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Sample records for dft calculation isomeros

  1. DFT calculations with the exact functional

    Science.gov (United States)

    Burke, Kieron

    2014-03-01

    I will discuss several works in which we calculate the exact exchange-correlation functional of density functional theory, mostly using the density-matrix renormalization group method invented by Steve White, our collaborator. We demonstrate that a Mott-Hubard insulator is a band metal. We also perform Kohn-Sham DFT calculations with the exact functional and prove that a simple algoritm always converges. But we find convergence becomes harder as correlations get stronger. An example from transport through molecular wires may also be discussed. Work supported by DOE grant DE-SC008696.

  2. Exchange interactions and Tc in rhenium-doped silicon: DFT, DFT + U and Monte Carlo calculations.

    Science.gov (United States)

    Wierzbowska, Małgorzata

    2012-03-28

    Interactions between rhenium impurities in silicon are investigated by means of the density functional theory (DFT) and the DFT + U scheme. All couplings between impurities are ferromagnetic except the Re-Re dimers which in the DFT method are nonmagnetic, due to the formation of the chemical bond supported by substantial relaxation of the geometry. The critical temperature is calculated by means of classical Monte Carlo (MC) simulations with the Heisenberg Hamiltonian. The uniform ferromagnetic phase is obtained with the DFT exchange interactions at room temperature for the impurities concentration of 7%. With the DFT + U exchange interactions, the ferromagnetic clusters form above room temperature in MC samples containing only 3% Re.

  3. nmr spectroscopic study and dft calculations of giao nmr shieldings ...

    African Journals Online (AJOL)

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    various fields of science and industry such as microelectronic and aerospace ... GIAO/DFT (Gauge Including Atomic Orbitals/Density Functional Theory) approach is .... successfully by using NMR and quantum chemical calculations.

  4. Modelling Catalyst Surfaces Using DFT Cluster Calculations

    Directory of Open Access Journals (Sweden)

    Oliver Kröcher

    2009-09-01

    Full Text Available We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO2, γ-Al2O3, V2O5-WO3-TiO2 and Ni/Al2O3. Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies.

  5. Modelling catalyst surfaces using DFT cluster calculations.

    Science.gov (United States)

    Czekaj, Izabela; Wambach, Jörg; Kröcher, Oliver

    2009-11-20

    We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO(2), gamma-Al(2)O(3), V(2)O(5)-WO(3)-TiO(2) and Ni/Al(2)O(3). Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies.

  6. Wavelet-Based DFT calculations on Massively Parallel Hybrid Architectures

    Science.gov (United States)

    Genovese, Luigi

    2011-03-01

    In this contribution, we present an implementation of a full DFT code that can run on massively parallel hybrid CPU-GPU clusters. Our implementation is based on modern GPU architectures which support double-precision floating-point numbers. This DFT code, named BigDFT, is delivered within the GNU-GPL license either in a stand-alone version or integrated in the ABINIT software package. Hybrid BigDFT routines were initially ported with NVidia's CUDA language, and recently more functionalities have been added with new routines writeen within Kronos' OpenCL standard. The formalism of this code is based on Daubechies wavelets, which is a systematic real-space based basis set. As we will see in the presentation, the properties of this basis set are well suited for an extension on a GPU-accelerated environment. In addition to focusing on the implementation of the operators of the BigDFT code, this presentation also relies of the usage of the GPU resources in a complex code with different kinds of operations. A discussion on the interest of present and expected performances of Hybrid architectures computation in the framework of electronic structure calculations is also adressed.

  7. Understanding electrode materials of rechargeable lithium batteries via DFT calculations

    Institute of Scientific and Technical Information of China (English)

    Tianran Zhang; Daixin Li; Zhanliang Tao; Jun Chenn

    2013-01-01

    Rechargeable lithium batteries have achieved a rapid advancement and commercialization in the past decade owing to their high capacity and high power density. Different functional materials have been put forward progressively, and each possesses distinguishing structural features and electrochemical properties. In virtue of density functional theory (DFT) calculations, we can start from a specific structure to get a deep comprehension and accurate prediction of material properties and reaction mechanisms. In this paper, we review the main progresses obtained by DFT calculations in the electrode materials of rechargeable lithium batteries, aiming at a better understanding of the common electrode materials and gaining insights into the battery performance. The applications of DFT calculations involve in the following points of crystal structure modeling and stability investigations of delithiated and lithiated phases, average lithium intercalation voltage, prediction of charge distributions and band structures, and kinetic studies of lithium ion diffusion processes, which can provide atomic understanding of the capacity, reaction mechanism, rate capacity, and cycling ability. The results obtained from DFT are valuable to reveal the relationship between the structure and the properties, promoting the design of new electrode materials.

  8. BH-DFTB/DFT calculations for iron clusters

    Directory of Open Access Journals (Sweden)

    Abdurrahman Aktürk

    2016-05-01

    Full Text Available We present a study on the structural, electronic, and magnetic properties of Fen(n  =  2  −  20 clusters by performing density functional tight binding (DFTB calculations within a basin hopping (BH global optimization search followed by density functional theory (DFT investigations. The structures, total energies and total spin magnetic moments are calculated and compared with previously reported theoretical and experimental results. Two basis sets SDD with ECP and 6-31G** are employed in the DFT calculations together with BLYP GGA exchange-correlation functional. The results indicate that the offered BH-DFTB/DFT strategy collects all the global minima of which different minima have been reported in the previous studies by different groups. Small Fe clusters have three kinds of packing; icosahedral (Fe9−13, centered hexagonal antiprism (Fe14−17, Fe20, and truncated decahedral (Fe17(2, Fe18−19. It is obtained in a qualitative agreement with the time of flight mass spectra that the magic numbers for the small Fe clusters are 7, 13, 15, and 19 and with the collision induced dissociation experiments that the sizes 6, 7, 13, 15, and 19 are thermodynamically more stable than their neighboring sizes. The spin magnetic moment per atom of Fen(n = 2 − 20 clusters is between 2.4 and 3.6 μB for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe13 icosahedron, which have already been reported by experimental and theoretical studies, is verified by our calculations as well. The quantitative disagreements between the calculations and measurements of the magnetic moments of the individual sizes are still to be resolved.

  9. BH-DFTB/DFT calculations for iron clusters

    Science.gov (United States)

    Aktürk, Abdurrahman; Sebetci, Ali

    2016-05-01

    We present a study on the structural, electronic, and magnetic properties of Fen(n = 2 - 20) clusters by performing density functional tight binding (DFTB) calculations within a basin hopping (BH) global optimization search followed by density functional theory (DFT) investigations. The structures, total energies and total spin magnetic moments are calculated and compared with previously reported theoretical and experimental results. Two basis sets SDD with ECP and 6-31G** are employed in the DFT calculations together with BLYP GGA exchange-correlation functional. The results indicate that the offered BH-DFTB/DFT strategy collects all the global minima of which different minima have been reported in the previous studies by different groups. Small Fe clusters have three kinds of packing; icosahedral (Fe9-13), centered hexagonal antiprism (Fe14-17, Fe20), and truncated decahedral (Fe17(2), Fe18-19). It is obtained in a qualitative agreement with the time of flight mass spectra that the magic numbers for the small Fe clusters are 7, 13, 15, and 19 and with the collision induced dissociation experiments that the sizes 6, 7, 13, 15, and 19 are thermodynamically more stable than their neighboring sizes. The spin magnetic moment per atom of Fen(n = 2 - 20) clusters is between 2.4 and 3.6 μB for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe13 icosahedron, which have already been reported by experimental and theoretical studies, is verified by our calculations as well. The quantitative disagreements between the calculations and measurements of the magnetic moments of the individual sizes are still to be resolved.

  10. MP2, DFT and ab initio calculations on thioxanthone.

    Science.gov (United States)

    Beni, Alireza Salimi; Chermahini, Alireza Najafi; Sharghi, Hashem; Monfared, Setareh Mirzaei

    2011-11-01

    Density functional theory (DFT), HF and MP2 calculations have been carried out to investigate thioxanthone molecule using the standard 6-31+G(d,p) basis set. The results of MP2 calculations show a butterfly structure for thioxanthone. The calculated results show that the predicted geometry can well reproduce the structural parameters. The predicted vibrational frequencies were assigned and compared with experimental IR spectra. A good harmony between theory and experiment is found. The theoretical electronic absorption spectra have been calculated using CIS method. (13)C and (1)H NMR of the title compound have been calculated by means of B3LYP density functional method with 6-31+G(d,p) basis set. The comparison of the experimental and the theoretical results indicate that density functional B3LYP method is able to provide satisfactory results for predicting NMR properties. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Vibrational spectra and DFT calculations of sonderianin diterpene

    Science.gov (United States)

    Oliveira, I. M. M.; Santos, H. S.; Sena, D. M.; Cruz, B. G.; Teixeira, A. M. R.; Freire, P. T. C.; Braz-Filho, R.; Sousa, J. W.; Albuquerque, M. R. J. R.; Bandeira, P. N.; Bernardino, A. C. S. S.; Gusmão, G. O. M.; Bento, R. R. F.

    2015-11-01

    In the present study, the natural product sonderianin diterpene (C21H26O4), a diterpenoid isolated from Croton blanchetianus, with potential application in the drug industry, was characterized by nuclear magnetic resonance, infrared and Raman spectroscopy. Vibrational spectra were supported by Density Functional Theory calculations. Infrared and Raman spectra of sonderianin were recorded at ambient temperature in the regions from 400 cm-1 to 3600 cm-1 and from 40 cm-1 to 3500 cm-1, respectively. DFT calculations with the hybrid functional B3LYP and the basis set 6-31 G(d,p) were performed with the purpose of obtaining information on the structural and vibrational properties of this organic compound. A comparison with experimental spectra allowed us to assign all of the normal modes of the crystal. The assignment of the normal modes was carried out by means of potential energy distribution.

  12. Vibrational spectroscopy and DFT calculations of flavonoid derriobtusone A

    Science.gov (United States)

    Marques, A. N. L.; Mendes Filho, J.; Freire, P. T. C.; Santos, H. S.; Albuquerque, M. R. J. R.; Bandeira, P. N.; Leite, R. V.; Braz-Filho, R.; Gusmão, G. O. M.; Nogueira, C. E. S.; Teixeira, A. M. R.

    2017-02-01

    Flavonoids are secondary metabolites of plants which perform various functions. One subclass of flavonoid is auronol that can present immunostimulating activity. In this work Fourier-Transform Infrared with Attenuated Total Reflectance (FTIR-ATR) and Fourier-Transform Raman (FT-Raman) spectra of an auronol, derriobtusone A (C18H12O4), were obtained at room temperature. Theoretical calculations using Density Functional Theory (DFT) were performed in order to assign the normal modes and to interpret the spectra of the derriobtusone A molecule. The FTIR-ATR and FT-Raman spectra of the crystal, were recorded at room temperature in the regions 600 cm-1 to 4000 cm-1 and 40 cm-1 to 4000 cm-1, respectively. The normal modes of vibrations were obtained using Density Functional Theory with B3LYP functional and 6-31G+ (d,p) basis set. The calculated frequencies are in good agreement with those obtained experimentally. Detailed assignments of the normal modes present in both the Fourier-Transform infrared and the Fourier-Transform Raman spectra of the crystal are given.

  13. Synthesis, Crystal Structural Investigations, and DFT Calculations of Novel Thiosemicarbazones

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    Brian J. Anderson

    2016-02-01

    Full Text Available The crystal and molecular structures of three new thiosemicarbazones, 2-[1-(2-hydroxy-5-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide monohydrate (1, 2-[1-(2-hydroxy-5-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide (2 and 2-[1-(2-hydroxy-4-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide acetonitrile solvate (3, are reported and confirmed by single crystal X-ray diffraction, NMR and UV-vis spectroscopic data. Compound (1, C11H15N3O2S·H2O, crystallizes in the monoclinic with space group P21/c, with cell parameters a = 8.2304(3 Å, b = 16.2787(6 Å, c = 9.9708(4 Å, and β = 103.355(4°. Compound (2, C12H17N3O2S, crystallizes in the C2/c space group with cell parameters a = 23.3083(6 Å, b = 8.2956(2 Å, c = 13.5312(3 Å, β = 91.077(2°. Compound (3, C11H15N3O2S·C2H3N, crystallizes in the triclinic P-1 space group with cell constants a = 8.9384(7 Å, b = 9.5167(8 Å, c = 10.0574(8 Å, α = 110.773(7°, β = 92.413(6°, and γ = 90.654(7°. DFT B3LYP/6-31(G geometry optimized molecular orbital calculations were also performed and frontier molecular orbitals of each compound are displayed. The correlations between the calculated molecular orbital energies (eV for the surfaces of the frontier molecular orbitals to the electronic excitation transitions from the absorption spectra of each compound have been proposed. Additionally, similar correlations observed among three closely related compounds, (4, 2-[1-(2-hydroxy-4-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide, (5, 2-[1-(2-hydroxy-6-methoxyphenylethylidene]-N-methyl-hydrazinecarbothioamide acetonitrile monosolvate and (6, 2-[1-(2-hydroxy-6-methoxyphenylethylidene]-N-ethyl-hydrazinecarbothioamide, examining structural differences from the substitution of the methoxy group from the phenyl ring (4, 5, or 6 position and the substitution of the terminal amine (methyl or ethyl to their frontier molecular orbital surfaces and from their Density Functional

  14. Density functional theory (DFT)-based modified embedded atom method potentials: Bridging the gap between nanoscale theoretical simulations and DFT calculations

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A density functional theory (DFT)-calculation scheme for constructing the modified embedded atom method (MEAM) potentials for face-centered cubic (fcc) metals is presented. The input quantities are carefully selected and a more reliable DFT approach for surface energy determination is introduced in the parameterization scheme, enabling MEAM to precisely predict the surface and nanoscale properties of metallic materials. Molecular dynamics simulations on Pt and Au crystals show that the parameterization employed leads to significantly improved accuracy of MEAM in calculating the surface and nanoscale properties, with the results agreeing well with both DFT calculations and experimental observations. The present study implies that rational DFT parameterization of MEAM may lead to a theoretical tool to bridge the gap between nanoscale theoretical simulations and DFT calculations.

  15. Chemical Information revealed by Mössbauer spectroscopy and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Nakashima, Satoru, E-mail: snaka@hiroshima-u.ac.jp [Hiroshima University, Natural Science Center for Basic Research and Development (Japan)

    2017-11-15

    Mixed-valence state of binuclear metallocene derivatives and spin-crossover (SCO) phenomena of the assembled Fe(II) complexes have been studied by using Mössbauer spectroscopy. The understanding of the results obtained by Mössbauer spectra is well supported by means of X-ray structural analysis and density functional theory (DFT) calculation. Benchmark study of relativisitic DFT calculation by using Mössbauer isomer shifts of Eu, Np complexes reveals the validity of the calculation. Such study sheds light on the bonding character of 4f and 5f electron. These results are reviewed.

  16. DFT calculation for adatom adsorption on graphene sheet as a prototype of carbon nanotube functionalization

    Energy Technology Data Exchange (ETDEWEB)

    Ishii, A; Yamamoto, M; Asano, H; Fujiwara, K [Department of Applied Mathematics and Physics, Tottori University Koyama, Tottori 680-8552 (Japan)], E-mail: ishii@damp.tottori-u.ac.jp

    2008-03-15

    DFT calculation of various atomic species on graphene sheet is investigated as prototypes for formation of nano-structures on carbon nanotube (CNT) wall. We investigate computationally adsorption energies and adsorption sites on graphene sheet for a lot of atomic species including transition metals, noble metals, nitrogen and oxygen, using the DFT calculation as a prototype for CNT. The suitable atomic species can be chosen as each application from those results. The calculated results show us that Mo and Ru are bounded strongly on graphene sheet with large diffusion barrier energy. On the other hand, some atomic species has large binding energies with small diffusion barrier energies.

  17. Structural characterization of Am(III) formate complexes. Combining EXAFS spectroscopy with DFT and thermodynamical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Rossberg, Andre [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Molecular Structures; Froehlich, D.R. [Heidelberg Univ. (Germany). Physikalisch-Chemisches Inst.

    2017-06-01

    We used iterative transformation factor analysis (ITFA) in order to isolate the EXAFS spectral contributions of the complexing ligand from a Am(III)/formate pH-series. Thermodynamic calculations were used as constraint for ITFA and for density functional theory (DFT) calculations to identify the coordination mode within the formed complexes.

  18. Benchmarking the DFT+U method for thermochemical calculations of uranium molecular compounds and solids.

    Science.gov (United States)

    Beridze, George; Kowalski, Piotr M

    2014-12-18

    Ability to perform a feasible and reliable computation of thermochemical properties of chemically complex actinide-bearing materials would be of great importance for nuclear engineering. Unfortunately, density functional theory (DFT), which on many instances is the only affordable ab initio method, often fails for actinides. Among various shortcomings, it leads to the wrong estimate of enthalpies of reactions between actinide-bearing compounds, putting the applicability of the DFT approach to the modeling of thermochemical properties of actinide-bearing materials into question. Here we test the performance of DFT+U method--a computationally affordable extension of DFT that explicitly accounts for the correlations between f-electrons - for prediction of the thermochemical properties of simple uranium-bearing molecular compounds and solids. We demonstrate that the DFT+U approach significantly improves the description of reaction enthalpies for the uranium-bearing gas-phase molecular compounds and solids and the deviations from the experimental values are comparable to those obtained with much more computationally demanding methods. Good results are obtained with the Hubbard U parameter values derived using the linear response method of Cococcioni and de Gironcoli. We found that the value of Coulomb on-site repulsion, represented by the Hubbard U parameter, strongly depends on the oxidation state of uranium atom. Last, but not least, we demonstrate that the thermochemistry data can be successfully used to estimate the value of the Hubbard U parameter needed for DFT+U calculations.

  19. Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values.

    Science.gov (United States)

    Schober, Christoph; Reuter, Karsten; Oberhofer, Harald

    2016-02-07

    We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or "flavors" of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (-6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (-15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

  20. Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

    Energy Technology Data Exchange (ETDEWEB)

    Schober, Christoph; Reuter, Karsten; Oberhofer, Harald, E-mail: harald.oberhofer@ch.tum.de [Chair for Theoretical Chemistry, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching (Germany)

    2016-02-07

    We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or “flavors” of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (−6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (−15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

  1. Vibrational spectra of berberine and their interpretation by means of DFT quantum-mechanical calculations

    CERN Document Server

    Bashmakova, N; Zhurakivsky, R; Hovorun, D; Yashchuk, V

    2011-01-01

    Experimental vibrational spectra (Raman and infrared absorption) of berberine are obtained at room temperature. The vibrational spectra of berberine are calculated by the DFT method at the B3LYP/6-311++G(d,p) level. Based on the correlation between experimental and calculated data, the vibrational spectrum is interpreted in the frequency range of 800-1700 cm-1 in detail. The experimental and calculated spectra of intramolecular vibrations are found to correlate closely

  2. Calculation of the vibrational spectra of α-rdx using the grimme DFT potential

    Science.gov (United States)

    Perger, Warren; Slough, William J.; Valenzano, Loredana; Flurchick, K. M.

    2012-03-01

    The density-functional theory (DFT) potential by Grimme has been proposed for describing longrange dispersion corrections. This potential has been implemented into the CRYSTAL09 program and used to calculate the vibrational spectra in α-RDX at equilibrium. The frequencies and intensities are reported and compared with prior theory and experiment where possible.

  3. DFT calculation of core-electron binding energies

    Energy Technology Data Exchange (ETDEWEB)

    Takahata, Yuji; Chong, Delano P. E-mail: chong@chem.ubc.ca

    2003-11-01

    A total of 59 core-electron binding energies (CEBEs) were studied with the Amsterdam Density Functional Program (ADF) program and compared with the observed values. The results indicate that a polarized triple-zeta basis set of Slater-type orbitals is adequate for routine assessment of the performance of each method of computation. With such a basis set, seven density functionals were tested. In addition, the performance of 21 energy density functionals were computed from the density calculated with the statistical average of orbital potentials (SAOP). Among all the choices tested, the best density functional for core-electron binding energies of C to F turns out to be the combination of Perdew-Wang (1986) functional for exchange and the Perdew-Wang (1991) functional for correlation, confirming earlier studies based on contracted Gaussian-type orbitals. For this best functional, five Slater-type orbital basis sets were examined, ranging from polarized double-zeta quality to the largest set available in the ADF package. For the best functional with the best basis set, the average absolute deviation (AAD) of the calculated value from experiment is only 0.16 eV.

  4. Application of DFT in bi-static RCS calculation of complex electrically large targets

    Institute of Scientific and Technical Information of China (English)

    Kuisong Zheng; Tengjiang Ding; Hui Yu; Zhaoguo Hou

    2015-01-01

    To handle the electromagnetic problems of the bi-static radar cross section (RCS) calculation of scatterer in a wide fre-quency band, a finite-difference time-domain (FDTD) extrapolation method combining with discrete Fourier transform (DFT) is pro-posed. By comparing the formulas between the steady state field extrapolation method and the transient field extrapolation method, a novel extrapolation method combining with DFT used in FDTD is proposed when a transient field incident wave is introduced. With the proposed method, the ful-angle RCS distribution in a wide fre-quency band can be achieved through one-time FDTD calculation. Afterwards, the back-scattering RCS distributions of a double olive body and a sphere-cone body are calculated. Numerical results verify the validity of the proposed method.

  5. Zerovalent Selenium Adsorption Mechanisms on CaO Surface: DFT Calculation and Experimental Study.

    Science.gov (United States)

    Fan, Yaming; Zhuo, Yuqun; Zhu, Zhenwu; Du, Wen; Li, Liangliang

    2017-10-05

    Zerovalent Se (Se atom and small Se2 molecule) adsorption mechanisms on a CaO surface were studied by both density functional theory (DFT) calculations and adsorption experiments. Nonvalent Se adsorption on the CaO(001) surface was simulated using a slab model. The adsorption energy, adsorption structure, electron density clouds, and electron properties were calculated. Different Se surface coverages were investigated to elucidate the adsorption process. In the experiments, the Se adsorption products were prepared in a U-shaped quartz reactor at 300 °C. The properties were investigated by X-ray photoelectron spectroscopy (XPS), inductively coupled plasma atomic emission spectroscopy (ICP-AES), field emission scanning electron microscopy/energy dispersive X-ray spectroscopy (FE-SEM/EDS), and X-ray diffraction (XRD), respectively. The experimental results match up with the DFT results, which reveal fundamental monochemisorption mechanisms of zerovalent Se on the CaO surface.

  6. Stereochemical and conformational study on fenoterol by ECD spectroscopy and TD-DFT calculations.

    Science.gov (United States)

    Tedesco, Daniele; Zanasi, Riccardo; Wainer, Irving W; Bertucci, Carlo

    2014-03-01

    Fenoterol and its derivatives are selective β2-adrenergic receptor (β2-AR) agonists whose stereoselective biological activities have been extensively investigated in the past decade; a complete stereochemical characterization of fenoterol derivatives is therefore crucial for a better understanding of the effects of stereochemistry on β2-AR binding. In the present project, the relationship between chiroptical properties and absolute stereochemistry of the stereoisomers of fenoterol (1) was investigated by experimental ECD spectroscopy and time-dependent density functional theory (TD-DFT). DFT geometry optimizations were carried out at the RI-B97D/TZVP/IEFPCM(MeOH) level and subsequent TD-DFT calculations were performed using the PBE0 hybrid functional. Despite the large pool of equilibrium conformers found for the investigated compounds and the known limitations of the level of theory employed, the computational protocol was able to reproduce the experimental ECD spectra of the stereoisomers of 1. The main contribution to the overall chiroptical properties was found to arise from the absolute configuration of the chiral center in α-position to the resorcinol moiety. Based on this evidence, a thorough conformational analysis was performed on the optimized DFT conformers, which revealed the occurrence of a different equilibrium between conformational patterns for the diastereomers of fenoterol: the (R,R')/(S,S') enantiomeric pair showed a higher population of folded conformations than the (R,S')/(S,R') pair.

  7. Functionalized 4-Hydroxy Coumarins: Novel Synthesis, Crystal Structure and DFT Calculations

    Directory of Open Access Journals (Sweden)

    Olga Igglessi-Markopoulou

    2011-01-01

    Full Text Available A novel short-step methodology for the synthesis in good yields of functionalized coumarins has been developed starting from an activated precursor, the N-hydroxysuccinimide ester of O-acetylsalicylic acid. The procedure is based on a tandem C-acylation-cyclization process under mild reaction conditions. The structure of 3-methoxycarbonyl-4-hydroxy coumarin has been established by X-ray diffraction analysis and its geometry was compared with optimized parameters by means of DFT calculations.

  8. Artificial neural network prediction of the psychometric activities of phenylalkylamines using DFT-calculated molecular descriptors

    Directory of Open Access Journals (Sweden)

    MINA HAGHDADI

    2010-10-01

    Full Text Available In the present work, a quantitative structure–activity relationship (QSAR method was used to predict the psychometric activity values (as mescaline unit, log MU of 48 phenylalkylamine derivatives from their density functional theory (DFT calculated molecular descriptors and an artificial neural network (ANN. In the first step, the molecular descriptors were obtained by DFT calculation at the 6-311G level of theory. Then the stepwise multiple linear regression method was employed to screen the descriptor spaces. In the next step, an artificial neural network and multiple linear regressions (MLR models were developed to construct nonlinear and linear QSAR models, respectively. The standard errors in the prediction of log MU by the MLR model were 0.398, 0.443 and 0.427 for training, internal and external test sets, respectively, while these values for the ANN model were 0.132, 0.197 and 0.202, respectively. The obtained results show the applicability of QSAR approaches by using ANN techniques in prediction of log MU of phenylalkylamine derivatives from their DFT-calculated molecular descriptors.

  9. CO2 adsorption and separation from natural gason phosphorene surface: Combining DFT and GCMC calculations

    Science.gov (United States)

    Zhang, Yayun; Liu, Chao; Hao, Feng; Xiao, Hang; Zhang, Shiwei; Chen, Xi

    2017-03-01

    We have examined the performance of phosphorene-based material, phosphorene slit pores (PSP), in CO2 adsorption and separation from natural gas by using Density Function Theory (DFT) calculation and Grand Canonical Monte Carlo (GCMC) simulations. First, the adsorption of CH4 and CO2molecules on phosphorene sheet were conducted by DFT study. Then, adsorption performances of natural gas components as well as their binary CO2/CH4 gas mixture were investigated at 300 K with the pressure up to 3.0 MPa. The effects of slit pore width, H, and mole ratio of CO2/CH4in the gas phase on the separation of CO2 from mixtures of CO2/CH4 were also investigated. Our DFT calculation results show that the CO2 moleculehas higher adsorption energy than that of CH4, which implies that it can be easily adsorbed to the phosphorene surface than CH4. Detailed GCMC simulations reveal that the phosphorene slit pore has a high performance in separating CO2fromnature gas and achieves the highest gas selectivity at H = 1.0 nm at pressures lower than 0.1 MPa. Moreover, the selectivity of CO2 overCO2/CH4gas mixture increases with increasing the mole ratio of CO2/CH4due to the enhanced adsorbate-adsorbent interactions for the favorable component. Therefore, it is suggested that the phosphorene is a promising candidate for natural gas purification and possessing practical potential applications in gas adsorption.

  10. Vibrational, structural and electronic study of a pyridinium salt assisted by SXRD studies and DFT calculations

    Science.gov (United States)

    Labra-Vázquez, Pablo; Palma-Contreras, Miguel; Santillan, Rosa; Farfán, Norberto

    2017-03-01

    The molecular structure of 1-[2-oxo-2-(2-pyridinyl)ethyl]pyridinium iodide (C12H11IN2O) is discussed using an experimental (FT-IR/ATR, NMR, SXRD) and theoretical (DFT, B3LYP/6-311G**) approach. Compound 2 crystallized in the monoclinic P21/c space group with 4 molecules per unit cell and unit cell dimensions a = 7.5629 Å (3), b = 21.5694 Å (7), c = 7.8166 Å (3). The crystal packing is governed by ion-dipole contacts and π-π stacking. High electrostatic potential at the ethanone hydrogens was derived from DFT calculations, further explaining the acidity and reactivity of the molecule as a Michael donor.

  11. High-pressure behavior of solid nitrobenzene: Combined Raman spectroscopy and DFT-D calculations study

    Science.gov (United States)

    Wang, Wen-Peng; Liu, Fu-Sheng; Liu, Qi-Jun; Zhang, Lin-Ji; Wang, Yi-Gao; Liu, Zheng-Tang

    2016-09-01

    Nitrobenzene (NB), a simplest structure of the aromatic nitro compounds, was investigated as a model for understanding structural properties in nitro derivatives of benzene and anilines. Using the Raman spectroscopic technique, the vibrational modes of solid NB were examined under hydrostatic compression up to 10 GPa. The Raman spectra indicated that a subtle phase transition occurred around 5 GPa. Also, the dispersion corrected density functional theory (DFT-D) calculations were performed to provide further insight into pressure effects on the molecular geometry. The calculated data suggested that NB molecules were distorted, and molecular conformation was readjusted when the phase transition with vibrational changes took place under high-pressure.

  12. DFT calculations of magnetic anisotropy energy of Ge(1-x)Mn(x)Te ferromagnetic semiconductor.

    Science.gov (United States)

    Łusakowski, A; Bogusławski, P; Story, T

    2015-06-10

    Density functional theory (DFT) calculations of the energy of magnetic anisotropy for diluted ferromagnetic semiconductor Ge(1-x)Mn(x)Te were performed using OpenMX package with fully relativistic pseudopotentials. The influence of hole concentration and magnetic ion neighbourhood on magnetic anisotropy energy is presented. Analysis of microscopic mechanism of magnetic anisotropy is provided, in particular the role of spin-orbit coupling, spin polarization and spatial changes of electron density are discussed. The calculations are in accordance with the experimental observation of perpendicular magnetic anisotropy in rhombohedral Ge(1-x)Mn(x)Te (1 1 1) thin layers.

  13. DFT calculations of magnetic anisotropy energy of Ge1-xMnxTe ferromagnetic semiconductor

    Science.gov (United States)

    Łusakowski, A.; Bogusławski, P.; Story, T.

    2015-06-01

    Density functional theory (DFT) calculations of the energy of magnetic anisotropy for diluted ferromagnetic semiconductor Ge1-xMnxTe were performed using OpenMX package with fully relativistic pseudopotentials. The influence of hole concentration and magnetic ion neighbourhood on magnetic anisotropy energy is presented. Analysis of microscopic mechanism of magnetic anisotropy is provided, in particular the role of spin-orbit coupling, spin polarization and spatial changes of electron density are discussed. The calculations are in accordance with the experimental observation of perpendicular magnetic anisotropy in rhombohedral Ge1-xMnxTe (1 1 1) thin layers.

  14. Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations.

    Science.gov (United States)

    Chain, Fernando E; Romano, Elida; Leyton, Patricio; Paipa, Carolina; Catalán, César A N; Fortuna, Mario; Brandán, Silvia Antonia

    2015-01-01

    In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G(∗) basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay's scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (μ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings.

  15. DFT LCAO and plane wave calculations of SrZrO{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Evarestov, R.A.; Bandura, A.V.; Alexandrov, V.E. [Department of Quantum Chemistry, St. Petersburg State University, 26 Universitetskiy Prospekt, Stary Peterhof 198504 (Russian Federation); Kotomin, E.A. [Max-Planck-Institut fuer Festkoerperforschung, Heisenbergstr. 1, 70569, Stuttgart (Germany)

    2005-02-01

    The results of the density functional (DFT) LCAO and plane wave (PW) calculations of the electronic and structural properties of four known SrZrO{sub 3} phases (Pm3m, I4/mcm, Cmcm and Pbnm) are presented and discussed. The calculated unit cell energies and relative stability of these phases agree well with the experimental sequence of SrZrO{sub 3} phases as the temperature increases. The lattice structure parameters optimized in the PW calculations for all four phases are in good agreement with the experimental neutron diffraction data. The LCAO and PW results for the electronic structure, density of states and chemical bonding in the cubic phase (Pm3m) are discussed in detail and compared with the results of previous PW calculations. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  16. Cis/trans Coordination in olefin metathesis by static and molecular dynamic DFT calculations

    KAUST Repository

    Poater, Albert

    2014-05-25

    In regard to [(N-heterocyclic carbene)Ru]-based catalysts, it is still a matter of debate if the substrate binding is preferentially cis or trans to the N-heterocyclic carbene ligand. By means of static and molecular dynamic DFT calculations, a simple olefin, like ethylene, is shown to be prone to the trans binding. Bearing in mind the higher reactivity of trans isomers in olefin metathesis, this insight helps to construct small alkene substrates with increased reactivity. © 2014 Springer Science+Business Media New York.

  17. QSPR modeling of detonation parameters and sensitivity of some energetic materials: DFT vs. PM3 calculations.

    Science.gov (United States)

    Zhang, Jianying; Chen, Gangling; Gong, Xuedong

    2017-06-01

    The quantitative structure-property relationship (QSPR) methodology was applied to describe and seek the relationship between the structures and energetic properties (and sensitivity) for some common energy compounds. An extended series of structural and energetic descriptors was obtained with density functional theory (DFT) B3LYP and semi-empirical PM3 approaches. Results indicate that QSPR model constructed using quantum descriptors can be applied to verify the confidence of calculation results compared with experimental data. It can be extended to predict the properties of similar compounds.

  18. Hybrid DFT calculations of the F centers in cubic ABO{sub 3} perovskites

    Energy Technology Data Exchange (ETDEWEB)

    Kotomin, E A; Zhukovskii, Y F; Piskunov, S [Institute for Solid State Physics, University of Latvia, Kengaraga 8, Riga LV-1063 (Latvia); Ellis, D E [Materials Research Center, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208 (United States)], E-mail: kotomin@latnet.lv

    2008-06-01

    We employed the hybrid DFT-LCAO approach as implemented in the CRYSTAL code for 135 atom supercell calculations of O vacancies with trapped electrons (known as the F centers) in three cubic perovskite crystals: SrTiO{sub 3}, PbTiO{sub 3} and PbZrO{sub 3}. The local lattice relaxation, charge redistribution and defect energy levels in the optical gap are compared. We demonstrate how difference in a chemical composition of host materials leads to quite different defect properties.

  19. Conformational analysis of capsaicin using 13C, 15N MAS NMR, GIAO DFT and GA calculations

    Science.gov (United States)

    Siudem, Paweł; Paradowska, Katarzyna; Bukowicki, Jarosław

    2017-10-01

    Capsaicin produced by plants from genus Capsicum exerts multiple pharmacological effects and has found applications in food and pharmaceutical industry. The alkaloid was studied by a combined approach: solid-state NMR, GA conformational search and GIAO DFT methods. The 13C CPMAS NMR spectra were recorded using variable contact time and dipolar dephasing experiments. The results of cross-polarization (CP) kinetics, such as TCP values and long T1ρH (100-200 ms), indicated that the capsaicin molecule is fairly mobile, especially at the end of the aliphatic chain. The15N MAS NMR spectrum showed one narrow signal at -255 ppm. Genetic algorithm (GA) search with multi modal optimization was used to find low-energy conformations of capsaicin. Theoretical GIAO DFT calculations were performed using different basis sets to characterize five selected conformations. 13C CPMAS NMR was used as a validation method and the experimental chemical shifts were compared with those calculated for selected stable conformers. Conformational analysis suggests that the side chain can be bent or extended. A comparison of the experimental and the calculated chemical shifts indicates that solid capsaicin does not have the same structure as those established by PWXRD.

  20. Maximizing the solar energy storage of the four substituted norbornadiene-quadricyclane system: DFT calculations

    Science.gov (United States)

    Vessally, Esmail; Aryana, Soma

    2016-01-01

    The purpose of this research is to study the solar energy storage in norbornadiene ( 1)/quadricyclane ( 2) system by four direct attachments of substituents at two carbon atoms on both sides of the double bonds C2=C3 and C5=C6 in 1 X and 2 X; calculating the relative energies at B3LYP/6-311++G** level of theory. The solar energy storage of four electron donating substituents, (push-push effect), X (X =-NH2,-OH) and four electron withdrawing substituents, (pull-pull effect) X (X =-CO2H,-CONH2,-NO2 and CN) were examined. The solar absorption bands were calculated for 1 X. The DFT calculations reveal that the bands were shifted to the visible spectrum region when the electron withdrawing substituents were used rather than the electron donating substituents.

  1. Molecular structure and spectroscopic properties of 4-nitrocatechol at different pH: UV-visible, Raman, DFT and TD-DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Cornard, Jean-Paul [Laboratoire de Spectrochimie Infrarouge and Raman LASIR, CNRS UMR 8516, Universite des Sciences et Technologies de Lille Bat C5, 59655 Villeneuve d' Ascq Cedex (France)]. E-mail: cornard@univ-lille1.fr; Rasmiwetti [Laboratoire de Spectrochimie Infrarouge and Raman LASIR, CNRS UMR 8516, Universite des Sciences et Technologies de Lille Bat C5, 59655 Villeneuve d' Ascq Cedex (France); Merlin, Jean-Claude [Laboratoire de Spectrochimie Infrarouge and Raman LASIR, CNRS UMR 8516, Universite des Sciences et Technologies de Lille Bat C5, 59655 Villeneuve d' Ascq Cedex (France)

    2005-03-14

    We investigated theoretically, by density functional theoretical calculations and by vibrational and electronic spectroscopies, the structure and the molecular spectroscopic properties of the 4-nitrocatechol molecule with varying pH. The lower energy stable structures of the neutral, monoanion and dianion forms were compared, and influence of water solvation was examined. The Raman and UV-visible spectra of 4-nitrocatechol and of its singly deprotonated form were recorded by varying the pH from 2 to 9. A calculation of the vibrational frequencies has allowed a complete assignment of the Raman spectra of the two forms of 4-nitrocatechol, and has permitted to investigate the evolution of vibrational normal modes upon deprotonation. Based on the molecular orbital analysis and the time dependent DFT (TD-DFT) calculations, we discussed the electronic structure and the assignment of the absorption bands in the electronic spectra of 4-nitrocatechol and mono-deprotonated 4-nitrocatechol.

  2. Molecular structure and spectroscopic properties of 4-nitrocatechol at different pH: UV visible, Raman, DFT and TD-DFT calculations

    Science.gov (United States)

    Cornard, Jean-Paul; Rasmiwetti; Merlin, Jean-Claude

    2005-03-01

    We investigated theoretically, by density functional theoretical calculations and by vibrational and electronic spectroscopies, the structure and the molecular spectroscopic properties of the 4-nitrocatechol molecule with varying pH. The lower energy stable structures of the neutral, monoanion and dianion forms were compared, and influence of water solvation was examined. The Raman and UV-visible spectra of 4-nitrocatechol and of its singly deprotonated form were recorded by varying the pH from 2 to 9. A calculation of the vibrational frequencies has allowed a complete assignment of the Raman spectra of the two forms of 4-nitrocatechol, and has permitted to investigate the evolution of vibrational normal modes upon deprotonation. Based on the molecular orbital analysis and the time dependent DFT (TD-DFT) calculations, we discussed the electronic structure and the assignment of the absorption bands in the electronic spectra of 4-nitrocatechol and mono-deprotonated 4-nitrocatechol.

  3. Spectroscopic Investigations and DFT Calculations on 3-(Diacetylamino-2-ethyl-3H-quinazolin-4-one

    Directory of Open Access Journals (Sweden)

    Yusuf Sert

    2016-01-01

    Full Text Available The theoretical and experimental vibrational frequencies of 3-(diacetylamino-2-ethyl-3H-quinazolin-4-one (2 were investigated. The experimental Laser-Raman spectrum (4000–100 cm−1 and FT-IR spectrum (4000–400 cm−1 of the newly synthesized compound were recorded in the solid phase. Both the theoretical vibrational frequencies and the optimized geometric parameters such as bond lengths and bond angles have for the first time been calculated using density functional theory (DFT/B3LYP and DFT/M06-2X quantum chemical methods with the 6-311++G(d,p basis set using Gaussian 03 software. The vibrational frequencies were assigned with the help of potential energy distribution (PED analysis using VEDA 4 software. The calculated vibrational frequencies and the optimized geometric parameters were found to be in good agreement with the corresponding reported experimental data. Also, the energies of the lowest unoccupied molecular orbital (LUMO, highest occupied molecular orbital (HOMO, and other related molecular energies for 3-(diacetylamino-2-ethyl-3H-quinazolin-4-one (2 have been investigated using the same computational methods.

  4. 6-Aminocoumarin-naphthoquinone conjugates: design, synthesis, photophysical and electrochemical properties and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Miranda, Fabio S.; Ronconi, Celia M.; Sousa, Mikaelly O.B.; Silveira, Gleiciani Q.; Vargas, Maria D., E-mail: miranda@vm.uff.br, E-mail: mdvargascp@gmail.com [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Inst. de Quimica

    2014-01-15

    Four novel 6-aminocoumarin-naphthoquinone conjugates were synthesized and their photophysical and electrochemical properties, investigated. 2-Chloro-3-(2-oxo-2H-chromen-6- ylamino)-1,4-naphthoquinone 1 did not present appreciable fluorescence in solution in comparison with 6-aminocoumarin, 6-AC. In order to understand the reasons for the fluorescence quenching in this compound, two strategies were attempted. Firstly, compound 1 was N-methylated to remove the intramolecular N-H...O=C electrostatic interaction that maintained the two units fixed, but the emission properties of the product 2 were not significantly different from those of 1. Time-dependent density functional theory (TD-DFT) calculations of compounds 1 and 2 indicate that the fluorescence quenching is related to the electron acceptor character of the naphthoquinone ring. The second strategy, therefore, involved the substitution of the chlorine atom in position 2 of the naphthoquinone nucleus for different electron donor groups (compounds 3-5), but again the emission properties did not change significantly. To explain these experimental findings, TD-DFT calculations of the ground (S{sub 0}) and excited (S{sub 1}) states of all molecules in solution were carried out. The results suggest that the energy states in these conjugates are such that the fluorescent group (6-AC) donates electrons to the naphthoquinone LUMO resulting in an oxidative photoinduced electron transfer (oxidative-PET). (author)

  5. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

    Directory of Open Access Journals (Sweden)

    Sandeep Kumar Mishra

    2017-03-01

    Full Text Available The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

  6. Experimental investigation and DFT calculation of different amine/ammonium salts adsorption on kaolinite

    Science.gov (United States)

    Chen, Jun; Min, Fan-fei; Liu, Lingyun; Liu, Chunfu; Lu, Fangqin

    2017-10-01

    The adsorption of four different amine/ammonium salts of DDA (Dodecyl amine), MDA (N-methyldodecyl amine), DMDA (N,N-dimethyldodecyl amine) and DTAC (Dodecyl trimethyl ammonium chloride) on kaolinite particles was investigated in the study through the measurement of contact angles, zeta potentials, aggregation observation, adsorption and sedimentation. The results show that different amine/ammonium salts can adsorb on the kaolinite surface to enhance the hydrophobicity and reduce the electronegativity of kaolinite particle surface, and thus induce a strong hydrophobic aggregation of kaolinite particles which promotes the settlement of kaolinite. To explore the adsorption mechanism of these four amine/ammonium salts on kaolinite surfaces, the adsorptions of DDA+, MDA+, DMDA+ and DTAC+ on kaolinite (001) surface and (00 1 bar) surface are calculated with DFT (Density functional theory). The DFT calculation results indicate that different amine/ammonium cations can strongly adsorbed on kaolinite (001) surface and (00 1 bar) surface by forming Nsbnd H⋯O strong hydrogen bonds or Csbnd H⋯O weak hydrogen bonds, and there are strongly electrostatic attractions between different amine/ammonium cations and kaolinite surfaces. The main adsorption mechanism of amine/ammonium cations on kaolinite is hydrogen-bond interaction and electrostatic attraction.

  7. Vibrational spectroscopic studies and DFT calculations of 4-bromo-o-xylene.

    Science.gov (United States)

    Arivazhagan, M; Meenakshi, R

    2012-06-01

    In the present work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of 4-bromo-o-xylene (BOX). The FT-IR (400-4000 cm(-1)) and FT-Raman spectra (50-3500 cm(-1)) of BOX were recorded. The molecular geometry, harmonic vibrational frequencies and bonding features of BOX in the ground state have been calculated by using the density functional B3LYP method with 6-311++G(d,p)/6-311+G(d,p) higher basis sets. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT). To determine conformational flexibility, molecular energy profile of BOX was obtained by B3LYP method with 6-311++G(d,p) basis set with respect to selected degree of torsional freedom, which gives three stable conformers. Besides, molecular electrostatic potential (MEP), non-linear properties and NMR analysis were performed at DFT level of theory. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. A new vibrational study of Acetazolamide compound based on normal coordinate analysis and DFT calculations

    Science.gov (United States)

    Brandán, S. A.; Eroğlu, E.; Ledesma, A. E.; Oltulu, O.; Yalçınkaya, O. B.

    2011-05-01

    We have studied the 5-acetamido-1,3,4-thiadiazole-2-sulphonamide compound and characterized it by infrared and Raman spectroscopy in the solid phase. The Density Functional Theory (DFT) method together with Pople's basis set show that two stable molecules for the compound have been theoretically determined in the gas phase, and that only the more stable conformation is present in the solid phase, as was experimentally observed. The harmonic vibrational wavenumbers for the optimized geometry were calculated at B3LYP/6-31G ∗ and B3LYP/6-311++G ∗∗ levels at the proximity of the isolated molecule. For a complete assignment of the vibrational spectra in the compound solid, DFT calculations were combined with Pulaýs Scaled Quantum Mechanics Force Field (SQMFF) methodology in order to fit the theoretical wavenumber values to the experimental ones. In this way, a complete assignment of all of the observed bands in the infrared spectrum for the compound was performed. The natural bond orbital (NBO) study reveals the characteristics of the electronic delocalization of the two structures, while the corresponding topological properties of electronic charge density are analysed by employing Bader's Atoms in the Molecules theory (AIM).

  9. Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths.

    Science.gov (United States)

    Siiskonen, Antti; Priimagi, Arri

    2017-02-01

    In recent years, halogen bonding has become an important design tool in crystal engineering, supramolecular chemistry and biosciences. The fundamentals of halogen bonding have been studied extensively with high-accuracy computational methods. Due to its non-covalency, the use of triple-zeta (or larger) basis sets is often recommended when studying halogen bonding. However, in the large systems often encountered in supramolecular chemistry and biosciences, large basis sets can make the calculations far too slow. Therefore, small basis sets, which would combine high computational speed and high accuracy, are in great demand. This study focuses on comparing how well density functional theory (DFT) methods employing small, double-zeta basis sets can estimate halogen-bond strengths. Several methods with triple-zeta basis sets are included for comparison. Altogether, 46 DFT methods were tested using two data sets of 18 and 33 halogen-bonded complexes for which the complexation energies have been previously calculated with the high-accuracy CCSD(T)/CBS method. The DGDZVP basis set performed far better than other double-zeta basis sets, and it even outperformed the triple-zeta basis sets. Due to its small size, it is well-suited to studying halogen bonding in large systems.

  10. Using Density Functional Theory (DFT) for the Calculation of Atomization Energies

    Science.gov (United States)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.

  11. Synthesis, characterization and DFT calculations of electronic and optical properties of YbPO4

    Science.gov (United States)

    Khadraoui, Z.; Horchani-Naifer, K.; Ferhi, M.; Ferid, M.

    2015-08-01

    YbPO4 crystals were synthesized by solid-state reaction and characterized by X-ray diffraction, infrared and Raman spectroscopies. The electronic structure and optical properties of YbPO4 such as the energy band structures, density of states and chemical bonds were calculated with the Density Functional Theory (DFT) for the first time. We present a combination of the GGA and the LDA + U approaches in order to obtain appropriate results due to the strong Coulomb repulsion between the highly localized 4f electrons of rare earth atoms. The linear photon-energy-dependent dielectric functions, conductivity and some optical constants such as refractive index, reflectivity and absorption coefficients were determined. The calculated total and partial densities of states indicate that the top of valance band is built upon O-2p states with P-3p states via σ (P-O) interactions, and the conduction bands mostly originate from Yb-5d states.

  12. Vibrational study of tolazoline hydrochloride by using FTIR-Raman and DFT calculations

    Science.gov (United States)

    Contreras, C. D.; Ledesma, A. E.; Zinczuk, J.; Brandán, S. A.

    2011-09-01

    Quantum mechanical (QM) calculations have been carried out in order to study the tolazoline hydrochloride theoretical structure and vibrational properties. This compound was characterized by infrared and Raman spectroscopies in the solid phase. For a complete assignment of the IR and Raman spectra, the density functional theory (DFT) calculations were combined with Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology in order to fit the theoretical frequency values to the experimental ones. An agreement between theoretical and available experimental results was found. Three intense bands in the infrared spectrum characteristic of the protonated species of the compound were detected. Also, the possible charge-transfer and the topological properties for both benzyl and imidazoline rings were studied by means of Natural Bond Orbital (NBO) and Atoms in Molecules theory (AIM) investigation.

  13. SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Khabibullin, A.R.; Woods, L.M. [University of South Florida, Tampa, Florida (United States); Karolak, A.; Budzevich, M.M.; Martinez, M.V. [H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida (United States); McLaughlin, M.L.; Morse, D.L. [University of South Florida, Tampa, Florida (United States); H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida (United States)

    2016-06-15

    Purpose: Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio-nuclei. Methods: The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab-initio Simulation Package (VASP) with the projector-augmented wave method and a plane-wave basis set in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin-Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated. Results: Calculated binding energies for DOTA-radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF). Conclusion: DOTA-Gd, DOTA-Ac and DOTA-Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA

  14. A first-principles DFT study of UN bulk and (001) surface: comparative LCAO and PW calculations.

    Science.gov (United States)

    Evarestov, R A; Bandura, A V; Losev, M V; Kotomin, E A; Zhukovskii, Yu F; Bocharov, D

    2008-10-01

    LCAO and PW DFT calculations of the lattice constant, bulk modulus, cohesive energy, charge distribution, band structure, and DOS for UN single crystal are analyzed. It is demonstrated that a choice of the uranium atom relativistic effective core potentials considerably affects the band structure and magnetic structure at low temperatures. All calculations indicate mixed metallic-covalent chemical bonding in UN crystal with U5f states near the Fermi level. On the basis of the experience accumulated in UN bulk simulations, we compare the atomic and electronic structure as well as the formation energy for UN(001) surface calculated on slabs of different thickness using both DFT approaches.

  15. Chemisorption of Hydroxide on 2D Materials from DFT Calculations: Graphene versus Hexagonal Boron Nitride.

    Science.gov (United States)

    Grosjean, Benoit; Pean, Clarisse; Siria, Alessandro; Bocquet, Lydéric; Vuilleumier, Rodolphe; Bocquet, Marie-Laure

    2016-11-17

    Recent nanofluidic experiments revealed strongly different surface charge measurements for boron-nitride (BN) and graphitic nanotubes when in contact with saline and alkaline water (Nature 2013, 494, 455-458; Phys. Rev. Lett. 2016, 116, 154501). These observations contrast with the similar reactivity of a graphene layer and its BN counterpart, using density functional theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials-chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values, resulting in a favorable (nonfavorable) adsorption on BN (graphene). We also calculate a pKa ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echo the weaker surface charge measurements but point to an alternative scenario.

  16. Formation of a 6FDA-based ring polyimide with nanoscale cavity evaluated by DFT calculations

    Science.gov (United States)

    Fukuda, Mitsuhiro; Takao, Yoshimi; Tamai, Yoshinori

    2005-04-01

    The computer-aided molecular design of a rigid ring molecule has been performed. As a candidate molecule, the polyimide derived from 2,2-bis(3,4-carboxylphenyl) hexafluoropropane dianhydride (6FDA) with m-phenylenediamine (MDA) has been used. The optimized structures of the 6FDA-MDA model compounds including a precursor type amic acid model were investigated using the density functional theory (DFT) at the B3LYP/6-311G(d,p) level. Using the optimized structures of the model compounds, the probable combinations to form a flat ring polyimide are considered by taking the spatial angles between the respective aromatic groups into consideration. We selected several combinations with different conformations and the number of monomer units. We showed that the dimer, trimer and tetramer of not only the 6FDA-based ring imide but also the corresponding ring amic acid can have a stable geometry. Each of them contains a cavity of sub-nanometer size and characteristic shape. Among them, the interaction energy with some guest molecules are evaluated for the smallest ring imide constructed from two units of 6FDA-MDA using the DFT calculations.

  17. Synthesis, crystal structure, and spectroscopic characterization supported by DFT calculations of organoarsenic compound

    Science.gov (United States)

    Ennaceur, Nasreddine; Henchiri, Rokaya; Jalel, Boutheina; Cordier, Marie; Ledoux-Rak, Isabelle; Elaloui, Elimame

    2017-09-01

    A new semi-organic hydrogen bonding complex salt of 2-ammonium phenylarsonic acid and nitric acid has been synthesized, thus successfully growing good quality single crystals by means of slow solvent evaporation technique at ambient temperature. The 1H and 13C NMR spectra were recorded to establish the molecular structure. The conducted single crystal XRD analysis has shown that the title salt is crystalized in orthorhombic crystal system with centrosymmetric Pbcm space group. The structure consists of infinite parallel two-dimensional planes built of (C6H6NH3AsO3)+ organic cation and NO3- inorganic anions connected by hydrogen bonds and π-π interactions giving birth a three-dimensional network. The performed TG/DSC thermal analysis has established the thermal stability of the crystal. The optimized structural parameters and vibrational frequencies (the experimental and theoretical vibrational frequencies) were assigned and compared by the Density Functional Theory (DFT) using the Gaussian method (DFT/B3LYP). Good consistency results were found between the calculated and the experimental crystal structure and FT-IR spectra.

  18. On the Interactions of Fused Pyrazole Derivative with Selected Amino Acids: DFT Calculations

    Directory of Open Access Journals (Sweden)

    Kornelia Czaja

    2017-01-01

    Full Text Available Due to the increasing prevalence of neoplasms, there is a permanent need for new selective cytostatic compounds. Anticancer drugs can act in different ways, affecting protein expression and synthesis, including disruption of signaling pathways within cells. Continuing our previous research aiming at elucidating the mechanism of pyrazole’s anticancer activity, we carried out in silico studies on the interactions of fused pyrazole derivative with alanine, lysine, glutamic acid, and methionine. The objective of the study is to improve our understanding of the possible interactions of pyrazole derivatives with the above-mentioned amino acids. For this purpose, we apply the DFT formalism (optimization using the B3LYP, CAM-B3LYP, PBE0, and M06L functionals and interaction energy calculations (counterpoise corrected method based on the basis set superposition error, BSSE together with QTAIM approach and estimation of the 1H NMR chemical shifts of analyzed pyrazole derivative using different basis sets and DFT functionals in CPCM solvation model (and water used as a solvent.

  19. Vibrational spectra, DFT calculations, conformational stabilities and assignments of the fundamentals of the 1-butylpiperazine

    Science.gov (United States)

    Bağlayan, Özge; Kaya, Mehmet Fatih; Güneş, Esma; Şenyel, Mustafa

    2016-10-01

    FT-IR and FT-Raman spectra of 1-butylpiperazine (1bpa) were experimentally recorded in the region of 4000-10 cm-1 and 4000-100 cm-1, respectively. The optimized geometric parameters, conformational equilibria, normal mode frequencies and corresponding vibrational assignments of 1bpa (C8H18N2) are theoretically examined by means of B3LYP hybrid density functional theory (DFT) method together with 6-31++G(d,p) basis set. Also, reliable conformational investigation and vibrational assignments have been performed by the potential energy surface (PES) and potential energy distribution (PED) analysis, respectively. Calculations are made for four possible conformations. According to the experimental and theoretical data, density functional B3LYP method provides reliable results for predicting vibrational wavenumbers and equatorial-equatorial conformer is considered to be the most stable form of 1bpa.

  20. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    Science.gov (United States)

    Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.

    2016-05-01

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb -London -Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

  1. Basis Set Recommendations for DFT Calculations of Gas-Phase Optical Rotation at Different Wavelengths

    DEFF Research Database (Denmark)

    Hedegård, Erik D.; Jensen, Frank; Kongsted, Jacob

    2012-01-01

    of the optical rotation to the basis set limits for nine small or medium sized molecules, using basis sets developed specifically for DFT and magnetic properties (aug-pcS-n series). We suggest that assignment of absolute configuration by comparisons between theoretical and experimental optical rotations may......Even for pure substances, the deduction of the absolute configuration is not always straightforward since there is no direct link between the magnitude and sign of the optical rotation and the absolute configuration. It would be very useful to use computations of the optical rotation to link...... experimentally measured optical rotations to an absolute configuration. Such electronic structure calculations of the optical rotation typically employ regular energy optimized basis sets from wave function theory, and especially the aug-cc-pVDZ basis set has been popular. Here, we have carried out extrapolation...

  2. Synthesis, Crystal Structure, and DFT Calculations of 1,3-Diisobutyl Thiourea

    Directory of Open Access Journals (Sweden)

    Ataf A. Altaf

    2015-01-01

    Full Text Available 1,3-Diisobutyl thiourea was synthesized and characterized by single crystal X-ray diffraction. It gives a monoclinic (α = γ = 90 and β  ≠ 90 structure with the space group P21/c. The unit cell dimensions are a = 11.5131 (4 Å, b = 9.2355 (3 Å, c = 11.3093 (5 Å, α = 90°, β = 99.569° (2, γ = 90°, V = 1185.78 (8 Å3, and Z = 4. The crystal packing is stabilized by intermolecular (N–H⋯S hydrogen bonding in the molecules. The optimized geometry and Mullikan's charges of the said molecule calculated with the help of DFT using B3LYP-6-311G model support the crystal structure.

  3. Cis-trans isomerisation of azobenzenes studied by laser-coupled NMR spectroscopy and DFT calculations.

    Science.gov (United States)

    Wazzan, Nuha A; Richardson, Patricia R; Jones, Anita C

    2010-07-30

    In a combined experimental and computational study of a group of para-substituted azobenzenes, the effects of substituents and solvent on the kinetics of thermal cis-to-trans isomerisation have been examined and the success of DFT calculations in predicting kinetic parameters assessed. Mono-substituted species are predicted to isomerise by inversion in both non-polar and polar solvent, whereas for push-pull azobenzenes the mechanism is predicted to change from inversion to rotation on going from non-polar to polar solvent. Computed free energies of activation qualitatively reproduce experimental trends but do not quantitatively predict the kinetics of cis-trans isomerisation. The polarisable continuum model of solvation fails to predict the experimentally observed influence of solvent on the entropy of activation.

  4. Synthesis, characterization, DFT calculations and antibacterial activity of palladium(II) cyanide complexes with thioamides

    Science.gov (United States)

    Ahmad, Saeed; Nadeem, Shafqat; Anwar, Aneela; Hameed, Abdul; Tirmizi, Syed Ahmed; Zierkiewicz, Wiktor; Abbas, Azhar; Isab, Anvarhusein A.; Alotaibi, Mshari A.

    2017-08-01

    Palladium(II) cyanide complexes of thioamides (or thiones) having the general formula PdL2(CN)2, where L = Thiourea (Tu), Methylthiourea (Metu), N,N‧-Dimethylthiourea (Dmtu), Tetramethylthiourea (Tmtu), 2-Mercaptopyridine (Mpy) and 2-Mercaptopyrimidine (Mpm) were prepared by reacting K2[PdCl4] with potassium cyanide and thioamides in the molar ratio of 1:2:2. The complexes were characterized by elemental analysis, thermal and spectroscopic methods (IR, 1H and 13C NMR). The structures of three of the complexes were predicted by DFT calculations. The appearance of a band around 2100 cm-1 in IR and resonances around 120-130 ppm in the 13C NMR spectra indicated the coordination of cyanide to palladium(II). More than one resonances were observed for CN- carbon atoms in 13C NMR indicating the existence of equilibrium between different species in solution. DFT calculations revealed that in the case of the palladium(II) complex of Tmtu, the ionic dinuclear [Pd(Tmtu)4][Pd(CN)4] form was more stable than the dimer of mononuclear complex [Pd(Tmtu)2(CN)2] by 0.91 kcal mol-1, while for the complexes of Tu or Mpy ligands, the nonionic [Pd(L)2(CN)2] forms were more stable than the corresponding [Pd(L)4][Pd(CN)4] complexes by 1.26 and 6.49 kcal mol-1 for L = Tu and Mpy, respectively. The complexes were screened for antibacterial effects and some of them showed significant activities against both gram positive as well as gram negative bacteria.

  5. NO Chemisorption on Cu/SSZ-13: a Comparative Study from Infrared Spectroscopy and DFT Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Renqin; McEwen, Jean-Sabin; Kollar, Marton; Gao, Feng; Wang, Yilin; Szanyi, Janos; Peden, Charles HF

    2014-11-07

    The locations and energies of Cu ions in a Cu/SSZ-13 zeolite catalyst were investigated by density functional theory (DFT) calculations. For 'naked' Cu2+ ions (i.e., Cu2+ ions with no ligands in their coordination spheres other than zeolite lattice oxygen atoms), the more energetically favorable sites are within a 6-membered ring. However, with the presence of various adsorbates, the energy difference between 6- and 8-membered ring locations greatly diminishes. Specifically, Cu2+ ions are substantially stabilized by -OH ligands (as [CuII(OH)]+), making the extra-framework sites in an 8-membered ring energetically more favorable than 6-membered ring sites. Under fully dehydrated high vacuum conditions with different Si/Al and Cu/Al ratios, three chemisorbed NO species coexist upon exposure of NO to Cu/SSZ-13: NO+, Cu2+-NO and Cu+-NO. The relative signal intensities for these bands vary greatly with Si/Al ratios. The vibrational frequency of chemisorbed NO was found to be very sensitive to the location of Cu2+ ions. On the one hand, with the aid from DFT calculations, the nature for these vibrations can be assigned in detail. On the other hand, the relative intensities for various Cu2+-NO species provide a good measure of the nature of Cu2+ ions as functions of Si/Al and Cu/Al ratios and the presence of humidity. These new findings cast doubt on the generally accepted proposal that only Cu2+ ions located in 6-membered rings are catalytically active for NH3-SCR.

  6. FT-IR spectroscopy combined with DFT calculation to explore solvent effects of vinyl acetate.

    Science.gov (United States)

    Chen, Yi; Zhang, Hui; Liu, Qing

    2014-05-21

    The infrared vibration frequencies of vinyl acetate (VAc) in 18 different solvents were theoretically computed at Density Function Theory (DFT) B3LYP/6-311G(*) level based on Polarizable Continuum Model (PCM) and experimentally recorded by FT-IR spectroscopy. The solvent-induced long-range bulk electrostatic solvation free energies of VAc (ΔGelec) were calculated by the SMD model. The C=O stretching vibration frequencies of VAc were utilized as a measure of the chemical reactivities of the CC group in VAc. The calculated and experimental C=O stretching vibration frequencies of VAc (νcal(C=O) and νexp(C=O)) were correlated with empirical solvent parameters including the KBM equation, the Swain equation and the linear solvation energy relationships (LSER). Through ab initio calculation, assignments of the two C=O absorption bands of VAc in alcohol solvents were achieved. The PCM, SMD and ab initio calculation offered supporting evidence to explain the FT-IR experimental observations from differing aspects.

  7. Structural analysis of N,N-diacyl-1,4-dihydropyrazine by variable-temperature NMR and DFT calculation

    Science.gov (United States)

    Song, Xiu-qing; Tan, Hong-bo; Yan, Hong; Chang, Yu

    2017-04-01

    N,N-diacyl-1,4-dihydropyrazine derivatives (1) were prepared via an efficient microwave-assisted synthesis. 1 was isolated and unambiguously confirmed by NMR spectra and high-resolution mass spectrometry. The NMR spectra of 1 showed complicated rather than conventional spectroscopy. Variable-temperature experiments and DFT calculation (PES) were used to investigate this phenomenon. DFT calculations confirmed that the structures of the two rotamers of 1 correspond to those determined by NMR in solution, and gave the syn-anti interconversion barriers of rotamers. The results showed that two isomers exist in solution (deuterated solvent) at room temperature, resulting in complicated NMR spectra.

  8. DFT calculations of magnetic parameters for molybdenum complexes and hydroxymethyl intermediates trapped on silica surface

    Science.gov (United States)

    Sojka, Zbigniew; Pietrzyk, Piotr

    2006-03-01

    Density functional theory (DFT) calculations of EPR parameters and their structure sensitivity for selected surface paramagnetic species involved in oxidative dehydrogenation of methanol over silica grafted molybdenum catalyst were investigated. Two surface complexes, Mo 4 c/SiO 2 and {O -sbnd Mo 4 c}/SiO 2, as well as rad CH 2OH radical trapped on the SiO 2 matrix were taken as the examples. The spin-restricted zeroth order regular approximation (ZORA) implemented in the Amsterdam Density Functional suite was used to calculate the electronic g tensor for those species. The predicted values were in satisfactory agreement with experimental EPR results. Five different coordination modes of the rad CH 2OH radical on the silica surface were considered and the isotropic 13C, 17O, and 1H hyperfine coupling constants (HFCC) of the resultant surface complexes were calculated. Structure sensitivity of the HFCC values was discussed in terms of the angular deformations caused by hydrogen bonding with the silica surface.

  9. Structural and vibrational characterization of sugar arabinitol structures employing micro-Raman spectra and DFT calculations

    Science.gov (United States)

    Hédoux, Alain; Guinet, Yannick; Carpentier, Laurent; Paccou, Laurent; Derollez, Patrick; Brandán, Silvia Antonia

    2017-06-01

    In this work, three monomeric forms of arabinitol, usually named arabitol, and their dimeric species have been structural and vibrationally studied by using the micro-Raman spectra in the solid phase accomplished with theoretical calculations based on the theory of the functional of the density (DFT). The hybrid B3LYP method was used for all the calculations together with the 6-31G* and 6-311++g** basis sets. Two different L structures with minima energies were predicted in accordance to the two polymorphic structures revealed by recent X-ray diffraction experiments. The studies by natural bond orbital (NBO) calculations reveals high stabilities of the L form as compared with the D one but the topological properties by using the atoms in molecules (AIM) suggest a higher stability of the D form due to a strong H bond interactions. The scaled mechanical force fields (SQMFF) procedure was used to perform the complete vibrational assignments for the monomeric forms and their dimer. On the other hand, the similarity in the gap values computed for the three forms of arabitol with those observed for sucrose, trehalose, maltose and lactose in gas phase at the same level of theory could partially explain the sweetening property of this alcohol. In addition, the influences of the size of the basis set on some properties were evidenced.

  10. A strategy of integrating ultraviolet absorption and crosslinking in a single molecule: DFT calculation and experimental

    Science.gov (United States)

    Shan, Mingli; Liu, Yujing; Xia, Shuwei; Tang, Qunwei; Yu, Liangmin

    2016-03-01

    Creation of advanced ultraviolet light absorbers having crosslinking ability has been persistent objective for anti-ultraviolent aging polymers. We present here the integration of 2, 4-dihydroxybenzophenone (UV-0) and N-methylol acrylamide (NMA) for novel ultraviolet absorber namely (3,5-dimethacrylamide-2,4-dihydroxyphenyl) (phenyl)methanone (UV-CA), which is subsequently utilized as a crosslinking agent after suffering Friedel-Crafts reaction. The preliminary results demonstrate that quantum chemical calculations (DFT) is a promising avenue in demonstrating the optimized geometry, charges, energy levels and UV electronic absorption bands of the UV-CA in the singlet (steady and excited states). The structure parameters and natural band orbital (NBO) calculations suggest that the intramolecular hydrogen bond (IMHB) in the UV-0 group is significantly enhanced in comparison to that between UV-0 and NMA groups. The acrylic acid polymers functionalized with UV-CA yield high crosslinking degree and robust UV absorbing performance. The impressive results demonstrate that quantum chemical calculations are promising in organic synthesis to develop advanced compounds.

  11. Anionic fructose-related conformational and positional isomers assigned through PES experiments and DFT calculations.

    Science.gov (United States)

    Zeng, Zhen; Bernstein, Elliot R

    2017-08-30

    Gas phase, isolated fructose anionic species, fructose(-), (fructose-H)(-), (fructose-OH)(-), and (fructose-H2O)(-), are investigated employing anionic photoelectron spectroscopy (PES) combined with density functional theory (DFT) calculations. The PES vertical detachment energies (VDEs) for these anions are determined and, based on these experimental values, their calculated anionic structures are assigned. Generation of these four species through the matrix assisted laser desorption ionization (MALDI) process is sample desorption substrate dependent. The parent anion fructose(-) exists as a single, dominant open chain structure in the gas phase, with substrate dependent specific conformational isomers. (Fructose-H)(-) and (fructose-OH)(-) are mainly produced from the laser ablation process rather than from fragmentation reaction pathways associated with the parent anion species. Both conformational and positional isomers are identified in the gas phase for these latter anions. (Fructose-H2O)(-) has two types of positional isomers, both of which contribute to two different components of the observed PES feature. The fixed positions for losing an OH group and an H atom, in addition to thermodynamic calculations, provide reaction pathways for generating a dehydration product (open chain structures) from the parent anion (open chain and furanose structures), further demonstrating the active nature of fructose upon capturing an extra electron.

  12. Electronic and optical properties of AlN under pressure: DFT calculations

    Science.gov (United States)

    Javaheri, Sahar; Boochani, Arash; Babaeipour, Manuchehr; Naderi, Sirvan

    2017-01-01

    Structural, elastic, optical, and electronic properties of wurtzite (WZ), zinc-blende (ZB), and rocksalt (RS) structures of AlN are investigated using the first-principles method and within the framework of density functional theory (DFT). Lattice parameters, bulk modulus, shear modulus, Young’s modulus, and elastic constants are calculated at zero pressure and compared with other experimental and theoretical results. The wurtzite and zinc-blende structures have a transition to rocksalt phase at the pressures of 12.7 GPa and 14 GPa, respectively. The electronic properties are calculated using both GGA and EV-GGA approximations; the obtained results by EV-GGA approximation are in much better agreement with the available experimental data. The RS phase has the largest bandgap with an amount of 4.98 eV; by increasing pressure, this amount is also increased. The optical properties like dielectric function, energy loss function, refractive index, and extinction coefficient are calculated under pressure using GGA approximation. Inter-band transitions are investigated using the peaks of imaginary part of the dielectric function and these transitions mainly occur from N-2p to Al-3p levels. The results show that the RS structure has more different properties than the WZ and ZB structures.

  13. Copper(II) complexes with pyrazole derivatives - Synthesis, crystal structure, DFT calculations and cytotoxic activity

    Science.gov (United States)

    Kupcewicz, Bogumiła; Ciolkowski, Michal; Karwowski, Boleslaw T.; Rozalski, Marek; Krajewska, Urszula; Lorenz, Ingo-Peter; Mayer, Peter; Budzisz, Elzbieta

    2013-11-01

    The series of pyrazole derivatives (1a-4a) were used as bidentate N,N' ligands to obtain neutral Cu(II) complexes of ML2Cl2 type (1b-4b). The molecular structures of ligand 1a and Cu(II) complex 4b were determined by X-ray crystallography and theoretical DFT calculations. In this study, three functionals B3LYP, BP86 and mPW1PW91 with different basis sets and two effective core potentials Los Alamos and Stuttgart/Dresden were performed. The DFT study disclosed the usefulness of BP86 functional with SDD-ECP for Cu(II) ion and dedicated D95 basis set for other non-transition metal atoms, with the exclusion of Cl for which 6-31++G(2df,2pd) were used. The structural analysis shows that the presence of phenyl substituent in a pyrazole ring contributed to Cu-N bond elongation, which can result in different reactivity of complexes 1b and 3b. The cytotoxicity of the obtained compounds was evaluated on three cancer cells lines: HL-60, NALM-6 and WM-115. The complexes have exhibited similar moderate antiproliferative activity. All the complexes, except for 1b, were found to be more active against three cancer cell lines than uncomplexed pyrazoles. The lipophilicity and electrochemical properties of ligands and complexes was also studied. For complexes with ligand 1a and 3a only one reduction process at the metal centre occurs (Cu(II) → Cu(I)) with oxidization of Cu(I)-Cu(II) in the backward step.

  14. DFT calculations on electronic properties of ZnO thin films deposited by spray pyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Cordeiro, J.M.; Reynoso, V.C.; Azevedo, D.H.M. [Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), SP (Brazil)

    2016-07-01

    Full text: Introduction - Thin films of Zinc oxide (ZnO) has a wide range of technological applications, as transparent conducting electrodes in solar cells, flat panel displays, and sensors, for example. More recently applications in optoelectronics, like light emitter diodes and laser diodes, due to its large band gap, are been explored. Studies of ZnO thin films are important for these applications. Methodology - In this study thin films of ZnO have been deposited by spray pyrolysis on glass substrate. The films were characterized by XRD and UV-VIS techniques and the electronic properties as a function of the film thickness have been investigated by DFT calculations with B3LYP hybrid potential implemented in the CRYSTAL09 code. Results - The diffractograms obtained for the ZnO thin films as a function of the thickness are shown. The films exhibit a hexagonal wurtzite structure with preferred c-axis orientation in (002) direction of ZnO crystal. A quantum mechanical approach based on the periodic Density Functional Theory (DFT), with B3LYP hybrid potential was used to investigate the electronic structure of the films as a function of the thickness. The CRYSTAL09 code has been used for the calculations on the wurtzite hexagonal structure of ZnO - spatial group P63mc. For optimizing the geometry of the pure ZnO crystal, the experimental lattice parameters were got as follows: a= 0.325 nm, b= 0.325 nm, c= 0.5207 nm with c/a= 1.602. Considering to the calculations of the band structure, it is suggested that the semiconducting properties of ZnO arises from the overlapping of the 4s orbital of the conducting band of Zn and the 2p orbital of the top of valence band of O. Conclusions - The structure of ZnO thin film deposited on glass substrate present preferential orientation in (002) direction. Variation in the optical properties as a function of the film thickness was observed. The band gap energy was determined from optical analysis to be ∼ 3.27 eV. The refractive

  15. Optimal Location of Vanadium in Muscovite and Its Geometrical and Electronic Properties by DFT Calculation

    Directory of Open Access Journals (Sweden)

    Qiushi Zheng

    2017-02-01

    Full Text Available Vanadium-bearing muscovite is the most valuable component of stone coal, which is a unique source of vanadium manufacture in China. Numbers of experimental studies have been carried out to destroy the carrier muscovite’s structure for efficient extraction of vanadium. Hence, the vanadium location is necessary for exploring the essence of vanadium extraction. Although most infer that vanadium may substitute for trivalent aluminium (Al as the isomorphism in muscovite for the similar atomic radius, there is not enough experimental evidence and theoretical supports to accurately locate the vanadium site in muscovite. In this study, the muscovite model and optimal location of vanadium were calculated by density functional theory (DFT. We find that the vanadium prefers to substitute for the hexa-coordinated aluminum of muscovite for less deformation and lower substitution energy. Furthermore, the local geometry and relative electronic properties were calculated in detail. The basal theoretical research of muscovite contained with vanadium are reported for the first time. It will make a further influence on the technology development of vanadium extraction from stone coal.

  16. DFT calculations of EPR parameters for copper(II)-exchanged zeolites using cluster models.

    Science.gov (United States)

    Ames, William M; Larsen, Sarah C

    2010-01-14

    The coordination environment of Cu(II) in hydrated copper-exchanged zeolites was explored through the use of density functional theory (DFT) calculations of EPR parameters. Extensive experimental EPR data are available in the literature for hydrated copper-exchanged zeolites. The copper complex in hydrated copper-exchanged zeolites was previously proposed to be [Cu(H(2)O)(5)OH](+) based on empirical trends in tetragonal model complex EPR data. In this study, calculated EPR parameters for the previously proposed copper complex, [Cu(H(2)O)(5)OH](+), were compared to model complexes in which Cu(II) was coordinated to small silicate or aluminosilicate clusters as a first approximation of the impact of the zeolitic environment on the copper complex. Interpretation of the results suggests that Cu(II) is coordinated or closely associated with framework oxygen atoms within the zeolite structure. Additionally, it is proposed that the EPR parameters are dependent on the Si/Al ratio of the parent zeolite.

  17. DFT-based Theoretical Calculation of Nb- and W-doped Anatase TiO2

    Science.gov (United States)

    Suenaga, Takahiro; Kamisaka, Hideyuki; Nakamura, Hisao; Yamashita, Koichi

    2010-03-01

    The structure and electronic states in the Nb-doped TiO2 (TNO) and W-doped TiO2 (TWO) in anatase phase were investigated from the first-principle using DFT-based band structure method. In addition to the cases where the dopant substituting a Ti atom, cells containing a dopant (MTi; M = Nb, W) and an oxygen vacancy (VO) were calculated in order to clarify the role of the oxygen vacancy in the system. Furthermore, cells containing two dopants and an oxygen vacancy (2MTi--VO), and cells with a dopant and two oxygen vacancies (MTi--2VO) were calculated. Energetically stable structures were found among the sampled 2WTi--VO and WTi--2VO cells, while the corresponding structures in TNO did not show any significant energy stabilization. Impurity states were found in the stable 2WTi--VO and WTi--2VO structures, and an approach of the two WTi atoms was observed in the former. The present results rationalize the lower electronic conductivity of TWO than that of TNO, and suggest possible formation of complex structures consisting of the WTi dopants and the oxygen vacancies.

  18. Surface study of gallium- and aluminum- doped graphenes upon adsorption of cytosine: DFT calculations

    Science.gov (United States)

    Shokuhi Rad, Ali; Zareyee, Daryoush; Peyravi, Majid; Jahanshahi, Mohsen

    2016-12-01

    The adsorption of cytosine molecule on Al- and Ga- doped graphenes is studied using first-principles density functional theory (DFT) calculations. The energetically most stable geometries of cytosine on both Al- and Ga- doped graphenes are determined and the adsorption energies are calculated. The net charge of transfer as well as local charge of doped atoms upon adsorption of cytosine are studied by natural bond orbitals (NBO) analysis. Orbital hybridizing of complexes was searched by frontier molecular orbital theory (FMO), and density of states (DOS). Depending on the side of cytosine, there are four possible sites for its adsorption on doped graphene; denoted as P1, P2, P3, and P4, respectively. The order of binding energy in the case of Al-doped graphene is found as P1 ˃ P4 ˃ P3 ˃ P2. Interestingly, the order in the case of Ga-doped graphene changes to: P4 ∼ P1˃ P3˃ P2. Both surfaces show superior adsorbent property, resulting chemisorption of cytosine, especially at P1 and P4 position configurations. The NBO charge analysis reveals that the charge transfers from Al- and Ga- doped graphene sheets to cytosine. The electronic properties of both surfaces undertake important changes after cytosine adsorption, which indicates notable change in its electrical conductivity.

  19. Methemoglobinemia caused by 8-aminoquinoline drugs: DFT calculations suggest an analogy to H4B's role in nitric oxide synthase

    Science.gov (United States)

    We suggest a possible mechanism of how 8-aminoquinolines (8-AQ's) cause hemotoxicity by oxidizing hemoglobin to methemoglobin. In our DFT calculations, we found that 5-hydroxyprimaquine is able to donate an electron to O2 to facilitate its conversion to H2O2. Meanwhile, Fe(II) is oxidized to Fe(III)...

  20. FT-IR spectroscopy and DFT calculation study on the solvent effects of benzaldehyde in organic solvents.

    Science.gov (United States)

    Li, Yi; Zhang, Hui; Liu, Qing

    2012-02-01

    FT-IR spectra of benzaldehyde in 11 different organic solvents were recorded and analyzed. The density functional theory (DFT) B3LYP/6-31G* method was chosen to calculate the infrared spectrum of benzaldehyde in gaseous state. The electrostatic effects of different solvents in benzaldehyde solutions were calculated using DFT with the self-consistent isodensity polarizable continuum model (SCI-PCM). Two remarkable carbonyl (C=O) peaks of benzaldehyde were observed by FT-IR in alcohol solvents, which were caused by different hydrogen bond species and explained by ab initio calculation. The results showed that the combination of SCI-PCM model and ab initio calculation could give excellent agreements with FT-IR spectra of title compound in solutions.

  1. Genetic Functional Algorithm Prediction of Toxicity of some Polychlorinated Dioxins using DFT and Semi-empirical Calculated Molecular Descriptors

    Directory of Open Access Journals (Sweden)

    Hassan Samuel

    2016-03-01

    Full Text Available A set of twenty five compounds of polyhalogenated dioxins with toxicity data in EC50 was subjected to quantitative structure activity relationship studies using Material Studio software 7.0. Large number of molecular descriptors was calculated from the level of theory DFT (BLYP/6-31G* and semi-empirical (AM1 using the softwares Spartan 14v1.1.2 and PaDel descriptor. The correlation between the toxicities and the DFT and semi-empirical calculated descriptors was examined. Genetic Function Approximation (GFA technique was used to generate ten QSAR models for each of the two level of theory, out of these models the one with the highest statistical significance was selected as the best for the two methods. DFT (R2 = 0.9516, R2 adj = 0.9389, R2 cv = 0.9091, LOF = 0.5882, significance of regression F-value = 74.8019 and Semi-empirical (R2 = 0.96803, R2 adj = 0.9596, R2 cv = 0.9518, LOF = 0.3877, significance of regression F-value = 115.0703. These descriptors were found to be responsible for the toxicities of polyhalogenated dioxins. DFT (BCUTc-1h, VP-3, SssssGe, 0ETA_dAlpha_B and ETA_BetaP and semi-empirical (EHOMO, SP-7, ETA_Shape_P, ETA_EtaP_L and GRAV-4. From the comparison of the models generated using DFT and semi-empirical and based on their statistical parameters, semi-empirical (AM1 has slightly better predictive power than DFT (BLYP/6-31G*.

  2. Performance of DFT Methods in the Calculation of Optical Spectra of TCF-Chromophores.

    Science.gov (United States)

    Andzelm, Jan; Rinderspacher, Berend C; Rawlett, Adam; Dougherty, Joseph; Baer, Roi; Govind, Niranjan

    2009-10-13

    We present electronic structure calculations of the ultraviolet/visible (UV-vis) spectra of highly active push-pull chromophores containing the tricyanofuran (TCF) acceptor group. In particular, we have applied the recently developed long-range corrected Baer-Neuhauser-Livshits (BNL) exchange-correlation functional. The performance of this functional compares favorably with other density functional theory (DFT) approaches, including the CAM-B3LYP functional. The accuracy of UV-vis results for these molecules is best at low values of attenuation parameters (γ) for both BNL and CAM-B3LYP functionals. The optimal value of γ is different for the charge-transfer (CT) and π-π* excitations. The BNL and PBE0 exchange correlation functionals capture the CT states particularly well, while the π-π* excitations are less accurate and system dependent. Chromophore conformations, which considerably affect the molecular hyperpolarizability, do not significantly influence the UV-vis spectra on average. As expected, the color of chromophores is a sensitive function of modifications to its conjugated framework and is not significantly affected by increasing aliphatic chain length linking a chromophore to a polymer. For selected push-pull aryl-chromophores, we find a significant dependence of absorption spectra on the strength of diphenylaminophenyl donors.

  3. Experimental and ab initio DFT calculated Raman Spectrum of Sudan I, a Red Dye

    DEFF Research Database (Denmark)

    Kunov-Kruse, Andreas Jonas; Kristensen, Steffen Buus; Liu, Chuan

    2011-01-01

    The red dye Sudan I was investigated by Raman spectroscopy using different excitation wavelengths (1064, 532 and 244 nm). A calculation of the Raman spectrum based on quantum mechanical ab initio density functional theory (DFT) was made using the RB3LYP method with the 3-21G and 6-311+G(d,p) basis....... Comparison was made with other azo dyes in the literature on natural, abundant plant pigments. The results show that there is a possibility in foodstuff analysis to distinguish Sudan I from other dyes by using Raman spectroscopy with more than one laser wavelength for resonance enhancement of the different...... of the Sudan I molecule was involved in the majority of the vibrations through N N and C–N stretching and various bending modes. Low-intensity bands in the lower wavenumber range (at about 721, 616, 463 and 218 cm−1) were selectively enhanced by the resonance Raman effect when using the 532 nm excitation line...

  4. Theoretical study of atomic oxygen on gold surface by Hückel theory and DFT calculations.

    Science.gov (United States)

    Sun, Keju; Kohyama, Masanori; Tanaka, Shingo; Takeda, Seiji

    2012-09-27

    It is fundamental to understand the behavior of atomic oxygen on gold surfaces so as to elucidate the mechanism of nano gold catalysts for low-temperature CO oxidation reactions since the atomic oxygen on gold system is an important intermediate involved in both the processes of O(2) dissociation and CO oxidation. We performed theoretical analysis of atomic oxygen adsorption on gold by using Hückel theory. It is found that formation of linear O-Au-O structure on Au surfaces greatly stabilizes the atomic oxygen adsorption due to stronger bond energy and bond order, which is confirmed subsequently by density functional theory (DFT) calculations. The linear O-Au-O structure may explain the surprising first order kinetics behavior of O(2) desorption from gold surfaces. This view of the linear O-Au-O structure as the natural adsorption status is quite different from the conventional view, which may lead to new understanding toward the reaction mechanism of low-temperature CO oxidation reaction on nano gold catalysts.

  5. Salicylamide cocrystals: screening, crystal structure, sublimation thermodynamics, dissolution, and solid-state DFT calculations.

    Science.gov (United States)

    Manin, Alex N; Voronin, Alexander P; Manin, Nikolay G; Vener, Mikhail V; Shishkina, Anastasia V; Lermontov, Anatoly S; Perlovich, German L

    2014-06-19

    A new cocrystal of 2-hydroxybenzamide (A) with 4-acetamidobenzoic acid (B) has been obtained by the DSC screening method. Thermophysical analysis of the aggregate [A:B] has been conducted and a fusion diagram has been plotted. Cocrystal formation from melts was studied by using thermomicroscopy. A cocrystal single-crystal was grown and its crystal structure was determined. The pattern of noncovalent interactions has been quantified using the solid-state DFT computations coupled with the Bader analysis of the periodic electron density. The sublimation processes of A-B cocrystal have been studied and its thermodynamic functions have been calculated. The classical method of substance transfer by inert gas-carrier was chosen to investigate sublimation processes experimentally. The lattice energy is found to be 143 ± 4 kJ/mol. It is lower than the sum of the corresponding values of the cocrystal pure components. The theoretical value of the lattice energy, 156 kJ/mol, is in reasonable agreement with the experimental one. A ternary phase diagram of solubility (A-B-ethanol) has been plotted and the areas with solutions for growing thermodynamically stable cocrystals have been determined.

  6. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Chavda, Bhavin R., E-mail: chavdabhavin9@gmail.com; Dubey, Rahul P.; Patel, Urmila H. [Department of Physics, Sardar Patel University, Vallabh Vidyanagar-388120, Gujarat (India); Gandhi, Sahaj A. [Bhavan’s Shri I.L. Pandya Arts-Science and Smt. J.M. shah Commerce College, Dakar, Anand -388001, Gujarat, Indian (India); Barot, Vijay M. [P. G. Center in Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat 383 215 (India)

    2016-05-06

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb –London –Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

  7. The potential surface in the ground electronic state of HCP with the isomerization process: the validity of calculating potential surface with DFT methods

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The density functional theory (DFT) provides us an effective way to calculate large cluster systems with moderate computational demands. We calculate potential energy surfaces (PES) with several different approaches of DFT. The PES in the ground electronic state are related to HCP's isomerization process. The calculated PES are compared with the “experimental” PES obtained by fitting from the experimental vibrational spectra and that given by the “accurate” quantum chemistry calculation with more expensive computations. The comparisons show that the potential surfaces calculated with DFT methods can reach the accuracy of less than 0.1 eV.

  8. Electronic structure of O-doped SiGe calculated by DFT + U method

    Science.gov (United States)

    Zhao, Zong-Yan; Yang, Wen; Yang, Pei-Zhi

    2016-12-01

    To more in depth understand the doping effects of oxygen on SiGe alloys, both the micro-structure and properties of O-doped SiGe (including: bulk, (001) surface, and (110) surface) are calculated by DFT + U method in the present work. The calculated results are as follows. (i) The (110) surface is the main exposing surface of SiGe, in which O impurity prefers to occupy the surface vacancy sites. (ii) For O interstitial doping on SiGe (110) surface, the existences of energy states caused by O doping in the band gap not only enhance the infrared light absorption, but also improve the behaviors of photo-generated carriers. (iii) The finding about decreased surface work function of O-doped SiGe (110) surface can confirm previous experimental observations. (iv) In all cases, O doing mainly induces the electronic structures near the band gap to vary, but is not directly involved in these variations. Therefore, these findings in the present work not only can provide further explanation and analysis for the corresponding underlying mechanism for some of the experimental findings reported in the literature, but also conduce to the development of μc-SiGe-based solar cells in the future. Project supported by the Natural Science Foundation of Yunnan Province, China (Grant No. 2015FB123), the 18th Yunnan Province Young Academic and Technical Leaders Reserve Talent Project, China (Grant No. 2015HB015), and the National Natural Science Foundation of China (Grant No. U1037604).

  9. The screened pseudo-charge repulsive potential in perturbed orbitals for band calculations by DFT+U.

    Science.gov (United States)

    Huang, Bolong

    2017-03-06

    The conventional linear response overestimates the U in DFT+U calculations for solids with fully occupied orbitals. Here, we demonstrate that the challenge arises from the incomplete cancellation of the electron-electron Coulomb repulsion energy under external perturbation. We applied the second charge response, denoted as the "pseudo-charge" model, to offset such residue effects. Counteracting between these two charge response-induced Coulomb potentials, the U parameters are self-consistently obtained by fulfilling the conditions for minimizing the non-Koopmans energy. Moreover, the pseudo-charge-induced repulsive potential shows a screening behavior related to the orbital occupation and is potentially in compliance with the screened exact exchange-correlation of electrons. The resultant U parameters are self-consistent solutions for improved band structure calculations by the DFT+U method. This work extends the validity of the linear response method to both partially and fully occupied orbitals and gives a reference for estimating the Hubbard U parameter prior to other advanced methods. The U parameters were determined in a transferability test using both PBE and hybrid density functional methods, and the results showed that this method is independent of the functional. The electronic structures determined from the hybrid-DFT+U(hybrid) approach are provided. Comparisons are also made with the recently developed self-consistent hybrid-DFT+Uw method.

  10. Benchmark Calculations on the Atomization Enthalpy,Geometry and Vibrational Frequencies of UF6 with Relativistic DFT Methods

    Institute of Scientific and Technical Information of China (English)

    XIAO Hai; LI Jun

    2008-01-01

    Benchmark calculations on the molar atomization enthalpy, geometry, and vibrational frequencies of uranium hexafluoride (UF6) have been performed by using relativistic density functional theory (DFT) with various levels of relativistic effects, different types of basis sets, and exchange-correlation functionals. Scalar relativistic effects are shown to be critical for the structural properties. The spin-orbit coupling effects are important for the calculated energies, but are much less important for other calculated ground-state properties of closed-shell UF6. We conclude through systematic investigations that ZORA- and RECP-based relativistic DFT methods are both appropriate for incorporating relativistic effects. Comparisons of different types of basis sets (Slater, Gaussian, and plane-wave types) and various levels of theoretical approximation of the exchange-correlation functionals were also made.

  11. Molecular structure and vibrational and chemical shift assignments of 3'-chloro-4-dimethylamino azobenzene by DFT calculations.

    Science.gov (United States)

    Toy, Mehmet; Tanak, Hasan

    2016-01-05

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3'-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400cm(-1) for solid state. The (1)H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

  12. Molecular structure and vibrational and chemical shift assignments of 3‧-chloro-4-dimethylamino azobenzene by DFT calculations

    Science.gov (United States)

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3‧-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state. The 1H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

  13. Theoretical investigation of lead vapor adsorption on kaolinite surfaces with DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xinye [Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, School of Energy and Environment, Southeast University, Nanjing 210096 (China); Huang, Yaji, E-mail: heyyj@seu.edu.cn [Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, School of Energy and Environment, Southeast University, Nanjing 210096 (China); Pan, Zhigang [College of Materials Science and Engineering, Nanjing Tech University, Nanjing 210009 (China); Wang, Yongxing; Liu, Changqi [Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, School of Energy and Environment, Southeast University, Nanjing 210096 (China)

    2015-09-15

    Highlights: • Al surface after dehydroxylation is active while Si surface is inert. • The active sites are the unsaturated Al atoms and O atoms losing H atom. • PbO is the most suitable species for adsorption. • Increasing the activities of Al atoms can enhance the performance of kaolinite. • Produce of amorphous silica is a potential path to enhance the performance of kaolinite. - Abstract: Kaolinite can be used as the in-furnace sorbent/additive to adsorb lead (Pb) vapor at high temperature. In this paper, the adsorptions of Pb atom, PbO molecule and PbCl{sub 2} molecule on kaolinie surfaces were investigated by density functional theory (DFT) calculation. Si surface is inert to Pb vapor adsorption while Al surfaces with dehydroxylation are active for the unsaturated Al atoms and the O atoms losing H atoms. The adsorption energy of PbO is much higher than that of Pb atom and PbCl{sub 2}. Considering the energy barriers, it is easy for PbO and PbCl{sub 2} to adsorb on Al surfaces but difficult to escape. The high energy barriers of de–HCl process cause the difficulties of PbCl{sub 2} to form PbO·Al{sub 2}O{sub 3}·2SiO{sub 2} with kaolinite. Considering the inertia of Si atoms and the activity of Al atoms after dehydroxylation, calcination, acid/alkali treatment and some other treatment aiming at amorphous silica producing and Al activity enhancement can be used as the modification measures to improve the performance of kaolinite as the in-furnace metal capture sorbent.

  14. Interaction mechanisms of Ionizable Organic Pollutants with Aromatized Biochar: Adsorption Experiments and DFT Calculations

    Science.gov (United States)

    Zhang, Kun; Chen, Baoliang

    2017-04-01

    The molecular interaction between biochars and ionizable organic pollutants (IOPs) are of great concern in natural environments, however the underlying mechanisms and their quantification under different pH range are not vivid. The adsorption of IOPs onto high temperature biochars derived from bamboo wood biomass (BW700) was conducted to quantify the various interactions between sorbent surface and IOPs under different pH conditions. The aromatized surface of BW700 were characterized by Fourier Transformed Infrared spectroscopy (FT-IR), Brunauer-Emmet-Teller (BET) specific surface area with N2 and CHN elemental compositions. Seven IOPs were selected as model sorbates, and batch sorption experiments were conducted to quantify the ratio of π-π interactions and hydrogen bonding interactions. The pH-dependent adsorption curves and the adsorption isotherms not only indicated that the adsorption capacity was related with species of IOPs, but also showed the presence of adsorbing peak owing some of the other mechanisms when taking the ice-like adlayer into consideration. Finally, density functional theory (DFT) calculations provided a possible structure of the complex combined with ice-like adlayer with aromatic substrate of BW700, and indicated that the formation of extra adsorption sites originated from the X-H ... O-H ... π interactions. The contribution of π-π interactions, hydrogen bonding interactions and X-H ... O-H ... π interactions were distinguished by the pKa value of IOPs owing to their species. Our findings provide new insight for distinction and quantification of various interactions under different pH conditions, and it is the first time to put forward the X-H ... O-H ... π interactions for the interaction mechanism of IOPs with biochar.

  15. Study of the thermal stability of studtite by in situ Raman spectroscopy and DFT calculations

    Science.gov (United States)

    Colmenero, Francisco; Bonales, Laura J.; Cobos, Joaquín; Timón, Vicente

    2017-03-01

    The design of a safe spent nuclear fuel repository requires the knowledge of the stability of the secondary phases which precipitate when water reaches the fuel surface. Studtite is recognized as one of the secondary phases that play a key-role in the mobilization of the radionuclides contained in the spent fuel. Thereby, it has been identified as a product formed under oxidation conditions at the surface of the fuel, and recently found as a corrosion product in the Fukushima-Daiichi nuclear plant accident. Thermal stability is one of the properties that should be determined due to the high temperature of the fuel. In this work we report a detailed analysis of the structure and thermal stability of studtite. The structure has been studied both by experimental techniques (SEM, TGA, XRD and Raman spectroscopy) and theoretical DFT electronic structure and spectroscopic calculations. The comparison of the results allows us to perform for the first time the Raman bands assignment of the whole spectrum. The thermal stability of studtite has been analyzed by in situ Raman spectroscopy, with the aim of studying the effect of the heating rate and the presence of water. For this purpose, a new cell has been designed. The results show that studtite is stable under dry conditions only at temperatures below 30 °C, in contrast with the higher temperatures published up to date ( 130 °C). Opposite behaviour has been found when studtite is in contact with water; under these conditions studtite is stable up to 90 °C, what is consistent with the encounter of this phase after the Fukushima-Daiichi accident.

  16. Calculation of the vibrational spectra of RDX as a function of pressure using the Grimme DFT potential

    Science.gov (United States)

    Perger, Warren; Flurchick, K. M.; Slough, Wil; Valenzano, Loredana

    2011-06-01

    The density-functional theory (DFT) potential by Grimme has been proposed for describing long-range dispersion corrections. This potential has been implemented into the CRYSTAL09 program and used to calculate the vibrational spectra in RDX at equilibrium and as a function of pressure. The intensities, Born charge tensor, and high-frequency dielectric constant are reported and compared with prior theory and experiment where possible. Supported by ONR-MURI grant N00014-06-1-0459.

  17. Rapidly calculated density functional theory (DFT) relaxed Iso-potential Phi Si Maps: Beta-cellobiose

    Science.gov (United States)

    New cellobiose Phi-H/Si-H maps are rapidly generated using a mixed basis set DFT method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are made for different conformational states of cellobiose, showing how glycosidic bond dihe...

  18. How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase

    Directory of Open Access Journals (Sweden)

    Yanwei Li

    2016-08-01

    Full Text Available The quantum mechanics/molecular mechanics (QM/MM method (e.g., density functional theory (DFT/MM is important in elucidating enzymatic mechanisms. It is indispensable to study “multiple” conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case.

  19. Structural and theoretical investigations of short hydrogen bonds: neutron diffraction and plane-wave DFT calculations of urea phosphoric acid

    Science.gov (United States)

    Wilson, Chick C.; Morrison, Carole A.

    2002-08-01

    Low temperature neutron diffraction and high level computational methods have been applied to investigate the short hydrogen bond in urea-phosphoric acid. It is found that isolated molecule calculations predict a `normal' O-H⋯O hydrogen bond, in strong disagreement with the very short, 3 c-4 e hydrogen bond found from the neutron diffraction. Extending these calculations into a periodic environment using plane-wave DFT methods give much improved agreement with experiment, with a much shorter, stronger hydrogen bond, and significant elongation of the O-H `covalent' bond.

  20. Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.

    Science.gov (United States)

    Bielecki, Jakub; Lipiec, Ewelina

    2016-02-01

    Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople's basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.

  1. Electronic structure and optical properties of noncentrosymmetric LiGaSe2: Experimental measurements and DFT band structure calculations

    Science.gov (United States)

    Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Ananchenko, L. N.; Isaenko, L. I.; Yelisseyev, A. P.; Khyzhun, O. Y.

    2017-04-01

    We report on measurements of X-ray photoelectron (XP) spectra for pristine and Ar+ ion-irradiated surfaces of LiGaSe2 single crystal grown by Bridgman-Stockbarger method. Electronic structure of the LiGaSe2 compound is studied from a theoretical and experimental viewpoint. In particular, total and partial densities of states of LiGaSe2 are investigated by density functional theory (DFT) calculations employing the augmented plane wave + local orbitals (APW + lo) method and they are verified by data of X-ray spectroscopy measurements. The DFT calculations indicate that the main contributors to the valence band of LiGaSe2 are the Se 4p states, which contribute mainly at the top and in the upper portion of the valence band, with also essential contributions of these states in the lower portion of the band. Other substantial contributions to the valence band of LiGaSe2 emerge from the Ga 4s and Ga 4p states contributing mainly at the lower ant upper portions of the valence band, respectively. With respect to the conduction band, the calculations indicate that its bottom is composed mainly from contributions of the unoccupied Ga s and Se p states. The present calculations are confirmed experimentally when comparing the XP valence-band spectrum of the LiGaS2 single crystal on a common energy scale with the X-ray emission bands representing the energy distribution of the Ga 4p and Se 4p states. Measurements of the fundamental absorption edges at room temperature reveal that bandgap value, Eg, of LiGaSe2 is equal to 3.47 eV and the Eg value increases up to 3.66 eV when decreasing temperature to 80 K. The main optical characteristics of the LiGaSe2 compound are clarified by the DFT calculations.

  2. DFT-GIAO calculation of properties of {sup 19}F NMR and stability study of environmentally relevant perfluoroalkylsulfonamides (PFASAmide)

    Energy Technology Data Exchange (ETDEWEB)

    Mejia-Urueta, Rafael; Mestre-Quintero, Kleyber; Vivas-Reyes, Ricardo, E-mail: rvivasr@unicartagena.edu.co [Grupo de Quimica Cuantica y Teorica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena (Colombia)

    2011-09-15

    Perfluorinated organic compounds (POCs), such as perfluorooctanesulfonate (PFOS) and perfluoroalkylsulfonamide (PFASA) are compounds that have recently attracted considerable attention worldwide because of its high persistence and wide distribution in the environment. Among the spectroscopic methods used to study the PFASA, {sup 19}F nuclear magnetic resonance (NMR {sup 19}F) is very effective, due to its ability to determine concentrations of PFASA in biological samples and measure pollution in water samples. For this reason, a theoretical study of the properties of {sup 19}F NMR was performed. In this study we have determined the shielding constant ({sigma}) for different fluorine nucleus of the 18 molecules under study, using density functional theory (DFT) and GIAO method with the B3PW91/6-31+G(d,p) level of calculation. The {sigma} calculations were made at vacuum and in presence of a solvent. The values of chemical shifts ({delta}), were also calculated in a different level of theory. The best results were obtained with the level of calculation DFT-GIAO/B3PW91/6-31+G(d,p) by considering the solvent such as dimethylsulfoxide (DMSO), chloroform (CHCl{sub 3}), acetone (CH{sub 3}COCH{sub 3}) and methanol (CH{sup 3}OH). The results were interpreted in terms of calculated hardness at DFT/B3PW91/6-31+G(d, p) level. The behaviour of the hardness was higher in the molecules of four carbons PFASA than eight carbons. This explain theoretically resistance of four carbons PFAS to be transformed into perfluorobutanesulfonate (PFBS). (author)

  3. DFT calculations of electronic and optical properties of SrS with LDA, GGA and mGGA functionals

    Science.gov (United States)

    Sharma, Shatendra; Sharma, Jyotsna; Sharma, Yogita

    2016-05-01

    The theoretical investigations of electronic and optical properties of SrS are made using the first principle DFT calculations. The calculations are performed for the local-density approximation (LDA), generalized gradient approximation (GGA) and for an alternative form of GGA i.e. metaGGA for both rock salt type (B1, Fm3m) and cesium chloride (B2, Pm3m) structures. The band structure, density of states and optical spectra are calculated under various available functional. The calculations with LDA and GGA functional underestimate the values of band gaps with all functional, however the values with mGGA show reasonably good agreement with experimental and those calculated by using other methods.

  4. Spectroscopic investigations of 2,5-Difluoronitrobenzene using Hartree-Fock (HF) and density functional theory (DFT) calculations

    Science.gov (United States)

    Saravanan, S. P.; Sankar, A.; Parimala, K.

    2017-01-01

    The complete structural and vibrational analysis of the 2,5-Difluoronitrobenzene (DNB) was carried out by Hartree-Fock (HF) and density functional theory (DFT) method (B3LYP) with 6-311++G (d,p) basis set. The fundamental vibrations are assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. Using the time-dependent density functional theory (TD-DFT) method, electronic absorption spectra of the title compound have been predicted and a good agreement with the experimental ones is determined. 13C and 1H NMR spectra were recorded and chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The hyperconjugative interaction energy (E(2)) and electron densities of donor (i) and acceptor (j) bonds were calculated using natural bond orbital (NBO) analysis. In addition, molecular electrostatic potential (MEP) and atomic charges were calculated using B3LYP/6-311++G (d,p) level of theory. Moreover, thermodynamic properties (heat capacities, entropy, enthalpy and Gibb's free energy) of the title compound at different temperatures were calculated.

  5. Hydrogen Transfer in Energetic Materials from ReaxFF and DFT Calculations.

    Science.gov (United States)

    Sergeev, Oleg V; Yanilkin, Alexey V

    2017-04-27

    Energetic materials are characterized by fast and complex chemical reactions. It makes them hardly available for kinetic experiments in relevant conditions and a good target for reactive molecular dynamics simulations. In this work, unimolecular and condensed-phase thermal decomposition of pentaerythritol tetranitrate (PETN) are investigated by ReaxFF molecular dynamics. It is shown that the decomposition kinetics in condensed phase may be described with the activation barrier lower by a factor of 2 than that for isolated molecules. The effect of the intermolecular hydrogen transfer is revealed in condensed phase. Energetic barriers for hydrogen transfer in two energetic materials (methyl nitrate, which is a nitroester as well as PETN, and o-nitrotoluene) are studied with ReaxFF and DFT using nudged elastic band technique. The results indicate that ReaxFF gives significantly lower activation energy for intermolecular hydrogen transfer in nitroesters than different DFT approximations, which explains the molecular dynamics results for PETN.

  6. The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies

    Science.gov (United States)

    Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L.; Sinha, Chittaranjan

    2015-02-01

    Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)sbnd H(7A)---O(2), N(7)sbnd H(7B)---O(3), N(1)sbnd H(1)---N(2), C(5)sbnd H(5)---O(3)sbnd S(1) and N(7)sbnd (H7A)---O(2)sbnd S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37 × 104 M-1. The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

  7. The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies.

    Science.gov (United States)

    Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L; Sinha, Chittaranjan

    2015-02-25

    Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)-H(7A)-O(2), N(7)-H(7B)-O(3), N(1)-H(1)-N(2), C(5)-H(5)-O(3)-S(1) and N(7)-(H7A)-O(2)-S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37×10(4)M(-1). The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

  8. Enhancement of DFT-calculations at petascale: Nuclear Magnetic Resonance, Hybrid Density Functional Theory and Car-Parrinello calculations

    Science.gov (United States)

    Varini, Nicola; Ceresoli, Davide; Martin-Samos, Layla; Girotto, Ivan; Cavazzoni, Carlo

    2013-08-01

    One of the most promising techniques used for studying the electronic properties of materials is based on Density Functional Theory (DFT) approach and its extensions. DFT has been widely applied in traditional solid state physics problems where periodicity and symmetry play a crucial role in reducing the computational workload. With growing compute power capability and the development of improved DFT methods, the range of potential applications is now including other scientific areas such as Chemistry and Biology. However, cross disciplinary combinations of traditional Solid-State Physics, Chemistry and Biology drastically improve the system complexity while reducing the degree of periodicity and symmetry. Large simulation cells containing of hundreds or even thousands of atoms are needed to model these kind of physical systems. The treatment of those systems still remains a computational challenge even with modern supercomputers. In this paper we describe our work to improve the scalability of Quantum ESPRESSO (Giannozzi et al., 2009 [3]) for treating very large cells and huge numbers of electrons. To this end we have introduced an extra level of parallelism, over electronic bands, in three kernels for solving computationally expensive problems: the Sternheimer equation solver (Nuclear Magnetic Resonance, package QE-GIPAW), the Fock operator builder (electronic ground-state, package PWscf) and most of the Car-Parrinello routines (Car-Parrinello dynamics, package CP). Final benchmarks show our success in computing the Nuclear Magnetic Response (NMR) chemical shift of a large biological assembly, the electronic structure of defected amorphous silica with hybrid exchange-correlation functionals and the equilibrium atomic structure of height Porphyrins anchored to a Carbon Nanotube, on many thousands of CPU cores.

  9. FT-IR and Raman spectra and vibrational investigation of bis (4-acetylanilinium) hexachlorostannate using DFT (B3LYP) calculation

    Science.gov (United States)

    Tarchouna, S.; Chaabane, I.; Rahaiem, A. Ben

    2016-09-01

    4-acetylanilinium was used as a ligand for the synthesis of the organic/inorganic compound bis (4-acetylanilinium) hexachlorostannate. Vibrational study in the solid state was performed by FT-Raman of the free 4-acetylanilinium ligand C8H9ON+ and by FT-IR and FT-Raman spectroscopies of the [C8H10NO]2 SnCl6 compound. The comparative analysis of the Raman spectra of the title compound with that of the free ligand was discussed. The structure of the [C8H10NO]2SnCl6 was optimized by density functional theory (DFT) using B3LYP method and shows that the calculated values obtained by B3LYP/LanL2DZ basis are in a better agreement with the experimental data reported by Song et al. (2011) [1] than those obtained by B3LYP/LanL2MB basis. The vibrational frequencies are calculated using density functional theory (DFT) with the B3LYP/LanL2DZ basis, and scaled by various factors. Root mean square (RMS) value was calculated and the small difference between experimental and calculated modes has been interpreted by intermolecular interactions in the crystal.

  10. Electronic structure of interstitial hydrogen in lutetium oxide from DFT+U calculations and comparison study with μ SR spectroscopy

    Science.gov (United States)

    da Silva, E. Lora; Marinopoulos, A. G.; Vieira, R. B. L.; Vilão, R. C.; Alberto, H. V.; Gil, J. M.; Lichti, R. L.; Mengyan, P. W.; Baker, B. B.

    2016-07-01

    The electronic structure of hydrogen impurity in Lu2O3 was studied by first-principles calculations and muonium spectroscopy. The computational scheme was based on two methods which are well suited to treat defect calculations in f -electron systems: first, a semilocal functional of conventional density-functional theory (DFT) and secondly a DFT+U approach which accounts for the on-site correlation of the 4 f electrons via an effective Hubbard-type interaction. Three different types of stable configurations were found for hydrogen depending upon its charge state. In its negatively charged and neutral states, hydrogen favors interstitial configurations residing either at the unoccupied sites of the oxygen sublattice or at the empty cube centers surrounded by the lanthanide ions. In contrast, the positively charged state stabilized only as a bond configuration, where hydrogen binds to oxygen ions. Overall, the results between the two methods agree in the ordering of the formation energies of the different impurity configurations, though within DFT+U the charge-transition (electrical) levels are found at Fermi-level positions with higher energies. Both methods predict that hydrogen is an amphoteric defect in Lu2O3 if the lowest-energy configurations are used to obtain the charge-transition, thermodynamic levels. The calculations of hyperfine constants for the neutral interstitial configurations show a predominantly isotropic hyperfine interaction with two distinct values of 926 MHz and 1061 MHz for the Fermi-contact term originating from the two corresponding interstitial positions of hydrogen in the lattice. These high values are consistent with the muonium spectroscopy measurements which also reveal a strongly isotropic hyperfine signature for the neutral muonium fraction with a magnitude slightly larger (1130 MHz) from the ab initio results (after scaling with the magnetic moments of the respective nuclei).

  11. Structural Investigation of Methanol {6-[(2-oxidopropyliminomethyl] phenolato} dioxidomolybdenum(VI by X-Ray Crystallography and DFT Calculations

    Directory of Open Access Journals (Sweden)

    Iran SHEIKHSHOAIE

    2012-09-01

    Full Text Available This article presents the computational calculations of a cis-dioxomolybdenum(VI complex by using density functional theory (DFT with a DZP basis set (double zeta polarized basis set. The Schiff base 2-((E-(2-hydroxypropyliminomethyl-6-methoxyphenol was treated with MoO2(acac2 in dry methanol to produce the mononuclear complex methanol{2-methoxy-6-[(2-oxidopropyl iminomethyl]phenolato} dioxidomolybdenum(VI, whose structure has been solved and successfully refined in the monoclinic space group P21/c, with a = 6.755 Å, b = 15.835 Å, c = 13.119 Å, V = 1388.79 Å3, and Z = 4.

  12. Calculating hyperfine couplings in large ionic crystals containing hundreds of QM atoms: subsystem DFT is the key.

    Science.gov (United States)

    Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele

    2013-11-14

    We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

  13. Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals

    Science.gov (United States)

    Frau, Juan; Glossman-Mitnik, Daniel

    2017-01-01

    Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly. PMID:28361050

  14. Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals.

    Science.gov (United States)

    Frau, Juan; Glossman-Mitnik, Daniel

    2017-01-01

    Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly.

  15. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

    Science.gov (United States)

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

  16. Molecular structure, spectroscopic characterization, HOMO and LUMO analysis of 3,3'-diaminobenzidine with DFT quantum chemical calculations.

    Science.gov (United States)

    Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

    2015-11-05

    In this work, infrared, Raman and UV spectra of 3,3'-diaminobenzidine (3,3-DAB) were carried out by using density functional theory (DFT)/B3LYP method with 6-311G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the region 4000-400 and 4000-50 cm(-1), respectively. The geometrical parameters, energies and wavenumbers were obtained and fundamental vibrations were assigned on the basis of the potential energy distribution (PED) of the vibrational modes. The UV spectrum of the investigated compound was recorded in the range of 200-400 nm in ethanol and water solutions. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. Thermodynamic properties, Mulliken atomic charges and molecular electrostatic potential (MEP) were calculated for the title molecule. Also the nonlinear optical properties of 3,3-DAB molecule were explored theoretically. As a result, the calculated results were compared with the observed values and generally found to be in good agreement.

  17. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations.

    Science.gov (United States)

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as "pau branco". Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The (13)C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d,p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

  18. DFT calculations and experimental FT-IR, FT-Raman, NMR, UV-Vis spectral studies of 3-fluorophenylboronic acid.

    Science.gov (United States)

    Karabacak, M; Kose, E; Sas, E B; Kurt, M; Asiri, A M; Atac, A

    2015-02-05

    The spectroscopic (FT-IR, FT-Raman, (1)H and (13)C NMR, UV-Vis), structural, electronic and thermodynamical properties of 3-fluorophenylboronic acid (C6H4FB(OH)2), 3FPBA) were submitted by using both experimental techniques and theoretical methods (quantum chemical calculations) in this work. The experimental infrared and Raman spectra were obtained in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The equilibrium geometry and vibrational spectra were calculated by using DFT (B3LYP) with 6-311++G(d,p) basis set. The vibrational wavenumbers were also corrected with scale factor to take better results for the calculated data. The total energy distributions (TED) of the vibrational modes were performed for the assignments of the title molecule by using scaled quantum mechanics (SQM) method. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The (1)H and (13)C NMR spectra were computed by using the gauge-invariant atomic orbital (GIAO) method, showing a good agreement with the experimental ones. The last one UV-Vis absorption spectra were analyzed in two solvents (ethanol and water), saved in the range of 200-400 nm. In addition these, HOMO and LUMO energies, the excitation energies, density of states (DOS) diagrams, thermodynamical properties and molecular electrostatic potential surface (MEPs) were presented. Nonlinear optical (NLO) properties and thermodynamic features were performed. The experimental results are combined with the theoretical calculations using DFT calculations to fortification of the paper. At the end of this work, the results were proved our paper had been indispensable for the literature backing.

  19. DFT calculations on spectroscopic, structural and NLO properties of silver (I) complex with picolinamide

    Science.gov (United States)

    Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

    2017-02-01

    The molecular geometry optimization, vibrational frequencies, the molecular static polarizability (α), first-order static hyperpolarizability (β), second-order static hyperpolarizability (γ) and frontier molecular orbital (FMO) energies of silver (I) complex with picolinamide, [Ag(C6H6N2O)2](NO3).H2O, were investigated using density functional theory (DFT) HSEh1PBE and B3LYP methods with LANL2DZ basis set. The molecular hardness (η) and electronegativity (χ) parameters were also obtained by using FMO energies. The NLO parameters of the complex were compared with those of para-Nitroaniline (pNA) and urea which are typical NLO materials. Obtained data showed that there is an agreement between the predicted and experimental data.

  20. Anharmonic vibrational studies of L-aspartic acid using HF and DFT calculations

    Science.gov (United States)

    Alam, Mohammad Jane; Ahmad, Shabbir

    2012-10-01

    The experimental and theoretical studies on the structure, molecular properties and vibrational spectra of L-aspartic acid are presented. The molecular structure, harmonic and anharmonic vibrational frequencies, molecular properties, MEP mapping, NBO analysis and electronic spectra of L-aspartic acid have been reported. Computed geometrical parameters and anharmonic frequencies of fundamental, combination and overtone transitions were found in satisfactory agreement with the experimental data. The UV-Vis spectrum of present molecule has been recorded and the electronic properties such as HOMO and LUMO energies and few low lying excited states were carried out by using time dependent density functional theory (TD-DFT) approach. Natural Bond Orbital (NBO) analysis has been performed for analyzing charge delocalization throughout the molecule. Molecular electrostatic potential map has also been used for quantitative measure of the chemical activities of various sites of the molecule.

  1. Structure-activity study of thiazides by magnetic resonance methods (NQR, NMR, EPR) and DFT calculations.

    Science.gov (United States)

    Latosińska, J N

    2005-01-01

    The paper presents a comprehensive analysis of the relationship between the electronic structure of thiazides and their biological activity. The compounds of interest were studied in solid state by the resonance methods nuclear quadrupole resonance (NQR), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) and quantum chemistry (ab inito and DFT) methods. Detailed parallel analysis of the spectroscopic parameters such as quadrupole coupling constant (QCC) NQR chemical shift (delta), chemical shift anisotropy (CSA), asymmetry parameter (eta), NMR and hyperfine coupling constant (A), EPR was performed and the electronic effects (polarisation and delocalisation) were revealed and compared. Biological activity of thiazides has been found to depend on many factors, but mainly on the physico-chemical properties whose assessment was possible on the basis of electron density determination in the molecules performed by experimental and theoretical methods.

  2. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method.

    Science.gov (United States)

    Xu, Zhongnan; Joshi, Yogesh V; Raman, Sumathy; Kitchin, John R

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  3. Understanding the difference in cohesive energies between alpha and beta tin in DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Legrain, Fleur; Manzhos, Sergei, E-mail: mpemanzh@nus.edu.sg [Department of Mechanical Engineering, National University of Singapore, 117576 (Singapore)

    2016-04-15

    The transition temperature between the low-temperature alpha phase of tin to beta tin is close to the room temperature (T{sub αβ} = 13{sup 0}C), and the difference in cohesive energy of the two phases at 0 K of about ΔE{sub coh} =0.02 eV/atom is at the limit of the accuracy of DFT (density functional theory) with available exchange-correlation functionals. It is however critically important to model the relative phase energies correctly for any reasonable description of phenomena and technologies involving these phases, for example, the performance of tin electrodes in electrochemical batteries. Here, we show that several commonly used and converged DFT setups using the most practical and widely used PBE functional result in ΔE{sub coh} ≈0.04 eV/atom, with different types of basis sets and with different models of core electrons (all-electron or pseudopotentials of different types), which leads to a significant overestimation of T{sub αβ}. We show that this is due to the errors in relative positions of s and p –like bands, which, combined with different populations of these bands in α and β Sn, leads to overstabilization of alpha tin. We show that this error can be effectively corrected by applying a Hubbard +U correction to s –like states, whereby correct cohesive energies of both α and β Sn can be obtained with the same computational scheme. We quantify for the first time the effects of anharmonicity on ΔE{sub coh} and find that it is negligible.

  4. Molecular Structure, NMR, HOMO, LUMO, and Vibrational Analysis of O-Anisic Acid and Anisic Acid Based on DFT Calculations

    Directory of Open Access Journals (Sweden)

    R. Mathammal

    2013-01-01

    Full Text Available This work deals with the vibrational spectroscopy of O-Anisic acid (OAA and Anisic acid (AA. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT with standard B3LYP/6-31G** method and basis set combinations. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical force field. The infrared and Raman spectra were also predicted from the calculated intensities. The effects of carbonyl and methyl substitutions on the structure and vibrational frequencies have been investigated. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. The 13C and 1H NMR chemical shifts of the DFA and CA molecules were calculated using the gauge-invariant-atomic orbital (GIAO method in DMSO solution using IEF-PCM model and compared with experimental data.

  5. Molecular structure, vibrational spectral assignments (FT-IR and FT-RAMAN), NMR, NBO, HOMO-LUMO and NLO properties of O-methoxybenzaldehyde based on DFT calculations

    Science.gov (United States)

    Vennila, P.; Govindaraju, M.; Venkatesh, G.; Kamal, C.

    2016-05-01

    Fourier transform - Infra red (FT-IR) and Fourier transform - Raman (FT-Raman) spectroscopic techniques have been carried out to analyze O-methoxy benzaldehyde (OMB) molecule. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT). The vibrational analysis of stable isomer of OMB has been carried out by FT-IR and FT-Raman in combination with theoretical method simultaneously. The first-order hyperpolarizability and the anisotropy polarizability invariant were computed by DFT method. The atomic charges, hardness, softness, ionization potential, electronegativity, HOMO-LUMO energies, and electrophilicity index have been calculated. The 13C and 1H Nuclear magnetic resonance (NMR) have also been obtained by GIAO method. Molecular electronic potential (MEP) has been calculated by the DFT calculation method. Electronic excitation energies, oscillator strength and excited states characteristics were computed by the closed-shell singlet calculation method.

  6. (13)C, (15)N CPMAS NMR and GIAO DFT calculations of stereoisomeric oxindole alkaloids from Cat's Claw (Uncaria tomentosa).

    Science.gov (United States)

    Paradowska, Katarzyna; Wolniak, Michał; Pisklak, Maciej; Gliński, Jan A; Davey, Matthew H; Wawer, Iwona

    2008-11-01

    Oxindole alkaloids, isolated from the bark of Uncaria tomentosa [Willd. ex Schult.] Rubiaceae, are considered to be responsible for the biological activity of this herb. Five pentacyclic and two tetracyclic alkaloids were studied by solid-state NMR and theoretical GIAO DFT methods. The (13)C and (15)N CPMAS NMR spectra were recorded for mitraphylline, isomitraphylline, pteropodine (uncarine C), isopteropodine (uncarine E), speciophylline (uncarine D), rhynchophylline and isorhynchophylline. Theoretical GIAO DFT calculations of shielding constants provide arguments for identification of asymmetric centers and proper assignment of NMR spectra. These alkaloids are 7R/7S and 20R/20S stereoisomeric pairs. Based on the (13)C CP MAS chemical shifts the 7S alkaloids (delta C3 70-71ppm) can be easily and conveniently distinguished from 7R (deltaC3 74.5-74.9ppm), also 20R (deltaC20 41.3-41.7ppm) from the 20S (deltaC20 36.3-38.3ppm). The epiallo-type isomer (3R, 20S) of speciophylline is characterized by a larger (15)N MAS chemical shift of N4 (64.6ppm) than the allo-type (3S, 20S) of isopteropodine (deltaN4 53.3ppm). (15)N MAS chemical shifts of N1-H in pentacyclic alkaloids are within 131.9-140.4ppm.

  7. Molecular and supramolecular properties of nitroaromatic thiosemicarbazones: Synthesis, spectroscopy, X-ray structure elucidation and DFT calculations

    Science.gov (United States)

    Dias, L. C.; de Lima, G. M.; Pinheiro, C. B.; Nascimento, M. A. C.; Bitzer, R. S.

    2017-03-01

    The reactions of 6-nitropiperonal with H2Nsbnd NHsbnd C(S)sbnd NHR, R = Me, Et, Ph or H, afforded four nitroaromatic thiosemicarbazones 1-4, respectively. 1-4 were characterized by elemental analysis (CHN), FTIR, and 1H and 13C{1H} NMR spectroscopy. In addition, the crystal structures of 2 and 3 were determined by single-crystal X-ray diffraction. Our X-ray structural results have shown that the nitropiperonal and thiosemicarbazone moieties exhibit an almost coplanar arrangement for both 2 and 3. Moreover, they establish 2-D networks along the [111] base vector by means of classical and nonclassical hydrogen bonds. Electronic and spectroscopic properties of 1-4 were investigated at the DFT B3LYP/6-311G** level of calculation. The Cdbnd S group of 1-4 constitutes a nucleophilic region, whereas the NO2 group defines an electrophilic centre, as expected. Furthermore, a DFT vibrational analysis of 4 allowed a reliable assignment of the thiosemicarbazone-based vibrations. Also, a good agreement between theoretical and experimental 13C chemical shift values was obtained for 1-4.

  8. UV-Vis spectroscopic study and DFT calculation on the solvent effect of trimethoprim in neat solvents and aqueous mixtures.

    Science.gov (United States)

    Almandoz, M C; Sancho, M I; Duchowicz, P R; Blanco, S E

    2014-08-14

    The solvatochromic behavior of trimethoprim (TMP) was analyzed using UV-Vis spectroscopy and DFT methods in neat and binary aqueous solvent mixtures. The effects of solvent dipolarity/polarizability and solvent-solute hydrogen bonding interactions on the absorption maxima were evaluated by means of the linear solvation energy relationship concept of Kamlet and Taft. This analysis indicated that both interactions play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra of TMP and TMP:(solvent)n complexes in ACN and H2O using TD-DFT methods were in agreement with the experimental ones. Binary aqueous mixtures containing as co-solvents DMSO, ACN and EtOH were studied. Preferential solvation was detected as a nonideal behavior of the wavenumber curve respective to the analytical mole fraction of co-solvent in all binary systems. TMP molecules were preferentially solvated by the organic solvent over the whole composition range. Index of preferential solvation, as well as the influence of solvent parameters were calculated as a function of solvent composition.

  9. Mono azo dyes derived from 5-nitroanthranilic acid: Synthesis, absorption properties and DFT calculations

    Science.gov (United States)

    Karabacak Atay, Çiğdem; Gökalp, Merve; Kart, Sevgi Özdemir; Tilki, Tahir

    2017-08-01

    Four new azo dyes: 2-[(3,5-diamino-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (A), 2-[(3-hydroxy-5-methyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (B), 2-[(3,5-dimethyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (C) and 2-[(5-amino-3-methyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (D) which have the same 4-nitrobenzene/azo/pyrazole skeleton and different substituted groups are synthesized in this work. The structures and spectroscopic properties of these new azo dyes are characterized by using spectroscopic methods such as FT-IR, 1H NMR, 13C NMR and UV-vis. Their solvatochromic properties in chloroform, acetic acid, methanol, dimethylformamide (DMF) and dimethylsulphoxide (DMSO) are studied. Moreover, molecular structures and some spectroscopic properties of azo dyes are investigated by utilizing the quantum computational chemistry method based on Density Functional Theory (DFT) employing B3LYP hybrid functional level with 6-31G(d) basis set. It is seen that experimental and theoretical results are compatible with each other.

  10. A theoretical study on 2-chloro-5-(2-hydroxyethyl-4-methoxy-6-methylpyrimidine by DFT/ab initio calculations

    Directory of Open Access Journals (Sweden)

    Gümüs Hacer Pir

    2015-06-01

    Full Text Available Quantum chemical calculations have been performed to study the molecular geometry, 1H and 13C NMR chemical shifts, conformational, natural bond orbital (NBO and nonlinear optical (NLO properties of the 2-chloro-5-(2-hydroxyethyl-4- methoxy-6-methylpyrimidine molecule in the ground state using DFT and HF methods with 6-311++G(d,p basis set. The optimized geometric parameters and 1H and 13C NMR chemical shifts have been compared with the experimental values of the title molecule. The results of the calculations show excellent agreement between the experimental and calculated frequencies at B3LYP/6-311++G(d,p level. In order to provide a full understanding of the properties of the title molecule in the context of molecular orbital picture, the highest occupied molecular energy level (EHOMO, the lowest unoccupied molecular energy level (ELUMO, the energy difference (DE between EHOMO and ELUMO, electronegativity (χ, hardness (η and softness (S have been calculated using B3LYP/6-311++G(d,p and HF/6-311++G(d,p levels. The calculated HOMO and LUMO energies show that the charge transfer occurs within the title molecule.

  11. First principles study of Al-doped graphene as nanostructure adsorbent for NO2 and N2O: DFT calculations

    Science.gov (United States)

    Rad, Ali Shokuhi

    2015-12-01

    We studied the first principles adsorption phenomena of nitrogen dioxide (NO2) and nitrous oxide (N2O) molecules on the surface of pristine graphene and Al-doped graphene using density functional theory (DFT) calculations. The adsorption energies have been calculated for different possible configurations of the molecules on the surface of pristine and Al-doped graphene. Our calculations reveal that the Al-doped graphene has significant adsorption energy, elevated net charge transferring values and smaller bond distances to gases than that of pristine graphene because of the chemical interaction of the mentioned molecules. Furthermore, the calculated density of states (DOS) show the existing of noteworthy orbital hybridization between NO2 as well as N2O and Al-doped graphene during adsorption process which is proving to strong interaction while there is no evidence for hybridization between the those molecules and the pristine graphene. Our calculated adsorption energies for the most stable states for NO2 and N2O was -62.2 kJ mol-1 (-48.5 kJ mol-1 BSSE corrected energy) and -33.9 kJ mol-1 (-22.7 kJ mol-1 corrected energy), which are correspond to chemisorption process. These results point to the suitability of Al-doped graphene as a powerful sensor for practical applications.

  12. Effects of Fatty Acids on Low-Sulfur Diesel Lubricity:Experimental Investigation, DFT Calculation and MD Simulation

    Institute of Scientific and Technical Information of China (English)

    Luo Hui; Fan Weiyu; Li Yang; Zhao Pinhui; Nan Guozhi

    2013-01-01

    The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re-sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to low-sulfur diesel fuel. It was attempted to correlate the molecular structures of fatty acids, such as carbon chain length, degree of saturation and hy-droxylation, to their lubricity enhancement, which was evaluated by the High-Frequency Reciprocating Rig (HFRR) meth-od. The efifciency order was supported by the density functional theory (DFT) calculations and the molecular dynamics (MD) simulations. The lubricity enhancing properties of fatty acids are mainly determined by the cohesive energy of adsorbed iflms formed on iron surface. The greater the cohesive energy, the more efifciently the fatty acid would enhance the lubricity of low-sulfur diesel fuel.

  13. DFT calculations for the high-temperature structure of (EDO-TTF)2PF6: Identification of an electronic molecular dimer

    Science.gov (United States)

    Iwano, Kaoru; Shimoi, Yukihiro

    2009-02-01

    Density-functional theory (DFT) calculations are performed based on the high-temperature structure of (EDO-TTF)2PF6, a quasi-one-dimensional molecular compound that shows both thermal and photoinduced phase transitions. In this structure, the EDO-TTF molecules are one-dimensionally aligned, accompanied with weak dimerization. Contrary to a common sense, our DFT calculations reveal that the pair having a shorter mutual distance has a weaker intermolecular coupling than the pair with a longer one; the latter is appropriate to be called an electronic dimer. We also estimate the corresponding transfer energies and discuss their relevance to spin correlations and optical excitations.

  14. Study of conformational stability, structural, electronic and charge transfer properties of cladrin using vibrational spectroscopy and DFT calculations.

    Science.gov (United States)

    Singh, Swapnil; Singh, Harshita; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Bharti, Purnima; Kumar, Sudhir; Kumar, Padam; Maurya, Rakesh

    2014-11-11

    In the present work, a detailed conformational study of cladrin (3-(3,4-dimethoxy phenyl)-7-hydroxychromen-4-one) has been done by using spectroscopic techniques (FT-IR/FT-Raman/UV-Vis/NMR) and quantum chemical calculations. The optimized geometry, wavenumber and intensity of the vibrational bands of the cladrin in ground state were calculated by density functional theory (DFT) employing 6-311++G(d,p) basis sets. The study has been focused on the two most stable conformers that are selected after the full geometry optimization of the molecule. A detailed assignment of the FT-IR and FT-Raman spectra has been done for both the conformers along with potential energy distribution for each vibrational mode. The observed and scaled wavenumber of most of the bands has been found to be in good agreement. The UV-Vis spectrum has been recorded and compared with calculated spectrum. In addition, 1H and 13C nuclear magnetic resonance spectra have been also recorded and compared with the calculated data that shows the inter or intramolecular hydrogen bonding. The electronic properties such as HOMO-LUMO energies were calculated by using time-dependent density functional theory. Molecular electrostatic potential has been plotted to elucidate the reactive part of the molecule. Natural bond orbital analysis was performed to investigate the molecular stability. Non linear optical property of the molecule have been studied by calculating the electric dipole moment (μ) and the first hyperpolarizability (β) that results in the nonlinearity of the molecule.

  15. Structure of dimethylphenyl betaine hydrochloride studied by X-ray diffraction, DFT calculation, NMR and FTIR spectra

    Science.gov (United States)

    Szafran, M.; Katrusiak, A.; Dega-Szafran, Z.; Kowalczyk, I.

    2013-01-01

    The structure of dimethylphenyl betaine hydrochloride (1) has been studied by X-ray diffraction, DFT calculations, NMR and FTIR spectra. The crystals are monoclinic, space group P21/c. In the crystal, the Cl- anion is connected with protonated betaine through the O-H⋯Cl- hydrogen bond of 2.943(2) Å. The structures in the gas phase (2) and water solution (3) have been optimized by the B3LYP/6-311++G(d,p) approach and the geometrical results have been compared with the X-ray data of 1. The FTIR spectrum of the solid compound is consistent with the X-ray results. The probable assignments of the anharmonic experimental vibrational frequencies of the investigated chloride (1) based on the calculated harmonic frequencies in water solution (3) are proposed. The correlations between the experimental 1H and 13C NMR chemical shifts (δexp) of 1 in D2O and the magnetic isotropic shielding constants (σcalc) calculated by the GIAO/B3LYP/6-311G++(d,p) approach, using the screening solvation model (COSMO), δexp = a + b σcalc, for optimized molecule 3 in water solution are linear and correctly reproduce the experimental chemical shifts.

  16. Vibrational spectroscopic and DFT calculation studies of a new organic-inorganic compound of bis (4-acetylanilinium) tetrachlorocadmiate (II)

    Science.gov (United States)

    Jellibi, A.; Chaabane, I.; Guidara, K.

    2016-10-01

    The FT-IR and Raman vibrational spectra of bis (4-acetylanilinium) tetrachlorocadmiate (II) compound have been measured at room temperature by FT-infrared spectroscopy (4000-400 cm-1) on polycrystalline samples, and by Raman spectroscopy (3600-30 cm-1) on monocrystals. The structure of the [C8H10NO] 2CdCl4 formed by two cations [C8H10NO]+ of same type and one type of anion [CdCl4]2- was optimized by density functional theory (DFT) using the B3LYP method. The theoretical wavenumbers spectra were scaled by multiple scaling factors, yielding a good agreement between the experimentally recorded and the theoretically calculated values. Root mean square (rms) value was calculated and the small difference between experimental and calculated modes has been interpreted by intermolecular interactions in the crystal. The comparison between the [C8H9NO] ligand and the [C8H10NO]2[CdCl4] compound of the Raman spectra showed a decrease in the wavenumber of the bands assigned to the stretching vibration of (NH3) group in the compound due to the effect of the protonation of the nitrogen.

  17. Electronically excited states of chloroethylenes: Experiment and DFT calculations in comparison

    Energy Technology Data Exchange (ETDEWEB)

    Khvostenko, O.G., E-mail: khv@mail.ru

    2014-08-15

    Highlights: • B3LYP/6-311 + G(d,p) calculations of chloroethylenes molecules were performed. • Calculations were correlated with experiment on the molecules ground and excited states. • The general pattern of electron structure of chloroethylenes was obtained. • Necessity of this data for chloroethylenes negative ions study was noted. - Abstract: B3LYP/6-311 + G(d,p) calculations of ground and electronically excited states of ethylene, chloroethylene, 1,1-dichloroethylene, 1,2-dichloroethylene-cis, 1,2-dichloroethylene-trans trichloroethylene and tetrachloroethylene molecules have been performed. Molecular orbitals images and orbital correlation diagram are given. The calculation results for chloroethylenes electronically excited states were compared with experimental data from the energy-loss spectra obtained and generally considered previously by C.F. Koerting, K.N. Walzl and A. Kupperman. Several new additional triplet and singlet transitions were pointed out in these spectra considering the calculation results. The finding of the additional transitions was supported by the UV absorption spectrum of trichloroethylene recorded in big cuvette (10 cm), where the first three triplet and two low-intensive forbidden singlet transitions were registered. The first triplet of this compound was recorded to be at the same energy as was found with the energy-loss spectroscopy.

  18. Applicability of the wide-band limit in DFT-based molecular transport calculations

    NARCIS (Netherlands)

    Verzijl, C.J.O.; Seldenthuis, J.S.; Thijssen, J.M.

    2013-01-01

    Transport properties of molecular junctions are notoriously expensive to calculate with ab initio methods, primarily due to the semi-infinite electrodes. This has led to the introduction of different approximation schemes for the electrodes. For the most popular metals used in experiments, such as g

  19. To address surface reaction network complexity using scaling relations machine learning and DFT calculations

    Science.gov (United States)

    Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; Nørskov, Jens K.

    2017-01-01

    Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations. PMID:28262694

  20. To address surface reaction network complexity using scaling relations machine learning and DFT calculations

    Science.gov (United States)

    Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; Nørskov, Jens K.

    2017-03-01

    Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations.

  1. Obtaining the magnetic susceptibility of the heme complex from DFT calculations

    Science.gov (United States)

    Pereira, L. M. O.; Resende, S. M.; Leite Alves, H. W.

    2016-09-01

    Magnetic field interactions with particles, as observed in magnetophoresis, are becoming important tool to understand the nature of the iron role in heme molecular complex, besides other useful applications. Accurate estimations of some macroscopic magnetic properties from quantum mechanical calculations, such as the magnetic susceptibility, can also check the reliability of the heme microscopic models. In this work we report, by using the Stoner criterion, a simple way to obtain the magnetic susceptibility of the heme complex from Density Functional Theory calculations. Some of our calculated structural properties and electronic structure show good agreement with both the available experimental and theoretical data, and the results show that its groundstate is a triplet 3A state. From the obtained results, we have evaluated the exchange interaction energy, J = 0.98 eV, the associated magnetic energy gain, Δ EM =-0.68 eV, and the magnetic susceptibility, χ0=1.73 ×10-6 cm3/mol for the heme alone (with uncompleted Fe ligands). If we consider the heme complex with the two histidine residues (completing the Fe ligands), we have then obtained χ0=5.27 ×10-12 cm3/g, which is in good agreement with experimental magnetophoresis data.

  2. Al-doped graphene as a new nanostructure adsorbent for some halomethane compounds: DFT calculations

    Science.gov (United States)

    Rad, Ali Shokuhi

    2016-03-01

    We have studied the electronic structure and property of pristine as well as Al-doped graphene sheets towards adsorption of some halomethane compounds (trichloromethane, dichloromethane, and difluoromethane) using density functional theory (DFhsT) calculations. The adsorption energies have been calculated for each adsorbed-adsorbent system. Based on our results, compared to pristine graphene, the Al-doped graphene causes significant adsorption energy, higher charge transferring, and smaller bond distances to halomethane compounds. Our calculated adsorption energies of trichloromethane, dichloromethane, and difluoromethane on Al-doped graphene were - 54.1, - 68.3, and - 123.2 kJ mol- 1, respectively, which are categorized in the chemisorption region while the adsorption of these molecules on pristine graphene release insignificant energies which correspond to very weak adsorption on it. Furthermore, we used charge transfer analysis to search the amount of electron allocation. Orbital analysis including the density of states (DOS) was done to find the possible orbital hybridization between adsorbates and two graphene sheets. These results imply the suitability of Al-doped graphene as a good adsorbent/sensor for halomethane compounds.

  3. Quantitative analysis of weak interactions by Lattice energy calculation, Hirshfeld surface and DFT studies of sulfamonomethoxine

    Science.gov (United States)

    Patel, Kinjal D.; Patel, Urmila H.

    2017-01-01

    Sulfamonomethoxine, 4-Amino-N-(6-methoxy-4-pyrimidinyl) benzenesulfonamide (C11H12N4O3S), is investigated by single crystal X-ray diffraction technique. Pair of N-H⋯N and C-H⋯O intermolecular interactions along with π···π interaction are responsible for the stability of the molecular packing of the structure. In order to understand the nature of the interactions and their quantitative contributions towards the crystal packing, the 3D Hirshfeld surface and 2D fingerprint plot analysis are carried out. PIXEL calculations are performed to determine the lattice energies correspond to intermolecular interactions in the crystal structure. Ab initio quantum chemical calculations of sulfamonomethoxine (SMM) have been performed by B3LYP method, using 6-31G** basis set with the help of Schrodinger software. The computed geometrical parameters are in good agreement with the experimental data. The Mulliken charge distribution, calculated using B3LYP method to confirm the presence of electron acceptor and electron donor atoms, responsible for intermolecular hydrogen bond interactions hence the molecular stability.

  4. Obtaining the magnetic susceptibility of the heme complex from DFT calculations

    Directory of Open Access Journals (Sweden)

    L. M. O. Pereira

    2016-09-01

    Full Text Available Magnetic field interactions with particles, as observed in magnetophoresis, are becoming important tool to understand the nature of the iron role in heme molecular complex, besides other useful applications. Accurate estimations of some macroscopic magnetic properties from quantum mechanical calculations, such as the magnetic susceptibility, can also check the reliability of the heme microscopic models. In this work we report, by using the Stoner criterion, a simple way to obtain the magnetic susceptibility of the heme complex from Density Functional Theory calculations. Some of our calculated structural properties and electronic structure show good agreement with both the available experimental and theoretical data, and the results show that its groundstate is a triplet 3A state. From the obtained results, we have evaluated the exchange interaction energy, J = 0.98 eV, the associated magnetic energy gain, ΔEM=−0.68 eV, and the magnetic susceptibility, χ0=1.73×10−6 cm3/mol for the heme alone (with uncompleted Fe ligands. If we consider the heme complex with the two histidine residues (completing the Fe ligands, we have then obtained χ0=5.27×10−12 cm3/g, which is in good agreement with experimental magnetophoresis data.

  5. Structural, electronic and optical properties of ilmenite and perovskite CdSnO3 from DFT calculations.

    Science.gov (United States)

    Sesion, P D; Henriques, J M; Barboza, C A; Albuquerque, E L; Freire, V N; Caetano, E W S

    2010-11-03

    CdSnO(3) ilmenite and perovskite crystals were investigated using both the local density and generalized gradient approximations, LDA and GGA, respectively, of the density functional theory (DFT). The electronic band structures, densities of states, dielectric functions, optical absorption and reflectivity spectra related to electronic transitions were obtained, as well as the infrared absorption spectra after computing the vibrational modes of the crystals at q = 0. Dielectric optical permittivities and polarizabilities at ω = 0 and ∞ were also calculated. The results show that GGA-optimized geometries are more accurate than LDA ones, and the Kohn-Sham band structures obtained for the CdSnO(3) polymorphs confirm that ilmenite has an indirect band gap, while perovskite has a direct band gap, both being semiconductors. Effective masses for both crystals are obtained for the first time, being highly isotropic for electrons and anisotropic for holes. The optical properties reveal a very small degree of anisotropy of both crystals with respect to different polarization planes of incident light. The phonon calculation at q = 0 for perovskite CdSnO(3) does not show any imaginary frequencies, in contrast to a previous report suggesting the existence of a more stable crystal of perovskite CdSnO(3) with ferroelectric properties.

  6. Molecular size evaluation of linear and branched paraffins from the gasoline pool by DFT quantum chemical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Federico Jimenez-Cruz; Georgina C. Laredo [Instituto Mexicano del Petroleo, Mexico (Mexico). Programa de Tratamiento de Crudo Maya

    2004-11-01

    A good approach of the critical molecular dimensions of 35 linear and branched C5-C8 paraffins by DFT quantum chemical calculations at B3LYP/6-31G{asterisk}{asterisk} level of theory in gas phase is described. In this context, we found that either the determined molecular width or width-height average values can be used as critical measures in the analysis for selection of molecular sieves materials, depending on their pore size and shape. The molecular width values for linear and monosubstituted paraffins are 4.2 and 5.5 {angstrom}, respectively. In the case of disubstituted paraffins, the values are 5.5 for 2,3-, 2,4-, 2,5- and 3,4-disubstituted and for 2,2- and 3,3-disubstituted are 6.7-7.1 {angstrom}. The values for ethyl-substituted are 6.1-6.7 {angstrom} and for trisubstituted isoparaffins are 6.7. In order to select a porous material for selective separation of isoparaffins and paraffins, the zeolite diffusivity can be correlated with the critical diameter of the paraffins according to the geometry-limited diffusion concept and the effective minimum dimensions of the molecules. The calculated values of CPK molecular volume of the titled paraffins showed a good discrimination between the number of carbons and molecular size. 25 refs., 4 figs., 2 tabs.

  7. Structural, electronic and optical properties of ilmenite and perovskite CdSnO{sub 3} from DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sesion Jr, P D [Escola de Ciencias e Tecnologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, Rio Grande do Norte (Brazil); Henriques, J M [Departamento de Fisica Teorica e Experimental, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, Rio Grande do Norte (Brazil); Barboza, C A; Albuquerque, E L [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-900 Natal, Rio Grande do Norte (Brazil); Freire, V N [Departamento de Fisica, Universidade Federal do Ceara, 60455-970 Fortaleza, Ceara (Brazil); Caetano, E W S, E-mail: ewcaetano@gmail.co [Instituto Federal de Educacao, Ciencia e Tecnologia do Ceara, Avenida 13 de Maio, 2081, Benfica, 60040-531 Fortaleza, Ceara (Brazil)

    2010-11-03

    CdSnO{sub 3} ilmenite and perovskite crystals were investigated using both the local density and generalized gradient approximations, LDA and GGA, respectively, of the density functional theory (DFT). The electronic band structures, densities of states, dielectric functions, optical absorption and reflectivity spectra related to electronic transitions were obtained, as well as the infrared absorption spectra after computing the vibrational modes of the crystals at q = 0. Dielectric optical permittivities and polarizabilities at {omega} = 0 and {infinity} were also calculated. The results show that GGA-optimized geometries are more accurate than LDA ones, and the Kohn-Sham band structures obtained for the CdSnO{sub 3} polymorphs confirm that ilmenite has an indirect band gap, while perovskite has a direct band gap, both being semiconductors. Effective masses for both crystals are obtained for the first time, being highly isotropic for electrons and anisotropic for holes. The optical properties reveal a very small degree of anisotropy of both crystals with respect to different polarization planes of incident light. The phonon calculation at q = 0 for perovskite CdSnO{sub 3} does not show any imaginary frequencies, in contrast to a previous report suggesting the existence of a more stable crystal of perovskite CdSnO{sub 3} with ferroelectric properties.

  8. The structure of N-arylindazoles and their aza-derivatives in the solid state: A systematic analysis of the Cambridge Structural Database coupled with DFT calculations

    Science.gov (United States)

    Alkorta, Ibon; Elguero, José

    2017-06-01

    A search in the Cambridge Structural Database for N-aryl indazoles and their aza derivatives affords 227 structures (183 1-aryl and 44 2-aryl). To discuss their structures, DFT calculations on 20 model compounds were carried out. The geometry of the five-membered ring (the pyrazole) and the conformation if the N-aryl substituent were analyzed.

  9. Structure, spectroscopy and DFT calculations of 1,2-di(3-hydroxymethylpyridinium)ethane dibromide

    Science.gov (United States)

    Komasa, Anna; Barczyński, Piotr; Ratajczak-Sitarz, Małgorzata; Katrusiak, Andrzej; Dega-Szafran, Zofia; Szafran, Mirosław

    2016-09-01

    The molecular structure of 1,2-di(3-hydroxymethylpyridinium)ethane dibromide (1) has been characterized by X-ray diffraction, B3LYP/6-311++G(d,p) calculations, FTIR, Raman and NMR spectra. The crystals are monoclinic, space group C2/c. 1,2-Di(3-hydroxymethylpyridinium)ethane dication and hydrogen-bonded bromide anions in crystals are located at the inversion center. The both CH2OH groups are engaged in two equal length hydrogen bonds with bromide anions. Two structures (2) and (3) were optimized at the B3LYP/6-311++G(d,p) level of theory. The optimized complex (2) resembles the crystal structure, while complex (3) is preferred energetically. The O⋯Br- hydrogen bonds distances are: 3.289(2) Å in crystals (1), but in the optimized structures (2) and (3) they are 3.303 Å and 3.461 Å, respectively. The investigated complex is additionally stabilized by the N+⋯Br- electrostatic attractions. The potential energy distributions (PED) were used for the assignments of IR and Raman frequencies in the experimental and calculated spectra of the title compound. The FTIR spectrum of (1) is consistent with the X-ray results. Interpretation of the 1H and 13C NMR spectra in DMSO-d6 has been based on 2D experiments. The calculated GIAO/B3LYP/6-311++G(d,p) magnetic shielding constants have been used to predict 1H and 13C chemical shifts for the optimized structures of (2) and (3).

  10. TOPOLOGICAL ANALYSIS AND FREQUENCY DEPENDENT HYPERPOLARIZABILITY CALCULATIONS OF FDDNP: A DFT STUDY

    Directory of Open Access Journals (Sweden)

    Keivan Akhtari

    2016-12-01

    Full Text Available The topological and fi rst-hyperpolarizability properties of 2-(1-{6-[(2-fl uoroethyl(methylamino]-2-naphthyl}ethylidenemalononitrile (FDDNP were studied using DFTB3LYP method. The static and dynamic electronic (hyperpolarizabilities of conformers were calculated and a simple two-state model was employed to explain the fi rst hyperpolarizability differences in two conformers. The second harmonic generation property was evaluated at the typical wavelengths of Cr:forsterite, Nd:YAG(neodymium-doped yttrium aluminium garnet and Ti:sapphire lasers to predict the compound conformers potency for second harmonic generation imaging in biological studies.

  11. Gas phase infrared spectra and corresponding DFT calculations of α, ω-diphenylpolyenes

    Science.gov (United States)

    Biemann, Lars; Braun, Michaela; Kleinermanns, Karl

    2010-01-01

    We present gas phase Fourier Transform Infrared (FTIR) spectra of the homologue series of α, ω-diphenylpolyenes consisting of trans- and cis-stilbene, diphenylbutadiene (DPB) and diphenylhexatriene (DPH) obtained by a fast thermal heating technique that enables vaporization without decomposition. Infrared marker bands for the cis-isomers of the polyenes have been identified by density functional calculations at the B3LYP/TZVP level of theory. The all trans isomers of DPB and DPH do not interconvert to the cis-isomers in the gas phase at 200 °C.

  12. Ruthenium tetraoxide oxidations of alkanes: DFT calculations of barrier heights and kinetic isotope effects.

    Science.gov (United States)

    Drees, Markus; Strassner, Thomas

    2006-03-03

    The oxidation of C-H and C-C bonds by metal-oxo compounds is of general interest. We studied the RuO4-mediated catalytic oxidation of several cycloalkanes such as adamantane and cis- and trans-decalin as well as methane. B3LYP/6-31G(d) calculations on the experimentally proposed (3+2) mechanism are in good agreement with known experimental results. Comparison of experimental and theoretical kinetic isotope effects confirms the proposed mechanism. Besides RuO4, we also looked at RuO4(OH)- as a potential active species to account for ruthenium tetraoxide oxidations under strong basic conditions.

  13. Electronic band structure and specific features of Sm{sub 2}NiMnO{sub 6} compound: DFT calculation

    Energy Technology Data Exchange (ETDEWEB)

    Reshak, A.H. [Institute of complex systems, FFPW, CENAKVA, University of South Bohemia in CB, Nove Hrady 37333 (Czech Republic); Center of Excellence Geopolymer and Green Technology, School of Material Engineering, University Malaysia Perlis, 01007 Kangar, Perlis (Malaysia); Azam, Sikander, E-mail: sikander.physicst@gmail.com [Institute of complex systems, FFPW, CENAKVA, University of South Bohemia in CB, Nove Hrady 37333 (Czech Republic)

    2013-09-15

    The band structure, density of states, electronic charge density, Fermi surface and optical properties of Sm{sub 2}NiMnO{sub 6} compound have been investigated with the support of density functional theory (DFT). The atomic positions of Sm{sub 2}NiMnO{sub 6} compound were optimized by minimizing the forces acting on the atoms, using the full potential linear augmented plane wave method. We employed the local density approximation (LDA), generalized gradient approximation (GGA) and Engel–Vosko GGA (EVGGA) to treat the exchange correlation potential by solving Kohn–Sham equations. The calculation shows that the compound is metallic with strong hybridization near the Fermi energy level (E{sub F}). The calculated density of states at the E{sub F} is about 21.60, 24.52 and 26.21 states/eV, and the bare linear low-temperature electronic specific heat coefficient (γ) is found to be 3.74, 4.25 and 4.54 mJ/mol K{sup 2} for EVGGA, GGA and LDA, respectively. The Fermi surface is composed of two sheets. The bonding features of the compounds are analyzed using the electronic charge density in the (011) crystallographic plane. The dispersion of the optical constants was calculated and discussed. - Highlights: • The compound is metallic with strong hybridization near the Fermi energy. • The density of states at the Fermi energy is calculated. • The bare linear low-temperature electronic specific heat coefficient is obtained. • Fermi surface is composed of two sheets. • The bonding features are analyzed using the electronic charge density.

  14. Femtosecond spectroscopy and TD-DFT calculations of CuCl4(2-) excited states.

    Science.gov (United States)

    Golubeva, Elena N; Zubanova, Ekaterina M; Melnikov, Michail Ya; Gostev, Fedor E; Shelaev, Ivan V; Nadtochenko, Victor A

    2014-12-21

    Photoinduced processes of tetrahexylammonium tetrachlorocuprate [(C6H13)4N]2Cu(II)Cl4 in chloro-organic solvents were investigated by steady state photolysis and femtosecond transient absorption spectroscopy. The quantum yield of photoreduction of CuCl4(2-) was estimated to be about 1%; the process resulted in the formation of the copper(i) chlorocomplex Cu(I)Cl3(2-) and a chlorine atom. Femtosecond laser photolysis with a 422 nm, 40 fs pulse revealed a three-exponential decay of the LMCT excited state of [(C6H13)4N]2CuCl4. A global fitting SVD analysis of the femtosecond transient spectra suggested three relaxation times, ∼400 fs, ∼1.4 ps and ∼5.8 ps. Oscillations in transient absorption kinetic traces were documented for CuCl4(2-) solutions in 2-chlorobutane. The oscillation Fourier transform analysis of the oscillations and linear predictive singular value decomposition revealed peaks at 283 cm(-1) (damping time ∼600 fs) and 181 cm(-1) (damping time ∼400 fs). These peaks can be tentatively attributed to νs(Cu-Cl) symmetric stretching frequency A1 and T2 reflecting excited state vibrational coherence. Quantum chemical calculations suggest a possible scheme for relaxation pathways in CuCl4(2-). The observed transient excited state absorption bands agree semiquantitatively with the calculated transition bands of CuCl4(2-).

  15. Structural, mechanical and vibrational study of uranyl silicate mineral soddyite by DFT calculations

    Science.gov (United States)

    Colmenero, Francisco; Bonales, Laura J.; Cobos, Joaquín; Timón, Vicente

    2017-09-01

    Uranyl silicate mineral soddyite, (UO2)2(SiO4)·2(H2O), is a fundamental component of the paragenetic sequence of secondary phases that arises from the weathering of uraninite ore deposits and corrosion of spent nuclear fuel. In this work, soddyite was studied by first principle calculations based on the density functional theory. As far as we know, this is the first time that soddyite structure is determined theoretically. The computed structure of soddyite reproduces the one determined experimentally by X-Ray diffraction (orthorhombic symmetry, spatial group Fddd O2; lattice parameters a = 8.334 Å, b = 11.212 Å; c = 18.668 Å). Lattice parameters, bond lengths, bond angles and X-Ray powder pattern were found to be in very good agreement with their experimental counterparts. Furthermore, the mechanical properties were obtained and the satisfaction of the Born conditions for mechanical stability of the structure was demonstrated by means of calculations of the elasticity tensor. The equation of state of soddyite was obtained by fitting lattice volumes and pressures to a fourth order Birch-Murnahan equation of state. The Raman spectrum was also computed by means of density functional perturbation theory and compared with the experimental spectrum obtained from a natural soddyite sample. The results were also found in agreement with the experimental data. A normal mode analysis of the theoretical spectra was carried out and used in order to assign the main bands of the Raman spectrum.

  16. Infrared spectral evidence and DFT calculations of hydrogen-bonding and molecular structures of acetogenins

    Science.gov (United States)

    Afonso, Sabrina; Silva, Fabiano B.; Silva, Arnaldo F.; Scarminio, Ieda S.; Bruns, Roy E.

    2017-02-01

    FTIR spectra have been measured for 31 different five component - simplex centroid design solvent mixture extracts of shaded and sun-exposed Annonaceous leaves harvested in all four seasons. The spectral frequencies are characteristic of anonnaceous acetogenins known to be a major component of these leaves. Osbnd H stretching spectral bands in the 3100-3600 cm-1 region provide evidence of notable intensity changes for the shaded and sun-exposed leaves. Chemometric principal component analysis involving 264 spectra show that shaded samples tend to have more intense Osbnd H stretching bands than those grown in the sun. B3LYP density functional calculations indicate significant Osbnd H stretching band changes in this region owing to hydrogen bond formation. Weak Osbnd H intensity enhancements, around 40 km mol-1, occur when an Osbnd H group forms a hydrogen bond with the oxygen atom of an adjacent tetrahydrofuran ring oxygen atom. Much more intense enhancements, 400-500 km mol-1, are predicted to occur for acetogenins with two tetrahydrofuran rings for which the Osbnd H group hydrogen bonds with its fartherest removed tetrahydrofuran ring oxygen. Whereas weak or moderate H-bond stretching intensities are obtained for acetogenins with slightly bent carbon chain structures the strongest hydrogen bond intensities are calculated for molecules with a 45° V-type backbone structure. These important structural modifications as well as significant changes in bond lengths and angles owing to hydrogen bonding are detailed.

  17. Combined hybrid functional and DFT+U calculations for metal chalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Aras, Mehmet; Kılıç, Çetin, E-mail: cetin-kilic@gyte.edu.tr [Department of Physics, Gebze Institute of Technology, Gebze, Kocaeli 41400 (Turkey)

    2014-07-28

    In the density-functional studies of materials with localized electronic states, the local/semilocal exchange-correlation functionals are often either combined with a Hubbard parameter U as in the LDA+U method or mixed with a fraction of exactly computed (Fock) exchange energy yielding a hybrid functional. Although some inaccuracies of the semilocal density approximations are thus fixed to a certain extent, the improvements are not sufficient to make the predictions agree with the experimental data. Here, we put forward the perspective that the hybrid functional scheme and the LDA+U method should be treated as complementary, and propose to combine the range-separated Heyd-Scuseria-Ernzerhof (HSE) hybrid functional with the Hubbard U. We thus present a variety of HSE+U calculations for a set of II-VI semiconductors, consisting of zinc and cadmium monochalcogenides, along with comparison to the experimental data. Our findings imply that an optimal value U{sup *} of the Hubbard parameter could be determined, which ensures that the HSE+U{sup *} calculation reproduces the experimental band gap. It is shown that an improved description not only of the electronic structure but also of the crystal structure and energetics is obtained by adding the U{sup *} term to the HSE functional, proving the utility of HSE+U{sup *} approach in modeling semiconductors with localized electronic states.

  18. Vibrational spectra, DFT quantum chemical calculations and conformational analysis of P-iodoanisole.

    Science.gov (United States)

    Arivazhagan, M; Anitha Rexalin, D; Geethapriya, J

    2013-09-01

    The solid phase FT-IR and FT-Raman spectra of P-iodoanisole (P-IA) have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by ab initio (HF) and density functional theory (B3LYP) methods with LanL2DZ as basis set. The potential energy surface scan for the selected dihedral angle of P-IA has been performed to identify stable conformer. The optimized structure parameters and vibrational wavenumbers of stable conformer have been predicted by density functional B3LYP method with LanL2DZ (with effective core potential representations of electrons near the nuclei for post-third row atoms) basis set. The nucleophilic and electrophilic sites obtained from the molecular electrostatic potential (MEP) surface were calculated. The temperature dependence of thermodynamic properties has been analyzed. Several thermodynamic parameters have been calculated using B3LYP with LanL2DZ basis set.

  19. Correlating DFT-calculated energy barriers to experiments in nonheme octahedral Fe(IV)O species.

    Science.gov (United States)

    Cho, Kyung-Bin; Kim, Eun Jeong; Seo, Mi Sook; Shaik, Sason; Nam, Wonwoo

    2012-08-13

    The experimentally measured bimolecular reaction rate constant, k(2), should in principle correlate with the theoretically calculated rate-limiting free energy barrier, ΔG(≠), through the Eyring equation, but it fails quite often to do so due to the inability of current computational methods to account in a precise manner for all the factors contributing to ΔG(≠). This is further aggravated by the exponential sensitivity of the Eyring equation to these factors. We have taken herein a pragmatic approach for C-H activation reactions of 1,4-cyclohexadiene with a variety of octahedral nonheme Fe(IV)O complexes. The approach consists of empirically determining two constants that would aid in predicting experimental k(2) values uniformly from theoretically calculated electronic energy (ΔE(≠)) values. Shown in this study is the predictive power as well as insights into energy relationships in Fe(IV)O C-H activation reactions. We also find that the difference between ΔG(≠) and ΔE(≠) converges at slow reactions, in a manner suggestive of changes in the importance of the triplet spin state weight in the overall reaction.

  20. DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.

    Science.gov (United States)

    del Rosal, I; Maron, L; Poteau, R; Jolibois, F

    2008-08-14

    Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for

  1. A cobalt (II) complex with 6-methylpicolinate: Synthesis, characterization, second- and third-order nonlinear optical properties, and DFT calculations

    Science.gov (United States)

    Altürk, Sümeyye; Avcı, Davut; Tamer, Ömer; Atalay, Yusuf; Şahin, Onur

    2016-11-01

    A cobalt(II) complex of 6-methylpicolinic acid, [Co(6-Mepic)2(H2O)2]·2H2O, was prepared and fully determined by single crystal X-ray crystal structure analysis as well as FT-IR, FT-Raman. UV-vis spectra were recorded within different solvents, to illustrate electronic transitions and molecular charge transfer within complex 1. The coordination sphere of complex 1 is a distorted octahedron according to single crystal X-ray results. Moreover, DFT (density functional theory) calculations with HSEH1PBE/6-311 G(d,p) level were carried out to back up the experimental results, and form base for future work in advanced level. Hyperconjugative interactions, intramolecular charge transfer (ICT), molecular stability and bond strength were researched by the using natural bond orbital (NBO) analysis. X-ray and NBO analysis results demonsrate that O-H···O hydrogen bonds between the water molecules and carboxylate oxygen atoms form a 2D supramolecular network, and also adjacent 2D networks connected by C-H···π and π···π interactions to form a 3D supramolecular network. Additionally, the second- and third-order nonlinear optical parameters of complex 1 were computed at DFT/HSEH1PBE/6-311 G(d,p) level. The refractive index (n) was calculated by using the Lorentz-Lorenz equation in order to investigate polarization behavior of complex 1 in different solvent polarities. The first-order static hyperpolarizability (β) value is found to be lower than pNA value because of the inversion symmetry around Co (II). But the second-order static hyperpolarizability (γ) value is 2.45 times greater than pNA value (15×10-30 esu). According to these results, Co(II) complex can be considered as a candidate to NLO material. Lastly molecular electrostatic potential (MEP), frontier molecular orbital energies and related molecular parameters for complex 1 were evaluated.

  2. Optical absorption and DFT calculations in L-aspartic acid anhydrous crystals: Charge carrier effective masses point to semiconducting behavior

    Science.gov (United States)

    Silva, A. M.; Silva, B. P.; Sales, F. A. M.; Freire, V. N.; Moreira, E.; Fulco, U. L.; Albuquerque, E. L.; Maia, F. F., Jr.; Caetano, E. W. S.

    2012-11-01

    Density functional theory (DFT) computations within the local-density approximation and generalized gradient approximation in pure form and with dispersion correction (GGA+D) were carried out to investigate the structural, electronic, and optical properties of L-aspartic acid anhydrous crystals. The electronic (band structure and density of states) and optical absorption properties were used to interpret the light absorption measurements we have performed in L-aspartic acid anhydrous crystalline powder at room temperature. We show the important role of the layered spatial disposition of L-aspartic acid molecules in anhydrous L-aspartic crystals to explain the observed electronic and optical properties. There is good agreement between the GGA+D calculated and experimental lattice parameters, with (Δa, Δb, Δc) deviations of (0.029,-0.023,-0.024) (units in Å). Mulliken [J. Chem. Phys.JCPSA60021-960610.1063/1.1740588 23, 1833 (1955)] and Hirshfeld [Theor. Chim. ActaTCHAAM0040-574410.1007/BF00549096 44, 129 (1977)] population analyses were also performed to assess the degree of charge polarization in the zwitterion state of the L-aspartic acid molecules in the DFT converged crystal. The lowest-energy optical absorption peaks related to transitions between the top of the valence band and the bottom of the conduction band involve O 2p valence states and C 1p and O 2p conduction states, with the carboxyl and COOH lateral chain group contributing significantly to the energy band gap. Among the calculated band gaps, the lowest GGA+D (4.49-eV) gap is smaller than the experimental estimate of 5.02 eV, as obtained by optical absorption. Such a wide-band-gap energy together with the small carrier effective masses estimated from band curvatures allows us to suggest that an L-aspartic acid anhydrous crystal can behave as a wide-gap semiconductor. A comparison of effective masses among directions parallel and perpendicular to the L-aspartic molecules layers reveals that charge

  3. Synthesis, structure, spectral properties and DFT quantum chemical calculations of 4-aminoazobenzene dyes. Effect of intramolecular hydrogen bonding on photoisomerization

    Science.gov (United States)

    Georgiev, Anton; Bubev, Emil; Dimov, Deyan; Yancheva, Denitsa; Zhivkov, Ivaylo; Krajčovič, Jozef; Vala, Martin; Weiter, Martin; Machkova, Maria

    2017-03-01

    In this paper three different "push-pull" 4-aminoazobenzene dyes have been synthesized in order to characterize their photochromic behavior in different solvents. The molecular geometry was optimized by DFT/B3LYP functional combined with the standard 6-31 + G(d,p) basis set for trans (E) and cis (Z) isomers and the energy levels of HOMO and LUMO frontier orbitals were computed using IEFPCM solvation in CHCl3 and DMF. The calculated results were compared to the experimental optical band gap and HOMO values of cyclic voltammetry. The intramolecular six-membered hydrogen bond was formed in both isomers of the synthesized dyes. The thermodynamic parameters such as total electronic energy E (RB3LYP), enthalpy H298 (sum of electronic and thermal enthalpies), free Gibbs energy G298 (sum of electronic and thermal free Gibbs energies) and dipole moment μ were computed for trans (E) and cis (Z) isomers in order to estimate the ΔEtrans → cis, Δμtrans → cis, ΔHtrans → cis, ΔGtrans → cis and ΔStrans → cis values. The NBO analysis was performed in order to understand the intramolecular charge transfer and energy of resonance stabilization. The solvatochromic shift was evaluated by UV-VIS spectroscopy in CHCl3 (nonpolar), EtOH (polar protic) and DMF (polar aprotic) solvents to determine the electron withdrawing and donating properties of the substituents on electron transitions energy. Through the increasing solvent polarity a strong bathochromic shift is observed. The photoisomerization experiments have been performed in two solvents CHCl3 (nonpolar) and DMF (polar aprotic) by UV light irradiation with λ = 365 nm at equal concentrations and time of illuminations. The electronic spectra were computed by TD-DFT after geometry optimization using IEFPCM solvation in CHCl3 and DMF. The degree of photoisomerization was calculated for the three azo chromophores in both solvents. By using first derivative of the UV-VIS spectra it was possible to resolve the overlapped

  4. Hindered rotational energy barriers of BH4- tetrahedra in β-Mg(BH4)2 from quasielastic neutron scattering and DFT calculations

    DEFF Research Database (Denmark)

    Blanchard, Didier; Maronsson, Jon Bergmann; Riktor, M.D.;

    2012-01-01

    In this work, hindered rotations of the BH4- tetrahedra in Mg(BH4)2 were studied by quasielastic neutron scattering, using two instruments with different energy resolution, in combination with density functional theory (DFT) calculations. Two thermally activated reorientations of the BH4- units......, around the 2-fold (C2) and 3-fold (C3) axes were observed at temperatures from 120 to 440 K. The experimentally obtained activation energies (EaC2 = 39 and 76 meV and EaC3 = 214 meV) and mean residence times between reorientational jumps are comparable with the energy barriers obtained from DFT...... calculations. A linear dependency of the energy barriers for rotations around the C2 axis parallel to the Mg-Mg axis with the distance between these two axes was revealed by the DFT calculations. At the lowest temperature (120 K) only 15% of the BH4- units undergo rotational motion and from comparison with DFT...

  5. Nanocrystalline lanthanide nitride materials synthesised by thermal treatment of amido and ammine metallocenes: X-ray studies and DFT calculations.

    Science.gov (United States)

    Baisch, Ulrich; Pagano, Sandro; Zeuner, Martin; Barros, Noémi; Maron, Laurent; Schnick, Wolfgang

    2006-06-14

    The decomposition process of ammine lanthanide metallocenes was studied by X-ray diffractometry, spectroscopy and theoretical investigations. A series of ammine-tris(eta(5)-cyclopentadienyl)lanthanide(III) complexes 1-Ln (Lanthanide (Ln)=Sm, Gd, Dy, Ho, Er, Yb) was synthesised by the reaction of [Cp(3)Ln] complexes (Cp=cyclopentadienyl) with liquid ammonia at -78 degrees C and structurally characterised by X-ray diffraction methods, mass spectrometry and vibrational (IR, Raman) spectroscopy. Furthermore, amido-bis(eta(5)-cyclopentadienyl)lanthanide(III) complexes 2-Ln (Ln=Dy, Ho, Er, Yb) were synthesised by heating the respective ammine adduct 1-Ln in an inert gas atmosphere at temperatures of between 240 and 290 degrees C. X-ray diffraction studies, mass spectrometry and vibrational (IR, Raman) spectroscopy were carried out for several 2-Ln species and proved the formation of dimeric mu(2)-bridged compounds. Species 1-Ln are highly reactive coordination compounds and showed different behaviour regarding the decomposition to 2-Ln. The reaction of 1-Ln and 2-Ln with inorganic bases yielded lanthanide nitride LnN powders with an estimated crystallite size of between 40 and 90 nm at unprecedented low temperatures of 240 to 300 degrees C. Temperature-dependent X-ray powder diffraction and transmission electron microscopy (TEM) investigations were performed and showed that the decomposition reaction yielded nanocrystalline material. Structural optimisations were carried out for 1-Ln and 2-Ln by employing density functional (DFT) calculations. A good agreement was found between the observed and calculated structural parameters. Also, Gibbs free energies were calculated for 1-Ln, 2-Ln and the pyrolysis reaction to the nitride material, and were found to fit well with the expected ranges.

  6. Structures of a n * Ions Derived from Protonated Pentaglycine and Pentaalanine: Results from IRMPD Spectroscopy and DFT Calculations

    Science.gov (United States)

    Zhao, Junfang; Lau, Justin Kai-Chi; Grzetic, Josipa; Verkerk, Udo H.; Oomens, Jos; Siu, K. W. Michael; Hopkinson, Alan C.

    2013-12-01

    Infrared multiple-photon dissociation (IRMPD) spectroscopy and DFT calculations have been used to probe the most stable structures of a 3 * and a 4 * ions derived from both protonated pentaglycine (denoted G5) and pentaalanine (A5). The a 3 * and a 4 * ions derived from protonated A5 feature a CHR=N-CHR'- group at the N-terminus and an oxazolone ring at the C-terminus, as proposed previously [ J. Am. Soc. Mass Spectrom. 19, 1788-1798 (2008)]. The isomeric a 4 * ion derived from A5 with a 3,5-dihydro-4H-imidazol-4-one ring structure was calculated to have a slightly better energy than the oxazolone, but the barrier to its formation is higher and there was no evidence of this ion in the IRMPD spectrum. By contrast, the a 4 * and [ a 4 - H2O]+ (denoted a 4 0 ) ions from G5 gave strikingly similar IRMPD spectra and both have the 3,5-dihydro-4H-imidazol-4-one ring structure similar to that recently reported for the [GGGG + H - H2O]+ ion [ Int. J. Mass Spectrom. 316- 318, 268-272 (2012)]. In the absence of a solvent molecule, the pathway to the oxazolone is calculated to be lower than those to thermodynamically more stable products, the a 4 0 and the a 4 * with the 3,5-dihydro-4H-imidazol-4-one ring structure. Incorporation of one water molecule is sufficient to reduce the barrier to formation of the a 4 0 of G5 to below that for formation of the oxazolone. On the equivalent potential energy surface for protonated A5 the barrier to formation of the a 4 0 ion is 12.3 kcal mol-1 higher than that for oxazolone formation and the a 4 0 ion is not observed experimentally.

  7. Structures of a(n)* ions derived from protonated pentaglycine and pentaalanine: results from IRMPD spectroscopy and DFT calculations.

    Science.gov (United States)

    Zhao, Junfang; Lau, Justin Kai-Chi; Grzetic, Josipa; Verkerk, Udo H; Oomens, Jos; Siu, K W Michael; Hopkinson, Alan C

    2013-12-01

    Infrared multiple-photon dissociation (IRMPD) spectroscopy and DFT calculations have been used to probe the most stable structures of a3(*) and a4(*) ions derived from both protonated pentaglycine (denoted G5) and pentaalanine (A5). The a3(*) and a4(*) ions derived from protonated A5 feature a CHR=N-CHR'- group at the N-terminus and an oxazolone ring at the C-terminus, as proposed previously [J. Am. Soc. Mass Spectrom. 19, 1788-1798 (2008)]. The isomeric a4(*) ion derived from A5 with a 3,5-dihydro-4H-imidazol-4-one ring structure was calculated to have a slightly better energy than the oxazolone, but the barrier to its formation is higher and there was no evidence of this ion in the IRMPD spectrum. By contrast, the a4(*) and [a4 - H2O](+) (denoted a4(0)) ions from G5 gave strikingly similar IRMPD spectra and both have the 3,5-dihydro-4H-imidazol-4-one ring structure similar to that recently reported for the [GGGG + H - H2O](+) ion [Int. J. Mass Spectrom. 316-318, 268-272 (2012)]. In the absence of a solvent molecule, the pathway to the oxazolone is calculated to be lower than those to thermodynamically more stable products, the a4(0) and the a4(*) with the 3,5-dihydro-4H-imidazol-4-one ring structure. Incorporation of one water molecule is sufficient to reduce the barrier to formation of the a4(0) of G5 to below that for formation of the oxazolone. On the equivalent potential energy surface for protonated A5 the barrier to formation of the a4(0) ion is 12.3 kcal mol(-1) higher than that for oxazolone formation and the a4(0) ion is not observed experimentally.

  8. Comparison of repulsive interatomic potentials calculated with an all-electron DFT approach with experimental data

    Science.gov (United States)

    Zinoviev, A. N.; Nordlund, K.

    2017-09-01

    The interatomic potential determines the nuclear stopping power in materials. Most ion irradiation simulation models are based on the universal Ziegler-Biersack-Littmark (ZBL) potential (Ziegler et al., 1983), which, however, is an average and hence may not describe the stopping of all ion-material combinations well. Here we consider pair-specific interatomic potentials determined experimentally and by density-functional theory simulations with DMol approach (DMol software, 1997) to choose basic wave functions. The interatomic potentials calculated using the DMol approach demonstrate an unexpectedly good agreement with experimental data. Differences are mainly observed for heavy atom systems, which suggests they can be improved by extending a basis set and more accurately considering the relativistic effects. Experimental data prove that the approach of determining interatomic potentials from quasielastic scattering can be successfully used for modeling collision cascades in ion-solids collisions. The data obtained clearly indicate that the use of any universal potential is limited to internuclear distances R < 7 af (af is the Firsov length).

  9. Fluoridonitrosyl complexes of technetium(I) and technetium(II). Synthesis, characterization, reactions, and DFT calculations.

    Science.gov (United States)

    Balasekaran, Samundeeswari Mariappan; Spandl, Johann; Hagenbach, Adelheid; Köhler, Klaus; Drees, Markus; Abram, Ulrich

    2014-05-19

    A mixture of [Tc(NO)F5](2-) and [Tc(NO)(NH3)4F](+) is formed during the reaction of pertechnetate with acetohydroxamic acid (Haha) in aqueous HF. The blue pentafluoridonitrosyltechnetate(II) has been isolated in crystalline form as potassium and rubidium salts, while the orange-red ammine complex crystallizes as bifluoride or PF6(-) salts. Reactions of [Tc(NO)F5](2-) salts with HCl give the corresponding [Tc(NO)Cl4/5](-/2-) complexes, while reflux in neat pyridine (py) results in the formation of the technetium(I) cation [Tc(NO)(py)4F](+), which can be crystallized as hexafluoridophosphate. The same compound can be synthesized directly from pertechnetate, Haha, HF, and py or by a ligand-exchange procedure starting from [Tc(NO)(NH3)4F](HF2). The technetium(I) cation [Tc(NO)(NH3)4F](+) can be oxidized electrochemically or by the reaction with Ce(SO4)2 to give the corresponding Tc(II) compound [Tc(NO)(NH3)4F](2+). The fluorido ligand in [Tc(NO)(NH3)4F](+) can be replaced by CF3COO(-), leaving the "[Tc(NO)(NH3)4](2+) core" untouched. The experimental results are confirmed by density functional theory calculations on [Tc(NO)F5](2-), [Tc(NO)(py)4F](+), [Tc(NO)(NH3)4F](+), and [Tc(NO)(NH3)4F](2+).

  10. Effect of transition metal-doped Ni(211) for CO dissociation: Insights from DFT calculations

    Science.gov (United States)

    Yang, Kuiwei; Zhang, Minhua; Yu, Yingzhe

    2017-03-01

    Density functional theory slab calculations were performed to investigate the adsorption and dissociation of CO over pure and M-doped Ni(211) (M = Fe, Co, Ru and Rh) with the aim to elucidate the effect of transition metal doping for CO activation. Doping the step edge of Ni(211) with Fe, Co and Ru is found to enhance the binding of CO in the initial state (IS) (in the sequence by the improvement degree: Fe > Ru > Co) as well as the co-adsorption of C and O in the final state (FS) (Ru > Fe > Co). In contrast, Rh doping is unfavorable both in the IS and in the FS. Analysis of the overall potential energy surfaces (PES) suggests CO dissociation is facilitated by Fe, Ru and Co doping both kinetically and thermodynamically, wherein Fe and Ru behave extraordinary. Interestingly, Fe substitute is slightly superior to Ru in kinetics whereas the contrary is the case in thermodynamics. Rh doping elevates the energy height from 0.97 eV on Ni(211) to 1.32 eV and releases 0.39 eV less heat relative to Ni(211), again manifesting a negative effect. Besides the classical Brønsted-Evans-Polanyi relationship, we put forward another two neat linear relations, which can well describe the feature of CO dissociation. The differences of CO adsorption and activation in the IS over pure and doped Ni(211) surfaces are rationalized via electronic structure analysis. The findings presented herein are expected to provide theoretical guidance for catalyst design and optimization in relevant processes.

  11. Searching for DFT-based methods that include dispersion interactions to calculate the physisorption of H2 on benzene and graphene

    Science.gov (United States)

    Cabria, I.; López, M. J.; Alonso, J. A.

    2017-06-01

    Simulations of the hydrogen storage capacities of nanoporous carbons require an accurate treatment of the interaction of the hydrogen molecule with the graphite-like surfaces of the carbon pores, which is dominated by the dispersion forces. These interactions are described accurately by high level quantum chemistry methods, like the Coupled Cluster method with single and double excitations and a non-iterative correction for triple excitations (CCSD(T)), but those methods are computationally very expensive for large systems and for massive simulations. Density functional theory (DFT)-based methods that include dispersion interactions at different levels of complexity are less accurate, but computationally less expensive. In order to find DFT-methods that include dispersion interactions to calculate the physisorption of H2 on benzene and graphene, with a reasonable compromise between accuracy and computational cost, CCSD(T), Møller-Plesset second-order perturbation theory method, and several DFT-methods have been used to calculate the interaction energy curves of H2 on benzene and graphene. DFT calculations are compared with CCSD(T) calculations, in the case of H2 on benzene, and with experimental data, in the case of H2 on graphene. Among the DFT methods studied, the B97D, RVV10, and PBE+DCACP methods yield interaction energy curves of H2-benzene in remarkable agreement with the interaction energy curve obtained with the CCSD(T) method. With regards to graphene, the rev-vdW-DF2, PBE-XDM, PBE-D2, and RVV10 methods yield adsorption energies of the lowest level of H2 on graphene, very close to the experimental data.

  12. The lifetime of CFC substitutes studied by a network trained with chaotic mapping modified genetic algorithm and DFT calculations.

    Science.gov (United States)

    Lü, Q; Wu, H; Yu, R; Shen, G

    2004-08-01

    The hydrohaloalkanes have attracted much attention as potential substitutes of chlorofluorocarbons (CFCs) that deplete the ozone layer and lead to great high global warming. Having a short atmospheric lifetime is very important for the potential substitutes that may also induce ozone depletion and yield high global warming gases to be put in use. Quantitative structure-activity relationship (QSAR) studies were presented for their lifetimes aided by the quantum chemistry parameters including net charges, Mulliken overlaps, E(HOMO) and E(LUMO) based on the density functional theory (DFT) at B3PW91 level, and the C-H bond dissociation energy based on AM1 calculations. Outstanding features of the logistic mapping, a simple chaotic system, especially the inherent ability to search the space of interest exhaustively have been utilized. The chaotic mapping aided genetic algorithm artificial neural network training scheme (CGANN) showed better performance than the conventional genetic algorithm ANN training when the structure of the data set was not favorable. The lifetimes of HFCs and HCs appeared to be greatly dependent on their energies of the highest occupied molecular orbitals. The perference of the RMSRE comparing to RMSE as objective function of ANN training was better for the samples of interest with relatively short lifetimes. C(2)H(6) and C(3)H(8) as potential green substitutes of CFCs present relatively short lifetimes.

  13. Raman spectra and DFT calculations for tetraterpene hydrocarbons from the L race of the green microalga Botryococcus braunii

    Science.gov (United States)

    Chun, Hye Jin; Waqued, Sergio; Thapa, Hem R.; Han, Arum; Yakovlev, Vladislav V.; Laane, Jaan; Devarenne, Timothy P.

    2017-02-01

    The green microalga Botryococcus braunii produces large amounts of liquid hydrocarbons that can be used as a renewable source for producing transportation fuels. In the L race of B. braunii the tetraterpene known as lycopadiene accumulates as the main hydrocarbon. Lycopadiene biosynthesis begins with the production of the eight carbon-carbon double bond (C=C) containing molecule lycopaoctaene, which is reduced to lycopadiene through four intermediates containing less C=C bonds. While the biosynthetic pathway for these hydrocarbons has recently been deciphered, a spectroscopic understanding of the molecular structure for these molecules remains to be reported. Here we describe the vibrational frequency assignments for all six L race hydrocarbons using density functional theory (DFT) calculations, showing that these molecules have between 312 and 348 vibrational frequencies. Experimental Raman spectroscopy analysis shows the regions for ν(C=C) stretch and CH2/CH3 bending vibrations offer unique spectral signatures allowing for the differentiation of several of the hydrocarbons from each other.

  14. Mechanism of Formation of Copper(II) Chloro Complexes Revealed by Transient Absorption Spectroscopy and DFT/TDDFT Calculations.

    Science.gov (United States)

    Mereshchenko, Andrey S; Olshin, Pavel K; Karabaeva, Kanykey E; Panov, Maxim S; Wilson, R Marshall; Kochemirovsky, Vladimir A; Skripkin, Mikhail Yu; Tveryanovich, Yury S; Tarnovsky, Alexander N

    2015-07-16

    Copper(II) complexes are extremely labile with typical ligand exchange rate constants on the order of 10(6)-10(9) M(-1) s(-1). As a result, it is often difficult to identify the actual formation mechanism of these complexes. In this work, using UV-vis transient absorption when probing in a broad time range (20 ps to 8 μs) in conjunction with DFT/TDDFT calculations, we studied the dynamics and underlying reaction mechanisms of the formation of extremely labile copper(II) CuCl4(2-) chloro complexes from copper(II) CuCl3(-) trichloro complexes and chloride ions. These two species, produced via photochemical dissociation of CuCl4(2-) upon 420 nm excitation into the ligand-to-metal-charge-transfer electronic state, are found to recombine into parent complexes with bimolecular rate constants of (9.0 ± 0.1) × 10(7) and (5.3 ± 0.4) × 10(8) M(-1) s(-1) in acetonitrile and dichloromethane, respectively. In dichloromethane, recombination occurs via a simple one-step addition. In acetonitrile, where [CuCl3](-) reacts with the solvent to form a [CuCl3CH3CN](-) complex in less than 20 ps, recombination takes place via ligand exchange described by the associative interchange mechanism that involves a [CuCl4CH3CN](2-) intermediate. In both solvents, the recombination reaction is potential energy controlled.

  15. Synthesis, spectroscopic, DFT calculations and biological activity studies of ruthenium carbonyl complexes with 2-picolinic acid and a secondary ligand

    Science.gov (United States)

    Shohayeb, Shahera M.; Mohamed, Rania G.; Moustafa, H.; El-Medani, Samir M.

    2016-09-01

    Thermal reaction of [Ru3(CO)12] with 2-picolinic acid (Hpic) in the absence and presence of a secondary ligand (pyridine, Py, bipyridine, Bipy, or thiourea, Tu) was investigated. Four complexes with molecular formulae: [Ru(CO)3(Hpic)], 1, [Ru2(CO)5(Hpic)(Py)], 2, [Ru2(CO)5(Hpic)(Tu)], 3 and [Ru2(CO)4(Hpic)(Bipy)], 4, were isolated. All complexes were characterized based on elemental analyses, IR, 1H NMR, magnetic studies, mass spectrometry and thermal analysis. The ligand and its complexes have been screened for antibacterial activities. Density Functional Theory (DFT) calculations at the B3LYP/6-311G (d,p)_ level of theory have been carried out to investigate the equilibrium geometry of the ligands. The optimized geometry parameters of the complexes were evaluated using B3LYP method and LANL2DZ basis set. The extent of natural charge population (core, valence and rydberg), exact electronic configuration, total Lewis and total non-Lewis are estimated and discussed in terms of natural bond orbitals (NBO) analysis.

  16. Spectrum-splitting approach for Fermi-operator expansion in all-electron Kohn-Sham DFT calculations

    CERN Document Server

    Motamarri, Phani; Bhattacharya, Kaushik; Ortiz, Michael

    2016-01-01

    We present a spectrum-splitting approach to conduct all-electron Kohn-Sham density functional theory (DFT) calculations by employing Fermi-operator expansion of the Kohn-Sham Hamiltonian. The proposed approach splits the subspace containing the occupied eigenspace into a core-subspace, spanned by the core eigenfunctions, and its complement, the valence-subspace, and thereby enables an efficient computation of the Fermi-operator expansion by reducing the expansion to the valence-subspace projected Kohn-Sham Hamiltonian. The key ideas used in our approach are: (i) employ Chebyshev filtering to compute a subspace containing the occupied states followed by a localization procedure to generate non-orthogonal localized functions spanning the Chebyshev-filtered subspace; (ii) compute the Kohn-Sham Hamiltonian projected onto the valence-subspace; (iii) employ Fermi-operator expansion in terms of the valence-subspace projected Hamiltonian to compute the density matrix, electron-density and band energy. We demonstrate ...

  17. Three green luminescent cadmium complexes containing 8-aminoquinoline ligands: Syntheses, crystal structures, emission spectra and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Xu Heng; Huang Liangfang; Guo Limin; Zhang Yuanguang [Anhui Key Laboratory for Functional Coordination Compounds, Anqing Normal College, Anqing 246011 (China); Ren Xiaoming [Anhui Key Laboratory for Functional Coordination Compounds, Anqing Normal College, Anqing 246011 (China); Department of Applied Chemistry, Science College, Nanjing University of Technology, 5 Xin Mo Fan Road, Nanjing 210009 (China)], E-mail: xmren@njut.edu.cn; Song You [Coordination Chemistry Institute and State Key Laboratory, Nanjing University, Nanjing 210093 (China); Xie Jingli [School of Chemistry and Bio21 Institute, The University of Melbourne, Parkville, VIC 3010 (Australia)

    2008-10-15

    Three complexes, Cd(8-aminoql){sub 2}x{sub 2} (8-aminoql=8-aminoquinoline; X{sup -}=ClO{sub 4}{sup -}, SCN{sup -}, 1 and 2, respectively) and Cd(8-aminoql)(N{sub 3}){sub 2} (3), were synthesized and structurally characterized. For each complex, the Cd{sup 2+} ion exhibits distorted octahedral coordination geometry. Two 8-aminoquinoline molecules and two counter-anions are coordinated to the Cd{sup 2+} center to form a mononuclear species with two trans-ClO{sub 4}{sup -} anions for 1, while two SCN{sup -} anions adopt a cis-configuration for 2. The intermolecular H-bonding interactions between the -NH{sub 2} groups and the O atom (1) and the S atom (2) result in the formation of a 2-D layered structure. In the crystal of 3, the N{sub 3}{sup -} anions bridging the neighboring Cd(8-aminoql){sup 2+} units form a 1-D coordination polymer. The three complexes emit green luminescence. The emission bands possess a broad asymmetric feature, which can be assigned to L'LCT transitions based on DFT and TDDFT calculations.

  18. Crystal structure, vibrational, spectral investigation, quantum chemical DFT calculations and thermal behavior of Diethyl [hydroxy (phenyl) methyl] phosphonate

    Science.gov (United States)

    Ouksel, Louiza; Chafaa, Salah; Bourzami, Riadh; Hamdouni, Noudjoud; Sebais, Miloud; Chafai, Nadjib

    2017-09-01

    Single Diethyl [hydroxy (phenyl) methyl] phosphonate (DHPMP) crystal with chemical formula C11H17O4P, was synthesized via the base-catalyzed Pudovik reaction and Lewis acid as catalyst. The results of SXRD analyzes indicate that this compound crystallizes into a mono-clinic system with space group P21/n symmetry and Z = 4. The crystal structure parameters are a = 9.293 Å, b = 8.103 Å, c = 17.542 Å, β = 95.329° and V = 1315.2 Å3, the structure displays one inter-molecular O-H⋯O hydrogen bonding. The UV-Visible absorption spectrum shows that the crystal exhibits a good optical transmission in the visible domain, and strong absorption in middle ultraviolet one. The vibrational frequencies of various functional groups present in DHPMP crystal have been deduced from FT-IR and FT-Raman spectra and then compared with theoretical values performed with DFT (B3LYP) method using 6-31G (p, d) basis sets. Chemical and thermodynamic parameters such as: ionization potential (I), electron affinity (A), hardness (σ), softness (η), electronegativity (χ) and electrophilicity index (ω), are also calculated using the same theoretical method. The thermal decomposition behavior of DHPMP, studied by using thermogravimetric analysis (TDG), shows a thermal stability until to 125 °C.

  19. One new and six known triterpene xylosides from Cimicifuga racemosa: FT-IR, Raman and NMR studies and DFT calculations

    Science.gov (United States)

    Jamróz, Marta K.; Jamróz, Michał H.; Cz. Dobrowolski, Jan; Gliński, Jan A.; Gleńsk, Michał

    One new and six known triterpene xylosides were isolated from Cimicifuga racemosa (black cohosh, Actaea racemosa). The structure of a new compound, designated as isocimipodocarpaside (1), was established to be (24S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10-seco-9,19-cyclolanost-1(10),7(8),9(11)-trien 3-O-β-D-xylopyranoside, by means of 1H and 13C NMR, IR and Raman spectroscopies and Mass Spectrometry. The six known compounds are: 23-epi-26-deoxycimicifugoside (2), 23-epi-26-deoxyactein (3), 25-anhydrocimigenol xyloside (4), 23-O-acetylshengmanol xyloside (5), 25-O-acetylcimigenol xyloside (6) and 3'-O-acetylcimicifugoside H-1 (7). On the basis of NMR data supported by DFT calculations of NMR shielding constants of (2), its structure, previously described as 26-deoxycimicifugoside was corrected and determined as 23-epi-26-deoxycimicifugoside. The 13C CPMAS NMR spectra of the studied compounds (1)-(7) provided data on their solid-state interactions. The IR and Raman spectra in the Cdbnd O, Cdbnd C, and Csbnd H stretching vibration regions clearly discriminate different triterpenes found in C. racemosa.

  20. Pseudopotential and full-electron DFT calculations of thermodynamic properties of electrons in metals and semiempirical equations of state.

    Science.gov (United States)

    Levashov, P R; Sin'ko, G V; Smirnov, N A; Minakov, D V; Shemyakin, O P; Khishchenko, K V

    2010-12-22

    In the present work, we compare the thermal contribution of electrons to thermodynamic functions of metals in different models at high densities and electron temperatures. One of the theoretical approaches, the full-potential linear-muffin-tin-orbital method, treats all electrons in the framework of density functional theory (DFT). The other approach, VASP, uses projector-augmented-wave pseudopotentials for the core electrons and considers the valent electrons also in the context of DFT. We analyze the limitations of the pseudopotential approach and compare the DFT results with a finite-temperature Thomas-Fermi model and two semiempirical equations of state.

  1. Comparative theoretical study of the UV/Vis absorption spectra of styrylpyridine compounds using TD-DFT calculations.

    Science.gov (United States)

    Castro, Maria Eugenia; Percino, M Judith; Chapela, Victor M; Soriano-Moro, Guillermo; Ceron, Margarita; Melendez, Francisco J

    2013-05-01

    This study examined absorption properties of 2-styrylpyridine, trans-2-(m-cyanostyryl)pyridine, trans-2-[3-methyl-(m-cyanostyryl)]pyridine, and trans-4-(m-cyanostyryl)pyridine compounds based on theoretical UV/Vis spectra, with comparisons between time-dependent density functional theory (TD-DFT) using B3LYP, PBE0, and LC-ωPBE functionals. Basis sets 6-31G(d), 6-31G(d,p), 6-31+G(d,p), and 6-311+G(d,p) were tested to compare molecular orbital energy values, gap energies, and maxima absorption wavelengths. UV/Vis spectra were calculated from fully optimized geometry in B3LYP/6-311+G(d,p) in gas phase and using the IEFPCM model. B3LYP/6-311+G(d,p) provided the most stable form, a planar structure with parameters close to 2-styrylpyridine X-ray data. Isomeric structures were evaluated by full geometry optimization using the same theory level. Similar energetic values were found: ~4.5 kJ mol(-1) for 2-styrylpyridine and ~1 kJ mol(-1) for derivative compound isomers. The 2-styrylpyridine isomeric structure differed at the pyridine group N-atom position; structures considered for the other compounds had the cyano group attached to the phenyl ring m-position equivalent. The energy difference was almost negligible between m-cyano-substituted molecules, but high energy barriers existed for cyano-substituted phenyl ring torsion. TD-DFT appeared to be robust and accurate approach. The B3LYP functional with the 6-31G(d) basis set produced the most reliable λmax values, with mean errors of 0.5 and 12 nm respect to experimental values, in gas and solution, respectively. The present data describes effects on the λmax changes in the UV/Vis absorption spectra of the electron acceptor cyano substituent on the phenyl ring, the electron donor methyl substituent, and the N-atom position on the electron acceptor pyridine ring, causing slight changes respect to the 2-styrylpyridine title compound.

  2. Structural Rearrangement of Niobium Oxides from Lamellar Phases to Discrete Nanosheets and Nanoscrolls Probed by DFT Calculations

    Science.gov (United States)

    Adhikari, Jhashanath; Smith, Luis J.

    2012-02-01

    Inorganic niobates ACa2Nb3O10 (A= H and K) with layered structures are good photocatalytic materials due to their high surface areas accommodating a larger number of active sites and ease of processing through soft chemical techniques like exfoliation and restacking. Alkali metal phases can be ion-exchanged to the acid phase, which in turn can be easily exfoliated to individual nanosheets. The nanosheets can change their form to nanoscrolls with a curled geometry instead of a flat surface. During these morphological transformations, the local structure at the Nb-atom, H-atom and the interface may undergo rearrangement which is responsible for the alteration of properties of the materials. This presentation highlights the preliminary results on these structural modifications (interface variation, stacking of layers, lattice contraction and space group settings) and the possible positions of the proton. Our calculations show that the protons in the acid form are non-bridging and bonded to the same layer oxygen atoms unlike the K-atoms in its parent compound. The Electric field gradient (EFG) is a parameter very sensitive to the electron density around a quadrupolar nucleus ^2H and ^93Nb that can be detected using NMR. Changes in its magnitude/sign can be correlated to the change in the local environment (bond lengths and angles) around the sites of interest. EFG values from DFT calculations based on the proposed structural models will be used for the characterization of surface O-H bond lengths, H-bonding and Nb-O bond lengths and can be used to interpret NMR studies.

  3. Spectrum-splitting approach for Fermi-operator expansion in all-electron Kohn-Sham DFT calculations

    Science.gov (United States)

    Motamarri, Phani; Gavini, Vikram; Bhattacharya, Kaushik; Ortiz, Michael

    2017-01-01

    We present a spectrum-splitting approach to conduct all-electron Kohn-Sham density functional theory (DFT) calculations by employing Fermi-operator expansion of the Kohn-Sham Hamiltonian. The proposed approach splits the subspace containing the occupied eigenspace into a core subspace, spanned by the core eigenfunctions, and its complement, the valence subspace, and thereby enables an efficient computation of the Fermi-operator expansion by reducing the expansion to the valence-subspace projected Kohn-Sham Hamiltonian. The key ideas used in our approach are as follows: (i) employ Chebyshev filtering to compute a subspace containing the occupied states followed by a localization procedure to generate nonorthogonal localized functions spanning the Chebyshev-filtered subspace; (ii) compute the Kohn-Sham Hamiltonian projected onto the valence subspace; (iii) employ Fermi-operator expansion in terms of the valence-subspace projected Hamiltonian to compute the density matrix, electron density, and band energy. We demonstrate the accuracy and performance of the method on benchmark materials systems involving silicon nanoclusters up to 1330 electrons, a single gold atom, and a six-atom gold nanocluster. The benchmark studies on silicon nanoclusters revealed a staggering fivefold reduction in the Fermi-operator expansion polynomial degree by using the spectrum-splitting approach for accuracies in the ground-state energies of ˜10-4Ha/atom with respect to reference calculations. Further, numerical investigations on gold suggest that spectrum splitting is indispensable to achieve meaningful accuracies, while employing Fermi-operator expansion.

  4. Conformational studies on 2-substituted ethanesulfonates in aqueous solution by 1H NMR spectroscopy and DFT calculations

    Science.gov (United States)

    Musio, Roberta; Sciacovelli, Oronzo

    2009-09-01

    The conformation of some 2-substituted sodium ethanesulfonates exerting biological functions, XCH 2CH 2SO 3Na (X = S -, Br, Cl, OH, NH 2, SH), has been investigated in aqueous solution by 1H NMR spectroscopy. Potential energy curves for rotation about the C-C bond have been calculated at DFT level of theory (B3LYP/6-311++G(2d,p)) in vacuum and in water (by IEF-PCM method). As concerning dianionic coenzyme M (X = S -), 2-bromo- and 2-chloroethanesulfonate, in vacuum the torsional potential curves and the variations of atomic charges and geometric parameters suggest that electrostatic and steric repulsions between the substituent X and -SO3- moiety determine the preference for anti conformer. In isethionate (X = OH), anionic taurine (X = NH 2), and coenzyme M (X = SH), the formation of an intramolecular hydrogen bond stabilizes also gauche-like conformers and the torsional potential curves exhibit two minima. According to Natural Bond Orbital analysis, hydrogen bond can be ascribed to electron transfer from two oxygen lone-pairs of the -SO3- moiety to the antibonding Y-H orbital of the substituent X. In all the compounds examined, hyperconjugative interactions tend to stabilize the gauche conformers with respect to the anti one. This means that conformational preferences in vacuum are determined by a counterbalancing of electrostatic, steric, and hyperconjugative interactions. Calculations in vacuum are not in agreement with the experimental conformational behaviour of the compounds examined. In order to reproduce the experimental results at least qualitatively, solvent effect must be introduced.

  5. Synthesis, crystal structure, spectroscopic investigations and DFT calculations of the copper(II) complex of 4-(Trifluoromethyl)pyridine-2-carboxylic acid

    Science.gov (United States)

    Vural, Hatice; Orbay, Metin

    2017-10-01

    A novel polymeric complex of Cu(II) ion, [Cu(tfpc)2]n [tfpc: 4-(Trifluoromethyl)pyridine-2-carboxylate] has been prepared and characterized spectroscopically (by FT-IR) and structurally (by single-crystal XRD). The geometry around the Cu(II) center can be described as square planar made by tfpc ligand having nitrogen and oxygen atoms. Additionally, the Cu(II) complex has a one-dimensional double-bridged polymeric structure in which Cu(II) ions are bridged by two oxygen atoms of adjacent planes. The crystal packing has been stabilized by Csbnd H⋯O intra and intermolecular hydrogen bonds. The molecular structure of the Cu(II) complex has been optimized using the Density Functional Theory (DFT) B3LYP, B3PW91 and PBEPBE levels with 6-311+G(d,p) basis set. The calculated electronic spectra have been explained using the time dependent DFT (TD-DFT) method by applying the polarized continuum model (PCM). The vibrational spectral data have been calculated and compared with experimental ones. The non-linear optical (NLO) properties of the title compound have been investigated using the DFT method with three different levels. Natural Bond Orbital (NBO) property of the Cu(II) complex has been performed by the B3LYP density functional and the 6-311+G(d,p) basis set.

  6. Extinction coefficients of CC and CC bands in ethyne and ethene molecules interacting with Cu+ and Ag+ in zeolites--IR studies and quantumchemical DFT calculations.

    Science.gov (United States)

    Kozyra, Paweł; Góra-Marek, Kinga; Datka, Jerzy

    2015-02-05

    The values of extinction coefficients of CC and CC IR bands of ethyne and ethene interacting with Cu+ and Ag+ in zeolites were determined in quantitative IR experiments and also by quantumchemical DFT calculations with QM/MM method. Both experimental and calculated values were in very good agreement validating the reliability of calculations. The values of extinction coefficients of ethyne and ethene interacting with bare cations and cations embedded in zeolite-like clusters were calculated. The interaction of organic molecules with Cu+ and Ag+ in zeolites ZSM-5 and especially charge transfers between molecule, cation and zeolite framework was also discussed in relation to the values of extinction coefficients.

  7. Specific features of the electronic structure and optical properties of KPb2Br5: DFT calculations and X-ray spectroscopy measurements

    Science.gov (United States)

    Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Denysyuk, N. M.; Shkumat, P. N.; Tarasova, A. Y.; Isaenko, L. I.; Khyzhun, O. Y.

    2016-03-01

    Density functional theory (DFT) calculations are made in order to explore the total and partial densities of states of potassium dilead pentabromide, KPb2Br5, by using the augmented plane wave + local orbitals (APW + lo) method as incorporated in the WIEN2k package. The present calculations reveal that the principle contributors to the valence band of KPb2Br5 are the Pb 6s and Br 4p states contributing predominantly at the bottom and at the top of the band, respectively, while the bottom of the conduction band is formed mainly from contributions of the unoccupied Pb 6p states. The curves of total density of states derived by the present DFT calculations of KPb2Br5 are found to be in agreement with the experimental X-ray photoelectron valence-band spectrum of the compound studied. Comparison on a common energy scale of the X-ray emission bands representing the energy distribution of the valence Br p and K s states and the X-ray photoelectron valence-band spectrum of the KPb2Br5 single crystal indicate that the Br 4p and K 4s states contribute mainly at the top and in the upper portion of the valence band, respectively, being in agreement with data of the present DFT band-structure calculations of this compound. Principal optical characteristics of KPb2Br5, namely dispersion of the absorption coefficient, real and imaginary parts of dielectric function, electron energy-loss spectrum, refractive index, extinction coefficient and optical reflectivity are also studied by the DFT calculations.

  8. DFT electronic structure calculations, spectroscopic studies, and normal coordinate analysis of 2-[(5-nitro-1,3-thiazol-2-yl)carbamoyl]phenyl acetate.

    Science.gov (United States)

    Muthu, S; Elamuruguporchelvi, E; Varghese, Anitha

    2015-03-05

    The solid phase FTIR and FT-Raman spectra of 2-[(5-nitro-1,3-thiazol-2-yl)carbamoyl]phenyl acetate (25N2LCPA) have been recorded 450-4000cm(-1) and 100-4000cm(-1) respectively. The normal coordinate analysis was carried out to confirm the precision of the assignments. DFT calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies and IR intensities. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31+G(d,p) basis set. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The Vibrational frequencies are calculated in the above method and are compared with experimental frequencies which yield good agreement between observed and calculated frequencies. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. In addition, Frontiers molecular orbital and molecular electrostatic potential were computed by using Density Functional Theory (DFT) B3LYP/6-31+G(d,p) basis set. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule.

  9. Synthesis, crystal structure, DFT calculation and DNA binding studies of new water-soluble derivatives of dppz

    Science.gov (United States)

    Aminzadeh, Mohammad; Eslami, Abbas; Kia, Reza; Aleeshah, Roghayeh

    2017-10-01

    Diquaternarization of dipyrido-[2,3-a:2‧,3‧-c]-phenazine,(dppz) and its analogous dipyrido-[2,3-a:2‧,3‧-c]-dimethylphenazine,(dppx) using 1,3-dibromopropane afford new water-soluble derivatives of phenazine, propylene-bipyridyldiylium-phenazine (1) and propylene-bipyridyldiylium-dimethylphenazine (2). The compounds have been characterized by means of FT-IR, NMR, elemental analysis and conductometric measurements and their structure were determined by X-ray crystallography. The experimental studies on the compounds have been accompanied computationally by Density Functional Theory (DFT) calculations. The DNA binding properties of both compounds to calf thymus DNA (ctDNA) were investigated by UV-Vis absorption and emission methods. The expanded UV-Vis spectral data matrix was analyzed by multivariate curve resolution-alternating least squares (MCR-ALS) technique to obtain the concentration profile and pure spectra of all reaction species which existed in the interaction procedure. Multivariate curve resolution may help us to give a better understanding of the 1(Cl)2-ctDNA and 2(Cl)2-ctDNA interaction mechanism. The results suggest that both compounds bind tightly to DNA through intercalation mechanism and the DNA binding affinity of 2 is slightly lower than that of 1 due to steric hindrance of the methyl group. Also, thermal denaturation studies reveal that these compounds show strong affinity for binding with calf thymus DNA. The thermodynamic parameters of the DNA binding process were obtained from the temperature dependence of the binding constants and the results showed that binding of both compounds to DNA is an enthalpically driven process that is in agreement with proposed DNA intercalation capability of these compounds.

  10. Circular dichroism spectroscopy and DFT calculations in determining absolute configuration and E/Z isomers of conjugated oximes.

    Science.gov (United States)

    Rode, Joanna E; Frelek, Jadwiga

    2017-11-01

    The primary purpose of this work was to demonstrate the suitability of circular dichroism (CD) spectroscopy in stereochemical studies of α,β-unsaturated oximes, with particular emphasis on determination of E and Z geometry of the oxime double bond. As models for this study, O-phenyl and O-triphenylmethyl (trityl) oximes of 4-hydroxy-2-methylcyclopent-2-en-1-one were selected. These model compounds differ in both absolute configuration at C4 carbon atom and E-Z configuration of the oxime double bond. The basic dichroic technique applied was electronic circular dichroism (ECD) assisted by quantum-chemical calculations and vibrational circular dichroism (VCD) for selected cases. Such an approach enabled effective implementation of both goals. Thus, we were able to associate the signs of Cotton effects in the range of 190-240 nm with the absolute configuration at C4 and within 240-300 nm with the E- or Z-geometry of the oxime double bond. Within this work, optical activity of the protecting trityl group was also studied towards formation of the propeller-shaped conformations by using the same combined CD/DFT methodology. As shown, the helical structure of the trityl group has a considerable influence on the ECD spectra. However, the MPM and PMP conformers of the trityl group are in fact almost equally populated in the conformational equilibrium, making it impossible to distinguish them. On the other hand, rotamers of the hydroxyl group at C4 show a decisive impact on the VCD spectra in both phenoxy and trityl oximes. © 2017 Wiley Periodicals, Inc.

  11. Adsorption of SO{sub 2} on Li atoms deposited on MgO (1 0 0) surface: DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Eid, Kh.M., E-mail: Kheid98@hotmail.com [Physics Department, Faculty of Education, Ain Shams University, Cairo 11757 (Egypt); Ammar, H.Y. [Department of Physics, Faculty of Science, Najran University, Najran 1988 (Saudi Arabia)

    2011-05-01

    The adsorption of sulfur dioxide molecule (SO{sub 2}) on Li atom deposited on the surfaces of metal oxide MgO (1 0 0) on both anionic and defect (F{sub s}-center) sites located on various geometrical defects (terrace, edge and corner) has been studied using density functional theory (DFT) in combination with embedded cluster model. The adsorption energy (E{sub ads}) of SO{sub 2} molecule (S-atom down as well as O-atom down) in different positions on both of O{sup -2} and F{sub s} sites is considered. The spin density (SD) distribution due to the presence of Li atom is discussed. The geometrical optimizations have been done for the additive materials and MgO substrate surfaces (terrace, edge and corner). The oxygen vacancy formation energies have been evaluated for MgO substrate surfaces. The ionization potential (IP) for defect free and defect containing of the MgO surfaces has been calculated. The adsorption properties of SO{sub 2} are analyzed in terms of the E{sub ads}, the electron donation (basicity), the elongation of S-O bond length and the atomic charges on adsorbed materials. The presence of the Li atom increases the catalytic effect of the anionic O{sup -2} site of MgO substrate surfaces (converted from physisorption to chemisorption). On the other hand, the presence of the Li atom decreases the catalytic effect of the F{sub s}-site of MgO substrate surfaces. Generally, the SO{sub 2} molecule is strongly adsorbed (chemisorption) on the MgO substrate surfaces containing F{sub s}-center.

  12. Synthesis, characterization, electrochemical studies and DFT calculations of amino acids ternary complexes of copper (II) with isonitrosoacetophenone. Biological activities

    Science.gov (United States)

    Tidjani-Rahmouni, Nabila; Bensiradj, Nour el Houda; Djebbar, Safia; Benali-Baitich, Ouassini

    2014-10-01

    Three mixed complexes having formula [Cu(INAP)L(H2O)2] where INAP = deprotonated isonitrosoacetophenone and L = deprotonated amino acid such as histidine, phenylalanine and tryptophan have been synthesized. They have also been characterized using elemental analyses, molar conductance, UV-Vis, IR and ESR spectra. The value of molar conductance indicates them to be non-electrolytes. The spectral studies support the binding of the ligands with two N and two O donor sites to the copper (II) ion, giving an arrangement of N2O2 donor groups. Density Functional Theory (DFT) calculations were applied to evaluate the cis and trans coordination modes of the two water molecules. The trans form was shown to be energetically more stable than the cis one. The ESR data indicate that the covalent character of the metal-ligand bonding in the copper (II) complexes increases on going from histidine to phenylalanine to tryptophan. The electrochemical behavior of the copper (II) complexes was determined by cyclic voltammetry which shows that the chelate structure and electron donating effects of the ligands substituent are among the factors influencing the redox potentials of the complexes. The antimicrobial activities of the complexes were evaluated against several pathogenic microorganisms to assess their antimicrobial potentials. The copper complexes were found to be more active against Gram-positive than Gram-negative bacteria. Furthermore, the antioxidant efficiencies of the metal complexes were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity. The antioxidant activity of the complexes indicates their moderate scavenging activity against the radical DPPH.

  13. Structural Investigation of Methanol {6-[(2-oxidopropyl)iminomethyl] phenolato} dioxidomolybdenum(VI) by X-Ray Crystallography and DFT Calculations

    OpenAIRE

    Iran SHEIKHSHOAIE; Yousef EBRAHIMIPOUR; Mahdiyeh SHEIKHSHOAEE

    2012-01-01

    This article presents the computational calculations of a cis-dioxomolybdenum(VI) complex by using density functional theory (DFT) with a DZP basis set (double zeta polarized basis set). The Schiff base 2-((E)-(2-hydroxypropylimino)methyl)-6-methoxyphenol was treated with MoO2(acac)2 in dry methanol to produce the mononuclear complex methanol{2-methoxy-6-[(2-oxidopropyl) iminomethyl]phenolato} dioxidomolybdenum(VI), whose structure has been solved and successfully refined in the monoclinic sp...

  14. Versatile and green synthesis, spectroscopic characterizations, crystal structure and DFT calculations of 1,2,3‒triazole‒based sulfonamides

    Science.gov (United States)

    Saeidian, Hamid; Sadighian, Hamed; Abdoli, Morteza; Sahandi, Morteza

    2017-03-01

    A green, and practically reliable method for the synthesis of novel 1,2,3‒triazole-based sulfonamides via copper (I)‒catalyzed azide‒alkyne [3 + 2] cycloaddition reaction was reported. The desired products were characterized by CHN analysis, FT-IR, 1H and 13C NMR, ESI-MS spectroscopy, single crystal X-ray diffraction and density functional theory (DFT) geometry optimization and molecular orbital calculations. Mild and green reaction conditions, atom-economic and high yields (61-91%) make this protocol an attractive option for the synthesis of 1,2,3‒triazoles bearing sulfonamide moiety. Geometrical structures, vibrational frequencies, 1H and 13C chemical shift values, Mulliken charge distribution and electrophilicity index (HOMO-LUMO analysis) of the characterized structure of 3f in the ground state have been calculated with the aid of DFT studies. The calculated chemical shifts (NMR) and vibrational frequencies (FT-IR) are in compliance with the experimental findings. The aim of the DFT study was to make a reasonable assignment of vibrational bands and chemical shifts.

  15. Synthesis, Crystal Structures, and DFT Calculations of Three New Cyano(phenylsulfonylindoles and a Key Synthetic Precursor Compound

    Directory of Open Access Journals (Sweden)

    William L. Montgomery

    2015-09-01

    Full Text Available Three cyano-1-(phenylsulfonylindole derivatives, 3-cyano-1-(phenylsulfonyl indole, (I, 2-cyano-1-(phenylsulfonylindole, (II, and 2,3-dicyano-1-(phenylsulfonyl indole, (III, and a key synthetic precursor 1-(phenylsulfonyl-1-(1,1-dimethylethyl indole-3-carboxamide, (IV, have been synthesized and their structures determined by single crystal X-ray crystallography. (I, C15H10N2O2S, is orthorhombic with space group P 212121 and cell constants: a = 4.9459(3 Å, b = 10.5401(7 Å, c = 25.0813(14 Å, V = 1307.50(14 Å3 and Z = 4. (II, C15H10N2O2S, is monoclinic with space group C 2/c and cell constants: a = 18.062(2 Å, b = 11.293(2 Å, c = 15.922(3 Å, α = 90°, β = 124.49(2°, g = 90°, V = 2676.7 Å3 and Z = 8. (III, C16H9N3O2S, is triclinic with space group P-1 and cell constants: a = 8.1986(8 Å, b = 9.6381(11 Å, c = 9.8113(5 Å, α = 95.053(6°, β = 101.441(6°, g = 108.071(9°, V = 713.02(11 Å3 and Z = 2. (IV, C19H20N2O3S, is orthorhombic with space group P ccn and cell constants: a = 13.7605(8 Å, b = 27.3177(14 Å, c = 9.7584(6 Å, α = 90°, β = 90°, g =90°, V = 3668.2(4 Å3 and Z = 8. All four compounds have the same indole nitrogen phenylsulfonyl substituent and (I, (II, and (III are nitrile derivatives. (IV is a tert-butylamide. In the crystals, the dihedral angle between the mean planes of the indole and phenylsulfonyl groups are 85.4(2° (I, 87.2(7° (II, 75.1(7° (III, and 88.6(2° (IV, respectively. Additionally, DFT geometry-optimized molecular orbital calculations were performed and frontier molecular orbitals of each compound are displayed. Correlation between the calculated molecular orbital energies (eV for the surfaces of the frontier molecular orbitals to the electronic excitation transitions from the absorption spectra of each compound has been proposed.

  16. Synthesis, Characterization, Properties and DFT Calculations of 2-(Benzo[b]thiophen-2-yl)pyridine-based Iridium(III) Complexes with Different Ancillary Ligands.

    Science.gov (United States)

    Li, Gao-Nan; Zeng, Yong-Pi; Li, Kai-Xiu; Chen, Hao-Hua; Xie, Hui; Zhang, Fu-Lin; Chen, Guang-Ying; Niu, Zhi-Gang

    2016-01-01

    A series of new cyclometalated btp-based iridium(III) complexes with three different ancillary ligands, Ir(btp)2(bozp) (3a), Ir(btp)2(btzp) (3b) and Ir(btp)2(izp) (3c) (btp = 2-(benzo[b]thiophen-2-yl)pyridine, bozp =2-(benzo[d]oxazol-2-yl)phenol, btzp =2-(benzo[d]thiazol-2-yl)phenol, izp = 2-(2 H-indazol-2-yl)phenol), have been synthesized and fully characterized. The crystal structure of 3b has been determined by single crystal X-ray diffraction analysis. A comparative study has been carried out for complexes 3a - 3c by UV-vis absorption spectroscopy, photoluminescence spectroscopy, cyclic voltammetry and DFT calculations. This observation illustrates that the substitution of N or S in ancillary ligand can lead to a marked bathochromic shift of absorption and emission wavelengths. The spectroscopic characterisation of these complexes has been complemented by DFT and TD-DFT calculations, supporting the assignment of (3)MLCT/(3)LC to the lowest energy excited state.

  17. Comparison of the performance of different DFT methods in the calculations of the molecular structure and vibration spectra of serotonin (5-hydroxytryptamine, 5-HT)

    Science.gov (United States)

    Yang, Yue; Gao, Hongwei

    2012-04-01

    Serotonin (5-hydroxytryptamine, 5-HT) is a monoamine neurotransmitter which plays an important role in treating acute or clinical stress. The comparative performance of different density functional theory (DFT) methods at various basis sets in predicting the molecular structure and vibration spectra of serotonin was reported. The calculation results of different methods including mPW1PW91, HCTH, SVWN, PBEPBE, B3PW91 and B3LYP with various basis sets including LANL2DZ, SDD, LANL2MB, 6-31G, 6-311++G and 6-311+G* were compared with the experimental data. It is remarkable that the SVWN/6-311++G and SVWN/6-311+G* levels afford the best quality to predict the structure of serotonin. The results also indicate that PBEPBE/LANL2DZ level show better performance in the vibration spectra prediction of serotonin than other DFT methods.

  18. The inelastic neutron scattering spectra of [alpha]-3-amino-5-nitro-1,2,4-2H-triazole: Experiment and DFT calculations

    Science.gov (United States)

    Ciezak, Jennifer A.; Trevino, S. F.

    2005-02-01

    The inelastic neutron scattering (INS) spectrum of α-3-amino-5-nitro-1,2,4-triazole is presented through 1200 cm -1. A comparison of the INS spectrum with an isolated molecule B3LYP/6-311G** calculation reveals generally good frequency and intensity agreement with two notable differences in intensity. Periodic density functional theory (DFT) calculations are employed to determine whether the intermolecular hydrogen bonding is the origin of these differences between the B3LYP/6-311G** and INS spectrum.

  19. New heterocyclic green, blue and orange dyes from indazole: Synthesis, tautomerism, alkylation studies, spectroscopic characterization and DFT/TD-DFT calculations

    Science.gov (United States)

    Poorhaji, Soodabeh; Pordel, Mehdi; Ramezani, Shirin

    2016-09-01

    Tautomerism and alkylation studies on the green intermediate 2-(5-hydroxyimino-1-methyl-4,5-dihydro-1H-4-indazolyliden)-2-phenylacetonitrile led to the synthesis of new heterocyclic green, blue and orange dyes in high yields. The structures of all newly synthesized compounds were confirmed by spectral and analytical data. The optical properties of the dyes were spectrally characterized by using a UV-vis spectrophotometer and results show that they exhibited interesting photophysical properties. Solvent effects on the absorption spectra of these dyes have been studied and the absorption band in polar solvents undergoes a red shift. Density functional theory calculations of the dyes were performed to provide the optimized geometries and relevant frontier orbitals. Calculated electronic absorption spectra were also obtained by time-dependent density functional theory method.

  20. DFT calculations on molecular structure, spectral analysis, multiple interactions, reactivity, NLO property and molecular docking study of flavanol-2,4-dinitrophenylhydrazone

    Science.gov (United States)

    Singh, Ravindra Kumar; Singh, Ashok Kumar

    2017-02-01

    A new flavanol-2,4-dinitrophenylhydrazone (FDNP) was synthesized and its structure was confirmed by FT-IR, FT-Raman, 1H NMR, mass spectrometry and elemental analysis. All quantum chemical calculations were carried out at level of density functional theory (DFT) with B3LYP functional using 6-311++ G (d,p) basis atomic set. UV-Vis absorption spectra for the singlet-singlet transition computed for fully optimized ground state geometry using Time-Dependent-Density Functional Theory (TD-DFT) with CAM-B3LYP functional was found to be in consistent with that of experimental findings. Analysis of vibrational (FT-IR and FT-Raman) spectrum and their assignments has been done by computing Potential Energy Distribution (PED) using Gar2ped. HOMO-LUMO analysis was performed and reactivity descriptors were calculated. Calculated global electrophilicity index (ω = 7.986 eV) shows molecule to be a strong electrophile. 1H NMR chemical shift calculated with the help of gauge-including atomic orbital (GIAO) approach shows agreement with experimental data. Various intramolecular interactions were analysed by AIM approach. DFT computed total first static hyperpolarizability (β0 = 189.03 × 10-30 esu) indicates that title molecule can be used as attractive future NLO material. Solvent induced effects on the NLO properties studied by using self-consistent reaction field (SCRF) method shows that β0 value increases with increase in solvent polarity. To study the thermal behaviour of title molecule, thermodynamic properties such as heat capacity, entropy and enthalpy change at various temperatures have been calculated and reported. Molecular docking results suggests title molecule to be a potential kinase inhibitor and might be used in future for designing of new anticancer drug.

  1. Molecular structure, vibrational analysis (FT-IR, FT-Raman), NMR, UV, NBO and HOMO-LUMO analysis of N,N-Diphenyl Formamide based on DFT calculations.

    Science.gov (United States)

    Mathammal, R; Monisha, N R; Yasaswini, S; Krishnakumar, V

    2015-03-15

    In this work, the vibrational spectral analysis is carried out by using Raman and infrared spectroscopy in the range 4000-400 cm(-1) and 4000-50 cm(-1) respectively for N,N-Diphenyl Formamide (DPF) molecule. The optimized molecular structures, vibrational frequencies and corresponding vibrational assignments, nuclear magnetic resonance (NMR) and ultraviolet-visible (UV-VIS) spectra of the title molecule are evaluated using density functional theory (DFT) with standard B3LYP/6-31G(d,p) basis set. The harmonic vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The stability of the molecule arising from hyper conjugative interactions and the charge delocalization has been analyzed using natural bond (NBO) analysis. The possible electronic transitions are determined by HOMO-LUMO orbital shapes and their energies. Thermodynamic properties (heat capacity, entropy and enthalpy) and the first hyperpolarizability of the title compound are calculated. The Mulliken charges and electric dipole moment of the molecule are computed using DFT calculations. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shift of the molecules are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde.

    Science.gov (United States)

    Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M; Ben Altabef, Aída

    2015-02-05

    The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34°C and decomposes at temperatures higher than 193°C. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde

    Science.gov (United States)

    Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M.; Altabef, Aída Ben

    2015-02-01

    The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34 °C and decomposes at temperatures higher than 193 °C.

  4. Molecular structure (monomeric and dimeric) and hydrogen bonds in 5-benzyl 2-thiohydantoin studied by FT-IR and FT-Raman spectroscopy and DFT calculations.

    Science.gov (United States)

    Deval, Vipin; Kumar, Amit; Gupta, Vineet; Sharma, Anamika; Gupta, Archana; Tandon, Poonam; Kunimoto, Ko-Ki

    2014-11-11

    In the present work the structural and spectral characteristics of 5-benzyl-2-thiohydantoin (5-BTH) have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G++(d,p) basis set. Our results support the hydrogen bonding pattern proposed by reported crystalline structure. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV-vis spectrum of the compound was recorded in methanol solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using PCM and 6-311++G(d,p) basis set. In addition, the thermodynamic properties of the compound were calculated at different temperatures and corresponding relations between the properties and temperature were also studied.

  5. Analysis of valence XPS and AES of (PP, P4VP, PVME, PPS, PTFE) polymers by DFT calculations using the model molecules

    Science.gov (United States)

    Endo, Kazunaka; Shimada, Shingo; Kato, Nobuhiko; Ida, Tomonori

    2016-10-01

    We simulated valence X-ray photoelectron spectra (VXPS) of five [(CH2CH(CH3))n {poly(propyrene) PP}, ((CH2CH(C5NH4))n {poly(4-vinyl-pyridine) P4VP}, (CH2CHO(CH3))n {poly(vinyl methyl ether) PVME}, (C6H4S)n {poly(phenylene) sulphide PPS}, (CF2CF2)n {poly(tetrafluoroethylene) PTFE}] polymers by density-functional theory (DFT) calculations using the model oligomers. The spectra reflect the differences in the chemical structures between each polymer, since the peak intensities of valence band spectra are seen to be due to photo-ionization cross-section of (C, N, O, S, F) atoms by considering the orbital energies and cross-section values of the polymer models, individually. In the Auger electron spectra (AES) simulations, theoretical kinetic energies of the AES are obtained with our modified calculation method. The modified kinetic energies correspond to two final-state holes at the ground state and at the transition-state in DFT calculations, respectively. Experimental peaks of (C, N, O)- KVV, and S L2,3VV AES for each polymer are discussed in detail by our modified calculation method.

  6. Chemical synthesis, crystal structure, vibrational spectroscopy, non-linear optical properties and DFT calculation of bis (2,6-diaminopyridinium) sulfate monohydrate

    Science.gov (United States)

    Ben Hassen, Chaouki; Dammak, Thameur; Chniba-Boudjada, Nassira; Mhiri, Tahar; Boujelbene, Mohamed

    2017-01-01

    Single crystals of a new organic inorganic hybrid compound "bis (2,6-diaminopyridinium) sulfate monohydrate [C5H8N3]2SO4·H2O ([2,6-HDAP]2SO4·H2O)" was synthesized by slow evaporation method at room temperature and characterized by X-ray single crystal diffraction, infrared spectroscopy and DFT calculation. The new hybrid compound crystallizes in the orthorhombic system with the non-centro symmetric space group Pna21 and the following parameters a = 14.759(2) Å, b = 7.076 (2) Å and c = 28.159 (2) Å. The atomic arrangement can be described as inorganic chains following the b axis connected with the organic groups by means of Nsbnd H⋯O hydrogen bonds to form 3D network. Antiparallelly π-π stacked 2,6-HDAP cations form molecular columns in the spaces between the chains. The optimized molecular structure, vibrational spectra and the optical properties were calculated by the density functional theory (DFT) method using the B3LYP function with the LanL2DV basis set. The wavenumber calculated are in good agreement with the observed frequency values. The calculated hyperpolarizability βtot is about 4.5 times more than that of the reference crystal KDP. Hence, the large β value shows that the title compound is an attractive object for future studies of nonlinear optical properties.

  7. A new experimental and theoretical investigation on the structures of aminoethyl phosphonic acid in aqueous medium based on the vibrational spectra and DFT calculations

    Science.gov (United States)

    Roldán, María L.; Ledesma, Ana E.; Raschi, Ana B.; Castillo, María V.; Romano, Elida; Brandán, Silvia A.

    2013-06-01

    A new study on the structural and vibrational properties of the aminoethylphosphonic acid was performed in aqueous solution phase by using the self-consistent reaction field (SCRF) method. We have studied and characterized it by infrared and Raman spectroscopies in solid and aqueous solution phases. The Density Functional Theory (DFT) method with Pople's basis set show that three stable zwitterions for the title molecule have been theoretically determined in aqueous solution and that probably they are present in it medium. Here, the solvent effects were studied by means of the self-consistent reaction field (SCRF) method with the polarized continuum model (PCM). The harmonic vibrational frequencies for the optimized geometries of the three zwitterions were calculated at the B3LYP/6-31G∗ level of the theory. A complete assignment of the IR and Raman spectra of the compound in aqueous solution was performed combining the DFT calculations with Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology in order to fit the theoretical frequency values to the experimental ones. Moreover, Natural Bond Orbital (NBO) and topological properties calculations were performed to analyze the energies and geometrical parameters of its three zwitterions in aqueous medium as well as the magnitude of the intramolecular interactions. The bond orders, atomic charges, solvation energies, dipole moments, molecular electrostatic potentials and force constants parameters calculated for zwitterions in aqueous solution, may be used to gain chemical and vibrational insights into related compounds.

  8. DFT calculations of 2,6-dimethylpyrazine (26DMP) and its complex with chloranilic acid (CLA): Comparison to INS, IR and Raman vibration spectra

    Science.gov (United States)

    Pawlukojć, A.; Sobczyk, L.; Prager, M.; Bator, G.; Grech, E.; Nowicka-Scheibe, J.

    2008-12-01

    The inelastic neutron scattering (INS), infrared and Raman spectra of crystalline 2,6-dimethylpyrazine (26DMP) and its complex with chloranilic acid (26DMP·CLA) were measured. Simultaneously the DFT calculations of the molecular structures and frequencies of the normal vibrations were performed by using various functionals. The INS spectra were simulated in the energy range up to 1200 cm -1, on the basis of the calculated frequencies. A very good conformity was obtained between experimental and calculated data with respect to the structure as well as to frequencies, with exception, however, of the CH 3 torsional modes. The structural analysis based on the deviation from the sum of the van der Waals radii showed that the packing of the methyl groups in the 26DMP·CLA complex was markedly stronger than that in the neat 26DMP. However, the DFT calculations overestimated the role of this effect that may be due to a limitation of the applied methods. In addition the anharmonicity of the rotational potential led to the librational energies different from those obtained using a harmonic potential.

  9. Molecular structure and vibrational analysis of Trifluoperazine by FT-IR, FT-Raman and UV-Vis spectroscopies combined with DFT calculations.

    Science.gov (United States)

    Rajesh, P; Gunasekaran, S; Gnanasambandan, T; Seshadri, S

    2015-02-25

    The complete vibrational assignment and analysis of the fundamental vibrational modes of Trifluoperazine (TFZ) was carried out using the experimental FT-IR, FT-Raman and UV-Vis data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT-B3LYP gradient calculations employing 6-31G (d,p) basis set. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. The HOMO-LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as first hyperpolarizability of TFZ have been computed using B3LYP quantum chemical calculation.

  10. Fe2 and Fe4 clusters encapsulated in vacant polyoxotungstates: hydrothermal synthesis, magnetic and electrochemical properties, and DFT calculations.

    Science.gov (United States)

    Pichon, Céline; Dolbecq, Anne; Mialane, Pierre; Marrot, Jérôme; Rivière, Eric; Goral, Monika; Zynek, Monika; McCormac, Timothy; Borshch, Serguei A; Zueva, Ekaterina; Sécheresse, Francis

    2008-01-01

    While the reaction of [PW(11)O(39)](7-) with first row transition-metal ions M(n+) under usual bench conditions only leads to monosubstituted {PW(11)O(39)M(H(2)O)} anions, we have shown that the use of this precursor under hydrothermal conditions allows the isolation of a family of novel polynuclear discrete magnetic polyoxometalates (POMs). The hybrid asymmetric [Fe(II)(bpy)(3)][PW(11)O(39)Fe(2) (III)(OH)(bpy)(2)]12 H(2)O (bpy=bipyridine) complex (1) contains the dinuclear {Fe(micro-O(W))(micro-OH)Fe} core in which one iron atom is coordinated to a monovacant POM, while the other is coordinated to two bipyridine ligands. Magnetic measurements indicate that the Fe(III) centers in complex 1 are weakly antiferromagnetically coupled (J=-11.2 cm(-1), H=-JS(1)S(2)) compared to other {Fe(micro-O)(micro-OH)Fe} systems. This is due to the long distances between the iron center embedded in the POM and the oxygen atom of the POM bridging the two magnetic centers, but also, as shown by DFT calculations, to the important mixing of bridging oxygen orbitals with orbitals of the POM tungsten atoms. The complexes [Hdmbpy](2)[Fe(II)(dmbpy)(3)](2)[(PW(11)O(39))(2)Fe(4) (III)O(2)(dmbpy)(4)]14 H(2)O (2) (dmbpy=5,5'-dimethyl-2,2'-bipyridine) and H(2)[Fe(II)(dmbpy)(3)](2)[(PW(11)O(39))(2)Fe(4) (III)O(2)(dmbpy)(4)]10 H(2)O (3) represent the first butterfly-like POM complexes. In these species, a tetranuclear Fe(III) complex is sandwiched between two lacunary polyoxotungstates that are pentacoordinated to two Fe(III) cations, the remaining paramagnetic centers each being coordinated to two dmbpy ligands. The best fit of the chi(M)T=f(T) curve leads to J(wb)=-59.6 cm(-1) and J(bb)=-10.2 cm(-1) (H=-J(wb)(S(1)S(2)+S(1)S(2*)+S(1*)S(2)+S(1*)S(2*))-J(bb)(S(2)S(2*))). While the J(bb) value is within the range of related exchange parameters previously reported for non-POM butterfly systems, the J(wb) constant is significantly lower. As for complex 1, this can be justified considering Fe

  11. A study of transition-metal organometallic complexes combining 35Cl solid-state NMR spectroscopy and 35Cl NQR spectroscopy and first-principles DFT calculations.

    Science.gov (United States)

    Johnston, Karen E; O'Keefe, Christopher A; Gauvin, Régis M; Trébosc, Julien; Delevoye, Laurent; Amoureux, Jean-Paul; Popoff, Nicolas; Taoufik, Mostafa; Oudatchin, Konstantin; Schurko, Robert W

    2013-09-09

    A series of transition-metal organometallic complexes with commonly occurring metal-chlorine bonding motifs were characterized using (35)Cl solid-state NMR (SSNMR) spectroscopy, (35)Cl nuclear quadrupole resonance (NQR) spectroscopy, and first-principles density functional theory (DFT) calculations of NMR interaction tensors. Static (35)Cl ultra-wideline NMR spectra were acquired in a piecewise manner at standard (9.4 T) and high (21.1 T) magnetic field strengths using the WURST-QCPMG pulse sequence. The (35)Cl electric field gradient (EFG) and chemical shielding (CS) tensor parameters were readily extracted from analytical simulations of the spectra; in particular, the quadrupolar parameters are shown to be very sensitive to structural differences, and can easily differentiate between chlorine atoms in bridging and terminal bonding environments. (35)Cl NQR spectra were acquired for many of the complexes, which aided in resolving structurally similar, yet crystallographically distinct and magnetically inequivalent chlorine sites, and with the interpretation and assignment of (35)Cl SSNMR spectra. (35)Cl EFG tensors obtained from first-principles DFT calculations are consistently in good agreement with experiment, highlighting the importance of using a combined approach of theoretical and experimental methods for structural characterization. Finally, a preliminary example of a (35)Cl SSNMR spectrum of a transition-metal species (TiCl4) diluted and supported on non-porous silica is presented. The combination of (35)Cl SSNMR and (35)Cl NQR spectroscopy and DFT calculations is shown to be a promising and simple methodology for the characterization of all manner of chlorine-containing transition-metal complexes, in pure, impure bulk and supported forms.

  12. Rh-Catalyzed Decarbonylation of Conjugated Ynones via Carbon–Alkyne Bond Activation: Reaction Scope and Mechanistic Exploration via DFT Calculations

    Science.gov (United States)

    Dermenci, Alpay; Whittaker, Rachel E.; Gao, Yang; Cruz, Faben A.; Yu, Zhi-Xiang; Dong, Guangbin

    2015-01-01

    In this full article, detailed development of a catalytic decarbonylation of conjugated monoynones to synthesize disubstituted alkynes is described. The reaction scope and limitation has been thoroughly investigated, and a broad range of functional groups including heterocycles were compatible under the catalytic conditions. Mechanistic exploration via DFT calculations has also been executed. Through the computational study, a proposed catalytic mechanism has been carefully evaluated. These efforts are expected to serve as an important exploratory study for developing catalytic alkyne-transfer reactions via carbon−alkyne bond activation. PMID:26229587

  13. Characterizing the Solvated Structure of Photoexcited [Os(terpy)2]2+ with X-ray Transient Absorption Spectroscopy and DFT Calculations

    DEFF Research Database (Denmark)

    Zhang, Xiaoyi; Pápai, Mátyás Imre; Møller, Klaus Braagaard

    2016-01-01

    undergoes small photo-induced structural changes which are challenging to characterize. In this work, X-ray transient absorption spectroscopy with picosecond temporal resolution is employed to determine the geometric and electronic structures of the photoexcited triplet state of [Os(terpy)2]2+ (terpy: 2......,2':6',2″-terpyridine) solvated in methanol. From the EXAFS analysis, the structural changes can be characterized by a slight overall expansion of the first coordination shell [OsN6]. DFT calculations supports the XTA results. They also provide additional information about the nature of the molecular orbitals...

  14. Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations.

    Science.gov (United States)

    Holland, Gregory P; Mou, Qiushi; Yarger, Jeffery L

    2013-07-28

    Two-dimensional (2D) (1)H-(13)C heteronuclear correlation (HETCOR) solid-state NMR spectra collected with fast magic angle spinning (MAS) are used in conjunction with density functional theory (DFT) proton chemical shift calculations to determine the hydrogen-bonding strength for ordered β-sheet and disordered 310-helical structures in spider dragline silk. The hydrogen-bond strength is determined to be identical for both structures in spider silk with a 1.83-1.84 Å NH···OC hydrogen-bond distance.

  15. Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

    Science.gov (United States)

    Cai, Kaicong; Zheng, Xuan; Du, Fenfen

    2017-08-01

    The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

  16. DFT calculations and experimental FT-IR, dispersive-Raman and EPR spectral studies of Copper (II) chloride complex with 3-amino-1-methylbenzene.

    Science.gov (United States)

    Kumru, Mustafa; Bardakçı, Tayyibe; Güner, Sadik

    2014-04-05

    In this study, we present the synthesis and the characterization of Copper (II) chloride complex with 3-amino-1-methylbenzene (3A1MB). This complex was characterized by vibrational and EPR spectroscopic techniques and elemental analysis. The molecular structure and spectrometry of this complex: Cu(3A1MB)2Cl2 and its ligand: 3A1MB have been investigated theoretically by performing DFT/B3LYP calculations. Cu(3A1MB)2Cl2 has been optimized as two conformers and the more stable conformer is determined. The optimized geometries and calculated vibrational frequencies have been evaluated via comparison with experimental values, and the normal modes were assigned on the basis of the percent potential energy distribution (PED). A good agreement between calculated and experimental data is observed.

  17. Anisotropic lattice thermal expansion of PbFeBO{sub 4}: A study by X-ray and neutron diffraction, Raman spectroscopy and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Murshed, M. Mangir, E-mail: murshed@uni-bremen.de [Chemische Kristallographie fester Stoffe, Institut für Anorganische Chemie, Universität Bremen, Leobener Straße, D-28359 Bremen (Germany); Mendive, Cecilia B.; Curti, Mariano [Departamento de Química, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Dean Funes 3350, B7600AYL, Mar del Plata (Argentina); Nénert, Gwilherm [Institut Laue-Langevin, 6 rue Jules Horowitz, 38042 Grenoble (France); Kalita, Patricia E. [Department of Physics and Astronomy and High-Pressure Science and Engineering Center, University of Nevada Las Vegas, Box 4002, Las Vegas, NV 89154-4002 (United States); Lipinska, Kris [Department of Mechanical Engineering, University of Nevada Las Vegas, 4505 Maryland Parkway, Box 454009, Las Vegas, NV 89154-4009 (United States); Cornelius, Andrew L. [Department of Physics and Astronomy and High-Pressure Science and Engineering Center, University of Nevada Las Vegas, Box 4002, Las Vegas, NV 89154-4002 (United States); Huq, Ashfia [Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6475 (United States); Gesing, Thorsten M. [Chemische Kristallographie fester Stoffe, Institut für Anorganische Chemie, Universität Bremen, Leobener Straße, D-28359 Bremen (Germany)

    2014-11-15

    Highlights: • Mullite-type PbFeBO{sub 4} shows uni-axial negative coefficient of thermal expansion. • Anisotropic thermal expansion of the metric parameters was modeled using modified Grüneisen approximation. • The model includes harmonic, quasi-harmonic and intrinsic anharmonic contributions to the internal energy. • DFT calculation, temperature- and pressure-dependent Raman spectra help understand the phonon decay and associated anharmonicity. - Abstract: The lattice thermal expansion of mullite-type PbFeBO{sub 4} is presented in this study. The thermal expansion coefficients of the metric parameters were obtained from composite data collected from temperature-dependent neutron and X-ray powder diffraction between 10 K and 700 K. The volume thermal expansion was modeled using extended Grüneisen first-order approximation to the zero-pressure equation of state. The additive frame of the model includes harmonic, quasi-harmonic and intrinsic anharmonic potentials to describe the change of the internal energy as a function of temperature. The unit-cell volume at zero-pressure and 0 K was optimized during the DFT simulations. Harmonic frequencies of the optical Raman modes at the Γ-point of the Brillouin zone at 0 K were also calculated by DFT, which help to assign and crosscheck the experimental frequencies. The low-temperature Raman spectra showed significant anomaly in the antiferromagnetic regions, leading to softening or hardening of some phonons. Selected modes were analyzed using a modified Klemens model. The shift of the frequencies and the broadening of the line-widths helped to understand the anharmonic vibrational behaviors of the PbO{sub 4}, FeO{sub 6} and BO{sub 3} polyhedra as a function of temperature.

  18. A systematic study on hydrogen bond interactions in sulfabenzamide: DFT calculations of the N-14, O-17, and H-2 NQR parameters.

    Science.gov (United States)

    Nozad, Ahmad G; Najafi, Hamidreza; Meftah, Sakineh; Aghazadeh, Mustafa

    2009-02-01

    A systematic computational study was carried out to characterize the hydrogen bond, HB, interactions of sulfabenzamide crystal structure by DFT calculations of electric field gradient, EFG, tensors at the sites of 14N, 17O, and 2H nuclei. The computations were performed with the B3LYP and B3PW91 DFT methods and 6-311+G and 6-311++G* standard basis sets using the Gaussian 98 package. To perform the calculations, a hydrogen-bonded heptameric cluster of sulfabenzamide was created by X-ray coordinates where the hydrogen atom positions were optimized and the EFG tensors were calculated for the target molecule. Additional optimization and EFG calculations were also performed for crystalline monomer and an isolated gas-phase sulfabenzamide. The calculated EFG tensors were converted to the experimentally measurable nuclear quadrupole resonance, NQR, parameters: quadrupole coupling constant, C(Q), and asymmetry parameter, eta(Q). The results reveal that the geometrical and NQR parameters of the optimized isolated gas-phase and crystalline phase are different. In addition, the difference between the calculated NQR parameters of the monomer and the target molecule shows how much H-bonding interactions affect the EFG tensors of each nucleus. The evaluated NQR parameters reveal that due to the contribution of the target molecule to N-H...O and C-H...O hydrogen bond interactions, the EFG tensors at the sites of N1, O3 and H1 undergo significant changes from monomer to the target molecule in cluster. These features reveal the major role of N-H...O type intermolecular HBs in cluster model of sulfabenzamide which the presence of these interactions can lead to polymorphism directly related to the drug activity and related properties.

  19. VLSI Architectures for Computing DFT's

    Science.gov (United States)

    Truong, T. K.; Chang, J. J.; Hsu, I. S.; Reed, I. S.; Pei, D. Y.

    1986-01-01

    Simplifications result from use of residue Fermat number systems. System of finite arithmetic over residue Fermat number systems enables calculation of discrete Fourier transform (DFT) of series of complex numbers with reduced number of multiplications. Computer architectures based on approach suitable for design of very-large-scale integrated (VLSI) circuits for computing DFT's. General approach not limited to DFT's; Applicable to decoding of error-correcting codes and other transform calculations. System readily implemented in VLSI.

  20. Pyrazolo[4,3-a]quinindoline as a new highly fluorescent heterocyclic system: Design, synthesis, spectroscopic characterization and DFT calculations

    Science.gov (United States)

    Alikhani, Elaheh; Pordel, Mehdi; Daghigh, Leila Rezaei

    2015-02-01

    After obtaining the desired precursors in several reactions, new N-alkyl-substituted heterocyclic system pyrazolo[4,3-a]quinindolines (pyrazolo[4,3-f]-indolo[2,3-b]quinolines) were synthesized by one-pot reaction of 1-alkyl-5-nitro-1H-indazole with 2-(1-alkyl-1H-3-indolyl)acetonitrile in MeOH/KOH solution via the nucleophilic substitution of hydrogen in excellent yields. Spectral (UV-Vis, FT-IR, NMR and fluorescence) and analytical data allowed the structures of the synthesized compounds to be established. The values of absorption and fluorescence maxima, extinction coefficients and fluorescence quantum yield of these new heterocyclic fluorophores were obtained and they show highlighting interesting photophysical properties. Density functional theory (DFT) calculations of one structure by using the B3LYP hybrid functional and the 6-311 + G(d,p) basis set were performed to provide the optimized geometry, relevant frontier orbitals and the prediction of 1H NMR chemical shifts. Calculated electronic absorption spectrum of one structure was also obtained by time-dependent density functional theory (TD-DFT) method. Solvatochromic properties of these dyes have been discussed and the results showed that the absorption and emission bands in polar solvents undergo a modest red shift.

  1. Synthesis, Crystal and Molecular Structure Studies and DFT Calculations of Phenyl Quinoline-2-Carboxylate and 2-Methoxyphenyl Quinoline-2-Carboxylate; Two New Quinoline-2 Carboxylic Derivatives

    Directory of Open Access Journals (Sweden)

    Edakot Fazal

    2015-02-01

    Full Text Available The crystal and molecular structures of the title compounds, phenyl quinoline-2-carboxylate and 2-methoxyphenyl quinoline-2-carboxylate, two new derivatives of quinolone-2-carboxylic acid, are reported and confirmed by single crystal X-ray diffraction and spectroscopic data. Compound (I, C16H11NO2, crystallizes in the monoclinic space group P21/c, with 8 molecules in the unit cell. The unit cell parameters are a = 14.7910(3 Å; b = 5.76446(12 Å; c = 28.4012(6 Å; β = 99.043(2°; V = 2391.45(9 Å3. Compound (II, C17H13NO5, crystallizes in the monoclinic space group P21/n with 4 molecules in the unit cell. The unit cell parameters are a = 9.6095(3 Å; b = 10.8040(3 Å; c = 13.2427(4 Å; β = 102.012(3°; V = 1344.76(7 Å3. Density functional theory (DFT geometry optimized molecular orbital calculations were performed and frontier molecular orbitals of each compound are displayed. Correlation between the calculated molecular orbital energies (eV for the surfaces of the frontier molecular orbitals to the electronic excitation transitions from the absorption spectra of each compound has been proposed. Additionally, similar correlations observed among six closely related compounds examining small structural differences to their frontier molecular orbital surfaces and from their DFT molecular orbital energies, provide further support for the suggested assignments of the title compounds.

  2. Molecular structure, Normal Coordinate Analysis, harmonic vibrational frequencies, Natural Bond Orbital, TD-DFT calculations and biological activity analysis of antioxidant drug 7-hydroxycoumarin

    Science.gov (United States)

    Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

    2013-01-01

    In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

  3. Structural characterization, vibrational study, NLO and DFT calculations of a novel organic sulfate monohydrate templated with (S)-(-)-2,6-diammonium-4,5,6,7-tetrahydrobenzothiazole

    Science.gov (United States)

    Barhoumi, Abir; Mhiri, Tahar; Dammak, Thameur; Suñol, Joan Josep; Belhouchet, Mohamed

    2017-01-01

    A single crystal of (S)-(-)-2,6-diammonium-4,5,6,7-tetrahydrobenzothiazole sulfate monohydrate has been synthesized and grown at room temperature by slow evaporation of aqueous solution. The studied compound crystallizes in the space group P212121 of the orthorhombic system with cell parameters a = 7.0014(12), b = 8.7631(15), c = 19.773(3) Å. We report the molecular structure and the theoretical and experimental vibrational spectra of the synthesized compound. The atomic arrangement, which is an alternation of organic inorganic layers linked together through hydrogen bonds, gives rise to three types of rings formed by the interconnection of organic-inorganic entities. The experimental FT-IR and the Raman spectra the synthesized compound were recorded and analyzed. The peaks assignment has been made unambiguously from the literature. To confirm the assignment, the experimental spectra were compared with theoretical spectra obtained with the Gaussian 98 program by the Density Functional Theory (DFT) method using B3LYP function with the LanL2DZ basis set. Moreover, to study the nonlinear optical (NLO) property of this compound, the hyperpolarizability βtot, the electric dipole μtot and the polarizability αtot were calculated using the DFT. Based on our calculation the synthesized compound has a non-zero hyperpolarizability suggesting that it may be used in some NLO applications.

  4. The spectroscopic properties of anticancer drug Apigenin investigated by using DFT calculations, FT-IR, FT-Raman and NMR analysis

    Science.gov (United States)

    Mariappan, G.; Sundaraganesan, N.; Manoharan, S.

    2012-09-01

    The FT-Raman and FT-Infrared spectra of solid Apigenin sample were measured in order to elucidate the spectroscopic properties of title molecule in the spectral range of 3500-50 cm-1 and 4000-400 cm-1, respectively. The recorded FT-IR and FT-Raman spectral measurements favor the calculated (by B3LYP/6-31G(d,p) method) structural parameters which are further supported by spectral simulation. Additional support is given by the collected 1H and 13C NMR spectra recorded with the sample dissolved in DMSO. The predicted chemical shifts at the B3LYP/6-31G(d) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. The UV-visible absorption spectra of the compound that dissolved in Ethanol, Methanol and DMSO were recorded in the range of 800-200 nm. The formation of hydrogen bond and the most possible interaction are explained using natural bond orbital (NBO) analysis. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and atomic charges of the title compound were investigated using theoretical calculations. The results are discussed herein and compared with similar molecules whenever appropriate.

  5. Ti{sub 3}GaC{sub 2} and Ti{sub 3}InC{sub 2}: First bulk synthesis, DFT stability calculations and structural systematics

    Energy Technology Data Exchange (ETDEWEB)

    Cuskelly, Dylan T., E-mail: Dylan.cuskelly@uon.edu.au [School of Engineering, The University of Newcastle, Callaghan, NSW 2308 (Australia); Richards, Erin R.; Kisi, Erich H. [School of Engineering, The University of Newcastle, Callaghan, NSW 2308 (Australia); Keast, Vicki J. [School of Mathematical and Physical Sciences, The University of Newcastle, Callaghan, NSW 2308 (Australia)

    2015-10-15

    A simple methodology for identifying possible higher order M{sub n+1}AX{sub n} phases (n≥2) from the chemical characteristics of known phases was developed. The method was used to identify two potential M{sub 3}AC{sub 2} phases Ti{sub 3}GaC{sub 2} and Ti{sub 3}InC{sub 2}. After verifying that the n=1 MAX phases in these systems could be synthesised in bulk using a simple pressureless reactive sintering process, the new phases were synthesised using the same method. DFT calculations were used to test the thermodynamic stability of the new phases against the known competing phases within the same ternary systems. Both were found to be stable although Ti{sub 3}InC{sub 2} only marginally so. Crystal structure refinements and comparison to other MAX phases revealed a linear increase in the c-axis length as a function of the atomic radius of the A element. - Highlights: • Chemical systematics were used to highlight a search window for new MAX phases. • Two new higher order MAX phases, Ti{sub 3}InC{sub 2} and Ti{sub 3}GaC{sub 2}, were synthesised. • Pressureless reactive sintering was effective in producing bulk material. • DFT calculations indicate that the new phases are stable.

  6. Lithium choreography: intramolecular arylations of carbamate-stabilised carbanions and their mechanisms probed by in situ IR spectroscopy and DFT calculations.

    Science.gov (United States)

    Fournier, Anne M; Nichols, Christopher J; Vincent, Mark A; Hillier, Ian H; Clayden, Jonathan

    2012-12-14

    Deprotonation of O-allyl, O-propargyl or O-benzyl carbamates in the presence of a lithium counterion leads to carbamate-stabilised organolithium compounds that may be quenched with electrophiles. We now report that when the allylic, propargylic or benzylic carbamate bears an N-aryl substituent, an aryl migration takes place, leading to stereochemical inversion and C-arylation of the carbamate α to oxygen. The aryl migration is an intramolecular S(N) Ar reaction, despite the lack of anion-stabilising aryl substituents. Our in situ IR studies reveal a number of intermediates along the rearrangement pathway, including a "pre-lithiation complex," the deprotonated carbamate, the rearranged anion, and the final arylated carbamate. No evidence was obtained for a dearomatised intermediate during the aryl migration. DFT calculations predict that during the reaction the solvated Li cation moves from the carbanion centre, thus freeing its lone pair for nucleophilic attack on the remote phenyl ring. This charge separation leads to several alternative conformations. The one having Li(+) bound to the carbamate oxygen gives rise to the lowest-energy transition structure, and also leads to inversion of the configuration. In agreement with the IR studies, the DFT calculations fail to locate a dearomatised intermediate. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures).

    Science.gov (United States)

    Sas, E B; Kose, E; Kurt, M; Karabacak, M

    2015-02-25

    In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule.

  8. Synthesis, Spectroscopic Properties and DFT Calculation of Novel Pyrrolo[1',5'-a]-1,8-naphthyridine Derivatives through a Facile One-pot Process

    Indian Academy of Sciences (India)

    GAO-ZHANG GOU; BO ZHOU; HE-PING YAN; YONG HONG; WEI LIU; SHAO-MING CHI; CHAO-YONG MANG

    2016-11-01

    Novel pyrrolo[1',5'-a]-1,8-naphthyridine compounds (L1-L4) have been synthesized through a facile one-pot process by the reaction of the corresponding 1,8-naphthyridines with aliphatic anhydride. The structures were established by spectroscopic data. Further, X-ray crystal analysis of 7-diacetamino-2,4-dimethy-1,8-naphthyridine (L1) identifies its molecular structure and reveals π-π stacking. The synthetic mechanisms for L2, L3 were studied by density functional theory calculations. And a comprehensive study of spectroscopic properties involving experimental data and theoretical studies is presented. L1 exhibited electronic absorption spectrum with λmax at ∼320 nm. L2-L4 exhibited similar electronic absorption spectra with λmax at ∼390 nm that is tentatively assigned to π→π* transition. The assignment was further supported by density functional theory (DFT) calculations.

  9. Determination of thermodynamic parameters of tautomerization in gas phase by mass spectrometry and DFT calculations: Keto-enol versus nitrile-ketenimine equilibria.

    Science.gov (United States)

    Giussi, Juan M; Gastaca, Belen; Albesa, Alberto; Cortizo, M Susana; Allegretti, Patricia E

    2011-02-01

    The study of tautomerics equilibria is really important because the reactivity of each compound with tautomeric capacity can be determined from the proportion of each tautomer. In the present work the tautomeric equilibria in some γ,δ-unsaturated β-hydroxynitriles and γ,δ-unsaturated β-ketonitriles were studied. The first family of compounds presents two possible theoretical tautomers, nitrile and ketenimine, while the second one presents four possible theoretical tautomers, keto-nitrile, enol (E and Z)-nitrile and keto-ketenimine. The equilibrium in gas phase was studied by gas chromatography-mass spectrometry (GC-MS). Tautomerization enthalpies were calculated by this methodology, and results were compared with those obtained by density functional theory (DFT) calculations, observing a good agreement between them. Nitrile tautomers were favored within the first family of compounds, while keto-nitrile tautomers were favored in the second family. Copyright © 2010 Elsevier B.V. All rights reserved.

  10. On the nature of lithium biphenyl in ethereal solvents. A critical analysis unifying DFT calculations, physicochemical data in solution, and a X-ray structure.

    Science.gov (United States)

    de la Viuda, Mónica; Yus, Miguel; Guijarro, Albert

    2011-12-15

    The lithium ion is an important type of electrolyte that has technological applications in the manufacture of lithium ion cells; therefore, a better understanding of the nature of its solutions is desirable. When associated to the radical anion of biphenyl in an organic solvent, it forms conducting solutions comparable to strong electrolytes such as lithium perchlorate. We have studied the lithium biphenyl solution in dimethoxyethane using DFT calculations. The nature of these ionic solutions is described in terms of a dynamic equilibrium between different types of ionic associations, the composition of which depends on the solvent and the temperature. The X-ray structure of [Li(+)·4C(5)H(10)O][C(12)H(10)(•-)], a solvent-separated ion pair of lithium biphenyl complexed with tetrahydropyran, is reported. Its main structural characteristics coincide with the calculated one, which we think is the dominant species at room temperature, in agreement with the available physicochemical data.

  11. 13C CP MAS NMR and GIAO-CHF/DFT calculations of flavonoids: Morin, kaempferol, tricin, genistein, formononetin and 3,7-dihydroxyflavone

    Science.gov (United States)

    Zielińska, Agnieszka; Paradowska, Katarzyna; Jakowski, Jacek; Wawer, Iwona

    2008-02-01

    13C CP MAS NMR spectra of the flavonoids: morin, kaempferol, 3,7-dihydroxyflavone, tricin and isoflavones: genistein and formononetin were recorded to characterize solid-state conformations. Intramolecular hydrogen bonds forming five-, six- and seven-membered rings are present in the two morin molecules in the crystals - their 13C resonances have been assigned with the aid of the calculated shielding constants. Linear relationships between the calculated shielding constants σDFT (ppm) and chemical shifts ( δCPMAS, ppm) were obtained for all studied compounds. Higher correlation coefficients suggest that the conformation with "clockwise" orientation of both OH groups is more probable in the solid 3,7-dihydroxyflavone, whereas in the solid formononetin the OH and OCH 3 substituents are directed "anticlockwise". The barrier to the rotation of phenyl ring B decreases in the order: morin (2'-OH, 3-OH) > kaempferol (3-OH) > tricin.

  12. 1,3-Di(2-p-tolylvinyl)-2,4,6-trinitrobenzene: X-ray Crystallographic Analysis, Thermal Decomposition and DFT Calculations

    Institute of Scientific and Technical Information of China (English)

    WANG, Li-Qiong; LIU, Yan-Hong; ZHANG, Jian-Guo; ZHANG, Tong-Lai; YANG, Lia; QIAO, Xiao-Jing; HU, Xiao-Chun; GUO, Jin-Yu

    2007-01-01

    In this paper, the synthesis, crystal culturing and single-crystal X-ray crystallography of 1,3-di(2-p-tolylvingl)-2,4,6-trinitrobenzene (DTTB) were reported. FT-IR, 1H NMR and mass spectroscopy techniques were employed to characterize this compound. The results show that this single crystal belongs to triclinic system with space group P-1. Density functional theory (DFT) B3LYP was employed to optimize structure and calculate frequencies of the title compound. The calculated geometrical parameters were close to the corresponding experiment ones. The thermal decomposition of DTTB was investigated by DSC and TG-DTG methods at the heating rate of 10 ℃/min. It was observed that the initial decomposing temperature of DTTB was higher than that of TNTM, although its melting point was lower than that of TNTM, indicating that DTTB has higher heat resistant ability.

  13. Electronic structure and optical properties of Cs2HgCl4: DFT calculations and X-ray photoelectron spectroscopy measurements

    Science.gov (United States)

    Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Parasyuk, O. V.; Fedorchuk, A. O.; Khyzhun, O. Y.

    2016-10-01

    A high-quality single crystal of cesium mercury tetrabromide, Cs2HgCl4, was synthesized by using the vertical Bridgman-Stockbarger method and its electronic structure was studied from both experimental and theoretical viewpoints. In particular, X-ray photoelectron spectra were measured for both pristine and Ar+ ion-bombarded Cs2HgCl4 single crystal surfaces. The present XPS measurements indicate that the Cs2HgCl4 single crystal surface is sensitive with respect to Ar+ ion-bombardment: such a treatment changes substantially its elemental stoichiometry. With the aim of exploring total and partial densities of states within the valence band and conduction band regions of the Cs2HgCl4 compound, band-structure calculations based on density functional theory (DFT) using the augmented plane wave + local orbitals (APW + lo) method as incorporated within the WIEN2k package are performed. The calculations indicate that the Cl 3p states are the principal contributors in the upper portion of the valence band, while the Hg 5d and Cs 5p states dominate in its lower portion. In addition, the calculations allow for concluding that the unoccupied Cl p and Hg s states are the main contributors to the bottom of the conduction band. Furthermore, main optical characteristics of Cs2HgCl4, namely dispersion of the absorption coefficient, real and imaginary parts of dielectric function, electron energy-loss spectrum, refractive index, extinction coefficient and optical reflectivity, are elucidated based on the DFT calculations.

  14. Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations

    Science.gov (United States)

    Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet

    2013-11-01

    In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400 cm-1 and 3500-50 cm-1, respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The 1H, 13C and HMQC (1H-13C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400 nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement.

  15. Synthesis, spectroscopic and single crystal X-ray studies on three new mononuclear Ni(II) pincer type complexes: DFT calculations and their antimicrobial activities

    Science.gov (United States)

    Layek, Samaresh; Agrahari, Bhumika; Tarafdar, Abhrajyoti; Kumari, Chanda; Anuradha; Ganguly, Rakesh; Pathak, Devendra D.

    2017-08-01

    Three new mononuclear square planar Ni(II) complexes, containing pincer type tridentate Schiff base ligands, having general formula [(NiL1(4-MePy)] (1), [(NiL1(2-AzNp)] (2), and [(NiL2(4-MePy)] (3) [where L1 = anion of N-(2-hydroxy-3-methoxybenzylidene) benzoylhydrazide (HL1), L2 = anion of N-(2-hydroxy-3-methoxybenzylidene) thiosemicarbazide (HL2), 4-MePy = 4-Methylpyridine and 2-AzNp = 2-Azanapthalene] have been synthesized and fully characterized by FT-IR, UV-visible, NMR, single crystal X-ray diffraction studies and elemental analysis. All the three complexes show square planar geometry around the nickel atom. The pincer type ligand occupies three coordination sites, while the fourth site is occupied by the monodentate nitrogen containing ligand. The Quantum chemical DFT calculations have also been carried out using DFT/B3LYP method and 6-311++G(d,p) basis set. The synthesized nickel complexes were screened for antimicrobial activities by agar well diffusion method against E. coli bacteria. Out of three complexes, [(NiL2(4-MePy)] (3) only showed the antimicrobial activity against E. coli bacteria.

  16. Characterizing the Solvated Structure of Photoexcited [Os(terpy2]2+ with X-ray Transient Absorption Spectroscopy and DFT Calculations

    Directory of Open Access Journals (Sweden)

    Xiaoyi Zhang

    2016-02-01

    Full Text Available Characterizing the geometric and electronic structures of individual photoexcited dye molecules in solution is an important step towards understanding the interfacial properties of photo-active electrodes. The broad family of “red sensitizers” based on osmium(II polypyridyl compounds often undergoes small photo-induced structural changes which are challenging to characterize. In this work, X-ray transient absorption spectroscopy with picosecond temporal resolution is employed to determine the geometric and electronic structures of the photoexcited triplet state of [Os(terpy2]2+ (terpy: 2,2′:6′,2″-terpyridine solvated in methanol. From the EXAFS analysis, the structural changes can be characterized by a slight overall expansion of the first coordination shell [OsN6]. DFT calculations supports the XTA results. They also provide additional information about the nature of the molecular orbitals that contribute to the optical spectrum (with TD-DFT and the near-edge region of the X-ray spectra.

  17. Synthesis, spectroscopic studies, DFT calculations, electrochemical evaluation, BSA binding and molecular docking of an aroylhydrazone -based cis-dioxido Mo(VI) complex

    Science.gov (United States)

    Mohamadi, Maryam; Faghih-Mirzaei, Ehsan; Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Haase, Wolfgang; Foro, Sabine

    2017-07-01

    A cis-dioxido Mo(VI) complex, [MoO2(L)(MeOH)], [L2-: (3-methoxy-2-oxidobenzylidene) benzohydrazonate], has been synthesized and characterized using physicochemical and spectroscopic techniques including elemental analysis, FT-IR, 1HNMR, UV-Vis spectroscopy, molar conductivity and single crystal X-ray diffraction. DFT calculations in the ground state of the complex were carried out using hybrid functional B3LYP with DGDZVP as basis set. Non-linear optical properties including electric dipole moment (μ), polarizability (α) and molecular first hyperpolarizability (β) of the compound were also computed. The values of linear polarizability and first hyperpolarizability obtained for the studied molecule indicated that the compound could be a good candidate of nonlinear optical materials. TD-DFT calculation and molecular electrostatic potential (MEP) were also performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the complex at different temperatures have been calculated. The interaction of a synthesized complex, with bovine serum albumin was also thoroughly investigated using experimental and theoretical studies. UV-Vis absorption and fluorescence quenching techniques were used to determine the binding parameters as well as the mechanism of the interaction. The values of binding constants were in the range of 104-105 M-1 demonstrating a moderate interaction between the synthesized complex and BSA making the protein suitable for transportation and delivery of the compound. Thermodynamic parameters were also indicating a binding through van der Waals force or hydrogen bond of [MoO2(L)(MeOH)] to BSA. The results obtained from docking studies were consistent to those obtained from experimental studies.

  18. Piezoelectric, elastic, Infrared and Raman behavior of ZnO wurtzite under pressure from periodic DFT calculations

    Science.gov (United States)

    Marana, Naiara Letícia; Casassa, Silvia Maria; Sambrano, Julio Ricardo

    2017-03-01

    The influence of pressure on elastic, piezoelectric (total and clamped-ion contribution), dielectric constants, Infrared and Raman spectra, and topological properties of ZnO wurtzite structure was carried out via periodic DFT/B3LYP methodology. The computational simulation indicated that, as the pressure increases, the structure becomes more rigid and an enhancement of the direct piezoelectric response along the z-direction was observed. Bader topological analysis and Hirshfeld-I charges showed a slight increase in the ionic character of Zn-O bond. Besides that, changes in the piezoelectric response are mainly due to the approach between Zn and O than to charge transfer phenomena among the two atoms. Pressure induces a sensitive displacement in the Infrared and Raman frequencies and a decrease of the E2 mode. Nevertheless, the increase of pressure does not lead to a change in the semiconductor character, which proves that the ZnO support high pressures and can be applied in different devices.

  19. Three iodometalate organic-inorganic hybrid materials based on methylene blue cation: Syntheses, structures, properties and DFT calculations

    Science.gov (United States)

    Chai, Wen-Xiang; Lin, Jian; Song, Li; Qin, Lai-Shun; Shi, Hong-Sheng; Guo, Jia-Yu; Shu, Kang-Ying

    2012-08-01

    The functional dye of methylene blue (MB) has been employed for seeking new organic-inorganic hybrid photochromic materials. Although the photochromism has not been observed yet, three iodometalate compounds, namely (MB) (PbI3) (DMF) (1), (MB)4(Cu2I4)2 (2), and (MB)3(Bi2I9) (DMF)2 (3), have been synthesized and characterized. The iodometalate anion features as a [PbI3]∞- chain in 1, a dinuclear unit of Cu2I42- in 2, and a dinuclear unit of Bi2I93- in 3. Due to the synergy of cations and anions, the MB+ cations present supramolecular column stacks in 1 and 3, but a novel supramolecular octamer structure in 2. Their thermogravimetric analyses reveal that the polymeric inorganic anion structure is helpful to increase the stability of cation whereas the discrete structure is adverse. For seeking some clues which is significant to searching new photochromic systems, the density functional theory (DFT) studies have been performed on 1, in which the electronic structure analyses suggests that the stacking mode of cations and anions could be also an important factor influencing the charge transfer between them. In addition, dielectric hysteresis loop testing has been performed on 1 due to its polar space group of Cc.

  20. Application of localized reactivity index in combination with periodic DFT calculation to rationalize the swelling mechanism of clay type inorganic material

    Indian Academy of Sciences (India)

    Abhijit Chatterjee

    2005-09-01

    Clays are layered alumino-silicates. Clays swell and expand in aqueous solution. This property governs the usage of these materials in synthesis of nano-composites and is a source of many of its catalytic applications. We used both localized and periodic calculations within the realm of density functional theory (DFT) on a series of monovalent (Li+, Na+, K+, Rb+, Cs+), and divalent (Mg2+, Ca2+, Sr2+, Ba2+) cations, to monitor their effect on the swelling of clays. The activity order obtained for the exchangeable cations among all the monovalent and divalent series studied is: Mg2+ > Ca2+ > Sr2+ > Ba2+ > Cs+ > Rb+ > Na+ > Li+ > K+. We have studied two types of clays, montmorillonite and beidellite, with different surface structures and with/without water using periodic calculations. We have calculated the layer spacing at the first, second and third hydration shells of exchangeable cation, to compare with the experimental -spacing values to correlate with humidity. A novel quantitative scale is proposed in terms of the intermolecular relative nucleophilicity of the active cation sites in their hydrated state through Fukui functions using hard-soft acid base (HSAB) principle. Finally, a swelling mechanism is proposed. This is a unique study where a combination of periodic and localized calculations has been performed to validate the capability of reactivity index calculations in material designing.

  1. Binding modes of phosphonic acid derivatives adsorbed on TiO2 surfaces: Assignments of experimental IR and NMR spectra based on DFT/PBC calculations

    Science.gov (United States)

    Geldof, D.; Tassi, M.; Carleer, R.; Adriaensens, P.; Roevens, A.; Meynen, V.; Blockhuys, F.

    2017-01-01

    A DFT study on the adsorption of a series of phosphonic acids (PAs) on the TiO2 anatase (101) and (001) surfaces was performed. The adsorption energies and geometries of the most stable binding modes were compared to literature data and the effect of the inclusion of dispersion forces in the energy calculations was gauged. As the (101) surface is the most exposed surface of TiO2 anatase, the calculated chemical shifts and vibrational frequencies of PAs adsorbed on this surface were compared to experimental 31P and 17O NMR and IR data in order to assign the two possible binding modes (mono- and bidentate) to peaks and bands in these spectra; due to the corrugated nature of anatase (101) tridentate binding is not possible on this surface. Analysis of the calculated and experimental 31P chemical shifts indicates that both monodentate and bidentate binding modes are present. For the reactive (001) surface, the results of the calculations indicate that both bi- and tridentate binding modes result in stable systems. Due to the particular sensitivity of 17O chemical shifts to hydrogen bonding and solvent effects, the model used is insufficient to assign these spectra at present. Comparison of calculated and experimental IR spectra leads to the conclusion that IR spectroscopy is not suitable for the characterization of the different binding modes of the adsorption complexes.

  2. Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-dihydro-1,3,4-thiadiazol-2-ylidene)-4-methylbenzenesulfonamide using DFT-D calculations and (13)C solid-state NMR

    DEFF Research Database (Denmark)

    Li, Xiaozhou; Bond, Andrew D; Johansson, Kristoffer E;

    2014-01-01

    in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported quantitative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation...

  3. Supramolecular clusters and chains of 2,6-dimethylpyridine on Cu(110): Observation of dynamic configuration change with real-space surface science techniques and DFT calculations

    Science.gov (United States)

    Lee, Junseok; Sorescu, Dan C.; Lee, Jae-Gook; Dougherty, Dan

    2016-10-01

    The adsorption of 2,6-dimethylpyridine (2,6-DMP) on Cu(110) has been studied using low temperature scanning tunneling microscopy (LT-STM), time-of-flight electron stimulated desorption ion angular distribution (TOF-ESDIAD), and density functional theory (DFT) calculations. At low temperatures (T surface direction. At near-saturation coverage, a c(6 × 2) long-range ordered structure was observed. Upon annealing to T = 200 K, the 2,6-DMP molecules adopt an upright configuration with their pyridine ring plane oriented parallel to the azimuth. These upright 2,6-DMP molecules produce extended molecular chains where the repulsive interactions between the molecular chains give rise to coverage-dependent interchain distances.

  4. Spectroscopy (FT-IR, FT-Raman), hydrogen bonding, electrostatic potential and HOMO-LUMO analysis of tioxolone based on DFT calculations

    Science.gov (United States)

    Tao, Yaping; Li, Xiaofeng; Han, Ligang; Zhang, Weiying; Liu, Zhaojun

    2016-10-01

    Tioxolone possess antipsoriatic and antibacterial properties. Therefore, it has been used in treating various skin and scalp disorders for many years. Spectroscopic analysis of tioxolone was presented by using density functional theory (DFT) calculations and experiments (FT-IR, FT-Raman and UV-Vis). Molecular geometry and vibrational wavenumbers of tioxolone were investigated by using B3LYP method with aug-cc-pVTZ basis set. A complete vibrational spectra was made to analyze the potential energy distributions (PED). In addition, analysis of frontier molecular orbitals, electrostatic potential (ESP) and thermodynamic properties (heat capacity, entropy, enthalpy and Gibbs free energy) was presented with the same basis-set. Furthermore, the nature of molecular association through hydrogen bonding were discussed using atoms in molecules (AIM) and reduced density gradient (RDG) methods.

  5. Synthesis, characterization, X-ray crystal structure, DFT calculation, DNA binding, and antimicrobial assays of two new mixed-ligand copper(II) complexes

    Science.gov (United States)

    Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Mohamadi, Maryam; Suarez, Sebastian; Baggio, Ricardo; Khaleghi, Moj; Torkzadeh-Mahani, Masoud; Mostafavi, Ali

    2015-05-01

    Two new Cu(II) complexes, [Cu(L)(phen)] (1), [Cu(L)(bipy)] (2), where L2- = (3-methoxy-2oxidobenzylidene)benzohydrazidato, phen = 1,10 phenanthroline, and bipy = 2,2‧ bipyridine, were prepared and fully characterized using elemental analyses, FT-IR, molar conductivity, and electronic spectra. The structures of both complexes were also determined by X-ray diffraction. It was found that, both complexes possessed square pyramidal coordination environment in which, Cu(II) ions were coordinated by donor atoms of HL and two nitrogens of heterocyclic bases. Computational studies were performed using DFT calculations at B3LYP/6-311+G(d,p) level of theory. DNA binding activities of these complexes were also investigated using electronic absorption, competitive fluorescence titration and cyclic voltammetry studies. The obtained results indicated that binding of the complexes to DNA was of intercalative mode. Furthermore, antimicrobial activities of these compounds were screened against microorganisms.

  6. Synthesis, structural characterization and DFT calculation on a square-planar Ni(II) complex of a compartmental Schiff base ligand

    Science.gov (United States)

    Biswas, Surajit; Dolai, Malay; Dutta, Arpan; Ali, Mahammad

    2016-12-01

    Reaction of a symmetric compartmental Schiff-base ligand, (H2L) with nickel(II) perchlorate hexahydrate in 1:1 M ratio in methanol gives rise to a mononuclear nickel(II) compound, NiL (1). The compound has been characterized by C, H, N microanalyses and UV-Vis spectra. The single crystal X-ray diffraction studies reveal a square planar geometry around the Ni(II) center. The compound crystallizes in monoclinic system with space group C2/c with a = 21.6425(6), b = 9.9481(3), c = 13.1958(4) Å, β = 107.728(2)°, V = 2706.16(14) Å3 and Z = 4. Ground state DFT optimization and TDDFT calculations on the ligand and complex were performed to get their UV-Vis spectral pattern.

  7. Spectroscopy studies on Schiff base N,N‧-bis(salicylidene)-1,2-phenylenediamine by NMR, infrared, Raman and DFT calculations

    Science.gov (United States)

    de Toledo, T. A.; Pizani, P. S.; da Silva, L. E.; Teixeira, A. M. R.; Freire, P. T. C.

    2015-10-01

    N,N‧-bis(salicylidene)-1,2-phenylenediamine, also known as Salophen, is a Schiff base which crystallizes in monoclinic structure and space group P21/c, with four molecules per unit cell. It has been intensely studied in last decades because of its excellent properties with many potential applications. In the present study, the structural and vibrational properties of the Salophen were investigated combining scanning electronic microscopy (SEM), Raman, infrared, nuclear magnetic resonance (NMR) spectroscopy as experimental techniques and theoretical calculation based on density functional theory (DFT). The interpretation of the vibrational modes was carried out by means of potential energy distribution (PED). The theoretical results are in good agreement with experimental ones.

  8. Studies of the electronic structure and biological activity of chosen 1,4-benzodiazepines by {sup 35}Cl NQR spectroscopy and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Bronisz, K. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland); Ostafin, M. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland)], E-mail: ostifnqr@amu.edu.pl; Poleshchuk, O. Kh. [Department of Chemistry, Tomsk Pedagogical University, Komsomolskii 75, 634041 Tomsk (Russian Federation); Mielcarek, J. [Faculty of Pharmacy, University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan (Poland); Nogaj, B. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland)

    2006-11-08

    Selected derivatives of 1,4-benzodiazepine: lorazepam, lormetazepam, oxazepam and temazepam, used as active substances in anxiolytic drugs, have been studied by {sup 35}Cl NQR method in order to find the correlation between electronic structure and biological activity. The {sup 35}Cl NQR resonance frequencies ({nu} {sub Q}) measured at 77 K have been correlated with the following parameters characterising their biological activity: biological half-life period (t {sub 0.5}), affinity to benzodiazepine receptor (IC{sub 50}) and mean dose equivalent. The results of experimental study of some benzodiazepine derivatives by nuclear quadrupole resonance of {sup 35}Cl nuclei are compared with theoretical results based on DFT calculations which were carried out by means of Gaussian'98 W software.

  9. Studies of the electronic structure and biological activity of chosen 1,4-benzodiazepines by 35Cl NQR spectroscopy and DFT calculations

    Science.gov (United States)

    Bronisz, K.; Ostafin, M.; Poleshchuk, O. Kh.; Mielcarek, J.; Nogaj, B.

    2006-11-01

    Selected derivatives of 1,4-benzodiazepine: lorazepam, lormetazepam, oxazepam and temazepam, used as active substances in anxiolytic drugs, have been studied by 35Cl NQR method in order to find the correlation between electronic structure and biological activity. The 35Cl NQR resonance frequencies ( νQ) measured at 77 K have been correlated with the following parameters characterising their biological activity: biological half-life period ( t0.5), affinity to benzodiazepine receptor (IC 50) and mean dose equivalent. The results of experimental study of some benzodiazepine derivatives by nuclear quadrupole resonance of 35Cl nuclei are compared with theoretical results based on DFT calculations which were carried out by means of Gaussian'98 W software.

  10. Ruthenium(II) bipyridine complexes bearing new keto-enol azoimine ligands: synthesis, structure, electrochemistry and DFT calculations.

    Science.gov (United States)

    Al-Noaimi, Mousa; Awwadi, Firas F; Mansi, Ahmad; Abdel-Rahman, Obadah S; Hammoudeh, Ayman; Warad, Ismail

    2015-01-25

    The novel azoimine ligand, Ph-NH-N=C(COCH3)-NHPh(C≡CH) (H2L), was synthesized and its molecular structure was determined by X-ray crystallography. Catalytic hydration of the terminal acetylene of H2L in the presence of RuCl3·3H2O in ethanol at reflux temperature yielded a ketone (L1=Ph-N=N-C(COCH3)=N-Ph(COCH3) and an enol (L2=Ph-N=N-C(COCH3)=N-PhC(OH)=CH2) by Markovnikov addition of water. Two mixed-ligand ruthenium complexes having general formula, trans-[Ru(bpy)(Y)Cl2] (1-2) (where Y=L1 (1) and Y=L2 (2), bpy is 2.2'-bipyrdine) were achieved by the stepwise addition of equimolar amounts of (H2L) and bpy ligands to RuCl3·3H2O in absolute ethanol. Theses complexes were characterized by elemental analyses and spectroscopic (IR, UV-Vis, and NMR (1D (1)H NMR, (13)C NMR, (DEPT-135), (DEPT-90), 2D (1)H-(1)H and (13)C-(1)H correlation (HMQC) spectroscopy)). The two complexes exhibit a quasi-reversible one electron Ru(II)/Ru(III) oxidation couple at 604 mV vs. ferrocene/ferrocenium (Cp2Fe(0/+)) couple along with one electron ligand reduction at -1010 mV. The crystal structure of complex 1 showed that the bidentate ligand L1 coordinates to Ru(II) by the azo- and imine-nitrogen donor atoms. The complex adopts a distorted trans octahedral coordination geometry of chloride ligands. The electronic spectra of 1 and 1+ in dichloromethane have been modeled by time-dependent density functional theory (TD-DFT). Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Synthesis, physicochemical characterization, DFT calculation and biological activities of Fe(III) and Co(II)-omeprazole complexes. Potential application in the Helicobacter pylori eradication

    Science.gov (United States)

    Russo, Marcos G.; Vega Hissi, Esteban G.; Rizzi, Alberto C.; Brondino, Carlos D.; Salinas Ibañez, Ángel G.; Vega, Alba E.; Silva, Humberto J.; Mercader, Roberto; Narda, Griselda E.

    2014-03-01

    The reaction between the antiulcer agent omeprazole (OMZ) with Fe(III) and Co(II) ions was studied, observing a high ability to form metal complexes. The isolated microcrystalline solid complexes were characterized by elemental analysis, X-ray powder diffraction (XRPD), Scanning Electron Microscopy (SEM), magnetic measurements, thermal study, FTIR, UV-Visible, Mössbauer, electronic paramagnetic resonance (EPR), and DFT calculations. The metal-ligand ratio for both complexes was 1:2 determined by elemental and thermal analysis. FTIR spectroscopy showed that OMZ acts as a neutral bidentate ligand through the pyridinic nitrogen of the benzimidazole ring and the oxygen atom of the sulfoxide group, forming a five-membered ring chelate. Electronic, Mössbauer, and EPR spectra together with magnetic measurements indicate a distorted octahedral geometry around the metal ions, where the coordination sphere is completed by two water molecules. SEM and XRPD were used to characterize the morphology and the crystal nature of the complexes. The most favorable conformation for the Fe(III)-OMZ and Co(II)-OMZ complexes was obtained by DFT calculations by using B3LYP/6-31G(d)&LanL2DZ//B3LYP/3-21G(d)&LanL2DZ basis set. Studies of solubility along with the antibacterial activity against Helicobacter pylori for OMZ and its Co(II) and Fe(III) complexes are also reported. Free OMZ and both metal complexes showed antibacterial activity against H. pylori. Co(II)-OMZ presented a minimal inhibitory concentration ˜32 times lower than that of OMZ and ˜65 lower than Fe(III)-OMZ, revealing its promising potential use for the treatment of gastric pathologies associated with the Gram negative bacteria. The morphological changes observed in the cell membrane of the bacteria after the incubation with the metal-complexes were also analyzed by SEM microscopy. The antimicrobial activity of the complexes was proved by the viability test.

  12. Structural investigation of α-LaZr2F11 by coupling X-ray powder diffraction, 19F solid state NMR and DFT calculations

    Science.gov (United States)

    Martineau, Charlotte; Legein, Christophe; Body, Monique; Péron, Olivier; Boulard, Brigitte; Fayon, Franck

    2013-03-01

    α-LaZr2F11 has been synthesized by solid state reaction. Its crystal structure has been refined from X-ray powder diffraction data (space group no. 72 Ibam, a=7.785(1) Å, b=10.086(1) Å and c=11.102(1) Å). α-LaZr2F11 contains one La, one Zr and four F inequivalent crystallographic sites. F3 and F4 are shared between one ZrF73- polyhedron and one LaF85- polyhedron, while F1 and F2 bridge two ZrF73- polyhedra. 19F 1D MAS NMR spectra of α-LaZr2F11 are in agreement with the proposed structural model. Assignment of the 19F resonances to the corresponding crystallographic sites has been performed on the basis of both their relative intensities and their correlation patterns in a 19F 2D dipolar-based double-quantum recoupling MAS NMR spectrum. DFT calculations of the 19F chemical shielding tensors have been performed using the GIPAW method implemented in the NMR-CASTEP code, for the experimental structure and two PBE-DFT geometry optimized structures of α-LaZr2F11 (atomic position optimization and full geometry optimization with rescaling of the unit cell volume to the experimental value). Computations were done with and without using a modified La pseudopotential allowing the treatment of the 4f localized empty orbitals of La3+. A relatively nice agreement between the experimental 19F isotropic and anisotropic chemical shifts and the values calculated for the proposed structural model is obtained.

  13. Vibrational spectra, DFT calculations, unusual structure, anomalous CH2 wagging and twisting modes, and phase-dependent conformation of 1,3-disilacyclobutane.

    Science.gov (United States)

    Rishard, Mohamed Z M; Irwin, Richard M; Laane, Jaan

    2007-02-08

    Our previously published infrared and Raman spectra of 1,3-disilacyclobutane (13DSCB) and its 1,1,3,3-d4 isotopomer have been reexamined and partially reassigned on the basis of DFT and ab initio calculations. The calculations confirm previous microwave work that the CSiC angles in the ring are unexpectedly larger than the SiCSi angles. This may arise from the partial charges on the ring atoms. The calculations are in excellent agreement with the observed spectra in both frequency and intensity. They also demonstrate that this molecule has CH2 wagging and twisting vibrations with frequencies below 1000 cm-1, about 200 cm-1 lower than expected. These unprecedented low values can be explained by the decreased slope in the potential energy curves for these vibrations as the sideways motions of the CH2 groups result in attractive forces between the positively charged hydrogens on the carbon atoms and the negatively charged hydrogens on the silicon atoms. The theoretical calculations also confirm the previous conclusions that the individual molecules (vapor) have C2v symmetry whereas in the solid the molecules become planar with D2h symmetry. The vibrational coupling between the ring-angle bending mode and the SiH2 in-phase rocking, which is present for the C2v structure, is forbidden for D2h and hence disappears.

  14. DFT calculations of quadrupolar solid-state NMR properties: Some examples in solid-state inorganic chemistry.

    Science.gov (United States)

    Cuny, Jerome; Messaoudi, Sabri; Alonzo, Veronique; Furet, Eric; Halet, Jean-François; Le Fur, Eric; Ashbrook, Sharon E; Pickard, Chris J; Gautier, Regis; Le Polles, Laurent

    2008-10-01

    This article presents results of first-principles calculations of quadrupolar parameters measured by solid-state nuclear magnetic measurement (NMR) spectroscopy. Different computational methods based on density functional theory were used to calculate the quadrupolar parameters. Through a series of illustrations from different areas of solid state inorganic chemistry, it is shown how quadrupolar solid-state NMR properties can be tackled by a theoretical approach and can yield structural information.

  15. Vibrational spectroscopic analysis of cyanopyrazine-2-carboxamide derivatives and investigation of their reactive properties by DFT calculations and molecular dynamics simulations

    Science.gov (United States)

    Beegum, Shargina; Mary, Y. Sheena; Varghese, Hema Tresa; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Zitko, Jan; Dolezal, Martin; Van Alsenoy, C.

    2017-03-01

    Using density functional theory technique in the B3LYP approximation and cc-pVDZ (5D, 7F) basis set, the molecular structural parameters and vibrational wave numbers of two cyanopyrazine-2-carboxamide derivatives have been investigated. On the basis of potential energy distribution detailed vibrational assignments of observed FT-IR and FT-Raman bands have been proposed. Using molecular electrostatic potential map relative reactivities towards electrophilic and nucleophilic attack are predicted. The first and second hyperpolarizabilities are calculated and the first hyperpolarizability of the title compounds are greater than that of the standard NLO material urea. Molecular studies reveal that the predicted binding affinities of the best poses were -8.7 kcal/mol for BACPC, -9.0 kcal/mol for CBACPC, and -8.8 kcal/mol for the original inhibitor. Efforts were made in order to investigate local reactivity properties of title compounds as well. In order to do so we have calculated average local ionization energy (ALIE) surfaces, Fukui functions, bond dissociation energies (BDE) (within the framework of DFT calculations) and radial distribution functions (RDF) (within the molecular dynamics simulations). ALIE surfaces and Fukui functions gave us initial information on the site reactivity towards electrophilic and nucleophilic attacks. BDE indicated locations that might be prone to autoxidation mechanism, while RDF indicated which atoms of title molecules are having pronounced interactions with water.

  16. FT-IR, FT-Raman, UV/Vis spectra and fluorescence imaging studies on 2-(bromoacetyl)benzo(b)furan by ab initio DFT calculations.

    Science.gov (United States)

    Veeraiah, A

    2015-08-05

    The vibrational and electronic properties of 2-(bromoacetyl)benzo(b)furan have been studied in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-31G(d,p) basis set. The theoretically calculated optimized parameters, vibrational frequencies etc., were compared with the experimental values, which yield good agreement between the observed and calculated values. The complete assignments of fundamental modes were performed on the basis of the potential energy distribution (PED). UV-visible spectrum of the compound was recorded in the region 300-600 nm and compared with the theoretical spectrum obtained from SAC-CI calculations. A good agreement is observed between the experimental and theoretical spectra. Fluorescence microscopic imaging studies proved that the compound can be used as one of the potential light sources in the yellow region with suitable excitation. Further, the predicted electronic transitions between the MOs 47→64, 52→62, 56→65, 56→72, 56→77 of the compound show a strong line at 569.8 nm. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Molecular vibrational investigation [FT-IR, FT-Raman, UV-Visible and NMR] on Bis(thiourea) Nickel chloride using HF and DFT calculations.

    Science.gov (United States)

    Anand, S; Sundararajan, R S; Ramachandraraja, C; Ramalingam, S; Durga, R

    2015-03-05

    In the present research work, the FT-IR, FT-Raman spectra of the Bis(thiourea) Nickel chloride (BTNC) were recorded and analyzed. The observed fundamental frequencies in finger print and functional group regions were assigned according to their uniqueness region. The computational calculations were carried out by HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The present organo-metallic compound was made up of covalent and coordination covalent bonds. The modified vibrational pattern of the complex molecule associated with ligand group was analyzed. Furthermore, the (13)C NMR and (1)H NMR spectral data were calculated by using the gauge independent atomic orbital (GIAO) method with B3LYP/6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts linked to TMS were compared. A investigation on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies were carried out. The kubo gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The NLO properties related to Polarizability and hyperpolarizability based on the finite-field approach were also discussed. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  18. Atomic-Level Investigation of CHx and C2Hx Adsorption on β-SiC (111 Surface for CVD Diamond Growth from DFT Calculations

    Directory of Open Access Journals (Sweden)

    Naichao Chen

    2011-01-01

    Full Text Available The focus of this paper is on the adsorption of unsaturated hydrocarbon molecules on β-SiC (111 surfaces during diamond film growth. The CHx and C2Hx molecules have been investigated to obtain a specific insight into absorbing diamond processes on the atomic scale. Structural and electronic properties of CHx and C2Hx adsorption on the Si- and C-terminated surfaces have been studied by first-principles calculations based on density functional theory (DFT. From the calculated energetics and geometries, we find that C2Hx adsorption on the Si-terminated surfaces has six possible surface reconstructions. For the C-terminated surface, there exist eight possible surface reconstructions. Five surface reconstructions, including CH2 adsorption on the Si- and C-terminated surface, CH–CH2 and CH=CH2 adsorption on the C-terminated surface, and C2H5 adsorption on the Si-terminated surface, have the largest hydrogen adsorption energies and more stability of surface reconstructions. Calculations demonstrate that the Si-terminated surface is energetically more favorable for fabricating CVD diamond coatings than the C-terminated surface.

  19. Molecular structure, spectroscopic characterization, HOMO and LUMO analysis of PU and PCL grafted onto PEMA-co-PHEMA with DFT quantum chemical calculations

    Science.gov (United States)

    Demir, Pınar; Akman, Feride

    2017-04-01

    A newly synthesized polycaprolactone (PCL) and polyurethane (PU) polymers, which grafted onto poly (ethylmethacrylate-co-2-hydroxyethyl methacrylate) (PEMA-co-PHEMA) were characterized both theoretically and experimentally. The FTIR and 1H NMR spectra were recorded for the PCL and PU polymers and the experimental values were compared the theoretical values. The molecular structure evaluation, vibrational frequencies and 1H NMR chemical shift values, which carried out by using gauge including atomic orbital (GIAO) approach, of the PCL and PU polymers were calculated by using density functional method (DFT/B3LYP) with 6-311G (d, p) as a basis set in the ground state. The calculated data such as vibrational frequencies and chemical shift values show good agreement with experimental values. Besides, the thermodynamic properties such as rotational temperatures, rotational constants, zero-point vibrational energy, specific heat capacity, thermal energy, entropy, enthalpy, the electronic properties such as HOMO and LUMO energies, and molecular electrostatic potential (MEP) surfaces for the PCL and PU were calculated and interpreted.

  20. Vibrational, structural and electronic properties investigation by DFT calculations and molecular docking studies with DNA topoisomerase II of strychnobrasiline type alkaloids: A theoretical approach for potentially bioactive molecules

    Science.gov (United States)

    Costa, Renyer A.; Oliveira, Kelson M. T.; Costa, Emmanoel Vilaça; Pinheiro, Maria L. B.

    2017-10-01

    A combined experimental and theoretical DFT study of the structural, vibrational and electronic properties of strychnobrasiline and 12-hydroxy-10,11-dimethoxystrychnobrasiline is presented using the Becke three-parameter Lee-Yang-Parr function (B3LYP) and 6-311G(2d,p) basis set. The theoretical geometry optimization data were compared with the X-ray data for a similar structure in the associated literature, showing close values. The calculated HOMO-LUMO gap values showed that the presence of substituents in the benzene ring influences the quantum properties which are directly related to the reactive properties. Theoretical UV spectra agreed well with the measured experimental data, with bands assigned. In addition, Natural Bond Orbitals (NBOs), Mapped molecular electrostatic potential surface (MEPS) and NLO calculations were also performed at the same theory level. The theoretical vibrational analysis revealed several characteristic vibrations that may be used as a diagnostic tool for other strychnobrasiline type alkaloids, simplifying their identification and structural characterization. Molecular docking calculations with DNA Topoisomerase II-DNA complex showed binding free energies values of -8.0 and -9.5 kcal/mol for strychnobrasiline and 12-hydroxy-10,11-dimethoxystrychnobrasiline respectively, while for amsacrine, used for the treatment of leukemia, the binding free energy ΔG presented a value of -10.0 kcal/mol, suggesting that strychnobrasiline derivative alkaloids might exhibit an antineoplastic activity.

  1. Multichromophoric bimetallic Ru(II) terpyridine complexes based on pyrenyl-bis-phenylimidazole spacer: synthesis, photophysics, spectroelectrochemistry, and TD-DFT calculations.

    Science.gov (United States)

    Karmakar, Srikanta; Maity, Dinesh; Mardanya, Sourav; Baitalik, Sujoy

    2014-11-17

    A symmetrical bridging ligand, 5,11-bis(4-([2,2':6',2″-terpyridine]-4'-yl)phenyl)-4,12-dihydropyreno[4,5-d:9,10-d']diimidazole (tpy-H2PhImzPy-tpy), containing terpyridyl coordinating units connected via a pyrenyl-bis-phenylimidazole spacer have been designed to synthesize a new class of light harvesting bimetallic Ru(II) complexes. The electronic properties of this complexes can be fine-tuned by varying tridentate terminal ligands. Full characterization of the compounds has been done with the help of (1)H NMR spectroscopy, high-resolution mass spectrometry, and elemental analysis. Geometry optimization of the complexes was also carried out with density functional theory (DFT). Electronic absorption spectra exhibit a number of very intense π-π* and n-π* transitions in the UV and moderately intense MLCT and ILCT transitions in the visible region. Interestingly, the present bimetallic complexes exhibit moderately strong luminescence in the range between 657 and 703 nm and lifetimes (long component) between 5.8 and 67.0 ns at room temperature showing the dependence of the emission characteristics upon the type of terminal ligand and solvent. Detailed temperature-dependent emission measurements showed that an overall enhancement of photoluminescence intensity and lifetime occur in all three cases upon lowering of temperature. The redox behavior of the compounds is characterized by a single reversible anodic wave corresponding to two closely spaced one-electron processes. The appearance of intervalence charge transfer transition (IVCT) bands in the NIR region on electrochemical generation of Ru(II)Ru(II)/Ru(II)Ru(III) species indicates the presence of substantial electronic communication among the two ruthenium centers in the bimetallic complexes. DFT and TDDFT calculations were also done for better understanding of the absorption and emission spectral characteristics of the complexes.

  2. Effective Chirality Transfer in [3+2] Reaction between Allenyl-Rhodium and Enal: Mechanistic Study Based on DFT Calculations.

    Science.gov (United States)

    Qi, Xiaotian; Liu, Song; Zhang, Tao; Long, Rong; Huang, Jun; Gong, Jianxian; Yang, Zhen; Lan, Yu

    2016-09-16

    Theoretical calculation was performed to study the chirality transfer in a newly reported intramolecular [3+2] cycloaddition of enal and alleno rhodium species, generated in situ from an enynol precursor. [3.3.0] bicyclic system which contains two bridgehead quaternary carbons that can be achieved, the chirality of which are controlled by those of the starting material, and the product stereoselectivity is only determined by the α-position of the acetylene moiety. Density functional theory calculations predicted that only the cis [3.3.0] bicyclic product could be generated, regardless of either erythro or threo substrate, which was also confirmed by experimental observations.

  3. Electronic structure of BaFe2As2 as obtained from DFT/ASW first-principles calculations

    KAUST Repository

    Schwingenschlögl, Udo

    2010-07-02

    We use ab-initio calculations based on the augmented spherical wave method within density functional theory to study the magnetic ordering and Fermi surface of BaFe2As2, the parent compound of the hole-doped iron pnictide superconductors (K,Ba)Fe2As2, for the tetragonal I4/mmm as well as the orthorhombic Fmmm structure. In comparison to full potential linear augmented plane wave calculations, we obtain significantly smaller magnetic energies. This finding is remarkable, since the augmented spherical wave method, in general, is known for a most reliable description of magnetism. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Matei, Iulia; Ionescu, Sorana [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania); Hillebrand, Mihaela, E-mail: mihh@gw-chimie.math.unibuc.ro [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania)

    2011-08-15

    The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 10{sup 5} M{sup -1} was evidenced. Foerster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes in the CD band of HSA indicate a decrease in the {alpha}-helix content upon binding. An induced CD signal for bound fisetin was observed and rationalized in terms of density functional theory calculations. - Highlights: > Fisetin-BSA system was studied by fluorescence spectroscopy. > Binding parameters, association constant and number of sites were estimated. > Binding site of fisetin was identified by competitive experiments. > Conformational changes in HSA and fisetin were evidenced by circular dichroism. > TDDFT calculated CD spectra supported the experimental data.

  5. Glyphosate complexation to aluminium(III). An equilibrium and structural study in solution using potentiometry, multinuclear NMR, ATR-FTIR, ESI-MS and DFT calculations.

    Science.gov (United States)

    Purgel, Mihály; Takács, Zoltán; Jonsson, Caroline M; Nagy, Lajos; Andersson, Ingegärd; Bányai, István; Pápai, Imre; Persson, Per; Sjöberg, Staffan; Tóth, Imre

    2009-11-01

    The stoichiometries and stability constants of a series of Al(3+)-N-phosponomethyl glycine (PMG/H(3)L) complexes have been determined in acidic aqueous solution using a combination of precise potentiometric titration data, quantitative (27)Al and (31)P NMR spectra, ATR-FTIR spectrum and ESI-MS measurements (0.6M NaCl, 25 degrees C). Besides the mononuclear AlH(2)L(2+), Al(H(2)L)(HL), Al(HL)(2)(-) and Al(HL)L(2-), dimeric Al(2)(HL)L(+) and trinuclear Al(3)H(5)L(4)(2+) complexes have been postulated. (1)H and (31)P NMR data show that different isomers co-exist in solution and the isomerization reactions are slow on the (31)P NMR time scale. The geometries of monomeric and dimeric complexes likely double hydroxo bridged and double phosphonate bridged isomers have been optimized using DFT ab initio calculations starting from rational structural proposals. Energy calculations using the PCM solvation method also support the co-existence of isomers in solutions.

  6. EPR spectrum of the Y@C82 metallofullerene isolated in solid argon matrix: hyperfine structure from EPR spectroscopy and relativistic DFT calculations.

    Science.gov (United States)

    Misochko, Eugenii Ya; Akimov, Alexander V; Belov, Vasilii A; Tyurin, Daniil A; Bubnov, Vyacheslav P; Kareev, Ivan E; Yagubskii, Eduard B

    2010-08-21

    The EPR spectrum of the Y@C(82) molecules isolated in solid argon matrix was recorded for the first time at a temperature of 5 K. The isotropic hyperfine coupling constant (hfcc) A(iso) = 0.12 +/- 0.02 mT on the nucleus (89)Y as derived from the EPR spectrum is found in more than two times greater than that obtained in previous EPR measurements in liquid solutions. Comparison of the measured hfcc on a metal atom with that predicted by density-functional theory calculations (PBE/L22) indicate that relativistic method provides good agreement between experiment in solid argon and theory. Analysis of the DFT calculated dipole-dipole hf-interaction tensor and electron spin distribution in the endometallofullerenes with encaged group 3 metal atoms Sc, Y and La has been performed. It shows that spin density on the scandium atom represents the Sc d(yz) orbital lying in the symmetry plane of the C(2v) fullerene isomer and interacting with two carbon atoms located in the para-position on the fullerene hexagon. In contrast, the configuration of electron spin density on the heavier atoms, Y and La, is associated with the hybridized orbital formed by interaction of the metal d(yz) and p(y) electronic orbitals.

  7. Preparation and characterizations of SnO2 nanopowder and spectroscopic (FT-IR, FT-Raman, UV-Visible and NMR) analysis using HF and DFT calculations.

    Science.gov (United States)

    Ayeshamariam, A; Ramalingam, S; Bououdina, M; Jayachandran, M

    2014-01-24

    In this work, pure and singe phase SnO2 Nano powder is successfully prepared by simple sol-gel combustion route. The photo luminescence and XRD measurements are made and compared the geometrical parameters with calculated values. The FT-IR and FT-Raman spectra are recorded and the fundamental frequencies are assigned. The optimized parameters and the frequencies are calculated using HF and DFT (LSDA, B3LYP and B3PW91) theory in bulk phase of SnO2 and are compared with its Nano phase. The vibrational frequency pattern in nano phase gets realigned and the frequencies are shifted up to higher region of spectra when compared with bulk phase. The NMR and UV-Visible spectra are simulated and analyzed. Transmittance studies showed that the HOMO-LUMO band gap (Kubo gap) is reduced from 3.47 eV to 3.04 eV while it is heated up to 800°C. The Photoluminescence spectra of SnO2 powder showed a peak shift towards lower energy side with the change of Kubo gap from 3.73 eV to 3.229 eV for as-prepared and heated up to 800°C. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  8. General procedure for the calculation of accurate defect excitation energies from DFT-1/2 band structures: The case of the NV- center in diamond

    Science.gov (United States)

    Lucatto, Bruno; Assali, Lucy V. C.; Pela, Ronaldo Rodrigues; Marques, Marcelo; Teles, Lara K.

    2017-08-01

    A major challenge in creating a quantum computer is to find a quantum system that can be used to implement the qubits. For this purpose, deep centers are prominent candidates, and ab initio calculations are one of the most important tools to theoretically study their properties. However, these calculations are highly involved, due to the large supercell needed, and the computational cost can be even larger when one goes beyond the Kohn-Sham scheme to correct the band gap problem and achieve good accuracy. In this work, we present a method that overcomes these problems and provides the optical transition energies as a difference of Kohn-Sham eigenvalues; even more, provides a complete and accurate band structure of the defects in a semiconductor. Despite the original motivations, the presented methodology is a general procedure, which can be used to systematically study the optical transitions between localized levels within the band gap of any system. The method is an extension of the low-cost and parameter-free DFT-1/2 approximate quasiparticle correction, and allows it to be applied in the study of complex defects. As a benchmark, we apply the method to the NV- center in diamond. The agreement with experiments is remarkable, with an accuracy of 0.1 eV. The band structure agrees with the expected qualitative features of this system, and thus provides a good intuitive physical picture by itself.

  9. Structural, vibrational, electronic, NMR and reactivity analyses of 2-amino-4H-chromene-3-carbonitrile (ACC) by ab initio HF and DFT calculations.

    Science.gov (United States)

    Sridevi, C; Shanthi, G; Velraj, G

    2012-04-01

    This study represents an integrated approach towards understanding the vibrational, electronic, NMR, reactivity and structural aspects of 2-amino-4H-chromene-3-carbonitrile (ACC). A detailed interpretation of the FT IR, UV and NMR spectra were reported. Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. The electronic properties was also studied and the most prominent transition corresponds to π→π*. The lower frontier orbital energy gap and high dipole moment illustrates the high reactivity of the title molecule. The NMR results indicated that the observed chemical shifts depend not only on the structure of the molecule being studied, but also on the solvent used. ACC exhibited good nonlinear optical activity and was much greater than that of urea. Molecular electrostatic potential (MEP) results predicted that the enaminonitrile fragment of ACC to be the most reactive site for both electrophilic and nucleophilic attack. In addition, the thermodynamic properties of the compound were calculated at different temperatures and corresponding relations between the properties and temperature were also studied. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Synthesis, DFT calculations and cytotoxic investigation of platinum complexes with 3-thiolanespiro-5‧-hydantoin and 4-thio-1H-tetrahydropyranespiro-5‧-hydantoin

    Science.gov (United States)

    Bakalova, Adriana; Buyukliev, Rossen; Momekov, Georgi

    2015-07-01

    Two organic compounds - 3-thiolanespiro-5‧-hydantoin, 4-thio-1H-tetrahydropyranespiro-5‧-hydantoin and four new Pt(II) and Pt(IV) complexes with general formulas cis-[Pt(L)2Cl2] and cis-[Pt(L)2Cl4] were synthesized. The obtained compounds were characterized by elemental analysis, IR, 1H, 13C NMR spectroscopy. The hybrid DFT calculations were used for optimization of the structure geometries of the ligand (L1) and its Pt(II) complex (1). The calculated structural parameters such as bond lengths and angles are in good agreement with the experimental data for similar hydantoins and their platinum complexes. The obtained results showed that the geometry of the complex (1) is plane square and the bounding of the L1 with platinum ion is realized by sulfur atom from thiolane ring. The complexes were tested for cytotoxicity in vitro on four human tumor cell lines. The tested compounds exerted concentration-dependent cytotoxic effects against some of the tumor cell lines.

  11. Crystal structures, DFT calculations and Hirshfeld surface analyses of three new cobalt(III) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine

    Science.gov (United States)

    Masoudi, Mohaddeseh; Behzad, Mahdi; Arab, Ali; Tarahhomi, Atekeh; Rudbari, Hadi Amiri; Bruno, Giuseppe

    2016-10-01

    Three new Cobalt(III) Schiff base complexes were synthesized and characterized by spectroscopic methods and x-ray crystallography. The DFT optimized structures of the complexes agreed well with the corresponding x-ray structures. According to the calculated vibrational normal modes, the observed signals in the IR spectra of the complexes were assigned. The experimental UV-Vis spectra of the complexes were also discussed considering the calculated excited states and molecular orbitals. Hirshfeld surface analysis was carried out to study the inter-contact interactions in these complexes. These studies provided comprehensive description of such inter-contact interactions by means of an appealing graphical approach using 3D Hirshfeld surfaces and 2D fingerprint plots derived from the surfaces. It indicated the dominant role of various hydrogen intermolecular interactions such as H⋯H (above 60%), C⋯H/H⋯C (near 15%-20%), O⋯H/H⋯O (about 16% or 17% for structures with counter ion ClO4-) and H⋯F (17% for structure with counter ion PF6-) contacts into the crystal packing which are discussed in details.

  12. A theoretical study on the characteristics of the intermolecular interactions in the active site of human androsterone sulphotransferase: DFT calculations of NQR and NMR parameters and QTAIM analysis.

    Science.gov (United States)

    Astani, Elahe K; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L

    2016-07-01

    A theoretical study at the level of density functional theory (DFT) was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond interactions, in the active site of enzyme human androsterone sulphotransferase (SULT2A1/ADT). Geometry optimization, interaction energy, (2)H, (14)N, and (17)O electric field gradient (EFG) tensors, (1)H, (13)C, (17)O, and (15)N chemical shielding (CS) tensors, Natural Bonding Orbital (NBO) analysis, and quantum theory of atoms in molecules (QTAIM) analysis of this active site were investigated. It was found that androsterone (ADT) is able to form hydrogen bonds with residues Ser80, Ile82, and His99 of the active site. The interaction energy calculations and NBO analysis revealed that the ADT molecule forms the strongest hydrogen bond with Ser80. Results revealed that ADT interacts with the other residues through electrostatic and Van der Waals interactions. Results showed that these hydrogen bonds influence on the calculated (2)H, (14)N, and (17)O quadrupole coupling constants (QCCs), as well as (1)H, (13)C, (17)O, and (15)N CS tensors. The magnitude of the QCC and CS changes at each nucleus depends directly on its amount of contribution to the hydrogen bond interaction.

  13. Synthesis, X-ray single crystal structure, likelihood of occurrence of intermolecular contacts, spectroscopic investigation and DFT quantum chemical calculations of zwitterionic complex: 1-Ethylpiperaziniumtrichlorozincate (II)

    Science.gov (United States)

    Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

    2017-10-01

    The synthesis and the X-ray structure of the Zn(II) zwitterionic complex:1-ethylpiperaziniumtrichlorozincate (II) are described. In the atomic arrangement, the ZnCl3N entities, grouped in pairs, are deployed along the b-axis to form layers. The organic entities are inserted between these layers through Nsbnd H⋯Cl and Csbnd H⋯Cl hydrogen bonds to form infinite three-dimensional network. The 3D Hirshfeld surfaces were investigated for intermolecular interactions. The optimized geometry, Mulliken charge distribution, molecular electrostatic potential (MEP) maps and thermodynamic properties have been calculated using the Lee-Yang-Parr correlation functional B3LYP with the LanL2DZ basis set. The HOMO and LUMO energy gap and chemical reactivity parameters were made. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray crystal structure. The vibrational absorption bands were identified by infrared spectroscopy. DFT calculations allowed the attribution of the NMR peaks and of the IR bands.

  14. Molecular structure, spectroscopic characterization and DFT calculations of a novel (Z)-1-[(2-Ethylphenylamino)methylene]naphthalene-2(1H)-one

    Science.gov (United States)

    Alpaslan, Yelda Bingöl; Gökce, Halil; Macit, Mustafa; Alpaslan, Gökhan; Özdemir, Namık

    2015-09-01

    A novel Schiff base compound (Z)-1-[(2-Ethylphenylamino)methylene]naphthalene-2(1H)-one was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 2-ethylaniline. The structural properties of the compound have been characterized by using FT-IR, 1H and 13C NMR, UV-vis and X-ray single-crystal methods. According to X-ray diffraction result, the title compound exists in the keto-amine tautomeric form. The molecular geometry, vibrational frequencies, electronic absorption spectra and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the title compound in the ground state have been calculated by using density functional theory (DFT/B3LYP) method with 6-311G++(d,p) basis set, and compared with the experimental data. The obtained results indicate that optimized geometry can well reflect the crystal structural parameters. The theoretical values are in good agreement with the experimental ones. The energetic behavior of the compound in solvent media has been examined using B3LYP method with the 6-311G++(d,p) basis set by applying the polarizable continuum model (PCM). The total energy of the compound decreases with increasing polarity of the solvent. The molecular electrostatic potential (MEP), HOMO-LUMO energy gap and non-linear optical (NLO) properties of the compound were investigated using theoretical calculations.

  15. Experimental FTIR, FT-IR (gas phase), FT-Raman and NMR spectra, hyperpolarizability studies and DFT calculations of 3,5-dimethylpyrazole.

    Science.gov (United States)

    Sundaraganesan, N; Kavitha, E; Sebastian, S; Cornard, J P; Martel, M

    2009-10-15

    In the present study, structural properties of 3,5-dimethylpyrazole (3,5-DMP) have been studied extensively utilizing density functional theory (DFT) employing B3LYP exchange correlation. The Fourier transform infrared (solid phase and gas phase) and Fourier transform Raman spectra of 3,5-DMP were recorded. The Vibrational frequencies of 3,5-DMP in the ground state have been calculated by using density functional method (B3LYP) with 6-31G(d,p), 6-311G(d,p) and 6-311++G(d,p) as basis sets. Comparison of the observed fundamental vibrational frequencies of 3,5-DMP with calculated results show that 6-311++G(d,p) superior to other basis sets for molecular vibrational problems. Non linear optical NLO behavior of the examined molecule was investigated by the determination of the electric dipole moment mu, the polarizability alpha and the hyperpolarizability beta using the B3LYP/cc-pvdz method. The isotropic chemical shifts computed by (13)C and (1)H NMR analysis also show good agreement with experimental observations. The theoretically predicted FTIR and FT-Raman spectra of the title molecule have been constructed.

  16. A relativistic DFT methodology for calculating the structures and NMR chemical shifts of octahedral platinum and iridium complexes.

    Science.gov (United States)

    Vícha, Jan; Patzschke, Michael; Marek, Radek

    2013-05-28

    A methodology for optimizing the geometry and calculating the NMR shielding constants is calibrated for octahedral complexes of Pt(IV) and Ir(III) with modified nucleic acid bases. The performance of seven different functionals (BLYP, B3LYP, BHLYP, BP86, TPSS, PBE, and PBE0) in optimizing the geometry of transition-metal complexes is evaluated using supramolecular clusters derived from X-ray data. The effects of the size of the basis set (ranging from SVP to QZVPP) and the dispersion correction (D3) on the interatomic distances are analyzed. When structural deviations and computational demands are employed as criteria for evaluating the optimizations of these clusters, the PBE0/def2-TZVPP/D3 approach provides excellent results. In the next step, the PBE0/def2-TZVPP approach is used with the continuum-like screening model (COSMO) to optimize the geometry of single molecules for the subsequent calculation of the NMR shielding constants in solution. The two-component zeroth-order regular approximation (SO-ZORA) is used to calculate the NMR shielding constants (PBE0/TZP/COSMO). The amount of exact exchange in the PBE0 functional is validated for the nuclear magnetic shieldings of atoms in the vicinity of heavy transition metals. For the PBE0/TZP/COSMO setup, an exact exchange of 40% is found to accurately reproduce the experimental NMR shielding constants for both types of complexes. Finally, the effect of the amount of exact exchange on the NMR shielding calculations (which is capable of compensating for the structural deficiencies) is analyzed for various molecular geometries (SCS-MP2, BHLYP, and PBE0) and the influence of a trans-substituent on the NMR chemical shift of nitrogen is discussed. The observed dependencies for an iridium complex cannot be rationalized by visualizing the Fermi-contact (FC) induced spin density and probably originate from changes in the d-d transitions that modulate the spin-orbit (SO) part of the SO/FC term.

  17. Estimation of ΔR/R values by benchmark study of the Mössbauer Isomer shifts for Ru, Os complexes using relativistic DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Kaneko, Masashi [Japan Atomic Energy Agency, Nuclear Science and Engineering Center (Japan); Yasuhara, Hiroki; Miyashita, Sunao; Nakashima, Satoru, E-mail: snaka@hiroshima-u.ac.jp [Hiroshima University, Graduate School of Science (Japan)

    2017-11-15

    The present study applies all-electron relativistic DFT calculation with Douglas-Kroll-Hess (DKH) Hamiltonian to each ten sets of Ru and Os compounds. We perform the benchmark investigation of three density functionals (BP86, B3LYP and B2PLYP) using segmented all-electron relativistically contracted (SARC) basis set with the experimental Mössbauer isomer shifts for {sup 99}Ru and {sup 189}Os nuclides. Geometry optimizations at BP86 theory of level locate the structure in a local minimum. We calculate the contact density to the wavefunction obtained by a single point calculation. All functionals show the good linear correlation with experimental isomer shifts for both {sup 99}Ru and {sup 189}Os. Especially, B3LYP functional gives a stronger correlation compared to BP86 and B2PLYP functionals. The comparison of contact density between SARC and well-tempered basis set (WTBS) indicated that the numerical convergence of contact density cannot be obtained, but the reproducibility is less sensitive to the choice of basis set. We also estimate the values of ΔR/R, which is an important nuclear constant, for {sup 99}Ru and {sup 189}Os nuclides by using the benchmark results. The sign of the calculated ΔR/R values is consistent with the predicted data for {sup 99}Ru and {sup 189}Os. We obtain computationally the ΔR/R values of {sup 99}Ru and {sup 189}Os (36.2 keV) as 2.35×10{sup −4} and −0.20×10{sup −4}, respectively, at B3LYP level for SARC basis set.

  18. Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugate.

    Science.gov (United States)

    Zanuy, David; Hamley, Ian W; Alemán, Carlos

    2011-07-21

    The conformational properties of the hybrid amphiphile formed by the conjugation of a hydrophobic peptide with four phenylalanine (Phe) residues and hydrophilic poly(ethylene glycol), have been investigated using quantum mechanical calculations and atomistic molecular dynamics simulations. The intrinsic conformational preferences of the peptide were examined using the building-up search procedure combined with B3LYP/6-31G(d) geometry optimizations, which led to the identification of 78, 78, and 92 minimum energy structures for the peptides containing one, two, and four Phe residues. These peptides tend to adopt regular organizations involving turn-like motifs that define ribbon or helical-like arrangements. Furthermore, calculations indicate that backbone···side chain interactions involving the N-H of the amide groups and the π clouds of the aromatic rings play a crucial role in Phe-containing peptides. On the other hand, MD simulations on the complete amphiphile in aqueous solution showed that the polymer fragment rapidly unfolds maximizing the contacts with the polar solvent, even though the hydrophobic peptide reduce the number of waters of hydration with respect to an individual polymer chain of equivalent molecular weight. In spite of the small effect of the peptide in the hydrodynamic properties of the polymer, we conclude that the two counterparts of the amphiphile tend to organize as independent modules.

  19. The separation mechanism of Am(iii) from Eu(iii) by diglycolamide and nitrilotriacetamide extraction reagents using DFT calculations.

    Science.gov (United States)

    Kaneko, Masashi; Watanabe, Masayuki; Matsumura, Tatsuro

    2016-11-01

    Relativistic density functional calculations were applied to study the separation behaviors of the Am(iii) ion from the Eu(iii) ion by diglycolamide (DGA) and nitrilotriacetamide (NTA) ligands in order to understand the difference in the separation mechanism of their reagents. The complexation reaction was modeled on the basis of previous experimental studies. The calculated energies based on stabilization by complex formation at the ZORA-B2PLYP/SARC level predicted that the DGA reagent preferably coordinated to the Eu(iii) ion when compared with the Am(iii) ion. In contrast, the NTA reagent selectively coordinated to the Am(iii) ion when compared with the Eu(iii) ion. These results reproduced the experimental selectivity of DGA and NTA ligands toward Eu(iii) and Am(iii) ions. Mulliken's population analyses implied that the difference in the contribution of the bonding property between the f-orbital of Am and donor atoms determined the comparative stability of Eu and Am complexes.

  20. GHB光学性质的DFT理论计算研究%The Study on the Optical Properties of GHB by DFT Theoretical Calculation

    Institute of Scientific and Technical Information of China (English)

    唐利斌; 宋立媛; 陈雪梅; 马钰; 庄继胜; 姬荣斌; 刘树平; 王忆锋; 叶婧; 台国安; 魏长松; 陆志文; 许扬羽

    2011-01-01

    The geometry optimization, IR spectrum, Raman spectrum, UV-Vis spectrum as well as frontier molecular orbitals are calculated by using Density Functional Theory (DFT) at B3LYP/6-31G level. Research results show that the theoretical calculation results agree well with experimental data, the characteristic peaks in IR, THz, UV-Vis and Raman spectra have been assigned. It is found that GHB has four obvious absorption peaks in 0.1~10THz range, they are located at 0.85, 2.89, 7.21 and 8.61 THz. GHB has three UV absorption peaks which located at 235.50, 190.23 and 169.79 nm, respectively. Based on the characteristic IR, Raman, THz, UV-Vis optical properties, GHB may be detected, identified, analyzed, and inspected by means of spectroscopic technique.%采用密度泛函理论( DFT)方法对γ-羟基丁酸(GHB)进行了B3LYP/6-31G水平上的分子结构优化、红外光谱、Raman光谱、紫外-可见光谱及分子前线轨道理论等计算.研究结果表明:理论计算结果与实验数据吻合得较好,对IR、THz、UV-Vis吸收光谱和Raman散射光谱中的特征峰进行了归属,发现GHB在0.1 ~ 10 THz波谱范围内有四个明显的吸收峰,分别位于0.85、2.89、7.21以及8.61 THz,GHB在紫外波段的235.50、190.23及169.79 nm有3个吸收峰.基于GHB具有特征性的IR、Raman、THz、UV-Vis光谱性质,可以使用光谱技术对GHB进行探测、识别、分析和检测.

  1. Synthesis, characterization and DFT calculations of electronic and optical properties of CaMoO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Bouzidi, Chaker, E-mail: bouzidtc@yahoo.fr [Laboratoire de Physico-chimie des Matériaux Minéraux et leurs Applications, Centre National des Recherches en Sciences des Matériaux, BP No.73, 8027 Soliman (Tunisia); Horchani-Naifer, Karima; Khadraoui, Zied [Laboratoire de Physico-chimie des Matériaux Minéraux et leurs Applications, Centre National des Recherches en Sciences des Matériaux, BP No.73, 8027 Soliman (Tunisia); Elhouichet, Habib [Laboratoire de Physico-chimie des Matériaux Minéraux et leurs Applications, Centre National des Recherches en Sciences des Matériaux, BP No.73, 8027 Soliman (Tunisia); Département de Physique, Faculté des Sciences de Tunis, Université de Tunis-ElManar ElManar, 2092 Tunis (Tunisia); Ferid, Mokhtar [Laboratoire de Physico-chimie des Matériaux Minéraux et leurs Applications, Centre National des Recherches en Sciences des Matériaux, BP No.73, 8027 Soliman (Tunisia)

    2016-09-15

    The electronic and optical properties of calcium molybdate (CaMoO{sub 4}) have been determined by X-ray diffraction, spectroscopic measurements and calculations of energy-band structures, density of states, and optical response functions by density functional theory. The chemical bonding analysis indicates that Mo–O bonds exhibit more covalent character than the Ca–O bond. The linear photon-energy-dependent dielectric functions, conductivity, refractive index, reflectivity and extinction coefficients were investigated and analyzed. The results are in agreement with previous theoretical works and the experimental data. Reflectivity spectra revealed that the CaMoO{sub 4} promises as good coating materials in the energy region of 9.3–11.6 eV with reflectivity larger than 75%.

  2. Vibrational spectra and DFT calculations of the vibrational modes of Schiff base C18H17N3O2

    Science.gov (United States)

    Antunes, J. A.; Silva, L. E.; Bento, R. R. F.; Teixeira, A. M. R.; Freire, P. T. C.; Faria, J. L. B.; Ramos, R. J.; Silva, C. B.; Lima, J. A.

    2012-04-01

    The Schiff base 4-{[(1E)-(2-Hydroxyphenyl)methylidene]amino}-1,5-dimethyl-2-phenyl-1,2-dihydro-3H-pyrazol-3-one (C18H17N3O2) is a synthetic compound with a variety of scientific and technological applications, such as clinic, analytic and pharmacologic. In this work FT-Raman spectrum and FT-infrared spectrum of C18H17N3O2 were investigated at 300 K. Vibrational wavenumber and wave vector have been predicted using Density Functional Theory (B3LYP) calculations with the 6-31 G(d,p) basis set. The description of the normal modes was performed by means of the potential energy distribution. A comparison with experiment allowed us to assign most of the normal modes of the crystal.

  3. Synthesis, crystal structure, property research, and DFT calculation of 2,3-diphenylfuro[3,2-b]quinoxaline

    Science.gov (United States)

    Yao, Qi-Chao; Wu, Ding-Er; Xia, Min

    2013-06-01

    The title compound is obtained via the intramolecular condensation of 3-(2-oxo-1,2-diphenylethyl)quinoxalin-2(1H)-one in the presence of excessive boron trifluoride etherate and characterized by 1H NMR, 13C NMR, IR, and EI-MS. The solution-based and solid-state fluorescence along with the electrochemical property are studied in detail. The unique herring-bone arrangement which is revealed by the X-ray crystallography should account for the intense solid-state fluorescence. The theoretic calculations are employed to clarify the origin of the large Stokes shift and the positive solvatochromism in view of the geometric relaxation and the transition feature.

  4. Photoabsorption spectra of (Mo/W)@Au12Si60 clusters from time-dependent DFT calculations

    KAUST Repository

    Mokkath, Junais Habeeb

    2013-11-14

    The electronic structure and photoabsorption spectrum of encapsulated (Mo/W)@Au12Si60 clusters are theoretically investigated via static and time-dependent density functional theory. The photoabsorption spectrum is calculated both at the scalar relativistic and spin-orbit coupling levels. The encapsulated (Mo/W)@Au12 clusters interact with the Si and thus stabilize the Si60 cage. The spin-orbit coupling strongly affects the optical properties of (Mo/W)@Au12 clusters as it leads to a splitting of spectral lines together with an intensity redistribution, whereas the spectra of (Mo/W)@Au12Si60 clusters show hardly any difference. The nanoscale properties thus can be tuned by choosing the endohedral metal atom, while keeping the optical properties unaffected. © 2013 American Chemical Society.

  5. Spectroscopic [FT-IR and FT-Raman] and theoretical [UV-Visible and NMR] analysis on α-Methylstyrene by DFT calculations.

    Science.gov (United States)

    Karthikeyan, N; Joseph Prince, J; Ramalingam, S; Periandy, S

    2015-05-15

    In the present research work, the FT-IR, FT-Raman and (13)C and (1)H NMR spectra of the α-Methylstyrene were recorded. The observed fundamental frequencies in finger print as well as functional group regions were assigned according to their uniqueness region. The Gaussian computational calculations are carried out by HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The impact of the presence of vinyl group in phenyl structure of the compound is investigated. The modified vibrational pattern of the molecule associated vinyl group was analyzed. Moreover, (13)C NMR and (1)H NMR were calculated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts linked to TMS were compared. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies were carried out. The kubo gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The NLO properties related to Polarizability and hyperpolarizability based on the finite-field approach were also discussed. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

  6. Electronic structure investigations of 4-aminophthal hydrazide by UV-visible, NMR spectral studies and HOMO-LUMO analysis by ab initio and DFT calculations.

    Science.gov (United States)

    Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

    2015-08-05

    Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. A novel coordination polymer of 7-azaindole-3-carboxylic acid with sodium ions: crystal and molecular structures, vibrational spectra and DFT calculations

    Science.gov (United States)

    Morzyk-Ociepa, Barbara; Szmigiel, Ksenia; Petrus, Rafał; Turowska-Tyrk, Ilona; Michalska, Danuta

    2017-09-01

    A novel two-dimensional coordination polymer, catena-poly[(μ2-7-azaindole-3-carboxylato-O:N)-di-aqua-sodium], [Na(7AI3CAH)(H2O)2]n has been synthesized and investigated by a single crystal X-ray diffraction, vibrational spectroscopy and DFT calculations. The sodium complex crystallizes in the triclinic system, space group Pī with a = 7.2226 (4), b = 7.4342 (7), c = 8.8428 (8) Å, α = 103.568 (8), β = 93.425 (6), γ = 91.233 (6)°, V = 460.42 (7) A3 and Z = 2. The asymmetric unit contains two crystallographically independent, half occupied sodium cations surrounded by one 7AI3CAH anion and two water molecules. The O-deprotonated 7-azaindole-3-carboxylate ligand (7AI3CAH) bridges the adjacent Na ions via one oxygen atom of the carboxylate group and via the pyridine nitrogen atom of the 7-azaindole group, which is quite unusual. The sodium cations are six-coordinated in a distorted octahedral geometry, where two apical positions are occupied by two water molecules. Extensive intermolecular Nsbnd H⋯O and Osbnd H⋯O hydrogen bonds stabilize the crystal structure of the complex. The infrared and Raman spectra of [Na(7AI3CAH)(H2O)2]n were recorded in the solid state. The theoretical wavenumbers, infrared intensities, Raman scattering activities and Raman intensities were calculated at the B3LYP/6-311++G(d,p) level for a theoretical model of the title compound including an inter ligand Nsbnd H⋯O(aqua) interaction. A detailed vibrational assignment has been made on the basis of the calculated potential energy distribution.

  8. Synthesis and crystal structure of 3-(4‧-nitrophenyl)iminocoumarin, and cyclization reaction mechanism based on DFT calculation

    Science.gov (United States)

    Zhang, Chao-Zhi; Li, Shi-Juan; Cao, Hui; Song, Ming-Xia; Kong, Qing-Gang

    2015-05-01

    A convenient method was reported to synthesize 3-(4‧-nitrophenyl)iminocoumarin by a cyclization reaction following a Knoevenagel reaction of 2-hydroxybenzaldehyde with 4-nitrophenylacenitrile in an ethanol solution. Piperidine or piperazine was employed respectively as catalyst. Crystal structure of 3-(4‧-nitrophenyl)iminocoumarin shows that the molecules are H-aggregation due to π-π stacking and hydrogen bonds between adjacent molecules, as a result, electrons would transfer easily from a molecule to an adjacent molecule. Based on theoretical calculations of the electronic structures and thermodynamic parameters of the reactive intermediates in these cyclization reactions, the reaction mechanisms were postulated. Data of single crystal and spectrum of UV-vis absorption show that 3-(4‧-nitrophenyl)iminocoumarin is good π-conjugated compound and would be potentially employed as donor-acceptor polymer units for developing bulk heterojunction solar cell. This paper suggests a convenient and effective method for synthesizing ring-locked D-A copolymer units for developing solar cell materials.

  9. The far infrared spectrum of naphthalene characterized by high resolution synchrotron FTIR spectroscopy and anharmonic DFT calculations.

    Science.gov (United States)

    Pirali, O; Goubet, M; Huet, T R; Georges, R; Soulard, P; Asselin, P; Courbe, J; Roy, P; Vervloet, M

    2013-07-07

    Using synchrotron radiation, we performed the rotationally resolved Fourier transform infrared absorption spectroscopy of three bands of naphthalene C10H8, namely ν(46)-0 (centered at 782 cm(-1), 12.7 μm), ν(47)-0 (centered at 474 cm(-1), 21 μm), and ν(48)-0 (centered at 167 cm(-1), 60 μm). The intense CH bending out of plane ν(46)-0 band was recorded under supersonic jet-cooled conditions using a molecular beam (the Jet-AILES apparatus) and the low frequency ν(47)-0 and ν(48)-0 bands were measured at room temperature in a long absorption path cell. The simultaneous rotational analysis of these bands permitted us to refine the ground state (GS) and ν(46) rotational spectroscopic constants and to provide the first sets of constants for the ν(47) and ν(48) modes. The experimental rotational constants were then used as reference data to calibrate theoretical models in order to provide new insights into the accuracy of anharmonic calculations. The B97-1 functional associated with the cc-pVTZ and ANO-RCC basis sets gave a consistent set of results, for rotational constants and fundamental frequencies. The data presented here pave the way for the search of naphthalene through its far-infrared spectrum in different objects of the interstellar medium.

  10. Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of (1) H NMR chemical shifts.

    Science.gov (United States)

    Lomas, John S; Joubert, Laurent; Maurel, François

    2016-05-31

    Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen-bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge-including atomic orbital method to geometry-optimized conformers. For certain conformers, intramolecular OH···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms-in-molecules and non-covalent interaction plots. The computed OH and CH proton shifts for the diol and the two complexes correlate well with values obtained by analysing data from the NMR titration of the diols in benzene against pyridine. Shift values for the diols in neat pyridine are calculated by weighting the shifts of the various protons in the three forms (free diol, 1 : 1 and 1 : 2 diol/pyridine complexes) according to the experimentally determined association constants. The results are in good agreement with those observed, and after empirical scaling, the root mean square difference is 0.18 ppm. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  11. Effect of the components' interface on the synthesis of methanol over Cu/ZnO from CO2/H2: a microkinetic analysis based on DFT + U calculations.

    Science.gov (United States)

    Tang, Qian-Lin; Zou, Wen-Tian; Huang, Run-Kun; Wang, Qi; Duan, Xiao-Xuan

    2015-03-21

    The elucidation of chemical reactions occurring on composite systems (e.g., copper (Cu)/zincite (ZnO)) from first principles is a challenging task because of their very large sizes and complicated equilibrium geometries. By combining the density functional theory plus U (DFT + U) method with microkinetic modeling, the present study has investigated the role of the phase boundary in CO2 hydrogenation to methanol over Cu/ZnO. The absence of hydrogenation locations created by the interface between the two catalyst components was revealed based on the calculated turnover frequency under realistic conditions, in which the importance of interfacial copper to provide spillover hydrogen for remote Cu(111) sites was stressed. Coupled with the fact that methanol production on the binary catalyst was recently believed to predominantly involve the bulk metallic surface, the spillover of interface hydrogen atoms onto Cu(111) facets facilitates the production process. The cooperative influence of the two different kinds of copper sites can be rationalized applying the Brönsted-Evans-Polanyi (BEP) relationship and allows us to find that the catalytic activity of ZnO-supported Cu catalysts is of volcano type with decrease in the particle size. Our results here may have useful implications in the future design of new Cu/ZnO-based materials for CO2 transformation to methanol.

  12. QSPR Studies on lgKow and lgKoc of Fluorobenzenes and Property Parameters Based on HF and DFT Calculations

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xing-Chuan; YU Jing; WANG Zun-Yao; LIU Hong-Xia

    2006-01-01

    Quantum chemistry parameters of 22 fluorobenzenes were computed at six levels using Hartree-Fock and DFT methods. Based on the experimental data of n-octanol/water partition coefficient (lgKow), a three-parameter (dipole moments (μ), zero point energy (ZPE) and free energy (G°)) quantitative correlation equation that can predict lgKow was developed using structural and thermodynamic parameters as theoretical descriptors. Similarly, based on experimental data of soil organic carbon sorption coefficient (lgKoc), the other three-parameter (the most negative atomic net charge of molecule (q-), dipole moments (μ) and molecular volume (Vi)) quantitative correlation equation that can predict lgKoc was given. Quantitative correlation equations based on B3LYP/6-311G** calculation were validated by VIF (variance inflation factors) and t-test and used to predict lgKow and lgKoc of a series of compounds. The result showed that the correlation and prediction ability of lgKoc equations based on three levels of HF/STO-3G, B3LYP/6-31G* and B3LYP/6-311G** are all more advantageous than those based on AM1.

  13. Tracking Co(I) Intermediate in operando in Photocatalytic Hydrogen Evolution by X-ray transient Absorption Spectroscopy and DFT Calculation

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhi-Jun; Zhan, Fei; Xiao, Hongyan; Zhang, Xiaoyi; Kong, Qing-Yu; Fan, Xiang-Bing; Liu, Wen-Qiang; Huang, Mao-Yong; Huang, Cheng; Gao, Yu-Ji; Li, Xu-Bing; Meng, Qing-Yuan; Feng, Ke; Chen, Bin; Tung, Chen-Ho; Zhao, Hai-Feng; Tao, Ye; Wu, Li-Zhu

    2016-12-07

    X-ray transient absorption spectroscopy (XTA) and optical transient spectroscopy (OTA) were used to probe the Co(I) intermediate generated in situ from an aqueous photocatalytic hydrogen evolution system, with [RuII(bpy)3]Cl2·6H2O as the photosensitizer, ascorbic acid/ascorbate as the electron donor, and the Co-polypyridyl complex ([CoII(DPABpy) Cl]Cl) as the pre-catalyst. Upon exposure to light, the XTA measured at Co K-edge visualizes the grow and decay of the Co(I) intermediate, and reveals its Co-N bond contraction of 0.09 ± 0.03 Å. Density functional theory (DFT) calculations support the bond contraction and illustrate that the metal-to-ligand π back-bonding greatly stabilizes the penta-coordinated Co(I) intermediate, which provides easy photon access. To the best of our knowledge, this is the first example of capturing the penta-coordinated Co(I) intermediate in operando with bond contraction by XTA, thereby providing new insights for fundamental understanding of structure– function relationship of cobalt-based molecular catalysts.

  14. Advanced Photoemission Spectroscopy Investigations Correlated with DFT Calculations on the Self-Assembly of 2D Metal Organic Frameworks Nano Thin Films.

    Science.gov (United States)

    Elzein, Radwan; Chang, Chun-Min; Ponomareva, Inna; Gao, Wen-Yang; Ma, Shengqian; Schlaf, Rudy

    2016-11-16

    Metal-organic frameworks (MOFs) deposited from solution have the potential to form 2-dimensional supramolecular thin films suitable for molecular electronic applications. However, the main challenges lie in achieving selective attachment to the substrate surface, and the integration of organic conductive ligands into the MOF structure to achieve conductivity. The presented results demonstrate that photoemission spectroscopy combined with preparation in a system-attached glovebox can be used to characterize the electronic structure of such systems. The presented results demonstrate that porphyrin-based 2D MOF structures can be produced and that they exhibit similar electronic structure to that of corresponding conventional porphyrin thin films. Porphyrin MOF multilayer thin films were grown on Au substrates prefunctionalized with 4-mercaptopyridine (MP) via incubation in a glovebox, which was connected to an ultrahigh vacuum system outfitted with photoelectron spectroscopy. The thin film growth process was carried out in several sequential steps. In between individual steps the surface was characterized by photoemission spectroscopy to determine the valence bands and evaluate the growth mode of the film. A comprehensive evaluation of X-ray photoemission spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and inverse photoemission spectroscopy (IPES) data was performed and correlated with density functional theory (DFT) calculations of the density of states (DOS) of the films involved to yield the molecular-level insights into the growth and the electronic properties of MOF-based 2D thin films.

  15. Reversible Polymorphism, Liquid Crystallinity, and Stimuli-Responsive Luminescence in a Bola-amphiphilic π-System: Structure-Property Correlations Through Nanoindentation and DFT Calculations.

    Science.gov (United States)

    Roy, Syamantak; Hazra, Arpan; Bandyopadhyay, Arkamita; Raut, Devraj; Madhuri, P Lakshmi; Rao, D S Shankar; Ramamurty, Upadrasta; Pati, Swapan Kumar; Krishna Prasad, S; Maji, Tapas Kumar

    2016-10-03

    We report the design, synthesis, detailed characterization, and analysis of a new multifunctional π-conjugated bola-amphiphilic chromophore: oligo-(p-phenyleneethynylene)dicarboxylic acid with dialkoxyoctadecyl side chains (OPE-C18-1). OPE-C18-1 shows two polymorphs at 123 K (OPE-C18-1') and 373 K (OPE-C18-1″), whose crystal structures were characterized via single crystal X-ray diffraction. OPE-C18-1 also exhibits thermotropic liquid crystalline property revealing a columnar phase. The inherent π-conjugation of OPE-C18-1 imparts luminescence to the system. Photoluminescence measurements on the mesophase also reveal similar luminescence as in the crystalline state. Additionally, OPE-C18-1 shows mechano-hypsochromic luminescence behavior. Density functional theory (DFT)-based calculations unravel the origins behind the simultaneous existence of all these properties. Nanoindentation experiments on the single crystal reveal its mechanical strength and accurately correlate the molecular arrangement with the liquid crystalline and mechanochromic luminescence behavior.

  16. A unique manganese (II) complex of 4-methoxy-pyridine-2-carboxylate: Synthesis, crystal structure, FT-IR and UV-Vis spectra and DFT calculations

    Science.gov (United States)

    Tamer, Ömer

    2017-09-01

    The first metal complex of 4-Methoxy-pyridine-2-carboxylic acid, [Mn(4-mpic)2(H2O)2], has been synthesized, and its crystal structure has been determined by X-Ray diffraction method. The FT-IR spectrum for [Mn(4-mpic)2(H2O)2] complex has been presented in this paper, as compared with that of single 4-mpic ligand. The electronic absorption spectrum recorded in DMSO solvent revealed that the ligand metal charge transfer (LMCT) interactions occur in Mn(II) complex. In order to support experimental results, density functional theory (DFT) calculations have been also carried out with the hybrid B3LYP functional. The coordination sphere of central Mn(II) ion has been evaluated by using the hyperconjugative interactions between the lone pair electrons of metal and donor atoms (N and O). The natural charge of Mn(II) ion demonstrated that the electronic transitions from metal ion to 4-mpic are higher than those in reverse direction. The carboxylate group has been determined as the most reactive side of Mn(II) complex in chemical reactions. A comparison among Mulliken, NBO and APT charges has been carried out for Mn(II) complex system. The first static hyperpolarizability parameter for Mn(II) complex has been also investigated by using B3LYP level.

  17. A new mixed-ligand copper(II) complex of (E)-N";-(2-hydroxybenzylidene) acetohydrazide: Synthesis, characterization, NLO behavior, DFT calculation and biological activities

    Science.gov (United States)

    Yousef Ebrahimipour, S.; Sheikhshoaie, Iran; Crochet, Aurelien; Khaleghi, Moj; Fromm, Katharina M.

    2014-08-01

    A tridentate hydrazone Schiff base ligand, (E)-N";-(2-hydroxybenzylidene)acetohydrazide [HL], and its mixed-ligand Cu(II) complex [CuL(phen)], have been synthesized and characterized by elemental analyses, FT-IR, molar conductivity, UV-Vis spectroscopy. The structure of the complex has been determined by X-ray diffraction. This complex has square pyramidal geometry and the positions around central atom are occupied with donor atoms of Schiff base ligand and two nitrogens of 1,10-phenanthroline. Computational studies of compounds were performed by using DFT calculations. The linear polarizabilities and first hyperpolarizabilities of the studied molecules indicate that these compounds can be good candidates of nonlinear optical materials. It is in accordance with experimental data. In addition, invitro antimicrobial results show that these compounds specially [CuL(phen)] have great potential of antibacterial activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Listeria monocytogenes bacteria and antifungal activity against Candida Albicans in comparison to some standard drugs.

  18. Synthesis, Characterization and DFT Calculation of a New Silver(Ⅰ) Iodide Templated by Conjugated Cation: (ipq)4Ag4I8

    Institute of Scientific and Technical Information of China (English)

    XIAO Guang-Can

    2006-01-01

    A silver iodide, (ipq)4Ag4I8 1, has been synthesized in the presence of ipq (ipq =N-(isopentyl)-quinolinium) acting as a structure-directing reagent (SDA). Compound 1 crystallizes in the triclinic system, space group Pī, with a = 9.850(2), b = 11.564(2), c = 16.111(3) (A), α =104.64(3), β = 105.73(3), γ = 94.37(3)°, V= 1688.3(7) (A)3, Z = 2, Dc= 2.205 g/cm3, F(000) = 1042,C28H33Ag2I4N2, Mr= 1120.90,μ(MoKα) = 4.836 mm-1, the final R = 0.0363 and wR = 0.0761 for 5465 observed reflections with I > 2σ(Ⅰ). 1 consists of uncoordinated structure-directing molecule and inorganic moiety tuned by organic SDA. Tetrameric Ag4I84- anion in 1 is composed of edgesharing AgI4 tetrahedra and AgI3 planar triangles. Electrostatic interaction between organic counter cations and inorganic moieties is present and contributes to the crystal packing. 1 was further characterized with IR, UV-Vis, elemental analysis and cyclic voltammetry. Based on the crystal structure data, quantum chemical calculation with DFT method was used to reveal the electronic structure and optical property of 1.

  19. Understanding atomic-resolved STM images on TiO{sub 2}(110)-(1 x 1) surface by DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Sanchez, C; Gonzalez, C; Mendez, J; De Andres, P L; MartIn-Gago, J A; Lopez, M F [Instituto Ciencia de Materiales de Madrid (CSIC), C/Sor Juana Ines de la Cruz 3, 28049-Madrid (Spain); Jelinek, P, E-mail: mflopez@icmm.csic.es [Institute of Physics, Czech Academy of Sciences, Cukrovarnicka 10, 162 53-Prague (Czech Republic)

    2010-10-08

    We present a combination of experimental STM images and DFT calculations to understand the atomic scale contrast of features found in high-resolution STM images. Simulating different plausible structural models for the tip, we have been able to reproduce various characteristics previously reported in experimental images on TiO{sub 2}(110)-(1 x 1) under controlled UHV conditions. Our results allow us to determine the influence of different chemical and morphological tip terminations on the atomic-resolution STM images of the TiO{sub 2}(110)-(1 x 1) surface. The commonest images have been properly explained using standard models for a W tip, either clean or with a single O atom located at the apex. Furthermore, a double transfer of oxygen atoms can account for different types of bizarre atomic-resolution features occasionally seen, and not conclusively interpreted before. Importantly, we discuss how typical point-defects are imaged on this surface by different tips, namely bridging O vacancies and adsorbed OH groups.

  20. Ammonia-Containing Species Formed in Cu-Chabazite As Per In Situ EPR, Solid-State NMR, and DFT Calculations.

    Science.gov (United States)

    Moreno-González, Marta; Hueso, Beatriz; Boronat, Mercedes; Blasco, Teresa; Corma, Avelino

    2015-03-19

    Nowadays, the most attractive technology for the elimination of nitric oxides from the exhaust gas of diesel vehicles is the selective catalytic reduction with ammonia (NH3-SCR-NOx) using Cu zeolite with the chabazite structure as the catalyst. Isolated copper species are the active sites, but the reaction intermediates and the overall reaction mechanism are still under debate. Here, we study the interaction of ammonia with zeolite Cu-SSZ-13 (CHA topology) with a uniform distribution of Cu(2+) sites prepared in one pot and a conventional Cu-ZSM-5 (MFI topology) for comparison. In situ EPR and solid-state NMR spectroscopies combined with DFT calculations have allowed the identification of NH4(+), [Cu(NH3)5](2+), [Cu(Of)2(NH3)2](2+), [Cu(Of)3NH3](2+), [Cu(NH3)2](+), and [CuOf(NH3)](+) (Of being framework oxygen) under different conditions. The results demonstrate that ammonia is able to reduce Cu(2+) to Cu(+) and provide new information on the species formed in Cu-SSZ-13, which have important implications for the elucidation of the SCR reaction mechanism.

  1. Study of behaviour of Ni(III) macrocyclic complexes in acidic aqueous medium through kinetic measurement involving hydrogen peroxide oxidation and DFT calculations

    Indian Academy of Sciences (India)

    ANURADHA SANKARAN; E J PADMA MALAR; VENKATAPURAM RAMANUJAM VIJAYARAGHAVAN

    2017-02-01

    The Cu(II) ion-catalysed kinetics of oxidation of H ₂O ₂ by [NiIIIL] [where L = L₁ (cyclam) and L ₂ (1,8-bis(2-hydroxyethyl)-1,3,6,8,10,13-hexaazacyclotetradecane)] was studied in the pH range of 3.6–5.6 in acetic acid-acetate buffer medium at 25◦C in the presence of sulphate ion. The ionic strength (I) was maintained at 0.5 M (NaClO₄). The rate constants showed an inverse acid dependence and [NiIIIL ₂] was observed to be more stable than [NiIIIL₁]. The rate of the reaction of both complexes with hydrogen peroxide shows contrastingbehaviour at pH > 2.5 when compared to the same reaction in perchloric acid medium. DFT calculations performed on the complexes [NiIIIL₁ (SO₄)(OAc)] and [NiIIIL ₂ (SO₄)(OAc)] reveal that both the acetate and sulphate ligands are axially coordinated to the metal centre. In addition, there is strong hydrogen bonding between the axial ligand and NH hydrogen of the macrocyclic ligand. The computed covalent bond ordersin the aqueous medium predict that the acetate forms stronger coordinate bond with Ni ion than the sulphate ligand. The hydroxyl group present in one of the pendant groups of L ₂ forms a strong hydrogen bond with thesulphate ligand which leads to additional stability in [NiIIIL ₂ (SO₄)(OAc)].

  2. Structural determination of stable MoO{sub x} monolayers on O/Cu{sub 3}Au(1 0 0): DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Valadares, George C.S., E-mail: georgevaladares@if.ufrj.br [Instituto de Fisica, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, Rio de Janeiro, RJ 21941-972 (Brazil); Mendes, F.M.T. [Divisao de Metrologia de Materiais (DIMAT), Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial (Inmetro), CEP 25250-020, Xerem, Duque de Caxias, RJ (Brazil); Instituto Nacional de Tecnologia, Av. Venezuela 82, Centro, Rio de Janeiro, RJ 20081-312 (Brazil); Dionizio Moreira, M. [Divisao de Metrologia de Materiais (DIMAT), Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial (Inmetro), CEP 25250-020, Xerem, Duque de Caxias, RJ (Brazil); Universidade Federal do Triangulo Mineiro, Instituto de Ciencias Exatas, Naturais e Educacao, Av. Getulio Guarita, 159, Bairro Abadia, CEP.: 38025-180, Uberaba, MG (Brazil); Leitao, A.A. [Departamento de Quimica, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-330 (Brazil); Niehus, H. [Divisao de Metrologia de Materiais (DIMAT), Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial (Inmetro), CEP 25250-020, Xerem, Duque de Caxias, RJ (Brazil); Institut fuer Physik, Humboldt Universitaet zu Berlin, Newtonstrasse 15, Berlin 12489 (Germany); and others

    2012-10-08

    Highlights: Black-Right-Pointing-Pointer Molybdenum oxide is widely used in catalysis in the chemical industry. Black-Right-Pointing-Pointer Recently, ultra-thin (monolayer) films of MoO{sub x} have been produced on top of O-Cu{sub 3}Au substrates. Black-Right-Pointing-Pointer XPS measurements suggest an unusual +5 charge state of the Mo cation. Black-Right-Pointing-Pointer Seeking for a low-energy structure with good match to the experimental STM and XPS. Black-Right-Pointing-Pointer Bader charges indicate indeed an intermediate charge state as compared to the more common Mo{sup +4}O{sub 2} and Mo{sup +6}O{sub 3} bulk oxides. -- Abstract: Using ab initio calculations based on density functional theory (DFT), we propose a geometrical structure for MoO{sub x} monolayers recently grown on O/Cu{sub 3}Au(1 0 0) substrates. The proposed structure reproduces the p(2 Multiplication-Sign 2) symmetry found by scanning tunneling microscopy (STM) and low-energy electron diffraction (LEED), as well as the intermediate oxidation state between Mo(IV) and Mo(VI) identified by X-ray photoelectron spectroscopy (XPS). Simulated STM images assign the bright spots in the experimental images to oxygen 2p states.

  3. Synthesis, spectroscopic, thermal and DFT calculations of 2-(3-amino-2-hydrazono-4-oxothiazolidin-5-yl) acetic acid binuclear metal complexes.

    Science.gov (United States)

    Hassan, Walid M I; Badawy, M A; Mohamed, Gehad G; Moustafa, H; Elramly, Salwa

    2013-07-01

    The binuclear complexes of 2-(3-amino-2-hydrazono-4-oxothiazolidin-5-yl) acetic acid ligand (HL) with Fe(III), Co(II), Ni(II), Cu(II) and Zn(II) ions were prepared and their stoichiometry was determined by elemental analysis. The stereochemistry of the studied series of metal complexes was established by analyzing their infrared, (1)H NMR spectra and the magnetic moment measurements. According to the elemental analysis data, the complexes were found to have the formulae [Fe2L(H2O)8]Cl5 and [M2L(H2O)8]Cl3 (M=Co(II), Ni(II), Cu(II) and Zn(II)). The present analyses demonstrate that all metal ions coordinated to the ligand via O(9), O(11), N(16) and N(18) atoms. Thermal decomposition studies of the ligand-metal complexes have been performed to verify the status of water molecules present in these metal complexes and their general decomposition pattern. Density Functional Theory (DFT) calculations at the B3LYP/6-31G(*) level of theory have been carried out to investigate the equilibrium geometry of the ligand and complexes. Moreover, charge density distribution, extent of distortion from regular geometry, dipole moment and orientation have been performed and discussed.

  4. Analysis of the [CuL n ]2+ and [CuG n ]2+ ( n = 2-4) complex structures: Comparison with CID experiment and DFT calculation

    Science.gov (United States)

    Zhang, Shuqin; Liu, Hai; Cheng, Ping; Ren, Dajun; Gong, Xiangyi

    2016-12-01

    The collision-induced dissociation (CID) of the copper-cytidine complex [CuL n ]2+ (L is cytidine, n = 2-4) shows that the inter-ligand proton transfer (PT) is the dominating process. This is quite different from the CID of copper-guanosine complex [CuG n ]2+ (G is guanosine, n = 2-4), in which the inter-electron transfer (ET) dominates. The possible structures and zero-point energies for the majority of these structures were calculated using density functional theory (DFT) methods, and the Δ G Gibbs energy analysis of the CID processes also demonstrated the difference between the two complex structures. The results show that the steric hindrance effects and the intermolecular hydrogen bonds are the main reasons that cause the coordination between Cu(II) and the ligands of the cytidine and guanosine molecule. Cu(II) coordinates 4 ligands for [CuL n ]2+, forming the primary order sphere and presenting non-covalent bonding of the ligands. A greater steric effect was observed in the purine ring, which could be unstable if the guanosine molecules distributed around the copper ions to form coordination compounds. The [CuG n ]2+ complex tends to form intermolecular hydrogen bonds to enhance its structural stability by amino N and carbonyl O of purine ring.

  5. Synthesis, spectroscopic characterization and DFT calculations of monohydroxyalkylated derivatives of 1-phenyl-2H,6H-imidazo[1,5-c]quinazoline-3,5-dione

    Science.gov (United States)

    Szyszkowska, Agnieszka; Hęclik, Karol; Trzybiński, Damian; Woźniak, Krzysztof; Klasek, Antonin; Zarzyka, Iwona

    2017-01-01

    Synthesis of new derivatives with an imidazo[1,5-c]quinazoline-3,5-dione ring has been presented. Two new alcohols with the imidazo[1,5-c]quinazoline-3,5-dione ring were obtained and characterized by spectral (1H, 13C NMR, IR and UV) and crystallography methods. A reaction chemoselectivity has been observed with a formation of monohydroxyalkyl derivatives of 1-phenyl-2H,6H-imidazo[1,5-c]quinazoline-3,5-dione substituted at the 2. nitrogen atom. The absence of derivatives substituted at the 6. nitrogen atom was proven experimentally. The synthesis with chemoselectivity over 99% without control of the substituent effect happens very rarely. The HOMO-LUMO mappings are reported which reveals the different charge transfer possibilities within the molecule of 1-phenyl-2H,6H-imidazo[1,5-c]quinazoline-3,5-dione in the region of the 2. and the 6. nitrogen atoms. Quantum-mechanical DFT calculations proved to be very useful to explain the reason of selectivity reaction of 1-phenyl-2H,6H-imidazo[1,5-c]quinazoline-3,5-dione with oxiranes.

  6. Synthesis, growth, optical and DFT calculation of 2-naphthol derived Mannich base organic non linear optical single crystal for frequency conversion applications

    Science.gov (United States)

    Raj, A. Dennis; Jeeva, M.; Shankar, M.; Purusothaman, R.; Prabhu, G. Venkatesa; Potheher, I. Vetha

    2016-11-01

    2-naphthol derived Mannich base 1-((4-methylpiperazin-1-yl) (phenyl) methyl) naphthalen-2-ol (MPN) - a nonlinear optical single crystal was synthesized and successfully grown by slow evaporation technique at room temperature. The molecular structure was confirmed by single crystal XRD, FT-IR, 1H NMR and 13C NMR spectral studies. The single crystal X-ray diffraction analysis reveals that the crystal belongs to orthorhombic crystal system with non-centrosymmetric space group Pna21. The chemical shift of 5.34 ppm (singlet methine CH proton) in 1H NMR and signal for the CH carbon around δ70.169 ppm in 13C NMR confirms the formation of the title compound. The crystal growth pattern and dislocations of crystal are analyzed using chemical etching technique. UV cut off wavelength of the material was found to be 212 nm. The second harmonic generation (SHG) of MPN was determined from Kurtz Perry powder technique and the efficiency is almost equal to that of standard KDP crystal. The laser damage threshold was measured by passing Nd: YAG laser beam through the sample and it was found to be 1.1974 GW/cm2. The material was thermally stable up to 142 °C. The relationship between the molecular structure and the optical properties was also studied from quantum chemical calculations using Density Functional Theory (DFT) and reported for the first time.

  7. Synthesis and characterization of a new zinc(II) complex with tetradentate azo-thioether ligand: X-ray structure, DNA binding study and DFT calculation

    Science.gov (United States)

    Mondal, Apurba Sau; Pramanik, Ajoy Kumar; Patra, Lakshman; Manna, Chandan Kumar; Mondal, Tapan Kumar

    2017-10-01

    A new zinc(II) complex, [Zn(L)(H2O)](ClO4) (1) with azo-thioether containing NSNO donor ligand, 3-(2-(2-((pyridin-2-ylmethyl)thio)phenyl)hydrazono)pentane-2,4-dione (HL) is synthesized and characterized by several spectroscopic techniques. The distorted square based pyramidal (DSBP) geometry is confirmed by single crystal X-ray structure. The ability of the complex to bind with CT DNA is investigated by UV-vis method and the binding constant is found to be 4.16 × 104 M-1. Competitive binding study with ethidium bromide (EB) by fluorescence method suggests that the zinc(II) complex efficiently displaces EB from EB-DNA. The Stern-Volmer dynamic quenching constant, Ksv is found to be 1.2 × 104 M-1. Theoretical calculations by DFT and TDDFT/CPCM methods are used to interpret the electronic structure and UV-vis spectrum of the complex.

  8. Synthesis, electronic structure investigation of 3-pentyl-2,6-di(furan-2-yl)piperidin-4-one by FT-IR, FT-Raman and UV-Visible spectral studies and ab initio/DFT calculations.

    Science.gov (United States)

    Arockia Doss, M; Savithiri, S; Rajarajan, G; Thanikachalam, V; Anbuselvan, C

    2015-12-05

    FT-IR and FT-Raman spectra of 3-pentyl-2,6-di(furan-2-yl) piperidin-4-one (3-PFPO) were recorded in the solid phase. The structural and spectroscopic analyses of 3-PFPO were made by using B3LYP/HF level with 6-311++G(d, p) basis set. The fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Comparison of the observed fundamental vibrational frequencies of 3-PFPO with calculated results by HF and DFT methods indicates that B3LYP is superior to HF method for molecular vibrational problems. The electronic properties such as excitation energies, oscillator strength, wavelengths and HOMO-LUMO energies were obtained by time-dependent DFT (TD-DFT) approach. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The hyperconjugative interaction energy (E((2))) and electron densities of donor (i) and acceptor (j) bonds were calculated using NBO analysis. In addition, MEP and atomic charges of carbon, nitrogen, oxygen and hydrogen were calculated using B3LYP/6-311++G(d, p) level theory. Moreover, thermodynamic properties (heat capacities, entropy and enthalpy) of the title compound at different temperatures were calculated in gas phase. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. New insights into the origin of visible-light photocatalytic activity in Se-modified anatase TiO2 from screened coulomb hybrid DFT calculations

    KAUST Repository

    Harb, Moussab

    2013-12-05

    We report a systematic study on the optoelectronic properties of Se-modified anatase TiO2 investigated by DFT (including the perturbation theory approach DFPT) within the screened coulomb hybrid HSE06 formalism to guarantee accurate band gap and electronic excitation predictions. Various selenium species at substitutional sites for O or Ti, at interstitial sites, as well as at mixed substitutional/interstitial sites are studied. Among the explored structures, Ti(1-2x)O2Se2x (containing Se4+ species), TiO(2-x)Sex (containing Se2- species), and TiO(2-x)Se2x (containing Se2 2- species) reveal significant enhanced visible-light optical absorption spectra with new absorption features appearing at 500, 600, and 690 nm, respectively. Our calculated spectra are found to be in good agreement with those obtained in available experimental works. The band gap narrowing in these materials originates from incorporation of newly occupied electronic levels within 0.5-1.5 eV above the original valence band of TiO 2, leading to new narrowed band gaps of 2.5, 2.0, and 1.8 eV respectively. Our calculations also reveal suitable band positions of Ti (1-2x)O2Se2x and TiO(2-x)Se x for overall water splitting, whereas TiO(2-x)Se 2x shows an unsuitable valence band position for the oxygen evolution reaction. In contrast, the localized electronic character of the new occupied states on the Se 4p orbitals and only on the O 2p orbitals linked to the Se species makes the holes mobility limited in this material and the recombination rate of charge carriers greatly increased in the bulk. © 2013 American Chemical Society.

  10. Conformational stability, spectral analysis (infrared, Raman and NMR) and DFT calculations of 2-Amino-5-(ethylthio)-1,3,4-thiadiazole

    Science.gov (United States)

    Mohamed, Tarek A.; Hassan, Ahmed E.; Shaaban, Ibrahim A.; Abuelela, Ahmed M.; Zoghaib, Wajdi M.

    2017-02-01

    The infrared (4000-225 cm-1) and Raman (3500-60 cm-1) spectra of 2-Amino-5-(ethylthio)-1,3,4-thiadiazole (AEST; C4H7N3S2) have been recorded in the solid phase. In addition, the 1H and 13C NMR spectra of AEST were obtained in DMSO-d6. We have focused on five staggered conformers (1-5) resulting from rotations of the methyl, ethyl and thioethyl groups around Csbnd C and Csbnd S bonds with the sbnd NH2 group having a non-planar (sp3) geometry. DFT-B3LYP/6-31G(d) calculations proved that only conformers 4 and 5 produce real vibrational frequencies and conformer 5 is the favored one with an energy difference of 124 cm-1 (0.35 kcal/mol) in agreement with the observed ethyl torsion at 92 cm-1. The calculated frequencies, infrared intensities, Raman activities and potential energy distributions were compiled with spectral observations in favor of conformer 5. All vibrational modes were assigned to their corresponding vibrational bands. Applying the observed methyl torsions, the kinetic parameter F number was found to be 5.3263 cm-1 and an average V3 value of 1565 ± 14 cm-1 (4.48 ± 0.04 kcal/mol) was obtained. These values are close to the methyl barriers predicted from B3LYP/6-31G(d) potential surface scans. Moreover, the 1H and 13C NMR chemical shifts were also estimated for conformers 4 and 5 with DMSO as solvent implementing GIAO/PCM approximation utilizing B3LYP method at 6-311++G (d,p) basis set. The results are reported and discussed herein and compared with 2-Amino-5-ethyl-1,3,4-thiadiazole (AET) whenever appropriate.

  11. Vibrations and reorientations of NH3 molecules in [Mn(NH3)6](ClO4)2 studied by infrared spectroscopy and theoretical (DFT) calculations.

    Science.gov (United States)

    Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward

    2015-02-05

    The vibrational and reorientational motions of NH3 ligands and ClO4(-) anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385cm(-1), associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR≈10(-12)-10(-13)s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5kJmol(-1), in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TC(c)=137.6K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6](2+) cation and ClO4(-) anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Chiral vanadium(V) complexes with 2-aminoglucose Schiff-base ligands and their solution configurations: synthesis, structures, and DFT calculations.

    Science.gov (United States)

    Mohammadnezhad, Gholamhossein; Böhme, Michael; Geibig, Daniel; Burkhardt, Anja; Görls, Helmar; Plass, Winfried

    2013-09-01

    two diastereomers are observed for the carbon atoms C2 (2 ppm) and C3 (4 ppm). DFT calculations of the NMR chemical shift parameters have been performed which are in good agreement with the experimental data. Moreover, the isomerization mechanism between the diastereomers is analysed on the basis of DFT calculations which indicate the required presence of methanol molecules as protic donors.

  13. Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion

    Science.gov (United States)

    Singh, R.; Yadav, R. A.

    2014-09-01

    Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5sbnd C6 bond length increases and loses its double bond character while the C4sbnd C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled Nsbnd H stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled.

  14. Spin-transfer pathways in paramagnetic lithium transition-metal phosphates from combined broadband isotropic solid-state MAS NMR spectroscopy and DFT calculations.

    Science.gov (United States)

    Clément, Raphaële J; Pell, Andrew J; Middlemiss, Derek S; Strobridge, Fiona C; Miller, Joel K; Whittingham, M Stanley; Emsley, Lyndon; Grey, Clare P; Pintacuda, Guido

    2012-10-17

    Substituted lithium transition-metal (TM) phosphate LiFe(x)Mn(1-x)PO(4) materials with olivine-type structures are among the most promising next generation lithium ion battery cathodes. However, a complete atomic-level description of the structure of such phases is not yet available. Here, a combined experimental and theoretical approach to the detailed assignment of the (31)P NMR spectra of the LiFe(x)Mn(1-x)PO(4) (x = 0, 0.25, 0.5, 0.75, 1) pure and mixed TM phosphates is developed and applied. Key to the present work is the development of a new NMR experiment enabling the characterization of complex paramagnetic materials via the complete separation of the individual isotropic chemical shifts, along with solid-state hybrid DFT calculations providing the separate hyperfine contributions of all distinct Mn-O-P and Fe-O-P bond pathways. The NMR experiment, referred to as aMAT, makes use of short high-powered adiabatic pulses (SHAPs), which can achieve 100% inversion over a range of isotropic shifts on the order of 1 MHz and with anisotropies greater than 100 kHz. In addition to complete spectral assignments of the mixed phases, the present study provides a detailed insight into the differences in electronic structure driving the variations in hyperfine parameters across the range of materials. A simple model delimiting the effects of distortions due to Mn/Fe substitution is also proposed and applied. The combined approach has clear future applications to TM-bearing battery cathode phases in particular and for the understanding of complex paramagnetic phases in general.

  15. Identifying systematic DFT errors in catalytic reactions

    DEFF Research Database (Denmark)

    Christensen, Rune; Hansen, Heine Anton; Vegge, Tejs

    2015-01-01

    Using CO2 reduction reactions as examples, we present a widely applicable method for identifying the main source of errors in density functional theory (DFT) calculations. The method has broad applications for error correction in DFT calculations in general, as it relies on the dependence...

  16. 同时计算实序列的DFT和实序列的DFT的IDFT的新公式%The New Formulas of Simultaneously Calculating DFT of Real Sequence and IDFT of the DFT of Real Sequence

    Institute of Scientific and Technical Information of China (English)

    范安东

    2008-01-01

    通过对离散傅里叶变换(DFT)的一些性质的分析,利用DFT的对称性和将一个复序列分解为4个奇偶序列之和的方法,改正了Gunther关于直接计算双实序列的DFT和实序列的DFT和逆离散傅里叶变换(IDFT)的公式中的少数错误,给出了新的同时计算实序列的DFT和实序列的DFT的IDFT的直接公式,并给出了证明.

  17. Solvation structure and thermodynamics for Pr(III), Nd(III) and Dy(III) complexes in ionic liquids evaluated by Raman spectroscopy and DFT calculation

    Science.gov (United States)

    Kuribara, Keita; Matsumiya, Masahiko; Tsunashima, Katsuhiko

    2016-12-01

    The coordination states of trivalent praseodymium, neodymium, and dysprosium complexes in the ionic liquid, triethyl-n-pentylphosphonium bis(trifluoromethyl-sulfonyl) amide ([P2225][TFSA]) were investigated by Raman spectroscopy. The effect of the concentration of rare earth ions on the Raman spectra was investigated, ranging from 0.23 to 0.45 mol kg-1 of Pr(III), Nd(III), and Dy(III) in [P2225][TFSA]. Based on a conventional analysis, the solvation numbers, n, of Pr(III), Nd(III), and Dy(III) in [P2225][TFSA] were determined to be 4.99, 5.01, and 5.00 at 298 K and 5.04, 5.06, and 5.07 at 373 K, respectively. Thermodynamic properties such as ΔisoG, ΔisoH, and ΔisoS for the isomerism of [TFSA]- from trans- to cis-coordinated isomer in the bulk and the first solvation sphere of the central RE3+ (RE = Pr, Nd, and Dy) cation in [P2225][TFSA] were evaluated from the temperature dependence of the Raman bands, measured at temperatures ranging from 298 to 398 K. Regarding the bulk properties, ΔisoG(bulk), ΔisoH(bulk), and TΔisoS(bulk) at 298 K were found to be -1.06, 6.86, and 7.92 kJ mol-1, respectively. The trans-[TFSA]- was a dominant contributor to the enthalpy, as shown by the positive value of ΔisoH(bulk). The value of TΔisoS(bulk) was slightly larger than that of ΔisoH(bulk), and cis-[TFSA]- was, therefore, entropy-controlled in [P2225][TFSA]. In contrast, in the first solvation sphere of the RE3+ cation, ΔisoH(RE) became remarkably negative, suggesting that cis-[TFSA]- isomers were stabilized by enthalpic contributions. Furthermore, ΔisoH(RE) contributed to the remarkable decrease in ΔisoG(RE), and this result clearly indicates that cis-[TFSA]- conformers bound to RE3+ cations are the preferred coordination state of [RE(III)(cis-TFSA)5]2- in [P2225][TFSA]. Moreover, optimized geometries and binding energies of [Pr(III)(cis-TFSA)5]2-, [Nd(III)(cis-TFSA)5]2-, and [Dy(III)(cis-TFSA)5]2- clusters were also investigated by DFT calculations using the ADF

  18. Isomeros de Valencia del Benceno

    OpenAIRE

    Mata Jiménez, Alfonso

    2015-01-01

    Durante la mitad del siglo pasado se propusieron algunas hipótesis sobre la estructura del benceno. La mas importante fue Ia propuesta por Kekule en 1865, ya que fue la que reprodujo mejor, teórica y experimentalmente, sus propiedades (2).

  19. Synthesis, molecular structure and vibrational analysis of D-D-A based carbazole decorated phenothiazine-3-carbaldehyde: Experimental (FT-IR, UV and NMR) and density functional theory (DFT) calculations

    Science.gov (United States)

    Karuppasamy, Ayyanar; Gokula Krishnan, Kannan; Pillai Velayutham Pillai, Muthiah; Ramalingan, Chennan

    2017-01-01

    A novel molecule, 10-(9-hexyl-9H-carbazol-3yl)-10H-phenothiazine-3-carbaldehyde (CZPTZA) has been synthesized and characterized through FT-IR, UV-Vis, NMR spectroscopic studies and molecular orbital calculations. Optimized geometrical structure, harmonic vibrational frequencies and NMR are computed with B3LYP method using 6-311++G (d,p) basis set. The geometrical parameters of the title compound obtained from Single Crystal XRD studies have been found in accord with the calculated (DFT) values. The experimentally observed vibrational frequencies are compared with the calculated ones, which were found to be in good agreement with each other. UV-Vis spectra of the title compound have also been recorded and the electronic properties, viz. excitation energies, calculated energies, oscillator strengths, frontier orbital energies and band gap energies are computed with TD-DFT/CAM-B3LYP method using 6-311++G (d,p) as the basis set. The 1H and 13C NMR chemical shifts of the molecule have been calculated by the Gauge Independent Atomic Orbital (GIAO) method and compared with the experimental outcome. Also, the values of dipole moment, polarizabilities and first order hyperpolarizabilities have been computed.

  20. Investigation of C-H...O=C and N-H...OC hydrogen-bonding interactions in crystalline thymine by DFT calculations of O-17, N-14 and H-2 NQR parameters.

    Science.gov (United States)

    Mirzaei, Mahmoud; Hadipour, Nasser L; Ahmadi, Kamran

    2007-02-01

    A computational study at the level of density functional theory (DFT) was carried out to investigate C-H...O=C and N-H...O=C hydrogen-bonding interactions (HBs) in the real crystalline cluster of thymine by O-17, N-14 and H-2 calculated nuclear quadrupole resonance (NQR) parameters. To perform the calculations, a hydrogen-bonded pentameric cluster of thymine was created using X-ray coordinates where the hydrogen atoms positions are optimized and the electric field gradient (EFG) tensors were calculated for the target molecule. Additional EFG calculations were also performed for crystalline monomer and an optimized isolated gas-phase thymine. The calculated EFG tensors at the level of B3LYP and B3PW91 DFT methods and 6-311++G**and CC-pVTZ basis sets were converted to those experimentally measurable NQR parameters, quadrupole coupling constants and asymmetry parameters. The results reveal that because of strong contribution to N-H...O=C HBs, NQR parameters of O2, N1 and N3 undergo significant changes from monomer to the target molecule in cluster. Furthermore, the NQR parameters of O2 also undergo some changes because of non-classical C-H...O=C HBs.

  1. Definitive evidence for the existence of isomeric chlorophenyl radicals (C6H4Cl) from charge inversion mass spectrometry and DFT calculations

    Science.gov (United States)

    Hayakawa, Shigeo; Matsubara, Hiroshi; Kawamura, Yoshiaki; Iwamoto, Kenichi

    2007-05-01

    Free radical species are much more reactive than stable molecules, and so usually exist only as transient intermediates in chemical reactions. Charge inversion mass spectrometry using alkali metal targets is an effective method for determining the structure and dissociation processes of radicals, and can also enable differentiation between isomeric forms of compounds whose parent ions have similar mass spectra and similar collisionally activated dissociation spectra, such as the isomers of dichlorobenzene and chlorophenol. The charge inversion process using alkali metal targets proceeds via near-resonant neutralization, followed by spontaneous dissociation of the excited neutrals, and then endothermic negative ion formation. In the normalized charge inversion spectra of ortho-, meta-, and para-dichlorobenzene (C6H4Cl2) measured in this work, the intensities of the peaks associated with chlorine anions (Cl-) are almost same for each of the isomers, whereas the intensities of the peaks associated with the chlorophenyl anions (C6H4Cl-) display a strong dependence on the isomeric structure of the parent compound. The similarities of the Cl- ion peak intensities indicate that neutralization cross-sections and branching ratios to produce Cl radicals are the same for each of the isomeric precursor C6H4Cl2+ ions. The strong isomer-dependence of the peak intensities of C6H4Cl- anions suggests that the chlorophenyl radicals (C6H4Cl) formed from C6H4Cl2 by loss of Cl do not undergo isomerization, and that the electron transfer cross-sections to form the negative ions are strongly isomer-dependent. Density functional theory (DFT) calculations on the o-, m-, and p-C6H4Cl radicals show that the barriers to isomerization are in excess of 2.8 eV, and these high isomerization barriers are believed to be the reason for the absence of isomerization among the C6H4Cl radicals during the charge inversion process. Calculated adiabatic electron affinities and vertical electron affinities

  2. Influence of Exchange-Correlation Functional in the Calculations of Vertical Excitation Energies of Halogenated Copper Phthalocyanines using Time-Dependent Density Functional Theory (TD-DFT)

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sang Uck [Univ. of Ulsan, Ulsan (Korea, Republic of)

    2013-08-15

    The accurate prediction of vertical excitation energies is very important for the development of new materials in the dye and pigment industry. A time-dependent density functional theory (TD-DFT) approach coupled with 22 different exchange-correlation functionals was used for the prediction of vertical excitation energies in the halogenated copper phthalocyanine molecules in order to find the most appropriate functional and to determine the accuracy of the prediction of the absorption wavelength and observed spectral shifts. Among the tested functional, B3LYP functional provides much more accurate vertical excitation energies and UV-vis spectra. Our results clearly provide a benchmark calibration of the TD-DFT method for phthalocyanine based dyes and pigments used in industry.

  3. Asymmetric NHC-catalyzed aza-Diels-Alder reactions: Highly enantioselective route to α-amino acid derivatives and DFT calculations

    KAUST Repository

    Yang, Limin

    2014-08-01

    A facile N-heterocyclic carbene catalytic enantioselective aza-Diels-Alder reaction of oxodiazenes with α-chloroaldehydes as dienophile precursors is reported, with excellent enantioselectivity (ee > 99%) and excellent yield (up to 93%). DFT study showed that cis-TSa, formed from a top face approach of oxodiazene to cis-IIa, is the most favorable transition state and is consistent with the experimental observations. © 2014 American Chemical Society.

  4. A complete vibrational study on a potential environmental toxicant agent, the 3,3',4,4'-tetrachloroazobenzene combining the FTIR, FTRaman, UV-Visible and NMR spectroscopies with DFT calculations.

    Science.gov (United States)

    Castillo, María V; Pergomet, Jorgelina L; Carnavale, Gustavo A; Davies, Lilian; Zinczuk, Juan; Brandán, Silvia A

    2015-01-05

    In this study 3,3',4,4'-tetrachloroazobenzene (TCAB) was prepared and then characterized by infrared, Raman, multidimensional nuclear magnetic resonance (NMR) and ultraviolet-visible spectroscopies. The density functional theory (DFT) together with the 6-31G(*) and 6-311++G(**) basis sets were used to study the structures and vibrational properties of the two cis and trans isomers of TCAB. The harmonic vibrational wavenumbers for the optimized geometries were calculated at the same theory levels. A complete assignment of all the observed bands in the vibrational spectra of TCAB was performed combining the DFT calculations with the scaled quantum mechanical force field (SQMFF) methodology. The molecular electrostatic potentials, atomic charges, bond orders and frontier orbitals for the two isomers of TCAB were compared and analyzed. The comparison of the theoretical ultraviolet-visible spectrum with the corresponding experimental demonstrates a good concordance while the calculated (1)H and (13)C chemicals shifts are in good conformity with the corresponding experimental NMR spectra of TCAB in solution. The npp(*) transitions for both forms were studied by natural bond orbital (NBO) while the topological properties were calculated by employing Bader's Atoms in the Molecules (AIM) theory. This study shows that the cis and trans isomers exhibit different structural and vibrational properties and absorption bands. Copyright © 2014. Published by Elsevier B.V.

  5. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

    Energy Technology Data Exchange (ETDEWEB)

    Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurelien; Blumberger, Jochen; Elstner, Marcus

    2016-10-11

    In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

  6. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level.

    Science.gov (United States)

    Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurélien; Blumberger, Jochen; Elstner, Marcus

    2016-10-11

    In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated π-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

  7. 离散傅立叶变换(DFT)计算中一些问题的论证%Some Discussion On the Calculation of the Discrete Fourier Transform(DFT)

    Institute of Scientific and Technical Information of China (English)

    钟佑明; 汤宝平; 秦树人

    2001-01-01

    在时频信号分析领域中,DFT是一个常见的术语,尤其是在它的高效算法FFT出现以后,信号分析中的其他运算也常常尽可能转化为DFT以提高运算速度。但作者在开发虚拟频谱分析仪中了解到,对DFT及其逆变换(IDFT)的计算存在着两套公式,导致不同信号分析人员,或不同时频信号分析仪计算出的DFT结果不一致,其物理意义也不分明。作者首先阐述了以前文献中定义DFT时所依据的周期延拓原理,然后分别用待定系数法和类比演变法论证了在周期延拓原理的认识下,DFT的计算公式采用式(3)更具合理性,指出并纠正了以前诸多文献中定义DFT计算公式时,推导过程中存在的一个不当之处,对以前认为DFT及其IDFT的计算存在两套公式是一种习惯的不恰当观点加以了澄清,最后以三个算例直观地验证了作者观点的正确性。%In the field of signal analyies for time-frequency, the DFT is a familiar term. Especially,when its efficient algorithm FFT given, the other operations in signal analyses are also usually translated to DFT as soon as possible so as to enhance the calculating speed. But in our exploning the virtual instrument for time-frequency analyzing, two sorts of formulas to calculate DFT and its inverse transform (IDFT) are found. These results are in different value of operation from different signal analysts or from different instruments for time-frequency analyzing, their physical meaning are also not clear enough.The period extent theory some previous document based on when defined DFT is firstly expatiated. Then, separately with future defining coefficient method and analogy-evolvement method, the authors argue that, based on the period extent theory, it is more rational to calculate DFT with the formula given. A shortage is pointed out and corrected is appeared in some previous documents when having given the formula of DFT. The improper

  8. The molecular pathway to ZIF-7 microrods revealed by in situ time-resolved small- and wide-angle X-ray scattering, quick-scanning extended X-ray absorption spectroscopy, and DFT calculations.

    Science.gov (United States)

    Goesten, Maarten; Stavitski, Eli; Pidko, Evgeny A; Gücüyener, Canan; Boshuizen, Bart; Ehrlich, Steven N; Hensen, Emiel J M; Kapteijn, Freek; Gascon, Jorge

    2013-06-10

    We present an in situ small- and wide-angle X-ray scattering (SAXS/WAXS) and quick-scanning extended X-ray absorption fine-structure (QEXAFS) spectroscopy study on the crystallization of the metal-organic framework ZIF-7. In combination with DFT calculations, the self-assembly and growth of ZIF-7 microrods together with the chemical function of the crystal growth modulator (diethylamine) are revealed at all relevant length scales, from the atomic to the full crystal size.

  9. New insight into the hydrocarbon-pool chemistry of the methanol-to-olefins conversion over zeolite H-ZSM-5 from GC-MS, solid-state NMR spectroscopy, and DFT calculations.

    Science.gov (United States)

    Wang, Chao; Chu, Yueying; Zheng, Anmin; Xu, Jun; Wang, Qiang; Gao, Pan; Qi, Guodong; Gong, Yanjun; Deng, Feng

    2014-09-22

    Over zeolite H-ZSM-5, the aromatics-based hydrocarbon-pool mechanism of methanol-to-olefins (MTO) reaction was studied by GC-MS, solid-state NMR spectroscopy, and theoretical calculations. Isotopic-labeling experimental results demonstrated that polymethylbenzenes (MBs) are intimately correlated with the formation of olefin products in the initial stage. More importantly, three types of cyclopentenyl cations (1,3-dimethylcyclopentenyl, 1,2,3-trimethylcyclopentenyl, and 1,3,4-trimethylcyclopentenyl cations) and a pentamethylbenzenium ion were for the first time identified by solid-state NMR spectroscopy and DFT calculations under both co-feeding ([(13) C6 ]benzene and methanol) conditions and typical MTO working (feeding [(13) C]methanol alone) conditions. The comparable reactivity of the MBs (from xylene to tetramethylbenzene) and the carbocations (trimethylcyclopentenyl and pentamethylbenzium ions) in the MTO reaction was revealed by (13) C-labeling experiments, evidencing that they work together through a paring mechanism to produce propene. The paring route in a full aromatics-based catalytic cycle was also supported by theoretical DFT calculations.

  10. DFT study of NH{sub 3} adsorption on the (5,0), (8,0), (5,5) and (6,6) single-walled carbon nanotubes. Calculated binding energies, NMR and NQR parameters

    Energy Technology Data Exchange (ETDEWEB)

    Shirvani, Bahram B.; Beheshtian, Javad; Esrafili, Mehdi D. [Department of Chemistry, Tarbiat Modares University, P.O. Box: 14115-175, Tehran (Iran, Islamic Republic of); Hadipour, Nasser L., E-mail: hadipour@modares.ac.i [Department of Chemistry, Tarbiat Modares University, P.O. Box: 14115-175, Tehran (Iran, Islamic Republic of)

    2010-03-15

    Behavior of a single NH{sub 3} molecule adsorbed on external surface of H-capped (5,5), (6,6), (5,0), and (8,0) single-walled carbon nanotubes (SWCNTs) is studied via DFT calculations. Binding energies clearly exhibit adsorption dependence on tube diameter. {sup 13}C, {sup 15}N and {sup 1}H chemical shielding tensors are calculated at the B3LYP level using GIAO method. NMR calculations reveal that {sup 13}C chemical shielding of (8,0) is more sensitive to NH{sub 3} adsorption compared to (5,5), (6,6) and (5,0) tubes. {sup 15}N and {sup 1}H chemical shielding correlate noticeably with diameter of the nanotubes. {sup 14}N and {sup 2}H nuclear quadrupole coupling constants, C{sub Q}, and asymmetry parameter, eta, reveal the remarkable effect of NH{sub 3} adsorption on electronic structure of the SWCNTs.

  11. X-ray Single Crystal Structure, DFT Calculations and Biological Activity of 2-(3-Methyl-5-(pyridin-2’-yl-1H-pyrazol-1-yl Ethanol

    Directory of Open Access Journals (Sweden)

    Smaail Radi

    2016-08-01

    Full Text Available A pyridylpyrazole bearing a hydroxyethyl substituent group has been synthesized by condensation of (Z-4-hydroxy-4-(pyridin-2-ylbut-3-en-2-one with 2-hydroxyethylhydrazine. The compound was well characterized and its structure confirmed by single crystal X-ray diffraction. Density functional calculations have been performed using DFT method with 6-31G* basis set. The HOMO-LUMO energy gap, binding energies and electron deformation densities are calculated at the DFT (BLYP, PW91, PWC level. The electrophilic f(− and nucleophilic f(+ Fukui functions and also the electrophilic and nucleophilic Parr functions are well adapted to find the electrophile and nucleophile centers in the molecule. The title compound has been tested for its DPPH radical scavenging activity which is involved in aging processes, anti-inflammatory, anticancer and wound healing activity. Compound is also found with a significant antioxidant activity, probably due to the ability to donate a hydrogen atom to the DPPH radical.

  12. Progress in the Characterization of the Surface Species in Activated Carbons by means of INS Spectroscopy Coupled with Detailed DFT Calculations

    Directory of Open Access Journals (Sweden)

    Andrea Piovano

    2015-01-01

    Full Text Available Activated carbons are materials with relevance in different industrial applications. Due to the inherent complexity and heterogeneity of their structures, an easy assignment of the species present on their surface has a challenging result. Only recently, with the possibility to collect well-resolved inelastic neutron spectra and to simulate by DFT methods more or less extended graphitic clusters, this task is starting to become feasible. Here we report our investigation on a steam activated carbon and we show that different vibrations in the region of out-of-plane C-H bending modes are specifically connected to hydrogen terminations belonging to extended and regular borders or to short and defective ones. Furthermore, simulations including heteroatoms such as oxygen allowed us to point out spectral regions with a contribution from carboxyl species.

  13. Molecular interactions investigated with DFT calculations of QTAIM and NBO analyses: An application to dimeric structures of rice α-amylase/subtilisin inhibitor

    Science.gov (United States)

    Astani, Elahe K.; Hadipour, Nasser L.; Chen, Chun-Jung

    2017-03-01

    Characterization of the dimer interactions at the dimeric interface of the crystal structure of rice α-amylase/subtilisin inhibitor (RASI) were performed using the quantum theory of atoms in molecules (QTAIM) and natural bonding orbital (NBO) analyses at the density-functional theory (DFT) level. The results revealed that Gly27 and Arg151 of chain A are the main residues involved in hydrogen bonds, dipole-dipole, and charge-dipole interactions with Gly64, Ala66, Ala67 and Arg81 of chain B at the dimeric interface. Calcium ion of chain A plays the significant role in the stability of the dimeric structure through a strong charge-charge interaction with Ala66.

  14. Magnetic property, DFT calculation, and biological activity of bis[(μ(2)-chloro)chloro(1,10-phenanthroline)copper(II)] complex.

    Science.gov (United States)

    Mroueh, Mohammad; Daher, Costantine; Hariri, Essa; Demirdjian, Sally; Isber, Samih; Choi, Eun Sang; Mirtamizdoust, Babak; Hammud, Hassan H

    2015-04-25

    The dinuclear complex bis[(μ(2)-chloro)chloro(1,10-phenanthroline)copper(II)] (1) was synthesized, and characterized by X-ray, FTIR and thermal analysis. The fitting of magnetic susceptibility and magnetization curve of (1) indicates the occurrence of weak antiferromagnetic exchange interaction between copper(II) ions. The electronic structure has been also determined by density functional theory (DFT) method. Complex (1) displayed potent anticancer activity against B16 (Melanoma), MDA-MB-32 (Breast Adenocarcinoma), A549 (Lung Adenocarcinoma), HT-29 (Colon Adenocarcinoma) and SF (Astrocytoma) cell lines with an average IC50 value of 0.726 μg/ml compared to 4.88 μg/ml for cisplatin. Complex (1) has a better therapeutic index and toxicological profile than cisplatin, and has demonstrated a potential chemotherapeutic property.

  15. The effect of Cu(2+) chelation on the direct photolysis of oxytetracycline: A study assisted by spectroscopy analysis and DFT calculation.

    Science.gov (United States)

    Jin, Xin; Qiu, Shanshan; Wu, Ke; Jia, Mingyun; Wang, Fang; Gu, Chenggang; Zhang, Aiqian; Jiang, Xin

    2016-07-01

    The extensive usage of OTC and Cu(2+) in livestock and poultry industry caused high residues in natural environment. Co-contamination of OTC and Cu(2+) was a considerable environmental problem in surface waters. In this study, Cu(2+) mediated direct photolysis of OTC was studied. Cu(2+) chelating with OTC was found to greatly inhibit OTC photodegradation. To reveal the chelation mechanism of OTC-Cu complexes, multiple methods including UV-Vis absorption spectra, Infrared (IR) spectra, mass spectroscopy, and density functional theoretical (DFT) modeling were performed. Four OTC-Cu complexes were proposed. Cu(2+) preferably bond to O11O12 site with the binding constants logK = 8.19 and 7.86 for CuHL+ and CuL±, respectively. The second chelating site was suggested to be O2O3 with the binding constants of logK = 4.41 and 4.62 for Cu2HL3+ and Cu2L2+, respectively. The suppressed quantum yield of OTC by Cu2+ chelation was accused for their intra-/inter-molecular electron transfer, by which the energy in activated states was distributed. The occurrence of electron transfer between BCD ring and A ring also from BCD ring to Cu was evidenced by the TD-DFT result only for the OTC-Cu complexes. Besides, the cyclic voltammetry measurement also suggested one OTC-Cu(II)/OTC-Cu(I) redox couple. These results suggested that the persistence of OTC in environmental surface waters will probably be underestimated for neglecting the chelating effect of Cu2+. The photolysis quantum yield of OTC-Cu complexes, as well as the specific molar absorption constants, the equilibrium binding constants of Cu2+ with OTC could contribute to more accurate kinetic models of OTC. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Co(II), Ni(II), Cu(II) and Zn(II) complexes of tridentate ONO donor Schiff base ligand: Synthesis, characterization, thermal, non-isothermal kinetics and DFT calculations

    Science.gov (United States)

    Kusmariya, Brajendra S.; Mishra, A. P.

    2017-02-01

    We report here four mononuclear Co(II), Ni(II), Cu(II) and Zn(II) coordination compounds of general formula [M(L)2] {L = dcp; M = CoII, CuII & ZnII} and [M(L)(H2O)]·H2O {L = dcp; M = NiII} derived from tridentate 2,4-dichloro-6-{[(3-chloro-2-hydroxy-5-nitrophenyl)imino]methyl}phenol (dcp) ligand. These compounds were synthesized and characterized by elemental analysis, FT-IR, uv-vis, 1H NMR, molar conductance, magnetic moment, thermal, PXRD and SEM-EDX. The Powder X-ray Diffraction patterns and SEM analyses showed the crystalline nature of synthesized compounds. The peak broadening was explained in terms of crystallite size and the lattice strain using Scherrer and Williamson-Hall method. Thermogravimetric analysis was performed to determine the thermal stability of synthesized compounds under nitrogen atmosphere up to 820 K at 10 Kmin-1 heating rate. The kinetic and thermodynamic parameters of thermal decomposition were calculated using Coats-Redfern (C-R), Piloyan-Novikova (P-N) and Horowitz-Metzger (H-M) methods assuming first order degradation. The calculated optical band gap values of complexes were found to be in semiconducting range. To support the experimental findings, and derive some fruitful information viz. frequency calculations, HOMO-LUMO, energy gap (ΔE), molecular electrostatic potential (MEP), spin density, absorption spectra etc.; theoretical calculations by means of DFT and TD-DFT at B3LYP level were incorporated.

  17. Crystal structure, spectral property, antimicrobial activity and DFT calculation of N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea

    Science.gov (United States)

    Zhang, Hong-Song; Zhang, Kong-Yan; Chen, Li-Chuan; Li, Yao-Xin; Chai, Lan-Qin

    2017-10-01

    N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea was synthesized and characterized by elemental analysis, IR, 1H NMR, 13C NMR, UV-Vis and emission spectroscopy, as well as by single-crystal X-ray diffraction. X-ray crystallographic analyses have indicated that the crystal structure consists of two dimethyl sulfoxide (DMSO) solvent molecules and the structural geometry of DMSO is a trigonal pyramid in shape. In the crystal structure, a self-assembling two-dimensional (2-D) layer supramolecular architecture is formed through intermolecular hydrogen bonds, Cdbnd O···π (thiadiazole ring) and π···π stacking interactions. The geometry of the compound has been optimized by the DFT method and the results are compared with the X-ray diffraction data. The electronic transitions and spectral features of the compound were carried out by using DFT/B3LYP method. In addition, the antimicrobial activity was also studied, and the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and HOMO-LUMO gap were also calculated.

  18. Calculation of the optical spectra of the copper(I) complex with triphenylphosphine, iodine, and 3-pyridine-2-yl-5-phenyl-1 H-1,2,4-triazole by the DFT method

    Science.gov (United States)

    Minaeva, V. A.; Minaev, B. F.; Baryshnikov, G. V.

    2017-02-01

    The IR and UV spectra of the [CuIL(PPh3)] complex (PPh3 = triphenylphosphine, L = 3-pyridine- 2-yl-5-phenyl-1 H-1,2,4-triazole) have been analyzed in detail within the density functional theory (DFT) and its time-dependent version TD DFT. The standard functional B3LYP and sets of basis orbitals 6-311G(d,p) and Lanl2DZ are used for the atoms of the elements of periods I and II and for the iodine atom, respectively. The calculated IR spectra of the complex and free ligands coincide with the observed IR bands, due to which one can completely interpret all normal modes and confirm X-ray diffraction (XRD) data. Particular attention is paid to the structure of excited triplet ( T 1) state in order to explain the role of copper and iodine ions in the formation of photo- and electroluminescence spectra. It is shown that the equilibrium T 1 state undergoes structural relaxation after the vertical excitation and significantly changes its electronic nature and the charge transfer structure.

  19. Raman and infrared spectroscopy, DFT calculations, and vibrational assignment of the anticancer agent picoplatin: performance of long-range corrected/hybrid functionals for a platinum(II) complex.

    Science.gov (United States)

    Malik, Magdalena; Wysokiński, Rafał; Zierkiewicz, Wiktor; Helios, Katarzyna; Michalska, Danuta

    2014-08-28

    Picoplatin, cis-[PtCl2(NH3)(2-picoline)], is a new promising anticancer agent undergoing clinical trials, which reveals high efficacy against many tumors and greatly reduced toxicity, in comparison to cisplatin. In this work, we present for the first time the Fourier-transform Raman and infrared spectra of picoplatin, in the region of 3500-50 cm(-1). The comprehensive theoretical studies on the molecular structure, the nature of Pt-ligand bonding, vibrational frequencies, and intensities were performed by employing different DFT methods, including hybrid (PBE0, mPW1PW, and B3LYP) and long-range-corrected hybrid density functionals (LC-ωPBE, CAM-B3LYP). Various effective core potentials (ECP) and basis sets have been used. In the prediction of the molecular structure of picoplatin, the best results have been obtained by LC-ωPBE, followed by PBE0, mPW1PW, and CAM-B3LYP density functionals, while the least accurate is B3LYP. The use of the LanL2TZ(f) ECP/basis set for Pt, in conjunction with all tested DFT methods, improves the calculated geometry of the title complex. The PBE0, mPW1PW, and CAM-B3LYP methods have shown the best performance in the calculations of the frequencies of Pt-ligand vibrations. A clear-cut assignment of all the bands in the IR and Raman spectra have been made on the basis of the calculated potential energy distribution (PED). The nature of the "vibrational signatures" of picoplatin have been determined. These results are indispensable for further investigation on drug-target interactions using vibrational spectroscopy.

  20. The synergetic effect of V and Fe-co-doping in TiO2 studied from the DFT + U first-principle calculation

    Science.gov (United States)

    Liu, Baoshun; Zhao, Xiujian

    2017-03-01

    Based on the density functional theory (DFT + U), a detailed study on the energetic, electronic, and optical properties of Fe-, V-, and Fe & V-co-doping anatase and rutile TiO2 was performed The synergetic effect of Fe & V bimetal co-doping on the optical absorption was discussed on electronic level. Two kinds of co-dopants were considered, which included edge-shared and corner-shared co-doping. It was shown that Fe and V atoms prefer to replace Ti atom in the O-rich contions than in the Ti-rich conditions. Co-doping in anatase reduces the formation energies in both cases, while the formation energies for rutile cannot be decreased. The Bader charge analysis indicates the +3 of Fe atom and +4 of V atom, and the obvious electron exchange between Fe and V atom in co-doping cases can be identified, which indicates the presence of synergetic effect induced by co-doping. The cooperation of Fe & V co-dopants was also supported by the result of projected density of states and spin charge density differences, as the hybridization of Fe3d with V3d orbitals was seen within the TiO2 forbidden band. Different from single-dopant systems, the V3d-Fe3d co-interaction leads to the formation of some spin mid-gap states, which have an obvious effect on the optical absorptions.

  1. Co(II), Ni(II) and Cu(II) complexes of methyl-5-(Phenylthio) benzimidazole-2-carbamate: Molecular structures, spectral and DFT calculations

    Science.gov (United States)

    Mansour, Ahmed M.; El Bakry, Eslam M.; Abdel-Ghani, Nour T.

    2016-05-01

    [Co(FBZ)2(H2O)]·2NO3·0.5H2O (1), [Ni(FBZ)2X2]·zH2O (X = Cl​-, z = 0.5 (2) and X = CH3COO-, z = 1 (3)) and [Cu(FBZ)2(H2O) (NO3)]·NO3·1.5H2O (4) (FBZ = methyl-5-(Phenylthio) benzimidazole-2-carbamate; Fenbendazole) complexes were synthesized and characterized by elemental analysis, thermal, IR, EPR, UV-Vis, magnetic and conductance measurements. Geometry optimization, molecular electrostatic potential maps and natural bond orbital analysis were carried out at DFT/B3LYP/6-31G∗ level of theory. FBZ behaves as a neutral bidentate ligand via the pyridine-type nitrogen of the benzimidazole moiety and the carbamate group. Three-step ionization with pKa values of 3.38, 4.06 and 10.07 were reported for FBZ. The coordination of FBZ to the metal ions led to an increase in the antibacterial activity against the tested Staphylococcus aureus and Escherichia coli bacteria.

  2. Montecrinanes A-C: Triterpenes with an Unprecedented Rearranged Tetracyclic Skeleton from Celastrus vulcanicola. Insights into Triterpenoid Biosynthesis Based on DFT Calculations.

    Science.gov (United States)

    Purino, Martín; Ardiles, Alejandro E; Callies, Oliver; Jiménez, Ignacio A; Bazzocchi, Isabel L

    2016-05-23

    Three new triterpenoids with an unprecedented 6/6/6/6-fused tetracyclic carbon skeleton, montecrinanes A-C (1-3), were isolated from the root bark of Celastrus vulcanicola, along with known D:B-friedobaccharanes (4-6), and lupane-type triterpenes (7-12). The stereostructures of the new metabolites were elucidated based on spectroscopic (1D and 2D NMR) and spectrometric (HR-EIMS and HR-ESIMS) techniques. Their absolute configurations were determined by both NMR spectroscopy, with (R)-(-)-α-methoxyphenylacetic acid as a chiral derivatizing agent, and biogenetic considerations. Biogenetic pathways for montecrinane and D:B-friedobaccharane skeletons were proposed and studied by DFT methods. The theoretical results support the energetic feasibility of the putative biogenetic pathways, in which the 1,2-methyl shift from the secondary baccharenyl cation represents a novel and key reaction step for a new montecrinane skeleton. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Isomeric ruthenium terpyridine complexes [Ru(trpy)(L)Cl]n+ containing the unsymmetrically bidentate acceptor L=3-amino-6-(3,5-dimethylpyrazol-1-yl)-1,2,4,5-tetrazine. Synthesis, structures, electrochemistry, spectroscopy and DFT calculations.

    Science.gov (United States)

    Patra, Srikanta; Sarkar, Biprajit; Ghumaan, Sandeep; Patil, Mahendra P; Mobin, Shaikh M; Sunoj, Raghavan B; Kaim, Wolfgang; Lahiri, Goutam Kumar

    2005-04-07

    The isomeric title complexes were obtained in almost equimolar ratio from the reaction of Ru(trpy)Cl3 and L. Crystal structure analyses of the perchlorate hemihydrates, electrochemical and spectroscopic (NMR, UV/VIS, EPR) studies, supported by DFT calculations, reveal distinct differences between the isomeric redox series [1]n+(tetrazine-Nt trans to Cl) and [2]n+(pyrazolyl-Np trans to Cl; n= 0, 1, 2). The latter system with the pi acceptors trpy and tetrazine in the equatorial plane and the pyrazolyl and chloride donors in the axial positions exhibits facilitated oxidation, lower energy MLCT transitions, more balanced chelate coordination, and a higher g anisotropy in the oxidised (RuIII) state. According to partially resolved EPR spectra of one-electron reduced neutral compounds and they have the unpaired electron predominantly in the tetrazine ring of L.

  4. Electronic structures of TiO2-TCNE, -TCNQ, and -2,6-TCNAQ surface complexes studied by ionization potential measurements and DFT calculations: Mechanism of the shift of interfacial charge-transfer bands

    Science.gov (United States)

    Fujisawa, Jun-ichi; Hanaya, Minoru

    2016-06-01

    Interfacial charge-transfer (ICT) transitions between inorganic semiconductors and π-conjugated molecules allow direct charge separation without loss of energy. This feature is potentially useful for efficient photovoltaic conversions. Charge-transferred complexes of TiO2 nanoparticles with 7,7,8,8-tetracyanoquinodimethane (TCNQ) and its analogues (TCNX) show strong ICT absorption in the visible region. The ICT band was reported to be significantly red-shifted with extension of the π-conjugated system of TCNX. In order to clarify the mechanism of the red-shift, in this work, we systematically study electronic structures of the TiO2-TCNX surface complexes (TCNX; TCNE, TCNQ, 2,6-TCNAQ) by ionization potential measurements and density functional theory (DFT) calculations.

  5. Explicitly correlated benchmark calculations on C8H8 isomer energy separations: how accurate are DFT, double-hybrid, and composite ab initio procedures?

    Science.gov (United States)

    Karton, Amir; Martin, Jan M. L.

    2012-10-01

    Accurate isomerization energies are obtained for a set of 45 C8H8 isomers by means of the high-level, ab initio W1-F12 thermochemical protocol. The 45 isomers involve a range of hydrocarbon functional groups, including (linear and cyclic) polyacetylene, polyyne, and cumulene moieties, as well as aromatic, anti-aromatic, and highly-strained rings. Performance of a variety of DFT functionals for the isomerization energies is evaluated. This proves to be a challenging test: only six of the 56 tested functionals attain root mean square deviations (RMSDs) below 3 kcal mol-1 (the performance of MP2), namely: 2.9 (B972-D), 2.8 (PW6B95), 2.7 (B3PW91-D), 2.2 (PWPB95-D3), 2.1 (ωB97X-D), and 1.2 (DSD-PBEP86) kcal mol-1. Isomers involving highly-strained fused rings or long cumulenic chains provide a 'torture test' for most functionals. Finally, we evaluate the performance of composite procedures (e.g. G4, G4(MP2), CBS-QB3, and CBS-APNO), as well as that of standard ab initio procedures (e.g. MP2, SCS-MP2, MP4, CCSD, and SCS-CCSD). Both connected triples and post-MP4 singles and doubles are important for accurate results. SCS-MP2 actually outperforms MP4(SDQ) for this problem, while SCS-MP3 yields similar performance as CCSD and slightly bests MP4. All the tested empirical composite procedures show excellent performance with RMSDs below 1 kcal mol-1.

  6. Study on the adsorption properties of O{sub 3}, SO{sub 2}, and SO{sub 3} on B-doped graphene using DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Rad, Ali Shokuhi, E-mail: a.shokuhi@gmail.com [Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr (Iran, Islamic Republic of); Shabestari, Sahand Sadeghi [Department of Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Mohseni, Soheil; Aghouzi, Samaneh Alijantabar [Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr (Iran, Islamic Republic of)

    2016-05-15

    We investigated the structure, adsorption, electronic states, and charge transfer of O{sub 3}, SO{sub 2} and SO{sub 3} molecules on the surface of a B-doped graphene using density functional theory (DFT). We found weak physisorption of SO{sub 2} (−10.9 kJ/mole, using B3LYP-D) and SO{sub 3} (−15.7 kJ/mole, using B3LYP-D) on the surface of B-doped graphene while there is strong chemisorption for O{sub 3} (−96.3 kJ/mole, using B3LYP-D ) on this surface. Our results suggest the potential of B-doped graphene as a selective sensor/adsorbent for O{sub 3} molecule. We noticed some change in hybridizing of boron from sp{sup 2} to sp{sup 3} upon adsorption of O{sub 3} which cases transformation of the adsorbent from 2D to 3D. - Graphical abstract: The electronic property of B-doped graphene is responsible to highly adsorption of O{sub 3} molecules while the adsorption of SO{sub 2} and SO{sub 3} molecules on this surface exhibits only a weak interaction. - Highlights: • B-doped graphene clearly is n-type semiconductor. • High negatively charge of C-atoms neighboring the boron dopant. • Chemisorption of O{sub 3} and physisorption of SO{sub 2} and SO{sub 3} on the surface of B-doped graphene.

  7. TD-DFT Study on Pyrazoline Derivatives

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The molecular structures of ground state and first single excited state for pyrazoline derivatives are optimized with DFT B3LYP method and ab initio "configuration interaction with single excitations"(CIS) method, respectively. The frontier molecular orbital characteristics have been analyzed systematically, and the electronic transition mechanism has been discussed. Electronic spectra are calculated by using TD-DFT method. These results are consistent with those from the experiment.

  8. Spectroscopic characterization of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea and assessment of reactive and optoelectronic properties employing DFT calculations and molecular dynamics simulations

    Science.gov (United States)

    War, Javeed Ahmad; Jalaja, K.; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Srivastava, Santosh Kumar; Van Alsenoy, C.

    2017-02-01

    IR and Raman spectra of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea (HIPPT) have been recorded in the solid phase and the vibrational wave numbers are calculated theoretically by B3LYP/6-31G(d,p) (6D, 7F) method. All the fundamental vibrational modes have been assigned using potential energy distribution values and the molecular structure was analyzed in terms of parameters like bond length, bond angles and dihedral angles. The ring breathing mode of the phenyl ring is observed at 1016 cm-1 in the IR spectrum, 1014 cm-1 in the Raman spectrum and at 1014 cm-1 theoretically. The values of polarizability and hyperpolarizabilities were calculated and nonlinear optical properties are discussed. The HOMO-LUMO plot reveals the charge transfer possibilities in the molecule. The NBO analysis was computed and possible transitions were correlated with the electronic transitions. In the title compound, the imidazole ring and CH2 groups are tilted from each other and the thiourea group is tilted from the phenyl ring. Using MEP plot the electrophilic and nucleophilic regions are identified. Local reactivity properties were investigated by analysis of ALIE surfaces and Fukui functions. Oxidation and degradation properties were initially assessed by calculation of bond dissociation energies of all single acyclic bonds. Determination of atoms with pronounced interactions with water molecules was performed by calculation of radial distribution functions after molecular dynamics simulations. Chargehopping rates were calculated within Marcus semi-empiric approach, employing both DFT calculations and MD simulations. The molecular docking computational predictions were complemented by the in vitro antibacterial activity evaluation.

  9. Hydrogen-bridge Si(μ-H)3CeH and inserted H3SiCeH molecules: Matrix infrared spectra and DFT calculations for reaction products of silane with Ce atoms

    Science.gov (United States)

    Xu, Bing; Shi, Peipei; Huang, Tengfei; Wang, Xuefeng

    2017-10-01

    Reactions of laser-ablated cerium atoms with silane were investigated by matrix isolation infrared spectroscopy and theoretical calculations. The reaction products, Si(μ-H)3CeH, H3SiCeH, H2Si(μ-H)CeH and HSi(μ-H)2CeH were identified on the basis of the SiD4 isotopic substitutions and DFT frequency calculations. In the solid argon or krypton matrix, the inserted H3SiCeH molecule was observed as initial product on deposition, which rearranged to hydrogen bridge species Si(μ-H)3CeH on follow-up annealing through H2Si(μ-H)CeH and HSi(μ-H)2CeH species. The Sisbnd Hsbnd Ce hydrogen bridge was investigated by NBO and ELF analysis. Calculation suggested that in Si(μ-H)3CeH molecule Ce atom donated one electron to Si atom, resulting in electron-rich SiH3 subunit, which was confirmed by ESP and AIM analysis. The increased basicity of Sisbnd H bond facilitates the formation of hydrogen bridge bond between Si and Ce. For comparison only insertion H3CCeH structure was obtained from the reaction of Ce atoms with CH4.

  10. Vibrational spectroscopy [FTIR and FTRaman] investigation, computed vibrational frequency analysis and IR intensity and Raman activity peak resemblance analysis on 4-chloro 2-methylaniline using HF and DFT [LSDA, B3LYP and B3PW91] calculations.

    Science.gov (United States)

    Ramalingam, S; Periandy, S

    2011-03-01

    In the present study, the FT-IR and FT-Raman spectra of 4-chloro-2-methylaniline (4CH2MA) have been recorded in the range of 4000-100 cm(-1). The fundamental modes of vibrational frequencies of 4CH2MA are assigned. All the geometrical parameters have been calculated by HF and DFT (LSDA, B3LYP and B3PW91) methods with 6-31G (d, p) and 6-311G (d, p) basis sets. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values for aniline and some substituted aniline. The harmonic and anharmonic vibrational wavenumbers, IR intensities and Raman activities are calculated at the same theory levels used in geometry optimization. The calculated frequencies are scaled and compared with experimental values. The scaled vibrational frequencies at LSDA/B3LYP/6-311G (d, p) seem to coincide with the experimentally observed values with acceptable deviations. The impact of substitutions on the benzene structure is investigated. The molecular interactions between the substitutions (Cl, CH(3) and NH(2)) are also analyzed.

  11. Molecular structure and computational studies on 2-((2-(4-(3-(2,5-dimethylphenyl)-3-methylcyclobutyl)thiazol-2-yl)hydrazono)methyl)phenol monomer and dimer by DFT calculations

    Science.gov (United States)

    Karakurt, Tuncay; Cukurovali, Alaaddin; Subasi, Nuriye Tuna; Kani, Ibrahim

    2016-12-01

    The title compound, 2-((2-(4-(3-(2,5-Dimethylphenyl)-3-methylcyclobutyl)thiazol-2-yl)hydrazono)methyl)phenol, was characterized by single-crystal X-ray diffraction. In order to calculate molecular geometry along with the infrared, Atoms in Molecules (AIM) analysis and 1H and 13C NMR chemical shift values, the density functional theory (DFT) method with 6-311G++(d,p) basis set was utilized. Experimental data were then used for comparison. While the title crystal structure is photochromic, the molecule is nonplanar. It takes on an enol form including a forceful intramolecular Osbnd H⋯N hydrogen bond as well as a forceful intermolecular Nsbnd H⋯N hydrogen bond. The 6-311G++(d,p) basis function was used to examine the intramolecular tautomerism single proton transfer reaction of the hydrogen-bonded enol-imine and keto-amine monomer in the title crystal structure at the B3LYP theory level. Further, the frontier molecular orbitals (FMO), molecular docking and NLO properties were studied by using theoretical calculations. The calculated NLO properties of title compound are much greater than urea. The title compound generates a stable complex with CDK2 as is distinct from the binding energy values. These results proposed that the compound might exhibit inhibitory effect against CDK2. These are important in development of new antitumor agent.

  12. Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-dihydro-1,3,4-thiadiazol-2-ylidene)-4-methylbenzenesulfonamide using DFT-D calculations and (13)C solid-state NMR.

    Science.gov (United States)

    Li, Xiaozhou; Bond, Andrew D; Johansson, Kristoffer E; Van de Streek, Jacco

    2014-08-01

    The crystal structure of the title compound, C11H13N3O2S2, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated (13)C solid-state NMR spectra [Hangan et al. (2010). Acta Cryst. B66, 615-621]. The molecule is tautomeric, and was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thiadiazol-2-yl)-p-toluenesulfonamide], rather than the correct imine tautomer. The protonation site on the molecule's 1,3,4-thiadiazole ring is indicated by the intermolecular contacts in the crystal structure: N-H...O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable intermolecular interactions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported quantitative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the (13)C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured (13)C SS-NMR spectrum.

  13. G4MP2, DFT and CBS-Q calculation of proton and electron affinities, gas phase basicities and ionization energies of hydroxylamines and alkanolamines

    Indian Academy of Sciences (India)

    Younes Valadbeigi; Hossein Farrokhpour; Mahmoud Tabrizchi

    2014-07-01

    The proton affinities, gas phase basicities and adiabatic ionization energies and electron affinities of some important hydroxylamines and alkanolamines were calculated using B3LYP, CBS-Q and G4MP2 methods. Also, the B3LYP method was used to calculate vertical ionization energies and electron affinities of the molecules. The calculated ionization energies are in the range of 8-10.5 eV and they decrease as the number of carbon atoms increases. Computational results and ion mobility spectrometry study confirm that some alkanolamines lose a water molecule due to protonation at oxygen site and form cationic cyclic compounds. Effect of different substitutions on the cyclization of ethanolamine was studied theoretically.

  14. Studies on the synthesis, spectroscopic analysis, molecular docking and DFT calculations on 1-hydroxy-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazol 3-oxide

    Science.gov (United States)

    Benzon, K. B.; Sheena, Mary Y.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Pradhan, Kiran; Nanda, Ashis Kumar; Van Alsenoy, C.

    2017-02-01

    In this work we have investigated in details the spectroscopic and reactive properties of newly synthesized imidazole derivative, namely the 1-hydroxy-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazole 3-oxide (HHPDI). FT-IR and NMR spectra were measured and compared with theoretically obtained data provided by calculations of potential energy distribution and chemical shifts, respectively. Insight into the global reactivity properties has been obtained by analysis of frontier molecular orbitals, while local reactivity properties have been investigated by analysis of charge distribution, ionization energies and Fukui functions. NBO analysis was also employed to understand the stability of molecule, while hyperpolarizability has been calculated in order to assess the nonlinear optical properties of title molecule. Sensitivity towards autoxidation and hydrolysis mechanisms has been investigated by calculations of bond dissociation energies and radial distribution functions, respectively. Molecular docking study was also performed, in order to determine the pharmaceutical potential of the investigated molecule.

  15. The interactions of phenylalanines in β-sheet-like structures from molecular orbital calculations using density functional theory (DFT), MP2, and CCSD(T) methods.

    Science.gov (United States)

    Pohl, Gabor; Plumley, Joshua A; Dannenberg, J J

    2013-06-28

    We present density functional theory calculations designed to evaluate the importance of π-stacking interactions to the stability of in-register Phe residues within parallel β-sheets, such as amyloids. We have used a model of a parallel H-bonded tetramer of acetylPheNH2 as a model and both functionals that were specifically designed to incorporate dispersion effects (DFs), as well as, several traditional functionals which have not been so designed. None of the functionals finds a global minimum for the π-stacked conformation, although two of the DFs find this to be a local minimum. The stacked phenyls taken from the optimized geometries calculated for each functional have been evaluated using MP2 and CCSD(T) calculations for comparison. The results suggest that π-stacking does not make an important contribution to the stability of this system and (by implication) to amyloid formation.

  16. Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Bratholm, L.A.; Olsen, Jógvan Magnus Haugaard

    2017-01-01

    Full-protein nuclear magnetic resonance (NMR) shielding constants based on ab initio calculations are desirable, because they can assist in elucidating protein structures from NMR experiments. In this work, we present NMR shielding constants computed using a new automated fragmentation (J. Phys. ...... can obtain a representative subset of snapshots that gives the smallest predicted error, compared to experiment. Finally, we use this subset of snapshots to calculate the NMR shielding constants at the PE-KT3/pcSseg-2 level of theory for all atoms in the protein GB3....

  17. Electronic structure of BaFe{sub 2}As{sub 2} as obtained from DFT/ASW first-principles calculations

    Energy Technology Data Exchange (ETDEWEB)

    Schwingenschloegl, U.; Di Paola, C. [KAUST, PSE Division, Thuwal (Saudi Arabia)

    2010-08-15

    We use ab-initio calculations based on the augmented spherical wave method within density functional theory to study the magnetic ordering and Fermi surface of BaFe{sub 2}As{sub 2}, the parent compound of the hole-doped iron pnictide superconductors (K,Ba)Fe{sub 2}As{sub 2}, for the tetragonal I4/mmm as well as the orthorhombic Fmmm structure. In comparison to full potential linear augmented plane wave calculations, we obtain significantly smaller magnetic energies. This finding is remarkable, since the augmented spherical wave method, in general, is known for a most reliable description of magnetism. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  18. The atomic structure of protons and hydrides in Sm1.92Ca0.08Sn2O7-δ pyrochlore from DFT calculations and FTIR spectroscopy

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Eurenius, K. E. J.; Rossmeisl, Jan

    2012-01-01

    ) oxygen atoms closely associated with a Ca dopant. Further, the unexpected presence of Ho hydride defects in undoped, oxygen deficient Sm2Sn2O7 is reported. Finally, the stretching frequencies and relative intensities for these and other sites are calculated. The main features of the Fourier transform...

  19. Electronic Structure, Electronic Charge Density, and Optical Properties Analysis of GdX3 (X = In, Sn, Tl, and Pb Compounds: DFT Calculations

    Directory of Open Access Journals (Sweden)

    Jisha Annie Abraham

    2015-01-01

    Full Text Available The electronic properties of magnetic cubic AuCu3 type GdX3 (X = In, Sn, Tl, and Pb have been studied using first principles calculations based on density functional theory. Because of the presence of strong on-site Coulomb repulsion between the highly localized 4f electrons of Gd atoms, we have used LSDA + U approach to get accurate results in the present study. The electronic band structures as well as density of states reveal that the studied compounds show metallic behavior under ambient conditions. The calculated density of states at the Fermi level N(EF shows good agreement with the available experimental results. The calculated electronic charge density plots show the presence of ionic bonding in all the compounds along with partial covalent bonding except in GdIn3. The complex optical dielectric function’s dispersion and the related optical properties such as refractive indices, reflectivity, and energy-loss function were calculated and discussed in detail.

  20. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T)

    Science.gov (United States)

    Caldararu, Octav; Olsson, Martin A.; Riplinger, Christoph; Neese, Frank; Ryde, Ulf

    2017-01-01

    We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO-CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by 50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11-16 kJ/mol. DLPNO-CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates

  1. Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide using DFT-D calculations and {sup 13}C solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiaozhou; Bond, Andrew D.; Johansson, Kristoffer E.; Van de Streek, Jacco, E-mail: jacco.vandestreek@sund.ku.dk [Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100 (Denmark)

    2014-08-01

    The crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide contains an imine tautomer, rather than the previously reported amine tautomer. The tautomers can be distinguished using dispersion-corrected density functional theory calculations and by comparison of calculated and measured {sup 13}C solid-state NMR spectra. The crystal structure of the title compound, C{sub 11}H{sub 13}N{sub 3}O{sub 2}S{sub 2}, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated {sup 13}C solid-state NMR spectra [Hangan et al. (2010 ▶). Acta Cryst. B66, 615–621]. The mol@@ecule is tautomeric, and was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thia@@diazol-2-yl)-p-toluene@@sulfonamide], rather than the correct imine tautomer. The protonation site on the mol@@ecule’s 1,3,4-thia@@diazole ring is indicated by the inter@@molecular contacts in the crystal structure: N—H⋯O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable inter molecular inter@@actions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported qu@@anti@@tative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the {sup 13}C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured {sup 13}C SS-NMR spectrum.

  2. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation.

    Science.gov (United States)

    Mao, Yuezhi; Horn, Paul R; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin

    2016-07-28

    Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.

  3. Tailoring the electronic structure of anatase TiO2(001) surface through W and N codoping: a DFT calculation

    Science.gov (United States)

    Li, Zongbao; Wang, Xia; Xing, Xiaobo; Wang, Ying

    2017-02-01

    Using density functional theory, we calculated the geometries, band structures and densities of states of W-doped, N-doped, and W/N-codoped anatase TiO4 (001) and (101) surfaces, as well as while the formation energies, based on the overall reaction energy diagram. The calculated results reveal that, on the two surfaces, the absorption of W atoms are more stable than that of N atoms while a larger energy barrier blocks the transfer of W atoms from the surfaces to the body. For TiO2(001), the W-doping and the N/W-codoping lead to a visible lattice distortion while the recombination of photo-generated electron-holes pairs is reduced. A comprehensive analysis of the electronic structures show that the band-gap narrows and a new W-N bond appears, which obviously enhance the photocatalytic activity.

  4. Using simple molecular orbital calculations to predict disease: fast DFT methods applied to enzymes implicated in PKU, Parkinson's disease and Obsessive Compulsive Disorder

    Science.gov (United States)

    Hofto, Laura; Hofto, Meghan; Cross, Jessica; Cafiero, Mauricio

    2007-09-01

    Many diseases can be traced to point mutations in the DNA coding for specific enzymes. These point mutations result in the change of one amino acid residue in the enzyme. We have developed a model using simple molecular orbital calculations which can be used to quantitatively determine the change in interaction between the enzyme's active site and necessary ligands upon mutation. We have applied this model to three hydroxylase proteins: phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase, and we have obtained excellent correlation between our results and observed disease symptoms. Furthermore, we are able to use this agreement as a baseline to screen other mutations which may also cause onset of disease symptoms. Our focus is on systems where the binding is due largely to dispersion, which is much more difficult to model inexpensively than pure electrostatic interactions. Our calculations are run in parallel on a sixteen processor cluster of 64-bit Athlon processors.

  5. Vibrational spectrum of the spin crossover complex [Fe(phen)(2)(NCS)(2)] studied by IR and Raman spectroscopy, nuclear inelastic scattering and DFT calculations.

    Science.gov (United States)

    Ronayne, Kate L; Paulsen, Hauke; Höfer, Andreas; Dennis, Andrew C; Wolny, Juliusz A; Chumakov, Aleksandr I; Schünemann, Volker; Winkler, Heiner; Spiering, Hartmut; Bousseksou, Azzedine; Gütlich, Philipp; Trautwein, Alfred X; McGarvey, John J

    2006-10-28

    The vibrational modes of the low-spin and high-spin isomers of the spin crossover complex [Fe(phen)(2)(NCS)(2)] (phen = 1,10-phenanthroline) have been measured by IR and Raman spectroscopy and by nuclear inelastic scattering. The vibrational frequencies and normal modes and the IR and Raman intensities have been calculated by density functional methods. The vibrational entropy difference between the two isomers, DeltaS(vib), which is--together with the electronic entropy difference DeltaS(el)--the driving force for the spin-transition, has been determined from the measured and from the calculated frequencies. The calculated difference (DeltaS(vib) = 57-70 J mol(-1) K(-1), depending on the method) is in qualitative agreement with experimental values (20-36 J mol(-1) K(-1)). Only the low energy vibrational modes (20% of the 147 modes of the free molecule) contribute to the entropy difference and about three quarters of the vibrational entropy difference are due to the 15 modes of the central FeN(6) octahedron.

  6. Dispersion of the second harmonic generation from CdGa{sub 2}X{sub 4} (X = S, Se) defect chalcopyrite: DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Reshak, A.H. [New Technologies – Research Center, University of West Bohemia, Univerzitni 8, 306 14 Pilsen (Czech Republic); Center of Excellence Geopolymer and Green Technology, School of Material Engineering, University Malaysia Perlis, 01007 Kangar, Perlis (Malaysia); Khan, Saleem Ayaz, E-mail: sayaz_usb@yahoo.com [New Technologies – Research Center, University of West Bohemia, Univerzitni 8, 306 14 Pilsen (Czech Republic)

    2014-05-15

    Highlights: • Nonlinear optical properties of CdGa{sub 2}X{sub 4} (X = S, Se) were investigated. • The compounds have large uniaxial anisotropy and large negative birefringence. • The second order susceptibility and the first hyperpolarizability were calculated. • CdGa{sub 2}Se{sub 4} posses huge second harmonic generation. - Abstract: All electron full potential linear augmented plane wave method was used for calculating the nonlinear optical susceptibilities of CdGa{sub 2}X{sub 4} (X = S, Se) within the framework of density functional theory. The exchange correlation potential was solved by recently developed modified Becke and Johnson (mBJ) approximation. The crystal structure of CdGa{sub 2}S{sub 4} and CdGa{sub 2}Se{sub 4} reveals a large uniaxial dielectric anisotropy ensuing the birefringence of −0.036 and −0.066 which make it suitable for second harmonic generation. The second order susceptibility |χ{sub ijk}{sup (2)}(ω)| and microscopic first hyperpolarizability β{sub ijk}(ω) were calculated. The calculated |χ{sub 123}{sup (2)}(ω)| and |χ{sub 312}{sup (2)}(ω)| static values for the dominant components found to be 18.36 pm/V and 22.23 pm/V for CdGa{sub 2}S{sub 4} and CdGa{sub 2}Se{sub 4}. Both values shifted to be 60.12 pm/V and 108.86 pm/V at λ = 1064 nm. The calculated values of β{sub 123}(ω) is 6.47 × 10{sup −30} esu at static limit and 12.42 × 10{sup −30} esu at λ = 1064 nm for CdGa{sub 2}S{sub 4}, whereas it is 8.82 × 10{sup −30} esu at static limit and 20.51 × 10{sup −30} esu at λ = 1064 nm for CdGa{sub 2}Se{sub 4}. The evaluation of second order susceptibilities and first hyperpolarizabilties suggest that CdGa{sub 2}X{sub 4} possess huge second harmonic generation.

  7. Vibrational investigation on FT-IR and FT-Raman spectra, IR intensity, Raman activity, peak resemblance, ideal estimation, standard deviation of computed frequencies analyses and electronic structure on 3-methyl-1,2-butadiene using HF and DFT (LSDA/B3LYP/B3PW91) calculations.

    Science.gov (United States)

    Ramalingam, S; Jayaprakash, A; Mohan, S; Karabacak, M

    2011-11-01

    FT-IR and FT-Raman (4000-100 cm(-1)) spectral measurements of 3-methyl-1,2-butadiene (3M12B) have been attempted in the present work. Ab-initio HF and DFT (LSDA/B3LYP/B3PW91) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, IR intensities and Raman activities. Complete vibrational assignments on the observed spectra are made with vibrational frequencies obtained by HF and DFT (LSDA/B3LYP/B3PW91) at 6-31G(d,p) and 6-311G(d,p) basis sets. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The potential energy distribution (PED) corresponding to each of the observed frequencies are calculated which confirms the reliability and precision of the assignment and analysis of the vibrational fundamentals modes. The oscillation of vibrational frequencies of butadiene due to the couple of methyl group is also discussed. A study on the electronic properties such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The thermodynamic properties of the title compound at different temperatures reveal the correlations between standard heat capacities (C) standard entropies (S), and standard enthalpy changes (H).

  8. Structural, Electronic, and Optical Properties of BiOX1-xYx (X, Y = F, Cl, Br, and I) Solid Solutions from DFT Calculations.

    Science.gov (United States)

    Zhao, Zong-Yan; Liu, Qing-Lu; Dai, Wen-Wu

    2016-08-23

    Six BiOX1-xYx (X, Y = F, Cl, Br, and I) solid solutions have been systematically investigated by density functional theory calculations. BiOCl1-xBrx, BiOBr1-xIx, and BiOCl1-xIx solid solutions have very small bowing parameters; as such, some of their properties increase almost linearly with increasing x. For BiOF1-xYx solid solutions, the bowing parameters are very large and it is extremely difficult to fit the related calculated data by a single equation. Consequently, BiOX1-xYx (X, Y = Cl, Br, and I) solid solutions are highly miscible, while BiOF1-xYx (Y = Cl, Br, and I) solid solutions are partially miscible. In other words, BiOF1-xYx solid solutions have miscibility gaps or high miscibility temperature, resulting in phase separation and F/Y inhomogeneity. Comparison and analysis of the calculated results and the related physical-chemical properties with different halogen compositions indicates that the parameters of BiOX1-xYx solid solutions are determined by the differences of the physical-chemical properties of the two halogen compositions. In this way, the large deviation of some BiOX1-xYx solid solutions from Vegard's law observed in experiments can be explained. Moreover, the composition ratio of BiOX1-xYx solid solutions can be measured or monitored using optical measurements.

  9. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

    Science.gov (United States)

    Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin

    2016-07-01

    Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces modern density functionals.

  10. Structural and spectroscopic study of a pectin isolated from citrus peel by using FTIR and FT-Raman spectra and DFT calculations

    Science.gov (United States)

    Bichara, Laura C.; Alvarez, Patricia E.; Fiori Bimbi, María V.; Vaca, Hugo; Gervasi, Claudio; Brandán, Silvia Antonia

    2016-05-01

    In this work, pectin isolated from citrus peel with a degree of esterification of 76% was characterized by Fourier Transform Infrared (FTIR) and Fourier Transform Raman (FT-Raman) spectroscopies. Structural studies were carried out taking into account their partial degree of esterification and considering the polygalacturonic acid chain as formed by two different subunits, one with both COOH and COOsbnd CH3 groups (Ac) and the other one as constituted by two subunits with two COOsbnd CH3 groups (Es). Their structural properties, harmonic frequencies, force fields and force constants in gas and aqueous solution phases were calculated by using the hybrid B3LYP/6-31G∗ method. Then, their complete vibrational analyses were performed by using the IR and Raman spectra accomplished with the scaled quantum mechanical (SQM) methodology. Reactivities and behaviors in both media were predicted for Ac and Es by using natural bond orbital (NBO), atoms in molecules (AIM), and frontier orbitals calculations. We report for first time the complete assignments of those two different units of polygalacturonic acid chain which are the 132 normal vibration modes of Ac and the 141 normal vibration modes of Es, combining the normal internal coordinates with the SQM methodology. In addition, three subunits were also studied. Reasonable correlations between the experimental and theoretical spectra were obtained. Thus, this work would allow the quick identification of pectin by using infrared and Raman spectroscopies and also provides new insight into the interactions that exist between subunits of a large pectin chain.

  11. Crystal structure, DFT and HF calculations and radical scavenging activities of (E)-4,6-dibromo-3-methoxy-2-[(3-methoxyphenylimino)methyl]phenol

    Science.gov (United States)

    Alaşalvar, Can; Soylu, Mustafa Serkan; Güder, Aytaç; Albayrak, Çiğdem; Apaydın, Gökhan; Dilek, Nefise

    In this study, (E)-4,6-dibromo-3-methoxy-2-[(3-methoxyphenylimino)methyl]phenol has been synthesized and characterized by using X-ray technique and FT-IR experimentally and using B3LYP/6-31G(d,p) and HF/6-31G(d,p) methods theoretically. The intermolecular and intramolecular interactions of the title compound have been determined according to X-ray results. The molecular geometry, vibrational frequencies of the title compound in the ground state have been calculated using the density functional B3LYP and HF method with the 6-31G(d,p) basis set and calculated bond parameters and vibrational frequencies values show good agreement with experimental values. Theoretical and experimental results show that tautomeric form of the structure is phenol-imine form. Besides HOMO-LUMO energy gap, molecular electrostatic potential map were performed at B3LYP/6-31G(d,p) level. It is worthy note of that, the free radical scavenging activities of the title compound were assessed using DPPHrad , DMPDrad +, and ABTSrad + assays. The obtained results show that the title compound has effective DPPHrad (SC50 2.61 ± 0.09 μg/mL), DMPDrad + (SC50 2.82 ± 0.14 μg/mL), and ABTSrad + (SC50 4.91 ± 0.18 μg/mL) radical scavenging activities when compared with standard antioxidants (BHA, rutin, and trolox).

  12. Crystal structure and DFT calculations of 5-(4-Chlorophenyl)-1-(6-methoxypyridazin-3-yl)-1H-pyrazole-3-carboxylic acid

    Science.gov (United States)

    Alaşalvar, Can; Soylu, Mustafa Serkan; Ünver, Hüseyin; Ocak İskeleli, Nazan; Yildiz, Mustafa; Çiftçi, Murat; Banoğlu, Erden

    2014-11-01

    The title compound, 5-(4-Chlorophenyl)-1-(6-methoxypyridazin-3-yl)-1H-pyrazole-3-carboxylic acid, has been characterized by using elemental analysis, MS, FT-IR, 1H NMR and 13C NMR spectroscopic, and crystallographic techniques. The title compound crystallizes in the triclinic space group P-1 with a = 9.612(1), b = 9.894(1), c = 17.380(1) Å, α = 90.213(5)°, β = 104.99(1)°, γ = 111.072(5)°, V = 1481.3(2) Å3 and Dx = 1.483 g cm-3 respectively. The structure of the compound has also been examined by using quantum chemical methods. The molecular geometry and vibrational frequencies of monomeric and dimeric form of the title compound in the ground state have been calculated by using the B3LYP/6-31G(d,p) level of the theory. The calculated results show that the optimized geometry and the theoretical vibration frequencies of the dimeric form are good agreement with experimental data. In addition, HOMO-LUMO energy gap, molecular electrostatic potential map, thermodynamic properties of the title compound were performed at B3LYP/6-31G(d,p) level of theory.

  13. Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields.

    Science.gov (United States)

    Xiao, Yuming; Koutmos, Markos; Case, David A; Coucouvanis, Dimitri; Wang, Hongxin; Cramer, Stephen P

    2006-05-14

    We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies. The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT

  14. On the crystal energy and structure of A2TinO2n+1 (A=Li, Na, K) titanates by DFT calculations and neutron diffraction

    Science.gov (United States)

    Catti, Michele; Pinus, Ilya; Scherillo, Antonella

    2013-09-01

    First-principles quantum-mechanical calculations (CRYSTAL09 code, B3LYP functional) were performed on alkali titanates A2TinO2n+1 with layered structure (n=3,4,6). Monoclinic structural types with unshifted (P21/m) and with shifted (C2/m) layers were considered. Crystal energies and full structural details were obtained for all Li, Na, and K phases. Neutron diffraction data were collected on powder samples of P21/m-Li2Ti3O7 (a=9.3146(3), b=3.7522(1), c=7.5447(3) Å, β=97.611(4)°) and C2/m-K2Ti4O9 (a=18.2578(8), b=3.79160(9), c=12.0242(4) Å, β=106.459(4)°) and their structures were Rietveld-refined. Computed energies show the P21/m arrangement as favoured over the C2/m one for n=3, and the opposite holds for n=6. In the n=4 case the P21/m configuration is predicted to be more stable for Li and Na, and the C2/m one for K titanates. Analysis of Li-O and K-O crystal-chemical environments from experiment and theory shows that the alkali atom bonding is stabilized/destabilized in the different phases consistently with the energy trend.

  15. Thiazole-based nitrogen mustards: Design, synthesis, spectroscopic studies, DFT calculation, molecular docking, and antiproliferative activity against selected human cancer cell lines

    Science.gov (United States)

    Łączkowski, Krzysztof Z.; Świtalska, Marta; Baranowska-Łączkowska, Angelika; Plech, Tomasz; Paneth, Agata; Misiura, Konrad; Wietrzyk, Joanna; Czaplińska, Barbara; Mrozek-Wilczkiewicz, Anna; Malarz, Katarzyna; Musioł, Robert; Grela, Izabela

    2016-09-01

    Synthesis, characterization and investigation of antiproliferative activity of ten thiazole-based nitrogen mustard against human cancer cells lines (MV4-11, A549, MCF-7 and HCT116) and normal mouse fibroblast (BALB/3T3) is presented. The structures of novel compounds were determined using 1H and 13C NMR, FAB(+)-MS, and elemental analyses. Among the derivatives, 5b, 5c, 5e, 5f and 5i were found to exhibit high activity against human leukaemia MV4-11 cells with IC50 values of 2.17-4.26 μg/ml. The cytotoxic activity of compound 5c and 5f against BALB/3T3 cells is up to 20 times lower than against cancer cell lines. Our results also show that compounds 5e and 5i have very strong activity against MCF-7 and HCT116 with IC50 values of 3.02-4.13 μg/ml. Moreover, spectroscopic characterization and cellular localization for selected compound were performed. In order to identify potential drug targets we perform computer simulations with DNA-binding site of hTopoI and hTopoII and quantum chemical calculation of interaction and binding energies in complexes of the five most active compounds with guanine.

  16. Investigation of H-bonding and halogen-bonding effects in dichloroacetic acid: DFT calculations of NQR parameters and QTAIM analysis.

    Science.gov (United States)

    Esrafili, Mehdi D

    2012-12-01

    A theoretical study was performed to examine hydrogen and halogen bonds properties in gas phase and crystalline dichloroacetic acid (DCAA). The specific pattern of O-H∙∙∙O, C-H∙∙∙O, HCl, Cl∙∙∙O and Cl∙∙∙Cl interactions in DCAA dimers is described within the quantum theory of atoms in molecules (QTAIM) formalism. Based on QTAIM results, a partial covalent character is attributed to the O-H∙∙∙O hydrogen bonds in DCAA, whereas all the C-H∙∙∙O, Cl···O and Cl∙∙∙Cl intermolecular interactions are weak and basically electrostatic in nature. MP2/6-311++G** calculations indicate that the interaction energies for DCAA dimers lie in the range between -0.40 and -14.58 kcal mol(-1). One of the most important results of this study is that, according to energy decomposition analyses, halogen bonds are largely dependent on both electrostatic and dispersion interactions. For those nuclei participating in the hydrogen-bonding and halogen-bonding interactions, nuclear quadrupole coupling constants exhibit significant changes on going from the isolated molecule model to the crystalline DCAA. Of course, the magnitude of these changes at each nucleus depends directly on its amount of contribution to the interactions.

  17. U2 center, adsorption, coadsorption and epitaxial growth of Cu, Ag and Au on LiH(0 0 1) surface: DFT calculations

    Science.gov (United States)

    Shalabi, A. S.; El-Mahdy, A. M.; Eid, Kh. M.; Kamel, M. A.; El-Barbary, A. A.

    2001-08-01

    U2 center, adsorption, coadsorption and epitaxial growth of Cu, Ag and Au on LiH(0 0 1) surface have been studied using quantum clusters embedded in a simulated coulomb field that closely approximates the Madelung potential of the host surface and density functional theory calculations with effective core potentials on Ag, Cu and Au. The metal atoms are preferentially adsorbed on the top of the anionic species and the physical adsorption of metal atoms is enhanced by ≈0.0147 hartrees under the effect of U2 center imperfection. No barrier heights were detected for diffusion of metal atoms on the surface. The adsorption energies follow the trend Au>Cu>Ag and are correctly explained in terms of the band structure. In several cases the coadsorption is greater than the adsorption of a single adsorbate and metal atoms grows expitaxially on the surface following the growth mode mechanism: (i) M/H, (ii) M 2/LiH, (iii) M 3/Li 2H, (iv) M 4/Li 2H 2.

  18. Understanding the Adsorption of PFOA on MIL-101(Cr)-Based Anionic-Exchange Metal-Organic Frameworks: Comparing DFT Calculations with Aqueous Sorption Experiments.

    Science.gov (United States)

    Liu, Kai; Zhang, Siyu; Hu, Xiyue; Zhang, Kunyang; Roy, Ajay; Yu, Gang

    2015-07-21

    To examine the effects of different functionalization methods on adsorption behavior, anionic-exchange MIL-101(Cr) metal-organic frameworks (MOFs) were synthesized using preassembled modification (PAM) and postsynthetic modification (PSM) methods. Perfluorooctanoic acid (PFOA) adsorption results indicated that the maximum PFOA adsorption capacity was 1.19 and 1.89 mmol g(-1) for anionic-exchange MIL-101(Cr) prepared by PAM and PSM, respectively. The sorption equilibrium was rapidly reached within 60 min. Our results indicated that PSM is a better modification technique for introducing functional groups onto MOFs for adsorptive removal because PAM places functional groups onto the aperture of the nanopore, which hinders the entrance of organic contaminants. Our experimental results and the results of complementary density functional theory calculations revealed that in addition to the anion-exchange mechanism, the major PFOA adsorption mechanism is a combination of Lewis acid/base complexation between PFOA and Cr(III) and electrostatic interaction between PFOA and the protonated carboxyl groups of the bdc (terephthalic acid) linker.

  19. Location of protons in anhydrous Keggin heteropolyacids H(3)PMo(12)O(40) and H(3)PW(12)O(40) by (1)H[(31)P]/(31)P[(1)H] REDOR NMR and DFT quantum chemical calculations.

    Science.gov (United States)

    Ganapathy, S; Fournier, M; Paul, J F; Delevoye, L; Guelton, M; Amoureux, J P

    2002-07-03

    HeteroPolyAcids (HPA's) are a class of solid acids that have broad applications in many fields of science and technology, including catalysis and chemical engineering. The proton locations within the thermally stable and commonly known Keggin unit, which is the primary structure building unit/block, has remained undetermined in anhydrous HPAs, despite numerous theoretical and experimental efforts. However, Rotational Echo DOuble Resonance (REDOR) NMR and Density Functional Theory (DFT) quantum chemical calculations offer a new opportunity to determine the exact locations of protons within the Keggin unit. The crucial experimental evidence is provided for the basic and very extensively studied acidic form of H(8-n)X(n+)M(12)O(40), X = Si, P and M = Mo, W, belonging to the Keggin structure. While showing that the acidic protons are located in the bridging oxygen positions (R(P-H) = 520 +/- 20 pm) in H(3)PMo(12)O(40) and in the terminal oxygen positions (R(P-H) = 570 +/- 20 pm) in H(3)PW(12)O(40), REDOR measurements also provide for the first time the structural basis to consistently rank the acid strength for the important class of Keggin solid catalysts.

  20. Bonding Study on the Chemical Separation of Am(III) from Eu(III) by S-, N-, and O-Donor Ligands by Means of All-Electron ZORA-DFT Calculation.

    Science.gov (United States)

    Kaneko, Masashi; Miyashita, Sunao; Nakashima, Satoru

    2015-07-20

    We performed a theoretical investigation for the selectivity of Eu(III)/Am(III) ions depending on the donor atoms by means of all-electron ZORA-DFT calculation. We estimated their selectivity as the relative stability in the complex formation reaction. The B2PLYP functional reproduced the experimental selectivity in which S- and N-donor ligands favor Am(III) ion, but O-donor ligand favors Eu(III) ion. Mulliken's bond overlap population analysis revealed that the contribution of the f orbital to the bonding was small or zero for Eu complex, whereas it was large for Am complex. The bonding nature of the f orbital for Am ion was the bonding type to S- and N-donor ligands, while it was the antibonding type to O-donor ligand. It was suggested that the difference in the bonding nature between the f orbital in the metal and the donor atoms determines the selectivity of Eu(III)/Am(III) by donor ligands.

  1. Relativistic four-component DFT calculations of 1H NMR chemical shifts in transition-metal hydride complexes: unusual high-field shifts beyond the Buckingham-Stephens model.

    Science.gov (United States)

    Hrobárik, Peter; Hrobáriková, Veronika; Meier, Florian; Repiský, Michal; Komorovský, Stanislav; Kaupp, Martin

    2011-06-09

    State-of-the-art relativistic four-component DFT-GIAO-based calculations of (1)H NMR chemical shifts of a series of 3d, 4d, and 5d transition-metal hydrides have revealed significant spin-orbit-induced heavy atom effects on the hydride shifts, in particular for several 4d and 5d complexes. The spin-orbit (SO) effects provide substantial, in some cases even the dominant, contributions to the well-known characteristic high-field hydride shifts of complexes with a partially filled d-shell, and thereby augment the Buckingham-Stephens model of off-center paramagnetic ring currents. In contrast, complexes with a 4d(10) and 5d(10) configuration exhibit large deshielding SO effects on their hydride (1)H NMR shifts. The differences between the two classes of complexes are attributed to the dominance of π-type d-orbitals for the true transition-metal systems compared to σ-type orbitals for the d(10) systems.

  2. Metal-organic frameworks in cadmium(II) complexes with 5-methoxyindole-2-carboxylic acid: structure, vibrational spectra and DFT calculations

    Science.gov (United States)

    Morzyk-Ociepa, Barbara; Szmigiel, Ksenia; Dysz, Karolina; Turowska-Tyrk, Ilona; Michalska, Danuta

    2016-11-01

    Two new complexes of Cd(II) with an O-deprotonated anion of 5-methoxyindole-2-carboxylic acid (5-MeOI2CA), of the formulas [Cd(5-MeOI2CA)2(H2O)2]n (1) and [Cd3(5-MeOI2CA)6(H2O)4(DMSO)4]ṡ2DMSO (2) were synthesized. In the polymeric complex 1, the 5-MeOI2CA anion acts as a bidentate bridging ligand and the coordination environment around the Cd(II) ion can be described as a distorted octahedron. Single crystal X-ray diffraction analysis of 2 has revealed that this complex is a trimer and it crystallizes in the monoclinic system (space group P21/c with a = 20.3403(4), b = 14.3079(2), c = 15.0603(3) Å, β = 92.4341(17)°, V = 4379.00(14) Å3 and Z = 2). In 2, the 5-MeOI2CA anions act as bidentate bridging and bidentate chelating ligands. The asymmetric unit of 2 contains two crystallographically independent Cd(II) cations. One of the cations is coordinated to six oxygen atoms and shows an octahedral geometry with a rhombic deformation. The other Cd(II) cation adopts a distorted seven-coordinate pentagonal-bipyramidal geometry involving seven oxygen atoms. In 2, the DMSO solvent molecules play a key role in the formation of metal-organic frameworks by filling voids, which are created by the bridging and chelating 5-MeOI2CA anions, the cadmium cations and the other DMSO molecules coordinated to cadmium. Comprehensive theoretical calculations (including the optimized structural parameters, harmonic frequencies and vibrational intensities) were performed for 2 using the B3LYP method with the 6-311++G(d,p)/LanL2DZ basis sets. The infrared and Ramana spectra were measured and a detailed assignment of the experimental spectra of 2 was performed. All cadmium-oxygen stretching vibrations occur in the range below 400 cm-1.

  3. Conventional and microwave-assisted synthesis, characterization, DFT calculations, in vitro DNA binding and cleavage studies of potential chemotherapeutic diorganotin(IV) mandelates.

    Science.gov (United States)

    Mridula; Nath, Mala

    2016-09-01

    Diorganotin(IV) complexes of the general formulae {[R2Sn(L)]2O}(R=Me (1), n-Bu (2), and n-Oct (3); L=anion of mandelic acid) and {[R2Sn(L)]2Cl2}(R=Ph (4)) have been synthesized by conventional thermal method (1a-3a), except 4a and by microwave-assisted reactions (1b-4b). The elemental analysis, IR, NMR ((1)H, (13)C and (119)Sn) and ESI-MS/DART-mass spectral studies revealed that dimeric 1:1 complexes with SnOSn bridges (1-3) are formed possessing distorted trigonal bipyramidal geometry around the Sn atoms, except 4b which exhibits octahedral geometry with SnClSn bridges. The proposed geometries have been validated by density functional theory calculations. Thermal behavior of 1b-4b, studied by using thermogravimetry (TG), differential thermal analysis (DTA) and derivative thermogravimetric (DTG) techniques, indicated that all except 4b are stable up to 200°C. In vitro interaction studies of 1b-4b with CT-DNA were performed by UV-Vis, fluorescence titrations and results suggest that the complexes are binding to DNA via an intercalative mode. The binding affinity and quenching ability were quantified in terms of intrinsic binding constant (Kb) (3.74×10(4)M(-1), 2b; >3.67×10(4)M(-1), 4b; >3.03×10(4)M(-1), 3b; >0.72×10(4)M(-1), 1b) and Stern-Volmer quenching constant (Ksv) (2.16×10(5), 2b; >1.73×10(5), 4b; >1.66×10(5)3b; >1.51×10(5), 1b) which showed high binding affinity of 2b with CT-DNA. The cleavage studies of 1b-4b with pBR322 plasmid DNA was ascertained by agarose gel electrophoresis. They exhibited effective cleavage of supercoiled plasmid DNA into its nicked form (1b, 3b, 4b) and even into its linear form in presence of 2b.

  4. Synthesis, structures and DFT calculations of 2-(4,6-dimethyl pyrimidyl)selenolate complexes of Cu(I), Ag(I) and Au(I) and their conversion into metal selenide nanocrystals.

    Science.gov (United States)

    Sharma, Rakesh K; Wadawale, Amey; Kedarnath, G; Manna, Debashree; Ghanty, Tapan K; Vishwanadh, B; Jain, Vimal K

    2014-05-07

    The complexes [M{SeC4H(Me-4,6)2N2}]6 (M = Cu (1), Ag (2)) and [Au{SeC4H(Me-4,6)2N2}(PEt3)] (3) have been prepared and characterized by elemental analyses, UV-vis, NMR ((1)H, (13)C, (77)Se) spectroscopy and single crystal X-ray diffraction. The crystal structures of [Cu{SeC4H(Me-4,6)2N2}]6·H2O (1·H2O), [Ag{SeC4H(Me-4,6)2N2}]6·6MeOH·H2O (2·6MeOH·H2O) and [Au{SeC4H(Me-4,6)2N2}(PEt3)] (3) revealed that their metal centers acquire distorted square-pyramidal, trigonal and linear geometries, respectively. DFT calculations have been carried out to rationalize nuclearity in copper(i) chalcogenolate complexes. The calculations suggest that there is hardly any energy difference between the tetrameric and hexameric forms. Thermal behavior of [Cu{SeC4H(Me-4,6)2N2}]6 was studied by thermogravimetric analysis. Thermolysis of [M{SeC4H(Me-4,6)2N2}]6 (M = Cu, Ag) in 1-dodecanethiol (DDT) at 150 °C gave a cubic phase of Cu7Se4 and an orthorhombic phase of Ag2Se, respectively. Copper selenide (Cu7Se4) thin films were deposited on glass and silicon substrates by using [Cu{SeC4H(Me-4,6)2N2}]6 at 400 °C by AACVD.

  5. The new Schiff base 4-[(4-Hydroxy-3-fluoro-5-methoxy-benzylidene)amino]-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one: Experimental, DFT calculational studies and in vitro antimicrobial activity

    Science.gov (United States)

    İskeleli, Nazan Ocak; Alpaslan, Yelda Bingöl; Direkel, Şahin; Ertürk, Aliye Gediz; Süleymanoğlu, Nevin; Ustabaş, Reşat

    2015-03-01

    The synthesized Schiff base, 4-[(4-Hydroxy-3-fluoro-5-methoxy-benzylidene)amino]-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one (I), has been characterized by 13C NMR, 1H NMR, 2D NMR (1H-1H COSY and 13C APT), FT-IR, UV-vis and X-ray single-crystal techniques. Molecular geometry of the compound I in the ground state, vibrational frequencies and chemical shift values have been calculated by using the density functional method (DFT) with 6-311++G(d,p) basis set. The obtained results indicate that optimized geometry can well reflect the crystal structural parameters. The differences between experimental and calculated results of FT-IR and NMR have supported the existence of intermolecular (O-H⋯O type) and intramolecular (C-H⋯O type) hydrogen bonds in the crystal structure. Molecular electrostatic potential (MEP), frontier molecular orbital analysis (HOMO-LUMO) and electronic absorption spectra were carried out at B3LYP/6-311G++(d,p). HOMO-LUMO electronic transition of 3.92 eV is due to contribution of the bands the n → π∗. The antimicrobial activity of the compound I was determined against the selected 11 bacteria and 8 fungi by microdilution broth assay with Alamar Blue. In vitro studies showed that the compound I has no antifungal effect for selected fungal isolates. However, the compound I shows remarkable antibacterial effect for the bacteria; Streptococcus pneumoniae, Haemophilus influenzae and Enterococcus faecalis.

  6. Photo release of nitrous oxide from the hyponitrite ion studied by infrared spectroscopy. Evidence for the generation of a cobalt-N2O complex. Experimental and DFT calculations

    Science.gov (United States)

    Chacón Villalba, M. Elizabeth; Franca, Carlos A.; Güida, Jorge A.

    2017-04-01

    The solid state photolysis of sodium, silver and thallium hyponitrite (M2N2O2, M = Na, Ag, Tl) salts and a binuclear complex of cobalt bridged by hyponitrite ([Co(NH3)5-N(O)-NO-Co(NH3)5]4 +) were studied by irradiation with visible and UV light in the electronic absorption region. The UV-visible spectra for free hyponitrite ion and binuclear complex of cobalt were interpreted in terms of Density Functional Theory calculations in order to explain photolysis behavior. The photolysis of each compound depends selectively on the irradiation wavelength. Irradiation with 340-460 nm light and with the 488 nm laser line generates photolysis only in silver and thallium hyponitrite salts, while 253.7 nm light photolyzed all the studied compounds. Infrared spectroscopy was used to follow the photolysis process and to identify the generated products. Remarkably, gaseous N2O was detected after photolysis in the infrared spectra of sodium, silver, and thallium hyponitrite KBr pellets. The spectra for [Co(NH3)5-N(O)-NO-Co(NH3)5]4 + suggest that one cobalt ion remains bonded to N2O from which the generation of a [(NH3)5CoNNO]+ 3 complex is inferred. Density Functional Theory (DFT) based calculations confirm the stability of this last complex and provide the theoretical data which are used in the interpretation of the electronic spectra of the hyponitrite ion and the cobalt binuclear complex and thus in the elucidation of their photolysis behavior. Carbonate ion is also detected after photolysis in all studied compounds, presumably due to the reaction of atmospheric CO2 with the microcrystal surface reaction products. Kinetic measurements for the photolysis of the binuclear complex suggest a first order law for the intensity decay of the hyponitrite IR bands and for the intensity increase in the N2O generation. Predicted and experimental data are in very good agreement.

  7. A structural study of [CpM(CO)3H] (M = Cr, Mo and W) by single-crystal X-ray diffraction and DFT calculations: sterically crowded yet surprisingly flexible molecules.

    Science.gov (United States)

    Burchell, Richard P L; Sirsch, Peter; Decken, Andreas; McGrady, G Sean

    2009-08-14

    The single-crystal X-ray structures of the complexes [CpCr(CO)3H] 1, [CpMo(CO)3H] 2 and [CpW(CO)3H] 3 are reported. The results indicate that 1 adopts a structure close to a distorted three-legged piano stool geometry, whereas a conventional four-legged piano stool arrangement is observed for 2 and 3. Further insight into the equilibrium geometries and potential energy surfaces of all three complexes was obtained by DFT calculations. These show that in the gas phase complex 1 also prefers a geometry close to a four-legged piano stool in line with its heavier congeners, and implying strong packing forces at work for 1 in the solid state. Comparison with their isolelectronic group 7 tricarbonyl counterparts [CpM(CO)3] (M = Mn 4 and Re 5) illustrates that 1, 2 and 3 are sterically crowded complexes. However, a surprisingly soft bending potential is evident for the M-H moiety, whose order (1 approximately = 2 < 3) correlates with the M-H bond strength rather than with the degree of congestion at the metal centre, indicating electronic rather than steric control of the potential. The calculations also reveal cooperative motions of the hydride and carbonyl ligands in the M(CO)3H unit, which allow the M-H moiety to move freely, in spite of the closeness of the four basal ligands, helping to explain the surprising flexibility of the crowded coordination sphere observed for this family of high CN complexes.

  8. Improved DFT Potential Energy Surfaces via Improved Densities.

    Science.gov (United States)

    Kim, Min-Cheol; Park, Hansol; Son, Suyeon; Sim, Eunji; Burke, Kieron

    2015-10-01

    Density-corrected DFT is a method that cures several failures of self-consistent semilocal DFT calculations by using a more accurate density instead. A novel procedure employs the Hartree-Fock density to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear molecules. We show that this works for both neutral and charged molecules. We explain why and explore more difficult cases, for example, CH(+), where density-corrected DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases.

  9. Indirect "no-bond" ³¹P···³¹P spin-spin couplings in P,P-[3]ferrocenophanes: insights from solid-state NMR spectroscopy and DFT calculations.

    Science.gov (United States)

    Wiegand, Thomas; Eckert, Hellmut; Ren, Jinjun; Brunklaus, Gunther; Fröhlich, Roland; Daniliuc, Constantin G; Lübbe, Gerrit; Bussmann, Kathrin; Kehr, Gerald; Erker, Gerhard; Grimme, Stefan

    2014-03-27

    No-bond (31)P-(31)P indirect dipolar couplings, which arise from the transmission of nuclear spin polarization through interaction of proximal nonbonded electron pairs have been investigated in the solid state for a series of closely related substituted P,P-[3]ferrocenophanes and model systems. Through variation and combination of ligands (phenyl, cyclohexyl, isopropyl) at the two phosphorus sites, the P···P distances in these compounds can be varied from 3.49 to 4.06 Å. Thus, the distance dependence of the indirect no-bond coupling constant J(nb) can be studied in a series of closely related compounds. One- and two-dimensional solid-state NMR experiments serve to establish the character of these couplings and to measure the isotropic coupling constants J(iso), which were found to range between 12 and 250 Hz. To develop an understanding of the magnitude of J(nb) in terms of molecular structure, their dependences on intramolecular internuclear distances and relative orbital orientations is discussed by DFT-calculations on suitable models. In agreement with the literature the dependence of J(nb) on the P···P distance is found to be exponential; however, the steepness of this curve is highly dependent on the internuclear equilibrium distance. For a quantitative description, the off-diagonal elements of the expectation value of the Kohn-Sham-Fock operator in the LMO basis for the LMOs of the two phosphorus lone-pairs is proposed. This parameter correlates linearly with the calculated J(nb) values and possesses the same distance-dependence. In addition, the simulations indicate a distinct dependence of J(nb) on the dihedral angle defined by the two C-P bonds providing ligation to the molecular backbone. For disordered materials or those featuring multiple sites, conformers, and/or polymorphism, a new double-quantum NMR method termed DQ-DRENAR can be used to conveniently measure internuclear (31)P-(31)P distances. If conducted on compounds with known P

  10. Investigation of the Electronic and pH-Sensing properties of Hydroxyl-Functionalized Imine-Linked Polymers via the UV-vis Absorption Spectra and the Density Functional Theory (DFT Calculations

    Directory of Open Access Journals (Sweden)

    Ibtesam Y. Aljaafreh

    2017-01-01

    Full Text Available In this report, a synergetic computational and experimental studies were demonstrated on examples of poly-imine polymers; P(PI-IPI and P(PIOH-IPI to explore the role of hydroxyl substituent on their sensing and electronic properties. The polymer P(PIOH-IPI bearing the OH-group on the ortho-position to the imine-bond, while the structure of the polymer P(PI-IPI reveal the imine-bond only. The sensing property of the polymers was investigated via the UV-vis absorption in different solvents, acidic and basic solutions. Both polymers have shown significant sensing behavior in the acidic medium, while unpronounced behavior was noticed in the case of the polymer P(PI-IPI in basic medium. Upon the incorporation of the OH-group, the polymer P(PIOH-IPI has indistinguishable sensing behavior, a similar blue-shift in the acidic and basic medium, which can be attributed to the presence and the position of OH-group. The optical band gap of the polymers was determined experimentally and theoretically from the UV-vis absorption spectra and DFT calculations in the DMSO solvent. Other factors that affect the band gap values such as the structural conformation and length of conjugation were explored theoretically. In general, as the length of the optimized chain increased, the spectrum is red-shifted and the band gap decreased, which is attributed to the possible loss of chain planarity and conjugation beyond the monomer structure. Interestingly, the UV-vis spectra of the monomer-optimized structures were in a good match with the experimental UV-vis spectra. However, the band gap difference can be attributed to the method of band gap determination.

  11. Synthesis, characterization, DFT calculations and biological studies of Mn(II), Fe(II), Co(II) and Cd(II) complexes based on a tetradentate ONNO donor Schiff base ligand

    Science.gov (United States)

    Abdel-Rahman, Laila H.; Ismail, Nabawia M.; Ismael, Mohamed; Abu-Dief, Ahmed M.; Ahmed, Ebtehal Abdel-Hameed

    2017-04-01

    This study highlights synthesis and characterization of a tetradentate ONNO Schiff base ligand namely (1, 1‧- (pyridine-2, 3-dimethyliminomethyl) naphthalene-2, 2‧-diol) and hereafter denotes as "HNDAP″ and selected metal complexes including Mn(II), Fe(II), Co(II) and Cd(II) as a central metal. HNDAP was synthesized from 1:2 M ratio condensation of 2, 3-diaminopyridine and 2- hydroxy-1-naphthaldhyde, respectively. The stoichiometric ratios of the prepared complexes were estimated using complementary techniques such as; elemental analyses (-C, H, N), FT-IR, magnetic measurements and molar conductivity. Furthermore, their physicochemical studies were carried out using thermal TGA, DTA and kinetic-thermodynamic studies along with DFT calculations. The results of elemental analyses showed that these complexes are present in a 1:1 metal-to- ligand molar ratio. Moreover, the magnetic susceptibilities values at room temperature revealed that Mn(II), Fe(II) and Co(II) complexes are paramagnetic in nature and have an octahedral (Oh) geometry. In contrast, Cd(II) is diamagnetic and stabilizes in square planar sites. The molar conductivity measurements indicated that all complexes are nonelectrolytes in dimethyl formamide. Spectral data suggested that the ligand is as tetradentate and coordinated with Co(II) ion through two phenolic OH and two azomethine nitrogen. However, for Mn(II), Fe(II) and Cd(II) complexes, the coordination occurred through two phenolic oxygen and two azomethine nitrogen with deprotonation of OH groups. The proposed chemical structures have been validated by quantum mechanics calculations. Antimicrobial activities of both the HNDAP Schiff base ligand and its metal complexes were tested against strains of Gram (-ve) E. coli and Gram (+ve) B. subtilis and S. aureus bacteria and C. albicans, A. flavus and T. rubrum fungi. All the prepared compounds showed good results of inhibition against the selected pathogenic microorganisms. The investigated

  12. Unveiling the non-covalent interactions of molecular homodimers by dispersion-corrected DFT calculations and collision-induced broadening of ro-vibrational transitions: application to (CH2F2)2 and (SO2)2.

    Science.gov (United States)

    Tasinato, Nicola; Grimme, Stefan

    2015-02-28

    Thermodynamic and spectroscopic properties of molecular complexes featuring non-covalent interactions, such as van der Waals forces and hydrogen bonds, are of fundamental interest in many fields, ranging from chemistry and biology to nanotechnology. In the present work the homodimers of difluoromethane (CH2F2) and sulfur dioxide (SO2) are investigated theoretically using dispersion-corrected density functional theory (DFT-D3) and experimentally by tunable diode laser (TDL) infrared (IR) spectroscopy. The dissociation energies of (CH2F2)2 and (SO2)2 are determined experimentally from the broadening of the ro-vibrational transitions of the corresponding monomers collisionally perturbed by a range of damping gases. The resulting dissociation energies are 2.79 ± 0.32 and 2.62 ± 0.16 kcal mol(-1) for the CH2F2 and SO2 dimers, respectively. Six to nine different stationary points on the PES of the two complexes are investigated theoretically at the DFT-D3 level, retrieving the corresponding dissociation energies, structures and rotational constants. Computations are carried out by employing six different density functionals (BLYP, TPSS, B3LYP, PBE0, TPSSh, and PW6B95) in conjunction with def2-TZVP and in a few cases def2-QZVP basis sets. DFT-D3 dissociation energies are benchmarked against reference values from CCSD(T)/CBS computations, and furthermore compared to experimental ones. A very good agreement between theory and experiment is attained, showing that DFT-D3 provides a significant improvement over standard DFT. This work shows that dissociation energies of homodimers can be consistently derived from collisional broadening cross sections and that interaction energies at various DFT-D3 levels (nearly) reach the accuracy of highly correlated wavefunction methods.

  13. On the molecular and supramolecular properties of N,N‧-disubstituted iminoisoindolines: Synthesis, spectroscopy, X-ray structure and Hirshfeld surface analyses, and DFT calculations of two (E)-N,N‧-bis(aryl)iminoisoindolines (aryl = 2-tert-butylphenyl or perfluorophenyl)

    Science.gov (United States)

    Bitzer, Rodrigo S.; Visentin, Lorenzo C.; Hörner, Manfredo; Nascimento, Marco A. C.; Filgueiras, Carlos A. L.

    2017-02-01

    Supramolecular studies of iminoisoindoline-derived compounds have been prompted by their biological and photophysical properties. In this article, we report the synthesis, spectroscopy, X-ray structural characterization, and DFT study of two N,N‧-(aryl)-disubstituted 1-iminoisoindolines, namely (E)-N,N‧-bis(2-tert-butylphenyl)iminoisoindoline (2-t-BuPhimiso) and (E)-N,N‧-bis(perfluorophenyl)iminoisoindoline (F5Phimiso). Our X-ray structural analyses have shown that the isoindoline N2 atom of 2-t-BuPhimiso is slightly pyramidalized whereas the respective atom of F5Phimiso displays the expected trigonal planar geometry. The supramolecular arrangement of 2-t-BuPhimiso comprises one-dimensional chains along the [101] direction formed by Csbnd H···πarene interactions, in which the isoindoline ring behaves as a hydrogen-bond donor. For 2-t-BuPhimiso, DFT calculations at the B97-D3/6-311G** level have shown that the dimer formed by this Csbnd H···πarene contact displays a binding energy of -12.83 kcal mol-1. Product F5Phimiso assembles in the crystal state through type-I F3 synthons in addition to Csbnd H⋯F, C-Fδ-···πF+, and πarene/F-πarene/F stacking interactions. Accordingly, our DFT-D3 calculations have confirmed that these interactions synergistically play a dominating role in the crystal packing of F5Phimiso. Finally, the relative stability of the (Z) and (E) isomers of each product has been evaluated at the DFT level of theory. Our calculations have shown that the (E) forms are the most stable ones.

  14. A DFT Calculation Screening of Pt-Based Bimetallic Catalysts for Oxygen Reduction%Pt基合金氧还原催化剂设计的密度泛函理论计算研究

    Institute of Scientific and Technical Information of China (English)

    欧利辉; 陈胜利

    2013-01-01

    Developing Pt-lean catalysts for oxygen reduction reaction (ORR) is the key for the large-scale application of the proton exchange membrane fuel cell (PEMFC). In this paper, we have proposed a multiple-descriptor strategy for screening efficient and durable ORR alloy catalysts of low Pt content. We demonstrate that an ideal Pt-based bimetallic alloy catalyst for ORR should possess simultaneously negative alloy formation energy, negative surface segregation energy of Pt and a lower oxygen binding ability than pure Pt. By performing detailed DFT calculations on the thermodynamics, surface chemical and electronic properties of various Pt-M alloys (M refers to non-precious transition metals in the periodic table), Pt-V,Pt-Fe,Pt-Co,Pt-Ni,Pt-Cu,Pt-Zn, Pt-Mo, Pt-W alloys are predicted to have improved catalytic activity and durability for ORR, most of which have indeed been reported to have excellent ORR catalytic performance in the literature. It is suggested that the ORR performance of Pt-Zn and Pt-Mo systems deserve detailed theoretical and experimental investigations.%本文提出以合金形成能、Pt表面偏析能和氧原子吸附能作为依据筛选具有高活性和高稳定性的表面富Pt氧还原合金催化剂.利用DFT计算对Pt与各种过渡金属形成的合金的热力学、表面化学和电子性质进行了系统研究,在此基础上预测Pt-V、Pt-Fe、Pt-Co、Pt-Ni、Pt-Cu、Pt-Zn、Pt-Mo和Pt-W等合金可能具有好的氧还原催化活性和稳定性.所预期的大部分催化剂已有文献研究结果支持.另外,Pt-Zn和Pt-Mo体系目前报道尚不多,值得进一步细致研究.

  15. Selective activation of C-F and C-H bonds with iron complexes, the relevant mechanism study by DFT calculations and study on the chemical properties of hydrido iron complex.

    Science.gov (United States)

    Xu, Xiaofeng; Jia, Jiong; Sun, Hongjian; Liu, Yuxia; Xu, Wengang; Shi, Yujie; Zhang, Dongju; Li, Xiaoyan

    2013-03-14

    The reactions of (2,6-difluorophenyl)phenylmethanone (2,6-F(2)C(6)H(3)-C(=O)-C(6)H(5)) (1) and (2,6-difluorophenyl)phenylmethanimine (2,6-F(2)C(6)H(3)-C(=NH)-C(6)H(5)) (3) with Fe(PMe(3))(4) afforded different selective C-F/C-H bond activation products. The reaction of 1 with Fe(PMe(3))(4) gave rise to bis-chelate iron(II) complex [C(6)H(5)-C(=O)-3-FC(6)H(3))Fe(PMe(3))](2) (2) via C-F bond activation. The reaction of 3 with Fe(PMe(3))(4) delivered chelate hydrido iron(II) complex 2,6-F(2)C(6)H(3)-C(=NH)-C(6)H(4))Fe(H)(PMe(3))(3) (4) through C-H bond activation. The DFT calculations show the detailed elementary steps of the mechanism of formation of hydrido complex 4 and indicate 4 is the kinetically preferred product. Complex 4 reacted with HCl, CH(3)Br and CH(3)I delivered the chelate iron halides (2,6-F(2)C(6)H(3)-C(=NH)-C(6)H(4))Fe(PMe(3))(3)X (X = Cl (5); Br (6); I (7)). A ligand (PMe(3)) replacement by CO of 4 was observed giving (2,6-F(2)C(6)H(3)-C(=NH)-C(6)H(4))Fe(H)(CO)(PMe(3))(2) (8). The chelate ligand exchange occurred through the reaction of 4 with salicylaldehydes. The reaction of 4 with Me(3)SiC[triple bond, length as m-dash]CH afforded (2,6-F(2)C(6)H(3)-C([double bond, length as m-dash]N)-C(6)H(5))Fe(C≡C-SiMe(3))(PMe(3))(3) (11). A reaction mechanism from 4 to 11 was discussed with the support of IR monitoring. The molecular structures of complexes 2, 4, 6, 7, 10 and 11 were determined by X-ray diffraction.

  16. DFT calculation of core- and valence-shell electron excitation and ionization energies of 2,1,3-benzothiadiazole C{sub 6}H{sub 4}SN{sub 2}, 1,3,2,4-benzodithiadiazine C{sub 6}H{sub 4}S{sub 2}N{sub 2}, and 1,3,5,2,4-benzotrithiadiazepine C{sub 6}H{sub 4}S{sub 3}N{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Takahata, Yuji, E-mail: taka@iqm.unicamp.br [Amazonas State University, Av. Darcy Vargas, 1200, Parque 10, 69065-020 Manaus, AM (Brazil); Institute of Chemistry, University of Campinas - UNICAMP, 13084-862 Campinas, SP (Brazil); Chong, Delano P. [Department of Chemistry, 2036 Main Mall, University of British Columbia, Vancouver, BC, Canada V6T 1Z1 (Canada)

    2012-11-15

    Highlights: Black-Right-Pointing-Pointer DFT calculations resulted average error of 0.14 eV for VIP, and 0.4 for CEBE. Black-Right-Pointing-Pointer The multiplet approximation (MA) resulted average error of 0.56 eV for core excitation energies. Black-Right-Pointing-Pointer A shifted energy method to calculated core-electron excitation energy was proposed. Black-Right-Pointing-Pointer The method is based on a combination between MA and TDDFT. Black-Right-Pointing-Pointer Convoluted spectra reproduce observed spectra in low energy region. -- Abstract: The vertical core- and valence-shell electron excitation and ionization energies of the three title molecules, 1-3, were calculated by density functional theory (DFT) using adequate functional for each type of processes and atoms under study. The inner shells treated were C1s, N1s, S1s, S2s, S2p. Molecular geometry was optimized by DFT B3LYP/6-311 + (d,p). The basis set of triple zeta plus polarization (TZP) Slater-type orbitals was employed for DFT calculations. The {Delta}SCF method was used to calculate ionization energies. The average absolute deviation (AAD) from experiment of 26 valence-electron ionization energies calculated by DFT for the three molecules 1-3 was 0.14 eV; while that of 24 calculated core-electron binding energies (CEBEs) from experiment was 0.4 eV. Selected core excitation energies were calculated by the multiplet approximation for the three molecules. The AAD of twelve calculated core excitation energies by the multiplet approximation that exclude S2s cases was 0.56 eV. Time-dependent DFT (TDDFT) was employed to calculate the excitation energies and corresponding oscillator strengths of core- and valence-electrons of the molecules. Some selected occupied core orbitals were used to calculate the core-excitation energies with the TDDFT (Sterner-Frozoni-Simone scheme). The core excitation energies thus calculated were in an average error of ca. 28 eV compared to observed values. They were shifted

  17. Synthesis, DFT calculations, electronic structure, electronic absorption spectra, natural bond orbital (NBO) and nonlinear optical (NLO) analysis of the novel 5-methyl-8H-benzo[h]chromeno[2,3-b][1,6] naphthyridine-6(5H),8-dione (MBCND)

    Science.gov (United States)

    Halim, Shimaa Abdel; Ibrahim, Magdy A.

    2017-02-01

    New derivative of heteroannulated chromone identified as 5-methyl-8H-benzo[h]chromeno[2,3-b][1,6]naphthyridine-6(5H),8-dione (5, MBCND) was easily and efficiently synthesized from DBU catalyzed condensation reaction of 2-aminochromone-3-carboxaldehyde (1) with 4-hydroxy-1-methylquinolin-2(1H)-one (2). The same product 5 was isolated from condensation reaction of aldeyde 1 with 3-(4-hydroxy-1-methyl-2-oxo-1,2-dihydroquinolin-3-yl)-3-oxopropanoic acid (3) or ethyl 4-(4-hydroxy-1-methyl-2-oxo-1,2-dihydroquinolin-3-yl)-2,4-dioxobutanoate (4). Structure of compound (5, MBCND) was deduced based on their elemental analyses and spectral data (IR, 1H NMR and mass spectra). Density Functional Theory (DFT) calculations at the B3LYP/6-311G (d,p) level of theory have been carried out to investigate the equilibrium geometry of the novel compound (5, MBCND). Moreover, total energy, energy of HOMO and LUMO and Mullikan atomic charges were calculated. In addition, the dipole moment, theoretical study of the electronic structure, nonlinear optical properties (NLO), and natural bonding orbital (NBO) analysis and orientation have been performed and discussed. Also the electronic absorption spectra were measured in polar (methanol) as well as non polar (dioxane) solvents and the assignment of the observed bands has been discussed by TD-DFT calculations. The correspondences between calculated and experimental transitions energies are satisfactory.

  18. Adaptive DFT-based Interferometer Fringe Tracking

    Science.gov (United States)

    Wilson, Edward; Pedretti, Ettore; Bregman, Jesse; Mah, Robert W.; Traub, Wesley A.

    2004-01-01

    An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA) observatory at Mt. Hopkins, Arizona. The system can minimize the optical path differences (OPDs) for all three baselines of the Michelson stellar interferometer at IOTA. Based on sliding window discrete Fourier transform (DFT) calculations that were optimized for computational efficiency and robustness to atmospheric disturbances, the algorithm has also been tested extensively on off-line data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately 2.0 milliseconds per scan (including all three interferograms), using the science camera and piezo scanners to measure and correct the OPDs. The adaptive DFT-based tracking algorithm should be applicable to other systems where there is a need to detect or track a signal with an approximately constant-frequency carrier pulse.

  19. Generalized gravity from modified DFT

    CERN Document Server

    Sakatani, Yuho; Yoshida, Kentaroh

    2016-01-01

    Recently, generalized equations of type IIB supergravity have been derived from the requirement of classical kappa-symmetry of type IIB superstring theory in the Green-Schwarz formulation. These equations are covariant under generalized T-duality transformations and hence one may expect a formulation similar to double field theory (DFT). In this paper, we consider a modification of the DFT equations of motion by relaxing a condition for the generalized covariant derivative with an extra generalized vector. In this modified double field theory (mDFT), we show that the flatness condition of the modified generalized Ricci tensor leads to the NS-NS part of the generalized equations of type IIB supergravity. In particular, the extra vector fields appearing in the generalized equations correspond to the extra generalized vector in mDFT. We also discuss duality symmetries and a modification of the string charge in mDFT.

  20. Computational Molecular Electronic Spectroscopy with TD-DFT.

    Science.gov (United States)

    Jacquemin, Denis; Adamo, Carlo

    2016-01-01

    In this chapter we present applications of TD-DFT aiming at reproducing and rationalizing the optical signatures of molecules, and, more precisely, the absorption and fluorescence spectra of conjugated compounds belonging to both organic and inorganic families. We particularly focus on the computations going beyond the vertical approximation, i.e., on the calculation of 0-0 energies and vibronic spectra with TD-DFT, and on large applications performed for "real-life" structures (organic and inorganic dyes, optimization of charge-transfer structures, rationalization of excited-state proton transfer, etc.). We present a series of recent applications of TD-DFT methodology for these different aspects. The main conclusions of TD-DFT benchmarks aiming at pinpointing the most suited exchange-correlation functionals are also discussed.

  1. Semiempirical and DFT Investigations of the Dissociation of Alkyl Halides

    Science.gov (United States)

    Waas, Jack R.

    2006-01-01

    Enthalpy changes corresponding to the gas phase heats of dissociation of 12 organic halides were calculated using two semiempirical methods, the Hartree-Fock method, and two DFT methods. These calculated values were compared to experimental values where possible. All five methods agreed generally with the expected empirically known trends in the…

  2. New bisphosphomide ligands, 1,3-phenylenebis((diphenylphosphino)methanone) and (2-bromo-1,3-phenylene)bis((diphenylphosphino)methanone): synthesis, coordination behavior, DFT calculations and catalytic studies.

    Science.gov (United States)

    Kumar, Pawan; Siddiqui, Mujahuddin M; Reddi, Yerrnaidu; Mague, Joel T; Sunoj, Raghavan B; Balakrishna, Maravanji S

    2013-08-28

    )}AuCl] (19), in good yield. The structures of complexes 5, 7-10, 12 and 14a were confirmed by single-crystal X-ray diffraction studies. DFT calculations were performed in order to gain additional insights into the structure and bonding of the pincer complexes. An additional analysis of the orbital interactions in the case of palladium complex 9 is also included. The in situ generated rhodium complex of bisphosphomide 1 showed moderate to good selectivity in the hydroformylation of hex-1-ene and styrene derivatives.

  3. Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions.

    Science.gov (United States)

    Morgado, Claudio A; Jurecka, Petr; Svozil, Daniel; Hobza, Pavel; Sponer, Jirí

    2010-04-14

    We have performed reference quantum-chemical calculations for about 130 structures of adenine dimers in stacked conformations, with special attention given to dimers that are either vertically compressed (parallel structures) or contain close interatomic contacts (non-parallel structures). Such geometries are sampled during thermal fluctuations of nucleic acids and contribute to the local conformational variability of these systems. Their theoretical characterization requires a good description of interaction energies in the short-range repulsion region. The reference calculations have been performed with the CBS(T) method, i.e., MP2/CBS computations corrected for higher-order electron-correlation effects using the CCSD(T) method. These benchmark data have been used to examine the performance of the DFT-D, SCS(MI)-MP2, MP2.5, M06-2X and CBS(SCS-D) quantum-mechanical methods, and of the AMBER Cornell et al. force field. The present results, as well as those of our previous study on stacked uracil dimers, confirm that the force field severely exaggerates the repulsion at short intermolecular distances. This behavior complicates the use of the force field in scans of the stacking-energy dependence on local conformational parameters in nucleic acids. Compared against the previous results obtained in the uracil dimer study, the performance of DFT-D to describe stacking at short intermolecular distances has worsened, showing for the adenine dimers a larger exaggeration of the repulsion, especially for structures where the monomers are parallel to each other. Despite these deviations, the performance of DFT-D is still reasonably good and this method provides, for example, a relatively inexpensive way to monitor stacking energies along molecular dynamics trajectories. The best performers are the MP2.5, SCS(MI)-MP2, and CBS(SCS-D) methods. In addition, the energy profiles given by the SCS(MI)-MP2 and CBS(SCS-D) methods are the ones that most closely resemble the CBS(T) data

  4. Vibrational spectroscopic studies, NMR, HOMO-LUMO, NLO and NBO analysis of 1-(2-nitrobenzoyl)-3,5-diphenyl-4,5-dihydro-1H-pyrazole with use X-ray diffractions and DFT calculations

    Science.gov (United States)

    Demir, Sibel; Tinmaz, Feyza; Dege, Necmi; Ilhan, Ilhan Ozer

    2016-03-01

    The crystal and molecular structure of the title compound, 1-(2-nitrobenzoyl)-3,5-diphenyl-4,5-dihydro-1H-pyrazole, was reported and confirmed by single crystal X-ray diffraction and spectroscopic data. The structure, geometry optimization, vibrational frequencies and nuclear magnetic resonance were also investigated. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation was analysed using natural bond orbital analysis. The results show that charge in electron density (ED) in the σ∗ and π∗ antibonding orbitals and second-order delocalisation energies E(2) confirms the occurrence of intramolecular charge transfer within the molecule. Satisfactory theoretical aspects were made for the stable conformer of the molecule using density functional theory DFT-B3LYP methods with the 6-311G++(d,p) basis set.

  5. New Fe(III) complex with 8-(4-chlorophenyl)-3-butyl-3H-imidazo[4‧,5‧:3,4]benzo[1,2-c]isoxazol-5-amine (5-AIBI) ligand: Synthesis, spectroscopic characterization and DFT calculations

    Science.gov (United States)

    Agheli, Zahra; Pordel, Mehdi; Beyramabadi, S. Ali

    2017-02-01

    The new heterocyclic ligand 8-(4-chlorophenyl)-3-butyl-3H-imidazo[4‧,5‧:3,4]benzo [1,2-c]isoxazol-5-amine (5-AIBI) was synthesized from the reduction of 3-butyl-8-(4-chlorophenyl)-5-nitro-3H-imidazo[4‧,5‧:3,4]benzo[1,2-c]isoxazole in high yield. The coordination ability of the ligand with some cations was examined by spectrophotometric method at rt condition. Results showed that only the absorption spectra of the Fe3+-5-AIBI complex show a high redshift of the absorption maximum in the aqueous ethanol solution. The effect of pH on the absorption spectrum of the green iron-5-AIBI complex was also investigated. In addition, density functional theory (DFT) calculations are performed to provide the optimized geometries, structural parameters, calculated chemical shifts and vibrational frequencies of the investigated Fe(III) complex.

  6. Assessment of DFT functionals with fluorine-fluorine coupling constants

    Science.gov (United States)

    García de la Vega, J. M.; San Fabián, J.

    2015-07-01

    Density functional theory (DFT) calculations of nuclear magnetic resonance (NMR) spin-spin coupling constants (SSCCs) provide an important contribution for understanding experimentally observed values. It is known that calculated SSCCs using DFT methods correlate well with those experimentally measured. Unlike most of SSCCs, in fluorine compounds, fluorine-fluorine SSCC JFF shows that the Fermi contact (FC) term is not dominant, particularly for JFF in polyfluorinated organic molecules. In order to devise a DFT approach that would correctly reproduce the variation of SSCCs within a series of fluorine compounds, we test several DFT-based approaches, using different exchange and correlation functionals. Isotropic contributions to NMR fluorine-fluorine coupling constants (FC, spin-dipolar, SD, paramagnetic spin-orbit, PSO, and diamagnetic spin-orbit, DSO) have been calculated. Results show that DFT methods give appropriate values for nJFF (n = 4 to 7), while for geminal and vicinal JFF present large deviations from experimental values. For the latter SSCCs (2JFF and 3JFF), the four contributions (FC, SD, PSO and DSO) are analysed as a function of the local and nonlocal exchange in 1,1- and 1,2-difluoroethylene. Although FC term is not dominant for these SSCCs, the variation of this contribution with exchange is remarkable. On the other hand, SD and PSO contributions can be suitably computed without and with exact exchange, respectively. This article is dedicated to the memory of Prof. N. C. Handy, whose contributions to the development of Theoretical Chemistry have been widely recognized.

  7. Rigid Coumarins: a Complete DFT, TD-DFT and Non Linear Optical Property Study.

    Science.gov (United States)

    Lanke, Sandip K; Sekar, Nagaiyan

    2015-09-01

    The electronic structures and photophysical properties of rigid coumarin dyes have been studied by using quantum chemical methods. The ground-state geometries of these dyes were optimized using the Density Functional Theory (DFT) methods. The lowest singlet excited state was optimized using Time -Dependent Density Functional Theory [TD-B3LYP/6-31G(d)]. On the basis of ground- and excited-state geometries, the absorption and emission spectra have been calculated using the DFT and TD-DFT method. All the calculations were carried out in gas phase and in acetonitrile medium. The results show that the absorption maxima and fluorescence emission maxima calculated using the Time-Dependent Density Functional Theory is in good agreement with the available experimental results. To understand the Non- Linear Optical properties of coumarin dyes we computed dipole moment (μ), electronic polarizability (α), mean first hyperpolarizability (βo) and second hyperpolarizability (γ) using B3LYP density functional theory method in conjunction with 6-31G(d) basis set.

  8. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine.

    Science.gov (United States)

    Srivastava, Santosh K; Singh, Vipin B

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  9. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

    Science.gov (United States)

    Srivastava, Santosh K.; Singh, Vipin B.

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  10. Infinite-basis calculations of binding energies for the hydrogen bonded and stacked tetramers of formic acid and formamide and their use for validation of hybrid DFT and ab initio methods.

    Science.gov (United States)

    Zhao, Yan; Truhlar, Donald G

    2005-08-04

    Benchmark stabilization energies for planar H-bonded and stacked structures of formic acid tetramers and formamide tetramers were determined as the sum of the infinite basis set limit of MP2 energies and a CCSD(T) correction term evaluated with the 6-31G*(0.25) basis set. The infinite basis (IB) set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and separate extrapolation of the Hartree-Fock and correlation energies with new IB parameters for augmented basis sets determined here. Final stabilization energies (kcal/mol) for the tetramer studied are in the range of 4.6 to approximately 6.7 kcal/mol and they were used as reference data to test 14 density functionals. Among the tested DFT methods, PWB6K gives the best performance with an average error equal to only 30% of the average binding energy. In contrast, the popular B3LYP functional has an average error of 85%. We recommend the PWB6K method for exploring the potential energy surfaces of organic complexes and clusters and supramolecular assemblies.

  11. TD-DFT and DFT/MRCI study of electronic excitations in Violaxanthin and Zeaxanthin

    Science.gov (United States)

    Götze, Jan Philipp; Thiel, Walter

    2013-03-01

    We report vibrationally broadened Franck-Condon (FC) spectra of Violaxanthin (Vx) and Zeaxanthin (Zx) for the lowest-energy 1Ag → 1Bu band that arises from the bright HOMO → LUMO single-electron excitation. Geometries were optimized using standard (1Ag) and time-dependent (1Bu) density functional theory (DFT) at the (TD-)CAM-B3LYP/6-31G(d) level, both in the gas phase and in acetone using a polarizable continuum model (PCM). DFT/MRCI multireference calculations were performed at the optimized (TD)-CAM-B3LYP structures to evaluate the energies of doubly excited states that are not accessible to linear response TD-DFT theory. The FC spectra were calculated using the time-independent (TI) scheme. The calculated spectra of Vx and Zx are very similar, with a red shift of about 0.1 eV for Zx relative to Vx, which is in agreement with the experimental data. The predicted spectral peaks of Vx and Zx deviate from experiment by less than 0.1 eV when performing the calculations in the gas phase. In the presence of acetone (PCM model), there are larger deviations so that a state specific correction scheme needs to be applied, which accounts for non-equilibrium solvent relaxation. The 1Ag → 1Bu vertical absorption energies and the corresponding vertical fluorescence energies from TD-CAM-B3LYP and DFT/MRCI agree reasonably well. The DFT/MRCI absorption and fluorescence energies for the doubly excited 2Ag and 2Bu states are found to be rather sensitive to the underlying geometry, in particular to the bond length alternation in the polyene chain. In acetone (PCM), Vx and Zx show little bond alternation, and thus the doubly excited Bu state becomes the lowest excited Bu state. (TD)-CAM-B3LYP appears to be suitable for generating realistic geometries for higher-level calculations in such molecules.

  12. Synthesis, characterization of (3E)-1-(6-chloro-2-methyl-4-phenyl quinolin-3-Yl)-3-aryl prop-2-en-1-ones through IR, NMR, single crystal X-ray diffraction and insights into their electronic structure using DFT calculations

    Science.gov (United States)

    Sarveswari, S.; Srikanth, A.; Arul Murugan, N.; Vijayakumar, V.; Jasinski, Jerry P.; Beauchesne, Hanna C.; Jarvis, Ethan E.

    2015-02-01

    3E-1-(6-Chloro-2-methyl-4-phenylquinolin-3-yl)-3-arylprop-2-en-1-ones were synthesized and characterized by FTIR, 1H NMR, 13C NMR, HSQC, DEPT-135. In addition the compound 3E-1-(6-chloro-2-methyl-4-phenylquinolin-3-yl)-3-(2,5-dimethoxyphenyl)prop-2-en-1-one was subjected to the single crystal X-ray diffraction studies. Density functional theory calculations were carried out for this chalcone and its derivatives to investigate into their electronic structure, chemical reactivity, linear and non-linear optical properties. The structure predicted from DFT for chalcone is in good agreement with the structure from XRD measurement.

  13. Identification of mixed bromidochloridotellurate anions in disordered crystal structures of (bdmim)2[TeX2Y4] (X, Y=Br, Cl; bdmim=1-butyl-2,3-dimethylimidazolium) by combined application of Raman spectroscopy and solid-state DFT calculations.

    Science.gov (United States)

    Närhi, Sari M; Kutuniva, Johanna; Lajunen, Marja K; Lahtinen, Manu K; Tuononen, Heikki M; Karttunen, Antti J; Oilunkaniemi, Raija; Laitinen, Risto S

    2014-01-03

    The discrete mixed [TeBrxCl6-x](2-) anions in their disordered crystal structures have been identified by using the phases prepared by the reaction of 1-butyl-2,3-dimethylimidazolium halogenides (bdmim)X with tellurium tetrahalogenides TeX4 (X=Cl, Br) as examples. Homoleptic (bdmim)2[TeX6] [X=Cl (1), Br (2)] and mixed (bdmim)2[TeBr2Cl4] (3), and (bdmim)2[TeBr4Cl2] (4) are formed depending on the choice of the reagents, and their crystal structures have been determined by single-crystal X-ray diffraction. The coordination environments of tellurium in all hexahalogenidotellurates are almost octahedral. Because of the crystallographic disorder, the mixed [TeBr2Cl4](2-) and [TeBr4Cl2](2-) anions in 3 and 4 cannot be identified in their crystal structures. Pawley refinement of the X-ray powder diffraction patterns of 1-4 indicates the presence of single phases in all four products. The solid state Raman spectra of 1-4 were assigned with help of DFT calculations that were performed both for the discrete anions in vacuum and for the complete crystal structures employing periodic boundary conditions. The fundamental vibrations of the homoleptic [TeX6](2-) (X=Cl, Br) anions could be well reproduced by the solid-state DFT computations and enabled a complete assignment of the Raman spectra. While the presence of cis-isomers in both [TeBr2Cl4](2-) and [TeBr4Cl2](2-) could be inferred by the computed fundamental vibrations, that of trans-isomers among the reaction products is, however, also possible. The pathway of the formation of [TeX4Y2](2-) isomers from TeX4 and Y(-) (X, Y=Cl, Br) was also explored by DFT calculations both in vacuum and in solution and indicated that both reactions afforded 80 mol% of cis-isomers and 20 mol% of trans-isomers.

  14. First Principle Study of Uranium Nitrides UN and UN2 Using DFT and DFT + U

    Directory of Open Access Journals (Sweden)

    T. Zergoug

    2015-12-01

    Full Text Available First principle calculation based on density functional theory (DFT was used to evaluate some physical properties of Uranium Nitrides. Adsorption of oxygen O atom and O2 molecule on/in (001 surfaces of both Uranium monoNitride (UN and diNitride (UN2 was then studied and compared mutually. To treat the strong correlation effects caused by 5f Uranium valence electrons, Hubbard-U advanced (DFT + U approach was employed to correct the exchange correlation functional GGA and PBE which are based on generalized gradient approximation. The functional are developed for the Vienna Abinitio Simulation Package (VASP and were used with the projector-augmented wave (PAW pseudo potentials. The structural and elastic-mechanical UN and UN2 properties were calculated within DFT and DFT + U methods. Then, Potential Energy Surfaces (PES concepts which correspond to the interaction between O atom (respectively O2 molecule and (001 on-surfaces / sub-surfaces uranium nitrides for several positions were determined to identify favorable adsorption sites. Physical properties calculation results of UN or UN2 are in order of magnitude of other theoretical values and show an acceptable precision compared to experiments. Hubbard U value of the DFT + U formalism was optimized to achieve Antiferromagnetic (AFM UN configuration and was effective at U = 1.625 eV. Optimization of UN2 was accomplished to attain experimental cell parameter of 5.31 A° and was reached for U = 2.6 eV. According to our calculation results, O2 diffusion through UN(001 and UN2(001 clean surfaces have demonstrated dissociation of the molecule from a distance of approximately d = 1.5 Å. Favored on surface modes for O atom adsorption were found to be near the bridge site for UN(001 and UN2(001. The O incorporation through UN(001 surface was at the bridge site, nevertheless, for UN2, merging of O atom in the (001 surface bridge site was not allowed.

  15. Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

    Science.gov (United States)

    Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

    2016-04-01

    A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd.

  16. Structure, IR and Raman spectra of phosphotrihydrazide studied by DFT.

    Science.gov (United States)

    Furer, V L; Vandyukov, A E; Majoral, J P; Caminade, A M; Kovalenko, V I

    2016-09-05

    The FTIR and FT Raman measurements of the phosphotrihydrazide (S)P[N(Me)-NH2]3 have been performed. This compound is a zero generation dendrimer G0 with terminal amine groups. Structural optimization and normal mode analysis were obtained for G0 by the density functional theory (DFT). Optimized geometric bond length and angles obtained by DFT show good agreement with experiment. The amine terminal groups are characterized by the well-defined bands at 3321, 3238, 1614cm(-1) in the experimental IR spectrum and by bands at 3327, 3241cm(-1) in the Raman spectrum of G0. The experimental frequencies of asymmetric and symmetric NH2 stretching vibrations of amine group are lower than theoretical values due to intramolecular NH⋯S hydrogen bond. This hydrogen bond is also responsible for higher experimental infrared intensity of these bands as compared with theoretical values. Relying on DFT calculations a complete vibrational assignment is proposed for the studied dendrimer.

  17. Theoretical investigation on the effect of protonation on the absorption and emission spectra of two amine-group-bearing, red "push-pull" emitters, 4-dimethylamino-4'-nitrostilbene and 4-(dicyanomethylene)-2-methyl-6-p-(dimethylamino) styryl-4H-pyran, by DFT and TDDFT calculations.

    Science.gov (United States)

    Petsalakis, I D; Georgiadou, D G; Vasilopoulou, M; Pistolis, G; Dimotikali, D; Argitis, P; Theodorakopoulos, G

    2010-05-06

    A theoretical investigation on the electronic structure of 4-dimethylamino-4'-nitrostilbene (DANS), 4-(dicyanomethylene)-2-methyl-6-p-(dimethylamino) styryl-4H-pyran (DCM), and their protonated forms is presented in an effort to rationalize recent experimental results on the tuning of the emitted color of organic light-emitting diodes through photochemically induced protonation. Density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations have been carried out on the neutral and protonated forms of DANS and DCM, employing both the B3LYP and the CAM-B3LYP functionals. It was found that the CAM-B3LYP functional leads to better agreement than the B3LYP of the calculated with the experimental absorption lambda(max) for DANS, whereas B3LYP is more appropriate than CAM-B3LYP for DCM. The results of the calculations aid in a rationalization of the observed differences of the spectra of DANS and DCM upon protonation, and in particular those differences that make DANS a more attractive system for absorbance and emission tuning.

  18. A conceptual DFT approach towards analysing toxicity

    Indian Academy of Sciences (India)

    U Sarkar; D R Roy; P K Chattaraj; R Parthasarathi; J Padmanabhan; V Subramanian

    2005-09-01

    The applicability of DFT-based descriptors for the development of toxicological structure-activity relationships is assessed. Emphasis in the present study is on the quality of DFT-based descriptors for the development of toxicological QSARs and, more specifically, on the potential of the electrophilicity concept in predicting toxicity of benzidine derivatives and the series of polyaromatic hydrocarbons (PAH) expressed in terms of their biological activity data (50). First, two benzidine derivatives, which act as electron-donating agents in their interactions with biomolecules are considered. Overall toxicity in general and the most probable site of reactivity in particular are effectively described by the global and local electrophilicity parameters respectively. Interaction of two benzidine derivatives with nucleic acid (NA) bases/selected base pairs is determined using Parr’s charge transfer formula. The experimental biological activity data (50) for the family of PAH, namely polychlorinated dibenzofurans (PCDF), polyhalogenated dibenzo--dioxins (PHDD) and polychlorinated biphenyls (PCB) are taken as dependent variables and the HF energy (), along with DFT-based global and local descriptors, viz., electrophilicity index () and local electrophilic power (+) respectively are taken as independent variables. Fairly good correlation is obtained showing the significance of the selected descriptors in the QSAR on toxins that act as electron acceptors in the presence of biomolecules. Effects of population analysis schemes in the calculation of Fukui functions as well as that of solvation are probed. Similarly, some electron-donor aliphatic amines are studied in the present work. We see that global and local electrophilicities along with the HF energy are adequate in explaining the toxicity of several substances

  19. A self-consistent DFT + DMFT scheme in the projector augmented wave method: applications to cerium, Ce2O3 and Pu2O3 with the Hubbard I solver and comparison to DFT + U.

    Science.gov (United States)

    Amadon, B

    2012-02-22

    An implementation of full self-consistency over the electronic density in the DFT + DMFT framework on the basis of a plane wave–projector augmented wave (PAW) DFT code is presented. It allows for an accurate calculation of the total energy in DFT + DMFT within a plane wave approach. In contrast to frameworks based on the maximally localized Wannier function, the method is easily applied to f electron systems, such as cerium, cerium oxide (Ce2O3) and plutonium oxide (Pu2O3). In order to have a correct and physical calculation of the energy terms, we find that the calculation of the self-consistent density is mandatory. The formalism is general and does not depend on the method used to solve the impurity model. Calculations are carried out within the Hubbard I approximation, which is fast to solve, and gives a good description of strongly correlated insulators. We compare the DFT + DMFT and DFT + U solutions, and underline the qualitative differences of their converged densities. We emphasize that in contrast to DFT + U, DFT + DMFT does not break the spin and orbital symmetry. As a consequence, DFT + DMFT implies, on top of a better physical description of correlated metals and insulators, a reduced occurrence of unphysical metastable solutions in correlated insulators in comparison to DFT + U.

  20. Ethylene dissociation on flat and stepped Ni(111): A combined STM and DFT study

    DEFF Research Database (Denmark)

    Vang, R.T.; Honkala, Johanna Karoliina; Dahl, S.;

    2006-01-01

    The dissociative adsorption of ethylene (C(2)H(4)) on Ni(111) was studied by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The STM studies reveal that ethylene decomposes exclusively at the step edges at room temperature. However, the step edge sites...... are poisoned by the reaction products and thus only a small brim of decomposed ethylene is formed. At 500 K decomposition on the (111) facets leads to a continuous growth of carbidic islands, which nucleate along the step edges. DFT calculations were performed for several intermediate steps...... and DFT results. (c) 2005 Elsevier B.V. All rights reserved....

  1. Calculation of Vibrational and Electronic Excited-State Absorption Spectra of Arsenic-Water Complexes Using Density Functional Theory

    Science.gov (United States)

    2016-06-03

    IR and UV-visible ranges. The absorption spectrum corresponding to excitation states of As-H2O complexes consisting of relatively small numbers of...complexes consisting of relatively small numbers of water molecules using DFT and TD- DFT. Calculation of excited state resonance structure using DFT and TD...absorption spectra. A significant aspect of using DFT and TD-DFT for the calculation of absorption spectra is that it adopts the perspective of computational

  2. Computing m DFT's over GF(q) with one DFT over GF(q^m)

    OpenAIRE

    Hong, Jonathan; Vetterli, Martin

    1993-01-01

    Over the field of complex numbers, it is well-known that if the input is real then it is possible to compute 2 real DFT's with one complex DFT. We extend the result to finite fields and show how to compute m DFT's over GF(q) with one DFT over GF(qm)

  3. Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (M(p+) = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+).

    Science.gov (United States)

    Gourlaouen, Christophe; Piquemal, Jean-Philip; Saue, Trond; Parisel, Olivier

    2006-01-30

    Hartree-Fock and DFT (B3LYP) nonrelativistic (scalar relativistic pseudopotentials for the metallic cation) and relativistic (molecular four-component approach coupled to an all-electron basis set) calculations are performed on a series of six nd10 (n+1)s0 [M(H2O)]p+ complexes to investigate their geometry, either planar C2v or nonplanar C(s). These complexes are, formally, entities originating from the complexation of a water molecule to a metallic cation: in the present study, no internal reorganization has been found, which ensures that the complexes can be regarded as a water molecule interacting with a metallic cation. For [Au(H2O)]+ and [Hg(H2O)]2+, it is observed that both electronic correlation and relativistic effects are required to recover the C(s) structures predicted by the four-component relativistic all-electron DFT calculations. However, including the zero-point energy corrections makes these shallow C(s) minima vanish and the systems become floppy. In all other systems, namely [Cu(H2O)]+, [Zn(H2O)]2+, [Ag(H2O)]+, and [Cd(H2O)]2+, all calculations predict a C2v geometry arising from especially flat potential energy surfaces related to the out-of-plane wagging vibration mode. In all cases, our computations point to the quasi-perfect transferability of the atomic pseudopotentials considered toward the molecular species investigated. A rationalization of the shape of the wagging potential energy surfaces (i.e., single well vs. double well) is proposed based on the Constrained Space Orbital Variation decompositions of the complexation energies. Any way of stabilizing the lowest unoccupied orbital of the metallic cation is expected to favor charge-transfer (from the highest occupied orbital(s) of the water ligand), covalence, and, consequently, C(s) structures. The CSOV complexation energy decompositions unambiguously reveal that such stabilizations are achieved by means of relativistic effects for [Au(H2O)]+, and, to a lesser extent, for [Hg(H2O)]2

  4. Spectroscopic, DNA binding ability, biological activity, DFT calculations and non linear optical properties (NLO) of novel Co(II), Cu(II), Zn(II), Cd(II) and Hg(II) complexes with ONS Schiff base

    Science.gov (United States)

    Abdel Aziz, Ayman A.; Elantabli, Fatma M.; Moustafa, H.; El-Medani, Samir M.

    2017-08-01

    The reaction of Co(II), Cu(II), Zn(II), Cd(II) and Hg(II) with the synthesized N-(2-hydroxy-1-naphthylidene)-2-aminothiophenol Schiff base ligand (H2L) at room temperature resulted in the formation of the five complexes; [Co(HL)2]H2O, 1; [M(HL)2] (M = Cu, Zn and Cd), (2-4) and [Hg(HL)Cl], 5. The ligand and its complexes were characterized based on elemental analyses, IR, 1H NMR, magnetic measurement, molar conductance, and thermal analysis. Coats and Redfern method was used to compute the kinetic and thermodynamic parameters. Antimicrobial activities of H2L and its complexes have been studied. The binding of Co(II), Cu(II) and Zn(II) complexes to calf thymus DNA (CT-DNA) has been investigated using UV-Vis and fluorescence absorption spectra. The results indicated that the ligand and its complexes may bind to DNA by intercalation modes, with a much higher binding affinity of the complexes than that of the ligand. The equilibrium geometries of the studied complexes are investigated theoretically at the B3LYP/LANL2DZ level of theory, and it was found that these geometries are non-linear. The calculated EHOMO and ELUMO energies of the studied complexes can be used to calculate the global properties. The calculated nonlinear optical parameters (NLO); first order hyperpolarizibility (β) of the studied complexes show promising optical properties.

  5. FT-IR, FT-Raman and NMR characterization of 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate and investigation of its reactive and optoelectronic properties by molecular dynamics simulations and DFT calculations

    Science.gov (United States)

    Menon, Vidya V.; Fazal, Edakot; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Nagarajan, Subban; Van Alsenoy, C.

    2017-01-01

    The FT-IR and FT-Raman spectra of the synthesized compound, 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate is recorded and analyzed. Optimized molecular structure, wave numbers, corresponding assignments regarding 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate has become screened tentatively as well as hypothetically using Gaussian09 program package. Natural bonding orbital assessment has been completed with a reason to clarify charge transfer or conjugative interaction, the intra-molecular re-hybridization and delocalization of electron density within the molecule. The NMR spectral assessment had been made choosing structure property relationship by chemical shifts along with the magnetic shielding effects regarding the title compound. The first and second hyperpolarizabilities were calculated. The calculated first order hyperpolarizability is commensurate with the documented worth of very similar derivatives and could be an interesting object for more experiments on nonlinear optics. Local reactivity properties have been investigated using average local ionization energies and Fukui functions. Investigation of optoelectronic properties encompassed calculations of reorganization energies and hopping rates of charge carriers within the framework of Marcus semi-empiric approach. The docked ligand title compound forms a stable complex with CDK inhibitors and gives a binding affinity value of -9.7 kcal/mol and molecular docking results suggest that the compound might exhibit inhibitory activity against CDK inhibitors.

  6. Chemoenzymatic approach to optically active 4-hydroxy-5-alkylcyclopent-2-en-1-one derivatives: an application of a combined circular dichroism spectroscopy and DFT calculations to assignment of absolute configuration.

    Science.gov (United States)

    Frelek, Jadwiga; Karchier, Michał; Madej, Daria; Michalak, Karol; Różański, Paweł; Wicha, Jerzy

    2014-06-01

    A series of representative optically active derivatives of 4-hydroxy-5-alkylcyclopent-2-en-1-one were prepared from the respective 2-furyl methyl carbinols via the Piancatelli rearrangement followed by the enzymatic kinetic resolution of racemates. Applicability of chiroptical methods (experimental and calculated electronic circular dichroism [ECD] and vibrational circular dichroism [VCD] spectra) to determine the absolute configuration of both stereogenic centers in 4-hydroxy-5-methylcyclopent-2-en-1-one was demonstrated. It was also demonstrated that the concurrent application of ECD and VCD spectroscopy can be used for the determination of the configuration of two stereogenic centers. © 2014 Wiley Periodicals, Inc.

  7. Self-interaction error in DFT-based modelling of ionic liquids.

    Science.gov (United States)

    Lage-Estebanez, Isabel; Ruzanov, Anton; García de la Vega, José M; Fedorov, Maxim V; Ivaništšev, Vladislav B

    2016-01-21

    The modern computer simulations of potential green solvents of the future, involving the room temperature ionic liquids, heavily rely on density functional theory (DFT). In order to verify the appropriateness of the common DFT methods, we have investigated the effect of the self-interaction error (SIE) on the results of DFT calculations for 24 ionic pairs and 48 ionic associates. The magnitude of the SIE is up to 40 kJ mol(-1) depending on the anion choice. Most strongly the SIE influences the calculation results of ionic associates that contain halide anions. For these associates, the range-separated density functionals suppress the SIE; for other cases, the revPBE density functional with dispersion correction and triple-ζ Slater-type basis is suitable for computationally inexpensive and reasonably accurate DFT calculations.

  8. Copper(II) and nickel(II) complexes of tetradentate Schiff base ligand: UV-Vis and FT-IR spectra and DFT calculation of electronic, vibrational and nonlinear optical properties

    Science.gov (United States)

    Zarei, Seyed Amir; Khaledian, Donya; Akhtari, Keivan; Hassanzadeh, Keyumars

    2015-11-01

    The experimental fourier transform infrared (FT-IR) and ultraviolet-visible (UV-Vis) spectra of copper(II) and nickel(II) complexes of the deprotonated tetradentate Schiff base ligand N,N‧-bis(2-hydroxybenzylidene)-2,2-dimethyl-1,3-propanediamine (H2L) are compared with their corresponding theoretical ones. The applied theoretical method is based on the density functional theory and time-dependent density functional theory at the UPBE0/PBE0 levels using Def2-TZVP basis set. The computational optimised geometric parameters of the complexes are in good agreement with their corresponding experimental data. The FT-IR and UV-Vis spectra of the complexes were reproduced on the basis of their optimised structures. The vibrational assignments of some fundamental modes of the complexes are performed. The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies are calculated. The analyses of the calculated electronic absorption spectra of the complexes are carried out to elucidate the electronic transitions assignments and their characters. Second-order nonlinear optical property of the complexes is evaluated by the above-mentioned theoretical method that implies much greater values for the complexes in comparison with the corresponding value of urea.

  9. A comparative study of 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under high pressures using Raman spectroscopy and DFT calculations

    Science.gov (United States)

    Zeng, Yangyang; Song, Yunfei; Yu, Guoyang; Zheng, Xianxu; Guo, Wencan; Zhao, Jun; Yang, Yanqiang

    2016-09-01

    High pressure Raman experiment was performed to compare RDX and HMX crystals. Ab initio calculations using B3LYP Density Functional Theory method with Sadlej's medium-sized polarized basis set (SadlejpVTZ) were carried out for Caae RDX and 1,5-diaxial-3,7-diequatorial chair HMX molecules. Our calculations and measured Raman vibrational spectra reveal both molecules have similarities on bonding and vibrational properties at ambient pressure. However, high pressure responses for both molecules aren't the same. For RDX, at pressure near 4 GPa, a number of changes become apparent in the Raman spectra, such as modes splitting, intensity modification, and discontinuity of pressure-dependence of frequency shifts, which are consistent with previous experiment and believed to associate with α-γ phase transition. For HMX, only slight conformational deformation involving NO2 group was observed, and was considered as an onset of β-ε phase transition. It is proposed that the markedly different behavior under high pressure for these two molecules results from different molecular packing in unit cell.

  10. Dynamics of an [Fe{sub 4}S{sub 4}(SPh){sub 4}{sup 2-} cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using {sup 36}S substitution, DFT calculations, and empirical force fields.

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Y.; Koutmos, M.; Case, D.A.; Coucouvanis, D.; Wang, H.; Cramer, S.P.; X-Ray Science Division; Univ. of California; LBNL; The Scripps Research Inst.; Univ. of Michigan

    2006-01-01

    We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and {sup 57}Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu){sub 4}N]{sub 2}[Fe{sub 4}S{sub 4}(SPh){sub 4}]. This [Fe{sub 4}S{sub 4}(SR){sub 4}]{sup 2-} complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with {sup 36}S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies.The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after {sup 36}S substitution were used as an additional constraint. A D{sub 2d} symmetry Fe{sub 4}S{sub 4}S{sub 4} model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D{sub 2d} Fe{sub 4}S{sub 4}(SPh){sub 4} model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between 50 and 100 cm{sup -1} were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe{sub 4}S{sub 4} cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to rotational lattice modes. We also reassign the 430 cm{sup -1} band as primarily an elongation of the thiophenolate ring, with 10% terminal Fe-S stretch character. This study illustrates the

  11. Development and implementation of a DFT/MIA method

    Science.gov (United States)

    Rousseau, Bart

    2001-11-01

    In the last half of the century that has passed since the advent of the quantum chemical era the computational quantum chemistry methods have matured into valuable tools for researchers in industry and academia alike. However, for these methods to be competitive with e.g. the high-throughput experimental techniques used in the pharmaceutical industry, they must not only be accurate but at the same time must be computationally inexpensive. Most of the contemporary computational methods succeed only in fulfilling one of these criteria. Therefore the goal of this Ph.D. project was to combine the MIA approach, which allows efficient SCF calculations on large systems, and the DFT method, that takes electron correlation into account at a moderate computational cost. The new DFT method thus obtained, the DFT/MIA method, allows for efficient correlated calculations on large systems. The MIA method, an efficient combination of the Multiplicative Integral Approximation and the direct SCF procedure, is implemented in the ab-initio quantum chemical program package BRABO. In the MIA approximation the product of two basis functions is expanded in terms of an auxiliary basis set. This reduces the N4 four-center two-electron integrals to a sum of N3 three-center two-electron integrals. In addition this allows for a very fast build- up of the Fock matrix. The MIA approach has already proven its effectiveness in calculations on systems that belong to the largest that have been calculated at this level of theory, such as the calculation on the 46- peptide crambin. In addition this method was implemented using the `Parallel Virtual Machine' method, allowing parallel execution on a heterogeneous cluster of workstations. The MIA approach is applied to both the calculation of the electron density and the calculation of the exchange-correlation contribution to the Fock matrix. For both these quantities a recursive procedure is used. Test calculations on water clusters ranging in size from

  12. Study of E/Z isomerization of (arylamino)methylidenefuran-2(3H)-ones by (1) H, (13) C, (15) N spectroscopy and DFT calculations in different solvents.

    Science.gov (United States)

    Osipov, Alexander K; Anis'kov, Alexander A; Grinev, Vyacheslav S; Yegorova, Alevtina Yu

    2017-08-01

    The structure and configuration of the series of previously unknown arylaminomethylidenefuran-2(3H)-ones have been determined in solution by (1) H, (13) C, (15) N nuclear magnetic resonance spectroscopy including two-dimensional experiments such as (1) H─(1) H COSY, dqCOSY, (1) H─(13) C HSQC, (1) H─(13) C HMBC. It was found that synthesized substances exist as an equilibrium mixture of E- and Z-enamines in solution. It was established on the basis of density functional theory calculations that the exchange between the two push-pull enamines is a simple rotation around an exocyclic partial double bond that depends on the effect of the solvents. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  13. DFT investigations of hydrogen storage materials

    Science.gov (United States)

    Wang, Gang

    Hydrogen serves as a promising new energy source having no pollution and abundant on earth. However the most difficult problem of applying hydrogen is to store it effectively and safely, which is smartly resolved by attempting to keep hydrogen in some metal hydrides to reach a high hydrogen density in a safe way. There are several promising metal hydrides, the thermodynamic and chemical properties of which are to be investigated in this dissertation. Sodium alanate (NaAlH4) is one of the promising metal hydrides with high hydrogen storage capacity around 7.4 wt. % and relatively low decomposition temperature of around 100 °C with proper catalyst. Sodium hydride is a product of the decomposition of NaAlH4 that may affect the dynamics of NaAlH4. The two materials with oxygen contamination such as OH- may influence the kinetics of the dehydriding/rehydriding processes. Thus the solid solubility of OH - groups (NaOH) in NaAlH4 and NaH is studied theoretically by DFT calculations. Magnesium boride [Mg(BH4)2] is has higher hydrogen capacity about 14.9 wt. % and the decomposition temparture of around 250 °C. However one flaw restraining its application is that some polyboron compounds like MgB12H12 preventing from further release of hydrogen. Adding some transition metals that form magnesium transition metal ternary borohydride [MgaTMb(BH4)c] may simply the decomposition process to release hydrogen with ternary borides (MgaTMbBc). The search for the probable ternary borides and the corresponding pseudo phase diagrams as well as the decomposition thermodynamics are performed using DFT calculations and GCLP method to present some possible candidates.

  14. CO oxidation on PdO catalysts with perfect and defective rutile-TiO2 as supports: Elucidating the role of oxygen vacancy in support by DFT calculations

    Science.gov (United States)

    Li, Xiao; Sun, Xiongfei; Xu, Xianglan; Liu, Wenming; Peng, Honggen; Fang, Xiuzhong; Wang, Hongming; Wang, Xiang

    2017-04-01

    To explore metal oxide-oxide support interactions and their effects, the mechanism of CO oxidation on PdO catalysts with rutile TiO2 or TiO2-x (TiO2 with a bridging oxygen vacancy) as the support, was studied by density functional theory calculations, compared with that on pure PdO surface. For TiO2 as the support, support effect leads to the change of the preferential CO adsorption sites from the coordinatively unsaturated Pd (Pdcus) site on pure PdO surface to the bridging site of coordinatively unsaturated Pd and O atoms (Pdcus and Ocus), thus altering the reaction pathway of CO oxidation, whereas the support effect has little influence on the energy barrier. However, for TiO2-x as the support, the presence of the oxygen vacancy leads to the energy barrier remarkably decreased compared with that on pure or TiO2-supported PdO surface. The change of Bader charges indicates the oxygen vacancy in the support can tune the oxidizability of PdO surface active oxygen Ocus, thus adjusting the CO adsorption strength at the bridging site of Pdcus and Ocus to be favorable for the extraction process of Ocus. Tuning oxygen vacancies in supports can be used as a new perspective to design improved supported oxide catalysts.

  15. O sbnd H⋯O and O sbnd H⋯N hydrogen bonds in the complex of DABCO mono-betaine with p-hydroxybenzoic acid studied by X-ray diffraction, DFT calculations and spectroscopic methods

    Science.gov (United States)

    Barczyński, P.; Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.

    2011-08-01

    DABCO mono-betaine (1,4-diazabicyclo[2.2.2]octane-1-acetate) forms a complex with p-hydroxybenzoic acid (HBA) at the 1:1 ratio. The crystals are monoclinic, space group P2 1/ m. The HBA and DABCO mono-betaine molecules are linked into infinite chains through the COOH⋯OOC and O sbnd H⋯N hydrogen bonds of 2.604(1) and 2.771(2) Å, respectively. The DABCO mono-betaine is located on a mirror plane and the HBA molecule lies on this plane. In the structure of the 1:1 complex optimized by the B3LYP/6-31G(d,p) approach, the DABCO ring has a planar conformation, while in the chains formed by two complexes, the DABCO moieties assume the propeller conformations. The FTIR spectrum shows several bands attributed to the O sbnd H, O sbnd H⋯O, O sbnd H⋯N, C dbnd O and COO stretching vibrations. 1H and 13C chemical shifts assignments were confirmed by the magnetic isotropic shielding constants, calculated by the GIAO/B3LYP/6-31G(d,p) approach.

  16. Novel and unusual triterpene from Black Cohosh. Determination of structure of 9,10- seco-9,19-cyclolanostane xyloside (cimipodocarpaside) by NMR, IR and Raman spectroscopy and DFT calculations

    Science.gov (United States)

    Jamróz, Marta K.; Jamróz, Michał H.; Dobrowolski, Jan Cz.; Gliński, Jan A.; Davey, Matthew H.; Wawer, Iwona

    2011-01-01

    A new triterpene xyloside, designated cimipodocarpaside was isolated from a Black Cohosh ( Actea racemosa L.) extract and its structure was elucidated by means of 1H, 13C NMR, IR and Raman spectroscopy supported by B3LYP/6-31G** calculations. The vibrational spectra were interpreted using the PED analysis of 273 fundamentals. Its structure comprises four condensed rings A-D which are 6, 7, 6, and 5-membered, respectively. An oxiirane ring is located in the side chain and a xylose moiety is attached to the A-ring. Comparison of the experimental 13C NMR data with the theoretical chemical shifts of 24 S- and 24 R-cimipodocarpaside isomers revealed that the isolated compound has the 24 S-configuration. Combined spectroscopic and computational studies enabled the determination of the structure of cimipodocarpaside as (24 S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10- seco-9,19-cyclolanost-7(8),9(11),10(19)-trien-3-O-β- D-xylopyranoside. Triterpenes with 7-membered ring were thus far isolated from only Actea podocarpa DC. plants. This is the first report on the isolation of such a compound from Black Cohosh.

  17. Calculate Electric Field Gradient of TiO2 Within Density Functional Theory

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>TiO2 electric field gradient has been calculated utilizing WIEN2K program, which is ab initio based on density function theory (DFT). DFT uses the charge density as a variable instead of electronic wave

  18. Halide ligated iron porphines: a DFT+U and UB3LYP study.

    Science.gov (United States)

    Panchmatia, Pooja M; Ali, Md Ehesan; Sanyal, Biplab; Oppeneer, Peter M

    2010-12-30

    We apply the density functional theory + U (DFT+U) and unrestricted hybrid functional DFT-UB3LYP methods to study the electronic structure and magnetic properties of two prototypical iron porphines: iron(III) porphine chloride (FePCl) and difluoro iron(III-IV) porphine. Plain DFT within the generalized gradient approximation (GGA) implementation fails in describing the correct high-spin ground state of these porphine molecules, whereas DFT+U and UB3LYP provide an improved description. For a range of U values (4-8 eV), we compare the results of the DFT+U approach to those obtained previously with the hybrid functional (B3LYP) and with the CASPT2 approach. The DFT+U and UB3LYP methods successfully predict the molecular high spin (S = 5/2) ground state of FePCl, and also provide the nontrivial S = 3 high spin ground state for FePF(2). For the latter six-coordinated Fe porphine, our DFT+U calculations show that the S = 2, S = 5/2, and S = 3 states are energetically very close together (differences of 30 meV). Nonetheless, S = 3 is obtained as the ground state of the whole molecule, in accordance with the spin expected from the electron count. Our DFT+U calculations show furthermore that the Fe 3d occupancy is similar for FePF(2) and FePCl, i.e., DFT+U does not support Fe(IV) for FePF(2), but rather an Fe(III) porphyrin π-cation radical species, with an Fe high spin S(Fe) = 5/2, and an additional S = 1/2 stemming from spin density distributed over the porphine ring. This observation is also supported by our UB3LYP calculations.

  19. Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What Is Missing In, and Corrections To, the TD-DFT Adiabatic Approximation.

    Science.gov (United States)

    Casida, Mark E; Huix-Rotllant, Miquel

    2016-01-01

    In their famous paper, Kohn and Sham formulated a formally exact density-functional theory (DFT) for the ground-state energy and density of a system of N interacting electrons, albeit limited at the time by certain troubling representability questions. As no practical exact form of the exchange-correlation (xc) energy functional was known, the xc-functional had to be approximated, ideally by a local or semilocal functional. Nowadays, however, the realization that Nature is not always so nearsighted has driven us up Perdew's Jacob's ladder to find increasingly nonlocal density/wavefunction hybrid functionals. Time-dependent (TD-) DFT is a younger development which allows DFT concepts to be used to describe the temporal evolution of the density in the presence of a perturbing field. Linear response (LR) theory then allows spectra and other information about excited states to be extracted from TD-DFT. Once again the exact TD-DFT xc-functional must be approximated in practical calculations and this has historically been done using the TD-DFT adiabatic approximation (AA) which is to TD-DFT very similar to what the local density approximation (LDA) is to conventional ground-state DFT. Although some of the recent advances in TD-DFT focus on what can be done within the AA, others explore ways around the AA. After giving an overview of DFT, TD-DFT, and LR-TD-DFT, this chapter focuses on many-body corrections to LR-TD-DFT as one way to build hybrid density-functional/wavefunction methodology for incorporating aspects of nonlocality in time not present in the AA.

  20. DFT study with inclusion of the Grimme potential on anatase TiO2: structure, electronic, and vibrational analyses.

    Science.gov (United States)

    Albuquerque, Anderson R; Garzim, Marcos L; Santos, Iêda M G dos; Longo, Valeria; Longo, Elson; Sambrano, Julio R

    2012-11-29

    Periodic DFT/B3LYP calculations for TiO(2) anatase bulk were carried out including semiempirical dispersive interactions (DFT-D2) to pure Khon-Sham DFT energy. From this standard methodology, van der Waals (vdW) radii were optimized to 1.4214 Å for titanium and 1.3420 Å for oxygen centers in order to achieve a better structural description. The results from this approach (here named DFT/B3LYP-D*) showed a better description for lattice constants, vibrational IR and Raman, energy band gaps, and bulk modulus than default DFT/B3LYP and DFT/B3LYP-D. The dispersion correction showed more reliable results and was necessary to achieve a good agreement with reported single crystal results, without new formalism or additional computational cost.

  1. X-ray and DFT calculated structures of 2-(1 H-imidazol-1-yl)-1-(2-naphthyl)ethan-1-one N-phenylthiosemicarbazone and 2-(1 H-imidazol-1-yl)-1-(2-naphthyl)ethan-1-one N-(4-chlorophenyl)thiosemicarbazone

    Science.gov (United States)

    Sahin, Z. S.; Septioglu, E.; Calis, U.; Isik, S.

    2014-12-01

    Crystal and molecular structures of two new compounds 2-(1 H-imidazol-1-yl)-1-(2-naphthyl)ethan-1-one N-phenylthiosemicarbazone, C22H19N5S, ( I) and 2-(1 H-imidazol-1-yl)-1-(2-naphthyl)ethan-1-one N-(4-chlorophenyl)thiosemicarbazone, C22H18ClN5S, ( II) have been determined by single-crystal X-ray diffraction. Molecular geometries from X-ray experiment of I and II have been compared with those calculated using the Density Functional Theory (DFT) with B3LYP/6-31G( d, p) basis set. Both compounds crystallize in the monoclinic space group P21/ c with Z = 4: a = 13.2880(5), 14.2648(3) Å, b = 9.4122(2), 9.3892(3) Å, c = 15.6341(6), 15.6268(4) Å, β = 101.779(3)°, 104.926(2)°, for I and II, respectively. An extensive two-dimensional network of N-H⋯N hydrogen bonds and π-ring interactions are responsible for crystal stabilization in both structures.

  2. Normal coordinate analysis and DFT calculations of the vibrational spectra for lanthanide(III) complexes with 3-bromo-4-methoxy-2,6-lutidine N-oxide: LnCl 3(3Br4CH 3OC 7H 7NO) 3 (Ln=Pr, Nd, Sm, Eu, Gd, Dy)

    Science.gov (United States)

    Godlewska, P.; Ban-Oganowska, H.; Macalik, L.; Hanuza, J.; Oganowski, W.; Roszak, S.; Lipkowski, P.

    2006-01-01

    The results of the FT-Raman and FT-IR studies of the LnCl 3(LNO) 3 type complexes (where Ln=Pr, Nd, Sm, Eu, Gd, Dy and LNO=3-Br-4-CH 3OC 7H 7NO) are presented. The spectral contours observed in the regions of the lanthanide-oxygen, lanthanide-chlorine and nitrogen-oxygen vibrations are employed in the discussion of the molecular structure of the complex ions and the local symmetry of the LnCl 3(ON) 3 polyhedron. The discussion of the vibrational spectra is based on the classical normal coordinate analysis and its results are compared to the results of DFT quantum chemical calculations performed for complete molecule. The normal coordinate analysis has been performed for PrCl 3(ON) 3 and DyCl 3(ON) 3 molecular systems, which have been treated as a different 'isotopic units'. Basing on the predominant PED contributions of the respective internal coordinates the assignment of the normal vibrations has been proposed.

  3. DFT Modelling of Tripeptides (Lysine-Tryptophan-Lysine Interacting with Single Walled Carbon Nanotubes

    Directory of Open Access Journals (Sweden)

    Navaratnarajah Kuganathan

    2010-01-01

    Full Text Available Model calculations are performed to predict the nature of interaction between SWNT and a tripeptide (Lys-Trp-Lys and to calculate the binding energies and charge transfer between these two species using density functional theory. DFT calculations indicate that the interaction is of a non covalent nature. Minimal charge transfer is observed between SWNT and Lys-Trp-Lys.

  4. On the crystal energy and structure of A{sub 2}Ti{sub n}O{sub 2n+1} (A=Li, Na, K) titanates by DFT calculations and neutron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Catti, Michele, E-mail: catti@mater.unimib.it [Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 53, 20125 Milano (Italy); Pinus, Ilya [Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 53, 20125 Milano (Italy); Scherillo, Antonella [ISIS Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxon, OX11 0QX (United Kingdom)

    2013-09-15

    First-principles quantum-mechanical calculations (CRYSTAL09 code, B3LYP functional) were performed on alkali titanates A{sub 2}Ti{sub n}O{sub 2n+1} with layered structure (n=3,4,6). Monoclinic structural types with unshifted (P2{sub 1}/m) and with shifted (C2/m) layers were considered. Crystal energies and full structural details were obtained for all Li, Na, and K phases. Neutron diffraction data were collected on powder samples of P2{sub 1}/m-Li{sub 2}Ti{sub 3}O{sub 7} (a=9.3146(3), b=3.7522(1), c=7.5447(3) Å, β=97.611(4)°) and C2/m-K{sub 2}Ti{sub 4}O{sub 9} (a=18.2578(8), b=3.79160(9), c=12.0242(4) Å, β=106.459(4)°) and their structures were Rietveld-refined. Computed energies show the P2{sub 1}/m arrangement as favoured over the C2/m one for n=3, and the opposite holds for n=6. In the n=4 case the P2{sub 1}/m configuration is predicted to be more stable for Li and Na, and the C2/m one for K titanates. Analysis of Li–O and K–O crystal-chemical environments from experiment and theory shows that the alkali atom bonding is stabilized/destabilized in the different phases consistently with the energy trend. - Graphical abstract: Display Omitted - Highlights: • The P2{sub 1}/m structure-type is found to be more stable for A{sub 2}Ti{sub 3}O{sub 7} layer titanates. • The C2/m structure-type is found to be more stable for A{sub 2}Ti{sub 6}O{sub 13} layer titanates. • Tetratitanates are predicted to prefer the P2{sub 1}/m (Li and Na) or C2/m (K) structure. • Li–O and K–O bond distances follow a trend consistent with computed phase energies.

  5. Intermolecular Interaction Induced Multi-Polymers of Aceclofenac with Flexible Conformation:Crystal Structure, Thermostability, Solubility and DFT Calculations%分子间作用力构筑的具有柔性结构的醋氯芬酸多聚物:晶体结构,热稳定性,溶解度和DFT计算

    Institute of Scientific and Technical Information of China (English)

    孙盼盼; 刘翔宇; 孙琳; 张盛; 魏青; 尹琰; 杨奇; 陈三平

    2015-01-01

    非甾体类抗炎药物醋氯芬酸(ACF)的水溶性差,导致其生物利用度较低。本文制备了三种多聚物,分别是醋氯芬酸与4,4ʹ-联吡啶(BIPY)共晶(1),与3-氨基苯甲酸(3-ABA)盐(2)和与二甲基亚砜(DMSO)的溶剂化物(3),利用红外光谱、粉末X射线衍射和单晶X射线衍射对它们的结构进行了表征。结果表明,化合物1-3的超分子结构是通过氢键、C―H…π和π…π堆积作用构筑而成,三个多聚物具有良好的热稳定性。从热力学角度分析和密度泛函理论(DFT)计算说明ACF在化合物3中的构象比其在化合物1和2中更稳定。此外, ACF形成共晶、盐和溶剂化物后有效提高了其溶解度。%The non-steroidal anti-inflammatory drug aceclofenac (ACF) has low bioavailability because of its poor water solubility. To enhance its water solubility we synthesized three compounds:a co-crystal of ACF-0.5BIPY (4,4'-bipyridine) (1), a salt of ACF-3-ABA (3-aminobenzoic acid) (2), and a solvate of ACF-DMSO (dimethyl sulfoxide) (3). These compounds were characterized by infrared spectroscopy, powder and single crystal X-ray diffractions. The supramolecular structures of 1-3 are sustained by hydrogen bonding C―H…πandπ…πstacking interactions and they have favorable thermal stabilities. Thermodynamical y, DFT calculations revealed that the most stable conformation of ACF exists in compound 3 and this structure is more stable than 1 and 2. Furthermore, upon the formations of the co-crystal, the salt or the solvate the solubility of ACF improves significantly.

  6. Calculating NMR parameters in aluminophosphates: evaluation of dispersion correction schemes.

    Science.gov (United States)

    Sneddon, Scott; Dawson, Daniel M; Pickard, Chris J; Ashbrook, Sharon E

    2014-02-14

    Periodic density functional theory (DFT) calculations have recently emerged as a popular tool for assigning solid-state nuclear magnetic resonance (NMR) spectra. However, in order for the calculations to yield accurate results, accurate structural models are also required. In many cases the structural model (often derived from crystallographic diffraction) must be optimised (i.e., to an energy minimum) using DFT prior to the calculation of NMR parameters. However, DFT does not reproduce weak long-range "dispersion" interactions well, and optimisation using some functionals can expand the crystallographic unit cell, particularly when dispersion interactions are important in defining the structure. Recently, dispersion-corrected DFT (DFT-D) has been extended to periodic calculations, to compensate for these missing interactions. Here, we investigate whether dispersion corrections are important for aluminophosphate zeolites (AlPOs) by comparing the structures optimised by DFT and DFT-D (using the PBE functional). For as-made AlPOs (containing cationic structure-directing agents (SDAs) and framework-bound anions) dispersion interactions appear to be important, with significant changes between the DFT and DFT-D unit cells. However, for calcined AlPOs, where the SDA-anion pairs are removed, dispersion interactions appear much less important, and the DFT and DFT-D unit cells are similar. We show that, while the different optimisation strategies yield similar calculated NMR parameters (providing that the atomic positions are optimised), the DFT-D optimisations provide structures in better agreement with the experimental diffraction measurements. Therefore, it appears that DFT-D calculations can, and should, be used for the optimisation of calcined and as-made AlPOs, in order to provide the closest agreement with all experimental measurements.

  7. DFT Studies of Mo-C Heterocyclic Rings

    Institute of Scientific and Technical Information of China (English)

    RAN Xiao-Rong; ZHAO Hai-Tao; ZHANG Wen-Qin

    2003-01-01

    @@ Eleven clusters of the six-membered Mo-C heterocyclic rings were calculated and compared with corresponding organic compounds. The structure, stability and the electronic properties of these clusters are discussed. All calcu- lations were carried out within the framework of the density functional theory (DFT) with a plane wave basis set, which encoded in VASP (Vienna Ab-initio Simulation Package). [1,2

  8. Why Is MP2-Water "Cooler" and "Denser" than DFT-Water?

    Science.gov (United States)

    Willow, Soohaeng Yoo; Zeng, Xiao Cheng; Xantheas, Sotiris S; Kim, Kwang S; Hirata, So

    2016-02-18

    Density functional theory (DFT) with a dispersionless generalized gradient approximation (GGA) needs much higher temperature and pressure than the ambient conditions to maintain water in the liquid phase at the correct (1 g/cm(3)) density during first-principles simulations. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water require lower temperature and pressure than DFT/GGA to keep water liquid. Here we present a unifying explanation of these trends derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the different temperatures and pressures between DFT/GGA and MP2 at which the simulated water displays the experimentally observed liquid structure under the ambient conditions can be largely explained by their differences in polarizability and dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for DFT-water to be liquid. MP2 gives a stronger dispersion interaction and thus shorter intermolecular distances than dispersionless DFT/GGA, which is why MP2-water is denser than DFT-water under the same external pressure.

  9. Temperature dependent Raman and DFT study of creatine.

    Science.gov (United States)

    Gangopadhyay, Debraj; Sharma, Poornima; Singh, Ranjan K

    2015-01-01

    Temperature dependent Raman spectra of creatine powder have been recorded in the temperature range 420-100K at regular intervals and different clusters of creatine have been optimized using density functional theory (DFT) in order to determine the effect of temperature on the hydrogen bonded network in the crystal structure of creatine. Vibrational assignments of all the 48 normal modes of the zwitterionic form of creatine have been done in terms of potential energy distribution obtained from DFT calculations. Precise analysis gives information about thermal motion and intermolecular interactions with respect to temperature in the crystal lattice. Formation of higher hydrogen bonded aggregates on cooling can be visualized from the spectra through clear signature of phase transition between 200K and 180K.

  10. Vibrational modes of aminothiophenol: a TERS and DFT study.

    Science.gov (United States)

    Merlen, A; Chaigneau, M; Coussan, S

    2015-07-15

    We report Tip Enhanced Raman Spectroscopy (TERS) mapping and Density Functional (DFT) calculations of aminothiophenol (ATP) grafted on a gold surface. The TERS mapping has demonstrated Raman modes of (ATP) and its dimerised derivative Dimercaptoazobenzene (DMAB). This feature confirms that the plasmon activated chemical reaction of ATP has occurred during TERS measurements. In some specific part of the samples some unidentified Raman modes are observed. We suggest that they could come from intermediate species formed during the conversion of ATP into DMAB. These modes are compared with calculated Raman spectra of some possible intermediate species. These results confirm the high potentiality of TERS measurements for nanochemistry.

  11. Charged vanadium-benzene multidecker clusters: DFT and quantum Monte Carlo study.

    Science.gov (United States)

    Tokár, K; Derian, R; Mitas, L; Štich, I

    2016-02-14

    Using explicitly correlated fixed-node quantum Monte Carlo and density functional theory (DFT) methods, we study electronic properties, ground-state multiplets, ionization potentials, electron affinities, and low-energy fragmentation channels of charged half-sandwich and multidecker vanadium-benzene systems with up to 3 vanadium atoms, including both anions and cations. It is shown that, particularly in anions, electronic correlations play a crucial role; these effects are not systematically captured with any commonly used DFT functionals such as gradient corrected, hybrids, and range-separated hybrids. On the other hand, tightly bound cations can be described qualitatively by DFT. A comparison of DFT and quantum Monte Carlo provides an in-depth understanding of the electronic structure and properties of these correlated systems. The calculations also serve as a benchmark study of 3d molecular anions that require a balanced many-body description of correlations at both short- and long-range distances.

  12. Charged vanadium-benzene multidecker clusters: DFT and quantum Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    Tokár, K.; Derian, R. [Institute of Physics, CCMS, Slovak Academy of Sciences, 84511 Bratislava (Slovakia); Mitas, L. [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Štich, I., E-mail: ivan.stich@savba.sk [Institute of Physics, CCMS, Slovak Academy of Sciences, 84511 Bratislava (Slovakia); Ruprecht A. Institute of Technology, Bratislava (Slovakia)

    2016-02-14

    Using explicitly correlated fixed-node quantum Monte Carlo and density functional theory (DFT) methods, we study electronic properties, ground-state multiplets, ionization potentials, electron affinities, and low-energy fragmentation channels of charged half-sandwich and multidecker vanadium-benzene systems with up to 3 vanadium atoms, including both anions and cations. It is shown that, particularly in anions, electronic correlations play a crucial role; these effects are not systematically captured with any commonly used DFT functionals such as gradient corrected, hybrids, and range-separated hybrids. On the other hand, tightly bound cations can be described qualitatively by DFT. A comparison of DFT and quantum Monte Carlo provides an in-depth understanding of the electronic structure and properties of these correlated systems. The calculations also serve as a benchmark study of 3d molecular anions that require a balanced many-body description of correlations at both short- and long-range distances.

  13. The solvatochromic, spectral, and geometrical properties of nifenazone: a DFT/TD-DFT and experimental study.

    Science.gov (United States)

    Bani-Yaseen, Abdulilah Dawoud; Al-Balawi, Mona

    2014-08-07

    The solvatochromic, spectral, and geometrical properties of nifenazone (NIF), a pyrazole-nicotinamide drug, were experimentally and computationally investigated in several neat solvents and in hydro-organic binary systems such as water-acetonitrile and water-dioxane systems. The bathochromic spectral shift observed in NIF absorption spectra when reducing the polarity of the solvent was correlated with the orientation polarizability (Δf). Unlike aprotic solvents, a satisfactory correlation between λ(max) and Δf was determined (linear correlation of regression coefficient, R, equal to 0.93) for polar protic solvents. In addition, the medium-dependent spectral properties were correlated with the Kamlet-Taft solvatochromic parameters (α, β, and π*) by applying a multiple linear regression analysis (MLRA). The results obtained from this analysis were then employed to establish MLRA relationships for NIF in order to estimate the spectral shift in different solvents, which in turn exhibited excellent correlation (R > 0.99) with the experimental values of ν(max). Density functional theory (DFT) and time-dependent DFT theory calculations coupled with the integral equation formalism-polarizable continuum model (IEF-PCM) were performed to investigate the solvent-dependent spectral and geometrical properties of NIF. The calculations showed good and poor agreements with the experimental results using the CAM-B3LYP and B3LYP functionals, respectively. Experimental and theoretical results confirmed that the chemical properties of NIF are strongly dependent on the polarity of the chosen medium and its hydrogen bonding capability. This in turn supports the hypothesis of the delocalization of the electron density within the pyrazole ring of NIF.

  14. Established DFT methods lose sigma/pi separation in double bonds having hyperconjugative interactions

    CERN Document Server

    Sharley, John N

    2015-01-01

    Accurate treatment of amide resonance is important in electronic structure calculation of protein, for Resonance Assisted Hydrogen Bonding in hydrogen bonded chains of backbone amides in protein secondary structure types such as beta sheet and alpha helix is determined by amide resonance. Variation in amide resonance is the means by which the hydrogen bonding in these chains is cooperative. Amide carbonyl orbitals are revealed by Natural Bond Orbital analysis to substantially maintain sigma/pi separation in the presence of non-amide plane hyperconjugative interactions with wavefunction methods but not with established DFT methods. This DFT error is most pronounced with small basis sets such as are used with DFT for proteins to reduce the basis function count. This error disturbs calculation of a range of amide donor/acceptor and steric interactions. This finding has important implications for the selection of electronic structure methods and basis sets for protein calculations. For example, great caution is n...

  15. DFT Studies on Hydrogen Overfall Mechanism for Catalyzed Hydroisomerization of Pentane

    Institute of Scientific and Technical Information of China (English)

    AI Chun-Zhi; SUN Ren-An; WANG Chang-Sheng

    2007-01-01

    The mechanism and related reaction paths in the hydroisomerization of n-pentane were studied by DFT calculations at the B3LYP/6-311++G** level. Two possible transition states were theoretically predicted and verified by the vibration frequency analysis as well as the calculations of intrinsic reaction coordinates (IRC). Furthermore, the related reaction barriers were evaluated by single point energy at the MP2/6-311++G** level with zero point vibration correction of DFT method. Thus, it is concluded that the isomerization might go through two pathways.

  16. Assessment of TD-DFT and LF-DFT for study of d - d transitions in first row transition metal hexaaqua complexes.

    Science.gov (United States)

    Vlahović, Filip; Perić, Marko; Gruden-Pavlović, Maja; Zlatar, Matija

    2015-06-07

    Herein, we present the systematic, comparative computational study of the d - d transitions in a series of first row transition metal hexaaqua complexes, [M(H2O)6](n+) (M(2+/3+) = V (2+/3+), Cr(2+/3+), Mn(2+/3+), Fe(2+/3+), Co(2+/3+), Ni(2+)) by the means of Time-dependent Density Functional Theory (TD-DFT) and Ligand Field Density Functional Theory (LF-DFT). Influence of various exchange-correlation (XC) approximations have been studied, and results have been compared to the experimental transition energies, as well as, to the previous high-level ab initio calculations. TD-DFT gives satisfactory results in the cases of d(2), d(4), and low-spin d(6) complexes, but fails in the cases when transitions depend only on the ligand field splitting, and for states with strong character of double excitation. LF-DFT, as a non-empirical approach to the ligand field theory, takes into account in a balanced way both dynamic and non-dynamic correlation effects and hence accurately describes the multiplets of transition metal complexes, even in difficult cases such as sextet-quartet splitting in d(5) complexes. Use of the XC functionals designed for the accurate description of the spin-state splitting, e.g., OPBE, OPBE0, or SSB-D, is found to be crucial for proper prediction of the spin-forbidden excitations by LF-DFT. It is shown that LF-DFT is a valuable alternative to both TD-DFT and ab initio methods.

  17. Assessment of ten DFT methods in predicting structures of sheet silicates: importance of dispersion corrections.

    Science.gov (United States)

    Tunega, Daniel; Bučko, Tomáš; Zaoui, Ali

    2012-09-21

    The performance of ten density functional theory (DFT) methods in a prediction of the structure of four clay minerals, in which non-bonding interactions dominate in the layer stacking (dispersive forces in talc and pyrophyllite, and hydrogen bonds in lizardite and kaolinite), is reported. In a set of DFT methods following functionals were included: standard local and semi-local (LDA, PW91, PBE, and RPBE), dispersion corrected (PW91-D2, PBE-D2, RPBE-D2, and vdW-TS), and functionals developed specifically for solids and solid surfaces (PBEsol and AM05). We have shown that the standard DFT functionals fail in the correct prediction of the structural parameters, for which non-bonding interactions are important. The remarkable improvement leading to very good agreement with experimental structures is achieved if the dispersion corrections are included in the DFT calculations. In such cases the relative error for the most sensitive lattice vector c dropped below 1%. Very good performance was also observed for both DFT functionals developed for solids. Especially, the results achieved with the PBEsol are qualitatively similar to those with DFT-D2.

  18. Accurate potential energy surfaces with a DFT+U(R) approach.

    Science.gov (United States)

    Kulik, Heather J; Marzari, Nicola

    2011-11-21

    We introduce an improvement to the Hubbard U augmented density functional approach known as DFT+U that incorporates variations in the value of self-consistently calculated, linear-response U with changes in geometry. This approach overcomes the one major shortcoming of previous DFT+U studies, i.e., the use of an averaged Hubbard U when comparing energies for different points along a potential energy surface is no longer required. While DFT+U is quite successful at providing accurate descriptions of localized electrons (e.g., d or f) by correcting self-interaction errors of standard exchange correlation functionals, we show several diatomic molecule examples where this position-dependent DFT+U(R) provides a significant two- to four-fold improvement over DFT+U predictions, when compared to accurate correlated quantum chemistry and experimental references. DFT+U(R) reduces errors in binding energies, frequencies, and equilibrium bond lengths by applying the linear-response, position-dependent U(R) at each configuration considered. This extension is most relevant where variations in U are large across the points being compared, as is the case with covalent diatomic molecules such as transition-metal oxides. We thus provide a tool for deciding whether a standard DFT+U approach is sufficient by determining the strength of the dependence of U on changes in coordinates. We also apply this approach to larger systems with greater degrees of freedom and demonstrate how DFT+U(R) may be applied automatically in relaxations, transition-state finding methods, and dynamics.

  19. ANTIBACTERIAL ACTIVITIES, DFT AND QSAR STUDIES OF ...

    African Journals Online (AJOL)

    geometries have been optimized by using density functional theory (DFT) at ..... the molecular weight < 500, molar refractivity from 40-130 having hydrogen bond donor .... Cioslowski, J.; Fox, D.J. Gaussian 09, Revision A. 01, Gaussian Inc.: ...

  20. DFT Techniques in DSP Chip Core NDSP25

    Institute of Scientific and Technical Information of China (English)

    XUE Jing; BAI Yong-qiang; DENG Zheng-hong; ZHENG Wei

    2004-01-01

    Design for Testability(DFT) is critical in chip design.DFT techniques insert hardware logic to an original design,in order to improve testability of the chip,and thus reduce test cost significantly.In this paper,we introduces the most frequently used DFT techniques,then put emphasis on the DFT policy and the DFT realization of the NDSP25 chip core,and analyses the result at last.

  1. DFT studies of CNT-functionalized uracil-acetate hybrids

    Science.gov (United States)

    Mirzaei, Mahmoud; Gulseren, Oguz

    2015-09-01

    Calculations based on density functional theory (DFT) have been performed to investigate the stabilities and properties of hybrid structures consisting of a molecular carbon nanotube (CNT) and uracil acetate (UA) counterparts. The investigated models have been relaxed to minimum energy structures and then various physical properties and nuclear magnetic resonance (NMR) properties have been evaluated. The results indicated the effects of functionalized CNT on the properties of hybrids through comparing the results of hybrids and individual structures. The oxygen atoms of uracil counterparts have been seen as the detection points of properties for the CNT-UA hybrids.

  2. Spectral and conformational studies on 3-pyridinealdazine by DFT approach

    Science.gov (United States)

    Arulmani, R.; Balachander, R.; Vijaya, P.; Sankaran, K. R.

    2015-03-01

    3-Pyridinealdazine was synthesized and characterized by FT-IR, 1H, 13C NMR and mass spectroscopy. The conformations of azine was determined theoretically besides selected geometrical parameters, HOMO-LUMO energies, polarizability, hyperpolarizability, natural bond orbital (NBO), atomic charges, Mulliken charges and atom in molecule (AIM) analysis were also calculated. The optimized geometry of the symmetrical azine, HOMO-LUMO and molecular electrostatic potential (MEP) surface were also evaluated using B3LYP/6-31G(d,p) basis set. 13C NMR data were also computed using Gaussian-03 package and compared with the observed values according to density functional theory (DFT) method and analyzed.

  3. Hydrogen molecule on lithium adsorbed graphene: A DFT study

    Science.gov (United States)

    Kaur, Gagandeep; Gupta, Shuchi; Gaganpreet, Dharamvir, Keya

    2016-05-01

    Electronic structure calculations for the adsorption of molecular hydrogen on lithium (Li) decorated and pristine graphene have been studied systematically using SIESTA code [1] within the framework of the first-principle DFT under the Perdew-Burke-Ernzerhof (PBE) form of the generalized gradient approximation (GGA)[2], including spin polarization. The energy of adsorption of hydrogen molecule on graphene is always enhanced by the presence of co-adsorbed lithium. The most efficient adsorption configuration is when H2 is lying parallel to lithium adsorbed graphene which is in contrast to its adsorption on pristine graphene (PG) where it prefers perpendicular orientation.

  4. Why is MP2-Water "Cooler" and "Denser" than DFT-Water?

    Energy Technology Data Exchange (ETDEWEB)

    Willow, Soohaeng Y.; Zeng, Xiao Cheng; Xantheas, Sotiris S.; Kim, Kwang S.; Hirata, So

    2016-02-18

    To maintain water in the liquid phase at the correct (1 g/cm3) density during first-principles simulations, density-functional theory (DFT) with a dispersionless generalized-gradient-approximation (GGA) functional requires a much higher temperature and pressure than the ambient conditions. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water performed by Del Ben et al. [J. Chem. Phys. Lett. 4, 3753 (2013); J. Chem. Phys. 143, 054506 (2015)] and by us [Willow et al., Sci. Rep. 5, 14358 (2015)] required a lower temperature and a negative pressure than DFT to keep water liquid. Here, we present a unifying explanation of these trends derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the calculated temperature and pressure of the liquid phase are strongly correlated with the polarizability of water and the dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for water to be liquid. In MP2 and DFT/GGA, the dispersion interaction is stronger and weaker (or lacking), respectively. This explains why liquid water contracts uniformly and becomes too dense in MP2, whereas the opposite is the case for dispersionless DFT/GGA.

  5. Investigation of the torsional barrier of EDOT using molecular mechanics and DFT methods.

    Science.gov (United States)

    Durães, Jussara A; da Silva Filho, Demétrio A; Ceschin, Artemis M; Sales, Maria J A; Martins, João B L

    2014-08-01

    When heterocyclic monomers are polymerized by electrochemical or chemical methods, they form fully conjugated polymers which have a wide range of applications due to their outstanding electronic properties. Among this class of compounds, thiophene derivatives are widely used due to their chemical stability and synthesis flexibility. With the goal to investigate the torsion barrier of polymer chains, a few units of 3,4-ethylenedioxythiophene (EDOT) were chosen and submitted to molecular mechanics (MM), density functional theory (DFT) and coupled cluster CCSD(T) calculations. This study helps to understand the performance and transferability of force fields used in molecular mechanics and molecular dynamics simulations often used to describe structure-property relationships of those systems. Determination of inter-ring torsion angle was performed in a comparative study using both force field, DFT and CCSD(T) methods. A good agreement was noticed between MM and QC results and highlights the importance of the description of the interactions involving the oxygen atoms present in the structure of EDOT. These observations are related to the α,α-coupling that occurs between the monomer units and yields a linear polymer. DFT HOMO and LUMO orbitals were also presented. Finally, UV-vis spectra of EDOT units were obtained using several levels of theory by means of time-dependent DFT calculations (TD-DFT).

  6. Charge Transfer Couplings and Excitation Energies From Subsystem DFT: The Ultimate Divide and Conquer Approach to DFT

    Science.gov (United States)

    Pavanello, Michele

    2013-03-01

    The subsystem formulation of DFT known as Frozen Density Embedding (FDE) offers an excellent platform for studying charge transfer reactions in solvated systems, such as biosystems. I present new theory and software development for the calculation of the electronic couplings as well as the charge transfer excitations from FDE derived densities. The method presented scales linearly with the number of non-covalently bound subsystems considered in the calculation. Proof-of-principle calculations of water and ethylene clusters with up to 56 monomers are presented. In addition, DNA oligomers radical cations, including donor-acceptor, donor-bridge-acceptor, as well as a prototype of the phothosynthetic reaction center are tackled and preliminary results are presented.

  7. Can the Closed-Shell DFT Methods Describe the Thermolysis of 1,2-Dioxetanone?

    Science.gov (United States)

    Yue, Ling; Roca-Sanjuán, Daniel; Lindh, Roland; Ferré, Nicolas; Liu, Ya-Jun

    2012-11-13

    The chemiluminescent decomposition of 1,2-dioxetanone has in the past been studied by state-of-the-art multireference quantum chemical calculations, and a stepwise biradical mechanism was established. Recently, this decomposition has been reinvestigated, and a concerted mechanism has been proposed based on calculations performed at the closed-shell density functional theory (DFT) level of theory. In order to solve this apparent mechanistic contradiction, the present paper presents restricted and unrestricted DFT results obtained using functionals including different amounts of Hartree-Fock (HF) exchange, repeating and complementing the above-mentioned DFT calculations. The calculated results clearly indicate that the closed-shell DFT methods cannot correctly describe the thermolysis of 1,2-dioxetanone. It is found that unrestricted Kohn-Sham reaction energies and barriers are always lower than the ones obtained using a restricted formalism. Hence, from energy principles, the biradical mechanism is found to be prevailing in the understanding of the 1,2-dioxetanone thermolysis.

  8. DFT Investigation of the Palladium-Catalyzed Ene-Yne Coupling

    DEFF Research Database (Denmark)

    Henriksen, Signe Teuber; Tanner, David Ackland; Skrydstrup, T.

    2010-01-01

    The mechanism of the recently developed palladium-catalyzed ene-yne coupling has been evaluated by DFT methods. The calculations validate the previously proposed reaction mechanism and explain the stereoselectivity of the reaction (exclusive formation of the E isomer of the disubstituted alkene...

  9. A polarizable embedding DFT study of one-photon absorption in fluorescent proteins

    DEFF Research Database (Denmark)

    Beerepoot, Maarten; Steindal, Arnfinn H.; Kongsted, Jacob;

    2013-01-01

    A theoretical study of the one-photon absorption of five fluorescent proteins (FPs) is presented. The absorption properties are calculated using a polarizable embedding approach combined with density functional theory (PE-DFT) on the wild-type green fluorescent protein (wtGFP) and several of its...

  10. Hydrogen rotational and translational diffusion in calcium borohydride from quasielastic neutron scattering and DFT

    DEFF Research Database (Denmark)

    Blanchard, Didier; Riktor, M.D.; Maronsson, Jon Bergmann;

    2010-01-01

    with different time scales in combination with density functional theory (DFT) calculations. Two thermally activated reorientational motions were observed, around the 2-fold (C2) and 3-fold (C3) axes of the BH4− units, at temperature from 95 to 280K. The experimental energy barriers (EaC2 = 0.14 eV and EaC3 = 0...

  11. Electronic Absorption Spectra of Tetrapyrrole-Based Pigments via TD-DFT: A Reduced Orbital Space Study.

    Science.gov (United States)

    Shrestha, Kushal; Virgil, Kyle A; Jakubikova, Elena

    2016-07-28

    Tetrapyrrole-based pigments play a crucial role in photosynthesis as principal light absorbers in light-harvesting chemical systems. As such, accurate theoretical descriptions of the electronic absorption spectra of these pigments will aid in the proper description and understanding of the overall photophysics of photosynthesis. In this work, time-dependent density functional theory (TD-DFT) at the CAM-B3LYP/6-31G* level of theory is employed to produce the theoretical absorption spectra of several tetrapyrrole-based pigments. However, the application of TD-DFT to large systems with several hundreds of atoms can become computationally prohibitive. Therefore, in this study, TD-DFT calculations with reduced orbital spaces (ROSs) that exclude portions of occupied and virtual orbitals are pursued as a viable, computationally cost-effective alternative to conventional TD-DFT calculations. The effects of reducing orbital space size on theoretical spectra are qualitatively and quantitatively described, and both conventional and ROS results are benchmarked against experimental absorption spectra of various tetrapyrrole-based pigments. The orbital reduction approach is also applied to a large natural pigment assembly that comprises the principal light-absorbing component of the reaction center in purple bacteria. Overall, we find that TD-DFT calculations with proper and judicious orbital space reductions can adequately reproduce conventional, full orbital space, TD-DFT results of all pigments studied in this work.

  12. DFT computational analysis of piracetam

    Science.gov (United States)

    Rajesh, P.; Gunasekaran, S.; Seshadri, S.; Gnanasambandan, T.

    2014-11-01

    Density functional theory calculation with B3LYP using 6-31G(d,p) and 6-31++G(d,p) basis set have been used to determine ground state molecular geometries. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of piracetam is calculated using B3LYP/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO/NLMO analysis. The calculation of first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. Molecular electrostatic potential (MEP) at a point in the space around a molecule gives an indication of the net electrostatic effect produced at that point by the total charge distribution of the molecule. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charge is also calculated. Because of vibrational analysis, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-Vis spectra and electronic absorption properties are explained and illustrated from the frontier molecular orbitals.

  13. Iodine adsorption on Ni(111): STM and DFT study

    Science.gov (United States)

    Komarov, N. S.; Pavlova, T. V.; Andryushechkin, B. V.

    2016-09-01

    Iodine adsorption on the Ni(111) surface has been studied in ultra-high vacuum conditions with scanning tunneling microscopy (STM), Auger electron spectroscopy (AES), low-energy electron diffraction (LEED) and density functional theory (DFT) calculations. At the first stage of adsorption, iodine was found to form a simple commensurate (√{ 3 } ×√{ 3 }) R 30∘ structure at the coverage of 0.33 ML. According to DFT calculations, all iodine atoms in the (√{ 3 } ×√{ 3 }) R 30∘ structure occupy fcc hollow sites. Increase of the coverage in the range of (0.333 ML <θ < 0.364 ML) results in the uniaxial compression of the iodine lattice and the formation of the high-order commensurate structure (11 ×√{ 3 } R 30∘). The mechanism of compression involves the formation and the development of the striped super-heavy domain wall network. Further iodine dosing gives rise to nucleation and growth of flat 2D islands of surface nickel iodide. Atomic resolution STM images of iodide islands, in addition to atomic modulation, exhibit clear visible moiré-like superstructures with a period about 26 Å. The origin of the moiré-patterns was explained by the incommensurability of lattices of the surface nickel iodide and underlying Ni(111).

  14. Evaluation of DFT-D3 dispersion corrections for various structural benchmark sets

    Science.gov (United States)

    Schröder, Heiner; Hühnert, Jens; Schwabe, Tobias

    2017-01-01

    We present an evaluation of our newly developed density functional theory (DFT)-D3 dispersion correction D3(CSO) in comparison to its predecessor D3(BJ) for geometry optimizations. Therefore, various benchmark sets covering bond lengths, rotational constants, and center of mass distances of supramolecular complexes have been chosen. Overall both corrections give accurate structures and show no systematic differences. Additionally, we present an optimized algorithm for the computation of the DFT-D3 gradient, which reduces the formal scaling of the gradient calculation from O (N3) to O (N2) .

  15. Assessment of Charge-Transfer Excitations in Organic Dyes obtained from TD-srDFT Based on Long-Range MP2 and MCSCF Wave Functions

    CERN Document Server

    Hedegård, Erik D; Knecht, Stefan; Fromager, Emmanuel; Jensen, Hans Jørgen Aa

    2013-01-01

    Charge transfer excitations can be described within TD-DFT, not only by means of long-range corrected exchange functionals but also with a combination of wave function theory and TD-DFT based on range separation. The latter approach enables a rigorous formulation of multi-determinantal TD-DFT schemes where excitation classes, which are absent in conventional TD-DFT spectra (like for example double excitations), can be addressed. This paper investigates the combination of both the long-range MCSCF and SOPPA ans\\"atze with a short-range DFT (srDFT) description. We find that the combinations of SOPPA or MCSCF with TD-DFT yield better results than could be expected from the pure wave function schemes. For the Time-Dependent MCSCF short-range DFT ansatz (TD-MC-srDFT) excitation energies calculated over a larger benchmark set of molecules with predominantly single reference character yield good agreement with their reference values, and are in general comparable to the long-range corrected functional CAM-B3LYP. The...

  16. Comparative Assessment of DFT Performances in Ru- and Rh-Promoted σ-Bond Activations.

    Science.gov (United States)

    Sun, Yuanyuan; Hu, Lianrui; Chen, Hui

    2015-04-14

    In this work, the performances of 19 density functional theory (DFT) methods are calibrated comparatively on Ru- and Rh-promoted σ-bond (C-H, O-H, and H-H) activations. DFT calibration reference is generated from explicitly correlated coupled cluster CCSD(T)-F12 calculations, and the 4s4p core-valence correlation effect of the two 4d platinum group transition metals is also included. Generally, the errors of DFT methods for calculating energetics of Ru-/Rh-mediated reactions appear to correlate more with the magnitude of energetics itself than other factors such as metal identity. For activation energy calculations, the best performing functionals for both Ru and Rh systems are MN12SX DFT empirical dispersion correction on the performance of the DFT methods is beneficial for most density functionals tested in this work, reducing their MUDs to different extents. After including empirical dispersion correction, ωB97XD, B3LYP-D3, and CAM-B3LYP-D3 (PBE0-D3, B3LYP-D3, and ωB97XD) are the three best performing DFs for activation energy (reaction energy) calculations, from which B3LYP-D3 and ωB97XD can notably be recommended uniformly for both the reaction energy and reaction barrier calculations. The good performance of B3LYP-D3 in quantitative description of the energetic trends further adds value to B3LYP-D3 and singles this functional out as a reasonable choice in the Ru/Rh-promoted σ-bond activation processes.

  17. The Nature of Noncovalent Interactions in Catenane Supramolecular Complexes: Calibrating the MM3 Force Field with ab initio, DFT and SAPT Methods

    Science.gov (United States)

    Simeon, Tomekia M.; Ratner, Mark A.; Schatz, George C.

    2013-01-01

    The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H⋯O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3] catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H⋯O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H⋯O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, and we find that electrostatic interactions dominate the [C-H⋯O] hydrogen-bonding interactions while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interactions energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correct have important differences compared to DFT-SAPT while HF and even MP2 results are in poor agreement with DFT-SAPT. PMID:23941280

  18. Nature of noncovalent interactions in catenane supramolecular complexes: calibrating the MM3 force field with ab initio, DFT, and SAPT methods.

    Science.gov (United States)

    Simeon, Tomekia M; Ratner, Mark A; Schatz, George C

    2013-08-22

    The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H···O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3]catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H···O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H···O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, we find that electrostatic interactions dominate the [C-H···O] hydrogen-bonding interactions, while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interaction energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correction have important differences compared to DFT-SAPT, while HF and even MP2 results are in poor agreement with DFT-SAPT.

  19. A DFT investigation of methanolysis and hydrolysis of triacetin

    CERN Document Server

    Limpanuparb, Taweetham; Tantirungrotechai, Yuthana; 10.1016/j.theochem.2010.05.022

    2012-01-01

    The thermodynamic and kinetic aspects of the methanolysis and hydrolysis reactions of glycerol triacetate or triacetin, a model triacylglycerol compound, were investigated by using Density Functional Theory (DFT) at the B3LYP/6-31++G(d,p) level of calculation. Twelve elementary steps of triacetin methanolysis were studied under acid-catalyzed and base-catalyzed conditions. The mechanism of acid-catalyzed methanolysis reaction which has not been reported yet for any esters was proposed. The effects of substitution, methanolysis/hydrolysis position, solvent and face of nucleophilic attack on the free energy of reaction and activation energy were examined. The prediction confirmed the facile position at the middle position of glycerol observed by NMR techniques. The calculated activation energy and the trends of those factors agree with existing experimental observations in biodiesel production.

  20. Assessing the density functional theory-based multireference configuration interaction (DFT/MRCI) method for transition metal complexes.

    Science.gov (United States)

    Escudero, Daniel; Thiel, Walter

    2014-05-21

    We report an assessment of the performance of density functional theory-based multireference configuration interaction (DFT/MRCI) calculations for a set of 3d- and 4d-transition metal (TM) complexes. The DFT/MRCI results are compared to published reference data from reliable high-level multi-configurational ab initio studies. The assessment covers the relative energies of different ground-state minima of the highly correlated CrF6 complex, the singlet and triplet electronically excited states of seven typical TM complexes (MnO4(-), Cr(CO)6, [Fe(CN)6](4-), four larger Fe and Ru complexes), and the corresponding electronic spectra (vertical excitation energies and oscillator strengths). It includes comparisons with results from different flavors of time-dependent DFT (TD-DFT) calculations using pure, hybrid, and long-range corrected functionals. The DFT/MRCI method is found to be superior to the tested TD-DFT approaches and is thus recommended for exploring the excited-state properties of TM complexes.

  1. Combined ATR-FTIR and DFT Study of Cyclohexanone Adsorption on Hydrated TiO2 Anatase Surfaces

    NARCIS (Netherlands)

    Almeida, Ana Rita; Calatayud, Monica; Tielens, Frederik; Moulijn, Jacob A.; Mul, Guido

    2011-01-01

    The adsorption of cyclohexanone on different planes ((100), (101), and (001)) of anatase TiO2, with variable level of hydration, was evaluated by density functional theory (DFT) calculations. Surface hydration was found to affect the cyclohexanone adsorption enthalpy and the calculated infrared abso

  2. Interactions between metal cations with H2 in the M+- H2 complexes: Performance of DFT and DFT-D methods

    Indian Academy of Sciences (India)

    Srimanta Pakhira; Tanay Debnath; Kaushik Sen; Abhijit K Das

    2016-04-01

    The interactions between metal cations (Ni+, Cu+, Zn+) and H2 molecule have been investigated in detail using dispersion-corrected and -uncorrected double hybrid density functional (DHDF), gradient corrected density functional, ordinary density functional and CCSD(T) methods in conjunction with the correlation consistent triple- quality basis sets. Structural properties, depth of the potential well and dissociation energies are calculated using DFT, DFT-D and CCSD(T) methods and are compared with experimental results. A comparative analysis has been made among DFT, DFT-D and CCSD(T) methods with respect to experiments. The energy components of the interaction energy have been estimated by the symmetry-adapted perturbation theory (SAPT) to analyze the effect of various components on the interaction of the complexes. The dispersion-corrected DHDF, mPW2PLYP-D method shows the best agreement with the experimental values. An NBO analysis has been performed to understand the orbital participation in metal ligand interaction and charge transfer process in these complexes.

  3. DFT CONFORMATIONAL STUDIES OF ALPHA-MALTOTRIOSE

    Science.gov (United States)

    Recent DFT optimization studies on alpha-maltose improved our understanding of the preferred conformations of alpha-maltose and the present study extends these studies to alpha-maltotriose with three alpha-D-glucopyranose residues linked by two alpha-[1-4] bridges, denoted herein as DP-3's. Combina...

  4. z-transform DFT filters and FFT's

    DEFF Research Database (Denmark)

    Bruun, G.

    1978-01-01

    of DFT filter banks which utilize a minimum of complex coefficients. These implementations lead to new forms of FFT's, among which is acos/sinFFT for a real signal which only employs real coefficients. The new FFT algorithms use only half as many real multiplications as does the classical FFT....

  5. Noise Tracking Using DFT Domain Subspace Decompositions

    NARCIS (Netherlands)

    Hendriks, R.C.; Jensen, J.; Heusdens, R.

    2008-01-01

    All discrete Fourier transform (DFT) domain-based speech enhancement gain functions rely on knowledge of the noise power spectral density (PSD). Since the noise PSD is unknown in advance, estimation from the noisy speech signal is necessary. An overestimation of the noise PSD will lead to a loss in

  6. DFT STUDIES OF DP-3 AMYLOSE FRAGMENTS

    Science.gov (United States)

    This study extends our work on mono- and disaccharides to structures with three glucose residues by two alpha-[1-4] bridges, denoted herein as DP-3's. DFT optimization studies of DP-3 fragments have been carried out at the B3LYP/6-311++G** level of theory. Different hydroxymethyl conformations (gg...

  7. Noise Tracking Using DFT Domain Subspace Decompositions

    NARCIS (Netherlands)

    Hendriks, R.C.; Jensen, J.; Heusdens, R.

    2008-01-01

    All discrete Fourier transform (DFT) domain-based speech enhancement gain functions rely on knowledge of the noise power spectral density (PSD). Since the noise PSD is unknown in advance, estimation from the noisy speech signal is necessary. An overestimation of the noise PSD will lead to a loss in

  8. Introduction to Density Functional Theory: Calculations by Hand on the Helium Atom

    Science.gov (United States)

    Baseden, Kyle A.; Tye, Jesse W.

    2014-01-01

    Density functional theory (DFT) is a type of electronic structure calculation that has rapidly gained popularity. In this article, we provide a step-by-step demonstration of a DFT calculation by hand on the helium atom using Slater's X-Alpha exchange functional on a single Gaussian-type orbital to represent the atomic wave function. This DFT…

  9. Introduction to Density Functional Theory: Calculations by Hand on the Helium Atom

    Science.gov (United States)

    Baseden, Kyle A.; Tye, Jesse W.

    2014-01-01

    Density functional theory (DFT) is a type of electronic structure calculation that has rapidly gained popularity. In this article, we provide a step-by-step demonstration of a DFT calculation by hand on the helium atom using Slater's X-Alpha exchange functional on a single Gaussian-type orbital to represent the atomic wave function. This DFT…

  10. System-dependent dispersion coefficients for the DFT-D3 treatment of adsorption processes on ionic surfaces.

    Science.gov (United States)

    Ehrlich, Stephan; Moellmann, Jonas; Reckien, Werner; Bredow, Thomas; Grimme, Stefan

    2011-12-09

    Dispersion-corrected density functional theory calculations (DFT-D3) were performed for the adsorption of CO on MgO and C(2) H(2) on NaCl surfaces. An extension of our non-empirical scheme for the computation of atom-in-molecules dispersion coefficients is proposed. It is based on electrostatically embedded M(4)X(4) (M=Na, Mg) clusters that are used in TDDFT calculations of dynamic dipole polarizabilities. We find that the C(MM)(6) dispersion coefficients for bulk NaCl and MgO are reduced by factors of about 100 and 35 for Na and Mg, respectively, compared to the values of the free atoms. These are used in periodic DFT calculations with the revPBE semi-local density functional. As demonstrated by calculations of adsorption potential energy curves, the new C(6) coefficients lead to much more accurate energies (E(ads)) and molecule-surface distances than with previous DFT-D schemes. For NaCl/C(2) H(2) we obtained at the revPBE-D3(BJ) level a value of E(ads) =-7.4 kcal mol(-1) in good agreement with experimental data (-5.7 to -7.1 kcal mol(-1)). Dispersion-uncorrected DFT yields an unbound surface state. For the MgO/CO system, the computed revPBE-D3(BJ) value of E(ads) =-4.1 kcal mol(-1) is also in reasonable agreement with experimental results (-3.0 kcal mol(-1)) when thermal corrections are taken into account. Our new dispersion correction also improves computed lattice constants of the bulk systems significantly compared to plain DFT or previous DFT-D results. The extended DFT-D3 scheme also provides accurate non-covalent interactions for ionic systems without empirical adjustments and is suggested as a general tool in surface science.

  11. Error compensation of IQ modulator using two-dimensional DFT

    Energy Technology Data Exchange (ETDEWEB)

    Ohshima, Takashi, E-mail: ohshima@spring8.or.jp [RIKEN, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Maesaka, Hirokazu [RIKEN, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Matsubara, Shinichi [Japan Synchrotron Radiation Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Otake, Yuji [RIKEN, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan)

    2016-06-01

    It is important to precisely set and keep the phase and amplitude of an rf signal in the accelerating cavity of modern accelerators, such as an X-ray Free Electron Laser (XFEL) linac. In these accelerators an acceleration rf signal is generated or detected by an In-phase and Quadrature (IQ) modulator, or a demodulator. If there are any deviations of the phase and the amplitude from the ideal values, crosstalk between the phase and the amplitude of the output signal of the IQ modulator or the demodulator arises. This causes instability of the feedback controls that simultaneously stabilize both the rf phase and the amplitude. To compensate for such deviations, we developed a novel compensation method using a two-dimensional Discrete Fourier Transform (DFT). Because the observed deviations of the phase and amplitude of an IQ modulator involve sinusoidal and polynomial behaviors on the phase angle and the amplitude of the rf vector, respectively, the DFT calculation with these basis functions makes a good approximation with a small number of compensation coefficients. Also, we can suppress high-frequency noise components arising when we measure the deviation data. These characteristics have advantages compared to a Look Up Table (LUT) compensation method. The LUT method usually demands many compensation elements, such as about 300, that are not easy to treat. We applied the DFT compensation method to the output rf signal of a C-band IQ modulator at SACLA, which is an XFEL facility in Japan. The amplitude deviation of the IQ modulator after the DFT compensation was reduced from 15.0% at the peak to less than 0.2% at the peak for an amplitude control range of from 0.1 V to 0.9 V (1.0 V full scale) and for a phase control range from 0 degree to 360 degrees. The number of compensation coefficients is 60, which is smaller than that of the LUT method, and is easy to treat and maintain.

  12. Antibacterial activities, DFT and QSAR studies of quinazolinone compounds

    Directory of Open Access Journals (Sweden)

    A. G. Al-Sehemi

    2016-08-01

    Full Text Available The quinazolinone compounds (1 and 2 in this work were examined for their in vitro antibacterial activities against gram-positive (Staphylococcus aureus and gram-negative bacteria (Klebsiella pneumonia, Proteus bacilli and Shigella flexneri. Compared to the reference antibiotic chloramphenicol, these compounds showed high antibacterial activities against studied strains with inhibition zones observation. The ground state geometries have been optimized by using density functional theory (DFT at B3LYP/6-31G* level of theory. The absorption spectra have been calculated by using time dependent density functional theory (TDDFT with and without solvent. The effect of different functionals (B3LYP, MPW1PW91, and PBE1PBE on the absorption wavelengths has been studied. The ionization potential (IP, electron affinity (EA, energy gap (Egap, electronegativity (χ, hardness (η, electrophilicity (ω, softness (S and electrophilicity index (ωi were computed and discussed. The nonlinear optical (NLO properties vary by changing the theory (DFT to HF or functional (B3LYP to CAM-B3LYP. The physicochemical parameters have been studied by quantitative structure–activity relationship (QSAR. The computed properties of investigated compounds have been compared with the Chloramphenicol as well as available experimental data.

  13. Investigation of pyrite surface state by DFT and AFM

    Institute of Scientific and Technical Information of China (English)

    先永骏; 聂琪; 文书明; 刘建; 邓久帅

    2015-01-01

    The surface states of pyrite (FeS2) were theoretically investigated using first principle calculation based on the density functional theory (DFT). The results indicate that both the (200) and (311) surfaces of pyrite undergo significant surface atom relaxation after geometry optimization, which results in a considerable distortion of the surface region. In the normal direction, i.e., perpendicular to the surface, S atoms in the first surface layer move outward from the bulk, while Fe atoms move toward the bulk, forming an S-rich surface. The surface relaxation processes are driven by electrostatic interaction, which is evidenced by a relative decrease in the surface energy after surface relaxation. Such a relaxation process is visually interpreted through the qualitative analysis of molecular mechanics. Atomic force microscopy (AFM) analysis reveals that only sulfur atom is visible on the pyrite surface. This result is consistent with the DFT data. Such S-rich surface has important influence on the flotation properties of pyrite.

  14. Ions in solution: density corrected density functional theory (DC-DFT).

    Science.gov (United States)

    Kim, Min-Cheol; Sim, Eunji; Burke, Kieron

    2014-05-14

    Standard density functional approximations often give questionable results for odd-electron radical complexes, with the error typically attributed to self-interaction. In density corrected density functional theory (DC-DFT), certain classes of density functional theory calculations are significantly improved by using densities more accurate than the self-consistent densities. We discuss how to identify such cases, and how DC-DFT applies more generally. To illustrate, we calculate potential energy surfaces of HO·Cl(-) and HO·H2O complexes using various common approximate functionals, with and without this density correction. Commonly used approximations yield wrongly shaped surfaces and/or incorrect minima when calculated self consistently, while yielding almost identical shapes and minima when density corrected. This improvement is retained even in the presence of implicit solvent.

  15. Theoretical DFT and experimental NMR studies on uracil and 5-fluorouracil

    Science.gov (United States)

    Blicharska, Barbara; Kupka, Teobald

    2002-08-01

    The results of extended MO calculations using density functional theory (DFT) approximation and multinuclear HR NMR studies on uracil (U) and 5-fluorouracil (5FU) are reported. The performance of the B3PW91 hybrid density functional was compared with the ab initio restricted Hartree-Fock (RHF) method. With the basis set 6-31G ∗, or better quality, the DFT calculated bond lengths, dipole moments and harmonic stretching vibrations were predicted in good agreement with available experimental data. Structure and harmonic vibrations of U and 5FU were also calculated in the presence of water within a simple Onsager model. A linear correlation between proton and carbon GIAO NMR shieldings of uracil and 5FU and experimental data was shown.

  16. Ions in solution: Density Corrected Density Functional Theory (DC-DFT)

    CERN Document Server

    Kim, Min-Cheol; Burke, Kieron

    2014-01-01

    Standard density functional approximations often give questionable results for odd-electron radical complexes, with the error typically attributed to self-interaction. In density corrected density functional theory (DC-DFT), certain classes of density functional theory calculations are significantly improved by using densities more accurate than the self-consistent densities. We discuss how to identify such cases, and how DC-DFT applies more generally. To illustrate, we calculate potential energy surfaces of HO$\\cdot$Cl$^-$ and HO$\\cdot$H$_2$O complexes using various common approximate functionals, with and without this density correction. Commonly used approximations yield wrongly shaped surfaces and/or incorrect minima when calculated self consistently, while yielding almost identical shapes and minima when density corrected. This improvement is retained even in the presence of implicit solvent.

  17. Conformational analysis of menthol diastereomers by NMR and DFT computation

    Science.gov (United States)

    Härtner, Julia; Reinscheid, Uwe M.

    2008-01-01

    Correlations between experimental and calculated 13C chemical shifts were performed with the series of all menthol diastereomers. In this way it could be shown that identification problems with newly isolated natural products can be solved. Starting from simulated, low energy conformers of menthol, neomenthol, isomenthol, and neoisomenthol the 13C chemical shifts were obtained using DFT calculations [functional: B3LYP, basis set: 6-31G(d,p)]. Due to differences in chemical shifts, the prochiral methyl groups of the isopropyl substituent of menthol could be differentiated using the correlations between experimental and calculated values. A conformational scan of the dihedral angle of the isopropyl group allowed the determination of the dominating rotamers of menthol (+68.4°) and neomenthol (+172.5°) using 13C chemical shifts. The results were supported by energy calculations, 1JCH and 3JHH measurements. The correlations and 3JHH measurements for isomenthol indicate conformational averaging impeding the determination of the isopropyl group rotamer. For neoisomenthol, MD simulations showed two chair conformations. However, in contrast to calculated energies and correlations between theoretical and experimental 13C chemical shifts, the measured 3JH3H2 coupling of 6.3 Hz indicates an equally populated equilibrium of both conformers.

  18. Dissociation curves of diatomic molecules: A DC-DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Sim, Eunji; Kim, Min-Cheol [Department of Chemistry and Institute of Nano-Bio Molecular Assemblies, Yonsei University, Seoul 120-749 (Korea, Republic of); Burke, Kieron [Department of Chemistry, University of California, Irvine, CA, 92697 (United States)

    2015-12-31

    We investigate dissociation of diatomic molecules using standard density functional theory (DFT) and density-corrected density functional theory (DC-DFT) compared with CCSD(T) results as reference. The results show the difference between the HOMO values of dissociated atomic species often can be used as an indicator whether DFT would predict the correct dissociation limit. DFT predicts incorrect dissociation limits and charge distribution in molecules or molecular ions when the fragments have large HOMO differences, while DC-DFT and CCSD(T) do not. The criteria for large HOMO difference is about 2 ∼ 4 eV.

  19. Synthesis, Characterization and DFT-Based Investigation of a Novel Trinuclear Singly-Chloro-Bridged Copper(II)-1-Vinylimidazole Complex.

    Science.gov (United States)

    Yolcu, Zuhal; Demir, Serkan; Andaç, Ömer; Büyükgüngör, Orhan

    2016-01-01

    A novel trinuclear copper(II) complex [Cu3(μ-Cl)2Cl4(1-Vim)6] with monodentate 1-vinylimidazole (1-Vim) and chloro ligands has been prepared and experimentally characterized by elemental analysis, thermogravimetry (TGA, DTG, DTA), X-ray single crystal diffractometry, TOF-MS and FT-IR spectroscopies. The electronic and structural properties of the complex were further investigated by DFT/TD-DFT methods. Density functional hybrid method (B3LYP) was applied throughout the calculations. The calculated UV-Vis results based on TD-DFT approach were simulated and compared with experimental spectrum. Based on the data obtained, DFT calculations have been found in reasonable accordance with experimental data.

  20. Structure and spectroscopy of water-fluoride microclusters: a combined genetic algorithm and DFT-based study.

    Science.gov (United States)

    Neogi, Soumya Ganguly; Chaudhury, Pinaki

    2012-03-05

    In this article, we explore the efficiency of using a coupled genetic algorithm (GA) and density functional theory (DFT) based strategy to evaluate probable structures of (H(2) O)(n) F(-) micro-clusters, with n = 1 - 6. We use the stochastic optimization technique of GA to arrive at structures of the cluster systems and once the structures are obtained, do a DFT calculation with the optimized coordinates from the GA calculation as input to get the infra-red spectrum of all the systems. The results of our work closely resembles the pure quantum chemical results obtained by Baik et al. (J Chem Phys 1999, 110, 9116-9127).