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Sample records for previous dft calculations

  1. Synthesis, Spectroscopic Properties and DFT Calculation of Novel ...

    Indian Academy of Sciences (India)

    excited states were calculated by using the TD-DFT method. In all calculations, squeezed self-consistent field. (SCF) convergence standards, the self-consistent reac- tion field (SCRF) method and polarized continuum model (PCM)33,34 were adopted. The UV-Vis spectra were computed from TD-DFT calculations in differ-.

  2. BH-DFTB/DFT calculations for iron clusters

    Energy Technology Data Exchange (ETDEWEB)

    Aktürk, Abdurrahman; Sebetci, Ali, E-mail: asebetci@mevlana.edu.tr [Mechanical Engineering Department, Mevlana (Rumi) University, Konya 42003 (Turkey)

    2016-05-15

    We present a study on the structural, electronic, and magnetic properties of Fe{sub n}(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 (Fe{sub 9−13}), centered hexagonal antiprism (Fe{sub 14−17}, Fe{sub 20}), and truncated decahedral (Fe{sub 17(2)}, Fe{sub 18−19}). 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 Fe{sub n}(n = 2 − 20) clusters is between 2.4 and 3.6 μ{sub B} for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe{sub 13} 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.

  3. 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.

  4. Polydiphenylenephthalide: Optical Spectroscopy and DFT Calculations

    Directory of Open Access Journals (Sweden)

    Alexander KUKHTA

    2011-09-01

    Full Text Available The results of spectral and luminescent studies of polydiphenylenphthalide (PDF solutions and thin films as well as molecule structure and its energy levels DFT modelling within the Gaussian-03 software package are presented. It is shown that structural unit (diphenylenephthalide can form four polymer conformations with a similar energy gap. The most probable polymer conformation is the spiral cis-form with phthalide groups turned in opposite directions. At long-wave optical transition the electronic density moves on a chain of a molecule from diphenyl part to somehow distant phthalide one. Fluorescence excitation spectra reveal a transition band on a long-wave tail of the absorption spectrum. Spectral and time measurements of the luminescence allow to assume the presence of conformation transformations of PDF molecule under its optical excitation.http://dx.doi.org/10.5755/j01.ms.17.3.591

  5. nmr spectroscopic study and dft calculations of vibrational analyses ...

    African Journals Online (AJOL)

    Preferred Customer

    Furthermore, GIAO/DFT (Gauge Including Atomic Orbitals/Density. Functional Theory) approach is extensively used for the calculations of chemical shifts for various types of compounds [14-20]. During the last decade an important breakthrough in the calculation of NMR spin-spin coupling constants took place when the ...

  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. Synthesis and DFT calculations of some 2-aminothiazoles

    Science.gov (United States)

    Rezania, Jafar; Behzadi, Hadi; Shockravi, Abbas; Ehsani, Morteza; Akbarzadeh, Elahe

    2018-04-01

    A series of 2-aminothiazole derivatives have been synthesized by the reaction of acetyl compounds with thiourea and iodine as catalyst under solvent-free condition, a green chemistry method. The quantum chemical calculations at the DFT/B3LYP level of theory in gas phase were carried out for starting acetyl derivatives. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and related reactivity descriptor of acetyl derivatives, as well as, enthalpy of reactions are calculated in order to investigate the reaction properties of acetyl compounds and yields of the reactions. The calculated reactivity descriptors are well correlated to activity of different acetyl derivatives.

  8. Advantages of GPU technology in DFT calculations of intercalated graphene

    International Nuclear Information System (INIS)

    Pešić, J; Gajić, R

    2014-01-01

    Over the past few years, the expansion of general-purpose graphic-processing unit (GPGPU) technology has had a great impact on computational science. GPGPU is the utilization of a graphics-processing unit (GPU) to perform calculations in applications usually handled by the central processing unit (CPU). Use of GPGPUs as a way to increase computational power in the material sciences has significantly decreased computational costs in already highly demanding calculations. A level of the acceleration and parallelization depends on the problem itself. Some problems can benefit from GPU acceleration and parallelization, such as the finite-difference time-domain algorithm (FTDT) and density-functional theory (DFT), while others cannot take advantage of these modern technologies. A number of GPU-supported applications had emerged in the past several years (www.nvidia.com/object/gpu-applications.html). Quantum Espresso (QE) is reported as an integrated suite of open source computer codes for electronic-structure calculations and materials modeling at the nano-scale. It is based on DFT, the use of a plane-waves basis and a pseudopotential approach. Since the QE 5.0 version, it has been implemented as a plug-in component for standard QE packages that allows exploiting the capabilities of Nvidia GPU graphic cards (www.qe-forge.org/gf/proj). In this study, we have examined the impact of the usage of GPU acceleration and parallelization on the numerical performance of DFT calculations. Graphene has been attracting attention worldwide and has already shown some remarkable properties. We have studied an intercalated graphene, using the QE package PHonon, which employs GPU. The term ‘intercalation’ refers to a process whereby foreign adatoms are inserted onto a graphene lattice. In addition, by intercalating different atoms between graphene layers, it is possible to tune their physical properties. Our experiments have shown there are benefits from using GPUs, and we reached an

  9. Electronic structure of crystalline uranium nitride: LCAO DFT calculations

    International Nuclear Information System (INIS)

    Evarestov, R.A.; Losev, M.V.; Panin, A.I.; Mosyagin, N.S.; Titov, A.V.

    2008-01-01

    The results of the first LCAO DFT calculations of cohesive energy, band structure and charge distribution in uranium nitride (UN) crystal are presented and discussed. The calculations are made with the uranium atom relativistic effective core potentials, including 60, 78 and 81 electrons in the core. It is demonstrated that the chemical bonding in UN crystal has a metallic-covalent nature. Three 5f-electrons are localized on the U atom and occupy the states near the Fermi level. The metallic nature of the crystal is due to the f-character of both the valence-band top and the conduction-band bottom. The covalent bonds are formed by the interaction of 7s- and 6d-states of the uranium atom with the 2p-states of the nitrogen atom. It is shown that the inclusion of 5f-electrons in the atomic core introduces small changes in the calculated cohesive energy of UN crystal and electron charge distribution. However, the inclusion of 5s-, 5p-, 5d-electrons in the valence shell allows the better agreement with the calculated and experimental cohesive-energy value. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  10. Accurate structures and energetics of neutral-framework zeotypes from dispersion-corrected DFT calculations

    Science.gov (United States)

    Fischer, Michael; Angel, Ross J.

    2017-05-01

    Density-functional theory (DFT) calculations incorporating a pairwise dispersion correction were employed to optimize the structures of various neutral-framework compounds with zeolite topologies. The calculations used the PBE functional for solids (PBEsol) in combination with two different dispersion correction schemes, the D2 correction devised by Grimme and the TS correction of Tkatchenko and Scheffler. In the first part of the study, a benchmarking of the DFT-optimized structures against experimental crystal structure data was carried out, considering a total of 14 structures (8 all-silica zeolites, 4 aluminophosphate zeotypes, and 2 dense phases). Both PBEsol-D2 and PBEsol-TS showed an excellent performance, improving significantly over the best-performing approach identified in a previous study (PBE-TS). The temperature dependence of lattice parameters and bond lengths was assessed for those zeotypes where the available experimental data permitted such an analysis. In most instances, the agreement between DFT and experiment improved when the experimental data were corrected for the effects of thermal motion and when low-temperature structure data rather than room-temperature structure data were used as a reference. In the second part, a benchmarking against experimental enthalpies of transition (with respect to α-quartz) was carried out for 16 all-silica zeolites. Excellent agreement was obtained with the PBEsol-D2 functional, with the overall error being in the same range as the experimental uncertainty. Altogether, PBEsol-D2 can be recommended as a computationally efficient DFT approach that simultaneously delivers accurate structures and energetics of neutral-framework zeotypes.

  11. Vibrational spectroscopic and DFT calculation studies of cobalt(II) complexes with 3-hydroxypicolinic acid.

    Science.gov (United States)

    Furić, Krešimir; Kodrin, Ivan; Kukovec, Boris-Marko; Mihalić, Zlatko; Popović, Zora

    2013-01-15

    Two cobalt(II) complexes with 3-hydroxypicolinic acid (3-hydroxypyridine-2-carboxylic acid, 3-OHpicH), trans-[Co(3-OHpic)2(py)2] (2) and cis-[Co(3-OHpic)2(4-pic)2] (3) (py=pyridine; 4-pic=4-picoline or 4-methylpyridine), previously synthesized and characterized by X-ray diffraction, are here studied by Raman and mid-infrared spectroscopy with the help from the corresponding DFT vibrational calculations using B3LYP/6-311G(d,p) computational model. Intramolecular O-H⋯O hydrogen bond appears in both complexes 2 and 3, while weak C-H⋯O hydrogen bonds assemble molecules of 2 or 3 into 3D architecture. A complete presentation of all Raman, infrared and theoretical results is given for complex 3. The measured spectra are shown, relative intensities and bandwidths are discussed and the assignment of vibrational bands is given on the basis of the DFT calculations. The calculated spectra agree very well with the presented experimental findings, thanks to the suitable grouping of modes. The same vibrational calculations also reveal insignificant influence of H→CH3 substitution for the spectroscopic characterization of the complex. A careful study of differences between calculated and observed wavenumbers suggests that modified single-factor scaling is actually better than the classic multi-factor scaling approach. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. DFT LCAO and plane wave calculations of SrZrO3

    International Nuclear Information System (INIS)

    Evarestov, R.A.; Bandura, A.V.; Alexandrov, V.E.; Kotomin, E.A.

    2005-01-01

    The results of the density functional (DFT) LCAO and plane wave (PW) calculations of the electronic and structural properties of four known SrZrO 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 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.)

  13. DFT and TD-DFT calculation of new thienopyrazine-based small molecules for organic solar cells.

    Science.gov (United States)

    Bourass, Mohamed; Benjelloun, Adil Touimi; Benzakour, Mohammed; Mcharfi, Mohammed; Hamidi, Mohammed; Bouzzine, Si Mohamed; Bouachrine, Mohammed

    2016-01-01

    Novel six organic donor-π-acceptor molecules (D-π-A) used for Bulk Heterojunction organic solar cells (BHJ), based on thienopyrazine were studied by density functional theory (DFT) and time-dependent DFT (TD-DFT) approaches, to shed light on how the π-conjugation order influence the performance of the solar cells. The electron acceptor group was 2-cyanoacrylic for all compounds, whereas the electron donor unit was varied and the influence was investigated. The TD-DFT method, combined with a hybrid exchange-correlation functional using the Coulomb-attenuating method (CAM-B3LYP) in conjunction with a polarizable continuum model of salvation (PCM) together with a 6-31G(d,p) basis set, was used to predict the excitation energies, the absorption and the emission spectra of all molecules. The trend of the calculated HOMO-LUMO gaps nicely compares with the spectral data. In addition, the estimated values of the open-circuit photovoltage (V oc ) for these compounds were presented in two cases/PC 60 BM and/PC 71 BM. The study of structural, electronics and optical properties for these compounds could help to design more efficient functional photovoltaic organic materials.

  14. Self-Consistent Constricted Variational Theory RSCF-CV(∞)-DFT and Its Restrictions To Obtain a Numerically Stable ΔSCF-DFT-like Method: Theory and Calculations for Triplet States.

    Science.gov (United States)

    Park, Young Choon; Senn, Florian; Krykunov, Mykhaylo; Ziegler, Tom

    2016-11-08

    In this paper, the relaxed self-consistent field infinite order constricted variational density functional theory (RSCF-CV(∞)-DFT) for triplet calculations is presented. Here, we focus on two main features of our implementation. First, as an extension of our previous work by Krykunov and Ziegler ( J. Chem. Theory Comput. 2013 , 9 , 2761 ), the optimization of the transition matrix representing the orbital transition is implemented and applied for vertical triplet excitations. Second, restricting the transition matrix, we introduce RSCF-CV(∞)-DFT-based numerically stable ΔSCF-DFT-like methods, the most general of them being SVD-RSCF-CV(∞)-DFT. The reliability of the different methods, RSCF-CV(∞)-DFT and its restricted versions, is examined using the benchmark test set of Silva-Junior et al. ( J. Chem. Phys. 2008 , 129 , 104103 ). The obtained excitation energies validate our approach and implementation for RSCF-CV(∞)-DFT and also show that SVD-RSCF-CV(∞)-DFT mimics very well ΔSCF-DFT, as the root-mean-square deviations between these methods are less than 0.1 eV for all functionals examined.

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

    International Nuclear Information System (INIS)

    Ishii, A; Yamamoto, M; Asano, H; Fujiwara, K

    2008-01-01

    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

  16. 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.

  17. Electronic annealing Fermi operator expansion for DFT calculations on metallic systems

    Science.gov (United States)

    Aarons, Jolyon; Skylaris, Chris-Kriton

    2018-02-01

    Density Functional Theory (DFT) calculations with computational effort which increases linearly with the number of atoms (linear-scaling DFT) have been successfully developed for insulators, taking advantage of the exponential decay of the one-particle density matrix. For metallic systems, the density matrix is also expected to decay exponentially at finite electronic temperature and linear-scaling DFT methods should be possible by taking advantage of this decay. Here we present a method for DFT calculations at finite electronic temperature for metallic systems which is effectively linear-scaling (O(N)). Our method generates the elements of the one-particle density matrix and also finds the required chemical potential and electronic entropy using polynomial expansions. A fixed expansion length is always employed to generate the density matrix, without any loss in accuracy by the application of a high electronic temperature followed by successive steps of temperature reduction until the desired (low) temperature density matrix is obtained. We have implemented this method in the ONETEP linear-scaling (for insulators) DFT code which employs local orbitals that are optimised in situ. By making use of the sparse matrix machinery of ONETEP, our method exploits the sparsity of Hamiltonian and density matrices to perform calculations on metallic systems with computational cost that increases asymptotically linearly with the number of atoms. We demonstrate the linear-scaling computational cost of our method with calculation times on palladium nanoparticles with up to ˜13 000 atoms.

  18. Electronic annealing Fermi operator expansion for DFT calculations on metallic systems.

    Science.gov (United States)

    Aarons, Jolyon; Skylaris, Chris-Kriton

    2018-02-21

    Density Functional Theory (DFT) calculations with computational effort which increases linearly with the number of atoms (linear-scaling DFT) have been successfully developed for insulators, taking advantage of the exponential decay of the one-particle density matrix. For metallic systems, the density matrix is also expected to decay exponentially at finite electronic temperature and linear-scaling DFT methods should be possible by taking advantage of this decay. Here we present a method for DFT calculations at finite electronic temperature for metallic systems which is effectively linear-scaling (O(N)). Our method generates the elements of the one-particle density matrix and also finds the required chemical potential and electronic entropy using polynomial expansions. A fixed expansion length is always employed to generate the density matrix, without any loss in accuracy by the application of a high electronic temperature followed by successive steps of temperature reduction until the desired (low) temperature density matrix is obtained. We have implemented this method in the ONETEP linear-scaling (for insulators) DFT code which employs local orbitals that are optimised in situ. By making use of the sparse matrix machinery of ONETEP, our method exploits the sparsity of Hamiltonian and density matrices to perform calculations on metallic systems with computational cost that increases asymptotically linearly with the number of atoms. We demonstrate the linear-scaling computational cost of our method with calculation times on palladium nanoparticles with up to ∼13 000 atoms.

  19. 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.

  20. Synthesis, Spectroscopic Properties and DFT Calculation of Novel ...

    Indian Academy of Sciences (India)

    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 ...

  1. Electronic structure of crystalline uranium nitride: LCAO DFT calculations

    International Nuclear Information System (INIS)

    Ehvarestov, R.A.; Panin, A.I.; Losev, M.V.

    2007-01-01

    The results of electronic structure calculations performed for the first time for crystalline uranium nitride and using a LCAO basis are discussed. For calculations we used the density functional method with the PW91 exchange correlation potential and a variety of relativistic core potentials for the uranium atom. The calculated atomization energy of the crystal agrees well with the experimental data and with the results of calculations with the plane wave basis. It is shown that a chemical bond in crystalline uranium nitride is a metal covalent bond. The metal component of the bond is due to the 5f electrons localized on the uranium atom and having energies near the Fermi level and the bottom of the conduction band. The covalent component of the chemical bond results from an overlap between the uranium 6d and 7s valence orbitals and the nitrogen 2p atomic orbitals. Inclusion of the 5f electrons in the core of the uranium atom introduces relatively minor changes in the calculated binding energy and electron density distribution [ru

  2. NMR spectroscopic study and DFT calculations of GIAO NMR ...

    African Journals Online (AJOL)

    1H, 13C NMR chemical shifts and 1JCH coupling constants of danon have been calculated by means of B3LYP density functional method with 6-311++G(d,p) basis set. Comparison between the experimental and the theoretical results indicates that density functional B3LYP method is able to provide satisfactory results for ...

  3. Exploring Systematic Discrepancies in DFT Calculations of Chlorine Nuclear Quadrupole Couplings

    Czech Academy of Sciences Publication Activity Database

    Socha, Ondřej; Hodgkinson, P.; Widdifield, C. M.; Yates, J. R.; Dračínský, Martin

    2017-01-01

    Roč. 121, č. 21 (2017), s. 4103-4113 ISSN 1089-5639 R&D Projects: GA ČR GA15-11223S Institutional support: RVO:61388963 Keywords : NMR spectroscopy * DFT calculations * quadrupolar coupling Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 2.847, year: 2016

  4. A DFT based method for calculating the surface energies of asymmetric MoP facets

    Science.gov (United States)

    Tian, Xinxin; Wang, Tao; Fan, Lifang; Wang, Yuekui; Lu, Haigang; Mu, Yuewen

    2018-01-01

    MoP is a promising catalyst in heterogeneous catalysis. Understanding its surface stability and morphology is the first and essential step in exploring its catalytic properties. However, traditional surface energy calculation method does not work for the asymmetric termination of MoP. In this work, we reported a useful DFT based method to get the surface energies of asymmetric MoP facets. Under ideal condition, the (101) surface with mixed Mo/P termination is most stable, followed by the (100) surface, while the (001) surface is least stable. Wulff construction reveals the exposure of six surfaces on the MoP nanoparticle, where the (101) has the largest contribution. Atomistic thermodynamics results reveal the changes in surface stability orders with experimental conditions, and the (001)-P termination becomes more and more stable with increasing P chemical potential, which indicates its exposure is possible at defined conditions. Our results agree well with the previous experimental XRD and TEM data. We believe the reported method for surface energy calculation could be extended to other similar systems with asymmetric surface terminations.

  5. 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

  6. Matrix isolation studies and DFT calculations on molecular alkali metal bromates.

    Science.gov (United States)

    Ogden, J Steven; Graham, John T; Joy, Jon T; Ferrante, Francesco

    2009-01-28

    DFT and MP2 calculations have been carried out on a series of molecular alkali metal bromates MBrO3 (M = Na, K, Rb, Cs), and the results compared with matrix isolation IR studies on the vaporisation of the solid salts. For M = Na, K or Rb, no ternary molecular species were detected in the low temperature matrix, but vaporisation of solid caesium bromate at 730 K resulted in the formation of molecular CsBrO3, which was identified as having a C3v structure involving tridentate coordination. Additionally, the DFT and MP2 calculations provide estimates of the molecular parameters for all four MBrO3 species, and for the related MXO3 species CsClO3 and CsIO3. The proven stability of MBrO3 molecules may have a bearing on the atmospheric chemistry of bromine oxo-species.

  7. Thermodynamic study of complexation of thorium with pyridine monocarboxylates by calorimetry and DFT calculations

    International Nuclear Information System (INIS)

    Rama Mohana Rao, D.; Rawat, Neetika; Sawant, R.M.; Tomar, B.S.; Manna, D.; Ghanty, T.K.

    2013-01-01

    Stability constants of Th(IV) complexes with pyridine mono-carboxylates, namely, picolinate, nicotinate and isonicotinate have been determined following potentiometric titration of the metal ion and ligand mixtures with NaOH solution of known concentration. These data were used during the analysis of the calorimetric titration data to obtain the enthalpy of complexation reactions. The experimental data have been compared with that obtained from the DFT based theoretical calculations. (author)

  8. DFT calculations on 1,4-dithiine and S-oxygenated derivatives ...

    African Journals Online (AJOL)

    The molecular structures of 1,4-dithiine and S-oxygenated derivatives are studied using B3LYP/6-311++G** level of theory. These compounds have 8π-electrons in the ring. This led to stabilization of non-planar conformation. DFT calculations show that 1,4-dithiine, C4H4SS, 1,4-dithiine-1-oxide, C4H4SOS, 1,4-dithiine-1 ...

  9. DFT calculation and vibrational spectroscopic studies of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine

    Science.gov (United States)

    Premkumar, S.; Jawahar, A.; Mathavan, T.; Kumara Dhas, M.; Sathe, V. G.; Milton Franklin Benial, A.

    2014-08-01

    The molecular structure of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine (BABP) was optimized by the DFT/B3LYP method with 6-311G (d,p), 6-311++G (d,p) and cc-pVTZ basis sets using the Gaussian 09 program. The most stable optimized structure of the molecule was predicted by the DFT/B3LYP method with cc-pVTZ basis set. The vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals and thermodynamical parameters were calculated. These calculations were done at the ground state energy level of BABP without applying any constraint on the potential energy surface. The vibrational spectra were experimentally recorded using Fourier Transform-Infrared (FT-IR) and micro-Raman spectrometer. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies. The complete theoretically calculated and experimentally observed vibrational frequencies were assigned on the basis of Potential Energy Distribution (PED) calculation using the VEDA 4.0 program. The vibrational modes assignments were performed by using the animation option of GaussView 05 graphical interface for Gaussian program. The Mulliken atomic charge distribution was calculated for BABP molecule. The molecular reactivity and stability of BABP were also studied by frontier molecular orbitals (FMOs) analysis.

  10. Structure evolution of mononuclear tungsten and molybdenum species in the protonation process: Insight from FPMD and DFT calculations

    Science.gov (United States)

    Zhang, Ning; Yi, Haibo; Zeng, Dewen; Zhao, Zhongwei; Wang, Wenlei; Costanzo, Francesca

    2018-03-01

    In this work, we apply static density functional theory (DFT) calculations, as well as classical and first-principles molecular dynamics (FPMD) simulations, using the free-energy perturbation method to study the protonation ability, active site and structures of W(VI) and Mo(VI) in acidic aqueous solution. Using FPMD simulations, utilizing the pKa's calculation technique, we concluded that the octahedral WO2(OH)2(H2O)2 is the true formula for tungstic acid (H2WO4), and the hydroxyl ligands are the acidic site. This aqueous structure of H2WO4 is analogous to the previously reported structure of molybdic acid (H2MoO4). The FPMD trajectories of the tungstic acid deprotonation show that the mono-protonated monotungstate ion (HWO4-) may partially exist as a five-coordinated WO3(OH)(H2O)- species except for the four-coordinated WO3(OH)- species. This result is supported by DFT calculations, with an isoenergetic point (ΔE = 1.9 kcal·mol-1) for the WO3(OH)(H2O)- and WO3(OH)- species, when explicit solvent molecules are taken into account. In contrast, for the H2MoO4 acid, FPMD trajectories during the deprotonation process show that two H2O ligands immediately escape from the first coordinated sphere of Mo(VI) to form the four-coordinated MoO3(OH)- species. This difference indicates that structural expansion of W(VI) began in the first protonated step, while that of Mo(VI) only occurs in the second step. In addition, our calculated first and second acid constants for tungstic acid are higher than previously reported values for molybdic acid. This result suggests that WO42- is more easily protonated than the MoO42- anion in the same acidic solution, which is further confirmed by DFT calculations of hydrated oxoanions and its protonated species, based upon the hydration energy.

  11. Internal dynamics in helical molecules studied by X-ray diffraction, NMR spectroscopy and DFT calculations

    Czech Academy of Sciences Publication Activity Database

    Dračínský, Martin; Storch, Jan; Církva, Vladimír; Císařová, I.; Sýkora, Jan

    2017-01-01

    Roč. 19, č. 4 (2017), s. 2900-2907 ISSN 1463-9076 R&D Projects: GA ČR GA15-11223S; GA ČR GA15-12719S Institutional support: RVO:61388963 ; RVO:67985858 Keywords : helicene * NMR spectroscopy * DFT calculations Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry; Physical chemistry (UCHP-M) Impact factor: 4.123, year: 2016 http://pubs.rsc.org/en/content/articlehtml/2013/cp/c6cp07552e

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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)

  17. Association of aescin with β- and γ-cyclodextrins studied by DFT calculations and spectroscopic methods

    Directory of Open Access Journals (Sweden)

    Ana I. Ramos

    2017-02-01

    Full Text Available Background: Aescin, a natural mixture of saponins occurring in Aesculus hippocastanum, exhibits important flebotonic properties, being used in the treatment of chronic venous insufficiency in legs. The inclusion of aescin into cyclodextrins (CDs is a technical solution for its incorporation into the textile of stockings, but details of the physicochemistry of these host–guest systems are lacking. This work investigates the inclusion of aescin into the cavities of two native cyclodextrins, β-CD and γ-CD.Results: The continuous variation method applied to aqueous-phase 1H nuclear magnetic resonance (1H NMR has demonstrated that the preferred CD/aescin inclusion stoichiometries are 2:1 with β-CD and 1:1 with γ-CD. The affinity constant calculated for γ-CD·aescin was 894 M−1, while for 2β-CD·aescin it was estimated to be 715 M−1. Density functional theory (DFT calculations on the interaction of aescin Ib with CDs show that an inclusion can indeed occur and it is further demonstrated that the wider cavity of γ-CD is more adequate to accommodate this large guest. ROESY spectroscopy is consistent with the formation of a complex in which the triterpenic moiety of aescin is included into the cavity of γ-CD. The higher stability of this geometry was confirmed by DFT. Furthermore, DFT calculations were applied to determine the chemical shifts of the protons H3 and H5 of the CDs in the optimised structures of the inclusion complexes. The calculated values are very similar to the experimental data, validating the approach made in this study by NMR.Conclusion: The combination of experimental data from aqueous-state NMR measurements and theoretical calculations has demonstrated that γ-CD is the most suitable host for aescin, although the inclusion also occurs with β-CD. The geometry of the γ-CD·aescin complex is characterised by the inclusion of the triterpene segment of aescin into the host cavity.

  18. Association of aescin with β- and γ-cyclodextrins studied by DFT calculations and spectroscopic methods.

    Science.gov (United States)

    Ramos, Ana I; Vaz, Pedro D; Braga, Susana S; Silva, Artur M S

    2017-01-01

    Background: Aescin, a natural mixture of saponins occurring in Aesculus hippocastanum , exhibits important flebotonic properties, being used in the treatment of chronic venous insufficiency in legs. The inclusion of aescin into cyclodextrins (CDs) is a technical solution for its incorporation into the textile of stockings, but details of the physicochemistry of these host-guest systems are lacking. This work investigates the inclusion of aescin into the cavities of two native cyclodextrins, β-CD and γ-CD. Results: The continuous variation method applied to aqueous-phase 1 H nuclear magnetic resonance ( 1 H NMR) has demonstrated that the preferred CD/aescin inclusion stoichiometries are 2:1 with β-CD and 1:1 with γ-CD. The affinity constant calculated for γ-CD·aescin was 894 M -1 , while for 2β-CD·aescin it was estimated to be 715 M -1 . Density functional theory (DFT) calculations on the interaction of aescin Ib with CDs show that an inclusion can indeed occur and it is further demonstrated that the wider cavity of γ-CD is more adequate to accommodate this large guest. ROESY spectroscopy is consistent with the formation of a complex in which the triterpenic moiety of aescin is included into the cavity of γ-CD. The higher stability of this geometry was confirmed by DFT. Furthermore, DFT calculations were applied to determine the chemical shifts of the protons H3 and H5 of the CDs in the optimised structures of the inclusion complexes. The calculated values are very similar to the experimental data, validating the approach made in this study by NMR. Conclusion: The combination of experimental data from aqueous-state NMR measurements and theoretical calculations has demonstrated that γ-CD is the most suitable host for aescin, although the inclusion also occurs with β-CD. The geometry of the γ-CD·aescin complex is characterised by the inclusion of the triterpene segment of aescin into the host cavity.

  19. 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.

  20. 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

  1. 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 pK a ≃ 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.

  2. DFT Calculations of Hydrogen Adsorption inside Single-Walled Carbon Nanotubes

    Directory of Open Access Journals (Sweden)

    Igor K. Petrushenko

    2018-01-01

    Full Text Available DFT calculations have been performed to study noncovalent interactions of a hydrogen molecule and single-walled carbon nanotubes (SWCNTs of various diameters. Understanding these interactions is crucial for the development of systems for hydrogen storage and delivery. The barrier and barrier-free introduction of a hydrogen molecule into SWCNTs is observed. It has been found that hydrogen molecules bind differently onto SWCNTs, depending on their diameters and the orientation of an H2 molecule inside the SWCNT. The binding inside SWCNTs with small diameters ((3,3; (4,4 is very unfavorable; the opposite situation is in the case of larger ((5,5; (6,6 SWCNTs. Finally, in the case of ((7,7; (8,8 SWCNTs, the hydrogen binding energies decrease, and their values approach to those of graphene.

  3. 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.

  4. 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.

  5. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    Science.gov (United States)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  6. Electronic and optical properties of GaN under pressure: DFT calculations

    Science.gov (United States)

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

    2017-12-01

    Optical and electronic properties of ZB, RS and WZ structures of gallium nitride (GaN) are studied in equilibrium and under pressure using the first-principles calculation in the density functional theory (DFT) framework to obtain quantities like dielectric function, loss function, reflectance and absorption spectra, refractive index and their relation parameters. The electronic properties are studied using EV-GGA and GGA approximations and the results calculated by EV-GGA approximation were found to be much closer to the experimental results. The interband electron transitions are studied using the band structure and electron transition peaks in the imaginary part of the dielectric function; these transitions occur in three structures from N-2p orbital to Ga-4s and Ga-4p orbitals in the conduction band. Different optical properties of WZ structure were calculated in two polarization directions of (100) and (001) and the results were close to each other. Plasmon energy corresponding to the main peak of the energy-loss function in RS with the value of 26 eV was the highest one, which increased under pressure. In general, RS shows more different properties than WZ and ZB.

  7. Synthesis, crystal structure of and DFT calculations on bisglycinato-bis[p-(hydroxymethylpyridine]nickel(II

    Directory of Open Access Journals (Sweden)

    FANG FANG JIAN

    2010-09-01

    Full Text Available The main aim of this study was to investigate the relationship between mIn tA new Ni(II complex of bisglycinato-bis[p-(hydroxylmethylpy-ridine] was synthesized and characterized by elemental analysis, IR, UV–Vis spectroscopy and X-ray single crystal diffraction analysis. The thermal stability of the title complex was also determined. The complex adopts a distorted octahedral geometry and possesses inversion symmetry with the Ni(II ion as the center of inversion. Density function theory (DFT calculations of the structure, electronic absorption spectra, electron structure and natural population analysis (NPA at the B3LYP/LANL2DZ level of theory were performed. The predicted geometric parameters and electronic spectra were compared with the experimental values and they supported each other. The NPA results indicate that the electronic transitions were mainly derived from the contribution of an intra-ligand (IL transition, a ligand-to-metal charge transfer (LMCT transition and a d-d transition. The electron structure calculations suggest that the central Ni(II ion uses its 4s and 3d orbitals to form covalent bonds with coordinated N and O atoms. The calculated bond orders are also consistent with the thermal decomposition results. Based on vibrational analysis, the thermodynamic properties of the title complex were predicted and the correlative equations between these thermodynamic properties and temperature are also reported.

  8. Structural and Thermodynamic Analysis of the First Mononuclear Aqueous Aluminum Citrate Complex Using DFT Calculations.

    Science.gov (United States)

    de Noronha, Antonio Luiz Oliveira; Guimarães, Luciana; Duarte, Hélio Anderson

    2007-05-01

    Structural and thermodynamic properties of the mononuclear Al/citrate complexes have been theoretically investigated aiming to understand the coordination mechanism at an atomic level. GGA-DFT/PCM calculations have been performed for the different conformations and tautomers arising from the Al(3+) and citric acid (H3L) interaction in aqueous solution. The Gibbs reaction energies were estimated based on the reaction of the trigonal planar Al(OH)3 and H3L to form different Al-citrate complexes. The estimated Gibbs free reaction energies for the [AlL], [AlHL](+), and [Al(OH)L](-) species are in good agreement with the experimental values. In these species, the Al(3+) center is coordinated by two carboxylic and the tertiary hydroxyl groups of the citrate. Conversely to what has been proposed based on the experiments, the present theoretical calculations indicate that the citric acid hydroxyl group remains protonated upon the coordination of Al(3+). In fact, our model turns out to be more consistent with the relative pKa values of citrate protonation groups and with the hydrolysis constant of the H2O bound to Al(3+) leading to better agreement with the available experimental data.

  9. Theoretical calculation (DFT), Raman and surface-enhanced Raman scattering (SERS) study of ponceau 4R

    Science.gov (United States)

    Xie, Yunfei; Li, Yan; Sun, Yingying; Wang, Heya; Qian, He; Yao, Weirong

    2012-10-01

    Ponceau 4R is used as a coloring agent in many different products, such as food, drinks, medicines, cosmetics and tobacco. However, ponceau 4R also shows carcinogenic, teratogenic and mutagenic behavior in high doses. In this work, standard Raman, theoretical Raman and surface-enhanced Raman scattering (SERS) spectra have been used to investigate ponceau 4R. More specifically, density functional theory (DFT) calculations have been used to calculate the optimized Raman spectrum of ponceau 4R at the B3LYP/6-31G(d) level. This has provided a better understanding of the optimized geometry and vibrational frequencies of this dye. In addition, the experimental spectrum of ponceau 4R has been compared with the theoretical spectrum; good agreement was obtained. Finally, it has shown that using SERS the detection limit of the ponceau 4R solution can be as low as 5 μg/mL. This has been achieved by SERS measurements of ponceau 4R on a substrate of gold nanoparticles. The SERS peaks at 1030, 1236, 1356 and 1502 cm-1 were chosen as index for semi-quantitative analysis, showing that the SERS technique provided a useful ultrasensitive method for the detection of ponceau 4R.

  10. DFT calculations for anharmonic force field and spectroscopic constants of YC2 and its 13C isotopologues

    Science.gov (United States)

    Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Li, Jing

    2018-02-01

    The construction of the complete third and the semi-diagonal quartic force fields including the anharmonicity of the ground state (X˜2A1) for yttrium dicarbide (YC2) is carried out employing the vibrational second-order perturbation theory (VPT2) in combination with the density functional theory (DFT). The equilibrium geometries optimization, anharmonic force field and vibrational spectroscopic constants of YC2 are calculated by B3LYP, B3PW91 and B3P86 methods. Aug-cc-pVnZ (n = D, T, Q) and cc-pVnZ-PP (n = D, T, Q) basis sets are chosen for C and Y atoms, respectively. The calculated geometry parameters of YC2 agree well with the corresponding experimental and previous theoretical results. The bonding characters of Ysbnd C2 or Csbnd C are discussed. Based on the optimized equilibrium geometries, the spectroscopic constants and anharmonic force field of YC2 are calculated. Comparing with the spectroscopic constants of YC2 derived from the experiment, the calculated results show that the B3PW91 and B3P86 methods are superior to B3LYP for YC2. The Coriolis coupling constants, cubic and quartic force constants of YC2 are reasonably predicted. Besides, the spectroscopic constants and anharmonic force field of Y13C2 (X˜2A1) and Y13CC (X˜2A‧) are calculated for the first time, which are expected to guide the high resolution experimental work for YC2 and its 13C isotopologues.

  11. DFT calculations for anharmonic force field and spectroscopic constants of YC2and its13C isotopologues.

    Science.gov (United States)

    Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Li, Jing

    2018-02-15

    The construction of the complete third and the semi-diagonal quartic force fields including the anharmonicity of the ground state (X˜ 2 A 1 ) for yttrium dicarbide (YC 2 ) is carried out employing the vibrational second-order perturbation theory (VPT2) in combination with the density functional theory (DFT). The equilibrium geometries optimization, anharmonic force field and vibrational spectroscopic constants of YC 2 are calculated by B3LYP, B3PW91 and B3P86 methods. Aug-cc-pVnZ (n=D, T, Q) and cc-pVnZ-PP (n=D, T, Q) basis sets are chosen for C and Y atoms, respectively. The calculated geometry parameters of YC 2 agree well with the corresponding experimental and previous theoretical results. The bonding characters of YC 2 or CC are discussed. Based on the optimized equilibrium geometries, the spectroscopic constants and anharmonic force field of YC 2 are calculated. Comparing with the spectroscopic constants of YC 2 derived from the experiment, the calculated results show that the B3PW91 and B3P86 methods are superior to B3LYP for YC 2 . The Coriolis coupling constants, cubic and quartic force constants of YC 2 are reasonably predicted. Besides, the spectroscopic constants and anharmonic force field of Y 13 C 2 (X˜ 2 A 1 ) and Y 13 CC (X˜ 2 A ' ) are calculated for the first time, which are expected to guide the high resolution experimental work for YC 2 and its 13 C isotopologues. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. 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.

  13. Calculating the geometry and Raman spectrum of physiological bis(L-histidinato)copper(II): an assessment of DFT functionals for aqueous and isolated systems.

    Science.gov (United States)

    Sabolović, Jasmina; Ramek, Michael; Marković, Marijana

    2017-09-26

    Reliable density functional theory (DFT) calculations can be performed in conjuction with spectroscopic measurements to elucidate the structural properties of physiologically important bis(amino acidato)copper(II) compounds in solutions. They can provide insight into the influence of intermolecular interactions on the molecular geometry in the crystal lattice or solution when compared with a DFT gas-phase minimum. Our previous paper [Marković et al. (2014) Eur J Inorg Chem 198] reported the DFT-determined geometries and Raman spectra for different conformers of physiological bis(L-histidinato)copper(II) with 20 explicit water molecules, as calculated using the B3LYP functional. The present study examined the reliability of those B3LYP results by applying the M06 functional instead, as it should better account for noncovalent interactions. The water molecules were positioned more compactly around the complex by M06 than by B3LYP. The accuracies of the two functionals when compared to relevant experimental data showed that M06 was better at reproducing in-plane Cu-N bond lengths but B3LYP gave more accurate axial Cu-O distances. Both functionals reproduced the experimental Raman spectrum at pH 8 to similar levels of accuracy and provided precise information on the Cu(II) coordination mode and conformation in aqueous solution. Additionally, we assessed several DFT and DFT-D functionals (BP86, B3LYP, B3LYP-D, M06, M06 L, wB97XD, mPW2PLYPD) by using them to model the geometries of experimental bis(L-histidinato)copper(II) crystalline conformations as isolated systems, and then benchmarking the results against those from high-level second-order pertubation Møller-Plesset (MP2) calculations. Although this assessment resulted in an equivocal conclusion because the MP2 results for the isolated complex were inconsistent with the corresponding DFT outcomes, it does provide new information on future benchmark options.

  14. Design of Pd-Based Bimetallic Catalysts for ORR: A DFT Calculation Study

    Directory of Open Access Journals (Sweden)

    Lihui Ou

    2015-01-01

    Full Text Available Developing Pd-lean catalysts for oxygen reduction reaction (ORR is the key for large-scale application of proton exchange membrane fuel cells (PEMFCs. In the present paper, we have proposed a multiple-descriptor strategy for designing efficient and durable ORR Pd-based alloy catalysts. We demonstrated that an ideal Pd-based bimetallic alloy catalyst for ORR should possess simultaneously negative alloy formation energy, negative surface segregation energy of Pd, and a lower oxygen binding ability than pure Pt. By performing detailed DFT calculations on the thermodynamics, surface chemistry and electronic properties of Pd-M alloys, Pd-V, Pd-Fe, Pd-Zn, Pd-Nb, and Pd-Ta, are identified theoretically to have stable Pd segregated surface and improved ORR activity. Factors affecting these properties are analyzed. The alloy formation energy of Pd with transition metals M can be mainly determined by their electron interaction. This may be the origin of the negative alloy formation energy for Pd-M alloys. The surface segregation energy of Pd is primarily determined by the surface energy and the atomic radius of M. The metals M which have smaller atomic radius and higher surface energy would tend to favor the surface segregation of Pd in corresponding Pd-M alloys.

  15. 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...... 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....... 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...

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

    Science.gov (United States)

    Wang, Xinye; Huang, Yaji; Pan, Zhigang; Wang, Yongxing; Liu, Changqi

    2015-09-15

    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 PbCl2 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 PbCl2. Considering the energy barriers, it is easy for PbO and PbCl2 to adsorb on Al surfaces but difficult to escape. The high energy barriers of de-HCl process cause the difficulties of PbCl2 to form PbO·Al2O3·2SiO2 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Indium local geometry in In-Sb-Te thin films using XANES and DFT calculations

    Science.gov (United States)

    Bilovol, V.; Gil Rebaza, A. V.; Mudarra Navarro, A. M.; Errico, L.; Fontana, M.; Arcondo, B.

    2017-12-01

    In-Sb-Te when is a thin film presents a huge difference in its electrical resistivity when transform from the amorphous (insulating) to the crystalline (conducting) phase. This property made this system one of the main phase-change materials used in the data storage industry. The change in the electrical conductivity is probably associated to a change in the bonding geometry of some of its constituents. To explore this point, we present in this work an study of the bonding geometry of In atoms in In-Sb-Te films by means of In K-edge X-ray absorption near edge structure (XANES) spectroscopy using synchrotron radiation in both as deposited (amorphous) and crystalline thin films obtained as a result of resistance (R) vs temperature (T) measurements. Comparison of the XANES spectra obtained for ternary amorphous films and binary crystalline reference films suggests that in amorphous films the bonding geometry of In atoms is tetrahedral-like. After the thermal annealing has been carried out the differences in the XANES spectra of the as deposited and the annealed films indicate that the bonding geometry of In atoms changes. Based on X-ray diffraction results and ab initio calculations in the framework of the Density Functional Theory (DFT) we show that the new coordination geometry is associated with a tendency of In atoms towards octahedral-like.

  18. 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.

  19. Synthesis, spectroscopic characterization and DFT calculations of novel Schiff base containing thiophene ring

    Science.gov (United States)

    Ermiş, Emel

    2018-03-01

    In this study, a new Schiff base derivative, 2-[(2-hydroxy-5-thiophen-2-yl-benzylidene)-amino]-6-methyl-benzoic acid (5), which has a thiophene ring and N, O donor groups, was successfully prepared by the condensation reaction of 2-hydroxy-5-(thiophen-2-yl)benzaldehyde (3) and 2-amino-6-methylbenzoic acid (4). The characterization of a Schiff base derivative (5) was performed by experimentally the UV-Vis., FTIR, 1H and 13C NMR spectroscopic methods and elemental analysis. Density Functional Theory (DFT/B3LYP/6-311+G(d, p)) calculations were used to examine the optimized molecular geometry, vibrational frequencies, 1H and 13C NMR chemical shifts, UV-Vis. spectroscopic parameters, HOMO-LUMO energies and molecular electrostatic potential (MEP) map of the compound (5) and the theoretical results were compared to the experimental data. In addition, the energetic behaviors such as the sum of electronic and thermal free energy (SETFE), atomic charges, dipole moment of the compound (5) in solvent media were investigated using the B3LYP method with the 6-311+G(d, p) basis set. The obtained experimental and theoretical results were found to be compatible with each other and they were supported the proposed molecular structure for the synthesized Schiff base derivative (5).

  20. Energetics of the spin-state transition in LaCoO3: Total energy calculations using DFT +DMFT

    Science.gov (United States)

    Nanguneri, Ravindra; Park, Hyowon

    In this talk, we will present the energetics of the spin-state transition in strongly correlated LaCoO3 by adopting total energy calculations within density functional theory plus dynamical mean field theory (DFT +DMFT). We computed total energy curves as a function of volume for different spin states including low spin (LS), high spin (HS), and 1:1 mixed HS-LS states. We will show that as the volume is expanded, the mixed HS-LS state becomes energetically stable with a reasonable energy gap to the ground-state LS state. The nature of the HS-LS state is a paramagnetic insulator consistent with experiment while the homogeneous HS state is energetically much higher compared to the LS state. To analyze the dynamical fluctuation effect on the energetics, we also computed DFT +U energy curves by adopting the maximally localized Wannier function as correlated orbitals, same as used in DFT +DMFT calculations. The static correlation effect treated in DFT +U overestimates the tendency to higher spin states and the mixed spin state is wrongly predicted to be the ground state. The effect of the Coulomb interaction U, the Hund's coupling J, and the double counting potential on the energetics will be also discussed.

  1. Structure of molybdenum and tungsten sulfide M(x)S(y)+ clusters: experiment and DFT calculations.

    Science.gov (United States)

    Patterson, Melissa J; Lightstone, James M; White, Michael G

    2008-11-27

    A combination of experiment and density functional theory was used to investigate the energetics of CO adsorption onto several small M(x)S(y)(+) (M = Mo, W; x/y = 2/6, 3/7, 5/7, 6/8) clusters as a probe of their atomic and electronic structure. Experimentally, tandem mass spectrometry was used to measure the relative yields of M(x)S(y)(+)(CO)(n) cluster adducts formed by collisions between a beam of mass-selected M(x)S(y)(+) cluster ions and CO molecules in a high-pressure collision cell (hexapole ion guide). The most probable M(x)S(y)(+)(CO)(n) adducts observed are those with n cluster, for which the n = 6 adduct is found to have nearly the same intensity as the n = x = 5 adduct. Density functional calculations were used to search for the lowest energy structures of the bare M(x)S(y)(+) clusters and to obtain their relative stability for sequential CO binding. The calculated trends in CO binding energies were then compared to the experimental adduct distributions for assigning the ground-state structures. In this way, it was possible to distinguish between two nearly isoenergetic ground-state isomers for the M(2)S(6)(+) and M(3)S(7)(+) clusters, as only one isomer gave a calculated CO stabilization energy trend that was consistent with the experimental data. Similar comparisons of predicted and observed CO adsorption trends also provide evidence for assigning the ground-state structures of the M(5)S(7)(+) and M(6)S(8)(+) clusters. The latter contain metallic cores with most of the sulfur atoms bonded along the edges or in the faces of the metal core structure. The n = 6 and 7 adducts of M(5)S(7)(+) are predicted to be more stable than the n = x = 5 adduct, but only the n = 6 adduct is observed experimentally. The DFT calculations show that the n = 7 adduct undergoes internal bond breaking whereas the n = 6 framework is stable, albeit highly distorted. For the M(6)S(8)(+) cluster, the calculations predict that the two lowest energy isomers can bind more than six CO

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

    Energy Technology Data Exchange (ETDEWEB)

    Shokuhi Rad, Ali, E-mail: a.shokuhi@gmail.com [Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr (Iran, Islamic Republic of); Zareyee, Daryoush [Department of Chemistry, Qaemshahr Branch, Islamic Azad University, Qaemshahr (Iran, Islamic Republic of); Peyravi, Majid; Jahanshahi, Mohsen [Faculty of Chemical Engineering, Babol University of Technology, Babol (Iran, Islamic Republic of)

    2016-12-30

    Highlights: • P1 and P4 are the most stable adsorption configurations for cytosine. • NBO analysis show n-type semiconductor property for both Al- and Ga-doped graphenes. • Important changes in the HOMO and LUMO of doped graphene upon adsorption of cytosine. • Increase in the conductivity of system when cytosine is adsorbed on doped graphenes. - Abstract: 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.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    Highlights: • P1 and P4 are the most stable adsorption configurations for cytosine. • NBO analysis show n-type semiconductor property for both Al- and Ga-doped graphenes. • Important changes in the HOMO and LUMO of doped graphene upon adsorption of cytosine. • Increase in the conductivity of system when cytosine is adsorbed on doped graphenes. - Abstract: 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.

  4. Value of NMR Parameters and DFT Calculations for Quantum Information Processing Utilizing Phosphorus Heterocycles.

    Science.gov (United States)

    Lino, Jéssica B R; Rocha, Eduardo P; Ramalho, Teodorico C

    2017-06-15

    Quantum computing is the field of science that uses quantum-mechanical phenomena, such as superposition and entanglement, to perform operations on data. The fundamental information unit used in quantum computing is the quantum bit or qubit. It is well-known that quantum computers could theoretically be able to solve problems much more quickly than any classical computers. Currently, the first and still the most successful implementations of quantum information processing (QIP) have been based on nuclear spins in liquids. However, molecules that enable many qubits NMR QIP implementations should meet some conditions: have large chemical shifts and be appropriately dispersed for qubit addressability, appreciable spin-spin coupling between any pair of spins, and a long relaxation time. In this line, benzyldene-2,3-dihydro-1H-[1,3]diphosphole (BDF) derivatives have been theoretically tested for maximizing large chemical shifts, spin-spin coupling, and minimizing the hyperfine coupling constant. Thus, the structures were optimized at the B3LYP/6-311G(d,p) level and showed a significant similarity with the experimental geometrical parameters. The NMR spectroscopic parameters (δ and J) were calculated with six different DFT functionals. The τ-HCTH/6-31G(2d) level is in better agreement with the experimental data of 31 P and 13 C chemical shifts, while PCM-B3LYP/cc-pVDZ level shows a decrease on deviation between calculated and experimental values for P-P and P-C SSCC. The surface response technique was employed to rationalize how the hyperfine constant varies with the chemical shifts and coupling constants values. From our findings, BDF-NO 2 was the best candidate for NMR quantum computations (NMR-QC) among the studied series.

  5. 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.

  6. Structural analysis of flavonoids in solution through DFT 1H NMR chemical shift calculations: Epigallocatechin, Kaempferol and Quercetin

    Science.gov (United States)

    De Souza, Leonardo A.; Tavares, Wagner M. G.; Lopes, Ana Paula M.; Soeiro, Malucia M.; De Almeida, Wagner B.

    2017-05-01

    In this work, we showed that comparison between experimental and theoretical 1H NMR chemical shift patterns, calculated using Density Functional Theory (DFT), can be used for the prediction of molecular structure of flavonoids in solution, what is experimentally accessible for gas phase (electron diffraction methods) and solid samples (X-ray diffraction). The best match between B3LYP/6-31G(d,p)-PCM 1H NMR calculations for B ring rotated structures and experimental spectra can provide information on the conformation adopted by polyphenols in solution (usually DMSO-d6, acetone-d6 as solvents), which may differ from solid state and gas phase observed structures, and also DFT optimized geometry in the vacuum.

  7. Understanding the interfacial properties of graphene-based materials/BiOI heterostructures by DFT calculations

    Science.gov (United States)

    Dai, Wen-Wu; Zhao, Zong-Yan

    2017-06-01

    Heterostructure constructing is a feasible and powerful strategy to enhance the performance of photocatalysts, because they can be tailored to have desirable photo-electronics properties and couple distinct advantageous of components. As a novel layered photocatalyst, the main drawback of BiOI is the low edge position of the conduction band. To address this problem, it is meaningful to find materials that possess suitable band gap, proper band edge position, and high mobility of carrier to combine with BiOI to form hetertrostructure. In this study, graphene-based materials (including: graphene, graphene oxide, and g-C3N4) were chosen as candidates to achieve this purpose. The charge transfer, interface interaction, and band offsets are focused on and analyzed in detail by DFT calculations. Results indicated that graphene-based materials and BiOI were in contact and formed van der Waals heterostructures. The valence and conduction band edge positions of graphene oxide, g-C3N4 and BiOI changed with the Fermi level and formed the standard type-II heterojunction. In addition, the overall analysis of charge density difference, Mulliken population, and band offsets indicated that the internal electric field is facilitate for the separation of photo-generated electron-hole pairs, which means these heterostructures can enhance the photocatalytic efficiency of BiOI. Thus, BiOI combines with 2D materials to construct heterostructure not only make use of the unique high electron mobility, but also can adjust the position of energy bands and promote the separation of photo-generated carriers, which provide useful hints for the applications in photocatalysis.

  8. Synthesis, characterization, DFT calculations and molecular docking studies of metal (II) complexes

    Science.gov (United States)

    Ekennia, Anthony C.; Osowole, Aderoju A.; Olasunkanmi, Lukman O.; Onwudiwe, Damian C.; Olubiyi, Olujide O.; Ebenso, Eno E.

    2017-12-01

    Two novel ligands, 2-methyl-6-[(5-methyl benzothiazol-2-ylimino)-methyl]-2-methoxycyclohexa-1,5-dienol (HL1) and 2-methyl-6-[(5-floro-benzothiazol-2-ylimino)-methyl]-2-methoxycyclohexa-1,5-dienol (HL2) were synthesized from the condensation reaction of 2-hydroxy-3-methoxybenzaldehyde with 2-amino-6-methylbenzothiazole and 2-amino-6-florobenzothiazole respectively. Mononuclear Cu(II), Ni(II) and Co(II) complexes of the ligands were synthesized and characterized using elemental analysis, magnetic susceptibility, thermogravimetric, conductance, infrared and UV-visible spectroscopic measurements. The 1H NMR, 13C NMR, Dept-90 NMR spectroscopy of the ligands was also recorded to establish the formation of the Schiff bases. The analytical data of the complexes showed that the metal to ligand ratio was 1:1 for Cu(II), Ni(II) and Co(II) complexes of HL1 and Cu(II) complexes of HL2, while Ni(II) and Co(II) complexes of HL2 was 1:2. The infrared spectral data showed that the chelation behaviour of the ligands towards transition metal ions was through phenolic oxygen and azomethine nitrogen atoms. Molar conductivity revealed the non-electrolytic nature of all chelates in DMSO solution. The geometry of the complexes was deduced from thermal, magnetic susceptibility and UV-visible spectroscopic results and was further confirmed with DFT calculations. The compounds were subjected to in-vitro antibacterial screening using agar well diffusion method on some clinically isolated Gram positive and Gram negative bacteria strains. The compounds showed varied antibacterial activities. Molecular docking studies were carried out to study the molecular interaction between the compounds and different enzymes of the bacterial strains. The antioxidant potentials of the compounds were studied using ferrous ion chelating assay and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay. However, the complexes had better antioxidant potentials compared to the ligands.

  9. Raman spectra and DFT calculations for botryococcene and methylsqualene hydrocarbons from the B race of the green microalga Botryococcus braunii

    Science.gov (United States)

    Tatli, Mehmet; Chun, Hye Jin; Camp, Charles H.; Li, Jingting; Cicerone, Marcus T.; Shih, Wei-Chuan; Laane, Jaan; Devarenne, Timothy P.

    2017-11-01

    Botryococcus braunii, a green colonial microalga, is a prodigious producer of liquid hydrocarbon oils that can be used as renewable feedstocks for producing combustion engine fuels. The B race of B. braunii mainly produces the triterpene hydrocarbons known as botryococcenes, which have over twenty known structures. Minor hydrocarbons in the B race include the triterpene methylsqualenes. Here we report an examination of the molecular structure for ten botryococcenes and five methylsqualenes using Raman spectroscopy and density functional theory (DFT) calculations in an effort to distinguish between these structurally similar molecules by spectroscopic approaches. The DFT calculations show that these molecules have between 243 and 271 vibrational frequencies. A comparison of the experimental Raman spectroscopy and DFT calculations indicates several spectral regions such as those for ν(Cdbnd C) stretching, CH2/CH3 bending, and ring bending can be used to distinguish between these molecules. In an extension of this analysis, a broadband coherent anti-Stokes Raman spectroscopy (BCARS) analysis was used to clearly distinguish between several botryococcenes isomers.

  10. 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.

  11. Electron, hole and exciton self-trapping in germanium doped silica glass from DFT calculations with self-interaction correction

    International Nuclear Information System (INIS)

    Du Jincheng; Rene Corrales, L.; Tsemekhman, Kiril; Bylaska, Eric J.

    2007-01-01

    Density functional theory (DFT) calculations were employed to understand the refractive index change in germanium doped silica glasses for the trapped states of electronic excitations induced by UV irradiation. Local structure relaxation and excess electron density distribution were calculated upon self-trapping of an excess electron, hole, and exciton in germanium doped silica glass. The results show that both the trapped exciton and excess electron are highly localized on germanium ion and, to some extent, on its oxygen neighbors. Exciton self-trapping is found to lead to the formation of a Ge E' center and a non-bridging hole center. Electron trapping changes the GeO 4 tetrahedron structure into trigonal bi-pyramid with the majority of the excess electron density located along the equatorial line. The self-trapped hole is localized on bridging oxygen ions that are not coordinated to germanium atoms that lead to elongation of the Si-O bonds and change of the Si-O-Si bond angles. We carried out a comparative study of standard DFT versus DFT with a hybrid PBE0 exchange and correlation functional. The results show that the two methods give qualitatively similar relaxed structure and charge distribution for electron and exciton trapping in germanium doped silica glass; however, only the PBE0 functional produces the self-trapped hole

  12. Synthesis, X-ray crystallography, and DFT calculations of a novel phosphoramide

    Czech Academy of Sciences Publication Activity Database

    Shariatinia, Z.; Dušek, Michal; Eigner, Václav

    2014-01-01

    Roč. 640, č. 14 (2014), 2945-2955 ISSN 0044-2313 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : phosphoramide * x-ray structure * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.160, year: 2014

  13. 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...

  14. Basis set recommendations for DFT calculations of gas-phase optical rotations at different wavelengths

    DEFF Research Database (Denmark)

    Hedegård, Erik Donovan; 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...

  15. A systematic theoretical study of the electronic structures of porphyrin dimers: DFT and TD-DFT calculations on diporphyrins linked by ethane, ethene, ethyne, imine, and azo bridges.

    Science.gov (United States)

    Rintoul, Llew; Harper, Shannon R; Arnold, Dennis P

    2013-11-21

    Theoretical calculations of the geometries, electronic structures and electronic absorption spectra of a series of covalently-linked porphyrin dimers are reported. The diporphyrins comprise 5,10,15-triphenylporphyrinatozinc(II) (ZnTriPP) units linked through the meso carbons by two-atom bridges, namely 1,2-ethanediyl (1), trans-1,2-ethenediyl (2), ethynediyl (3), 1,2-iminomethenediyl (4), and transdiazenediyl (5). The structures were optimised in toluene solvent by Density Functional Theory (DFT), using the integral equation formalism variant of the polarizable continuum model. The calculations were performed using the B3LYP functional and the 6-31G(d,p) basis set. The complete molecules were modelled, with no substitution of smaller groups on the periphery. In parallel, the compounds 2–5 were prepared by known or novel synthetic routes, to enable comparisons of experimental electronic absorption spectra with those calculated using time dependent-DFT at the same level of theory. As the ethane dimer 1 is not yet synthetically accessible, the model monomer meso-2-phenylethylZnTriPP was used for comparisons with the theoretical predictions. The results form a self-consistent set, enabling for the first time legitimate comparisons of the electronic structures of the series, especially regarding the degree to which the porphyrin p-systems interact by conjugation across the bridges. The theoretical calculations of the electronic transitions match the observed spectra in toluene to a remarkable degree, especially with respect to the peak maximum of the Q band, which represents to a large degree the energy of the HOMO–LUMO transition. The imine 4 is intrinsically polar due to the asymmetric bridge, and the HOMO is located almost exclusively on the ZnTriPP unit attached to the nitrogen of the imine, and the LUMO on the C-attached ring. Thus the Q-band transition is mapped as a comprehensive charge-transfer from the former ring to the latter. This may have consequences

  16. Understanding the interfacial properties of graphene-based materials/BiOI heterostructures by DFT calculations

    International Nuclear Information System (INIS)

    Dai, Wen-Wu; Zhao, Zong-Yan

    2017-01-01

    Highlights: • Heterostructure constructing is an effective way to enhance the photocatalytic performance. • Graphene-like materials and BiOI were in contact and formed van der Waals heterostructures. • Band edge positions of GO/g-C 3 N 4 and BiOI changed to form standard type-II heterojunction. • 2D materials can promote the separation of photo-generated electron-hole pairs in BiOI. - Abstract: Heterostructure constructing is a feasible and powerful strategy to enhance the performance of photocatalysts, because they can be tailored to have desirable photo-electronics properties and couple distinct advantageous of components. As a novel layered photocatalyst, the main drawback of BiOI is the low edge position of the conduction band. To address this problem, it is meaningful to find materials that possess suitable band gap, proper band edge position, and high mobility of carrier to combine with BiOI to form hetertrostructure. In this study, graphene-based materials (including: graphene, graphene oxide, and g-C 3 N 4 ) were chosen as candidates to achieve this purpose. The charge transfer, interface interaction, and band offsets are focused on and analyzed in detail by DFT calculations. Results indicated that graphene-based materials and BiOI were in contact and formed van der Waals heterostructures. The valence and conduction band edge positions of graphene oxide, g-C 3 N 4 and BiOI changed with the Fermi level and formed the standard type-II heterojunction. In addition, the overall analysis of charge density difference, Mulliken population, and band offsets indicated that the internal electric field is facilitate for the separation of photo-generated electron-hole pairs, which means these heterostructures can enhance the photocatalytic efficiency of BiOI. Thus, BiOI combines with 2D materials to construct heterostructure not only make use of the unique high electron mobility, but also can adjust the position of energy bands and promote the separation of

  17. Understanding the interfacial properties of graphene-based materials/BiOI heterostructures by DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Wen-Wu [Faculty of Materials Science and Engineering, Kunming University of Science and Technology, Kunming 650093 (China); Zhao, Zong-Yan, E-mail: zzy@kmust.edu.cn [Faculty of Materials Science and Engineering, Kunming University of Science and Technology, Kunming 650093 (China); Jiangsu Provincial Key Laboratory for Nanotechnology, Nanjing University, Nanjing 210093 (China)

    2017-06-01

    Highlights: • Heterostructure constructing is an effective way to enhance the photocatalytic performance. • Graphene-like materials and BiOI were in contact and formed van der Waals heterostructures. • Band edge positions of GO/g-C{sub 3}N{sub 4} and BiOI changed to form standard type-II heterojunction. • 2D materials can promote the separation of photo-generated electron-hole pairs in BiOI. - Abstract: Heterostructure constructing is a feasible and powerful strategy to enhance the performance of photocatalysts, because they can be tailored to have desirable photo-electronics properties and couple distinct advantageous of components. As a novel layered photocatalyst, the main drawback of BiOI is the low edge position of the conduction band. To address this problem, it is meaningful to find materials that possess suitable band gap, proper band edge position, and high mobility of carrier to combine with BiOI to form hetertrostructure. In this study, graphene-based materials (including: graphene, graphene oxide, and g-C{sub 3}N{sub 4}) were chosen as candidates to achieve this purpose. The charge transfer, interface interaction, and band offsets are focused on and analyzed in detail by DFT calculations. Results indicated that graphene-based materials and BiOI were in contact and formed van der Waals heterostructures. The valence and conduction band edge positions of graphene oxide, g-C{sub 3}N{sub 4} and BiOI changed with the Fermi level and formed the standard type-II heterojunction. In addition, the overall analysis of charge density difference, Mulliken population, and band offsets indicated that the internal electric field is facilitate for the separation of photo-generated electron-hole pairs, which means these heterostructures can enhance the photocatalytic efficiency of BiOI. Thus, BiOI combines with 2D materials to construct heterostructure not only make use of the unique high electron mobility, but also can adjust the position of energy bands and

  18. Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches

    Science.gov (United States)

    2015-01-01

    Quantum mechanical (QM) calculations of noncovalent interactions are uniquely useful as tools to test and improve molecular mechanics force fields and to model the forces involved in biomolecular binding and folding. Because the more computationally tractable QM methods necessarily include approximations, which risk degrading accuracy, it is essential to evaluate such methods by comparison with high-level reference calculations. Here, we use the extensive Benchmark Energy and Geometry Database (BEGDB) of CCSD(T)/CBS reference results to evaluate the accuracy and speed of widely used QM methods for over 1200 chemically varied gas-phase dimers. In particular, we study the semiempirical PM6 and PM7 methods; density functional theory (DFT) approaches B3LYP, B97-D, M062X, and ωB97X-D; and symmetry-adapted perturbation theory (SAPT) approach. For the PM6 and DFT methods, we also examine the effects of post hoc corrections for hydrogen bonding (PM6-DH+, PM6-DH2), halogen atoms (PM6-DH2X), and dispersion (DFT-D3 with zero and Becke–Johnson damping). Several orders of the SAPT expansion are also compared, ranging from SAPT0 up to SAPT2+3, where computationally feasible. We find that all DFT methods with dispersion corrections, as well as SAPT at orders above SAPT2, consistently provide dimer interaction energies within 1.0 kcal/mol RMSE across all systems. We also show that a linear scaling of the perturbative energy terms provided by the fast SAPT0 method yields similar high accuracy, at particularly low computational cost. The energies of all the dimer systems from the various QM approaches are included in the Supporting Information, as are the full SAPT2+(3) energy decomposition for a subset of over 1000 systems. The latter can be used to guide the parametrization of molecular mechanics force fields on a term-by-term basis. PMID:24803867

  19. 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)

  20. DFT-GIAO calculation of properties of 19F NMR and stability study of environmentally relevant perfluoroalkylsulfonamides (PFASAmide)

    International Nuclear Information System (INIS)

    Mejia-Urueta, Rafael; Mestre-Quintero, Kleyber; Vivas-Reyes, Ricardo

    2011-01-01

    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, 19 F nuclear magnetic resonance (NMR 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 19 F NMR was performed. In this study we have determined the shielding constant (σ) 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 σ calculations were made at vacuum and in presence of a solvent. The values of chemical shifts (δ), 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 3 ), acetone (CH 3 COCH 3 ) and methanol (CH 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)

  1. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. 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).

  3. Role of dbnd NOH intermolecular interactions in oxime derivatives via Crystal structure, Hirshfeld surface, PIXELC and DFT calculations

    Science.gov (United States)

    Purushothaman, Gayathri; Thiruvenkatam, Vijay

    2017-11-01

    Oximes are building block of organic synthesis and they have wide range applications in laboratories, industries, and pharmaceutical as antidotes. Herein we report the crystal structures of oxime derivative Beta-p-Dimethylaminodeoxybenzionoxime (I) and o-Chloro-p-dimethylaminodeoxybenzion (II) the precursor molecule of o-Chloro-p-dimethylaminodeoxybenzionoxime and their intermolecular interactions studies through Hirshfeld surface & 2D-fingerprint plot analysis along with PIXELC and DFT calculations. The packing arrangements in I and II are driven by Osbnd H⋯N and Osbnd H⋯C interactions respectively. The Osbnd H⋯N hydrogen bonding in I facilitates the formation of the dimer with the motif of R (22(6)), whereas in II absence of oxime moiety (dbnd NOH) restricts the dimer formation. The 2D-fingerprint plot shows the close contacts for the intermolecular interactions in I & II. The PIXELC calculation of II suggests Osbnd H⋯C contributes for intermolecular interaction that stabilizes the crystal packing with the total energy value of 60.4 kcal/mol. The DFT calculation using B3LYP with 6-311G (d, p) functional set for both the derivatives shows a small deviation in the benzene ring (I) and chlorobenzene ring (II) with the RMSD value of 0.5095 Å and 0.8472 Å respectively.

  4. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Theoretical study of the adsorption energy of some linear saturated hydrocarbons on SWCNT: DFT calculations

    Science.gov (United States)

    Abdullah, Hewa; Abdallah, Hassan H.

    2017-04-01

    Carbon nanotubes represent one of the building blocks of innovation across most industries. Carbon nanotubes have many applications based on the aspect ratio, mechanical strength, electrical and thermal conductivity of these nano materials. In this study the adsorption of a single molecule of the some linear saturated hydrocarbons inside and on the surface of a tube of single-walled carbon nanotubes (SWCNT) was investigated using Density Function Theory (DFT). The results showed that all guest molecules prefer to be adsorbed into the surface of SWCNT rather than into the CNT tube. Upon adsorption of the guest molecules, the energy gap was considerably reduced, resulting in improved electrical conductivity. DOS and NBO analysis were performed to discover intermolecular interactions. Chemical reactivity was investigated in terms of chemical hardness, softness and absolute electronegativity

  6. Treating dispersion effects in extended systems by hybrid MP2:DFT calculations--protonation of isobutene in zeolite ferrierite.

    Science.gov (United States)

    Tuma, Christian; Sauer, Joachim

    2006-09-14

    We propose use of a hybrid method to study problems that involve both bond rearrangements and van-der-Waals interactions. The method combines second-order Møller-Plesset perturbation theory (MP2) calculations for the reaction site with density functional theory (DFT) calculations for a large system under periodic boundary conditions. Hybrid MP2:DFT structure optimisation for a cluster embedded in the periodic model is the first of three steps in a multi-level approach. The second step is extrapolation of the MP2 energy to the complete basis set limit. The third step is extrapolating the high-level (MP2) correction to the limiting case of the full periodic structure. This is done by calculating the MP2 correction for a series of cluster models of increasing size, fitting an analytic expression to these energy corrections, and applying the fitted expression to the full periodic structure. We assume that, up to a constant, the high-level correction is described by a damped dispersion expression. Combining the results of all three steps yields an estimate of the MP2 reaction energy for the full periodic system at the complete basis set level. The method is designed for a reaction between a small or medium sized substrate molecule and a very large chemical system. For adsorption of isobutene in zeolite H-ferrierite, the energies obtained for the formation of different structures, the pi-complex, the isobutoxide, the tert-butoxide, and the tert-butyl carbenium ion, are -78, -73, -48, and -21 kJ mol(-1), respectively. This corresponds to corrections of the pure DFT (PBE functional) results by -62, -70, -67, and -29 kJ mol(-1), respectively. Hence, the MP2 corrections are substantial and, perhaps more importantly, not the same for the different hydrocarbon species in the zeolite. Coupled-cluster (CCSD(T)) calculations change the MP2 energies by -4 kJ mol(-1) (tert-butyl cation) or less (below +/-1 kJ mol(-1) for the other species).

  7. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. (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.

  9. Study on the Reactivity of Amino Acid Chemosensor, NPFNP, with Ethanol: Structural Elucidation through Single Crystal XRD and DFT Calculations

    Directory of Open Access Journals (Sweden)

    Beena Varghese

    2017-01-01

    Full Text Available A novel ethoxy derivative of an amino acid chemosensor, 3-naphthyl-1-phenyl-5-(2ʹ-fluoro-5ʹ-nitrophenyl-2-pyrazoline (NPFNP, has been synthesized and characterized by different spectroscopic methods.  A single crystal of the ethoxy derivative, 3-naphthyl-1-phenyl-5-(2ʹ-ethoxy-5ʹ-nitrophenyl-2-pyrazoline NPENP, has been obtained and characterized.  The structure holds interest as it carries biologically active pyrazoline as a central ring attaching to electron donating and withdrawing substituents. The major motivation for this work was to gain detailed insight into the structural parameters of this compound for investigating the influence of crystal packing and geometrical dimensions on optical properties. Time-dependent DFT calculations have been employed for comparing the XRD data with theoretical parameters. The results show that the DFT method at B3LYP/6-31G level can well reproduce the structure of the title compound.

  10. Electronic and optical properties of 2D graphene-like ZnS: DFT calculations

    International Nuclear Information System (INIS)

    Lashgari, Hamed; Boochani, Arash; Shekaari, Ashkan; Solaymani, Shahram; Sartipi, Elmira; Mendi, Rohollah Taghavi

    2016-01-01

    Graphical abstract: - Highlights: • DFT has been applied to investigate the optical properties of 2D-ZnS and 3D-ZnS. • The electronic and the optical properties of 3D-ZnS and 2D-ZnS are compared. • At visible range of energies the transparency of 2D-ZnS is more than the 3D. - Abstract: Density-functional theory has been applied to investigate the electronic and optical properties of graphene-like two-dimensional ZnS in the (0001) direction of its Wurtzite phase. A comparison with 3D-ZnS has been carried out within the PBE- and EV-GGA. The electronic properties of 2D- and 3D-ZnS have been derived by the examination of the electronic band structures and density of states. The optical properties have been determined through the study of the dielectric function, reflectivity, electron loss function, refractive and extinction indices, the absorption index and optical conductivity. It is found that the transparency of 2D-ZnS is greater than the 3D over the visible range. A thorough study of the dielectric function has been performed so that the peaks and the transition bands have been specified. The electron loss function demonstrates that the plasmonic frequency for 2D- and 3D-ZnS is accrued at 11.22 and 19.93 eV within the PBE-GGA, respectively.

  11. Electronic and optical properties of 2D graphene-like ZnS: DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Lashgari, Hamed [Department of Physics, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Boochani, Arash, E-mail: arash_bch@yahoo.com [Department of Physics, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Shekaari, Ashkan [Department of Physics, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Solaymani, Shahram [Young Researchers and Elite Club, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Sartipi, Elmira [Department of Physics, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Mendi, Rohollah Taghavi [Department of Physics, Mashhad Branch, Islamic Azad University, Mashhad (Iran, Islamic Republic of)

    2016-04-30

    Graphical abstract: - Highlights: • DFT has been applied to investigate the optical properties of 2D-ZnS and 3D-ZnS. • The electronic and the optical properties of 3D-ZnS and 2D-ZnS are compared. • At visible range of energies the transparency of 2D-ZnS is more than the 3D. - Abstract: Density-functional theory has been applied to investigate the electronic and optical properties of graphene-like two-dimensional ZnS in the (0001) direction of its Wurtzite phase. A comparison with 3D-ZnS has been carried out within the PBE- and EV-GGA. The electronic properties of 2D- and 3D-ZnS have been derived by the examination of the electronic band structures and density of states. The optical properties have been determined through the study of the dielectric function, reflectivity, electron loss function, refractive and extinction indices, the absorption index and optical conductivity. It is found that the transparency of 2D-ZnS is greater than the 3D over the visible range. A thorough study of the dielectric function has been performed so that the peaks and the transition bands have been specified. The electron loss function demonstrates that the plasmonic frequency for 2D- and 3D-ZnS is accrued at 11.22 and 19.93 eV within the PBE-GGA, respectively.

  12. The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations

    Science.gov (United States)

    2011-01-01

    The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and graphene has been studied using post Hartree–Fock wave function theory (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE, vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene–M (M = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively. We found that the nature of binding of the three metals is different: While silver binds predominantly through dispersion interactions, the binding of palladium has a covalent character, and the binding of gold involves a subtle combination of charge transfer and dispersion interactions as well as relativistic effects. We demonstrate that the CCSD(T) benchmark binding energies for benzene–M complexes can be reproduced in plane-wave density functional theory calculations by including a fraction of the exact exchange and a nonempirical van der Waals correction (EE+vdW). Applying the EE+vdW method, we obtained binding energies for the graphene–M (M = Pd, Au, Ag) complexes of 17.4, 5.6, and 4.3 kcal/mol, respectively. The trends in binding energies found for the benzene–M complexes correspond to those in coronene and graphene complexes. DFT methods that use empirical corrections to account for the effects of vdW interactions significantly overestimate binding energies in some of the studied systems. PMID:22076121

  13. The electronic spectra and the structures of the individual copper(II) chloride and bromide complexes in acetonitrile according to steady-state absorption spectroscopy and DFT/TD-DFT calculations

    Science.gov (United States)

    Olshin, Pavel K.; Myasnikova, Olesya S.; Kashina, Maria V.; Gorbunov, Artem O.; Bogachev, Nikita A.; Kompanets, Viktor O.; Chekalin, Sergey V.; Pulkin, Sergey A.; Kochemirovsky, Vladimir A.; Skripkin, Mikhail Yu.; Mereshchenko, Andrey S.

    2018-03-01

    The results of spectrophotometric study and quantum chemical calculations for copper(II) chloro- and bromocomplexes in acetonitrile are reported. Electronic spectra of the individual copper(II) halide complexes were obtained in a wide spectral range 200-2200 nm. Stability constants of the individual copper(II) halide complexes in acetonitrile were calculated: log β1 = 8.5, log β2 = 15.6, log β3 = 22.5, log β4 = 25.7 for [CuCln]2-n and log β1 = 17.0, log β2 = 24.6, log β3 = 28.1, log β4 = 30.4 for [CuBrn]2-n. Structures of the studied complexes were optimized and electronic spectra were simulated using DFT and TD-DFT methodologies, respectively. According to the calculations, the more is the number of halide ligands the less is coordination number of copper ion.

  14. 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.

  15. DFT Calculations using WIEN2K to determine oxygen defect structure of rare earth doped ceria

    CERN Document Server

    Khalife, Ali Rida

    2014-01-01

    We perform density functional calculations using the program WIEN2K in order to study oxygen vacancies in rare earth doped ceria. The calculation for all rare earth elements were prepared, however only those foe Cadmium and Europium were performed due to lack of time. Also a short description of my stay at CERN was presented

  16. G4MP2, DFT and CBS-Q calculation of proton and electron affinities ...

    Indian Academy of Sciences (India)

    Abstract. The proton affinities, gas phase basicities and adiabatic ionization energies and electron affini- ties 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.

  17. Synthesis, spectral and luminescence study, crystal structure determination and DFT calculation of binuclear palladium(II) complexes

    Science.gov (United States)

    Seyfi, S.; Alizadeh, R.; Darvish Ganji, M.; Amani, V.

    2018-02-01

    Binuclear palladium(II) complexes with metal-metal (d8-d8) bonding interaction were synthesized by reactions of the 1-methyl-1H-1,2,3,4-tetrazole-5-thiol (Hmtzt) or a mixture of Hmtzt and 1,3-propanediamine (1,3-pda) ligands. Complex [Pd2(μ-mtzt)4]·2CH3CN (1) was synthesized by the reaction of Pd(OAc)2 with Hmtzt dissolved in acetonitrile and complex [Pd2(μ-mtzt)2(mtzt)2(1,3-pda)] (2) was synthesized by reaction of a mixture of Hmtzt and 1,3-propanediamine (dissolved in methanol) with PdCl2 (dissolved in acetonitrile) and were identified through elemental analysis, IR, UV-Vis, 1H NMR, luminescence spectroscopy as well as single-crystal X-ray diffraction method. A single-crystal of complex 1 shows that two Pd(II) centers are linked together by four bridging tetrazole ligands providing a paddle wheel-like arrangement. Also a crystal structure of complex 2 shows that this complex possesses a symmetric structure in which one Pd atom is tetra-coordinated by four sulfur atoms to forms PdS4 and other Pd atom is tetra-coordinated by four nitrogen to forms PdN4 coordination sphere. Density functional theory (DFT) was performed in this study for the Hmtzt ligand and binuclear palladium(II) complexes (1) and (2). The DFT calculation shows PdII-PdII bond lengths of 2.831 and 3.086 Å in complex 1 and 2, respectively which are close to the observed bond lengths of 2.802(11) and 3.0911(17) Å from single-crystal X-ray structure. The optimized geometry of the complexes is shown good agreement by X-ray data. Structural properties and molecular descriptors including bond lengths, bond angles, chemical hardness, dipole moment, HOMO-LUMO energy levels, electron transfer were analyzed. The IR spectroscopy was performed using VEDA4 software and UV-Vis spectra were analyzed using time-dependent density functional theory (TD-DFT) method. The theoretical and experimental data were also compared with each other.

  18. Synthesis, spectral and luminescence study, crystal structure determination and DFT calculation of binuclear palladium(II) complexes.

    Science.gov (United States)

    Seyfi, S; Alizadeh, R; Darvish Ganji, M; Amani, V

    2018-02-05

    Binuclear palladium(II) complexes with metal-metal (d 8 -d 8 ) bonding interaction were synthesized by reactions of the 1-methyl-1H-1,2,3,4-tetrazole-5-thiol (Hmtzt) or a mixture of Hmtzt and 1,3-propanediamine (1,3-pda) ligands. Complex [Pd 2 (μ-mtzt) 4 ]·2CH 3 CN (1) was synthesized by the reaction of Pd(OAc) 2 with Hmtzt dissolved in acetonitrile and complex [Pd 2 (μ-mtzt) 2 (mtzt) 2 (1,3-pda)] (2) was synthesized by reaction of a mixture of Hmtzt and 1,3-propanediamine (dissolved in methanol) with PdCl 2 (dissolved in acetonitrile) and were identified through elemental analysis, IR, UV-Vis, 1 H NMR, luminescence spectroscopy as well as single-crystal X-ray diffraction method. A single-crystal of complex 1 shows that two Pd(II) centers are linked together by four bridging tetrazole ligands providing a paddle wheel-like arrangement. Also a crystal structure of complex 2 shows that this complex possesses a symmetric structure in which one Pd atom is tetra-coordinated by four sulfur atoms to forms PdS 4 and other Pd atom is tetra-coordinated by four nitrogen to forms PdN 4 coordination sphere. Density functional theory (DFT) was performed in this study for the Hmtzt ligand and binuclear palladium(II) complexes (1) and (2). The DFT calculation shows Pd II -Pd II bond lengths of 2.831 and 3.086Å in complex 1 and 2, respectively which are close to the observed bond lengths of 2.802(11) and 3.0911(17)Å from single-crystal X-ray structure. The optimized geometry of the complexes is shown good agreement by X-ray data. Structural properties and molecular descriptors including bond lengths, bond angles, chemical hardness, dipole moment, HOMO-LUMO energy levels, electron transfer were analyzed. The IR spectroscopy was performed using VEDA4 software and UV-Vis spectra were analyzed using time-dependent density functional theory (TD-DFT) method. The theoretical and experimental data were also compared with each other. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Crystal structure, DFT study, hirshfeld surface and PIXEL energy calculations of benzimidazolium and hexadecylaminium hydrogen maleate salts

    Science.gov (United States)

    Padmavathy, R.; Karthikeyan, N.; Sathya, D.; Jagan, R.; Kumar, R. Mohan; Sivakumar, K.

    2017-05-01

    Two new organic dicarboxylate salts, namely Benzimidazolium hydrogen maleate (BHM) (1) and Hexadecylaminium hydrogen maleate (HDHM) (2) have been prepared and characterized by single crystal X-ray diffraction, FT-IR and TG/DTA analysis. The crystal structures of both the compounds are stabilized by intramolecular Osbnd H⋯O and intermolecular Nsbnd H⋯O,Csbnd H⋯O hydrogen bonds. The supramolecular structure of the salts consists of various ring motifs generating diverse 2D and 3D architectures. The structural parameters were correlated with computed geometrical parameters obtained from DFT/B3LYP quantum chemical calculations using 6-31++g(d,p) basis set. The experimentally determined vibrational frequencies were matched with theoretically achieved FTIR modes and the complete vibrational assignments were done based on PED calculations. The TG/DTA studies reveal the thermal stability of the title compounds. Molecular electrostatic potential mapping were drawn to understand the chemical reactivity based on their charge distribution. The Frontier Molecular orbitals and other related molecular energies were evaluated using the same theoretical calculations. Hirshfeld surface analysis and its associated fingerprint plots were visualised to make clear signs on entity of intermolecular contacts and their impact on crystal packing. The intermolecular and lattice energies of the compounds were studied using PIXELC method to elucidate the quantitative information on interactions appeared between the molecules.

  20. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. X-ray crystallographic analysis and DFT calculations of three 'propylene linker' dimers linked by one polystep reaction

    Science.gov (United States)

    Shi, Yan; Tan, Xue-Jie; Xing, Dian-Xiang; Sui, Qi-Cheng; Liu, Bin; Feng, Wen-Quan; Liu, Yun

    2017-06-01

    In this manuscript, we report the synthesis, NMR and single-crystal structures of three propylene linking dimers related with the hydrolytic degradation of one 5,6-dehydronorcantharimide dimer. Special attention was paid to the conformation of propylene linkers in order to understand their changes in the reaction. Statistical analysis of CSD database revealed that a-a, g-a and g-g conformations may have similar stability in most cases and various complicated unpredictable non-covalent interactions may play important role in the formation of final rotamers. In order to reproduce all stable conformations and the energy barriers separating them, full range two-dimensional fully relaxed potential-energy surfaces (PES) scans of six 'propylene linker' dimers were calculated starting from the most stable crystal structures. The PES were scanned along both bridge Csbnd C single bond torsional angles (denoted as θ1 and θ2), while all other internal coordinates were optimized at the DFT/B3LYP/3-21G* level in gas phase. Then all energy minima were re-optimized again at the DFT/B3LYP/6-311 + G(d,p) level both in gas and ethanol solutions in order to evaluate the really stable rotamers. At last, 1D or 2D relaxed PES scans were performed between local stable rotamers to get reliable energy barriers. This method represents a less time-consuming and more reliable approach to the determination of conformational stability of propanediyl bridging chains. The combination of experimental, statistical and theoretical results shows that the observed conformation is jointly determined by the energy levels of the minima, energy barriers separating them, non-covalent interactions and somewhat randomness.

  2. A novel alkaloid isolated from Crotalaria paulina and identified by NMR and DFT calculations

    Science.gov (United States)

    Oliveira, Ramon Prata; Demuner, Antonio Jacinto; Alvarenga, Elson Santiago; Barbosa, Luiz Claudio Almeida; de Melo Silva, Thiago

    2018-01-01

    Pyrrolizidine alkaloids (PAs) are secondary metabolites found in Crotalaria genus and are known to have several biological activities. A novel macrocycle bislactone alkaloid, coined ethylcrotaline, was isolated and purified from the aerial parts of Crotalaria paulina. The novel macrocycle was identified with the aid of high resolution mass spectrometry and advanced nuclear magnetic resonance techniques. The relative stereochemistry of the alkaloid was defined by comparing the calculated quantum mechanical hydrogen and carbon chemical shifts of eight candidate structures with the experimental NMR data. The best fit between the eight candidate structures and the experimental NMR chemical shifts was defined by the DP4 statistical analyses and the Mean Absolute Error (MAE) calculations.

  3. PEEM microscopy and DFT calculations of catalytically active platinum surfaces and interfaces

    International Nuclear Information System (INIS)

    Spiel, C.

    2012-01-01

    CO, pO2, T) in one of both steady states depending on the system's prehistory. The bistable reaction kinetics can be studied globally with QMS, and the positions of the global transition points τ A and τ B in parameter space can be obtained this way. Based on a series of experiments, a global kinetic phase diagram can be established that is a useful tool to characterize the average behavior of a heterogeneous sample. In turn, using PEEM the kinetic phase transition points can also be obtained in a laterally-resolved way for each individual surface domain by analyzing local PEEM intensity variations. In the present work, QMS and PEEM experiments were performed, from which both global and laterally-resolved kinetic phase diagrams of polycrystalline platinum foil and, correspondingly, its [100]-, [110]- and [111]-oriented domains were obtained. The kinetic phase diagrams were measured both for constant oxygen partial pressure and varying temperatures as well as for constant temperature and varying oxygen partial pressure. Besides that, kinetic transitions that trigger catalytic ignition and extinction of the CO oxidation reaction were also studied in situ on the same sample and compared to results from experiments using field ion microscopy (FIM). The second part of this thesis consisted of a theoretical study of CeO 2 monolayers adsorbed on the Pt(111) surface. For this purpose, density functional theory (DFT) was applied in the implementation of the WIEN2k software package. (author) [de

  4. Scaling tests of a new algorithm for DFT hybrid-functional calculations on Trinity Haswell

    Energy Technology Data Exchange (ETDEWEB)

    Wright, Alan F. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Modine, Normand A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-09-01

    We show scaling results for materials of interest in Sandia Radiation-Effects and High-Energy-Density-Physics Mission Areas. Each timing is from a self-consistent calculation for bulk material. Two timings are given: (1) walltime for the construction of the CR exchange operator (Exchange-Operator) and (2) walltime for everything else (non-Exchange-Operator).

  5. Synthesis, crystal structure and DFT calculations of a new Hg (II) metal-organic polymer

    Czech Academy of Sciences Publication Activity Database

    Mirtamizdoust, B.; Roodsari, M.S.; Shaabani, B.; Dušek, Michal; Fejfarová, Karla

    2016-01-01

    Roč. 15, č. 3 (2016), s. 257-266 ISSN 1024-1221 Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : mercury (II) iodide * coordination polymer * square planar * tetrahedral geometry * density functional calculation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.565, year: 2016

  6. The determination of sulfoxide configuration in six-membered rings using NMR specroscopy and DFT calculations

    Czech Academy of Sciences Publication Activity Database

    Dračínský, Martin; Pohl, Radek; Slavětínská, Lenka; Janků, J.; Buděšínský, Miloš

    2011-01-01

    Roč. 22, č. 3 (2011), s. 356-366 ISSN 0957-4166 R&D Projects: GA ČR GA203/09/1919 Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR * calculation of NMR parameters * sulfoxides * configuration Subject RIV: CC - Organic Chemistry Impact factor: 2.652, year: 2011

  7. Relativistic DFT calculations of hyperfine coupling constants in the 5d hexafluorido complexes

    DEFF Research Database (Denmark)

    Haase, Pi Ariane Bresling; Repisky, Michal; Komorovsky, Stanislav

    2017-01-01

    We have investigated the performance of the most popular relativistic density functional theory methods, zeroth order regular approximation (ZORA) and 4-component Dirac-Kohn-Sham (DKS), in the calculation of the recently measured hyperfine coupling constants of ReIV and IrIV in their hexafluorido...

  8. Characterisation of different polymorphs of tris(8-hydroxyquinolinatoaluminium(III using solid-state NMR and DFT calculations

    Directory of Open Access Journals (Sweden)

    Periasamy N

    2009-11-01

    Full Text Available Abstract Background Organic light emitting devices (OLED are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato-aluminium(III, known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D and two-dimensional (2D multiple-quantum magic-angle spinning (MQMAS NMR studies of the meridional (α-phase and the facial (δ-phase isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer from the solid-state NMR studies

  9. 13C GIAO DFT calculation as a tool for configuration prediction of N-O group in saturated heterocyclic N-oxides

    Czech Academy of Sciences Publication Activity Database

    Pohl, Radek; Potmischil, F.; Dračínský, Martin; Vaněk, Václav; Slavětínská, Lenka; Buděšínský, Miloš

    2012-01-01

    Roč. 50, č. 6 (2012), s. 415-423 ISSN 0749-1581 R&D Projects: GA ČR GA203/09/1919 Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR * 13C * 1H * saturated heterocyclic N-oxides * chemical shift calculations * DFT Subject RIV: CC - Organic Chemistry Impact factor: 1.528, year: 2012

  10. 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...

  11. Modelling the matrix shift on the vibrational frequency of ThO by DFT-D3 calculations.

    Science.gov (United States)

    Kovács, Attila; Rode, Joanna E

    2017-03-28

    Benchmark calculations with a goal to find dispersion-corrected DFT-D3 methods suitable for a reliable estimation of matrix shifts on the vibrational frequency were carried out on the ThO molecule in three rare gas (Rg = Ne, Ar, and Kr) matrices. The matrices were modelled by the explicit approach, in which a single and a double shell of Rg atoms around ThO was considered. The selection of exchange-correlation functionals was based on test calculations on triatomic ThO⋯Rg models. The B3LYP, PBE0, CAM-B3LYP, and LC-ωPBE functionals were found to be the best suited for the estimation of matrix shifts. The single shell of Rg's around ThO accounted for a major part of the shifts; the addition of a second Rg shell resulted only in a minor improvement. Continuum solvation models considerably overestimated the effect of Rg matrices both when the whole matrix was treated by the model and when the first shell was treated explicitly and the rest with a continuum solvation model.

  12. Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

    Czech Academy of Sciences Publication Activity Database

    Přecechtělová, J.; Munzarová, M. L.; Vaara, J.; Novotný, J.; Dračínský, Martin; Sklenář, V.

    2013-01-01

    Roč. 9, č. 3 (2013), s. 1641-1656 ISSN 1549-9618 Grant - others:GA MŠk(CZ) LM2010005; GA MŠk(CZ) LC06030 Program:LC Institutional support: RVO:61388963 Keywords : density-funtional calculations * molecular-dynamics simulations * phosphate group * B-DNA Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013

  13. 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.

  14. 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.

  15. Steric effect studies on solar energy storage of norbornadiene-quadracyclane system: DFT calculations

    Directory of Open Access Journals (Sweden)

    E. Vessally

    2009-08-01

    Full Text Available The aim of this research is to determine the possible solar energy storage in the norbornadiene (1 / quadricyclane (2 system, through involving steric effects on various position of carbon C1, C2 or C7 for 1 and 2; calculating the corresponding energies at B3LYP/6-311G** level of theory. The extent of the solar energy storage is the least for 11-i-Pr (-21.018, 12-t-Bu (-22.525 and 17-i-Pr (-17.753 when the bulk substituents (X were occured at C1, C2 and C7, respectively.

  16. Thermodynamic characterization of lithium monosilicide (LiSi) by means of calorimetry and DFT-calculations

    Energy Technology Data Exchange (ETDEWEB)

    Taubert, Franziska; Seidel, Juergen; Huettl, Regina; Mertens, Florian [TU Bergakademie Freiberg (Germany). Inst. of Physical Chemistry; Schwalbe, Sebastian; Gruber, Thomas; Kortus, Jens [TU Bergakademie Freiberg (Germany). Inst. of Theoretical Chemistry; Janot, Raphael [Univ. de Picardie Jules Verne UMR 7314 CNRS, Amiens (France). Lab. de Reactivity et Chimie des Solides; Bobnar, Matej [Max-Planck-Institute for Chemical Physics of Solids, Dresden (Germany); Gumeniuk, Roman [TU Bergakademie Freiberg (Germany). Inst. of Experimental Physics

    2017-11-15

    In this work we summarize a symbiotic approach to combine experimental and theoretical investigations for the derivation of high quality thermodynamic data for the description of potential lithium ion battery materials. The methodology of this concept was demonstrated in detail by exploring and describing the properties of the lithium monosilicide phase LiSi. The procedures were also applied in a series of investigations to all major Li{sub x}Si{sub y}-phases which will be reviewed briefly. Regarding the LiSi phase, the measured and calculated isobaric heat capacity, which may enable further thermodynamic investigations (e.g. with CALPHAD method) of the phase diagram of the Li-Si-system is presented. The heat capacity of the stable phase LiSi was measured as a function of temperature in a range from (2 to 673) K and compared with corresponding ab-initio and molecular dynamic calculations resulting in values for absolute entropies. The heat of formation of the system was determined in an unconventional manner via hydrogenation experiments.

  17. 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

    2017-06-07

    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 H 2 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 H 2 on benzene and graphene. DFT calculations are compared with CCSD(T) calculations, in the case of H 2 on benzene, and with experimental data, in the case of H 2 on graphene. Among the DFT methods studied, the B97D, RVV10, and PBE+DCACP methods yield interaction energy curves of H 2 -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 H 2 on graphene, very close to the experimental data.

  18. Analyzing the vibrational signatures of thiophenol adsorbed on small gold clusters by DFT calculations.

    Science.gov (United States)

    Tetsassi Feugmo, Conrard Giresse; Liégeois, Vincent

    2013-06-03

    Using density functional theory, we calculate the IR and Raman signatures of the thiophenol (TP) molecule adsorbed on gold clusters by mimicking the different types of adsorption sites, and we analyze these signatures by using advanced tools implemented into the pyvib2 program. First, we follow the evolution of the vibrational normal modes from the isolated TP molecule to those of TP adsorbed on different clusters to highlight the influence of the site of adsorption on the vibrational motions. The use of the overlap matrix between the modes enables mode permutations, mode mixings, and mode splittings to be highlighted, all of which depend not only on the adsorption but also on the type of cluster and its symmetry. Second, the IR and Raman signatures were analyzed by using group coupling matrices and atomic contribution patterns based on the Hug decomposition scheme. Key results include 1) the fact that Raman spectroscopy is more sensitive than IR spectroscopy with respect to the nature of the coordination site, 2) an IR criterion that distinguishes between on-top coordination (onefold coordinated) with respect to the bridge (twofold coordinated) and hexagonal close-packed hollow site coordination (threefold coordinated), and 3) the best agreement to the experimental Raman spectrum with regard to signatures in the 500 to 1200 cm(-1) region is obtained for bridged, twofold coordination. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. 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.

  20. 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.

  1. Structure of [Ru(bpy)n(AP)(6-2n)]2+ homogeneous complexes: DFT calculation vs. EXAFS

    International Nuclear Information System (INIS)

    Salassa, Luca; Sadler, Peter J; Gianolio, Diego; Garino, Claudio; Salassa, Giovanni; Borfecchia, Elisa; Ruiu, Tiziana; Nervi, Carlo; Gobetto, Roberto; Lamberti, Carlo; Bizzarri, Ranieri

    2009-01-01

    We used EXAFS and DFT calculations to investigate the structure of [Ru(bpy)(AP) 4 ] 2+ and [Ru(bpy) 2 (AP) 2 ] 2+ (bpy=2-2'-bipyridyne, AP=4-aminopyridyne) in aqueous solution (10 mM). These derivatives are of potential interest since, upon direct irradiation, they can form reactive aqua-species able to bind to macromolecules. An attempt has been made to determine with EXAFS the structure of the photodissociation product of the [Ru(bpy) 2 (AP) 2 ] 2+ complex, where a water molecule fill the coordination vacancy left by an AP ligand resulting in [Ru(bpy) 2 (AP)(H 2 O)] 2+ . Unfortunately, co-presence in the experimental sample of both original and photodissociated complexes, causes the failure of the analysis. This failure was due to the structural complexity of both systems and to the similarity in their EXAFS signals. This work underlines the potentialities and the limits of EXAFS spectroscopy when dealing with highly diluted samples where the local environment of the adsorbing atom is characterized by structured ligands: the local environment of Ru is correctly reproduced when dealing with homogeneous samples, while the co-presence of two or more different species makes the data analysis highly critical.

  2. Syntheses, spectroscopic properties and molecular structure of silver phytate complexes - IR, UV-VIS studies and DFT calculations

    Science.gov (United States)

    Zając, A.; Dymińska, L.; Lorenc, J.; Ptak, M.; Hanuza, J.

    2018-03-01

    Silver phytate IP6, IP6Ag, IP6Ag2 and IP6Ag3 complexes in the solid state have been synthesized changing the phosphate to metal mole ratio. The obtained products have been characterized by means of chemical and spectroscopic studies. Attenuated total reflection Fourier transform infrared technique and Raman microscope were used in the measurements. These results were discussed in terms of DFT (Density Functional Theory) quantum chemical calculations using the B3LYP/6-31G(d,p) approach. The molecular structures of these compounds have been proposed on the basis of group theory and geometry optimization taking into account the shape and the number of the observed bands corresponding to the stretching and bending vibrations of the phosphate group and metal-oxygen polyhedron. The role of inter- and intra-hydrogen bonds in stabilization of the structure has been discussed. It was found that three types of hydrogen bonds appear in the studied compounds: terminal, and those engaged in the inter- and intra-molecular interactions. The Fermi resonance as a result of the strong intra-molecular Osbnd H⋯O hydrogen bonds was discovered. Electron absorption spectra have been measured to characterize the electron properties of the studied complexes and their local symmetry.

  3. Synthesis and spectral properties of Methyl-Phenyl pyrazoloquinoxaline fluorescence emitters: Experiment and DFT/TDDFT calculations

    Science.gov (United States)

    Gąsiorski, P.; Matusiewicz, M.; Gondek, E.; Uchacz, T.; Wojtasik, K.; Danel, A.; Shchur, Ya.; Kityk, A. V.

    2018-01-01

    Paper reports the synthesis and spectroscopic studies of two novel 1-Methyl-3-phenyl-1H-pyrazolo[3,4-b]quinoxaline (PQX) derivatives with 6-substituted methyl (MeMPPQX) or methoxy (MeOMPPQX) side groups. The optical absorption and fluorescence emission spectra are recorded in solvents of different polarity. Steady state and time-resolved spectroscopy provide photophysical characterization of MeMPPQX and MeOMPPQX dyes as materials for potential luminescence or electroluminescence applications. Measured optical absorption and fluorescence emission spectra are compared with quantum-chemical DFT/TDDFT calculations using long-range corrected xc-functionals, LRC-BLYP and CAM-B3LYP in combination with self-consistent reaction field model based on linear response (LR), state specific (SS) or corrected linear response (CLR) solvations. Performances of relevant theoretical models and approaches are compared. The reparameterized LRC-BLYP functional (ω = 0.231 Bohr-1) in combination with CLR solvation provides most accurate prediction of both excitation and emission energies. The MeMPPQX and MeOMPPQX dyes represent efficient fluorescence emitters in blue-green region of the visible spectra.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Kuiwei; Zhang, Minhua [Key Laboratory for Green Chemical Technology of Ministry of Education, R& D Center for Petrochemical Technology, Tianjin University, Tianjin 300072 (China); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072 (China); Yu, Yingzhe, E-mail: yzhyu@tju.edu.cn [Key Laboratory for Green Chemical Technology of Ministry of Education, R& D Center for Petrochemical Technology, Tianjin University, Tianjin 300072 (China)

    2017-03-31

    Highlights: • Doping the step edge of Ni(211) with Fe or Ru observably enhances CO dissociation. • Rh doping is unfavorable for CO activation both kinetically and thermodynamically. • Two neat linear relations are proposed besides the Brønsted–Evans–Polanyi relation. • The differences of CO adsorption are rationalized via the Blyholder model. - Abstract: 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.

  5. 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+).

  6. 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.

  7. A new method suitable for calculating accurately wetting temperature over a wide range of conditions: Based on the adaptation of continuation algorithm to classical DFT

    Science.gov (United States)

    Zhou, Shiqi

    2017-11-01

    A new scheme is put forward to determine the wetting temperature (Tw) by utilizing the adaptation of arc-length continuation algorithm to classical density functional theory (DFT) used originally by Frink and Salinger, and its advantages are summarized into four points: (i) the new scheme is applicable whether the wetting occurs near a planar or a non-planar surface, whereas a zero contact angle method is considered only applicable to a perfectly flat solid surface, as demonstrated previously and in this work, and essentially not fit for non-planar surface. (ii) The new scheme is devoid of an uncertainty, which plagues a pre-wetting extrapolation method and originates from an unattainability of the infinitely thick film in the theoretical calculation. (iii) The new scheme can be similarly and easily applied to extreme instances characterized by lower temperatures and/or higher surface attraction force field, which, however, can not be dealt with by the pre-wetting extrapolation method because of the pre-wetting transition being mixed with many layering transitions and the difficulty in differentiating varieties of the surface phase transitions. (iv) The new scheme still works in instance wherein the wetting transition occurs close to the bulk critical temperature; however, this case completely can not be managed by the pre-wetting extrapolation method because near the bulk critical temperature the pre-wetting region is extremely narrow, and no enough pre-wetting data are available for use of the extrapolation procedure.

  8. Efficient, approximate and parallel Hartree-Fock and hybrid DFT calculations. A 'chain-of-spheres' algorithm for the Hartree-Fock exchange

    International Nuclear Information System (INIS)

    Neese, Frank; Wennmohs, Frank; Hansen, Andreas; Becker, Ute

    2009-01-01

    In this paper, the possibility is explored to speed up Hartree-Fock and hybrid density functional calculations by forming the Coulomb and exchange parts of the Fock matrix by different approximations. For the Coulomb part the previously introduced Split-RI-J variant (F. Neese, J. Comput. Chem. 24 (2003) 1740) of the well-known 'density fitting' approximation is used. The exchange part is formed by semi-numerical integration techniques that are closely related to Friesner's pioneering pseudo-spectral approach. Our potentially linear scaling realization of this algorithm is called the 'chain-of-spheres exchange' (COSX). A combination of semi-numerical integration and density fitting is also proposed. Both Split-RI-J and COSX scale very well with the highest angular momentum in the basis sets. It is shown that for extended basis sets speed-ups of up to two orders of magnitude compared to traditional implementations can be obtained in this way. Total energies are reproduced with an average error of <0.3 kcal/mol as determined from extended test calculations with various basis sets on a set of 26 molecules with 20-200 atoms and up to 2000 basis functions. Reaction energies agree to within 0.2 kcal/mol (Hartree-Fock) or 0.05 kcal/mol (hybrid DFT) with the canonical values. The COSX algorithm parallelizes with a speedup of 8.6 observed for 10 processes. Minimum energy geometries differ by less than 0.3 pm in the bond distances and 0.5 deg. in the bond angels from their canonical values. These developments enable highly efficient and accurate self-consistent field calculations including nonlocal Hartree-Fock exchange for large molecules. In combination with the RI-MP2 method and large basis sets, second-order many body perturbation energies can be obtained for medium sized molecules with unprecedented efficiency. The algorithms are implemented into the ORCA electronic structure system

  9. Oligothiophene-based colorimetric and ratiometric fluorescence dual-channel cyanide chemosensor: Sensing ability, TD-DFT calculations and its application as an efficient solid state sensor

    Science.gov (United States)

    Lan, Linxin; Li, Tianduo; Wei, Tao; Pang, He; Sun, Tao; Wang, Enhua; Liu, Haixia; Niu, Qingfen

    2018-03-01

    An oligothiophene-based colorimetric and ratiometric fluorescence dual-channel cyanide chemosensor 3 T-2CN was reported. Sensor 3 T-2CN showed both naked-eye recognition and ratiometric fluorescence response for CN- with an excellent selectivity and high sensitivity. The sensing mechanism based on the nucleophilic attack of CN- on the vinyl Cdbnd C bond has been successfully confirmed by the optical measurements, 1H NMR titration, FT-IR spectra as well as the DFT/TD-DFT calculations. Moreover, the detection limit was calculated to be 0.19 μM, which is much lower than the maximum permission concentration in drinking water (1.9 μM). Importantly, test strips (filter paper and TLC plates) containing 3 T-2CN were fabricated, which could act as a practical and efficient solid state optical sensor for CN- in field measurements.

  10. Synthesis, characterization, nano-sized binuclear nickel complexes, DFT calculations and antibacterial evaluation of new macrocyclic Schiff base compounds

    Science.gov (United States)

    Parsaee, Zohreh; Mohammadi, Khosro

    2017-06-01

    Some new macrocyclic bridged dianilines tetradentate with N4coordination sphere Schiff base ligands and their nickel(II)complexes with general formula [{Ni2LCl4} where L = (C20H14N2X)2, X = SO2, O, CH2] have been synthesized. The compounds have been characterized by FT-IR, 1H and 13C NMR, mass spectroscopy, TGA, elemental analysis, molar conductivity and magnetic moment techniques. Scanning electron microscopy (SEM) shows nano-sized structures under 100 nm for nickel (II) complexes. NiO nanoparticle was achieved via the thermal decomposition method and analyzed by FT-IR, SEM and X-ray powder diffraction which indicates closeaccordance to standard pattern of NiO nanoparticle. All the Schiff bases and their complexes have been detected in vitro both for antibacterial activity against two gram-negative and two gram-positive bacteria. The nickel(II) complexes were found to be more active than the free macrocycle Schiff bases. In addition, computational studies of three ligands have been carried out at the DFT-B3LYP/6-31G+(d,p) level of theory on the spectroscopic properties, including IR, 1HNMR and 13CNMR spectroscopy. The correlation between the theoretical and the experimental vibrational frequencies, 1H NMR and 13C NMR of the ligands were 0.999, 0.930-0.973 and 0.917-0.995, respectively. Also, the energy gap was determined and by using HOMO and LUMO energy values, chemical hardness-softness, electronegativity and electrophilic index were calculated.

  11. Establishing the NO Oxidation State in Complexes [Cl5(NO)M]n-, M = Ru or Ir, trough Experiments and DFT Calculations

    Czech Academy of Sciences Publication Activity Database

    Sieger, M.; Sarkar, B.; Záliš, Stanislav; Fiedler, Jan; Escola, N.; Doctorovich, F.; Olabe, J. A.; Kaim, W.

    -, č. 12 (2004), s. 1797-1800 ISSN 1477-9226 R&D Projects: GA ČR GA203/03/0821; GA MŠk OC D14.20; GA MŠk OC D15.10 Institutional research plan: CEZ:AV0Z4040901 Keywords : NO oxidation * DFT calculations * spectroelectrochemistry Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.926, year: 2004

  12. 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.

  13. Encapsulation of Cadmium Selenide Nanocrystals in Biocompatible Nanotubes: DFT Calculations, X‐ray Diffraction Investigations, and Confocal Fluorescence Imaging

    Science.gov (United States)

    Calatayud, David G.; Ge, Haobo; Kuganathan, Navaratnarajah; Mirabello, Vincenzo; Jacobs, Robert M. J.; Rees, Nicholas H.; Stoppiello, Craig T.; Khlobystov, Andrei N.; Tyrrell, Rex M.; Como, Enrico Da

    2018-01-01

    Abstract The encapsulation of CdSe nanocrystals within single‐walled carbon nanotube (SWNT) cavities of varying dimensions at elevated temperatures under strictly air‐tight conditions is described for the first time. The structures of CdSe nanocrystals under confinement inside SWNTs was established in a comprehensive study, combining both experimental and DFT theoretical investigations. The calculated binding energies show that all considered polymorphs [(3:3), (4:4), and (4:2)] may be obtained experimentally. The most thermodynamically stable structure (3:3) is directly compared to the experimentally observed CdSe structures inside carbon nanotubes. The gas‐phase DFT‐calculated energy difference between “free” 3:3 and 4:2 structures (whereby 3:3 models a novel tubular structure in which both Cd and Se form three coordination, as observed experimentally for HgTe inside SWNT, and 4:2 is a motif derived from the hexagonal CuI bulk structure in which both Cd and Se form 4 or 2 coordination) is surprisingly small, only 0.06 eV per formula unit. X‐ray powder diffraction, Raman spectroscopy, high‐resolution transmission electron microscopy, and energy‐dispersive X‐ray analyses led to the full characterization of the SWNTs filled with the CdSe nanocrystals, shedding light on the composition, structure, and electronic interactions of the new nanohybrid materials on an atomic level. A new emerging hybrid nanomaterial, simultaneously filled and beta‐d‐glucan coated, was obtained by using pristine nanotubes and bulk CdSe powder as starting materials. This displayed fluorescence in water dispersions and unexpected biocompatibility was found to be mediated by beta‐d‐glucan (a biopolymer extracted from barley) with respect to that of the individual inorganic material components. For the first time, such supramolecular nanostructures are investigated by life‐science techniques applied to functional nanomaterial characterization, opening the door

  14. Molecular structure and vibrational investigation of benzenesulfonic acid methyl ester using DFT (LSDA, B3LYP, B3PW91 and MPW1PW91) theory calculations

    Science.gov (United States)

    Babu, P. David Suresh; Periandy, S.; Mohan, S.; Ramalingam, S.; Jayaprakash, B. G.

    2011-01-01

    The FT-Raman and FT-IR spectra for benzenesulfonic acid methyl ester (BSAME) have been recorded in the region 4000-100 cm -1 and compared with the harmonic vibrational frequencies calculated using DFT (LSDA, B3LYP, B3PW91 and MPW1PW91) method by employing 6-311G (d, p) basis set with appropriate scale factors. IR intensities and Raman activities are also calculated by DFT (LSDA, B3LYP, B3PW91 and MPW1PW91) methods. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values for sulfonic acid and some substituted sulfonic acids. The experimental geometrical parameters show satisfactory agreement with the theoretical prediction from DFT. The scaled vibrational frequencies at LSDA/B3LYP/6-311G (d, p) seem to coincide with the experimentally observed values with acceptable deviations. The theoretical spectrograms (IR and Raman) have been constructed and compared with the experimental FT-IR and FT-Raman spectra. Some of the vibrational frequencies of the sulfonic acid are effected upon profusely with the methyl substitution in comparison to benzene sulfonamide and these differences are interpreted.

  15. DFT calculation for elastic constants of orthorhombic structure within WIEN2K code: A new package (ortho-elastic)

    International Nuclear Information System (INIS)

    Reshak, Ali H.; Jamal, Morteza

    2012-01-01

    Highlights: ► A new package for calculating elastic constants of orthorhombic structure is released. ► The package called ortho-elastic. ► It is compatible with [FP-(L)APW+lo] method implemented in WIEN2k code. ► Several orthorhombic structure compounds were used to test the new package. ► Elastic constants calculated using this package show good agreement with experiment. - Abstract: A new package for calculating the elastic constants of orthorhombic structure is released. The package called ortho-elastic. The formalism of calculating the ortho-elastic constants is described in details. The package is compatible with the highly accurate all-electron full-potential (linearized) augmented plane-wave plus local orbital [FP-(L)APW+lo] method implemented in WIEN2k code. Several orthorhombic structure compounds were used to test the new package. We found that the calculated elastic constants using the new package show better agreement with the available experimental data than the previous theoretical results used different methods. In this package the second-order derivative E ″ (ε) of polynomial fit E=E(ε) of energy vs strains at zero strain (ε=0), used to calculate the orthorhombic elastic constants.

  16. Combined EXAFS and DFT Structure Calculations Provide Structural Insights into the 1:1 Multi-Histidine Complexes of CuII, CuI and ZnII with the Tandem Octarepeats of the Mammalian Prion Protein

    Science.gov (United States)

    Pushie, M. Jake; Nienaber, Kurt H.; McDonald, Alex; Millhauser, Glenn L.; George, Graham N.

    2014-01-01

    The metal coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of copper interaction with PrP just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, and yet the structural details of the various metal coordination modes have not been fully elucidated in some cases. Herein we employ X-ray absorption near edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for CuII, CuI and ZnII with an N-terminal fragment of PrP. The PrP fragment constitutes four tandem repeats representative of the mammalian octarepeat domain, designated OR4, which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations provide additional structural and thermodynamic data, and candidate structures are used to inform EXAFS data analysis. The optimized geometries from DFT calculations are used to identify potential coordination complexes for multi-histidine coordination of CuII, CuI and ZnII in an aqueous medium, modeled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve fitting, using full multiple scattering on candidate structures from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of CuII, CuI and ZnII with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as a square planar [CuII(His)4]2+, digonal [CuI(His)2]+ and tetrahedral [ZnII(His)3(OH2)]2+, respectively. PMID:25042361

  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. 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.

  19. FT-IR, FT-Raman and UV spectral investigation: computed frequency estimation analysis and electronic structure calculations on chlorobenzene using HF and DFT.

    Science.gov (United States)

    Govindarajan, M; Karabacak, M; Udayakumar, V; Periandy, S

    2012-03-01

    In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 100-4000 cm(-1) and 400-4000 cm(-1) respectively, for the title molecule. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on Hartree Fock (HF) and density functional theory (DFT) method and different basis sets combination. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The scaled B3LYP/6-311++G(d,p) results show the best agreement with the experimental values over the other methods. The effects due to the substitution of halogen bond were investigated. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complements with the experimental findings. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), and thermodynamic properties were performed. The thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between heat capacity (C), entropy (S), and enthalpy changes (H) and temperatures. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. 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.

  2. Refinement of labile hydrogen positions based on DFT calculations of 1H NMR chemical shifts: comparison with X-ray and neutron diffraction methods.

    Science.gov (United States)

    Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

    2017-05-31

    Numerous gas phase electron diffraction, ultra-fast electron diffraction, X-ray and neutron diffraction experiments on β-dicarbonyl compounds exhibiting enol-enol tautomeric equilibrium, with emphasis on acetylacetone and dibenzoylmethane, have so far been reported with conflicting results on the structural details of the O-HO intramolecular hydrogen bond and resulted in alternative hypotheses on the intramolecular hydrogen bond potential function either a double minimum potential corresponding to two tautomeric forms in equilibrium or a single symmetrical one. We demonstrate herein, firstly, that the DFT calculated OH 1 H NMR chemical shifts of acetylacetone and dibenzoylmethane exhibit a strong linear dependence on the computed OO hydrogen bond length of ∼-50 ppm Å -1 and as a function of the O-HO bond angle of ∼1 ppm per degree, upon the transfer of the hydrogen atom from the ground state toward the transition state. Secondly, the refinement of labile hydrogen atomic positions in intramolecular hydrogen bonds based on the root-mean-square deviation between experimentally determined and DFT calculated 1 H NMR chemical shifts in solution can provide high resolution structures of O-H and O(H)O bond lengths and O-HO bond angles with an accuracy of ∼10 -2 Å and ∼0.5°, respectively. Thirdly, the calculated 1 H NMR chemical shifts in solution of the two ground state tautomers in equilibrium of acetylacetone and dibenzoylmethane are in excellent agreement with the experimental value, even for moderate basis sets for energy minimization. In contrast, the single symmetrical structure in a strongly delocalized system is a transition state with calculated 1 H NMR chemical shifts which strongly deviate from the experimental value. Fourth, the DFT calculated ground state O-H bond lengths of acetylacetone and dibenzoylmethane are in quantitative agreement with the literature data which take into account the effect of quantum nuclear motion. The DFT structural

  3. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Solution Speciation, DFT Calculations, Luminescence Properties and Promoted Nitrophenyl-phosphate Hydrolysis Rates of Dinuclear Lanthanide(III)-m-ODO2A-dimer Macrocyclic Complexes.

    Science.gov (United States)

    Chang, C Allen; Lee, Hwa-Yu; Lin, Syue-Liang; Meng, Ching-Ning; Wu, Tsung-Ta

    2018-02-26

    Potentiometric speciation studies, mass spectrometry and density functional theory (DFT) calculations helped to predict the various structural possibilities of the dinuclear trivalent lanthanide ion (LnIII, Ln = La, Eu, Tb, Yb, Y) complexes of a novel macrocyclic ligand, m-ODO2A-dimer (H4L) to correlate with their luminescence properties and the promoted BNPP and HPNP phosphodiester bond hydrolysis reaction rates. The stability constants of the dinuclear Ln2(m-ODO2A-dimer) complexes and various hydrolytic species confirmed by mass spectrometry were determined. DFT calculations revealed that the Y2LH-1 and the Y2LH-2 species tended to form structures with the respective "closed-form" and "open-form" conformations. Luminescence lifetime data for the heterodimetallic TbEuL system confirmed the fluorescence resonance energy transfer from TbIII ion to EuIII ion. The internuclear distance RTbEu values were estimated to be in the range 9.4Å - 11.3Å (pH 6.7 - 10.6) which were comparable to those of the DFT calculated "open-form" conformations. Multiple linear regression analysis of the kobs data was performed using the equation: kobs,corr. = kobs - kobs,OH = kLn2LH-1[Ln2LH-1] + kLn2LH-2[Ln2LH-2] for the observed Ln2L-promoted BNPP/HPNP hydrolysis reactions in solution pH from 7 to 10.5 (Ln = Eu, Yb). The results showed that the second-order rate constants for the Eu2LH-2 and Yb2LH-2 species were about 50-400 times more reactive than the structural analogous Zn2(m-12N3O-dimer) system. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Sodium and potassium salts of dichloroisocyanuric acid and their hydrates as antimicrobials agents studied by 35Cl-NQR spectroscopy and DFT calculations

    International Nuclear Information System (INIS)

    Walczak, A.; Brycki, B.; Kaczmarek, M.; Poleshchuk, O.Kh.; Ostafin, M.; Nogaj, B.

    2006-01-01

    The electronic structure of dichloroisocyanuric acid derivatives was analysed by 35 Cl-NQR spectroscopy and DFT calculations. Here we concentrate our attention on three different factors: type of metallic substituent (sodium and potassium), temperature of the sample (liquid nitrogen and room) and degree of hydration (an amount of water molecules attached to analysed compounds). In particular, all the variations in 35 Cl-NQR frequencies upon hydration of salts containing sodium and potassium ions are explained as a consequence of H-bonds formation and accompanied effects of charge redistribution. Our studies can be useful in searching for the derivatives of dichloroisocyanuric acid revealing higher antimicrobial activity

  6. 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

    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......,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...

  7. Ion-pair structure of vaporized ionic liquid studied by matrix-isolation FTIR spectroscopy with DFT calculations: a case of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate.

    Science.gov (United States)

    Akai, Nobuyuki; Kawai, Akio; Shibuya, Kazuhiko

    2010-12-09

    The matrix-isolation infrared spectrum of a thermally evaporated ionic liquid, 1-ethyl-3-methylimidazolium trifluoromethanesulfonate ([Emim][OTf]), was measured by FTIR spectroscopy and analyzed with the aid of DFT calculations. The main chemical species in the observed IR spectrum was mainly identified as the 1:1 cation-anion pair, which corresponds to the second stable ion-pair structure bonded through five hydrogen bonds between three O atoms of the anion side and four H atoms of the cation.

  8. 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.

  9. Synthesis, molecular docking, DFT calculations and cytotoxicity activity of benzo[g]quinazoline derivatives in choline chloride-urea

    Science.gov (United States)

    Lakshmanan, Sivalingam; Govindaraj, Dharman; Ramalakshmi, Narayanan; Antony, S. Arul

    2017-12-01

    Green and highly efficient one-pot three component approach for the synthesis of benzo[g]quinazoline derivatives (6a-g) using Choline chloride-urea (DES). Synthesized compounds 6b and 6g showed the most potent biological activity against A549 lung cancer cell line. Docking simulation was performed to position compounds 6b and 6g showed the greater affinity for anaplastic lymphoma kinase (ALK) receptor. Quantum chemical studies were carried out on these compounds to understand the structural features essential for activity using DFT/6-31G level of theory.

  10. Benchmarking dispersion and geometrical counterpoise corrections for cost-effective large-scale DFT calculations of water adsorption on graphene.

    Science.gov (United States)

    Lorenz, Marco; Civalleri, Bartolomeo; Maschio, Lorenzo; Sgroi, Mauro; Pullini, Daniele

    2014-09-15

    The physisorption of water on graphene is investigated with the hybrid density functional theory (DFT)-functional B3LYP combined with empirical corrections, using moderate-sized basis sets such as 6-31G(d). This setup allows to model the interaction of water with graphene going beyond the quality of classical or semiclassical simulations, while still keeping the computational costs under control. Good agreement with respect to Coupled Cluster with singles and doubles excitations and perturbative triples (CCSD(T)) results is achieved for the adsorption of a single water molecule in a benchmark with two DFT-functionals (Perdew/Burke/Ernzerhof (PBE), B3LYP) and Grimme's empirical dispersion and counterpoise corrections. We apply the same setting to graphene supported by epitaxial hexagonal boron nitride (h-BN), leading to an increased interaction energy. To further demonstrate the achievement of the empirical corrections, we model, entirely from first principles, the electronic properties of graphene and graphene supported by h-BN covered with different amounts of water (one, 10 water molecules per cell and full coverage). The effect of h-BN on these properties turns out to be negligibly small, making it a good candidate for a substrate to grow graphene on. Copyright © 2014 Wiley Periodicals, Inc.

  11. 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%.

  12. 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.

  13. Expedient and click synthesis, spectroscopic characterizations and DFT calculations of novel 1,5-bis(N-substituted 1,2,3‒triazole) benzodiazepinedione scaffolds

    Science.gov (United States)

    Paghandeh, Hossein; Saeidian, Hamid

    2018-04-01

    A practically reliable procedure for synthesis of new 1,5-bis(N-substituted 1,2,3‒triazole) benzodiazepinedione derivatives was reported by sequential amidation, propargylation and a click azide‒alkyne [3 + 2] cycloaddition reaction in a one pot fashion. The desired products were characterized by CHN analysis, 1H and 13C NMR and ESI-MS spectroscopy. Short reaction time, good yields (55-91%), mild reaction conditions and easily available and less expensive starting materials are advantages of this protocol. Natural bond orbital charge distribution and HOMO-LUMO analysis of the characterized structure of 4e have been also calculated by density functional theory (DFT) calculations. The Li+ and Na+ ion affinities of 4e have been also investigated by DFT studies to find the applicability of these products as ligand in coordination chemistry. Sodium ion affinity of 4e was determined as 60 kJ mol-1 is less than its lithium ion affinity, indicating that the lithiation of 4e is more exothermic than the sodiation.

  14. The Effect of Substituent Position on Excited State Intramolecular Proton Transfer in Benzoxazinone Derivatives: Experiment and DFT Calculation.

    Science.gov (United States)

    Bian, Gao-Feng; Guo, Yun; Lv, Xiao-Jing; Zhang, Cheng

    2017-01-01

    The preparation and the photophysical behaviour of two benzoxazinone derivatives isomers 2-(1-hydroxynaphthalen-2-yl)-4H-benzo[e][1, 3]oxazin-4-one(1) and 2-(3-hydroxynaphthalen-2-yl)-4H-benzo[e][1, 3]oxazin-4-one(2) designed for displaying were reported. The effect of substituent position and solvent effect on the excited state intramolecular proton transfer (ESIPT) dynamics and the spectroscopic properties were investigated using a combined theoretical (i.e., time-dependent density function theory (DFT)) and experimental (i.e., steady-state absorption and emission spectra and time-resolved fluorescence spectra) study. The results showed that compound 1 would facilitate ESIPT process and favored the keto tautomer emission, while compound 2 suppressed the ESIPT process and favored the enol emission.

  15. 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.

  16. 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 3500-400cm(-1) and 3500-50cm(-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 (1)H, (13)C and HMQC ((1)H-(13)C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400nm 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Effects of Fe substitution on B3-B1 phase transition and structural, vibrational, and electronic properties of ZnS from DFT calculations

    Science.gov (United States)

    Das, Pratik Kr.; Mandal, Nibir; Arya, A.

    2017-02-01

    Naturally occurring zinc sulfide (ZnS) contains a substantial amount of iron (Fe) in its crystal structure. This study explores the possible effects of such Fe impurity on the physical properties of its two phases: B3 and B1, crystallizing in a cubic system with zinc blend (ZB, space group: F-43m) and rock salt (RS, space group: Fm-3m) structures. We have performed ab-initio calculations within density functional theory (DFT) to determine the equilibrium volumes of B3- and B1-ZnS phases, doped with Fe in varying concentrations (0% to 25%), and their corresponding lattice structures. Using the enthalpy cross-over, we determine the pressure-dependent B3 to B1 transition as a function of Fe concentration. Our DFT calculations suggest an inverse relation of the transition pressure with Fe content. For pure ZnS, the transition occurs at 17 GPa, which drops to ˜12 GPa for 25% Fe. This study also provides a first-hand analysis of the elastic constants (C11, C12, and C44) to show the effects of Fe impurity on the mechanical properties of ZnS phases. Their values generally drop due to Fe and the differences widen with increasing pressure. Fe causes large softening of C44, especially for the B1 phase. We have also performed phonon calculations to characterize the vibrational properties and explain the pressure dependent structural instability of the B3- ZnS. Finally, our calculations of the electronic structures show a transition of semi-conductor to conductor behavior of ZnS with incorporation of Fe impurity.

  18. FTIR, FT-RAMAN, NMR, spectra, normal co-ordinate analysis, NBO, NLO and DFT calculation of N,N-diethyl-4-methylpiperazine-1-carboxamide molecule.

    Science.gov (United States)

    Muthu, S; Elamurugu Porchelvi, E

    2013-11-01

    The Fourier Transform Infrared (FT-IR) and FT-Raman of N,N-diethyl-4-methylpiperazine-1-carboxamide (NND4MC) have been recorded and analyzed. The structure of the compound was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31G(d,p) and 6-311G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. 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. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that electron density (ED) in the σ(*) and π(*) antibonding orbitals and second order delocalization energies (E2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using Density Functional Theory (DFT/B3LYP) with 6-31G(d,p) and 6-311G(d,p) basis sets. The calculated results also show that the NND4MC molecule may have microscopy nonlinear optical (NLO) behavior with non zero values. Mulliken atomic charges of NND4MC were calculated. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. The UV-Vis spectrum of the compound was recorded. The theoretical electronic absorption spectra have been calculated by using CIS, TD-DFT methods. A study on the electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) were also performed. Copyright © 2013 Elsevier B

  19. 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.

  20. Antimicrobial activities, DNA interactions, spectroscopic (FT-IR and UV-Vis) characterizations, and DFT calculations for pyridine-2-carboxylic acid and its derivates

    Science.gov (United States)

    Tamer, Ömer; Tamer, Sevil Arabacı; İdil, Önder; Avcı, Davut; Vural, Hatice; Atalay, Yusuf

    2018-01-01

    In this paper, pyridine- 2- carboxylic acid, also known as picolinic acid (pic), and its two derivate, 4- methoxy-pyridine- 2- carboxylic acid (4-Mpic) and 4- chloro-pyridine- 2- carboxylic acid (4-Clpic) have been characterized by FT-IR and UV-Vis spectroscopy techniques as well as DFT calculations. B3LYP level of Density Functional Theory (DFT) method was used to obtain ground state geometries, vibration wavenumbers, first order hyperpolarizabilities and molecular electrostatic potential (MEP) surfaces for pic, 4Clpic and 4Mpic. The electronic absorption wavelengths and HOMO-LUMO energies were investigated by time dependent B3LYP (TD-B3LYP) level with the conductor-like polarizable continuum model (CPCM). The effects of Cl atom and OCH3 group on HOMO-LUMO energy gaps and first order hyperpolarizability parameters of pic, 4Clpic and 4Mpic molecules were examined. All molecules were screened for their antibacterial activities against Gram-positive and Gram-negative bacteria and for their antifungal activities against yeast strains by using minimal inhibitory concentration method (MIC). All compounds (pic, 4Mpic and 4Clpic) have been found to be very active against to the Gram (+) and Gram (-) bacteria. The DNA interactions of pic, 4Clpic and 4Mpic were analyzed by molecular docking simulations, and the interaction of the 4Mpic molecule with DNA is found to be higher than 4Clpic and pic.

  1. 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.

  2. B,N-Codoped graphene as catalyst for the oxygen reduction reaction: Insights from periodic and cluster DFT calculations.

    Science.gov (United States)

    Ricca, Chiara; Labat, Frédéric; Zavala, Claudia; Russo, Nino; Adamo, Carlo; Merino, Gabriel; Sicilia, Emilia

    2018-04-30

    A comprehensive theoretical study of the oxygen reduction reaction (ORR) over B,N-codoped graphene has been carried out in the framework of DFT using two different approaches based on periodic or cluster models. The comparison and integration of the information provided by the two approaches allow achieving a more complete description of the studied phenomena, combining the advantages of both models. On one hand, the analysis of the structure, stability, and electronic properties of this catalyst permits to identify and characterize the active sites and provides insights into the origin of its high catalytic activity that should be found in the synergistic coupling of the opposite effects of the two B and N heteroatoms used as dopants. On the other hand, the study of the reaction mechanisms evidences that the process is thermodynamically favorable due to the overall high exothermicity, and that the 4e - transfer is the favorite ORR pathway, being the OH hydrogenation the rate-determining step. Overall, all the reported results clearly underline the superior catalytic activity of B,N-codoped graphene toward this reaction. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  3. Accurate orbital-dependent correlation and exchange-correlation potentials from non-iterative ab initio dft calculations

    Science.gov (United States)

    Grabowski, Ireneusz; Lotrich, Victor

    2005-08-01

    A new approximate non-iterative procedure to obtain accurate correlation and exchange-correlation potentials of Kohn-Sham (KS) density functional theory (DFT) is presented. By carrying out only one step of the correlated optimized effective potential (OEP) iterations following the standard iterative exchange-only OEP, one can recover accurate correlation potentials corresponding to the orbital-dependent second-order many-body perturbation theory [MBPT(2)] energy functional that are hardly discernible from those obtained by the more expensive, fully iterative procedure. This new 'one-step' OEP-MBPT(2) algorithm reflects the non-iterative, perturbative algorithm of standard, canonical MBPT(2) of ab initio wave function theory, while it allows the correlation potentials to readjust and include the majority of the MBPT(2) correlation effect. It is also flexible in the treatment of exchange and the Hartree-Fock orbitals may be used in lieu of the exchange-only OEP orbitals, when the correlation or exchange-correlation potential is of interest.

  4. The Metal Effect on Self-Assembling of Oxalamide Gelators Explored by Mass Spectrometry and DFT Calculations

    Science.gov (United States)

    Dabić, Dario; Brkljačić, Lidija; Tandarić, Tana; Žinić, Mladen; Vianello, Robert; Frkanec, Leo; Kobetić, Renata

    2018-01-01

    Gels formed by self-assembly of small organic molecules are of wide interest as dynamic soft materials with numerous possible applications, especially in terms of nanotechnology for functional and responsive biomaterials, biosensors, and nanowires. Four bis-oxalamides were chosen to show if electrospray ionization mass spectrometry (ESI-MS) could be used as a prediction of a good gelator and also to shed light on the gelation processes. By inspecting the gelation of several solvent, we showed that bis(amino acid)oxalamide 1 proved to be the most efficient, also being able of forming the largest observable assemblies in the gas phase. The formation of singly charged assemblies holding from one up to six monomer units is the outcome of the strong intermolecular H-bonds, particularly among terminal carboxyl groups. The variation of solvents from polar aprotic towards polar protic did not have any significant effects on the size of the assemblies. The addition of a salt such as NaOAc or Mg(OAc)2, depending on the concentration, altered the assembling. Computational analysis at the DFT level aided in the interpretation of the observed trends and revealed that individual gelator molecules spontaneously assemble to higher aggregates, but the presence of the Na+ cation disrupts any gelator organization since it becomes significantly more favorable for gelator molecules to bind Na+ cations up to the 3:1 ratio than to self-assemble, being fully in line with experimental observations reported here. [Figure not available: see fulltext.

  5. 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.

  6. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  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. 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.

  10. Relative Stability of the La and Lb Excited States in Adenine and Guanine: Direct Evidence from TD-DFT Calculations of MCD Spectra.

    Science.gov (United States)

    Santoro, Fabrizio; Improta, Roberto; Fahleson, Tobias; Kauczor, Joanna; Norman, Patrick; Coriani, Sonia

    2014-06-05

    The relative position of La and Lb ππ* electronic states in purine nucleobases is a much debated topic, since it can strongly affect our understanding of their photoexcited dynamics. To assess this point, we calculated the absorption and magnetic circular dichroism (MCD) spectra of adenine, guanine, and their nucleosides in gas-phase and aqueous solution, exploiting recent developments in MCD computational technology within time-dependent density functional theory. MCD spectroscopy allows us to resolve the intense S0→ La transition from the weak S0→ Lb transition. The spectra obtained in water solution, by using B3LYP and CAM-B3LYP functionals and describing solvent effect by cluster models and by the polarizable continuum model (PCM), are in very good agreement with the experimental counterparts, thus providing direct and unambiguous evidence that the energy ordering predicted by TD-DFT, La Lb, is the correct one.

  11. Racemic crystals of trolox derivatives compared to their chiral counterparts: Structural studies using solid-state NMR, DFT calculations and X-ray diffraction

    Science.gov (United States)

    Wałejko, P.; Paradowska, K.; Szeleszczuk, Ł.; Wojtulewski, S.; Baj, A.

    2018-03-01

    Trolox C (6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid) is a water-soluble vitamin E analogue that is available in enantiomeric forms R or S. Enantiomerically pure Trolox 1, its derivatives 2, 3 (R and S enantiomers) and racemic forms 1-3 were studied using solid-state 13C cross-polarisation (CP) magic angle spinning (MAS) NMR (13C CPMAS NMR). Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of the shielding constants supported the assignment of 13C resonances in the solid-state NMR spectra. For the 13C CPMAS NMR spectra of 1, resonances of pure enantiomers were significantly broader than those of the racemic R/S form. In order to explain these effects, five of the available crystal structures were analysed (1R/S, 3R/S, 2S and the newly measured 2R/S and 3S). Cyclic dimers with one R and one S enantiomer linked by two OHsbnd Odbnd C2b hydrogen bonds were formed in 1R/S. Similar hydrogen-bonded dimers were present in 3S but not in 3R/S, in which interactions are water-mediated. A comparison of X-ray diffraction, CPMAS NMR data and the DFT GIPAW calculations of racemic forms and pure enantiomers was conducted for the first time. Our results, particularly the solid-state NMR data, were discussed in relation to Wallach's rule, that the racemic crystal appears as more ordered than its chiral counterpart.

  12. 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.

  13. 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.

  14. DFT calculations and electrochemical studies on azulene ligands for heavy metal ions detection using chemically modified electrodes

    Directory of Open Access Journals (Sweden)

    Amalia Stefaniu

    2018-03-01

    Full Text Available A computational study on three related derivatives of 5-[(azulen-1-ylmethylene]-2-thioxoimidazolidin-4-one was conducted using density functional theory by calculating a series of molecular descriptors and properties of their optimized geometries (electrostatic and local ionization potentials, molecular frontier orbitals, etc.. Thermodynamic properties (zero-point energy, enthalpy, constant volume heat capacity, entropy and Gibbs energy for these derivatives have been calculated and related to ligands electrochemical behavior. Reduction and oxidation potentials have been correlated to their calculated energy levels for LUMO and HOMO orbitals. Chemically modified electrodes based on these derivatives have been tested in view of heavy metal ions recognition, and their detection limits have been correlated to the calculated values of electron affinity.

  15. 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. (c) 2008 Wiley Periodicals, Inc.

  16. 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.

  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.

    2015-03-01

    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 13C NMR and 1H 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.

  18. 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.

    2015-05-01

    In the present research work, the FT-IR, FT-Raman and 13C and 1H 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, 13C NMR and 1H 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.

  19. 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.

  20. Structural characterization, vibrational spectroscopy accomplished with DFT calculation, thermal and dielectric behaviors in a new organic-inorganic tertrapropylammonium aquapentachlorostannate dihydrate compound

    Energy Technology Data Exchange (ETDEWEB)

    Hajlaoui, Sondes, E-mail: hajlaouisondes@yahoo.fr [Unité de recherche de la matière condensée, Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax (Tunisia); Chaabane, Iskandar [Unité de recherche de la matière condensée, Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax (Tunisia); Lhoste, Jérôme; Bulou, Alain [LUNAM Université, Université du Maine, CNRS UMR 6283, Institut des Molécules et Matériaux du Mans (IMMM), Avenue Olivier Messiaen, 72085, Le Mans, Cedex 9 (France); Guidara, Kamel [Unité de recherche de la matière condensée, Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax (Tunisia)

    2016-09-15

    In this work a novel compound tertrapropylammonium aquapentachlorostannate dihydrate was synthesized and characterized by; single crystal X-ray diffraction, vibrational spectroscopy, differential scanning calorimetric and dielectric measurement. The crystal structure refinement at room temperature reveled that this later belongs to the monoclinic compound with P121/c1 space group with the following unit cell parameters a = 8.2699(3) Å, b = 12.4665(4) Å, c = 22.3341(7) Å and β = 92.94(0)°. The crystal arrangement can be described by stacked organic-inorganic layers in the c direction with two independent water molecules placed between each two layers. The detailed interpretations of the vibrational properties of the studied compound were performed using density functional theory (DFT) with the B3LYP/LanL2DZ basis set, and has enabled us to make the detailed assignments by comparative study of the experimental and calculated Raman and IR spectra. The differential scanning calorimetry (DSC) measurement disclosed two anomalies in the temperature range 356–376 (T{sub 1}) K and at 393 K (T{sub 2}) characterized by the dehydration of the sample and probably a reconstruction of a new structure after T{sub 2} transition. The temperature dependences of dielectric permittivity show a relaxation process around T{sub 2} anomaly indicating the occurrence of the disorder at high temperature. The dependence of the exponent m(T) on temperature, extracted from the straight lines of log(ε″) with log (ω), suggests that the correlated barrier hopping is the appropriate model for the conduction mechanism. - Highlights: • The single-crystal X-ray diffraction has been performed. • The assignments of the vibration modes based on DFT were reported and discussed. • Differential scanning calorimetric reveals the presence of two endothermic peaks. • The electric permittivity was studied using the impedance measurements. • The CBH is the appropriate model for the conduction

  1. Reference values for spirometry, including vital capacity, in Japanese adults calculated with the LMS method and compared with previous values.

    Science.gov (United States)

    Kubota, Masaru; Kobayashi, Hirosuke; Quanjer, Philip H; Omori, Hisamitsu; Tatsumi, Koichiro; Kanazawa, Minoru

    2014-07-01

    Reference values for lung function tests should be periodically updated because of birth cohort effects and improved technology. This study updates the spirometric reference values, including vital capacity (VC), for Japanese adults and compares the new reference values with previous Japanese reference values. Spirometric data from healthy non-smokers (20,341 individuals aged 17-95 years, 67% females) were collected from 12 centers across Japan, and reference equations were derived using the LMS method. This method incorporates modeling skewness (lambda: L), mean (mu: M), and coefficient of variation (sigma: S), which are functions of sex, age, and height. In addition, the age-specific lower limits of normal (LLN) were calculated. Spirometric reference values for the 17-95-year age range and the age-dependent LLN for Japanese adults were derived. The new reference values for FEV(1) in males are smaller, while those for VC and FVC in middle age and elderly males and those for FEV(1), VC, and FVC in females are larger than the previous values. The LLN of the FEV(1)/FVC for females is larger than previous values. The FVC is significantly smaller than the VC in the elderly. The new reference values faithfully reflect spirometric indices and provide an age-specific LLN for the 17-95-year age range, enabling improved diagnostic accuracy. Compared with previous prediction equations, they more accurately reflect the transition in pulmonary function during young adulthood. In elderly subjects, the FVC reference values are not interchangeable with the VC values. Copyright © 2014 The Japanese Respiratory Society. Published by Elsevier B.V. All rights reserved.

  2. Determination of geometrical, spectroscopic, thermal and nonlinear optical parameters of (+)-Varitriol by DFT/ab initio calculations.

    Science.gov (United States)

    Vasantha Kumar, V; Nagabhushanam, M; Laxmikanth Rao, J

    2013-12-01

    Theoretical studies have been carried out on (+)-Varitriol using both the B3LYP/6-311+G and HF/6-311+G methods. The vibrational spectra of the title molecule have been recorded in solid state with FT-IR and Micro-Raman spectrometry. The calculated geometrical parameters of the title molecule, like bond length, bond angle and dihedral angles have been compared with the experimental data. The spectral frequencies have been calculated theoretically using both the above mentioned methods and are compared with the observed spectra. The complete vibrational assignments of wavenumbers have been made on the basis of potential energy distribution (PED). From this analysis, it is seen that the vibrational frequencies obtained from B3LYP method are in good agreement with the experiment, when compared to HF method. Nonlinear optical properties like dipole moment, hyperpolarizabilities and thermal properties like rotational constants, zero point vibrational energies are calculated. The effect of temperature on various thermodynamic properties have been calculated and reported. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Geometrical and ground state electronic structures of nitrosylcobalt complexes [(RNCHCHNR)Co(NO)(CO)] (R = isopropyl, 2,6-diisopropylphenyl or p-tolyl) from experiment and DFT-calculations

    Czech Academy of Sciences Publication Activity Database

    Sieger, M.; Hubler, K.; Scheiring, T.; Sixt, T.; Záliš, Stanislav; Kaim, W.

    2002-01-01

    Roč. 628, - (2002), s. 2360-2364 ISSN 0044-2313 R&D Projects: GA MŠk OC D14.20 Institutional research plan: CEZ:AV0Z4040901 Keywords : carbonyl complexes * cobalt compounds * DFT calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.196, year: 2002

  4. 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.

  5. Vibrational spectroscopic (FTIR and FT-Raman), first-order hyperpolarizablity, HOMO, LUMO, NBO, Mulliken charge analyses of 2-ethylimidazole based on Hartree-Fock and DFT calculations.

    Science.gov (United States)

    Arivazhagan, M; Manivel, S; Jeyavijayan, S; Meenakshi, R

    2015-01-05

    The FTIR and FT-Raman spectra of 2-ethylimidazole (2EIDZ) have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimized molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of 2EIDZ is also reported based on total energy distribution (TED). The values of the total dipole moment (μ) and the first-order hyperpolarizability (β) of the compound were computed. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. Besides, HOMO and LUMO analysis, Mulliken's charge analysis and several thermodynamic properties have been calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Structure and reactivity of oxalate surface complexes on lepidocrocite derived from infrared spectroscopy, DFT-calculations, adsorption, dissolution and photochemical experiments

    Science.gov (United States)

    Borowski, Susan C.; Biswakarma, Jagannath; Kang, Kyounglim; Schenkeveld, Walter D. C.; Hering, Janet G.; Kubicki, James D.; Kraemer, Stephan M.; Hug, Stephan J.

    2018-04-01

    Oxalate, together with other ligands, plays an important role in the dissolution of iron(hdyr)oxides and the bio-availability of iron. The formation and properties of oxalate surface complexes on lepidocrocite were studied with a combination of infrared spectroscopy (IR), density functional theory (DFT) calculations, dissolution, and photochemical experiments. IR spectra measured as a function of time, concentration, and pH (50-200 μM oxalate, pH 3-7) showed that several surface complexes are formed at different rates and in different proportions. Measured spectra could be separated into three contributions described by Gaussian line shapes, with frequencies that agreed well with the theoretical frequencies of three different surface complexes: an outer-sphere complex (OS), an inner-sphere monodentate mononuclear complex (MM), and a bidentate mononuclear complex (BM) involving one O atom from each carboxylate group. At pH 6, OS was formed at the highest rate. The contribution of BM increased with decreasing pH. In dissolution experiments, lepidocrocite was dissolved at rates proportional to the surface concentration of BM, rather than to the total adsorbed concentration. Under UV-light (365 nm), BM was photolyzed at a higher rate than MM and OS. Although the comparison of measured spectra with calculated frequencies cannot exclude additional possible structures, the combined results allowed the assignment of three main structures with different reactivities consistent with experiments. The results illustrate the importance of the surface speciation of adsorbed ligands in dissolution and photochemical reactions.

  7. Novel Zn(II) complexes of 1,3-diphenyl-4-(arylazo)pyrazol-5-one derivatives: Synthesis, spectroscopic properties, DFT calculations and first order nonlinear optical properties

    Science.gov (United States)

    Abdel-Latif, Samir A.; Mohamed, Adel A.

    2018-03-01

    Eight novel Zn(II) complexes with substituted 1,3-diphenyl-4-(arylazo)pyrazol-5-one (L1-L4) derivatives have been synthesized and elucidated using various physicochemical techniques. Quantum mechanical calculations of energies, geometries were done by DFT using B3LYP/GEN functional combined with 6.311G (d,p) and LAN2DZ basis sets. The analyses of HOMO and LUMO have been used to explain the charge transfer within the ligands and complexes. The calculated small energy gap between HOMO and LUMO energies shows that the charge transfer occurs within Zn(II) complexes. Geometrical parameters, molecular electrostatic potential maps (MEP) and total electron densities analyses of the ligands and their Zn complexes have been carried out. Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength has been investigated by the applying of natural bond orbital (NBO) analysis. Total static dipole moment (μ), the mean polarizability (), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability () have been also performed. The obtained values show that Zn(II) complexes is brilliant candidate to NLO materials. The analyses of the 1:1 complexes indicate that the Zn(II) ion is five-coordinated with water molecules at axial position in case of L1, L2 and L4 whereas, six-coordinated with L3 and non-electrolytic behaviour of complexes indicates the absence of counter ion.

  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. Morita-Baylis-Hillman reaction: ESI-MS(/MS) investigation with charge tags and ionic liquid effect origin revealed by DFT calculations.

    Science.gov (United States)

    Rodrigues, Thyago S; Silva, Valter H C; Lalli, Priscila M; de Oliveira, Heibbe C B; da Silva, Wender A; Coelho, Fernando; Eberlin, Marcos N; Neto, Brenno A D

    2014-06-06

    The use of a charge-tagged acrylate derivative bearing an imidazolium tag to study the Morita-Baylis-Hillman reaction via ESI-MS(/MS) monitoring and the effect of such tag (imidazolium cations and ion pairs) over TSs is described. The ionic nature of the substrate was meant to facilitate ESI transfer to the gas phase for direct mass spectrometric analysis. The detection and characterization of charged intermediates has suggested major reaction pathways. DFT calculations considering the effect of a polar and protic solvent (methanol), of a polar and aprotic solvent (acetonitrile), and of no solvent (gas phase) were used to predict possible TSs through a common accepted intermediate. The controversial proton transfer step, which may proceed via Aggarwal's or McQuade's proposals, was evaluated. Calculations predicted the formation of electrostatic intermediate complexes with both the cation and anion when charge-tagged reagents are used. These complexes contribute to the positive ionic liquid effect, and based on the formation of these unique complexes, a rationale for the ionic liquid effect is proposed. These complexes also pointed to a plausible explanation for the positive ionic liquid effect observed in several reactions that are difficult to be carried out in organic solvents but have shown a beneficial effect when performed in ionic liquids.

  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. Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations

    Science.gov (United States)

    2015-01-01

    Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals associated with the two Mn(II) centers located in the N- and C-terminal cupin domains of the enzyme. We now report a mutational strategy that has established the assignment of EPR fine structure parameters to each of these Mn(II) centers at pH 8.5. These experimental findings are also used to assess the performance of a multistep strategy for calculating the zero-field splitting parameters of protein-bound Mn(II) ions. Despite the known sensitivity of calculated D and E values to the computational approach, we demonstrate that good estimates of these parameters can be obtained using cluster models taken from carefully optimized DFT/MM structures. Overall, our results provide new insights into the strengths and limitations of theoretical methods for understanding electronic properties of protein-bound Mn(II) ions, thereby setting the stage for future EPR studies on the electronic properties of the Mn(II) centers in OxDC and site-specific variants. PMID:24444454

  12. 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.

  13. 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.

  14. DFT calculation of geometrical structure and electronic absorption spectra for neutral, mono-, and diprotonated forms of Risperidone (Risperdal)

    Science.gov (United States)

    Alparone, A.

    2012-09-01

    Vertical electronic transitions to singlet valence states of an antipsychotic drug, Risperidone (Risperdal), in its neutral, mono-, and diprotonated forms have been calculated within the time-dependent density functional theory using the PBE0 hybrid functional with the 6-31+G* basis set. The results of the computations show that the lowest-energy allowed π-π* electronic excitation is affected by protonation effects, the spectral shifts of this transition being potentially useful to individuate the different forms of risperidone

  15. The Raman and SERS spectra of indigo and indigo-Ag2complex: DFT calculation and comparison with experiment.

    Science.gov (United States)

    Ricci, Marilena; Lofrumento, Cristiana; Becucci, Maurizio; Castellucci, Emilio M

    2018-01-05

    Using time-dependent density functional theory in conjunction with B3LYP functional and LANL2DZ/6-31+g(d,p) basis sets, static and pre-resonance Raman spectra of the indigo-Ag 2 complex have been calculated. Structure optimization, excitation energies and pre-resonance Raman spectra of the indigo molecule have been obtained at the same level of theory. The available experimental Raman spectra at 1064, 785 and 514nm and the SERS spectra at 785 and 514nm have been well reproduced by the calculation. Experimental SERS spectra are confronted with the calculated pre-resonance Raman spectra obtained for the indigo-Ag 2 complex. The Raman activities calculated under the infinite lifetime approximation show a strong dependence upon the proximity to the energy and the oscillator strength of the excitation electronic transition. The comparison of the integrated EFs for indigo and indigo-Ag 2 calculated Raman spectra, gave some hints as to the enhancement mechanisms acting for the different excitation wavelengths. Whereas for excitation at a wavelength corresponding to 785nm, the enhancement mechanism for the Raman spectrum of the metal complex seems the chemical one, the strong increment (ten times) of the integrated EF of the Raman spectra of the complex in the case of 514nm excitation, suggests the onset of other enhancement mechanisms. Assuming that intra-cluster transitions with high oscillator strength can be thought of as to mimic surface plasmons excitations, we suggest the onset of the electromagnetic mechanisms (EM) as the origin of the Raman spectrum enhancement. Nevertheless, other enhancement effects cannot be ruled out, as a new molecular transition gains strength in the proximity of the excitation wavelength, as a consequence of the symmetry lowering of the molecule in the complex. A large variation across vibrational modes, by a factor of at least 10 4 , was found for the EFs. This large variation in the EFs can indicate that B-term Herzberg-Teller scattering

  16. 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.

  17. Novel CoIII complexes containing fluorescent coumarin-N-acylhydrazone hybrid ligands: Synthesis, crystal structures, solution studies and DFT calculations

    Science.gov (United States)

    Areas, Esther S.; Bronsato, Bruna Juliana da S.; Pereira, Thiago M.; Guedes, Guilherme P.; Miranda, Fábio da S.; Kümmerle, Arthur E.; da Cruz, Antônio G. B.; Neves, Amanda P.

    2017-12-01

    A series of new CoIII complexes of the type [Co(dien)(L1 -L3)]ClO4 (1-3), containing fluorescent coumarin-N-acylhydrazonate hybrid ligands, (E)-N‧-(1-(7-oxido-2-oxo-2H-chromen-3-yl)ethylidene)-4-R-benzohydrazonate [where R = H (L12 -), OCH3 (L22 -) or Cl (L32 -)], were obtained and isolated in the low spin CoIII configuration. Single-crystal X-ray diffraction showed that the coumarin-N-acylhydrazones act as tridentate ligands in their deprotonated form (L2 -). The cation (+ 1) complexes contain a diethylenetriamine (dien) as auxiliary ligand and their structures were calculated by DFT studies which were also performed for the CoII (S = 1/2 and S = 3/2) configurations. The LS CoII (S = 1/2) concentrated the spin density on the O-Co-O axis while the HS CoII (S = 3/2) exhibited a broad spin density distribution around the metallic center. Cyclic voltammetry studies showed that structural modifications made in the L2 - ligands caused a slight influence on the electronic density of the metal center, and the E1/2 values for the CoIII/CoII redox couple increased following the electronic effect of the R-substituent, in the order: 2 (R = OCH3) experimental values vs SHE (E°calc = - 0.37, - 0.36 and - 0.32 V vs E°exp. = - 0.371, - 0.406 and - 0.358 V, for 1-3 respectively). Complexes 1-3 exhibited a very intense absorption band around 470 nm, assigned by DFT calculations as π-π* transitions from the delocalized coumarin-N-acylhydrazone system. 1-3 were very stable in MeOH for several days. Likewise, 1-3 were stable in phosphate buffer containing sodium ascorbate after 15 h, which was attributed to the high chelate effect and σ-donor ability of the L2 - and dien ligands.

  18. Characterization of peroxide-based explosives using Raman spectroscopy: isotopic analysis and DFT calculations of triacetone triperoxide (TATP)

    Science.gov (United States)

    Brauer, Carolyn S.; Barber, Jeffrey; Weatherall, James C.; Smith, Barry T.; Tomlinson-Phillips, Jill; Wooten, Alfred

    2011-06-01

    The Raman spectra of triacetone triperoxide (TATP) and its fully deuterated isotopologue (d18-TATP) have been measured. Density functional theory calculations were performed using the EDF2/6-311++G** and B3LYP/6-311++G** methods/basis set to predict the Raman spectra of both the parent and deuterated isotopologues. The predicted isotopic shifts were used to identify frequency shifts in the experimental results and tentative assignments have been made for 10 fundamental vibrational modes of d18-TATP.

  19. High-throughput DFT calculations of formation energy, stability and oxygen vacancy formation energy of ABO3 perovskites

    Science.gov (United States)

    Emery, Antoine A.; Wolverton, Chris

    2017-10-01

    ABO3 perovskites are oxide materials that are used for a variety of applications such as solid oxide fuel cells, piezo-, ferro-electricity and water splitting. Due to their remarkable stability with respect to cation substitution, new compounds for such applications potentially await discovery. In this work, we present an exhaustive dataset of formation energies of 5,329 cubic and distorted perovskites that were calculated using first-principles density functional theory. In addition to formation energies, several additional properties such as oxidation states, band gap, oxygen vacancy formation energy, and thermodynamic stability with respect to all phases in the Open Quantum Materials Database are also made publicly available. This large dataset for this ubiquitous crystal structure type contains 395 perovskites that are predicted to be thermodynamically stable, of which many have not yet been experimentally reported, and therefore represent theoretical predictions. The dataset thus opens avenues for future use, including materials discovery in many research-active areas.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Tuning of Aggregation Enhanced Emission and Solid State Emission from 1,8-Naphthalimide Derivatives: Nanoaggregates, Spectra, and DFT Calculations.

    Science.gov (United States)

    Srivastava, Ashish Kumar; Singh, Avinash; Mishra, Lallan

    2016-07-07

    Four new 1,8-naphthalimide based compounds, 4-(1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-ylmethyl)-benzoic acid (LH), 4-(1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-ylmethyl)-benzoic acid methyl ester (LMe), 4-(1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-ylmethyl)-benzoyl chloride (LCl), and 4-(1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-ylmethyl)-benzoic acid hydrazide (LN) are synthesized and characterized using spectral data and X-ray crystallography. They form nanoaggregates in aqueous-DMF solution and exhibited aggregation enhanced emission. The nanoaggregates are characterized using their scanning electron and atomic force microscopy images. The emission intensity follows the order as LH > LMe > LCl > LN. Their photophysical properties are recorded both in solution and in the solid-state and are correlated with the nature of benzoic acid derivatives owing to the combinatorial effect of π-π stacking and intermolecular and intramolecular interactions. The density functional theory calculations empower the understanding of their molecular and cumulative electronic behaviors. Antiparallel dimeric interactions in the solid-state extend a herringbone arrangement to LH and 2D channel and stair-like arrangement for LCl and LN, respectively.

  5. Synthesis, growth, physicochemical properties and DFT calculations of 2-naphthol substituted Mannich base 1-(morpholino(phenyl) methyl) naphthalen-2-ol: A non linear optical single crystal

    Science.gov (United States)

    Dennis Raj, A.; Jeeva, M.; Shankar, M.; Venkatesa Prabhu, G.; Vimalan, M.; Vetha Potheher, I.

    2017-11-01

    2-Naphthol substituted Mannich base 1-morpholino(phenyl)methyl)naphthalen-2-ol (MPMN), a potential NLO active organic single crystal was developed using acetonitrile as a solvent by slow evaporation method. The experimental and theoretical analysis made towards the exploitation in the field of electro-optic and NLO applications. The cubic structure with non-centrosymmetric space group Cc was confirmed and cell dimensions of the grown crystal were obtained from single crystal X-ray diffraction (XRD) study. The formation of the Csbnd Nsbnd C vibrational band at 1115 cm-1 in Fourier Transform Infra-Red (FTIR) analysis confirms the formation of MPMN compound. The placement of protons and carbons of MPMN were identified from Nuclear Magnetic Resonance Spectroscopy (NMR) analysis. The wide optical absorption window and the lower cutoff wavelength of MPMN show the suitability of the material for the various laser related applications. The presence of dislocations and growth pattern of crystal were analyzed using chemical etching technique. The Second Harmonic Generation (SHG) of MPMN was found to be 1.57 times greater than the standard KDP crystal. The laser damage threshold was measured by using Nd: YAG laser beam passed through the sample and it was found to be 1.006 GW/cm2. The electronic structure of the molecular system and the optical properties were also studied from quantum chemical calculations using Density Functional Theory (DFT) and reported for the first time.

  6. Synthesis, crystal structure, spectroscopic characterization, Hirshfeld surface analysis, and DFT calculations of 1,4-dimethyl-2-oxo-pyrimido[1,2-a]benzimidazole hydrate

    Science.gov (United States)

    El Bakri, Youness; Anouar, El Hassane; Ramli, Youssef; Essassi, El Mokhtar; Mague, Joel T.

    2018-01-01

    Imidazopyrimidine derivatives are organic synthesized compounds with a pyrimido[1,2-a]benzimidazole as basic skeleton. They are known for their various biological properties and as an important class of compounds in medicinal chemistry. A new 1,4-dimethyl-2-oxo-pyrimido[1,2-a]benzimidazole hydrate derivative of the tilted group has been synthesized and characterized by spectroscopic techniques NMR and FT-IR; and by a single crystal X-ray diffraction. The X-ray results showed that the tricyclic core of the title compound, C12H11N3O·H2O, is almost planar. The molecules stack along the a-axis direction in head-to- tail fashion through π-stacking interactions involving all three rings. The stacks are tied together by direct Csbnd H⋯O hydrogen bonds and by Osbnd H⋯O, Osbnd N⋯N and Csbnd H⋯O hydrogen bonds with the lattice water. DFT calculations at B3LYP/6-311++G(d,p) in gas phase an polarizable continuum model have been carried out to predict the spectral and geometrical data of the tilted compound. The obtained results showed relatively good correlations between the predicted and experimental data with correlation coefficients higher than 98%.

  7. 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.

  8. 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.

  9. Molecular structure of mercury(II) thiocyanate complexes based on DFT calculations and experimental UV-electron spectroscopy and Raman studies.

    Science.gov (United States)

    Elijošiutė, Erika; Eicher-Lorka, Olegas; Griškonis, Egidijus; Matulaitienė, Ieva; Jankūnaitė, Dalia; Denafas, Gintaras

    2013-11-01

    In this work, we report a combined experimental and theoretical study on molecular structure, vibrational and electronic spectra of [Hg(SCN)n](2-)(n) complexes (where n=2, 3, 4) in the aqueous solution. Molecular modeling of the mercury(II) complexes were done by the density functional theory (DFT) method using B3LYP functional with Stuttgart relativistic ECP 78MWB basis set for Hg and 6-311++G(d,p) basis set for all other atoms. The effect of different solvation models with explicit (ligand) and/or implicit water environment upon its geometry, vibrational frequencies and UV spectrum have been studied. The influence of H2O/D2O exchange on the experimental and calculated vibrational frequencies of studied complexes has been established. The double-peak character of the νHgS vibrational mode of the all analyzed mercury complexes and νCN mode of [Hg(SCN)3H2O](-) complex, respectively, were proposed here for the first time. The formation of four-coordinated Hg(II) complexes with thiocyanate and (or) water ligands was verified. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. 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.

  11. Merging Kohn-Sham and Orbital-Free DFT Calculations to Extend the LiH Hugoniot to Very High Pressures

    Science.gov (United States)

    Kress, Joel

    2013-06-01

    Large-scale hydrodynamic simulations of fluids and plasmas under extreme conditions require knowledge of various properties such as the equation of state (EOS), mass diffusion, and shear viscosity. While many approaches exist for the determination of these properties, one of the most accurate employs quantum molecular dynamics (QMD) simulations on large samples of atoms of the various species. Examples include the shock compression of metal hydrides and the mixing of deuterium/tritium (DT) fuel with ablator materials (such as C/H plastics and Be) in inertial confinement fusion capsules. The quantum nature of the electrons is described with two flavors of finite-temperature density functional theory (DFT), namely orbital-based Kohn-Sham (KS) and Orbital Free (OF). EOSs for Lithium Hydride and Lithium 6 Deuteride (Li6D) have been calculated with both KSMD and with OFMD. The shock Hugoniot for Li6D has been determined for temperatures up to 25 eV (5000 GPa) using a KSMD based EOS, and for T = 5 eV and above (up to 10,000 GPa) using an OFMD based EOS. KSMD simulations here have a practical upper limit of T = 25 eV due to the scaling of the computational work. The OFMD simulations have a lower limit of T = 5 eV since the OF DFT yields a poor description at low temperatures. The KSMD and OFMD Hugoniots agree well in the region of overlap (T = 5 to 25 eV). Comparisons will be presented with experimental data and with shock Hugoniots constructed from both existing EOS tables and from a new, improved SESAME table. By utilizing the KSMD and OFMD results to guide the parameter choices, the new EOS overall is a better match to melt and shock experimental data. This work was performed in collaboration with L. A. Collins, S. Crockett, M. P. Desjarlais, and F. Lambert and under the auspices of an agreement between CEA/DAM and NNSA/DP on cooperation on fundamental science. LANL is operated by LANS, LLC for the NNSA of the USDoE under contract no. DE-AC52-06NA25396.

  12. 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.

  13. Determination of a complex crystal structure in the absence of single crystals: analysis of powder X-ray diffraction data, guided by solid-state NMR and periodic DFT calculations, reveals a new 2'-deoxyguanosine structural motif.

    Science.gov (United States)

    Hughes, Colan E; Reddy, G N Manjunatha; Masiero, Stefano; Brown, Steven P; Williams, P Andrew; Harris, Kenneth D M

    2017-05-01

    Derivatives of guanine exhibit diverse supramolecular chemistry, with a variety of distinct hydrogen-bonding motifs reported in the solid state, including ribbons and quartets, which resemble the G-quadruplex found in nucleic acids with sequences rich in guanine. Reflecting this diversity, the solid-state structural properties of 3',5'-bis- O -decanoyl-2'-deoxyguanosine, reported in this paper, reveal a hydrogen-bonded guanine ribbon motif that has not been observed previously for 2'-deoxyguanosine derivatives. In this case, structure determination was carried out directly from powder XRD data, representing one of the most challenging organic molecular structures (a 90-atom molecule) that has been solved to date by this technique. While specific challenges were encountered in the structure determination process, a successful outcome was achieved by augmenting the powder XRD analysis with information derived from solid-state NMR data and with dispersion-corrected periodic DFT calculations for structure optimization. The synergy of experimental and computational methodologies demonstrated in the present work is likely to be an essential feature of strategies to further expand the application of powder XRD as a technique for structure determination of organic molecular materials of even greater complexity in the future.

  14. Molecular and electron-spin structures of a ring-shaped mixed-valence polyoxovanadate (IV, V) studied by (11)B and (23)Na solid-state NMR spectroscopy and DFT calculations.

    Science.gov (United States)

    Iijima, Takahiro; Yamase, Toshihiro; Nishimura, Katsuyuki

    2016-01-01

    (11)B and (23)Na solid-state nuclear magnetic resonance (NMR) spectra of ring-shaped paramagnetic crystals of H15[V7(IV)V5(V)B32O84Na4]·13H2O containing seven d(1) electrons from V(IV) were studied. Magic-angle-spinning (MAS) and multiple-quantum MAS NMR experiments were performed at moderate (9.4T) and ultrahigh magnetic fields (21.6T). The NMR parameters for quadrupole and isotropic chemical shift interactions were estimated by simulation of the NMR spectra and from relativistic density functional theory (DFT) calculations. Four Na ions incorporated into the framework were found to occupy four distinct sites with different populations. The DFT calculation showed that d(1) electrons with effectively one up-spin caused by strong antiferromagnetic interactions were delocalized over the 12V ions. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Molecular structure and hydrogen bonding in liquid cyclohexanol and cyclohexanol/water mixtures studied by FT-NIR spectroscopy and DFT calculations

    Science.gov (United States)

    Czarnecki, Mirosław Antoni; Muszyński, Andrzej S.; Troczyńska, Helena

    2010-06-01

    The molecular structure and hydrogen bonding in liquid cyclohexanol and cyclohexanol/water mixtures has been examined by Fourier-transform near-infrared (FT-NIR) spectroscopy. FT-NIR spectra of pure cyclohexanol and binary mixtures with water at selected water mole fractions ( XO) from 30 to 80 °C and the spectra of the mixtures from XO = 0-0.4 at 30 °C were measured. Besides, FT-IR and FT-NIR spectra of cyclohexanol in CCl 4 and cyclohexane solutions were recorded. The experimental spectra were analyzed by two-dimensional (2D) correlation approach and chemometrics methods. Interpretation of the spectra was guided by DFT calculations. It has been shown that small to moderate water content has a negligible effect on the structure of liquid cyclohexanol at constant temperature. Water molecules predominantly act as double donors to different species of cyclohexanol and this hydrogen bonding is stronger than that in bulk water. At lower water content appears a noticeable amount of singly bonded water molecules, however, population of this species in cyclohexanol is significantly smaller as compared with that in butyl alcohols. This results from much higher viscosity of cyclohexanol that stabilizes the cyclohexanol-water interactions. Increasing water content leads to creation of small clusters of water, where the water-water interaction is much weaker than that in bulk water. The temperature-induced breaking of smaller associates of cyclohexanol occurs easier in the presence of water, while an opposite effect was observed for the higher associates. The hydrophobic interactions in the cyclohexanol/water mixtures are of minor importance.

  16. Synthesis, spectroscopic characterization, DFT calculations and biological evaluation of benzothiazole derivative bearing Mn(II) and Ni(II) metal ions

    Science.gov (United States)

    El-Gamel, Nadia E. A.; Ali, Korany A.

    2017-11-01

    N-(benzo[d]thiazol-2-yl)-3-oxo-3-phenylpropanamide ligand and its Nickel and Manganese complexes have been synthesized and characterized by elemental and thermal analyses, IR, diffuse reflectance, mass and UV-Vis spectra, molar conductance and magnetic moment measurements. The decomposition mechanism and thermal stability of the investigated complexes are interpreted in terms of their structures. The thermal behaviour of the complexes has been studied and different thermodynamic parameters are calculated using Coats-Redfern method. N-(benzo[d]thiazol-2-yl)-3-oxo-3-phenylpropanamide is a neutral bidentate ligand coordinating metal ions via thiazole ring nitrogen and amide carbonyl O forming high spin octahedral complexes with Mn(II) (2) and distorted square planar in case of Ni(II) (1). Natural bond orbital analysis and geometry optimization were carried out at DFT/B3LYP/6-31G(d) level of theory for the ligand and the mentioned complexes. Ab inito computations at the HF/6-31G(d) level of the theory is conducted in order to detect any probability of a hydrogen bond formation in the ligand. The dipole moment of the Ni(II) and Mn(II) complexes is recorded to be 9.69 and 7.39 Debye, respectively, indicating that the complexes are more polarized than the ligand 2.39 Debye. The in vitro biological activity of the metal chelates is screened against the Gram-positive bacteria (Staphylococcus aureus) and Gram-negative bacteria (Escherichia coli), fungus (Aspergillus flavus, Candida albicans). Ni(II) complexes displayed the highest activity against Candida albicans and Staphylococcus aureus with MIC values of 13, 30 μg/cm3, respectively.

  17. Spectroscopic (FT-IR, FT-Raman, UV-Vis) analysis, conformational, HOMO-LUMO, NBO and NLO calculations on monomeric and dimeric structures of 4-pyridazinecarboxylic acid by HF and DFT methods

    Science.gov (United States)

    Eşme, A.; Sağdınç, S. G.

    2017-11-01

    In this study, the Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 4-pyridazinecarboxylic acid (4PCA) in solid phase were recorded and analyzed. Quantum chemical calculations of the optimized molecular structure, energies, conformational, UV-Vis, nonlinear optical (NLO) and natural bond orbital (NBO) analysis, molecular surfaces, Mulliken charges, and vibrational studies for 4PCA were performed using the ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. Obtained results on the geometric structure and vibrational frequencies are compared with observed data. The dimeric structure of 4PCA with DFT/B3LYP/6-311++G(d,p) level caused by the shifts of Osbnd H and Cdbnd O bands in the vibrational spectra of 4PCA were also studied. Moreover, the spectroscopic and theoretical results were compared with the corresponding properties for monomeric and dimeric structures of 4PCA. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies also confirm that charge transfer occurs within the molecule. NBO analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. The detailed vibrational assignments were performed with the HF and DFT calculations, and the potential energy distribution (PED) was obtained by the Vibrational Energy Distribution Analysis (VEDA4) program.

  18. 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...

  19. Facile synthesis, crystal structure, DFT calculation and biological activities of 4-(2-fluorophenyl)-3-(3-methoxybenzyl)-1H-1,2,4-triazol-5(4H)-one (5).

    Science.gov (United States)

    Saleem, Muhammad; Rafiq, Muhammad; Jeong, Yeon Ki; Cho, Dae Won; Kim, Chong-Hyeak; Seo, Sung-Yum; Choi, Chang-Shik; Hong, Seong-Karp; Lee, Ki-Hwan

    2018-01-12

    In the past few decades, the design, synthesis and characterization of novel heterocyclic compounds with auspicious biological profile received the considerable attention of scientific community. Among them, the small and simple organic molecular backbone like triazole moiety have broad spectrum of applications in the medicinal as well as diagnostic areas. The objective of present study was the synthesis, characterization and exploration of biological profile of 4-(2-fluorophenyl)-3-(3-methoxybenzyl)-1H-1,2,4-triazol-5(4H)-one (5). The tautomeric interconversion of the molecule was observed by the single crystal XRD and DFT analysis. The N-(2-fluorophenyl)-2-[2-(3-methoxyphenyl)acetyl]hydrazine carboxamide (4) was synthesized by condensation of 2-(3-methoxyphenyl)acetohydrazide (3) with 1-fluoro-2-isocyanatobenzene. The dehydrocyclization of compound (4) yielded target compound (5) by refluxing in 2 N aqueous sodium hydroxide solutions. The target molecule was characterized by FT-IR, 1H NMR, 13C NMR, single crystal X-ray diffraction analysis and DFT calculation. The enzymatic assay measurements were carried out by using a micro plate reader (OPTI Max, Tunable Micro plate Reader; Wavelength range: 340-850 nm; for 96-well plates) while DFT calculation was performed by Gaussian 09 package. The XRD result and DFT calculations showed that the molecule 5 predominantly exist in thione conformation and crystallized in the triclinic system of P-1 space group. Furthermore, for the practical applicability of synthesized compound 5, the in vitro acetylcholinesterase as well as α-glucosidase inhibition activities were performed and found moderate enzyme inhibition potential comparable with that of reference inhibitors. This study might be helpful for future design and development of potent enzyme inhibitor to control alzheimer's as well as diabetic disease. The DFT and single crystal XRD analysis data might be helpful for understanding the mechanism of drug binding and its

  20. Single-case effect size calculation: comparing regression and non-parametric approaches across previously published reading intervention data sets.

    Science.gov (United States)

    Ross, Sarah G; Begeny, John C

    2014-08-01

    Growing from demands for accountability and research-based practice in the field of education, there is recent focus on developing standards for the implementation and analysis of single-case designs. Effect size methods for single-case designs provide a useful way to discuss treatment magnitude in the context of individual intervention. Although a standard effect size methodology does not yet exist within single-case research, panel experts recently recommended pairing regression and non-parametric approaches when analyzing effect size data. This study compared two single-case effect size methods: the regression-based, Allison-MT method and the newer, non-parametric, Tau-U method. Using previously published research that measured the Words read Correct per Minute (WCPM) variable, these two methods were examined by comparing differences in overall effect size scores and rankings of intervention effect. Results indicated that the regression method produced significantly larger effect sizes than the non-parametric method, but the rankings of the effect size scores had a strong, positive relation. Implications of these findings for research and practice are discussed. Copyright © 2014 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  1. On the spectral properties of methyl and methoxy derivatives of 1,3-diphenyl-1H-pyrazolo[3,4-b]quinoxalines: Experiment and DFT/TDDFT calculations.

    Science.gov (United States)

    Gasiorski, P; Matusiewicz, M; Gondek, E; Uchacz, T; Wojtasik, K; Danel, A; Shchur, Ya; Kityk, A V

    2017-11-05

    Paper reports the synthesis and spectroscopic studies of two novel 1,3-diphenyl pyrazoloquinoxaline (PQX) derivatives with 6-substituted methyl (MePQX) or methoxy (MeOPQX) side groups. The optical absorption and fluorescence emission spectra are recorded in solvents of different polarity. Other photophysical constants, such as the fluorescence lifetime and quantum yield, radiationless and radiative rate constants, electronic transition dipole moments, give complete characterization of MePQX and MeOPQX dyes as materials for potential luminescence or electroluminescence applications. Measured optical absorption and fluorescence emission spectra are compared with the results of quantum-chemical analysis using density functional theory (DFT/TDDFT) methods based on hybrid and long range corrected (LRC) exchange-correlation (xc) functionals in combination with solvation self consistent reaction field model. Comparing to conventional hybrid xc-functionals, the DFT/TDDFT calculations using LRC xc-functionals yield considerably more accurate description of optical absorption and fluorescence emission spectra. The best description of the absorption-emission circle provides the model assuming that optical absorption takes place from preferably flat or weakly twisted molecular conformations in the ground state, as particularly is suggested by the geometrical DFT optimization, whereas the fluorescence emission would be expected from more twisted molecular conformations in the excited state. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. 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.

  3. Does DFT-SAPT method provide spectroscopic accuracy?

    Energy Technology Data Exchange (ETDEWEB)

    Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl [Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań (Poland)

    2015-02-14

    Ground state potential energy curves for homonuclear and heteronuclear dimers consisting of noble gas atoms from He to Kr were calculated within the symmetry adapted perturbation theory based on the density functional theory (DFT-SAPT). These potentials together with spectroscopic data derived from them were compared to previous high-precision coupled cluster with singles and doubles including the connected triples theory calculations (or better if available) as well as to experimental data used as the benchmark. The impact of midbond functions on DFT-SAPT results was tested to study the convergence of the interaction energies. It was shown that, for most of the complexes, DFT-SAPT potential calculated at the complete basis set (CBS) limit is lower than the corresponding benchmark potential in the region near its minimum and hence, spectroscopic accuracy cannot be achieved. The influence of the residual term δ(HF) on the interaction energy was also studied. As a result, we have found that this term improves the agreement with the benchmark in the repulsive region for the dimers considered, but leads to even larger overestimation of potential depth D{sub e}. Although the standard hybrid exchange-correlation (xc) functionals with asymptotic correction within the second order DFT-SAPT do not provide the spectroscopic accuracy at the CBS limit, it is possible to adjust empirically basis sets yielding highly accurate results.

  4. 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.

  5. 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.

  6. The DFT Calculations of Structures and EPR Parameters for the Dinuclear Paddle-Wheel Copper(II) Complex {Cu2(μ2-O2CCH3)4}(OCNH2CH3) as Powder or Single Crystal

    Science.gov (United States)

    Ding, Chang-Chun; Wu, Shao-Yi; Xu, Yong-Qiang; Zhang, Li-Juan; Zhang, Zhi-Hong; Zhu, Qin-Sheng; Wu, Ming-He; Teng, Bao-Hua

    2017-10-01

    Density functional theory (DFT) calculations of the structures and the Cu2+ g factors (gx, gy and gz ) and hyperfine coupling tensor A (Ax , Ay and Az ) were performed for the paddle-wheel (PW)-type binuclear copper(II) complex {Cu2(μ2-O2CCH3)4}(OCNH2CH3) powder and single crystal. Calculations were carried out with the ORCA software using the functionals BHandHlyp, B3P86 and B3LYP with five different basis sets: 6-311g, 6-311g(d,p), VTZ, def-2 and def2-TZVP. Results were tested by the MPAD analysis to find the most suitable functional and basis sets. The electronic structure and covalency between copper and oxygen were investigated by the electron localisation function and the localised orbital locator as well as the Mayer bond order for the [CuO5] group. The optical spectra were theoretically calculated by the time-dependent DFT module and plotted by the Multiwfn program for the [CuO5] group and reasonably associated with the local structure in the vicinity of the central ion copper. In addition, the interactions between the OCNH2CH3, NH3 and H2O molecules and the uncoordinated PW copper(II) complex were studied, and the corresponding adsorption energies, the frequency shifts with respect to the free molecules and the changes of the Cu-Cu distances were calculated and compared with the relevant systems.

  7. Synthesis, crystallographic characterization, DFT and TD-DFT ...

    Indian Academy of Sciences (India)

    Their molecular structures were also calculated using DFT/B3LYP method. The optimized structures agreed well with the X-ray structures. Time-dependent density functional theory (TDDFT)was used to assign the electronic absorption bands observed experimentally. Pyridine derivative showed two bands at shorter λmax ...

  8. Synthesis, crystal structure, thermal analysis and vibrational spectroscopy accomplished with DFT calculation of new hybrid compound [2-CH3C6H4NH3]HSO4.H2O

    Science.gov (United States)

    Ben Hassen, C.; Boujelbene, M.; Marweni, S.; Bahri, M.; Mhiri, T.

    2015-10-01

    The present paper undertakes the study of a new organic/inorganic hybrid compound [2-CH3C6H4NH3]HSO4.H2O characterized by the X-ray diffraction, TG-DTA, IR and Raman spectroscopy accomplished with DFT calculation. It is crystallized in the monoclinic system with the centrosymmetric space group P 21/c, with a = 9.445 (5) Å, b = 10.499 Å, c = 10.073 Å, β = 90.627 (5)° and Z = 4. The atomic arrangement can be described as inorganic layers built by infinite chains, parallel to the (a c) planes between which the organic cations are inserted. In this atomic arrangement, hydrogen bonds and π-π interactions between the different species have an important role in the tri-dimensional network cohesion. Besides, the X-ray powder diffraction of the title compound confirms the existence of only one phase at room temperature. The thermal decomposition of precursors studied by thermo gravimetric analysis (TGA), the differential thermal analysis (DTA) and the temperature-dependent X-ray diffraction, show crystalline anhydrous compounds upon dehydration. DFT/BHHLYP calculations were performed, using the DZV (d,p) basis set, to determine the harmonic frequencies of the vibrational modes of an optimized cluster structure. The calculated modes were animated using the Molden graphical package to give tentative assignments of the observed IR and Raman spectra.

  9. New nano-complexes of Zn(II), Cu(II), Ni(II) and Co(II) ions; spectroscopy, thermal, structural analysis, DFT calculations and antimicrobial activity application

    Science.gov (United States)

    El-Shafiy, Hoda F.; Saif, M.; Mashaly, Mahmoud M.; Halim, Shimaa Abdel; Eid, Mohamed F.; Nabeel, A. I.; Fouad, R.

    2017-11-01

    This work presents synthesis, characterization, and application of several metal (II) complexes with (E)-2-hydroxy-N/-((thiophen-2-yl)methylene)benzohydrazide (H2L). Prepared complexes were identified by elemental, thermal, FT-IR, UV-Vis, 1H NMR, and XRD analysis, as well as molar conductivity and magnetic moment measurements. Changes in FT-IR and 1H NMR spectra of hydrazone ligand upon coordination indicated that the ligand behaves the same way as a monoanonic ligand with ONS donor sites. Kinetic parameters were determined for each thermal degradation stage of the ligand and its complexes using 'Coats-Redfern' method. All results confirm that all prepared compounds have 1:2 metal-to-ligand stoichiometry except Zn(II) complex, which has 1:1 metal-to-ligand stoichiometry. The antimicrobial activity for complexes was investigated. The antimicrobial activity results revealed that Zn(II) complex (1) has a good potency against gram positive bacteria (E. coli) and gram negative bacteria (P. vulgaris) in comparision with doxymycin standard, AT B3LYP/6-311G (d,p) level, Density Functional Theory (DFT) calculations were carried out to investigate the optimized structure of both, the ligand and the complexes. Total energy, energy of HOMO, and LUMO as well as Mullikan atomic charges were calculated. Dipole moment, orientation, and structure activity relationship were performed and discussed.DFT calculations, moreover, confirmed practical antimicrobial results.

  10. Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Otyepka, M.; Šponer, Jiří; Hobza, P.; Jurečka, P.

    2010-01-01

    Roč. 12, č. 35 (2010), s. 10476-10493 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA203/09/1476 Grant - others:GA MŠk(CZ) LC512; GA MŠk(CZ) GD203/09/H046 Program:LC; GD Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : amber empirical potential * DFT-SAPT * compensation of errors Subject RIV: BO - Biophysics Impact factor: 3.454, year: 2010

  11. Syntheses, crystal structures, spectral study and DFT calculation of three new copper(II) complexes derived from pyridoxal hydrochloride, N,N-dimethylethylenediamine and N,N-diethylethylenediamine

    Science.gov (United States)

    Mandal, Senjuti; Naskar, Barnali; Modak, Ritwik; Sikdar, Yeasin; Chatterjee, Sudipta; Biswas, Sujan; Mondal, Tapan Kumar; Modak, Debadrita; Goswami, Sanchita

    2015-05-01

    Two pyridoxal containing Schiff bases obtained by condensation of pyridoxal hydrochloride with N,N-dimethylethylenediamine (HL1) and N,N-diethylethylenediamine (HL2) are used for the syntheses of three new copper (II) complexes [Cu(HL1)(H2O)Cl]Cl (1), [Cu(L1)Cl] (2) and [Cu(L2)Cl] (3). The single crystal X-ray structures of all the three copper(II) complexes are determined. Redox potentials for the mononuclear complexes are measured by cyclic voltammetry experiments. The DFT and TDDFT results have been used to interpret the experimental properties.

  12. Highly efficient regioselective synthesis, spectroscopic characterizations and DFT calculations of novel hydroxymethylated 1,4-disubstituted-1,2,3-triazole-based sulfonamides

    Science.gov (United States)

    Taheri, Elmira; Mirjafary, Zohreh; Saeidian, Hamid

    2018-04-01

    The novel hydroxymethylated 1,4-disubstituted-1,2,3-triazole-based sulfonamides were synthesized in excellent yields and high regioselectivity via a one-pot, two-step, three-component reaction of N-propargylsulfonamides, sodium azide, and epoxide derivatives under green conditions. Green and mild reaction condition, commercially readily available and inexpensive starting materials, wide scope and easy work-up are the key features of the present method. The Li+ and Na+ ion affinities of the model structure have been also investigated by density functional theory (DFT) studies to find the applicability of these products as ligand in coordination chemistry.

  13. Rose-like I-doped Bi{sub 2}O{sub 2}CO{sub 3} microspheres with enhanced visible light response: DFT calculation, synthesis and photocatalytic performance

    Energy Technology Data Exchange (ETDEWEB)

    Zai, Jiantao; Cao, Fenglei; Liang, Na; Yu, Ke; Tian, Yuan; Sun, Huai; Qian, Xuefeng, E-mail: xfqian@sjtu.edu.cn

    2017-01-05

    Highlights: • DFT reveals I{sup −} can partially substitute CO{sub 3}{sup 2−}to narrow the bandgap of Bi{sub 2}O{sub 2}CO{sub 3}. • Sodium citrate play a key role on the formation of rose-like I-doped Bi{sub 2}O{sub 2}CO{sub 3}. • Rose-like I-doped Bi{sub 2}O{sub 2}CO{sub 3} show enhanced visible light response. • The catalyst has enhanced photocatalytic activity to organic and Cr(VI) pollutes. - Abstract: Based on the crystal structure and the DFT calculation of Bi{sub 2}O{sub 2}CO{sub 3}, I{sup −} can partly replace the CO{sub 3}{sup 2−}in Bi{sub 2}O{sub 2}CO{sub 3} to narrow its bandgap and to enhance its visible light absorption. With this in mind, rose-like I-doped Bi{sub 2}O{sub 2}CO{sub 3} microspheres were prepared via a hydrothermal process. This method can also be extended to synthesize rose-like Cl- or Br-doped Bi{sub 2}O{sub 2}CO{sub 3} microspheres. Photoelectrochemical test supports the DFT calculation result that I- doping narrows the bandgap of Bi{sub 2}O{sub 2}CO{sub 3} by forming two intermediate levels in its forbidden band. Further study reveals that I-doped Bi{sub 2}O{sub 2}CO{sub 3} microspheres with optimized composition exhibit the best photocatalytic activity. Rhodamine B can be completely degraded within 6 min and about 90% of Cr(VI) can be reduced after 25 min under the irradiation of visible light (λ > 400 nm).

  14. Molecular structure and vibrational assignment of 1-[N-(2-pyridyl) aminomethylidene}-2(1H)-Naphtalenone by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations.

    Science.gov (United States)

    Tanak, Hasan; Toy, Mehmet

    2016-01-05

    The molecular geometry and vibrational frequencies of 1-[N-(2-pyridyl)aminomethylidene}-2(1H)-Naphtalenone in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-311++G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. In addition, calculated results are related to the linear correlation plot of computed data versus experimental geometric parameters and IR data. From the results it was concluded that the B3LYP method is superior to the HF method for the vibrational frequencies. Using the time-dependent density functional theory (TD-DFT) and Hartree-Fock (TD-HF) methods, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and experimental ones is determined. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. 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.

  16. 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)....

  17. Spin-dependent structural, electronic and transport properties of armchair graphyne nanoribbons doped with single transition-metal atom, using DFT calculations

    Science.gov (United States)

    Golafrooz Shahri, S.; Roknabadi, M. R.; Radfar, R.

    2017-12-01

    In this present paper, the non-equilibrium Green function (NEGF) method along with the density functional theory (DFT) were used to investigate the effect of doping a single transition-metal atom on transport and electronic properties of armchair graphyne (γ-graphyne) nanoribbons. It can be deduced from the results that among the doped TM atoms, Mn and Fe cause stronger polarized currents comparing to Co and Ni. Mn-AGyNR represents the features of a half-semiconductor and behaves like a semiconductor in both up and down spin channels. On the other hand, Fe-AGyNR shows a great potential in spintronic applications due to its half-metal properties. Also our results show the promising application of armchair graphyne nanoribbons in nano-electrical devices.

  18. Molecular structure, vibrational spectral assignments, HOMO-LUMO, MESP, Mulliken analysis and thermodynamic properties of 2,6-xylenol and 2,5-dimethyl cyclohexanol based on DFT calculation

    Science.gov (United States)

    Arivazhagan, M.; Senthil kumar, J.

    2015-02-01

    The FT-IR and FT-Raman spectra of 2,6-xylenol and 2,5-dimethyl cyclohexanol are recorded in the region 4000-400 cm-1 and 3500-50 cm-1 respectively. The spectral data obtained are assigned to different normal modes by using of comparison with the theoretical values obtained by applying density functional theory (DFT/B3LYP) method with 6-31+G and 6-31++G basis set. The total energy distribution contributions of vibrations modes are distinguished through scaling factors. The calculated HOMO and LUMO energies shows that the charge transfers occur within the molecules. The harmonic frequencies obtained from these two methods are compared. The Mulliken, molecular electrostatic potentials analysis are calculated theoretically.

  19. Study on the adsorption properties of O3, SO2, and SO3 on B-doped graphene using DFT calculations

    International Nuclear Information System (INIS)

    Rad, Ali Shokuhi; Shabestari, Sahand Sadeghi; Mohseni, Soheil; Aghouzi, Samaneh Alijantabar

    2016-01-01

    We investigated the structure, adsorption, electronic states, and charge transfer of O 3 , SO 2 and SO 3 molecules on the surface of a B-doped graphene using density functional theory (DFT). We found weak physisorption of SO 2 (−10.9 kJ/mole, using B3LYP-D) and SO 3 (−15.7 kJ/mole, using B3LYP-D) on the surface of B-doped graphene while there is strong chemisorption for O 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 3 molecule. We noticed some change in hybridizing of boron from sp 2 to sp 3 upon adsorption of O 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 3 molecules while the adsorption of SO 2 and SO 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 3 and physisorption of SO 2 and SO 3 on the surface of B-doped graphene.

  20. Raman spectroscopy studies of temperature induced phase transitions in [N(CH3)3H]CdCl3 and DFT (B3LYP) calculations

    Science.gov (United States)

    Kchaou, H.; Karoui, K.; Bulou, A.; Ben Rhaiem, A.

    2017-04-01

    [N(CH3)3H]CdCl3 between 295 and 433 K possesses four phases. Three phase transition at T1=416 K, T2=373 K and T3=330 K (on heating) and T1=410 K, T2=386 K and T3=322 K (on cooling) was determined by differential scanning calorimetry. Thermal hysteresis of these transitions ΔT1=6 K, ΔT2=13 K and ΔT3=8 K, indicating a first order character. The X-ray diffraction study at room temperature revealed an orthorhombic system with Pbnm space group. The vibrational characteristics have been measured at room temperature by infrared spectroscopy (400-3800 cm-1) and by polarized Raman spectroscopy (10-3800 cm-1) on microcrystals orientated with respect to the organic and inorganic sublattice. The structure of this compound was optimized by density functional theory (DFT) using B3LYP with LanL2DZ and LanL2MB basis sets. The temperature dependence of the Raman line shifts ν and the half-width Δν detect the phase transitions (T1, T2 and T3).

  1. New mixed ligand palladium(II) complexes based on the antiepileptic drug sodium valproate and bioactive nitrogen-donor ligands: Synthesis, structural characterization, binding interactions with DNA and BSA, in vitro cytotoxicity studies and DFT calculations

    Science.gov (United States)

    Tabrizi, Leila; Chiniforoshan, Hossein; Tavakol, Hossein

    2015-04-01

    The complexes [Pd(valp)2(imidazole)2] (1), [Pd(valp)2(pyrazine)2] (2) (valp is sodium valproate) have been synthesized and characterized using IR, 1H NMR, 13C{1H} NMR and UV-Vis spectrometry. The interaction of complexes with CT-DNA has been investigated using spectroscopic tools and viscosity measurement. In each case, the association constant (Kb) was deduced from the absorption spectral study and the number of binding sites (n) and the binding constant (K) were calculated from relevant fluorescence quenching data. As a result, a non-covalent interaction between the metal complex and DNA was suggested, which could be assigned to an intercalative binding. In addition, the interaction of 1 and 2 was ventured with bovine serum albumin (BSA) with the help of absorption and fluorescence spectroscopy measurements. Through these techniques, the apparent association constant (Kapp) and the binding constant (K) could be calculated for each complex. Evaluation of cytotoxic activity of the complexes against four different cancer cell lines proved that the complexes exhibited cytotoxic specificity and significant cancer cell inhibitory rate. Moreover, density functional theory (DFT) calculations were employed to provide more evidence about the observed data. The majority of trans isomers were supported not only by energies, but also by the similarity of its calculated IR frequencies, UV adsorptions and NMR chemical shifts to the experimental values.

  2. DFT calculations of strain and interface effects on electronic structures and magnetic properties of L10-FePt/Ag heterojunction of GMR applications

    Science.gov (United States)

    Pramchu, Sittichain; Jaroenjittichai, Atchara Punya; Laosiritaworn, Yongyut

    2018-03-01

    In this work, density functional theory (DFT) was employed to investigate the effect of strain and interface on electronic structures and magnetic properties of L10-FePt/Ag heterojunction. Two possible interface structures of L10-FePt(001)/Ag(001), that is, interface between Fe and Ag layers (Fe/Ag) and between Pt and Ag layers (Pt/Ag), were inspected. It was found that Pt/Ag interface is more stable than Fe/Ag interface due to its lower formation energy. Further, under the lattice mismatch induced tensile strain, the enhancement of magnetism for both Fe/Ag and Pt/Ag interface structures has been found to have progressed, though the magnetic moments of "interfacial" Fe and Pt atoms have been found to have decreased. To explain this further, the local density of states (LDOS) analysis suggests that interaction between Fe (Pt) and Ag near Fe/Ag (Pt/Ag) interface leads to spin symmetry breaking of the Ag atom and hence induces magnetism magnitude. In contrast, the magnetic moments of interfacial Fe and Pt atoms reduce because of the increase in the electronic states near the Fermi level of the minority-spin electrons. In addition, the significant enhancements of the LDOS near the Fermi levels of the minority-spin electrons signify the boosting of the transport properties of the minority-spin electrons and hence the spin-dependent electron transport at this ferromagnet/metal interface. From this work, it is expected that this clarification of the interfacial magnetism may inspire new innovation on how to improve spin-dependent electron transport for enhancing the giant magnetoresistance (GMR) ratio of potential GMR-based spintronic devices.

  3. DFT calculations of strain and interface effects on electronic structures and magnetic properties of L10-FePt/Ag heterojunction of GMR applications

    Directory of Open Access Journals (Sweden)

    Sittichain Pramchu

    2018-03-01

    Full Text Available In this work, density functional theory (DFT was employed to investigate the effect of strain and interface on electronic structures and magnetic properties of L10-FePt/Ag heterojunction. Two possible interface structures of L10-FePt(001/Ag(001, that is, interface between Fe and Ag layers (Fe/Ag and between Pt and Ag layers (Pt/Ag, were inspected. It was found that Pt/Ag interface is more stable than Fe/Ag interface due to its lower formation energy. Further, under the lattice mismatch induced tensile strain, the enhancement of magnetism for both Fe/Ag and Pt/Ag interface structures has been found to have progressed, though the magnetic moments of “interfacial” Fe and Pt atoms have been found to have decreased. To explain this further, the local density of states (LDOS analysis suggests that interaction between Fe (Pt and Ag near Fe/Ag (Pt/Ag interface leads to spin symmetry breaking of the Ag atom and hence induces magnetism magnitude. In contrast, the magnetic moments of interfacial Fe and Pt atoms reduce because of the increase in the electronic states near the Fermi level of the minority-spin electrons. In addition, the significant enhancements of the LDOS near the Fermi levels of the minority-spin electrons signify the boosting of the transport properties of the minority-spin electrons and hence the spin-dependent electron transport at this ferromagnet/metal interface. From this work, it is expected that this clarification of the interfacial magnetism may inspire new innovation on how to improve spin-dependent electron transport for enhancing the giant magnetoresistance (GMR ratio of potential GMR-based spintronic devices.

  4. A new phosphorescent heteroleptic cuprous complex with a neutral 2-methylquinolin-8-ol ligand: synthesis, structure characterization, properties and TD-DFT calculations.

    Science.gov (United States)

    Shou, Rong Er; Song, Li; Chai, Wen Xiang; Qin, Lai Shun; Wang, Tian Gen

    2017-06-01

    Luminescent Cu I complexes have emerged as promising substitutes for phosphorescent emitters based on Ir, Pt and Os due to their abundance and low cost. The title heteroleptic cuprous complex, [9,9-dimethyl-4,5-bis(diphenylphosphanyl)-9H-xanthene-κ 2 P,P](2-methylquinolin-8-ol-κ 2 N,O)copper(I) hexafluorophosphate, [Cu(C 10 H 9 NO)(C 39 H 32 OP 2 )]PF 6 , conventionally abbreviated as [Cu(Xantphos)(8-HOXQ)]PF 6 , where Xantphos is the chelating diphosphine ligand 9,9-dimethyl-4,5-bis(diphenylphosphanyl)-9H-xanthene and 8-HOXQ is the N,O-chelating ligand 2-methylquinolin-8-ol that remains protonated at the hydroxy O atom, is described. In this complex, the asymmetric unit consists of a hexafluorophosphate anion and a whole mononuclear cation, where the Cu I atom is coordinated by two P atoms from the Xantphos ligand and by the N and O atoms from the 8-HOXQ ligand, giving rise to a tetrahedral CuP 2 NO coordination geometry. The electronic absorption and photoluminescence properties of this complex have been studied on as-synthesized samples, whose purity had been determined by powder X-ray diffraction. In the detailed TD-DFT (time-dependent density functional theory) studies, the yellow emission appears to be derived from the inter-ligand charge transfer and metal-to-ligand charge transfer (M+L')→LCT excited state (LCT is ligand charge transfer).

  5. 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.

  6. 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.

  7. Synthesis, DFT band structure calculations, optical and photoelectrical characterizations of the novel 5-hydroxy-4-methoxy-7-oxo-7H-furo[3,2-g]chromene-6-carbonitrile (HMOFCC)

    Science.gov (United States)

    Ibrahim, Magdy A.; Halim, Shimaa Abdel; Roushdy, N.; Farag, A. A. M.; El-Gohary, Nasser M.

    2017-11-01

    Reaction of 4-methoxy-5-oxo-5H-furo[3,2-g]chromene-6-carboxaldehyde (1) with hydroxylamine hydrochloride resulted in ring transformation producing the novel 5-hydroxy-4-methoxy-7-oxo-7H-furo[3,2-g]chromene-6-carbonitrile (HMOFCC). The structure was deduced based on its correct elemental analysis and spectral data (IR, 1H NMR, 13C NMR and mass spectra). The geometries of the HMOFCC were completely optimized by means of DFT-B3LYP/6-311++G (d,p) theoretical level. The ground state properties such as; total energy, the energy of HOMO and LUMO and Mulliken atomic charges were also determined. In addition, the two solvents; polar (methanol) and nonpolar (dioxane) were utilized to extract the electronic absorption spectra. The assignment of the detected bands was discussed by TD-DFT calculations. A cauliflower-like, as well as, needle-like leaves morphologies were observed using scanning electron microscope images. Two direct optical band gaps were extracted from the photon energy dependence of absorption coefficient at the band edges and found to be 1.16 and 2.56 eV. A characteristic emission peak of photoluminescence spectrum was observed and shifted depending on the solvent type. A remarkable rectification characteristic of HMOFCC/p-Si heterojunction confirms the diode-like behavior. The main important parameters like series resistance, shunt resistance and reverse saturation current show illumination dependence under influence of the illumination intensity range 20-100 mW/cm2. The heterojunction based HMOFCC showed phototransient properties under various illumination intensities which give the recommendation for the studied heterojunction in the field of optoelectronic device application.

  8. 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.

  9. 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...

  10. Electronic Structure, Optical and Transport Properties of Double Perovskite La2NbMnO6: A Theoretical Understanding from DFT Calculations

    Science.gov (United States)

    Parrey, Khursheed Ahmad; Khandy, Shakeel Ahmad; Islam, Ishtihadah; Laref, Amel; Gupta, Dinesh C.; Niazi, Asad; Aziz, Anver; Ansari, S. G.; Khenata, R.; Rubab, Seemin

    2018-03-01

    Double perovskite La2NbMnO6 was systematically studied using the first-principles calculations. The structural, electronic, optical and transport properties of this compound were calculated. Spin resolved band structure predicted this material as a half-metal with an energy gap of 3.75 eV in spin down state. The optical coefficients including optical conductivity, reflectivity and electron energy loss are calculated for photon energy up to 30.00 eV to understand the optical response of this perovskite. The strong absorption of all the ultraviolet and infrared frequencies of the spectrum by this material may suggest the potential application of this material for the optoelectronic devices in ultraviolet and infra-red region. Also, the thermoelectric properties with a speculation from the half-metallic electronic structure are reported. Subsequently, the Seebeck coefficient, electrical and thermal conductivity coefficients are calculated to predict the thermoelectric figure of merit (zT), the maximum of which is found out to be 0.14 at 800 K.

  11. Evaluation of uncertainty of ideal-gas entropy and heat capacity calculations by density functional theory (DFT) for molecules containing symmetrical internal rotors

    Czech Academy of Sciences Publication Activity Database

    Červinka, C.; Fulem, Michal; Růžička, K.

    2013-01-01

    Roč. 58, č. 5 (2013), s. 1382-1390 ISSN 0021-9568 Institutional support: RVO:68378271 Keywords : chemical thermodynamic properties * ab-initio calculation * vapor-pressure * xylene isomerization * organic -compounds * hindered rotation * methyl-groups * vaporization Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.045, year: 2013

  12. Dimethyl methylphosphonate adsorption and decomposition on MoO2 as studied by ambient pressure x-ray photoelectron spectroscopy and DFT calculations

    Science.gov (United States)

    Head, Ashley R.; Tsyshevsky, Roman; Trotochaud, Lena; Yu, Yi; Karslıoǧlu, Osman; Eichhorn, Bryan; Kuklja, Maija M.; Bluhm, Hendrik

    2018-04-01

    Organophosphonates range in their toxicity and are used as pesticides, herbicides, and chemical warfare agents (CWAs). Few laboratories are equipped to handle the most toxic molecules, thus simulants such as dimethyl methylphosphonate (DMMP), are used as a first step in studying adsorption and reactivity on materials. Benchmarked by combined experimental and theoretical studies of simulants, calculations offer an opportunity to understand how molecular interactions with a surface changes upon using a CWA. However, most calculations of DMMP and CWAs on surfaces are limited to adsorption studies on clusters of atoms, which may differ markedly from the behavior on bulk solid-state materials with extended surfaces. We have benchmarked our solid-state periodic calculations of DMMP adsorption and reactivity on MoO2 with ambient pressure x-ray photoelectron spectroscopy studies (APXPS). DMMP is found to interact strongly with a MoO2 film, a model system for the MoO x component in the ASZM-TEDA© gas filtration material. Density functional theory modeling of several adsorption and decomposition mechanisms assist the assignment of APXPS peaks. Our results show that some of the adsorbed DMMP decomposes, with all the products remaining on the surface. The rigorous calculations benchmarked with experiments pave a path to reliable and predictive theoretical studies of CWA interactions with surfaces.

  13. Inelastic and elastic neutron scattering studies of the vibrational and reorientational dynamics, crystal structure and solid-solid phase transition in [Mn(OS(CH₃)₂)₆](ClO₄)₂ supported by theoretical (DFT) calculations.

    Science.gov (United States)

    Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna

    2015-06-15

    The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5(c)=222.9K on cooling and at TC5(h)=225.4K on heating) the CH3 groups perform fast (τR≈10(-12)-10(-13)s) reorientational motions. These motions start to slow down below TC5(c) Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6](2+) cation and ClO4(-) anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. 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.

  15. Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: Correlated ab initio quantum-chemical, DFT and empirical calculations

    Czech Academy of Sciences Publication Activity Database

    Dobeš, Petr; Otyepka, M.; Strnad, Miroslav; Hobza, Pavel

    2006-01-01

    Roč. 12, č. 16 (2006), s. 4297-4304 ISSN 0947-6539 R&D Projects: GA ČR(CZ) GA203/05/0009; GA ČR(CZ) GA301/05/0418; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50380511 Keywords : ab initio calculations * cyclin -dependent kinase * roscovitine Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.015, year: 2006

  16. 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.

  17. Description of adenine and cytosine on Au(111) nano surface using different DFT functionals (PW91PW91, wB97XD, M06-2X, M06-L and CAM-B3LYP) in the framework of ONIOM scheme: Non-periodic calculations

    Science.gov (United States)

    Farrokhpour, Hossein; Jouypazadeh, Hamidreza

    2017-05-01

    In this work, the adsorption of the adenine (AD) and cytosine (CY) on the Au(111) nano surface (AD@Au and CY@Au) have been examined in the framework of combined quantum mechanics/molecular mechanics (QM/MM) methodology using two-layer ONIOM method and different density functional theory (DFT) functionals in the absence of periodic boundary conditions (PBC). It was found by selecting an appropriate size for the Au surface, the results obtained using QM/MM method were in good agreement with those obtained via the periodic DFT calculations with the same functional. The calculated adsorption energies (Ead) using M06-2X and M06-L functional were in good agreement with those, recently, obtained using periodic DFT calculations considering PBC and employing van der Waals (vdW) DFT functionals. The correlation diagram between the molecular orbitals of isolated deformed AD (AD-D) and CY (CY-D) and their molecular orbitals in AD@Au and CY@Au systems have also been investigated in this work.

  18. Elucidating adsorption mechanisms of phthalate esters upon carbon nanotubes/graphene and natural organic acid competitive effects in water by DFT and MD calculations

    International Nuclear Information System (INIS)

    Wang, Zhuang; Wang, Se; Chen, Min Dong; Xu, Defu; Tang, Lili; Wang, Degao

    2015-01-01

    Simulations at multiple levels were performed to investigate the aqueous adsorption of phthalate esters (PAEs) on carbon nanoparticles and to find the competitive effect of a low molecular weight natural organic acid (benzoic acid) on the adsorption process. Six PAEs of varying alkyl side chain lengths and three carbon-based nanomaterials including a single-walled carbon nanotube (SWNT), double-walled carbon nanotube (DWNT), and graphene (G) were studied. Results showed that the adsorption energies calculated using density functional theory increase with increasing length of the PAE alkyl chain. G exhibits higher adsorption capacity for the PAEs than SWNT and DWNT. The absolute adsorption energies of these systems also display a positive linear correlation with the hydrophobicity of the PAE molecules. Molecular dynamics simulations indicate that the presence of neutral/anionic benzoic acid in water alleviates the PAE adsorption. Furthermore, anionic benzoic acid exerts more impact on the PAE adsorption than the neutral form

  19. Interface charge transfer and enhanced visible light response of graphene/anatase TiO2 (110) systems with and without oxygen vacancy: A DFT+U calculation

    Science.gov (United States)

    Zhang, Hua-Xi; Zhu, Yong Fu; Zhao, Ming

    2017-10-01

    Interactions between graphene and anatase TiO2 (110) surface with and without oxygen vacancy (VO) are investigated by first-principle calculations. The close but non-destroyed contact at interface facilitates photo-excited electron transfer between graphene and TiO2. With a work function (WF) smaller than perfect TiO2 substrate, graphene is typically electron depleted. However, the introduction of surface VO decreases the WF of TiO2 remarkably and smaller than graphene, which induces electron transfer with reversed direction and accumulate at graphene sheet. Especially, the evident red shift of the optical absorption edge and obviously enhanced absorption intensity in the visible region for both combined configurations illustrate the enhancement mechanism of photocatalytic performance.

  20. The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations

    Science.gov (United States)

    Li, Yin; Lukács, András; Bordács, Sándor; Móczár, János; Nyitrai, Miklós; Hebling, János

    2018-02-01

    Low-frequency modes of L-Asp and L-Asn were studied in the range from 0.1 to 3.0 THz using time-domain Terahertz spectroscopy and density functional theory calculation. The results show that PBE-D2 shows more success than BLYP-D2 in prediction of THz absorption spectra. To compare their low-frequency modes, we adopted ;vibrational character ID strips; proposed by Schmuttenmaer and coworkers [Journal of Physical Chemistry B, 117, 10444(2013)]. We found that the most intense THz absorption peaks of two compounds both involve severe distortion of their hydrogen bonding networks. Due to less rigid hydrogen bonding network in L-Asp, the side chain (carboxyl group) of L-Asp exhibits larger motions than that (carboxamide group) of L-Asn in low-frequency modes.

  1. DFT calculations of the charged states of N@C60 and Fe4 single molecule magnets investigated in tunneling spectroscopy

    Science.gov (United States)

    Nossa, Javier; Islam, Fhokrul; Canali, Carlo; Pederson, Mark

    2012-02-01

    For device applications of single molecule magnets (SMMs) in high-density information storage and quantum-state control it is essential that the magnetic properties of the molecules remain stable under the influence of metallic contacts or surface environment. Recent tunneling experiments [1, 2] on N@C60 and Fe4 SMM have shown that these molecules preserve their magnetic characteristics when they are used as the central island of single-electron transistors. Although quantum spin models have been used extensively to study theoretically tunneling spectroscopy of SMMs, it has been shown recently that the orbital degrees of freedom, which is absent in spin models, can significantly affect the tunneling conductance [3]. In this work we present first-principles calculations of the neutral and charged states of N@C60 and Fe4 SMMs, and discuss a strategy to include their properties into a theory of quantum transport. We also present results of the magnetic anisotropy for the different charge states of Fe4 and discuss their relevance for experiments [2] in the sequential tunneling and cotunnelling regimes. [4pt] [1]. N. Roch et al., Phys. Rev. B 83, 081407 (2011). [0pt] [2]. A.S. Zyazin et al., Nano Lett. 10, 3307 (2010). [0pt] [3]. L. Michalak et al., Phys. Rev. Lett. 104, 017202 (2010).

  2. Formic acid decomposition on Pt1/Cu (111) single platinum atom catalyst: Insights from DFT calculations and energetic span model analysis

    Science.gov (United States)

    Wang, Ying-Fan; Li, Kun; Wang, Gui-Chang

    2018-04-01

    Inspired by the recent surface experimental results that the monatomic Pt catalysts has more excellent hydrogen production that Cu(111) surface, the mechanism of decomposition of formic acid on Cu(111) and single atom Pt1/Cu(111) surface was studied by periodic density functional theory calculations in the present work. The results show that the formic acid tends to undergo dehydrogenation on both surfaces to obtain the hydrogen product of the target product, and the selectivity and catalytic activity of Pt1/Cu (111) surface for formic acid dehydrogenation are better. The reason is that the single atom Pt1/Cu(111) catalyst reduces the reaction energy barrier (i.e., HCOO → CO2 + H) of the critical step of the dehydrogenation reaction due to the fact that the single atom Pt1/Cu(111) catalyst binds formate weakly compared to that of Cu (111) one. Moreover, it was found that the Pt1/Cu (111) binds CO more strongly than that of Cu (111) one and thus leading to the difficult for the formation of CO. These two factors would make the single Pt atom catalyst had the high selectivity for the H2 production. It is hoped that the present work may help people to design the efficient H2 production from HCOOH decomposition by reduce the surface binding strength of HCOO species, for example, using the low coordination number active site like single atom or other related catalytic system.

  3. Catalytic activity of gold nanoclusters supported by cerium oxide: interplay between cluster reactivity, size, and interface charge transfer revealed by DFT calculations

    Science.gov (United States)

    Fabris, Stefano; Farnesi Camellone, Matteo

    2010-03-01

    The parameters controlling the catalytic activity of oxide-supported Au atoms and clusters are studied by means of density functional theory calculations. CeO2(111) surfaces containing positively charged Au ions, either as supported Au^+ or as substitutional Au^3+ ions, are shown to activate molecular CO and to catalyze its oxidation to CO2 via participation of lattice O. For the Au^+ adatoms, the limiting rate is determined by the adsorbate spillover. The reaction proceeds with CO oxidation via O vacancy formation. These vacancies readily attract the Au^+ adatoms, turn them into negatively charged Au^δ- adspecies that prevent further CO adsorption, thus deactivating the catalyst. The reactivity of gold nanoparticles nucleated at O vacancies can be recovered for cluster sizes as small as Au2. Substitutional Au3+ ions dispersed into the ceria lattice can instead sustain a full catalytic cycle maintaining their charge state and activity along the reaction process. The interplay between the reversible Ce^4+/Ce^3+ and Au^3+/Au^+ redox couples underpins the high catalytic activity of dispersed Au atoms into the ceria substrate. Ab-initio surface thermodynamics is used to investigate the stability of different solid solutions and to predict more reactive catalysts.

  4. DFT and ENDOR Study of Bixin Radical Cations and Neutral Radicals on Silica-Alumina.

    Science.gov (United States)

    Tay-Agbozo, Sefadzi S; Krzyaniak, Matthew D; Bowman, Michael K; Street, Shane; Kispert, Lowell D

    2015-06-18

    Bixin, a carotenoid found in annatto (Bixa orellana), is unique among natural carotenoids by being water-soluble. We stabilized free radicals from bixin on the surface of silica-alumina (Si-Al) and characterized them by pulsed electron-nuclear double resonance (ENDOR). DFT calculations of unpaired electron spin distribution for various bixin radicals predict the EPR hyperfine couplings. Least-square fitting of experimental ENDOR spectra by spectra calculated from DFT hyperfine couplings characterized the radicals trapped on Si-Al. DFT predicts that the trans bixin radical cation is more stable than the cis bixin radical cation by 1.26 kcal/mol. This small energy difference is consistent with the 26% trans and 23% cis radical cations in the ENDOR spectrum. The remainder of the ENDOR spectrum is due to several neutral radicals formed by loss of a H(+) ion from the 9, 9', 13, or 13' methyl group, a common occurrence in all water-insoluble carotenoids previously studied. Although carboxyl groups of bixin strongly affect its solubility relative to other natural carotenoids, they do not alter properties of its free radicals based on DFT calculations and EPR measurements which remain similar to typical water-insoluble carotenoids.

  5. Synthesis, DFT calculations of structure, vibrational and thermal decomposition studies of the metal complex Pb[Mn(C3H2O4)2(H2O)2].

    Science.gov (United States)

    Gil, Diego M; Carbonio, Raúl E; Gómez, María Inés

    2015-04-15

    The metallo-organic complex Pb[Mn(C3H2O4)2(H2O)2] was synthesized and characterized by IR and Raman spectroscopy and powder X-ray diffraction methods. The cell parameters for the complex were determined from powder X-ray diffraction using the autoindexing program TREOR, and refined by the Le Bail method with the Fullprof program. A hexagonal unit cell was determined with a=b=13.8366(7)Å, c=9.1454(1)Å, γ=120°. The DFT calculated geometry of the complex anion [Mn(C3H2O4)2(H2O)2](2-) is very close to the experimental data reported for similar systems. The IR and Raman spectra and the thermal analysis of the complex indicate that only one type of water molecules is present in the structure. The thermal decomposition of Pb[Mn(C3H2O4)2(H2O)2] at 700 °C in air produces PbO and Pb2MnO4 as final products. The crystal structure of the mixed oxide is very similar to that reported for Pb3O4. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. [Fe(F20 TPP)Cl]-catalyzed amination with arylamines and {[Fe(F20 TPP)(NAr)](PhI=NAr)} + . Intermediate assessed by high-resolution ESI-MS and DFT calculations.

    Science.gov (United States)

    Liu, Yungen; Chen, Guo-Qiang; Tse, Chun-Wai; Guan, Xianguo; Xu, Zheng-Jiang; Huang, Jie-Sheng; Che, Chi-Ming

    2015-01-01

    Amination of CH bonds catalyzed by transition metal complexes via nitrene/imide insertion is an appealing strategy for CN bond formation, and the use of iminoiodinanes, or their in situ generated forms from 'PhI(OAc)2 +primary amides (such as sulfonamides, sulfamates, and carbamates)', as nitrogen sources for the amination reaction has been well documented. In this work, a 'metal catalyst+PhI(OAc)2 +primary arylamines' amination protocol has been developed using [Fe(F20 TPP)Cl] (H2 F20 TPP=meso-tetrakis(pentafluorophenyl)porphyrin) as a catalyst. This catalytic method is applicable for both intra- and intermolecular amination of sp(2) and sp(3) CH bonds (>27 examples), affording the amination products, including natural products such as rutaecarpine, in moderate-to-good yields. ESI-MS analysis and DFT calculations lend support for the involvement of {[Fe(F20 TPP)(NC6 H4 -p-NO2 )](PhI=NC6 H4 -p-NO2 )} + . intermediate in the catalysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Synthesis, structural characterization, thermal analysis, and DFT calculation of a novel zinc (II)-trifluoro-β-diketonate 3D supramolecular nano organic-inorganic compound with 1,3,5-triazine derivative

    Energy Technology Data Exchange (ETDEWEB)

    Mirtamizdoust, Babak, E-mail: babakm.tamizdoust@gmail.com [Department of Chemistry, Yasouj University, Yasouj, 75918-74831 (Iran, Islamic Republic of); Department of Chemistry, Faculty of Science, University of Qom, PO Box 37185-359, Qom, Islamic Republic of Iran (Iran, Islamic Republic of); Ghaedi, Mehrorang [Department of Chemistry, Yasouj University, Yasouj, 75918-74831 (Iran, Islamic Republic of); Hanifehpour, Younes, E-mail: y_hanifehpour@yu.ac.kr [School of Mechanical Engineering, WCU Nano Research Center, Yeungnam University, Gyongsan, 712-749 (Korea, Republic of); Mague, Joel T. [Department of Chemistry, Tulane University, New Orleans (United States); Joo, Sang Woo, E-mail: swjoo1@gmail.com [School of Mechanical Engineering, WCU Nano Research Center, Yeungnam University, Gyongsan, 712-749 (Korea, Republic of)

    2016-10-01

    A sonochemical method was used to synthesize a novel nano-structure of a zinc(II) organic-inorganic compound [Zn(dapt){sub 2}(ttfa){sub 2}] (1) [dapt = 2,4-diamino-6-phenyl-1,3,5-triazine and ttfa = 2-thenoyltrifluoroacetonate]. The new nanostructure was characterized by scanning electron microscopy, X-ray powder diffraction, elemental analysis, and thermal analysis. The single-crystal X-ray structure shows that 1 is a discrete coordination compound. Strong intra- and intermolecular hydrogen bonds are observed in the structure with the latter forming chains of molecules running parallel to (110). The chains are further extended into a three-dimensional supramolecular structure by intermolecular C−F⋯π interactions between trifluoromethyl and triazine moieties. The coordination number of the zinc(II) ion is six (ZnN{sub 2}O{sub 4}), and the coordination sphere is tetragonally elongated octahedral. The structure of the title complex was optimized by DFT calculations. - Highlights: • A new zinc(II) 3D coordination supramolecular compound was synthesized. • Ultrasound synthesis of nano coordination compound have been reported. • The X-ray crystal structure of the compound is reported.

  8. Synthesis, DFT calculations, spectroscopic and photovoltaic of the novel N″, N‴-bis[(4,9-dimethoxy-5-oxo-5H-furo[3,2-g]chromen-6-yl)methylidene] thiocarbonohydrazide (BFCMT) and its photodiode application

    Science.gov (United States)

    Farag, A. A. M.; Ibrahim, Magdy A.; Halim, Shimaa Abdel; Roushdy, N.; El-Gohary, Nasser M.

    2018-03-01

    Condensation reaction of 6-formylkhellin (1) with thiocarbohydrazide in 2:1 M ratio afforded the novel N″, N‴-bis [(4, 9-dimethoxy-5-oxo-5H-furo [3,2-g]chromen-6-yl) methylidene]thiocarbonohydrazide (BFCMT) and its electronic absorption spectrum was interpreted by TD-DFT calculations. The electronic transition is direct allowed with onset and fundamental energy gaps of 1.06 and 3.36 eV, respectively. The estimated optical constants were applied to evaluate the optical transition type as well as the effective optical parameters. The current density-voltage characteristics of BFCMT/p-Si heterojunction at 300 K in dark and under illumination of 100 mW/cm2 showed rectifying characteristics. The capacitance-voltage characteristic parameters under illumination showed a reduction in the built-in potential and increasing the active carrier concentration. The loaded J-V characteristics of BFCMT/p-Si heterojunction under illumination were investigated and showed a remarkable power conversion efficiency of 0.83% without consideration of the refection correction or losses from the upper electrode absorption.

  9. NMR spectroscopic characterization and DFT calculations of zirconium(IV)-3,3'-Br2-BINOLate and related complexes used in an enantioselective Friedel-Crafts alkylation of indoles with α,β-unsaturated ketones.

    Science.gov (United States)

    Blay, Gonzalo; Cano, Joan; Cardona, Luz; Fernández, Isabel; Muñoz, M Carmen; Pedro, José R; Vila, Carlos

    2012-12-07

    Experimental and theoretical studies on the structure of several complexes based on (R)-3,3'-Br(2)-BINOL ligand and group (IV) metals used as catalysts in an enantioselective Friedel-Crafts alkylation of indoles with α,β-unsaturated ketones have been carried out. NMR spectroscopic studies of these catalysts have been performed, which suggested that at room temperature the catalysts would form a monomeric structure in the case of Ti(IV) and a dimeric structure in the cases of Zr(IV) and Hf(IV). Density functional theory (DFT) calculations clearly corroborate the conclusions of these experimental spectroscopic studies. The dimeric structure with a doubly bridged motif [Zr(IV)(2)(μ-(R)-3,3'-Br(2)-BINOL)(2)] where each binaphthol ligand acts as bridge between the metal centers (Novak's model) is more stable than the dimeric structure with a doubly bridged motif [Zr(IV)(2)(μ-O(t)Bu)(2)] where the tert-butoxide groups act as bridging ligands (Kobayashi's model). The scope of the Friedel-Crafts alkylation with regard to the indole structure has been studied. Finally a plausible mechanism for the Friedel-Crafts reaction and a stereomodel for the mode of action of the catalyst that explain the observed stereochemistry of the reaction products have been proposed.

  10. 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.

  11. 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.

  12. Rate coefficients of the CF3CHFCF3 + H → CF3CFCF3 + H2 reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths.

    Science.gov (United States)

    Ng, Maggie; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M

    2013-03-15

    The minimum energy path (MEP) of the reaction, CF(3)CHFCF(3) + H → transition state (TS) → CF(3)CFCF(3) + H(2), has been computed at different ab initio levels and with density functional theory (DFT) using different functionals. The computed B3LYP/6-31++G**, BH&HLYP/cc-pVDZ, BMK/6-31++G**, M05/6-31+G**, M05-2X/6-31+G**, UMP2/6-31++G**, PUMP2/6-31++G**//UMP2/6-31++G**, RCCSD(T)/aug-cc-pVDZ//UMP2/6-31++G**, RCCSD(T)/aug-cc-pVTZ(spd,sp)//UMP2//6-31++G**, RCCSD(T)/CBS//M05/6-31+G**, and RCCSD(T)/CBS//UMP2/6-31++G** MEPs, and associated gradients and Hessians, were used in reaction rate coefficient calculations based on the transition state theory (TST). Reaction rate coefficients were computed between 300 and 1500 K at various levels of TST, which include conventional TST, canonical variational TST (CVT) and improved CVT (ICVT), and with different tunneling corrections, namely, Wigner, zero-curvature, and small-curvature (SCT). The computed rate coefficients obtained at different ab initio, DFT and TST levels are compared with experimental values available in the 1000-1200 K temperature range. Based on the rate coefficients computed at the ICVT/SCT level, the highest TST level used in this study, the BH&HLYP functional performs best among all the functionals used, while the RCCSD(T)/CBS//MP2/6-31++G** level is the best among all the ab initio levels used. Comparing computed reaction rate coefficients obtained at different levels of theory shows that, the computed barrier height has the strongest effect on the computed reaction rate coefficients as expected. Variational effects on the computed rate coefficients are found to be negligibly small. Although tunneling effects are relatively small at high temperatures (~1500 K), SCT corrections are significant at low temperatures (~300 K), and both barrier heights and the magnitudes of the imaginary frequencies affect SCT corrections. Copyright © 2012 Wiley Periodicals, Inc.

  13. 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.

  14. DFT Methods to Study the Reaction Mechanism of Iridium-Catalyzed Hydrogenation of Olefins: Which Functional Should be Chosen?

    Science.gov (United States)

    Sun, Yihua; Chen, Hui

    2016-01-04

    To enable the selection of more accurate computational methods for the future theoretical exploration of the reaction mechanism of Ir-catalyzed olefin hydrogenation, we compared high-level ab initio coupled cluster and DFT calculations with a simplified model of Pfaltz's Ir/P,N-type catalyst for all four previously proposed Ir(I) /Ir(III) and Ir(III) /Ir(V) mechanisms. Through the systematic assessment of the DFT performances, the DFT empirical dispersion correction (DFT-D3) is found to be indispensable for improving the accuracy of relative energies between the Ir(I) /Ir(III) and Ir(III) /Ir(V) mechanisms. After including the DFT-D3 correction, the three best performing density functionals (DFs) are B2-PLYP, BP86, and TPSSh. In these recommended DFs, the computationally more expensive double-hybrid functional B2-PLYP-D3 has a balanced and outstanding performance for calculations of the reaction barriers, reaction energies, and energy gaps between different mechanisms, whereas the less costly BP86-D3 and TPSSh-D3 methods have outstanding, but relatively less uniform performances. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Plane-Wave DFT Methods for Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Bylaska, Eric J.

    2017-08-01

    A detailed description of modern plane-wave DFT methods and software (contained in the NWChem package) are described that allow for both geometry optimization and ab initio molecular dynamics simulations. Significant emphasis is placed on aspects of these methods that are of interest to computational chemists and useful for simulating chemistry, including techniques for calculating charged systems, exact exchange (i.e. hybrid DFT methods), and highly efficient AIMD/MM methods. Sample applications on the structure of the goethite+water interface and the hydrolysis of nitroaromatic molecules are described.

  16. Investigating actinide compounds within a hybrid MCSCF-DFT model

    International Nuclear Information System (INIS)

    Fromager, E.; Jensen, H.J.A.; Wahlin, P.; Real, F.; Wahlgren, U.

    2007-01-01

    definition of an optimal μ opt parameter [3], independent of the approximate short-range functional and the approximate (MCSCF) wave function, is applied in this work. Recently reviewed calculations on light elements yielded μ opt ∼ 0.4 a.u [3], which is in agreement with previous calibration studies. A new numerical investigation of μ opt is now presented for actinides. A test set consisting of ThO 2 , PaO 2 + , UO 2 2+ , UCO and UN 2 (representing cases without significant static correlation) as well as NpO 2 3+ and PuO 2 4+ (representing cases with significant static correlation) has been considered. The bending problem of NpO 2 3+ and PuO 2 4+ observed in KS-DFT(B3LYP) is then addressed within the hybrid MCSCF-DFT approach. Calculations have been performed at the scalar relativistic level with the MCSCF-DFT code [4] implemented in a development version of the DALTON program package [5], using short-range LDA and PBE-type functionals [3. References [1] M. Straka, K.G. Dyall, and P. Pyykko, Theor. Chem. Acc., 106, 393 (2001); [2] A. Savin, in Recent Developments and Applications of Modern Density Functional Theory, edited by J.M. Seminario (Elsevier, Amsterdam, 1996), p. 327; [3] E. Fromager, J. Toulouse, and H. J. Aa. Jensen, J. Chem. Phys., in press; [4] J.K. Pedersen and H.J.A. Jensen, J. Chem. Phys., submitted; [5] T. Helgaker, H.J. Aa. Jensen, P. Jorgensen, J. Oelsen, K. Ruud, H. Agren, K.L. Bak, V. Bakken, O. Christiansen, S. Coriani, et al., Dalton release 2.0 (2005), an electronic structure program, www.kjemi.uio.no/software/dalton/dalton.html

  17. 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.

  18. 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

    2017-04-05

    The solid state photolysis of sodium, silver and thallium hyponitrite (M 2 N 2 O 2 , M=Na, Ag, Tl) salts and a binuclear complex of cobalt bridged by hyponitrite ([Co(NH 3 ) 5 -N(O)-NO-Co(NH 3 ) 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 340-460nm light and with the 488nm laser line generates photolysis only in silver and thallium hyponitrite salts, while 253.7nm light photolyzed all the studied compounds. Infrared spectroscopy was used to follow the photolysis process and to identify the generated products. Remarkably, gaseous N 2 O was detected after photolysis in the infrared spectra of sodium, silver, and thallium hyponitrite KBr pellets. The spectra for [Co(NH 3 ) 5 -N(O)-NO-Co(NH 3 ) 5 ] 4+ suggest that one cobalt ion remains bonded to N 2 O from which the generation of a [(NH 3 ) 5 CoNNO] +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 CO 2 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 N 2 O generation. Predicted and experimental data are in very good agreement. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. 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

  20. Unprecedented .pi. ... .pi. interaction between an aromatic ring and a pseudo-aromatic ring formed through intramolecular H-bonding in a bidentate Schiff base ligand: crystal structure and DFT calculations

    Czech Academy of Sciences Publication Activity Database

    Dutta, A.; Jana, A. D.; Gangopadhyay, S.; Das, K. K.; Marek, J.; Marek, R.; Brus, Jiří; Ali, M.

    2011-01-01

    Roč. 13, č. 35 (2011), s. 15845-15853 ISSN 1463-9076 Institutional research plan: CEZ:AV0Z40500505 Keywords : X-Ray diffraction * ss-NMR * DFT Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.573, year: 2011

  1. Microwave-assisted synthesis of mixed ligands organotin(IV) complexes of 1,10-phenanthroline and l-proline: Physicochemical characterization, DFT calculations, chemotherapeutic potential validation by in vitro DNA binding and nuclease activity.

    Science.gov (United States)

    Nath, Mala; Mridula; Kumari, Ranjana

    2017-09-01

    Diorganotin(IV) and triphenyltin(IV) derivatives of L-proline (HPro) having general formula R 2 Sn(Pro) 2 (R=n-Bu (1), Ph (2)) and Ph 3 Sn(Pro) (3), respectively, and the mixed ligands di-/triorganotin(IV) derivatives of L-proline and 1,10-phenanthroline (phen) with general formula [R 2 Sn(Pro)(Phen)Cl] and [R 3 Sn(Pro)(Phen)] (where R=Me (4 and 7), n-Bu (5 and 8), Ph (6 and 9)), respectively, have been synthesized by microwave-assisted method and characterized by elemental analysis, IR, NMR ( 1 H, 13 C and 119 Sn) and DART-mass spectral studies. The results suggest bicapped tetrahedron or a skew trapezoidal-bipyramid geometry for R 2 Sn(Pro) 2 , a distorted tetrahedral geometry for Ph 3 Sn(Pro) and a distorted octahedral geometry for [R 2 Sn(Pro)(Phen)Cl] and [Ph 3 Sn(Pro)(Phen)] around the Sn atom, and the same has been validated by density functional theory calculations (DFT). In vitro DNA binding studies of 1-9 have been investigated by UV-Vis, fluorescence and circular dichroism titrations, viscosity and DNA melting experiments. The observed hypochromic shift in UV-Vis and fluorescence studies evidenced a partial intercalative mode of binding of complexes to CT-DNA. The binding affinity and quenching ability have been quantified in terms of intrinsic binding constant (K b ) and Stern-Volmer quenching constant (Ksv). The determined values suggest that di- and triorganotin(IV) derivatives of L-proline possess lesser affinity to bind with CT-DNA in comparison to the mixed ligands di-/triorganotin(IV) derivatives of L-proline and 1,10-phenanthroline. The partial intercalative mode of binding of these complexes with CT DNA has also been supported by a change in the viscosity and melting point of DNA as well as a change in the intensity of positive and negative bands in circular dichroism spectra. The cleavage studies by agarose gel electrophoresis indicate effective cleavage of supercoiled plasmid DNA into its nicked form by all the complexes and even to its linear

  2. 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.

  3. 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

  4. OH-initiated transformation and hydrolysis of aspirin in AOPs system: DFT and experimental studies.

    Science.gov (United States)

    He, Lin; Sun, Xiaomin; Zhu, Fanping; Ren, Shaojie; Wang, Shuguang

    2017-08-15

    Advanced oxidation processes (AOPs) are widely used in wastewater treatment of pharmaceutical and personal care products (PPCPs). In this work, the OH-initiated transformation as well as the hydrolysis of a typical PPCPs, aspirin, was investigated using density functional theory (DFT) calculations and laboratory experiments. For DFT calculations, the frontier electron densities and bond dissociation energies were analyzed. Profiles of the potential energy surface were constructed, and all the possible pathways were discussed. Additionally, rate constants for each pathway were calculated with transition state theory (TST) method. UV/H 2 O 2 experiments of aspirin were performed and degradation intermediates were identified by UPLC-MS-MS analysis. Different findings from previous experimental works were reported that the H-abstraction pathways at methyl position were dominated and OH-addition pathways on benzene ring were also favored. Meantime, hydroxyl ASA was confirmed as the main stable intermediate. Moreover, it was the first time to use DFT method to investigate the hydrolysis mechanisms of organic ester compound. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Evolution of DFT studies in view of a scientometric perspective.

    Science.gov (United States)

    Haunschild, Robin; Barth, Andreas; Marx, Werner

    2016-01-01

    This bibliometric study aims to analyze the publications in which density functional theory (DFT) plays a major role. The bibliometric analysis is performed on the full publication volume of 114,138 publications as well as sub-sets defined in terms of six different types of compounds and nine different research topics. Also, a compound analysis is presented that shows how many compounds with specific elements are known to be calculated with DFT. This analysis is done for each element from hydrogen to nobelium. We find that hydrogen, carbon, nitrogen, and oxygen occur most often in compounds calculated with DFT in terms of absolute numbers, but a relative perspective shows that DFT calculations were performed rather often in comparison with experiments for rare gas elements, many actinides, some transition metals, and polonium. The annual publication volume of DFT literature continues to grow steadily. The number of publications doubles approximately every 5-6 years while a doubling of publication volume every 11 years is observed for the CAplus database (14 years if patents are excluded). Calculations of the structure and energy of compounds dominate the DFT literature.

  6. Synthesis of 5-alkyl-3,4-difluorofuran-2(5H)-ones by lactonisation. Effects of substituents on cyclisation ability of fluorinated 4-hydroxyalkanoates. DFT calculations of the cyclisation energies

    Czech Academy of Sciences Publication Activity Database

    Hajduch, Jan; Duda, Z.; Beran, J.; Kvíčala, J.; Paleta, O.

    2014-01-01

    Roč. 162, Jun (2014), s. 45-59 ISSN 0022-1139 Institutional support: RVO:61388963 Keywords : methyl 2,3,3-trifluoroacrylate * regioselective radical addition * photo-induced addition * dehydrofluorination * 5-alkyl-3,4-difluorofuran-2(5H)-ones * 5-alkyl-3-fluorofuran-2(5H)-ones * exo-trig lactonisations * DFT lactonisation energy Subject RIV: CC - Organic Chemistry Impact factor: 1.948, year: 2014

  7. DFT and TB study of the geometry of hydrogen adsorbed on graphynes.

    Science.gov (United States)

    Lee, Hunpyo; Koo, Jahyun; Capone, Massimo; Kwon, Yongkyung; Lee, Hoonkyung

    2014-09-24

    Using density-functional calculations (DFT) and a tight-binding model, we investigate the origin of distinct favorable geometries which depend on the type of graphyne used. The change in the H geometry is described in terms of the tuning of the hopping between sp(2)-bonded C atoms and sp-bonded C atoms hybridized with the H atoms. We find that the different preferred geometry for each type of graphyne is associated with the electronic effects due to different symmetries rather than a steric effect minimizing the repulsive interaction between the H atoms. The band gaps are significantly tuned as the hopping varies, except in α-graphyne, in agreement with the result of our previous DFT study (Koo J et al 2013 J. Phys. Chem. C 117 11960). Our model can be used to describe the geometry and electronic properties of hydrogenated graphynes.

  8. DFT and TB study of the geometry of hydrogen adsorbed on graphynes

    International Nuclear Information System (INIS)

    Lee, Hunpyo; Koo, Jahyun; Kwon, Yongkyung; Lee, Hoonkyung; Capone, Massimo

    2014-01-01

    Using density-functional calculations (DFT) and a tight-binding model, we investigate the origin of distinct favorable geometries which depend on the type of graphyne used. The change in the H geometry is described in terms of the tuning of the hopping between sp 2 -bonded C atoms and sp-bonded C atoms hybridized with the H atoms. We find that the different preferred geometry for each type of graphyne is associated with the electronic effects due to different symmetries rather than a steric effect minimizing the repulsive interaction between the H atoms. The band gaps are significantly tuned as the hopping varies, except in α-graphyne, in agreement with the result of our previous DFT study (Koo J et al 2013 J. Phys. Chem. C 117 11960). Our model can be used to describe the geometry and electronic properties of hydrogenated graphynes. (paper)

  9. Effects of Local Protein Environment on the Binding of Diatomic Molecules to Heme in Myoglobins. DFT and Dispersion-Corrected DFT Studies

    Science.gov (United States)

    Liao, Meng-Sheng; Huang, Ming-Ju; Watts, John D.

    2013-01-01

    The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersioncorrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly. PMID:23661270

  10. Combined spectroscopic, DFT, TD-DFT and MD study of newly synthesized thiourea derivative

    Science.gov (United States)

    Menon, Vidya V.; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Bielenica, Anna; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian

    2018-03-01

    A novel thiourea derivative, 1-(3-bromophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (ANF-22) is synthesized and characterized by FTIR, FT-Raman and NMR spectroscopy experimentally and theoretically. A detailed conformational analysis of the title molecule has been conducted in order to locate the lowest energy geometry, which was further subjected to the detailed investigation of spectroscopic, reactive, degradation and docking studies by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Time dependent DFT (TD-DFT) calculations have been used also in order to simulate UV spectra and investigate charge transfer within molecule. Natural bond orbital analysis has been performed analyzing the charge delocalization and using HOMO and LUMO energies the electronic properties are analyzed. Molecular electrostatic potential map is used for the quantitative measurement of active sites in the molecule. In order to determine the locations possibly prone to electrophilic attacks we have calculated average local ionization energies and mapped them to the electron density surface. Further insight into the local reactivity properties have been obtained by calculation of Fukui functions, also mapped to the electron density surface. Possible degradation properties by the autoxidation mechanism have been assessed by calculations of bond dissociation energies for hydrogen abstraction. Atoms of title molecule with significant interactions with water molecules have been determined by calculations of radial distribution functions. The title compound can be a lead compound for developing new analgesic drug.

  11. 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.

  12. Generalized gravity from modified DFT

    Energy Technology Data Exchange (ETDEWEB)

    Sakatani, Yuho [Department of Physics, Kyoto Prefectural University of Medicine,Kyoto 606-0823 (Japan); Fields, Gravity and Strings, CTPU,Institute for Basic Sciences, Daejeon 34047 (Korea, Republic of); Uehara, Shozo [Department of Physics, Kyoto Prefectural University of Medicine,Kyoto 606-0823 (Japan); Yoshida, Kentaroh [Department of Physics, Kyoto University,Kitashirakawa Oiwake-cho, Kyoto 606-8502 (Japan)

    2017-04-20

    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.

  13. 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…

  14. The DFT calculations of structures and EPR parameters for the dinuclear paddle-wheel copper(II) complex {Cu_2(μ_2-O_2CCH_3)_4}(OCNH{sub 2}CH{sub 3}) as powder or single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Chang-Chun; Wu, Shao-Yi; Xu, Yong-Qiang; Zhang, Li-Juan; Zhang, Zhi-Hong; Zhu, Qin-Sheng; Wu, Ming-He; Teng, Bao-Hua [Univ. of Electronic Science and Technology of China, Chengdu (China). School of Physical Electronics

    2017-07-01

    Density functional theory (DFT) calculations of the structures and the Cu{sup 2+} g factors (g{sub x}, g{sub y} and g{sub z}) and hyperfine coupling tensor A (A{sub x}, A{sub y} and A{sub z}) were performed for the paddle-wheel (PW)-type binuclear copper(II) complex {Cu_2(μ_2-O_2CCH_3)_4}(OCNH{sub 2}CH{sub 3}) powder and single crystal. Calculations were carried out with the ORCA software using the functionals BHandHlyp, B3P86 and B3LYP with five different basis sets: 6-311g, 6-311g(d,p), VTZ, def-2 and def2-TZVP. Results were tested by the MPAD analysis to find the most suitable functional and basis sets. The electronic structure and covalency between copper and oxygen were investigated by the electron localisation function and the localised orbital locator as well as the Mayer bond order for the [CuO{sub 5}] group. The optical spectra were theoretically calculated by the time-dependent DFT module and plotted by the Multiwfn program for the [CuO{sub 5}] group and reasonably associated with the local structure in the vicinity of the central ion copper. In addition, the interactions between the OCNH{sub 2}CH{sub 3}, NH{sub 3} and H{sub 2}O molecules and the uncoordinated PW copper(II) complex were studied, and the corresponding adsorption energies, the frequency shifts with respect to the free molecules and the changes of the Cu-Cu distances were calculated and compared with the relevant systems.

  15. The vibrational spectrum of parabanic acid by inelastic neutron scattering spectroscopy and simulation by solid-state DFT.

    Science.gov (United States)

    Hudson, Matthew R; Allis, Damian G; Hudson, Bruce S

    2010-03-18

    The incoherent inelastic neutron scattering spectrum of parabanic acid was measured and simulated using solid-state density functional theory (DFT). This molecule was previously the subject of low-temperature X-ray and neutron diffraction studies. While the simulated spectra from several density functionals account for relative intensities and factor group splitting regardless of functional choice, the hydrogen-bending vibrational energies for the out-of-plane modes are poorly described by all methods. The disagreement between calculated and observed out-of-plane hydrogen bending mode energies is examined along with geometry optimization differences of bond lengths, bond angles, and hydrogen-bonding interactions for different functionals. Neutron diffraction suggests nearly symmetric hydrogen atom positions in the crystalline solid for both heavy-atom and N-H bond distances but different hydrogen-bonding angles. The spectroscopic results suggest a significant factor group splitting for the out-of-plane bending motions associated with the hydrogen atoms (N-H) for both the symmetric and asymmetric bending modes, as is also supported by DFT simulations. The differences between the quality of the crystallographic and spectroscopic simulations by isolated-molecule DFT, cluster-based DFT (that account for only the hydrogen-bonding interactions around a single molecule), and solid-state DFT are considered in detail, with parabanic acid serving as an excellent case study due to its small size and the availability of high-quality structure data. These calculations show that hydrogen bonding results in a change in the bond distances and bond angles of parabanic acid from the free molecule values.

  16. 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.

  17. UV-Visible Absorption Spectra of [Ru(E)(E')(CO).sub.2./sub.(iPr-DAB)](E=E'=SnPh.sub.3./sub. or Cl; E=SnPh.sub.3./sub. or Cl, E'=CH.sub.3./sub.; iPr-DAB=N,N'-Di-isopropyl-1,4-diaza-1,3-butadiene): Combination of CASSCF/CASPT2 and TD-DFT Calculations

    Czech Academy of Sciences Publication Activity Database

    Turki, M.; Daniel, CH.; Záliš, Stanislav; Vlček, Antonín; Slageren van, J.; Stufkens, D. J.

    2001-01-01

    Roč. 123, č. 46 (2001), s. 11431-11440 ISSN 0002-7863 R&D Projects: GA MŠk OC D14.20 Institutional research plan: CEZ:AV0Z4040901 Keywords : diimine complexes * UV-Vis spectra * CASSCF/CASPT2 and TD-DFT calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.079, year: 2001

  18. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. Electronic and Optical Properties of CuO Based on DFT+U and GW Approximation

    International Nuclear Information System (INIS)

    Ahmad, F; Agusta, M K; Dipojono, H K

    2016-01-01

    We report ab initio calculations of electronic structure and optical properties of monoclinic CuO based on DFT+U and GW approximation. CuO is an antiferromagnetic material with strong electron correlations. Our calculation shows that DFT+U and GW approximation sufficiently reliable to investigate the material properties of CuO. The calculated band gap of DFT+U for reasonable value of U slightly underestimates. The use of GW approximation requires adjustment of U value to get realistic result. Hybridization Cu 3dxz, 3dyz with O 2p plays an important role in the formation of band gap. The calculated optical properties based on DFT+U and GW corrections by solving Bethe-Salpeter are in good agreement with the calculated electronic properties and the experimental result. (paper)

  20. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    and the new [Co(btmgn)Cl2] complex were charac- terized using different spectroscopic techniques. The. X-ray structure of the [Co(btmgn)Cl2] complex is deter- mined. The electronic and spectroscopic aspects of the ligands as well as the [Co(btmgn)Cl2] were discussed with the aid of DFT quantum chemical calculations.

  1. Oxovanadium(IV), cerium(III), thorium(IV) and dioxouranium(VI) complexes of 1-ethyl-4-hydroxy-3-(nitroacetyl)quinolin-2(1H)-one: Synthesis, spectral, thermal, fluorescence, DFT calculations, antimicrobial and antitumor studies

    Science.gov (United States)

    El-Shafiy, H. F.; Shebl, Magdy

    2018-03-01

    A new series of mononuclear oxovanadium(IV), cerium(III), thorium(IV) and dioxouranium(VI) complexes of a quinolinone ligand; 1-ethyl-4-hydroxy-3-(nitroacetyl)quinolin-2(1H)-one (H2L) have been synthesized. The metal complexes were characterized by different techniques such as elemental and thermal analyses, IR, 1H NMR, electronic, ESR, mass spectra and powder XRD, TEM in addition to magnetic susceptibility and conductivity measurements. The quinolinone ligand acts as a dibasic bidentate ligand forming mononuclear complexes, which can be formulated as: [(L)VO(H2O)2]·0.5H2O, [(L)M(NO3)x(H2O)y]·nH2O; M = Ce or Th, x = 1 or 2, y = 3 or 4 and n = 2 or 7 and [(L)UO2(H2O)x(MeOH)y]·nH2O; x = 2 or 3, y = 0 or 1 and n = 0.5 or 2.5. The photoluminescent properties of the prepared complexes were studied. The ligand and its thorium(IV) complex are characterized by an intense green emission. Kinetic parameters (Ea, A, ΔH, ΔS and ΔG) of the thermal decomposition stages have been evaluated using Coats-Redfern equations. The geometry of the ligand and its oxovanadium(IV) complex has been optimized using density functional theory (DFT). Total energy, energy of HOMO and LUMO, dipole moment and structure activity relationship were performed and confirmed practical antimicrobial and antitumor results. The antimicrobial activity of the ligand and its metal complexes was conducted against the microorganisms S. aureus, K. pnemonia, E. coli, P. vulgaris and C. albicans and the MIC values were determined. The antitumor activity of the ligand and its metal complexes was investigated against human Hepatocelluar carcinoma and human breast cancer cell lines.

  2. Vibrational spectroscopic analysis of aluminum phthalocyanine chloride. experimental and DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Soliman, I.M., E-mail: solidhima@gmail.com [Physics Department, Faculty of Science, Ain Shams University, Abbasia, Cairo (Egypt); El-Nahass, M.M. [Physics Department, Faculty of Education, Ain Shams University, Roxy, Cairo (Egypt); Eid, Kh.M. [Physics Department, Faculty of Education, Ain Shams University, Roxy, Cairo (Egypt); Physics department, Bukairiayh for Sciences & Arts, Quassim University, Quassim (Saudi Arabia); Ammar, H.Y. [Physics Department, Faculty of Arts and science, Najran University, Najran (Saudi Arabia)

    2016-06-15

    In this work, we report a combined experimental and theoretical study of aluminum phthalocyanine chloride (AlPcCl). The FT-IR and Raman spectra of AlPcCl were recorded and analyzed. The density functional theory (DFT) computations have been performed at B3LYP/6-31g and B3LYP/6-311g to derive equilibrium geometry, vibrational wavenumbers, intensity and NLO properties. All the observed vibrational bands have been discussed and assigned to normal mode or to combinations on the basis of our DFT calculations as a primary source of attribution and also by comparison with the previous results for similar compounds. The natural bond orbital (NBO) calculations were performed to study the atomic charge distribution of the investigated compound. The calculated results showed that dipole moment of the investigated compound was 4.68 Debye and HOMO-LUMO energy gap was 2.14 eV. The lowering of frontier orbital gap appears to be the cause of its enhanced charge transfer interaction.

  3. Implementation of DFT application on ternary optical computer

    Science.gov (United States)

    Junjie, Peng; Youyi, Fu; Xiaofeng, Zhang; Shuai, Kong; Xinyu, Wei

    2018-03-01

    As its characteristics of huge number of data bits and low energy consumption, optical computing may be used in the applications such as DFT etc. which needs a lot of computation and can be implemented in parallel. According to this, DFT implementation methods in full parallel as well as in partial parallel are presented. Based on resources ternary optical computer (TOC), extensive experiments were carried out. Experimental results show that the proposed schemes are correct and feasible. They provide a foundation for further exploration of the applications on TOC that needs a large amount calculation and can be processed in parallel.

  4. 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.

  5. Role of the lattice dynamics in La2-xBaxCuO4 superconductor based on DFT method

    Directory of Open Access Journals (Sweden)

    A Tavana

    2010-09-01

    Full Text Available Electron-phonon coupling parameters are calculated for La2-x BaxCuO4 cuprate superconductor in a wide range of dopings, from undoped to overdoped compounds. In this study we aim to study the quality of such calculations based on DFT method so, the results of σ GGA+U electronic structure calculations are also investigated. The obtained value for electron-phonon coupling is in the same order of previous calculations but, the value obtained for the Hubbard U parameter shows that, such methods are poor in the estimation of electronic correlations to decide about the role of phonons in these compounds based on their results. Moreover, existence of several structural phase transitions with temperature and doping, lead to larger error in these calculations. Based on the calculated phonon dispersions, structural phase transitions can be resulted which shows the ability of DFT in the study of structural properties and the weakness of the strongly correlations in this properties.

  6. First-principles calculations on third-order elastic constants and internal relaxation for monolayer graphene

    International Nuclear Information System (INIS)

    Wang Rui; Wang Shaofeng; Wu Xiaozhi; Liang Xiao

    2010-01-01

    The method of homogeneous deformation is combined with first-principles total-energy calculations on determining third-order elastic constants and internal relaxation for monolayer graphene. We employ density functional theory (DFT) within generalized-gradient-approximation (GGA). The elastic constants are obtained from a polynomial fitted to the calculations of strain-energy and strain-stress relations. Our results agree well with recent calculations by DFT calculations, tight-binding atomistic simulations, and experiments with an atomic force microscope. The internal relaxation displacement has also been determined from ab initio calculations. The details of internal lattice relaxation by first principles are basically consistent with the previous molecular dynamics (MD) simulation. But for tiny deformation, there is an anomalous region in which the behavior of internal relaxation is backward action. In addition, we have also demonstrated that the symmetry of the relationship between the internal displacement and the infinitesimal stains can be satisfied.

  7. Synthesis, crystallographic characterization, DFT and TD-DFT ...

    Indian Academy of Sciences (India)

    SAIED M SOLIMAN

    2017-08-29

    Aug 29, 2017 ... data. Natural charges, dipole moments and chemical reactivity of these molecules, as well as their non-linear optical activity, were computed and compared. Keywords. Oxyma; sulfonate ester; X-ray crystallography; TD-DFT; NLO; NBO. 1. Introduction. Sulfonate esters are considered as important precur-.

  8. Fluorine-induced local magnetic moment in graphene: A hybrid DFT study

    OpenAIRE

    Kim, Hyun-Jung; Cho, Jun-Hyung

    2013-01-01

    Recent experimental evidence that fluorinated graphene creates local magnetic moments around F adatoms has not been supported by semilocal density-functional theory (DFT) calculations where the adsorption of an isolated F adatom induces no magnetic moment in graphene. Here, we show that such an incorrect prediction of the nonmagnetic ground state is due to the self-interaction error inherent in semilocal exchange-correlation functionals. The present hybrid DFT calculation for an isolated F ad...

  9. 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)

  10. TD-DFT Insight into Photodissociation of Co-C Bond in Coenzyme B12

    Directory of Open Access Journals (Sweden)

    Pawel Michal Kozlowski

    2014-02-01

    Full Text Available Coenzyme B12 (AdoCbl is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM. Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo-C → σ*Co-C triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl. Furthermore, potential energy surfaces (PESs obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a MLCT (metal-to-ligand charge transfer and a σ bonding-ligand charge transfer (SBLCT states.

  11. Evidence for the dimer-of-(mixed-valent dimers) configuration in tetranuclear {(mu(4)-TCNX)[Ru(NH3)(5)](4)}(8+), TCNX = TCNE and TCNQ, from DFT calculations

    Czech Academy of Sciences Publication Activity Database

    Záliš, Stanislav; Sarkar, B.; Duboc, C.; Kaim, A.

    2009-01-01

    Roč. 140, č. 7 (2009), s. 765-773 ISSN 0026-9247 R&D Projects: GA MŠk OC 139; GA AV ČR KAN100400702 Institutional research plan: CEZ:AV0Z40400503 Keywords : Density functional calculations * Transition metal compounds * Ruthenium complexes * redox states Subject RIV: CG - Electrochemistry Impact factor: 1.312, year: 2009

  12. Adaptive DFT-Based Interferometer Fringe Tracking

    Directory of Open Access Journals (Sweden)

    Pedretti Ettore

    2005-01-01

    Full Text Available An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA Observatory at Mount 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 offline data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately 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. One example of such an application might be to the field of thin-film measurement by ellipsometry, using a broadband light source and a Fourier-transform spectrometer to detect the resulting fringe patterns.

  13. A torsional potential for graphene derived from fitting to DFT results

    Science.gov (United States)

    Chatzidakis, Georgios D.; Kalosakas, George; Fthenakis, Zacharias G.; Lathiotakis, Nektarios N.

    2018-01-01

    We present a simple torsional potential for graphene to accurately describe its out-of-plane deformations. The parameters of the potential are derived through appropriate fitting with suitable DFT calculations regarding the deformation energy of graphene sheets folded around two different folding axes, along an armchair or along a zig-zag direction. Removing the energetic contribution of bending angles, using a previously introduced angle bending potential, we isolate the purely torsional deformation energy, which is then fitted to simple torsional force fields. The presented out-of-plane torsional potential can accurately fit the deformation energy for relatively large torsional angles up to 0.5 rad. To test our proposed potential, we apply it to the problem of the vertical displacement of a single carbon atom out of the graphene plane and compare the obtained deformation energy with corresponding DFT calculations. The dependence of the deformation energy on the vertical displacement of the pulled carbon atom is indistinguishable in these two cases, for displacements up to about 0.5 Å. The presented potential is applicable to other sp2 carbon structures.

  14. IR, Raman, SERS and DFT study of amoxicillin

    Science.gov (United States)

    Bebu, Andreea; Szabó, László; Leopold, Nicolae; Berindean, Cătălin; David, Leontin

    2011-05-01

    In this work a joint experimental and theoretical study on amoxicillin is reported. The molecular vibrations of amoxicillin were investigated by FTIR, FT-Raman and SERS spectroscopies. In parallel, quantum chemical calculations based on density functional theory (DFT) were used to determine the geometrical, energetic and vibrational characteristics of the molecule with particular emphasis put on the interaction and adsorption geometry of the molecule to the silver colloidal surface. The SERS spectrum of amoxicillin was recorded using a 532 nm laser line and hydroxylamine reduced silver colloid as SERS substrate. FTIR, FT-Raman and SERS spectra of amoxicillin were assigned based on DFT calculations with the hybrid B3LYP exchange-correlation functional, coupled with the standard 6-31G(d) basis set. The calculated molecular electrostatic potential (MEP) was used in conjunction with SERS data to predict the adsorption geometry of the molecule on the silver surface.

  15. 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.

  16. On the subsystem formulation of linear-response time-dependent DFT.

    Science.gov (United States)

    Pavanello, Michele

    2013-05-28

    A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

  17. 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.

  18. DFT-SAPT intermolecular interaction energies employing exact-exchange Kohn-Sham response methods.

    Science.gov (United States)

    Hesselmann, Andreas

    2018-03-22

    Intermolecular interaction energies have been calculated by symmetry-adapted perturbation theory based on density-functional theory monomer properties (DFT-SAPT) employing response functions from time-dependent exact-exchange (TDEXX) kernels. Combined with a new asymptotic correction scheme for the xc potentials of the monomers, it is shown that this DFT-SAPT[TDEXX] method delivers highly accurate intermolecular interaction energies for the S22, S66 and IonHB benchmark data bases by Hobza et al.. A corresponding DFT-SAPT approach employing the adiabatic TDEXX kernel in the response calculations has also been tested. While exhibiting a similar performance than DFT-SAPT[TDEXX] for dispersion-dominated dimer systems, it was found found that the accuracies of the interaction energies for hydrogen-bonded dimers deteriorate with this DFT-SAPT[ATDEXX] method. Compared to this, the DFT-SAPT[TDEXX] yields a balanced description of the interaction energies for various interaction-type motifs, similar to the standard DFT-SAPT method that utilises the ALDA xc kernel to compute the response functions.

  19. Adsorption behavior and mechanism of acidic blue 25 dye onto cucurbit[8]uril: A spectral and DFT study

    Science.gov (United States)

    Luo, Hanhan; Huang, Xiangyu; Luo, Yuhan; Li, Zhuang; Li, Lan; Gao, Chao; Xiong, Jinyan; Li, Wei

    2018-03-01

    The acidic blue 25 (AB25) dye was efficiently adsorbed by CB [8]; the saturated adsorption capacity (qexp) reached 434.8 mg/g and was far higher than those of previous reported adsorbents. The Langmuir and Freundich isotherms were used to fit the equilibrium data, and the results showed that the Freundlich isotherm seemed to agree better with the AB25 adsorption. The adsorption kinetics followed the pseudo-second-order model. Calculated thermodynamic parameters showed that the adsorption of AB25 onto CB [8] was a spontaneous and enthalpy-driven process. The adsorption mechanism was explored by N2 adsorption-desorption, TG, FT-IR, UV-vis as well as MD simulation and DFT calculations. TG analysis revealed that a new inclusion complex was produced, and FT-IR,UV-vis spectrum and DFT calculations verify its structure. In this inclusion complex, the AB25 dye molecule inserted into cavities of CB [8] from portal, and the sulfonate and phenyl groups stayed in the hydrophobic cavity. TDDFT calculations indicated that all excitation arisen from π → π* transition.

  20. Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3 Thermus thermophilus.

    Science.gov (United States)

    Han Du, Wen-Ge; Noodleman, Louis

    2015-08-03

    The Fea3(3+)···CuB(2+) dinuclear center (DNC) structure of the as-isolated oxidized ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt) is still not fully understood. When the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through X-ray irradiation. Several X-ray crystal structures of reduced ba3 CcO from Tt are available. However, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent micelles, and whether the CcO's were chemically or radiolyticly reduced, the X-ray diffraction analysis of the crystals showed different Fea3(2+)···CuB(+) DNC structures. On the other hand, Mössbauer spectroscopic experiments on reduced and oxidized ba3 CcOs from Tt (Zimmermann et al., Proc. Natl. Acad. Sci. USA 1988, 85, 5779-5783) revealed multiple (57)Fea3(2+) and (57)Fea3(3+) components. Moreover, one of the (57)Fea3(3+) components observed at 4.2 K transformed from a proposed "low-spin" state to a different high-spin species when the temperature was increased above 190 K, whereas the other high-spin (57)Fea3(3+) component remained unchanged. In the current Article, in order to understand the heterogeneities of the DNC in both Mössbauer spectra and X-ray crystal structures, the spin crossover of one of the (57)Fea3(3+) components, and how the coordination and spin states of the Fea3(3+/2+) and Cu(2+/1+) sites relate to the heterogeneity of the DNC structures, we have applied density functional OLYP calculations to the DNC clusters established based on the different X-ray crystal structures of ba3 CcO from Tt. As a result, specific oxidized and reduced DNC structures related to the observed Mössbauer spectra and to spectral changes with temperature have been proposed. Our calculations also show that, in certain intermediate states, the His233 and His283 ligand side chains may dissociate from the CuB(+) site, and they may become potential proton loading sites

  1. Design, Synthesis, DFT Study and Antifungal Activity of Pyrazolecarboxamide Derivatives

    Directory of Open Access Journals (Sweden)

    Jin-Xia Mu

    2016-01-01

    Full Text Available A series of novel pyrazole amide derivatives were designed and synthesized by multi-step reactions from phenylhydrazine and ethyl 3-oxobutanoate as starting materials, and their structures were characterized by NMR, MS and elemental analysis. The antifungal activity of the title compounds was determined. The results indicated that some of title compounds exhibited moderate antifungal activity. Furthermore, DFT calculations were used to study the structure-activity relationships (SAR.

  2. Conformation of eight-membered benzoannulated lactams by combined NMR and DFT studies.

    Science.gov (United States)

    Witosińska, Agnieszka; Musielak, Bogdan; Serda, Paweł; Owińska, Maria; Rys, Barbara

    2012-11-02

    The title compounds were synthesized, and their structure and conformational behavior in solution (NMR and DFT), in the gas phase (DFT), and, for some of them, in the solid state (X-ray) were investigated. The variable-temperature NMR spectra were employed to determine the conformational equilibria and the activation energy of the conformational changes of the eight-membered ring. The coalescence effects are assigned to racemization of the chiral ground-state conformation with a ring inversion barrier in the range of 38-100 kJ mol(-1) depending on the relative setting of the two strong conformational constraints: benzoannulation and the amide function. The second conformational process, interconversion between two different conformers, in the molecules of benzo[c]azocin-3-one, benzo[d]azocin-2-one, and benzo[d]azocin-4-one was observed. The natures of the conformers observed in solution were elucidated by analysis of experimental and calculated NMR data. The present results are discussed in conjunction with previous experimental and theoretical data on (Z,Z)-cyclooctadienes and their benzo analogues.

  3. Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS and DFT Analyses

    Science.gov (United States)

    Mitra, Devrani; George, Simon J.; Guo, Yisong; Kamali, Saeed; Keable, Stephen; Peters, John W.; Pelmenschikov, Vladimir; Case, David A.; Cramer, Stephen P.

    2013-01-01

    Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm−1 decrease in Fe-S stretching frequencies with each added electron. The “oxidized” [4Fe-4S]2+ state spectrum is consistent with and extends previous resonance Raman spectra. For the “reduced” [4Fe-4S]1+ state in Fe protein, and for any “all-ferrous” [4Fe-4S]0 cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å−1 indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment. PMID:23282058

  4. 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.

  5. Predicting Intersystem Crossing Rates with AIMS-DFT Molecular Dynamics.

    Science.gov (United States)

    Fedorov, Dmitry A; Lykhin, Aleksandr O; Varganov, Sergey A

    2018-03-23

    Accurate prediction of the intersystem crossing rates is important for many different applications in chemistry, physics, and biology. Recently, we implemented the ab initio multiple spawning (AIMS) molecular dynamics method to describe the intersystem crossing processes, where nonradiative transitions between electronic states with different spin multiplicities are mediated by spin-orbit coupling. Our original implementation of the direct AIMS dynamics used the complete active space self-consistent field (CASSCF) method to describe multiple coupled electronic states on which multidimensional Gaussian wave packets were propagated. In this work, we improve the computational efficiency and versatility of the AIMS dynamics by interfacing it with the density functional theory (DFT). The new AIMS-DFT and the earlier AIMS-CASSCF implementations are used to investigate the effects of electronic structure methods on the predicted intersystem crossing rate constants and the lowest triplet state lifetime in the GeH 2 molecule. We also compare the rates and lifetimes obtained from the AIMS simulations with those predicted by the statistical nonadiabatic transition state theory (NA-TST). In NA-TST, the probabilities of spin transitions are calculated using the Landau-Zener, weak coupling, and Zhu-Nakamura formulas. Convergence of the AIMS rate constants with respect to the simulation time and the number of initial trajectories (Gaussian wave packets) is analyzed. An excellent agreement between AIMS-DFT and AIMS-CASSCF can be explained by cancelation of two effects: higher energy barriers and a stronger spin-orbit coupling in DFT relative to CASSCF. The rate constants obtained with the AIMS-DFT dynamics are about a factor of 2 larger than those predicted by the statistical NA-TST. This is likely due to the importance of the nonlocal interstate transitions missing from the NA-TST description.

  6. Triphenylamine-Based Fluorescent Styryl Dyes: DFT, TD-DFT and Non-Linear Optical Property Study.

    Science.gov (United States)

    Katariya, Santosh; Rhyman, Lydia; Alswaidan, Ibrahim A; Ramasami, Ponnadurai; Sekar, Nagaiyan

    2017-05-01

    The electronic structures and spectroscopic properties of triphenylamine-based monostyryl and bis(styryl) dyes were studied using quantum chemical methods. The ground-state geometries of these dyes were optimized using the density functional theory (DFT) method. The lowest singlet excited state was optimized using time-dependent density functional theory (TD-DFT). The absorption was also calculated using the ground-state geometries. All the calculations were carried out in the gas phase and in solvent. The results indicate that the absorption maxima calculated using the TD-DFT are in good agreement with those obtained experimentally. These dyes possess a large second-order non-linear property and this is mainly due to the strong donor-π-acceptor conjugation which is attributed to the excited state intramolecular charge transfer (ICT). There is a relationship between the hardness and first hyperpolarizability and second hyperpolarizability of mono- and bis(styryl) dyes. The efficiency of the intersystem crossing process can be improved by reducing the energy gap between the singlet and triplet excited states.

  7. Implementation of Constrained DFT for Computing Charge Transfer Rates within the Projector Augmented Wave Method.

    Science.gov (United States)

    Melander, Marko; Jónsson, Elvar Ö; Mortensen, Jens J; Vegge, Tejs; García Lastra, Juan Maria

    2016-11-08

    Combining constrained density function theory (cDFT) with Marcus theory is an efficient and promising way to address charge transfer reactions. Here, we present a general and robust implementation of cDFT within the projector augmented wave (PAW) framework. PAW pseudopotentials offer a reliable frozen-core electron description across the whole periodic table, with good transferability, as well as facilitate the extraction of all-electron quantities. The present implementation is applicable to two different wave function representations, atomic-centered basis sets (LCAO) and the finite-difference (FD) approximation utilizing real-space grids. LCAO can be used for large systems, molecular dynamics, or quick initialization, while more accurate calculations are achieved with the FD basis. Furthermore, the calculations can be performed with flexible boundary conditions, ranging from isolated molecules to periodic systems in one-, two-, or three-dimensions. As such, this implementation is relevant for a wide variety of applications. We also present how to extract the electronic coupling element and reorganization energy from the resulting diabatic cDFT-PAW wave functions for the parametrization of Marcus theory. Here, the combined method is applied to important test cases where practical implementations of DFT fail due to the self-interaction error, such as the dissociation of the helium dimer cation, and it is compared to other established cDFT codes. Moreover, for charge localization in a diamine cation, where it was recently shown that the commonly used generalized gradient and hybrid functionals of DFT failed to produce the localized state, cDFT produces qualitatively and quantitatively accurate results when benchmarked against self-interaction corrected DFT and high-level CCSD(T) calculations at a fraction of the computational cost.

  8. Communication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT cost

    Science.gov (United States)

    Bajaj, Akash; Janet, Jon Paul; Kulik, Heather J.

    2017-11-01

    The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i.e., Hartree-Fock exchange), it worsens FSE. To find an alternative strategy, we examine the shape of semi-local DFT deviations from the exact flat plane and we find this shape to be remarkably consistent across ions and molecules. We introduce the judiciously modified DFT (jmDFT) approach, wherein corrections are constructed from few-parameter, low-order functional forms that fit the shape of semi-local DFT errors. We select one such physically intuitive form and incorporate it self-consistently to correct semi-local DFT. We demonstrate on model systems that jmDFT represents the first easy-to-implement, no-overhead approach to recovering the flat plane from semi-local DFT.

  9. Communication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT cost.

    Science.gov (United States)

    Bajaj, Akash; Janet, Jon Paul; Kulik, Heather J

    2017-11-21

    The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i.e., Hartree-Fock exchange), it worsens FSE. To find an alternative strategy, we examine the shape of semi-local DFT deviations from the exact flat plane and we find this shape to be remarkably consistent across ions and molecules. We introduce the judiciously modified DFT (jmDFT) approach, wherein corrections are constructed from few-parameter, low-order functional forms that fit the shape of semi-local DFT errors. We select one such physically intuitive form and incorporate it self-consistently to correct semi-local DFT. We demonstrate on model systems that jmDFT represents the first easy-to-implement, no-overhead approach to recovering the flat plane from semi-local DFT.

  10. DFT

    Indian Academy of Sciences (India)

    Abstract. In the present investigation, interaction of ruthenium (Ru) atoms with fluorine (F) atoms was studied using the density functional theory utilizing B3LYP method. It was found that up to seven F atoms can bind to a single Ru atom which results in increase of electron affinities successively, reaching a peak value of ...

  11. DFT-Assisted Polymorph Identification from Lattice Raman Fingerprinting.

    Science.gov (United States)

    Bedoya-Martínez, Natalia; Schrode, Benedikt; Jones, Andrew O F; Salzillo, Tommaso; Ruzié, Christian; Demitri, Nicola; Geerts, Yves H; Venuti, Elisabetta; Della Valle, Raffaele Guido; Zojer, Egbert; Resel, Roland

    2017-08-03

    A combined experimental and theoretical approach, consisting of lattice phonon Raman spectroscopy and density functional theory (DFT) calculations, is proposed as a tool for lattice dynamics characterization and polymorph phase identification. To illustrate the reliability of the method, the lattice phonon Raman spectra of two polymorphs of the molecule 2,7-dioctyloxy[1]benzothieno[3,2-b]benzothiophene are investigated. We show that DFT calculations of the lattice vibrations based on the known crystal structures, including many-body dispersion van der Waals (MBD-vdW) corrections, predict experimental data within an accuracy of ≪5 cm -1 (≪0.6 meV). Due to the high accuracy of the simulations, they can be used to unambiguously identify different polymorphs and to characterize the nature of the lattice vibrations and their relationship to the structural properties. More generally, this work implies that DFT-MBD-vdW is a promising method to describe also other physical properties that depend on lattice dynamics like charge transport.

  12. DFT calculations of vibrational spectra of oxidized (111) diamond surface

    Czech Academy of Sciences Publication Activity Database

    Jirásek, Vít; Kozak, Halyna; Remeš, Zdeněk

    2015-01-01

    Roč. 7, č. 4 (2015), s. 275-278 ISSN 2164-6627 R&D Projects: GA ČR GPP205/12/P331; GA MŠk LH12186 Institutional support: RVO:68378271 Keywords : density functional theory * vibrational spectra * FTIR * diamond nanoparticles * functionalized diamond surface Subject RIV: JJ - Other Materials

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

    African Journals Online (AJOL)

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    NMR is a sensitive and versatile probe of molecular-scale structure and dynamics in solids and liquids. It has been widely used in chemistry, materials and geochemistry [21-23] and it enables one to get faster and easier structural information. The standard 1D and 2D hetero and homonuclear NMR experiments are enough ...

  14. The pink pigment prodigiosin: Vibrational spectroscopy and DFT calculations

    Czech Academy of Sciences Publication Activity Database

    Jehlička, J.; Němec, I.; Varnali, T.; Culka, A.; Svatoš, A.; Frank, Otakar; Oren, A.; Edwards, G.M.

    2016-01-01

    Roč. 134, NOV 2016 (2016), s. 234-243 ISSN 0143-7208 Institutional support: RVO:61388955 Keywords : prodigiosin * serratia marcescens * raman spectroscopy Subject RIV: CG - Electrochemistry Impact factor: 3.473, year: 2016

  15. NMR spectroscopic study and DFT calculations of GIAO NMR ...

    African Journals Online (AJOL)

    1H, proton coupled and decoupled 13C, DEPT, HETCOR NMR spectra, the magnitude of one bond 1JCH coupling constants and 13C NMR spin-lattice relaxation time (T1) of 1,9-diaminononane (danon, C9H22N2) have been reported for the first time. 1H, 13C NMR chemical shifts and 1JCH coupling constants of danon ...

  16. Ab Initio and DFT Potential Energy Surfaces for Cyanuric Chloride Reactions

    National Research Council Canada - National Science Library

    Pai, Sharmila

    1998-01-01

    ... on the potential energy surface were calculated using the 6-31G and 6-311 +Gbasis sets. DFT(B3LYP) geometry optimizations and zero-point corrections for critical points on the potential energy surface were calculated with the 6-31G, 6-311...

  17. DFT Study of the effects of counter ions on bonding, molecular and ...

    Indian Academy of Sciences (India)

    Abstract. The structures and properties of pentaflourophenyl xenonium diflouride cation (PFF) have been studied in their salts with 12 different counter ions using DFT calculations. The results demonstrated the huge effect of counter ion on all properties. The hybridization values, obtained from the NBO calculations, showed.

  18. PREVIOUS SECOND TRIMESTER ABORTION

    African Journals Online (AJOL)

    PNLC

    PREVIOUS SECOND TRIMESTER ABORTION: A risk factor for third trimester uterine rupture in three ... for accurate diagnosis of uterine rupture. KEY WORDS: Induced second trimester abortion - Previous uterine surgery - Uterine rupture. ..... scarred uterus during second trimester misoprostol- induced labour for a missed ...

  19. Complete assignment of the vibrational modes of C60 by inelastic neutron scattering spectroscopy and periodic-DFT.

    Science.gov (United States)

    Parker, Stewart F; Bennington, Stephen M; Taylor, Jon W; Herman, Henryk; Silverwood, Ian; Albers, Peter; Refson, Keith

    2011-05-07

    In this paper we exploit the complementarity of inelastic neutron scattering (INS), infrared and Raman spectroscopies with ab initio calculations to generate an updated assignment of the vibrational modes of C(60). We have carried out periodic-DFT calculations of the high temperature face centred cubic phase modelled as the standard structure and also of the low temperature simple cubic phase, the latter for the first time. Our assignment differs from all previous work, however, it is the only one that is able to successfully reproduce the INS spectrum in terms of both transition energies and intensities. In addition to the INS spectrum we are also able to quantitatively simulate the major features of the infrared and Raman spectra in the high temperature phase and the infrared spectrum in the low temperature phase. This journal is © the Owner Societies 2011

  20. Combined NMR and DFT studies for the absolute configuration elucidation of the spore photoproduct, a UV-induced DNA lesion.

    Science.gov (United States)

    Mantel, Claire; Chandor, Alexia; Gasparutto, Didier; Douki, Thierry; Atta, Mohamed; Fontecave, Marc; Bayle, Pierre-Alain; Mouesca, Jean-Marie; Bardet, Michel

    2008-12-17

    By irradiation of bacterial spores under UV radiation, a photoproduct (SP) bearing a covalent methylene link between two adjacent thymines is formed in DNA. Because of the presence of an asymmetric carbon on the aglycone and of two possible orientations for the formation of the cross-link, four isomers could in principle be obtained. Currently, no conclusive structural information of this photoproduct is available. The structure of the isolated SPTpT dinucleotide was revisited in order to determine the type of cross-link and the absolute configuration of the C5a carbon. For this purpose, a study combining NMR spectroscopy and DFT calculations was pursued on the spore photoproduct of the dinucleoside TpT since its structure was previously shown to be identical to the one produced in DNA. A full characterization of SPTpT by NMR analyses was performed in D2O and DMSO. 2D NMR measurements (1H-13C, 1H-31P, COSY, NOESY, and ROESY) and DFT calculations (geometries optimization of R and S isomers and theoretical chemical shifts) lead us to conclude without ambiguity that the absolute configuration of the C5a carbon is R and that the methylene bridge of the photoproduct corresponds to the methyl group of the thymine located on the 3'-end of the dinucleoside monophosphate.

  1. Basis set convergence on static electric dipole polarizability calculations of alkali-metal clusters

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Fabio A. L. de; Jorge, Francisco E., E-mail: jorge@cce.ufes.br [Departamento de Fisica, Universidade Federal do Espirito Santo, 29060-900 Vitoria-ES (Brazil)

    2013-07-15

    A hierarchical sequence of all-electron segmented contracted basis sets of double, triple and quadruple zeta valence qualities plus polarization functions augmented with diffuse functions for the atoms from H to Ar was constructed. A systematic study of basis sets required to obtain reliable and accurate values of static dipole polarizabilities of lithium and sodium clusters (n = 2, 4, 6 and 8) at their optimized equilibrium geometries is reported. Three methods are examined: Hartree-Fock (HF), second-order Moeller-Plesset perturbation theory (MP2), and density functional theory (DFT). By direct calculations or by fitting the directly calculated values through one extrapolation scheme, estimates of the HF, MP2 and DFT complete basis set limits were obtained. Comparison with experimental and theoretical data reported previously in the literature is done (author)

  2. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Docking and Molecular Dynamics Calculations of Some Previously Studied and newly Designed Ligands to Catalytic Core Domain of HIV-1 Integrase and an Investigation to Effects of Conformational Changes of Protein on Docking Results

    Directory of Open Access Journals (Sweden)

    Selami Ercan

    2016-10-01

    Full Text Available Nowadays, AIDS still remains as a worldwide pandemic and continues to cause many death which arise from HIV-1 virus. For nearly 35 years, drugs that target various steps of virus life cycle have been developed. HIV-1 integrase is the one of these steps which is essential for virus life cycle. Computer aided drug design is being used in many drug design studies as also used in development of the first HIV-1 integrase inhibitor Raltegravir. In this study 3 ligands which are used as HIV-1 integrase inhibitors and 4 newly designed ligands were docked to catalytic core domain of HIV-1 integrase. Each of ligands docked to three different conformations of protein. Prepared complexes (21 item were carried out by 50 ns MD simulations and results were analyzed. Finally, the binding free energies of ligands were calculated. Hereunder, it was determined that designed ligands L01 and L03 gave favorable results. The questions about the ligands which have low docking scores in a conformation of protein could give better scores in another conformation of protein and if the MD simulations carry the different oriented and different localized ligands in same position at the end of simulation were answered.

  4. DFT computations and spectroscopic analysis of a pesticide: Chlorothalonil

    Science.gov (United States)

    Dhas, D. Arul; Joe, I. Hubert; Roy, S. D. D.; Freeda, T. H.

    2010-09-01

    NIR FT-Raman and IR spectra of the biologically active molecule, chlorothalonil have been recorded and analyzed. The molecular geometry and vibrational wavenumbers of the title compound in the ground state have been calculated by density functional theory (DFT) with 6-31G(d) basis set. In order to obtain the information about the influence of intramolecular interaction on the molecule, the calculated geometries of chlorothalonil molecule was compared with the experimental data. The results of the optimized molecular structure gave clear evidence for the intramolecular charge transfer (ICT). Time-dependent density functional theory (TD-DFT) calculation of the electronic spectra has been performed and compared with the experimental UV-visible spectrum. Mulliken's net charges have been calculated and compared with the atomic natural charges. The effects of chlorine and cyanide group substituent in benzene ring in the vibrational wavenumbers have been analyzed. NBO analysis is useful to understand the intramolecular hyperconjugative interaction between lone pair Cl and σ*(C-C) bond orbital.

  5. Nanosecond CO Photodissociation and Excited-State Character of [Ru(X)(X´)(CO)2(N,N´-diisopropyl-1,4-diazabutadiene)] (X = X´ = Cl or I; X = Me, X´ = I; X = SnPh3, X´ = Cl) Studied by Time-Resolved Infrared Spectroscopy and DFT Calculations

    Czech Academy of Sciences Publication Activity Database

    Gabrielsson, A.; Towrie, M.; Záliš, Stanislav; Vlček, Antonín

    2008-01-01

    Roč. 47, č. 10 (2008), s. 4236-4242 ISSN 0020-1669 R&D Projects: GA MŠk 1P05OC068; GA AV ČR KAN100400702 Institutional research plan: CEZ:AV0Z40400503 Keywords : spectroscopy * DFT technique * ruthenium carbonrlydiimine complexes Subject RIV: CG - Electrochemistry Impact factor: 4.147, year: 2008

  6. DFT study of phonon dispersion in pure graphene

    Science.gov (United States)

    Mann, Sarita; Rani, Pooja; Kumar, Ranjan; Jindal, V. K.

    2015-08-01

    Ab-initio density functional perturbation theory (DFPT) study of pure graphene has been performed to study the phonon dispersion curve. The Specific heat at constant volume has been calculated and has been compared with theoretical and experimental results. The dynamical matrix has been calculated using VASP software under both simple DFT and DFPT approximation. The phonon frequencies have been calculated using phonopy code under harmonic approximation. The phonon frequencies are then used in calculating dispersion curve and specific heat at constant volume which is in reasonable agreement with available theoretical and experimental results for pure graphene. The specific heat of pristine graphene at constant value has been found to be 1.3 J g-1K-1.

  7. Laparoscopy After Previous Laparotomy

    Directory of Open Access Journals (Sweden)

    Zulfo Godinjak

    2006-11-01

    Full Text Available Following the abdominal surgery, extensive adhesions often occur and they can cause difficulties during laparoscopic operations. However, previous laparotomy is not considered to be a contraindication for laparoscopy. The aim of this study is to present that an insertion of Veres needle in the region of umbilicus is a safe method for creating a pneumoperitoneum for laparoscopic operations after previous laparotomy. In the last three years, we have performed 144 laparoscopic operations in patients that previously underwent one or two laparotomies. Pathology of digestive system, genital organs, Cesarean Section or abdominal war injuries were the most common causes of previouslaparotomy. During those operations or during entering into abdominal cavity we have not experienced any complications, while in 7 patients we performed conversion to laparotomy following the diagnostic laparoscopy. In all patients an insertion of Veres needle and trocar insertion in the umbilical region was performed, namely a technique of closed laparoscopy. Not even in one patient adhesions in the region of umbilicus were found, and no abdominal organs were injured.

  8. Hydrogen molecule on lithium adsorbed graphene: A DFT study

    International Nuclear Information System (INIS)

    Kaur, Gagandeep; Gupta, Shuchi; Gaganpreet; Dharamvir, Keya

    2016-01-01

    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 H 2 is lying parallel to lithium adsorbed graphene which is in contrast to its adsorption on pristine graphene (PG) where it prefers perpendicular orientation.

  9. Synthesis, X-ray, NMR, FT-IR, UV/vis, DFT and TD-DFT studies of N-(4-chlorobutanoyl)-N'-(2-, 3- and 4-methylphenyl)thiourea derivatives.

    Science.gov (United States)

    Abosadiya, Hamza M; Anouar, El Hassane; Hasbullah, Siti Aishah; Yamin, Bohari M

    2015-06-05

    A new isomers of thiourea derivatives, namely N-(4-chlorobutanoyl)-N'-(2-methylphenyl)-thiourea (1a), N-(4-chlorobutanoyl)-N'-(3-methylphenyl)thiourea (1b) and N-(4-chlorobutanoyl)-N'-(4-methylphenyl)thiourea (1c) have been synthesized by refluxing mixture of equimolar amounts of 4-chlorobutanoylisothiocyanate with 2, 3 or 4-toluidine, respectively. The three isomers were characterized by spectroscopic (UV/vis, FT-IR and NMR) and X-ray crystallography techniques. To investigate the isomerization effect on spectroscopic data, DFT and TD-DFT calculations have been carried out using five hybrid functionals (B3LYP, B3P86, CAM-B3LYP, M06-2X and PBE0) to predict UV/vis absorption bands (n→π∗ and π→π∗), (1)H and (13)C NMR chemical shifts, FT-IR vibration modes and X-ray parameters (bonds, bond angles and torsion angles) for 1a, 1b and 1c isomers. The results showed that the isomerization effect is significant on λ(MAX) absorption bands, while for IR and NMR the effect is negligible. In accordance with previous studies, B3LYP, B3P86 and PBE0 gave the most reliable to predict the excitation energies of thiourea derivatives. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. 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.

  11. A DFT and NBO Analysis of the Bonding in Titanocenyl Complexes ...

    African Journals Online (AJOL)

    NICO

    atoms L and L' containing different donor/acceptor properties, viz. L,L'= O,O'; S,S' or Se,Se'. An NBO analysis quantifies the degree of the Ti←ligand π-charge transfer. 2. Theoretical Approach. Density functional theory (DFT) calculations were carried out using the GAUSSIAN 03 program9 with the PW91 exchange and.

  12. DFT study of the reactions of Mo and Mo with CO2 in gas phase

    Indian Academy of Sciences (India)

    Abstract. Density functional theory (DFT) calculations have been performed to explore the potential energy surfaces of C–O bond activation in CO2 molecule by gas-phase Mo. + cation and Mo atom, in order to better understanding the mechanism of second-row metal reacting with CO2. The minimum energy reaction path is.

  13. Synthesis, spectroscopy, X-ray crystallography, and DFT computations of nanosized phosphazenes

    Czech Academy of Sciences Publication Activity Database

    Shariatinia, Z.; Moghadam, E.J.; Maghsoudi, N.; Mousavi, H.S.M.; Dušek, Michal; Eigner, Václav

    2015-01-01

    Roč. 641, č. 5 (2015), s. 967-978 ISSN 0044-2313 Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : phosphazene * ultrasonic * nanoparticle * x-ray crystallography * DFT calculation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.261, year: 2015

  14. A DFT study on the mechanism of palladium-catalyzed divergent ...

    Indian Academy of Sciences (India)

    Abstract. The reaction mechanisms of palladium-catalyzed divergent reactions of 1,6-enyne carbonates have been investigated using DFT calculations at the B3LYP/6-31G(d,p) (LanL2DZ for Pd) level. Solvent effects on these reactions have been considered by the polarizable continuum model (PCM) for the solvent (DMF).

  15. NMR, MP2 and DFT Study of Thiophenoxyketenimines (o-ThioSchiff bases)

    DEFF Research Database (Denmark)

    Saeed, Bahjat Ali; Elias, Rita Sabah; Kamounah, Fadhil S.

    2018-01-01

    Five new thiophenoxyketinimines have been synthesized. 1 H and 13 C NMR spectra as well as deuterium isotope effects on 13 C chemical shifts are determined, and spectra are assigned. DFT and MP2 calculations of both structures, chemical shifts, and isotope effects on chemical shifts are done. The...

  16. Complexation of the cesium cation with lithium ionophore VIII: extraction and DFT study

    Czech Academy of Sciences Publication Activity Database

    Makrlík, E.; Novák, Vít; Vaňura, P.; Bouř, Petr

    2013-01-01

    Roč. 298, č. 3 (2013), s. 2065-2068 ISSN 0236-5731 Institutional support: RVO:61388963 Keywords : cesium cation * lithium ionophore VIII * complexation * extraction and stability constants * water-nitrobenzene system * DFT calculations * structures Subject RIV: CB - Analytical Chemistry , Separation Impact factor: 1.415, year: 2013

  17. Efficacy of the DFT + U formalism for modeling hole polarons in perovskite oxides

    Science.gov (United States)

    Erhart, Paul; Klein, Andreas; Åberg, Daniel; Sadigh, Babak

    2014-07-01

    We investigate the formation of self-trapped holes (STH) in three prototypical perovskites (SrTiO3, BaTiO3, PbTiO3) using a combination of density functional theory (DFT) calculations with local potentials and hybrid functionals. First we construct a local correction potential for polaronic configurations in SrTiO3 that is applied via the DFT + U method and matches the forces from hybrid calculations. We then use the DFT + U potential to search the configuration space and locate the lowest energy STH configuration. It is demonstrated that both the DFT + U potential and the hybrid functional yield a piecewise linear dependence of the total energy on the occupation of the STH level, suggesting that self-interaction effects have been properly removed. The DFT + U model is found to be transferable to BaTiO3 and PbTiO3, and STH formation energies from DFT + U and hybrid calculations are in close agreement for all three materials. STH formation is found to be energetically favorable in SrTiO3 and BaTiO3 but not in PbTiO3, which can be rationalized by considering the alignment of the valence band edges on an absolute energy scale. In the case of PbTiO3 the strong coupling between Pb 6s and O 2p states lifts the valence band minimum (VBM) compared to SrTiO3 and BaTiO3. This reduces the separation between VBM and STH level and renders the STH configuration metastable with respect to delocalization (band hole state). We expect that the present approach can be adapted to study STH formation also in oxides with different crystal structures and chemical compositions.

  18. Post-DFT methods for Earth materials: Quantum Monte Carlo simulations of (Mg,Fe)O (Invited)

    Science.gov (United States)

    Driver, K. P.; Militzer, B.; Cohen, R. E.

    2013-12-01

    (Mg,Fe)O is a major mineral phase in Earth's lower mantle that plays a key role in determining the structural and dynamical properties of deep Earth. A pressure-induced spin-pairing transition of Fe has been the subject of numerous theoretical and experimental studies due to the consequential effects on lower mantle physics. The standard density functional theory (DFT) method does not treat strongly correlated electrons properly and results can have dependence on the choice of exchange-correlation functional. DFT+U, offers significant improvement over standard DFT for treating strongly correlated electrons. Indeed, DFT+U calculations and experiments have narrowed the ambient spin-transition between 40-60 GPa in (Mg,Fe)O. However, DFT+U, is not an ideal method due to dependence on Hubbard U parameter among other approximations. In order to further clarify details of the spin transition, it is necessary to use methods that explicitly treat effects of electron exchange and correlation, such as quantum Monte Carlo (QMC). Here, we will discuss methods of going beyond standard DFT and present QMC results on the (Mg,Fe)O elastic properties and spin-transition pressure in order to benchmark DFT+U results.

  19. Reactive sites influence in PMMA oligomers reactivity: a DFT study

    Science.gov (United States)

    Paz, C. V.; Vásquez, S. R.; Flores, N.; García, L.; Rico, J. L.

    2018-01-01

    In this work, we present a theoretical study of methyl methacrylate (MMA) living anionic polymerization. The study was addressed to understanding two important experimental observations made for Michael Szwarc in 1956. The unexpected effect of reactive sites concentration in the propagation rate, and the self-killer behavior of MMA (deactivating of living anionic polymerization). The theoretical calculations were performed by density functional theory (DFT) to obtain the frontier molecular orbitals values. These values were used to calculate and analyze the chemical interaction descriptors in DFT-Koopmans’ theorem. As a result, it was observed that the longest chain-length species (related with low concentration of reactive sites) exhibit the highest reactivity (behavior associated with the increase of the propagation rate). The improvement in this reactivity was attributed to the crosslinking produced in the polymethyl methacrylate chains. Meanwhile, the self-killer behavior was associated with the intermolecular forces present in the reactive sites. This behavior was associated to an obstruction in solvation, since the active sites remained active through all propagation species. The theoretical results were in good agreement with the Szwarc experiments.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. Palladium dimers adsorbed on graphene: A DFT study

    International Nuclear Information System (INIS)

    Kaur, Gagandeep; Gupta, Shuchi; Dharamvir, Keya

    2015-01-01

    The 2D structure of graphene shows a great promise for enhanced catalytic activity when adsorbed with palladium. We performed a systematic density functional theory (DFT) study of the adsorption of palladium dimer (Pd 2 ) on graphene using SIESTA package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, and charge transfer of Pd 2 -graphene system are calculated. Both horizontal and vertical orientations of Pd 2 on graphene are studied. Our calculations revealed that the minimum energy configuration for Pd dimer is parallel to the graphene sheet with its two atoms occupying centre of adjacent hexagonal rings of graphene sheet. Magnetic moment is induced for Pd dimer adsorbed on graphene in vertical orientation while horizontal orientation of Pd dimer on graphene do not exhibit magnetism. Insignificant energy differences among adsorption sites means that dimer mobility on the graphene sheet is high. There is imperceptible distortion of graphene sheet perpendicular to its plane. However, some lateral displacements are seen

  5. 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…

  6. Periodic DFT+U investigation of the bulk and surface properties of marcasite (FeS2)

    NARCIS (Netherlands)

    Dzade, Nelson Y.; de Leeuw, Nora H.

    2017-01-01

    Marcasite FeS2 and its surface properties have been investigated by Hubbard-corrected Density Functional Theory (DFT+U) calculations. The calculated structural parameters, interatomic bond distances, elastic constants and electronic properties of the bulk mineral were determined and compared with

  7. Accurate and efficient band gap predictions of metal halide perovskites using the DFT-1/2 method: GW accuracy with DFT expense.

    Science.gov (United States)

    Tao, Shu Xia; Cao, Xi; Bobbert, Peter A

    2017-10-30

    The outstanding optoelectronics and photovoltaic properties of metal halide perovskites, including high carrier motilities, low carrier recombination rates, and the tunable spectral absorption range are attributed to the unique electronic properties of these materials. While DFT provides reliable structures and stabilities of perovskites, it performs poorly in electronic structure prediction. The relativistic GW approximation has been demonstrated to be able to capture electronic structure accurately, but at an extremely high computational cost. Here we report efficient and accurate band gap calculations of halide metal perovskites by using the approximate quasiparticle DFT-1/2 method. Using AMX 3 (A = CH 3 NH 3 , CH 2 NHCH 2 , Cs; M = Pb, Sn, X = I, Br, Cl) as demonstration, the influence of the crystal structure (cubic, tetragonal or orthorhombic), variation of ions (different A, M and X) and relativistic effects on the electronic structure are systematically studied and compared with experimental results. Our results show that the DFT-1/2 method yields accurate band gaps with the precision of the GW method with no more computational cost than standard DFT. This opens the possibility of accurate electronic structure prediction of sophisticated halide perovskite structures and new materials design for lead-free materials.

  8. Error compensation of IQ modulator using two-dimensional DFT

    Science.gov (United States)

    Ohshima, Takashi; Maesaka, Hirokazu; Matsubara, Shinichi; Otake, Yuji

    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.

  9. 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....

  10. A conceptual DFT approach towards analysing toxicity

    Indian Academy of Sciences (India)

    ... 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 ...

  11. Structures and energetics of lithium adatom and its dimer on graphene–a DFT study

    International Nuclear Information System (INIS)

    Kaur, Gagandeep; Gupta, Shuchi; Dharamvir, Keya

    2015-01-01

    Highlights: • For single Li adatom adsorption on graphene, it prefers H-site followed by B-site. • By the examination of the calculated cohesive energies, it is possible to conclude that both Li/Li 2 binds strongly to graphene which corroborate previous results. • The calculations showed that the interaction between Li and graphene has minimal effects on the electronic states of the graphene sheet, in agreement with previous calculations. • Charge transfer (0.338e)upon adsorption also induces significant electric dipole moments and affect total magnetic moment at B-site and T-site. • For the Li dimer adsorption, we found that horizontal orientation is favored over the vertical. • Adsorption of lithium dimer to the HH-site alters graphene sheet only by small amount ∼0.0022 Å–0.0034 Å. • The methodology demonstrated in this paper maybe applied to larger lithium clusters on graphene sheet. - Abstract: We performed a systematic density functional theory (DFT) study of the adsorption of Lithium adatom and its dimer on graphene using SIESTA package [1], in the generalized gradient approximation (GGA). The adsorption energy, geometry, charge transfer and density of states of adatom/dimer-graphene system are calculated. The calculations showed that the interaction between Li adatom and graphene is strong (∼1.07 eV) and it prefers to adsorb on H-site. Further calculations of both horizontally and vertically aligned dimers show that the adsorption is also weak for the latter orientation. The preferred orientation of each dimer was found to be parallel to graphene sheet with the two atoms of the dimer occupying adjacent H-sites on the graphene. Significant charge transfer (∼0.388e) from Li adatom to graphene will induce electric dipole moments in the adatom/graphene system. We also calculated DOS for the stable Li -graphene system. The Fermi energy is seen to lie above the Dirac point inside the conduction band indicating that appreciable electrons

  12. Crystal structure relation between tetragonal and orthorhombic CsAlD{sub 4}: DFT and time-of-flight neutron powder diffraction studies

    Energy Technology Data Exchange (ETDEWEB)

    Bernert, Thomas; Krech, Daniel; Felderhoff, Michael; Weidenthaler, Claudia [Department of Heterogeneous Catalysis, Max-Planck-Institut fuer Kohlenforschung, Muelheim/Ruhr (Germany); Kockelmann, Winfried [Rutherford Appleton Laboratory, Harwell Oxford, Didcot (United Kingdom); Frankcombe, Terry J. [Research School of Chemistry, The Australian National University, Canberra, ACT (Australia); School of Physical, Environmental and Mathematic Sciences, The University of New South Wales, Canberra, ACT (Australia)

    2015-11-15

    The crystal structures of orthorhombic and tetragonal CsAlD{sub 4} were refined from time-of-flight neutron powder diffraction data starting from atomic positions predicted from DFT calculations. The earlier proposed crystal structure of orthorhombic CsAlH{sub 4} is confirmed. For tetragonal CsAlH{sub 4}, DFT calculations predicted a crystal structure in I4{sub 1}/amd as potential minimum structure, while from neutron diffraction studies of CsAlD{sub 4} best refinement is obtained for a disordered structure in the space group I4{sub 1}/a, with a = 5.67231(9) Aa, c = 14.2823(5) Aa. While the caesium atoms are located on the Wyckoff position 4b and aluminium at Wyckoff position 4a, there are two distinct deuterium positions at the Wyckoff position 16f with occupancies of 50 % each. From this structure, the previously reported phase transition between the orthorhombic and tetragonal polymorphs could be explained. (Copyright copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Tight-binding density functional theory: an approximate Kohn-Sham DFT scheme.

    Science.gov (United States)

    Seifert, G

    2007-07-05

    The DFTB method is an approximate KS-DFT scheme with an LCAO representation of the KS orbitals, which can be derived within a variational treatment of an approximate KS energy functional. But it may also be related to cellular Wigner-Seitz methods and to the Harris functional. It is an approximate method, but it avoids any empirical parametrization by calculating the Hamiltonian and overlap matrices out of DFT-derived local orbitals (atomic orbitals, AO's). The method includes ab initio concepts in relating the Kohn-Sham orbitals of the atomic configuration to a minimal basis of the localized atomic valence orbitals of the atoms. Consistent with this approximation, the Hamiltonian matrix elements can strictly be restricted to a two-center representation. Taking advantage of the compensation of the so-called "double counting terms" and the nuclear repulsion energy in the DFT total energy expression, the energy may be approximated as a sum of the occupied KS single-particle energies and a repulsive energy, which can be obtained from DFT calculations in properly chosen reference systems. This relates the method to common standard "tight-binding" (TB) schemes, as they are well-known in solid-state physics. This approach defines the density-functional tight-binding (DFTB) method in its original (non-self-consistent) version.

  14. Accuracy of Td-DFT in the Ultraviolet and Circular Dichroism Spectra of Deoxyguanosine and Uridine.

    Science.gov (United States)

    Miyahara, Tomoo; Nakatsuji, Hiroshi

    2018-01-11

    Accuracy of the time-dependent density functional theory (Td-DFT) was examined for the ultraviolet (UV) and circular dichroism (CD) spectra of deoxyguanosine (dG) and uridine, using 11 different DFT functionals and two different basis sets. The Td-DFT results of the UV and CD spectra were strongly dependent on the functionals used. The basis-set dependence was observed only for the CD spectral calculations. For the UV spectra, the B3LYP and PBE0 functionals gave relatively good results. For the CD spectra, the B3LYP and PBE0 with 6-311G(d,p) basis gave relatively permissible result only for dG. The results of other functionals were difficult to be used for the studies of the UV and CD spectra, though the symmetry adapted cluster-configuration interaction (SAC-CI) method reproduced well the experimental spectra of these molecules. To obtain valuable information from the theoretical calculations of the UV and CD spectra, the theoretical tool must be able to reproduce correctly both of the intensities and peak positions of the UV and CD spectra. Then, we can analyze the reasons of the changes of the intensity and/or the peak position to clarify the chemistry involved. It is difficult to recommend Td-DFT as such tools of science, at least from the examinations using dG and uridine.

  15. Probing the molecular and electronic structure of the lichen metabolite usnic acid: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Galasso, V., E-mail: galasso@univ.trieste.it [Dipartimento di Scienze Chimiche, Universita di Trieste, I-34127 Trieste (Italy)

    2010-08-23

    Graphical abstract: DFT calculations of structural preferences, acidic properties, carbonyl vibrations, {sup 13}C NMR chemical shifts, and absorption spectrum account for the unique structural backbone, chemical behaviour, and spectroscopic properties of usnic acid, the cortical pigment and potent reactive of lichens. - Abstract: The molecular structure of usnic acid was investigated by the density functional theory (DFT). Two keto-enol tautomers are nearly isoenergetic and more stable than other tautomers. Noteworthy is the energy difference among the three intramolecular O-H...O hydrogen bonds. The DFT/PCM calculated dissociation constants account for the acidic sequence of the three OH-groups. The electronic structure was also studied by calculating IR/Raman, NMR, and absorption features. A reliable assignment of the 'fingerprint' carbonyl stretching modes was supported by calculations on related molecules. The calculated NMR chemical shifts fit expectation in terms of a fast interconversion between the two most preferred tautomers. A variety of {pi} {yields} {pi}* and n {yields} {pi}* excitations, localized on a single ring or involving a charge-transfer between the two lateral rings of the molecule, gives rise to the broad UV-absorption bands. This property accounts for the efficient protection against damaging solar radiation provided by usnic acid for lichens.

  16. Benchmark CCSD-SAPT study of rare gas dimers with comparison to MP-SAPT and DFT-SAPT

    Science.gov (United States)

    Shirkov, Leonid; Sladek, Vladimir

    2017-11-01

    Symmetry-adapted perturbation theory (SAPT) based on coupled cluster approach with single and double excitations (CCSD) treatment of intramonomer electron correlation effects was applied to study rare gas homodimers from He2 to Kr2. The obtained benchmark CCSD-SAPT energies, including cumulant contributions to first order exchange and second-order exchange-induction terms, were then compared to their counterparts found using other methods—MP-SAPT based on many-body Møller-Plesset perturbation theory and DFT-SAPT based on density functional theory. The SAPT terms up to the second-order were calculated with the basis sets close to the complete basis set at the large range of interatomic distances R. It was shown that overestimation of the binding energies De found with DFT-SAPT reported in the work of Shirkov and Makarewicz [J. Chem. Phys. 142, 064102 (2015)] for Ar2 and Kr2 is mostly due to underestimation of the exchange energy Eexch(1 ) when comparing to the CCSD-SAPT benchmark. The CCSD-SAPT potentials were found to give the following values of the dissociation energies D0: 0.0006 cm-1 for He2, 16.71 cm-1 for Ne2, 85.03 cm-1 for Ar2, and 129.81 cm-1 for Kr2, which agree well with the values found from previously reported highly accurate ab initio supermolecular potentials and experimental data. The long-range dispersion coefficients C2n up to n = 6 that give the dispersion energy asymptotically equivalent to its SAPT counterpart were calculated from dynamic multipole polarizabilities at different levels of theory.

  17. Surface Pourbaix diagrams and oxygen reduction activity of Pt, Ag and Ni(111) surfaces studied by DFT

    DEFF Research Database (Denmark)

    Hansen, Heine Anton; Rossmeisl, Jan; Nørskov, Jens Kehlet

    2008-01-01

    The electrochemical most stable surface structures is investigated as function of pH and potential for Pt, Ag and Ni based on DFT calculations and constructed surface Pourbaix diagrams. It is also explained why metals such as Ag and Ni may be used successfully in alkaline fuel cells but not in ac......The electrochemical most stable surface structures is investigated as function of pH and potential for Pt, Ag and Ni based on DFT calculations and constructed surface Pourbaix diagrams. It is also explained why metals such as Ag and Ni may be used successfully in alkaline fuel cells...

  18. Synthesis and antibacterial activity of sulfonamides. SAR and DFT studies

    Science.gov (United States)

    Boufas, Wahida; Dupont, Nathalie; Berredjem, Malika; Berrezag, Kamel; Becheker, Imène; Berredjem, Hajira; Aouf, Nour-Eddine

    2014-09-01

    A series of substituted sulfonamide derivatives were synthesized from chlorosulfonyl isocyanate (CSI) in tree steps (carbamoylation, sulfamoylation and deprotection). Antibacterial activity in vitro of some newly formed compounds investigated against clinical strains Gram-positive and Gram-negative: Escherichia coli and Staphylococcus aureus applying the method of dilution and minimal inhibition concentration (MIC) methods. These compounds have significant bacteriostatic activity with totalities of bacterial strains used. DFT calculations with B3LYP/6-31G(d) level have been used to analyze the electronic and geometric characteristics deduced for the stable structure of three compounds presenting conjugation between a nitrogen atom N through its lone pair and an aromatic ring next to it. The principal quantum chemical descriptors have been correlated with the antibacterial activity.

  19. Accelerated DFT-Based Design of Materials for Ammonia Storage

    DEFF Research Database (Denmark)

    Jensen, Peter Bjerre; Bialy, Agata; Blanchard, Didier

    2015-01-01

    . Therefore, there is a need for new materials, releasing the ammonia in a narrow temperature interval. To search for new mixed metal halide chlorides, we use DFT calculations guided by a genetic algorithm (GA) to expedite the search, as the defined search space allowing up to three different metals contains...... more than 100,000 different structures. Here, we search for materials releasing the ammonia between 0 and 100 °C, a temperature range suitable for system integration with low-temperature polymer electrolyte membrane fuel cells (PEMFC). The efficiency of the implemented algorithm is verified by three...... trial runs capable of finding the same optimal mixtures starting from different random populations, testing

  20. Excited-state properties from ground-state DFT descriptors: A QSPR approach for dyes.

    Science.gov (United States)

    Fayet, Guillaume; Jacquemin, Denis; Wathelet, Valérie; Perpète, Eric A; Rotureau, Patricia; Adamo, Carlo

    2010-02-26

    This work presents a quantitative structure-property relationship (QSPR)-based approach allowing an accurate prediction of the excited-state properties of organic dyes (anthraquinones and azobenzenes) from ground-state molecular descriptors, obtained within the (conceptual) density functional theory (DFT) framework. The ab initio computation of the descriptors was achieved at several levels of theory, so that the influence of the basis set size as well as of the modeling of environmental effects could be statistically quantified. It turns out that, for the entire data set, a statistically-robust four-variable multiple linear regression based on PCM-PBE0/6-31G calculations delivers a R(adj)(2) of 0.93 associated to predictive errors allowing for rapid and efficient dye design. All the selected descriptors are independent of the dye's family, an advantage over previously designed QSPR schemes. On top of that, the obtained accuracy is comparable to the one of the today's reference methods while exceeding the one of hardness-based fittings. QSPR relationships specific to both families of dyes have also been built up. This work paves the way towards reliable and computationally affordable color design for organic dyes. Copyright 2009 Elsevier Inc. All rights reserved.

  1. DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

    Science.gov (United States)

    Stawoska, I.; Dudzik, A.; Wasylewski, M.; Jemioła-Rzemińska, M.; Skoczowski, A.; Strzałka, K.; Szaleniec, M.

    2017-06-01

    The reaction mechanism of ketone reduction by short chain dehydrogenase/reductase, ( S)-1-phenylethanol dehydrogenase from Aromatoleum aromaticum, was studied with DFT methods using cluster model approach. The characteristics of the hydride transfer process were investigated based on reaction of acetophenone and its eight structural analogues. The results confirmed previously suggested concomitant transfer of hydride from NADH to carbonyl C atom of the substrate with proton transfer from Tyr to carbonyl O atom. However, additional coupled motion of the next proton in the proton-relay system, between O2' ribose hydroxyl and Tyr154 was observed. The protonation of Lys158 seems not to affect the pKa of Tyr154, as the stable tyrosyl anion was observed only for a neutral Lys158 in the high pH model. The calculated reaction energies and reaction barriers were calibrated by calorimetric and kinetic methods. This allowed an excellent prediction of the reaction enthalpies (R2 = 0.93) and a good prediction of the reaction kinetics (R2 = 0.89). The observed relations were validated in prediction of log K eq obtained for real whole-cell reactor systems that modelled industrial synthesis of S-alcohols.

  2. A DFT study on the deprotonation antioxidant mechanistic step of ortho-substituted phenolic cation radicals

    International Nuclear Information System (INIS)

    Vafiadis, Anastasios P.; Bakalbassis, Evangelos G.

    2005-01-01

    The conformers of the 2-, 3- and 4-substituted phenolic cation radicals, 2-X-, 3-X- and 4-X-ArOH ·+ , and the respective phenoxyl radicals, ArO · , the intramolecular hydrogen bond strength (ΔH intra ) estimate along with the electronic effects of five electron withdrawing (EWG) and eight electron donating groups (EDG) on the gas-phase O-H proton dissociation enthalpies, (PDEs), of the short-lived, 2-X-ArOH ·+ , (involved in the single-electron transfer antioxidant mechanism), are studied at the DFT/B3LYP level of theory. EWG result to smaller PDEs, hence to stronger acidity; EDG to weaker acidity. The deprotonation antioxidant mechanistic step is not a rate-controlling step for 2-X-ArOH to scavenge free radicals. Approximate estimations of the ΔPDEs (hence acidities as well) can be derived from calculated structural and/or vibrational frequency values. ΔH intra s correlate reasonably with geometrical parameters for the closed-shell, neutral counterparts, in contrast with previous estimates

  3. DFT model cluster studies of O₂ adsorption on hydrogenated titania sub-nanoparticles.

    Science.gov (United States)

    Andreev, Alexey S; Kuznetsov, Vyacheslav N; Chizhov, Yuri V

    2013-11-01

    In the present paper, we examine the general applicability of different TiO2 model clusters to study of local chemical events on TiO2 sub-nanoparticles. Our previous DFT study of TiO2 activation through H adsorption and following deactivation by O2 adsorption using small amorphous Ti8O16 cluster were complemented by examination of rutile-type and spherical Ti15O30 nanoclusters. The obtained results were thoroughly compared with experimental data and results of related computational studies using other TiO2 models including periodic structures. It turned out that all considered model TiO2 model systems provide qualitatively similar results. It was shown that atomic hydrogen is adsorbed with negligible activation energy on surface O atoms, which is accompanied by the appearance of reduced Ti(3+) species and corresponding localized band gap 3d-Ti states. Oxygen molecule is adsorbed on Ti(3+) sites spontaneously forming molecular O2 (-) species by capturing an extra electron of Ti(3+) ion, which results in disappearance of Ti(3+) species and corresponding band gap states. Calculated g-tensor values of Ti(3+) and O2 (-) species agree well with the results of EPR studies and do not depend on the used TiO2 model cluster. Additionally, it was shown that the various cluster calculations provide results comparable with the calculations of periodic structures with respect to the modeling of chemical processes under study. As a whole, the present study approves the validity of molecular cluster approach to study of local chemical events on TiO2 sub-nanoparticles.

  4. DFT and TD-DFT study on geometries, electronic structures and electronic absorption of some metal free dye sensitizers for dye sensitized solar cells.

    Science.gov (United States)

    Mohr, T; Aroulmoji, V; Ravindran, R Samson; Müller, M; Ranjitha, S; Rajarajan, G; Anbarasan, P M

    2015-01-25

    The geometries, electronic structures, polarizabilities and hyperpolarizabilities of 2-hydroxynaphthalene-1,4-dione (henna1), 3-(5-((1E)-2-(1,4-dihydro-1,4-dioxonaphthalen-3-yloxy) vinyl) thiophen-2-yl)-2-isocyanoacrylic acid (henna2) and anthocyanin dye sensitizers were studied based on density functional theory (DFT) using the hybrid functional B3LYP. The Ultraviolet-Visible (UV-Vis) spectrum was investigated by using a hybrid method which combines the properties and dynamics of many-body in the presence of time-dependent (TD) potentials, i.e. TDSCF-DFT (B3LYP). Features of the electronic absorption spectrum in the visible and near-UV regions were plotted and assigned based on TD-DFT calculations. Due to the absorption, bands of the metal-organic compound are n→π(*) present. The calculated results suggest that the three lowest energy excited states of the investigated dye sensitizers are due to photoinduced electron transfer processes. The interfacial electron transfer between semiconductor TiO2 electrode and dye sensitizer is owing to an electron injection process from excited dye to the semiconductor's conduction band. The role of linking the henna1 dye with a carboxylic acid via a thiophene bridge was analyzed. The results are that using a stronger π-conjugate bridge as well as a strong donator and acceptor group enhances the efficiency. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Fractional Electron Loss in Approximate DFT and Hartree-Fock Theory.

    Science.gov (United States)

    Peach, Michael J G; Teale, Andrew M; Helgaker, Trygve; Tozer, David J

    2015-11-10

    Plots of electronic energy vs electron number, determined using approximate density functional theory (DFT) and Hartree-Fock theory, are typically piecewise convex and piecewise concave, respectively. The curves also commonly exhibit a minimum and maximum, respectively, in the neutral → anion segment, which lead to positive DFT anion HOMO energies and positive Hartree-Fock neutral LUMO energies. These minima/maxima are a consequence of using basis sets that are local to the system, preventing fractional electron loss. Ground-state curves are presented that illustrate the idealized behavior that would occur if the basis set were to be modified to enable fractional electron loss without changing the description in the vicinity of the system. The key feature is that the energy cannot increase when the electron number increases, so the slope cannot be anywhere positive, meaning frontier orbital energies cannot be positive. For the convex (DFT) case, the idealized curve is flat beyond a critical electron number such that any additional fraction of an electron added to the system is unbound. The anion HOMO energy is zero. For the concave (Hartree-Fock) case, the idealized curve is flat up to some critical electron number, beyond which it curves down to the anion energy. A minimum fraction of an electron is required before any binding occurs, but beyond that, the full fraction abruptly binds. The neutral LUMO energy is zero. Approximate DFT and Hartree-Fock results are presented for the F → F(-) segment, and results approaching the idealized behavior are recovered for highly diffuse basis sets. It is noted that if a DFT calculation using a highly diffuse basis set yields a negative LUMO energy then a fraction of an electron must bind and the electron affinity must be positive, irrespective of whether an electron binds experimentally. This is illustrated by calculations on Ne → Ne(-).

  6. Synthesis and spectroscopic characterization on 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid: A DFT approach.

    Science.gov (United States)

    Kurt, M; Sas, E Babur; Can, M; Okur, S; Icli, S; Demic, S; Karabacak, M; Jayavarthanan, T; Sundaraganesan, N

    2016-01-05

    A complete structural and vibrational analysis of the 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid (TPBA), was carried out by ab initio calculations, at the density functional theory (DFT) method. Molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO) (13)C NMR and (1)H NMR chemical shift values of (TPBA), in the ground state have been calculated by using ab initio density functional theory (DFT/B3LYP) method with 6-311G(d,p) as basis set for the first time. Comparison of the observed fundamental vibrational modes of (TPBA) and calculated results by DFT/B3LYP method indicates that B3LYP level of theory giving yield good results for quantum chemical studies. Vibrational wavenumbers obtained by the DFT/B3LYP method are in good agreement with the experimental data. The study was complemented with a natural bond orbital (NBO) analysis, to evaluate the significance of hyperconjugative interactions and electrostatic effects on such molecular structure. 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. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals analysis and thermodynamic properties of TPBA were investigated using theoretical calculations. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. The effect of zinc ion on the absorption and emission spectra of glutathione derivative: predication by ab initio and DFT methods.

    Science.gov (United States)

    Liu, Jianhua; Ma, Jie; Zhang, Hua; Wang, Haijun

    2012-06-01

    Relying on the reaction of o-phthalaldehyde (OPA) with glutathione (GSH) to form a highly fluorescence derivative GSH-OPA has been widely used to measure reduced glutathione. In order to better understand spectra property of the GSH-OPA and the effect of zinc ion on it, the ground and the lowest singlet excited state properties, the electronic absorption and emission spectra are predicted by ab initio and DFT methods. The absorption spectra are simulated using time dependent DFT method (TD-DFT) whereas the emission spectra are approximated by optimizing the lowest singlet excited state by HF/CI-Singles and then subsequently using this geometry for the TD-DFT calculations. The solvent effects on transition energies have been described within the conductor-like polarizable continuum model (CPCM). The calculated transition energies (absorption and emission) are in agreement with available experimental information. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Density functional theory calculations of Rh-β-diketonato complexes.

    Science.gov (United States)

    Conradie, J

    2015-01-28

    Density functional theory (DFT) results on the geometry, energies and charges of selected Rh-β-diketonato reactants, products and transition states are discussed. Various DFT techniques are used to increase our understanding of the orientation of ligands coordinated to Rh, to identify the lowest energy geometry of possible geometrical isomers and to get a molecular orbital understanding of ground and transition states. Trends and relationships obtained between DFT calculated energies and charges, experimentally measured values and electronic parameters describing the electron donating power of groups and ligands, enable the design of ligands and complexes of specific reactivity.

  9. DFT investigations of the piezoresistive effect of carbon nanotubes for sensor application

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, Christian [Center for Microtechnologies, Chemnitz University of Technology, 09126 Chemnitz (Germany); Schuster, Joerg [Fraunhofer Institute for Electronic Nanosystems (ENAS), Technologie-Campus 3, 09126 Chemnitz (Germany); Gessner, Thomas [Center for Microtechnologies, Chemnitz University of Technology, 09126 Chemnitz (Germany); Fraunhofer Institute for Electronic Nanosystems (ENAS), Technologie-Campus 3, 09126 Chemnitz (Germany)

    2012-12-15

    We investigate the piezoresistive effect of carbon nanotubes (CNTs) within density functional theory (DFT) aiming at application-relevant CNTs. CNTs are excellent candidates for the usage in nano-electromechanical sensors (NEMSs) due to their small band gap at zero strain leading to a finite resistivity at room temperature. The application of strain induces a band gap-opening leading to a tremendous change in the resistivity. DFT with the LDA approximation yields reasonable results for pure carbon systems like CNTs and is applied to calculate the electronic structure of experimentally relevant CNTs. For the transport part, a simple ballistic transport model based on the band gap is used. We compare our DFT results for the band gaps of strained CNTs to results of tight binding (TB) models. By introducing a scaling factor of {radical}2, an excellent agreement of the DFT data with TB model, published by Yang and Han [Phys. Rev. Lett. 85, 154 (2000)], is obtained. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  10. A novel correction scheme for DFT: A combined vdW-DF/CCSD(T) approach

    Science.gov (United States)

    Hermann, Jan; Bludský, Ota

    2013-07-01

    A system-specific but very accurate density functional theory (DFT) correction scheme is proposed for precise calculations of adsorbent-adsorbate interactions by combining the non-empirical van der Waals density functional (vdW-DF) method and the empirical DFT/CC correction scheme to reach accuracy of the coupled clusters method with single, double and perturbative triple excitations (CCSD(T)). The new approach is applied to small molecules (CH4, CO2, H2, H2O, N2) interacting with silica surfaces and purely siliceous microporous solids. The vdW-DF/CC results for a perfectly reconstructed α-quartz surface are consistent with other dispersion-corrected DFT methods. Corrected for ZPVE, the vdW-DF/CC enthalpies of adsorption in pure-silica zeolite LTA (ΔHads(0 K)) of 3.6 and 5.2 kcal/mol for methane and carbon dioxide, respectively, are in excellent agreement with experimental values of 3.6 and 5.0 kcal/mol. The very high accuracy of the new scheme and its relatively easy use and numerical stability as compared to the earlier DFT/CC scheme offer a straightforward solution for obtaining reliable predictions of adsorption energies.

  11. The nucleon localization function in static and time-dependent DFT

    Science.gov (United States)

    Schuetrumpf, Bastian; Zhang, Chunli

    2017-11-01

    Static and time-dependent density functional theory (DFT) calculations are often used to predict fission fragment distributions or fusion cross sections with great success. However, nuclear shell structure and clusterization effects are usually studied using the density distribution of the nucleons which is a poor indicator of these phenomena. In this work, we employ a measure called the localization function, which was first introduced in chemistry to visualize electronic bonds and recently applied to nuclear physics for light nuclei to reveal α-clustering. We show, that the localization function reveals the shell structure of the fragments in fission long before the scission point and also illustrates the shell structure of intermediate states in time-dependent DFT calculations.

  12. Computational Nutraceutics: Chemical Reactivity Properties of the Flavonoid Naringin by Means of Conceptual DFT

    Directory of Open Access Journals (Sweden)

    Jorge Ignacio Martínez-Araya

    2013-01-01

    Full Text Available The M06 family of density functionals has been assessed for the calculation of the molecular structure and properties of the Naringin molecule. The chemical reactivity descriptors have been calculated through Conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices and the dual descriptor f(2(r. A comparison between the descriptors calculated through vertical energy values and those arising from the Koopmans' theorem approximation has been performed in order to check for the validity of the last procedure.

  13. Pseudopotential for ab initio calculations of uranium compounds

    Science.gov (United States)

    Smirnov, G. S.; Pisarev, V. V.; Stegailov, V. V.

    2018-01-01

    The density functional theory (DFT) is a research tool of the highest importance for electronic structure calculations. It is often the only affordable method for ab initio calculations of complex materials. The pseudopotential approach allows reducing the total number of electrons in the model that speeds up calculations. However, there is a lack of pseudopotentials for heavy elements suitable for condensed matter DFT models. In this work, we present a pseudopotential for uranium developed in the Goedecker–Teter–Hutter form. Its accuracy is illustrated using several molecular and solid-state calculations.

  14. Graphene layer on Rh(111): combined DFT, STM, and NC-AFM studies

    OpenAIRE

    Stojanov, Petar; Voloshina, Elena; Dedkov, Yuriy; Schmitt, Stefan; Haenke, Torben; Thissen, Andreas

    2015-01-01

    The simultaneous combination of scanning probe methods (tunnelling and force microscopies, STM and AFM) is a unique way to get an information about crystallographic and electronic structure of the studied surface. Here we apply these methods accompanied by the state-of-the-art density functional theory (DFT) calculations to shed a light on the structure and electronic properties of the strongly-corrugated graphene/Rh(111) system. The atomically resolved images are obtained for both STM and AF...

  15. Theoretical investigation of loratadine reactivity in order to understand its degradation properties: DFT and MD study.

    Science.gov (United States)

    Armaković, Stevan; Armaković, Sanja J; Abramović, Biljana F

    2016-10-01

    Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding their fundamental reactive properties. In this study we have theoretically investigated reactive properties of LOR using both density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT study is used for collecting information related to the molecule stability, structure, frontier molecular orbitals, quantum molecular descriptors, charge distribution, molecular electrostatic potential surfaces, charge polarization, and local reactivity properties according to average local ionization energy surfaces. Based on these results, N24 atom of pyridine ring and oxygen atom O1 were identified with nucleophilic nature. In order to collect the information necessary for the proposition of degradation compounds we also calculated bond dissociation energies (BDE) for hydrogen abstraction and single acyclic bonds as well. According to BDE, the oxidation is likely to occur in the piperidine and cycloheptane rings. MD simulations were used in order to understand the interactions with water through radial distribution functions (RDF). Based on RDFs the most important interactions with solvent are determined for carbon atom C5, chlorine atom Cl15, and oxygen atom O1. Collected results based on DFT calculations and MD simulations provided information important for suggestion of possible degradation compounds. Covalent and noncovalent interactions between LOR and (•)OH have also been investigated.

  16. Computing the band structure and energy gap of penta-graphene by using DFT and G0W0 approximations

    OpenAIRE

    Einollahzadeh, H.; Dariani, R. S.; Fazeli, S. M.

    2015-01-01

    In this paper, we consider the optimum coordinate of the penta-graphene. Penta-graphene is a new stable carbon allotrope which is stronger than graphene. Here, we compare the band gap of penta-graphene with various density functional theory (DFT) methods. We plot the band structure of penta-graphene which calculated with the generalized gradient approximation functional, about Fermi energy.

  17. Electronic Structure and Physical-Chemistry Property Relationship for Oxazole Derivatives by Ab Initio and DFT Methods

    Directory of Open Access Journals (Sweden)

    Salah Belaidi

    2011-01-01

    Full Text Available The geometric, electronic structure, effect of the substitution, and structure physical-chemistry relationship for oxazoles derivatives have been studied by ab initio and DFT theory. In the present work, the calculated values, namely, net charges, bond lengths, dipole moments, electron affinities, heats of formation, and QSAR properties are reported and discussed in terms of the reactivity of oxazole derivatives.

  18. Recognition of switching on or off fluorescence emission spectrum on the Schiff-bases as a Mg2+ chemosensor: A first principle DFT and TD-DFT study

    Science.gov (United States)

    Taherpour, Avat Arman; Jamshidi, Morteza; Rezaei, Omid

    2017-11-01

    Today, due to convenience, rapid diagnosis and etc., chemosensors are widely used to detect metal ions. In the current research, through DFT and TD-DFT methods, 8-hydroxyquinoline-5-carbaldehyde-(benzotriazol-1‧-acetyl) (QCH) ligand was used to identify Mg2+ cation and investigate its fluorescence emission spectrum mechanism. In order to investigate electronic properties, natural bond orbital (NBO) analysis, reduced density gradient (RDG) plots and electron localization function (ELF) as well as, changes in energy gap of HOMO and LUMO orbitals in the ground state, in water solution were used. Energy gap underwent change about ΔE = 0.17 eV in the presence of Mg2+ cation. Using TD-DFT calculations the optical absorption and emission of QCH ligand was investigated in the presence and absence of Mg2+cation. QCH ligand lacks emission spectrum but in the presence of Mg2+cation shows an emission spectrum in the wavelength of λEmi = 611 nm. Using electron-hole theory, photoinduced electron transfer (PET) process and fluorescence emission spectrum mechanism were investigated. Turning on emission spectrum in the presence of Mg2+ cation is due to stopping charge transfer from chelator to fluorophore.

  19. Predictive DFT-based approaches to charge and spin transport in single-molecule junctions and two-dimensional materials: successes and challenges.

    Science.gov (United States)

    Quek, Su Ying; Khoo, Khoong Hong

    2014-11-18

    CONSPECTUS: The emerging field of flexible electronics based on organics and two-dimensional (2D) materials relies on a fundamental understanding of charge and spin transport at the molecular and nanoscale. It is desirable to make predictions and shine light on unexplained experimental phenomena independently of experimentally derived parameters. Indeed, density functional theory (DFT), the workhorse of first-principles approaches, has been used extensively to model charge/spin transport at the nanoscale. However, DFT is essentially a ground state theory that simply guarantees correct total energies given the correct charge density, while charge/spin transport is a nonequilibrium phenomenon involving the scattering of quasiparticles. In this Account, we critically assess the validity and applicability of DFT to predict charge/spin transport at the nanoscale. We also describe a DFT-based approach, DFT+Σ, which incorporates corrections to Kohn-Sham energy levels based on many-electron calculations. We focus on single-molecule junctions and then discuss how the important considerations for DFT descriptions of transport can differ in 2D materials. We conclude that when used appropriately, DFT and DFT-based approaches can play an important role in making predictions and gaining insight into transport in these materials. Specifically, we shall focus on the low-bias quasi-equilibrium regime, which is also experimentally most relevant for single-molecule junctions. The next question is how well can the scattering of DFT Kohn-Sham particles approximate the scattering of true quasiparticles in the junction? Quasiparticles are electrons (holes) that are surrounded by a constantly changing cloud of holes (electrons), but Kohn-Sham particles have no physical significance. However, Kohn-Sham particles can often be used as a qualitative approximation to quasiparticles. The errors in standard DFT descriptions of transport arise primarily from errors in the Kohn-Sham energy levels

  20. 1D magnetic interactions in Cu(II) oxovanadium phosphates (VPO), magnetic susceptibility, DFT, and single-crystal EPR.

    Science.gov (United States)

    Venegas-Yazigi, Diego; Spodine, Evgenia; Saldias, Marianela; Vega, Andrés; Paredes-García, Verónica; Calvo, Rafael; de Santana, Ricardo Costa

    2015-04-20

    We report the crystal face indexing and molecular spatial orientation, magnetic properties, electron paramagnetic resonance (EPR) spectra, and density functional theory (DFT) calculations of two previously reported oxovanadium phosphates functionalized with Cu(II) complexes, namely, [Cu(bipy)(VO2)(PO4)]n (1) and [{Cu(phen)}2(VO2(H2O)2)(H2PO4)2 (PO4)]n (2), where bipy = 2,2'-bipyridine and phen = 1,10-phenanthroline, obtained by a new synthetic route allowing the growth of single crystals appropriate for the EPR measurements. Compounds 1 and 2 crystallize in the triclinic group P1̅ and in the orthorhombic Pccn group, respectively, containing dinuclear copper units connected by two -O-P-O- bridges in 1 and by a single -O-P-O- bridge in 2, further connected through -O-P-O-V-O- bridges. We emphasize in our work the structural aspects related to the chemical paths that determine the magnetic properties. Magnetic susceptibility data indicate bulk antiferromagnetism for both compounds, allowing to calculate J = -43.0 cm(-1) (dCu-Cu = 5.07 Å; J defined as Hex(i,j) = -J Si·Sj), considering dinuclear units for 1, and J = -1.44 cm(-1) (dCu-Cu = 3.47 Å) using the molecular field approximation for 2. The single-crystal EPR study allows evaluation of the g matrices, which provide a better understanding of the electronic structure. The absence of structure of the EPR spectra arising from the dinuclear character of the compounds allows estimation of weak additional exchange couplings |J'| > 0.3 cm(-1) for 1 (dCu-Cu = 5.54 Å) and a smaller value of |J'| ≥ 0.15 cm(-1) for 2 (dCu-Cu = 6.59 Å). DFT calculations allow evaluating two different exchange couplings for each compound, specifically, J = -36.60 cm(-1) (dCu-Cu = 5.07 Å) and J' = 0.20 cm(-1) (dCu-Cu =5.54 Å) for 1 and J = -1.10 cm(-1) (dCu-Cu =3.47 Å) and J' = 0.01 cm(-1) (dCu-Cu = 6.59 Å) for 2, this last value being in the range of the uncertainties of the calculations. Thus, these values are in good agreement

  1. Colorimetric and fluorimetric response of salicylaldehyde dithiosemicarbazone towards fluoride, cyanide and copper ions: Spectroscopic and TD-DFT studies.

    Science.gov (United States)

    Harikrishnan, Vengayil K; Basheer, Sabeel M; Joseph, Nithin; Sreekanth, Anandaram

    2017-07-05

    The sensing mechanism of salicylaldehyde phenyldithiosemicarbazone (SDTSC) chemosensor has been investigated by spectroscopic and TD-DFT methods. The SDTSC shows colourimetric and spectral changes towards fluoride, cyanide and copper ions. The interaction between SDTSC with fluoride, cyanide and copper ions was examined through their absorption and fluorescence behaviour, and found that SDTSC has more sensing ability towards Cu 2+ ion than CN - and F - ions. The 1 H NMR titration with SDTSC and F - gives the structural changes in the sensing process. The reversibility of SDTSC was also evaluated and thus it is confirmed as a reusable chemosensor which can be clarified by the "Read-Erase-Read-Write" logic system. The DFT and TD-DFT calculations give the detailed sensing mechanism of SDTSC towards fluoride ion. The potential energy surface (PES) analysis confirms the excited state electron transfer mechanism. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. DFT studies of hydrocarbon combustion on metal surfaces.

    Science.gov (United States)

    Arya, Mina; Mirzaei, Ali Akbar; Davarpanah, Abdol Mahmood; Barakati, Seyed Masoud; Atashi, Hossein; Mohsenzadeh, Abas; Bolton, Kim

    2018-02-02

    Catalytic combustion of hydrocarbons is an important technology to produce energy. Compared to conventional flame combustion, the catalyst enables this process to operate at lower temperatures; hence, reducing the energy required for efficient combustion. The reaction and activation energies of direct combustion of hydrocarbons (CH → C + H) on a series of metal surfaces were investigated using density functional theory (DFT). The data obtained for the Ag, Au, Al, Cu, Rh, Pt, and Pd surfaces were used to investigate the validity of the Brønsted-Evans-Polanyi (BEP) and transition state scaling (TSS) relations for this reaction on these surfaces. These relations were found to be valid (R 2  = 0.94 for the BEP correlation and R 2  = 1.0 for the TSS correlation) and were therefore used to estimate the energetics of the combustion reaction on Ni, Co, and Fe surfaces. It was found that the estimated transition state and activation energies (E TS  = -69.70 eV and E a  = 1.20 eV for Ni, E TS  = -87.93 eV and E a  = 1.08 eV for Co and E TS  = -92.45 eV and E a  = 0.83 eV for Fe) are in agreement with those obtained by DFT calculations (E TS  = -69.98 eV and E a  = 1.23 eV for Ni, E TS  = -87.88 eV and E a  = 1.08 eV for Co and E TS  = -92.57 eV and E a  = 0.79 eV for Fe). Therefore, these relations can be used to predict energetics of this reaction on these surfaces without doing the time consuming transition state calculations. Also, the calculations show that the activation barrier for CH dissociation decreases in the order Ag ˃ Au ˃ Al ˃ Cu ˃ Pt ˃ Pd ˃ Ni > Co > Rh > Fe.

  3. Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

    Science.gov (United States)

    Behzadi, Hadi; Roonasi, Payman; Assle taghipour, Khatoon; van der Spoel, David; Manzetti, Sergio

    2015-07-01

    The quantum chemical calculations at the DFT/B3LYP level of theory were carried out on seven quinoxaline compounds, which have been synthesized as anti-Mycobacterium tuberculosis agents. Three conformers were optimized for each compound and the lowest energy structure was found and used in further calculations. The electronic properties including EHOMO, ELUMO and related parameters as well as electron density around oxygen and nitrogen atoms were calculated for each compound. The relationship between the calculated electronic parameters and biological activity of the studied compounds were investigated. Six similar quinoxaline derivatives with possible more drug activity were suggested based on the calculated electronic descriptors. A mechanism was proposed and discussed based on the calculated electronic parameters and bond dissociation energies.

  4. Is HAM/3 (hydrogenic atoms in molecules, version 3 a semiempirical version of dft (density functional theory for ionization processes?

    Directory of Open Access Journals (Sweden)

    Takahata Yuji

    2004-01-01

    Full Text Available We calculated valence-electron vertical ionization potentials (VIPs of nine small molecules, plus uracil and C2F4, by several different methods: semiempirical HAM/3 and AM1 methods, different nonempirical DFT models such as uDI(B88-P86/cc-pVTZ and -epsilon(SAOP/TZP, and ab initio Hartree-Fock (HF /cc-pVTZ. HAM/3 reproduced numerical values more closely to those calculated by the nonempirical DFTs than to those obtained by HF method. Core-electron binding energies (CEBEs of aniline, nitrobenzene and p-nitro aniline, were also calculated by HAM/3 and nonempirical DFT using DE method. A nonempirical DFT model, designated as deltaE KS (PW86-PW91/TZP model, resulted accurate CEBEs (average absolute deviation of 0.14 eV with high efficiency. Although absolute magnitude of HAM/3 CEBEs has error as much as 3 eV, the error in the chemical shifts deltaCEBE is much smaller at 0.55 eV. While the CEBE results do not lead to any definite answer to the question in the title, the trends in valence-electron VIPs indicate that HAM/3 does not approximate DFT with accurate exchange-correlation potentials, but seems to simulate approximate functionals such as B88-P86.

  5. Can Stereoclusters Separated by Two Methylene Groups Be Related by DFT Studies? The Case of the Cytotoxic Meroditerpenes Halioxepines.

    Science.gov (United States)

    Tarazona, Guillermo; Benedit, Gonzalo; Fernández, Rogelio; Pérez, Marta; Rodríguez, Jaime; Jiménez, Carlos; Cuevas, Carmen

    2018-02-23

    QM/NMR-DFT (quantum mechanics combined with nuclear magnetic resonance parameters calculated by density functional theory approximations) studies allowed us to link two stereoclusters separated by two methylene groups present in the new meroditerpenes halioxepine B (2) and halioxepine C (3) and the known halioxepine (1), isolated from two Indonesian sponges of the genus Haliclona (Reniera). DP4 and DP4+ probabilities were used to discriminate the two diastereotopic arrangements of the two stereoclusters, whose unconnected relative configurations were determined by ROESY and J-based configurational analysis. To confirm the DFT studies, the full relative configuration of 1 was deduced using a mixture of benzene-d 6 and pyridine-d 5 as the NMR solvent. ROESY measurements connected the two stereoclusters and demonstrated that DFT calculations accurately predict the configuration when two methylenes separate the two stereoclusters. The different arrangements of the distant stereoclusters C-1/C-2/C-7 and C-10/C-15 for compounds 2 and 3 were deduced by DFT calculations and explained the opposite optical rotations observed for the two compounds. Halioxepines B (2) and C (3) display moderate cytotoxicity against different human cancer cell lines.

  6. Modeling Excited States in TiO2 Nanoparticles: On the Accuracy of a TD-DFT Based Description

    Science.gov (United States)

    2014-01-01

    We have investigated the suitability of Time-Dependent Density Functional Theory (TD-DFT) to describe vertical low-energy excitations in naked and hydrated titanium dioxide nanoparticles. Specifically, we compared TD-DFT results obtained using different exchange-correlation (XC) potentials with those calculated using Equation-of-Motion Coupled Cluster (EOM-CC) quantum chemistry methods. We demonstrate that TD-DFT calculations with commonly used XC potentials (e.g., B3LYP) and EOM-CC methods give qualitatively similar results for most TiO2 nanoparticles investigated. More importantly, however, we also show that, for a significant subset of structures, TD-DFT gives qualitatively different results depending upon the XC potential used and that only TD-CAM-B3LYP and TD-BHLYP calculations yield results that are consistent with those obtained using EOM-CC theory. Moreover, we demonstrate that the discrepancies for such structures originate from a particular combination of defects that give rise to charge-transfer excitations, which are poorly described by XC potentials that do not contain sufficient Hartree–Fock like exchange. Finally, we consider that such defects are readily healed in the presence of ubiquitously present water and that, as a result, the description of vertical low-energy excitations for hydrated TiO2 nanoparticles is nonproblematic. PMID:24795544

  7. Conformational study of a bent-core liquid crystal: 13C NMR and DFT computation approach.

    Science.gov (United States)

    Dong, Ronald Y; Marini, Alberto

    2009-10-29

    A detailed conformational study is carried out by means of density functional theory (DFT) on a bent-core mesogen (A131) in order to shed light on its uniaxial-biaxial nematic phase transition. The most probable conformational states for this V-shaped core are found, from the potential energy surface (PES) of a five-ring model of A131, to fall into two distinct structural groups, namely, the banana-shaped and the hockey-stick-shaped forms. The chemical shielding tensors (CSTs) of the aromatic carbons, for the four prevalent conformers, have been calculated using the GIAO-DFT approach. The derived CSTs are found to compare well with the chemical shift anisotropy (CSA) tensors measured by the 2D-NMR SUPER technique. The CSA tensors are then used to aid the assignment of the aromatic carbon peaks, and the observed (13)C chemical shifts from its nematic phases are revisited to provide new structural and local orientational order parameters. In light of the conformational states found from the in vacuo DFT calculations, the "average" configuration shapes of the A131 molecule are found to be different in the nematic phases based on their new local order parameters S and D of the aromatic rings.

  8. Perspective: How good is DFT for water?

    Science.gov (United States)

    Gillan, Michael J.; Alfè, Dario; Michaelides, Angelos

    2016-04-01

    Kohn-Sham density functional theory (DFT) has become established as an indispensable tool for investigating aqueous systems of all kinds, including those important in chemistry, surface science, biology, and the earth sciences. Nevertheless, many widely used approximations for the exchange-correlation (XC) functional describe the properties of pure water systems with an accuracy that is not fully satisfactory. The explicit inclusion of dispersion interactions generally improves the description, but there remain large disagreements between the predictions of different dispersion-inclusive methods. We present here a review of DFT work on water clusters, ice structures, and liquid water, with the aim of elucidating how the strengths and weaknesses of different XC approximations manifest themselves across this variety of water systems. Our review highlights the crucial role of dispersion in describing the delicate balance between compact and extended structures of many different water systems, including the liquid. By referring to a wide range of published work, we argue that the correct description of exchange-overlap interactions is also extremely important, so that the choice of semi-local or hybrid functional employed in dispersion-inclusive methods is crucial. The origins and consequences of beyond-2-body errors of approximate XC functionals are noted, and we also discuss the substantial differences between different representations of dispersion. We propose a simple numerical scoring system that rates the performance of different XC functionals in describing water systems, and we suggest possible future developments.

  9. DFT research of methane preliminary dissociation on aluminum catalyst

    Science.gov (United States)

    Zhang, Minhua; Yu, Yingzhe; Zhang, Yongbo

    2013-09-01

    Using the quantum chemistry calculation module based on density functional theory (DFT), the stable adsorption states of Ni4 cluster on the surface of α-Al2O3(0 0 0 1) was investigated firstly, and then the most stable adsorption configuration was selected as the representative model of supported Ni4/α-Al2O3(0 0 0 1) catalyst to investigate the catalytic performance for methane preliminary dissociation. After theoretic calculation, it was found that the methane dissociation products prefer to be adsorbed on edge sites of Ni4 cluster, the adsorption priority sequence (from large to small) for the concerned species was H > O2 > CH3 ≫ CH4 > H2. Comparing with pure Ni4 cluster without support, the chemical adsorption ability of Ni4 cluster to H2 molecule is decreased after supporting on support, which would promote the desorption of product H2, and thus increase the H2 yield. The adsorption energy of O2 molecule on Ni4/α-Al2O3(0 0 0 1) is much higher than that of other molecules such as CH4 or H2 on Ni4 cluster surface. The Osbnd O bond length on the most stable adsorption site is elongated by 0.21 Å, which would promote the activation and dissociation of O2 molecule significantly and thus might facilitate the proceeding of further reaction.

  10. Optical Absorption Spectra and Electronic Properties of Symmetric and Asymmetric Squaraine Dyes for Use in DSSC Solar Cells: DFT and TD-DFT Studies

    Directory of Open Access Journals (Sweden)

    Reda M. El-Shishtawy

    2016-04-01

    Full Text Available The electronic absorption spectra, ground-state geometries and electronic structures of symmetric and asymmetric squaraine dyes (SQD1–SQD4 were investigated using density functional theory (DFT and time-dependent (TD-DFT density functional theory at the B3LYP/6-311++G** level. The calculated ground-state geometries reveal pronounced conjugation in these dyes. Long-range corrected time dependent density functionals Perdew, Burke and Ernzerhof (PBE, PBE1PBE (PBE0, and the exchange functional of Tao, Perdew, Staroverov, and Scuseria (TPSSh with 6-311++G** basis set were employed to examine optical absorption properties. In an extensive comparison between the optical data and DFT benchmark calculations, the BEP functional with 6-311++G** basis set was found to be the most appropriate in describing the electronic absorption spectra. The calculated energy values of lowest unoccupied molecular orbitals (LUMO were 3.41, 3.19, 3.38 and 3.23 eV for SQD1, SQD2, SQD3, and SQD4, respectively. These values lie above the LUMO energy (−4.26 eV of the conduction band of TiO2 nanoparticles indicating possible electron injection from the excited dyes to the conduction band of the TiO2 in dye-sensitized solar cells (DSSCs. Also, aromaticity computation for these dyes are in good agreement with the data obtained optically and geometrically with SQD4 as the highest aromatic structure. Based on the optimized molecular geometries, relative positions of the frontier orbitals, and the absorption maxima, we propose that these dyes are suitable components of photovoltaic DSSC devices.

  11. Substituted group and side chain effects for the porphyrin and zinc(II)–porphyrin derivatives: A DFT and TD-DFT study

    International Nuclear Information System (INIS)

    Tai, Chin-Kuen; Chuang, Wen-Hua; Wang, Bo-Cheng

    2013-01-01

    The DFT/B3LYP/LANL2DZ and TD-DFT calculations have been performed to generate the optimized structures, electronic and photo-physical properties for the porphyrin and zinc(II)–porphyrin (metalloporphyrin) derivatives. The substituted group and side chain effects for these derivatives are discussed in this study. According to the calculation results, the side chain moiety extends the π-delocalization length from the porphyrin core to the side chain moiety. The substituted group with a stronger electron-donating ability increases the energy level of highest occupied molecular orbital (E HOMO ). The side chain moiety with a lower resonance energy decreases E HOMO , the energy level of the lowest unoccupied molecular orbital (E LUMO ), and the energy gap (E g ) between HOMO and LUMO in the porphyrin and zinc(II)–porphyrin derivatives. The natural bonding orbital (NBO) analysis determines the possible electron transfer mechanism from the electron-donating to -withdrawing groups (the side chain moiety) in these porphyrin derivatives. The projected density of state (PDOS) analysis shows that the electron-donating group affects the electron density distribution in both HOMO and LUMO, and the side chain moiety influence the electron density distribution in LUMO. The calculated photo-physical properties (absorption wavelengths and the related oscillator strength, f) in dichloromethane environment for porphyrin and zinc(II)–porphyrin derivatives have been simulated by using the TD-DFT method within the Polarizable Continuum Model (PCM). The present of both of the substituted group and the side chain moiety in these derivatives results in a red shift and broadening of the range of the absorption peaks of the Q/Soret band as compared to porphin. -- Highlights: • Side chain moiety extends the π-delocalization for the porphyrins. • Substituted group increases the energy of highest occupied molecular orbital. • Side chain moiety influences the Q/Soret band of

  12. Optical Absorption Spectra and Electronic Properties of Symmetric and Asymmetric Squaraine Dyes for Use in DSSC Solar Cells: DFT and TD-DFT Studies.

    Science.gov (United States)

    El-Shishtawy, Reda M; Elroby, Shaaban A; Asiri, Abdullah M; Müllen, Klaus

    2016-04-01

    The electronic absorption spectra, ground-state geometries and electronic structures of symmetric and asymmetric squaraine dyes (SQD1-SQD4) were investigated using density functional theory (DFT) and time-dependent (TD-DFT) density functional theory at the B3LYP/6-311++G** level. The calculated ground-state geometries reveal pronounced conjugation in these dyes. Long-range corrected time dependent density functionals Perdew, Burke and Ernzerhof (PBE, PBE1PBE (PBE0)), and the exchange functional of Tao, Perdew, Staroverov, and Scuseria (TPSSh) with 6-311++G** basis set were employed to examine optical absorption properties. In an extensive comparison between the optical data and DFT benchmark calculations, the BEP functional with 6-311++G** basis set was found to be the most appropriate in describing the electronic absorption spectra. The calculated energy values of lowest unoccupied molecular orbitals (LUMO) were 3.41, 3.19, 3.38 and 3.23 eV for SQD1, SQD2, SQD3, and SQD4, respectively. These values lie above the LUMO energy (-4.26 eV) of the conduction band of TiO₂ nanoparticles indicating possible electron injection from the excited dyes to the conduction band of the TiO₂ in dye-sensitized solar cells (DSSCs). Also, aromaticity computation for these dyes are in good agreement with the data obtained optically and geometrically with SQD4 as the highest aromatic structure. Based on the optimized molecular geometries, relative positions of the frontier orbitals, and the absorption maxima, we propose that these dyes are suitable components of photovoltaic DSSC devices.

  13. Conformations and Conformational Processes of Hexahydrobenzazocines by NMR and DFT Studies.

    Science.gov (United States)

    Musielak, Bogdan; Holak, Tad A; Rys, Barbara

    2015-09-18

    Conformational processes that occur in hexahydrobenzazocines have been studied with the (1)H and (13)C dynamic nuclear magnetic resonance (DNMR) spectroscopy. The coalescence effects are assigned to two different conformational processes: the ring-inversion of the ground-state conformations and the interconversion between two different conformers. The barriers for these processes are in the range of 42-52 and 42-43 kJ mol(-1), respectively. Molecular modeling on the density functional theory (DFT) level and the gauge invariant atomic orbitals (GIAO)-DFT calculations of isotropic shieldings and coupling constants for the set of low-energy conformations were compared with the experimental NMR data. The ground-state of all compounds in solution is the boat-chair (BC) conformation. The BC form adopts two different conformations because the nitrogen atom can be in the boat or chair parts of the BC structure. These two conformers are engaged in the interconversion process.

  14. Downsampling of DFT Precoded Signals for the AWGN Channel

    DEFF Research Database (Denmark)

    Jensen, Tobias Lindstrøm; Fyhn, Karsten; Arildsen, Thomas

    2012-01-01

    In this paper we propose and analyze a method for downsampling discrete Fourier transform (DFT) precoded signals. Since the symbols (in frequency) are in the constellation set, which is a subset of the entire complex plane, it is possible to detect N symbols from the DFT precoded signal when...

  15. Electronic structure and spectral properties of selected trimethyl-alloxazines: Combined experimental and DFT study

    International Nuclear Information System (INIS)

    Bruszynska, Magdalena; Sikorska, Ewa; Komasa, Anna; Khmelinskii, Igor; Ferreira, Luis F.V.; Hernando, Jordi; Karolczak, Jerzy; Kubicki, Maciej; Bourdelande, Jose L.; Sikorski, Marek

    2009-01-01

    Electronic structure and S 0 -S i , T 1 -T i , and S 0 -T i transition energies and oscillator strengths were calculated using the TD-DFT method for a series of trimethyl substituted alloxazines. The general energy diagram of the excited states predicted by the calculations is generally the same in these and in other alloxazines, with the two lowest close-lying n, π * and π, π * singlet excited states, determining the photophysical properties, being isoenergetic in most cases. The theoretical predictions are compared to the experimentally determined spectral and photophysical properties.

  16. DFT study on the Raman spectra of Fe(II-porphin

    Directory of Open Access Journals (Sweden)

    Hovorun D. M.

    2009-02-01

    Full Text Available DFT quantum-chemical calculations of the Raman spectra of Fe(II-porphin in quintet (ground state were performed. Spin-unrestricted UB3LYP functional in 6-311G basis was used for geometry optimization and Raman calculation. All active modes of Raman spectrum were analyzed in detail. It was noted that the insertion of Fe(II ion into porphin leads to the considerable changes in frequencies and intensities for those vibrational modes which involve nitrogen atoms displacement. The Raman depolarization ratio for plane polarized incident light is discussed

  17. Study of a Conformational Equilibrium of Lisinopril by HPLC, NMR, and DFT

    Directory of Open Access Journals (Sweden)

    Sondes Bouabdallah

    2014-01-01

    Full Text Available The isomerization of lisinopril has been investigated using chromatographic, NMR spectroscopic, and theoretical calculations. The NMR data, particularly the NOEDIFF experiments, show that the major species that was eluted first is the trans form. The proportion was 77% and 23% for the trans and cis, respectively. The thermodynamic parameters (ΔH, ΔS, and ΔG were determined by varying the temperature in the NMR experiments. The interpretations of the experimental data were further supported by DFT/B3LYP calculations.

  18. Structural studies on Mannich bases of 2-Hydroxy-3,4,5,6-tetrachlorobenzene. An UV, IR, NMR and DFT study. A mini-review

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2016-01-01

    Mannich bases of 2-Hydroxy-3,4,5,6-tetrachlorobenzene are chosen as an exemplary case for tautomeric Mannich bases. Molecular structures are calculated. OH stretching frequencies are rationalized based on DFT calculations. Intrinsic deuterium isotope effects on 13C chemical shifts in the M-form a...

  19. Surface reactivity of Ge[111] for organic functionalization by means of a radical-initiated reaction: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Rubio-Pereda, Pamela, E-mail: rubio.pereda@gmail.com [Centro de Investigación Científica y de Educación Superior de Ensenada 3918, Código Postal 22860, Ensenada, Baja California (Mexico); Takeuchi, Noboru, E-mail: takeuchi@cnyn.unam.mx [Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Apartado Postal 14, Código Postal 22800, Ensenada, Baja California (Mexico)

    2016-08-30

    Highlights: • The surface reactivity of the Ge [111] surface is studied with DFT for the attachment of organic molecules by means of a radical-initiated reaction. • A hydrogen vacancy in the hydrogen terminated Ge [111] surface exhibits an accumulation of charge and electron pairing. • These characteristics make the hydrogen vacancy less reactive for the attachment of unsaturated organic molecules. • The adsorption of acetylene is probable to occur while the adsorption of ethylene and styrene is substantially less probable to occur. • The hydrogen terminated Ge [111] surface is found to be less reactive than its two-dimensional analogue, the hydrogen-terminated germanene. - Abstract: The study of interfacial chemistry at semiconductor surfaces has become an important area of research. Functionalities such as molecular recognition, biocompatibility of surfaces, and molecular computing, could be achieved by the combinations of organic chemistry with the semiconductor technology. One way to accomplish this goal is by means of organic functionalization of semiconductor surfaces such as the bulk-terminated germanium surfaces, more specifically the Ge[111]. In this work, we theoretically study, by applying density functional theory, the surface reactivity of the bulk-terminated Ge[111] surface for organic functionalization by means of a radical-initiated reaction of unsaturated molecules such as acetylene, ethylene and styrene with a hydrogen vacancy on a previously hydrogen-terminated Ge[111] surface. Results derived from this work are compared with those obtained in our previous calculations on the germanene surface, following the same chemical route. Our calculations show an accumulation of electronic charge at the H-vacancy having as a result electron pairing due to strong lattice-electron coupling and therefore a diminished surface reactivity. Calculation of the transition states for acetylene and ethylene indicates that the surface reactivity of the

  20. Surface reactivity of Ge[111] for organic functionalization by means of a radical-initiated reaction: A DFT study

    International Nuclear Information System (INIS)

    Rubio-Pereda, Pamela; Takeuchi, Noboru

    2016-01-01

    Highlights: • The surface reactivity of the Ge [111] surface is studied with DFT for the attachment of organic molecules by means of a radical-initiated reaction. • A hydrogen vacancy in the hydrogen terminated Ge [111] surface exhibits an accumulation of charge and electron pairing. • These characteristics make the hydrogen vacancy less reactive for the attachment of unsaturated organic molecules. • The adsorption of acetylene is probable to occur while the adsorption of ethylene and styrene is substantially less probable to occur. • The hydrogen terminated Ge [111] surface is found to be less reactive than its two-dimensional analogue, the hydrogen-terminated germanene. - Abstract: The study of interfacial chemistry at semiconductor surfaces has become an important area of research. Functionalities such as molecular recognition, biocompatibility of surfaces, and molecular computing, could be achieved by the combinations of organic chemistry with the semiconductor technology. One way to accomplish this goal is by means of organic functionalization of semiconductor surfaces such as the bulk-terminated germanium surfaces, more specifically the Ge[111]. In this work, we theoretically study, by applying density functional theory, the surface reactivity of the bulk-terminated Ge[111] surface for organic functionalization by means of a radical-initiated reaction of unsaturated molecules such as acetylene, ethylene and styrene with a hydrogen vacancy on a previously hydrogen-terminated Ge[111] surface. Results derived from this work are compared with those obtained in our previous calculations on the germanene surface, following the same chemical route. Our calculations show an accumulation of electronic charge at the H-vacancy having as a result electron pairing due to strong lattice-electron coupling and therefore a diminished surface reactivity. Calculation of the transition states for acetylene and ethylene indicates that the surface reactivity of the

  1. Combining DFT, Cluster Expansions, and KMC to Model Point Defects in Alloys

    Science.gov (United States)

    Modine, N. A.; Wright, A. F.; Lee, S. R.; Foiles, S. M.; Battaile, C. C.; Thomas, J. C.; van der Ven, A.

    In an alloy, defect energies are sensitive to the occupations of nearby atomic sites, which leads to a distribution of defect properties. When radiation-induced defects diffuse from their initially non-equilibrium locations, this distribution becomes time-dependent. The defects can become trapped in energetically favorable regions of the alloy leading to a diffusion rate that slows dramatically with time. Density Functional Theory (DFT) allows the accurate determination of ground state and transition state energies for a defect in a particular alloy environment but requires thousands of processing hours for each such calculation. Kinetic Monte-Carlo (KMC) can be used to model defect diffusion and the changing distribution of defect properties but requires energy evaluations for millions of local environments. We have used the Cluster Expansion (CE) formalism to ``glue'' together these seemingly incompatible methods. The occupation of each alloy site is represented by an Ising-like variable, and products of these variables are used to expand quantities of interest. Once a CE is fit to a training set of DFT energies, it allows very rapid evaluation of the energy for an arbitrary configuration, while maintaining the accuracy of the underlying DFT calculations. These energy evaluations are then used to drive our KMC simulations. We will demonstrate the application of our DFT/MC/KMC approach to model thermal and carrier-induced diffusion of intrinsic point defects in III-V alloys. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE.

  2. Characterizing Ni(II) hydration in aqueous solution using DFT and EXAFS.

    Science.gov (United States)

    Liu, H Y; Fang, C H; Fang, Y; Zhou, Y Q; Ge, H W; Zhu, F Y; Sun, P C; Miao, J T

    2016-01-01

    In the present work, a detailed investigation of Ni(II) hydration in water solutions was carried out using density functional theory (DFT) and extended X-ray absorption fine structure (EXAFS) spectroscopy. The hydrated characteristics of [Ni(H2O)n](2+) clusters, such as energy parameters, atomic charge distributions, and bond parameters, were explored using DFT with Becke's three-parameter exchange potential and the Lee-Yang-Parr correlation functional (B3LYP). DFT calculations indicated that the preferred structure of the first hydration shell of Ni(II) generally has a coordination number of six and is almost unaffected by the water molecules in the outer solvation shell, whereas the structure of the second solvation shell varies as the hydration proceeds. EXAFS measurements are reported for aqueous NiSO4 and Ni(NO3)2 solutions and the Ni(NO3)2·6H2O crystal. Analysis of the EXAFS spectra of these three systems using a multiparameter fitting procedure showed that, in each case, the first coordination shell consists of six water molecules with a Ni-O coordination distance of 2.04 Å, and that there is no Ni-S or Ni-N coordination in the first shell. There was no evidence of outer-shell SO4(2-) or NO3(-) ions substituting inner-sphere water molecules in NiSO4 and Ni(NO3)2. The characteristics of Ni(II) hydration obtained from DFT calculations agreed well with those obtained experimentally using EXAFS.

  3. Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT.

    Science.gov (United States)

    Bardak, F; Karaca, C; Bilgili, S; Atac, A; Mavis, T; Asiri, A M; Karabacak, M; Kose, E

    2016-08-05

    Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, (1)H and (13)C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400nm. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400cm(-1) and 3500-50cm(-1), respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The (13)C and (1)H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. First principle calculations for improving desorption temperature in ...

    Indian Academy of Sciences (India)

    3Centre National de l'Energie, des Sciences et des Techniques Nucléaires, Rabat 10000, Morocco. 4Département de Physique ... Electronic structure calculations; MgH2; formation energy; hydrogen storage capacity; DFT; first principle calculations. 1. ..... des Energies Renouvelables 10 545. Charbonnier J, de Rango P, ...

  5. Ab initio calculation of the structural, mechanical and ...

    African Journals Online (AJOL)

    An ab initio plane-wave Pseudopotential calculations using the density functional theory (DFT) implementing the generalised gradient approximation (GGA) to study the structural, elastic constants, phonon dispersion curves, density of state and thermal properties of BeS. Also we calculated the shear modulus, Young's ...

  6. Quantum chemical calculations of using density functional theory ...

    Indian Academy of Sciences (India)

    K RACKESH JAWAHER

    2018-02-15

    Feb 15, 2018 ... Abstract. Quantum chemical calculations have been employed to study the molecular effects produced by. Cr2O3/SnO2 optimised structure. The theoretical parameters of the transparent conducting metal oxides were calculated using DFT/B3LYP/LANL2DZ method. The optimised bond parameters such as ...

  7. DFT study of the molecular and crystal structure and vibrational analysis of cisplatin.

    Science.gov (United States)

    Georgieva, I; Trendafilova, N; Dodoff, N; Kovacheva, D

    2017-04-05

    DFT and periodic-DFT (PAW-PBE method, code VASP) calculations have been performed to study the structural and vibrational characteristics of cis-diamminedichloroplatinum(II) (cisplatin) at molecular and outside molecular level. To estimate the effect of the intermolecular interactions in crystal on the structural and vibrational properties of cisplatin, three theoretical models are considered in the present study: monomer (isolated molecule), hydrogen bonded dimer and periodic solid state structures. The work focused on the role of the theoretical models for correct modeling and prediction of geometrical and vibrational parameters of cisplatin. It has been found that the elaborate three-dimensional intermolecular hydrogen bonding network in the crystalline cisplatin significantly influences the structural and vibrational pattern of cisplatin and therefore the isolated cisplatin molecule is not the correct computational model regardless of the theoretical level used. To account for the whole intermolecular hydrogen bonding network in direction of both a and c axis and for more reliable calculations of structural and vibrational parameters periodic DFT calculations were carried out in the full crystalline periodic environment with the known lattice parameters for each cisplatin polymorph phase. The model calculations performed both at molecular level and for the periodic structures of alpha and beta cisplatin polymorph forms revealed the decisive role of the extended theoretical model for reliable prediction of the structural and vibrational characteristics of cisplatin. The powder diffraction pattern and the calculated IR and Raman spectra predicted beta polymorph form of our cisplatin sample freshly synthesized for the purposes of the present study using the Dhara's method. The various rotamers realized in the polymorph forms of cisplatin were explained by the low population of the large number of rotamers in solution as well as with the high rotamer

  8. Calculations of optical rotation: Influence of molecular structure

    Directory of Open Access Journals (Sweden)

    Yu Jia

    2012-01-01

    Full Text Available Ab initio Hartree-Fock (HF method and Density Functional Theory (DFT were used to calculate the optical rotation of 26 chiral compounds. The effects of theory and basis sets used for calculation, solvents influence on the geometry and values of calculated optical rotation were all discussed. The polarizable continuum model, included in the calculation, did not improve the accuracy effectively, but it was superior to γs. Optical rotation of five or sixmembered of cyclic compound has been calculated and 17 pyrrolidine or piperidine derivatives which were calculated by HF and DFT methods gave acceptable predictions. The nitrogen atom affects the calculation results dramatically, and it is necessary in the molecular structure in order to get an accurate computation result. Namely, when the nitrogen atom was substituted by oxygen atom in the ring, the calculation result deteriorated.

  9. Palladium(II) complexes of 2-pyridylmethylamine and 8-aminoquinoline: A crystallographic and DFT study

    Science.gov (United States)

    Akerman, Kate J.; Venter, Chané; Hunter, Leigh A.; Akerman, Matthew P.

    2015-07-01

    Two nominally square planar palladium(II) chelates: dichloro-(2-aminomethylpyridine-N,N‧)-palladium(II) ([Pd(L1)Cl2]) and dichloro-(8-aminoquinoline)-palladium(II) ([Pd(L2)Cl2]) have been synthesised and studied by X-ray crystallography and DFT methods. [Pd(L1)Cl2] crystallised in the monoclinic space group C2/c. In the solid state this compound exists as a one-dimensional supramolecular structure supported by Nsbnd H⋯Cl hydrogen bonds and metallophilic Pd⋯Pd interactions. The same hydrogen bonding motif leads to a two-dimensional supramolecular structure in the case of [Pd(L2)Cl2]; this structure is devoid of metallophilic interactions. DFT simulations show that the planar geometry of [Pd(L1)Cl2] in the solid state is not the lowest energy conformation. An out-of-plane distortion of the methylene group leads to a structure ca. 11 kJ mol-1 lower in energy. The NBO partial charges provide insight into the stability of the hydrogen bonding motif. TD-DFT calculations were used to delineate the experimental UV-visible spectra.

  10. Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C.

    Science.gov (United States)

    Witte, Jonathon; Neaton, Jeffrey B; Head-Gordon, Martin

    2017-06-21

    With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which-when stripped of BSSE-is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals-such as B97M-V-to recover large-basis results at a fraction of the cost.

  11. DFT application for chlorin derivatives photosensitizer drugs modeling

    Science.gov (United States)

    Machado, Neila; Carvalho, B. G.; Téllez Soto, C. A.; Martin, A. A.; Favero, P. P.

    2018-04-01

    Photodynamic therapy is an alternative form of cancer treatment that meets the desire for a less aggressive approach to the body. It is based on the interaction between a photosensitizer, activating light, and molecular oxygen. This interaction results in a cascade of reactions that leads to localized cell death. Many studies have been conducted to discover an ideal photosensitizer, which aggregates all the desirable characteristics of a potent cell killer and generates minimal side effects. Using Density Functional Theory (DFT) implemented in the program Vienna Ab-initio Simulation Package, new chlorin derivatives with different functional groups were simulated to evaluate the different absorption wavelengths to permit resonant absorption with the incident laser. Gaussian 09 program was used to determine vibrational wave numbers and Natural Bond Orbitals. The chosen drug with the best characteristics for the photosensitizer was a modified model of the original chlorin, which was called as Thiol chlorin. According to our calculations it is stable and is 19.6% more efficient at optical absorption in 708 nm in comparison to the conventional chlorin e6. Vibrational modes, optical and electronic properties were predicted. In conclusion, this study is an attempt to improve the development of new photosensitizer drugs through computational methods that save time and contribute to decrease the numbers of animals for model application.

  12. Synthesis, structural, catecholase, tyrosinase and DFT studies of pyrazoloquinoxaline derivatives

    Science.gov (United States)

    Bouanane, Zohra; Bounekhel, Mahmoud; Elkolli, Meriem; Abrigach, Farid; Khoutoul, Mohamed; Bouyala, Rabab; Touzani, Rachid; Hellal, Abdelkader

    2017-07-01

    Six functional multidentate ligands: 2,3-bis(3,5-dimethyl-1H-pyrazol-1-yl) quinoxaline, L1, 2,3-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-nitroquinoxaline, L2, 2,3-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-methylquinoxaline, L3, 2-(3,5-dimethyl-1H-pyrazol-1-yl)-3-hydrazinyl-6-nitroquinoxaline L4, 2-chloro-3-(3,5-dimethyl-1H-pyrazol-1-yl)-6-methylquinoxaline, L5, 2-chloro-3-(3,5-dimethyl-1H-pyrazol-1-yl) quinoxaline, L6, and a new copper (II) complex, were prepared and evaluated for their catecholase activities at aerobic conditions. We found that, the reaction rate depends on: The nature of the substituents in the quinoxaline ring, counter anion, metal, concentration of ligand and the used solvent. The complex obtained in-situ from reaction of one equivalent of ligand L1 and two equivalents of Cu(CH3COO)2 in methanol showed the highest oxidation rate activity (V = 33.48 μmol L-1. min-1). In addition, geometry optimizations of the complexes in order to get better insight into the geometry and the electronic structure and chemical reactivity were carried out by means of DFT calculations.

  13. Combined TD-DFT-SOS-CIS(D) Study of BOPHY Derivatives with Potential Application in Biosensing.

    Science.gov (United States)

    Ponce-Vargas, Miguel; Azarias, Cloé; Jacquemin, Denis; Le Guennic, Boris

    2017-12-07

    A set of 13 bis(difluoroboron)-1,2-bis((pyrrol-2-yl)methylene)hydrazine (BOPHY) dyes is studied through a hybrid time-dependent density functional theory (TD-DFT)-scaled opposite spin-configuration interaction singles with a double correction [SOS-CIS(D)] approach accounting for solvent effects, to shed light onto the structure-property relationships of these recently developed chromophores. In the first step, we calculate the absorption-fluorescence crossing points with refined TD-DFT models considering the influences of both vibrational and solvent contributions. We found that the systematic overestimation of the 0-0 energies is effectively reduced by combining polarizable continuum model-TD-DFT with a scaled opposite spin-configuration interaction singles with a double correction [SOS-CIS(D)]. Next, for a representative system, the vibrationally resolved spectrum within the harmonic approximation is computed on the basis of TD-DFT vibrational signatures and an excellent match with experiment is found. Finally, the influence of different lateral groups on the spectroscopic properties is rationalized by investigating charge transfer parameters and examining electronic density difference maps. It is found that one can tune the position of the absorption/emission maxima by a judicious choice of the lateral substituents or by using π-extended segments. The largest absorption and emission wavelengths as well as the largest Stokes shifts are obtained for BOPHYs containing strong electron-donor dimethylaminophenyl groups attached to the α-positions of the pyrrole units through vinyl linkers, making these chromophores promising candidates for bioluminescence applications.

  14. Communication: Hole localization in Al-doped quartz SiO{sub 2} within ab initio hybrid-functional DFT

    Energy Technology Data Exchange (ETDEWEB)

    Gerosa, Matteo [Department of Energy, Politecnico di Milano, via Ponzio 34/3, 20133 Milano (Italy); Di Valentin, Cristiana; Pacchioni, Gianfranco [Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milan (Italy); Bottani, Carlo Enrico, E-mail: carlo.bottani@polimi.it [Department of Energy, Politecnico di Milano, via Ponzio 34/3, 20133 Milano (Italy); Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, via Pascoli 70/3, 20133 Milano (Italy); Onida, Giovanni [Dipartimento di Fisica dell’ Universita’ degli Studi di Milano and European Theoretical Spectroscopy Facility (ETSF), Via Celoria 16, 20133 Milan (Italy)

    2015-09-21

    We investigate the long-standing problem of hole localization at the Al impurity in quartz SiO{sub 2}, using a relatively recent DFT hybrid-functional method in which the exchange fraction is obtained ab initio, based on an analogy with the static many-body COHSEX approximation to the electron self-energy. As the amount of the admixed exact exchange in hybrid functionals has been shown to be determinant for properly capturing the hole localization, this problem constitutes a prototypical benchmark for the accuracy of the method, allowing one to assess to what extent self-interaction effects are avoided. We obtain good results in terms of description of the charge localization and structural distortion around the Al center, improving with respect to the more popular B3LYP hybrid-functional approach. We also discuss the accuracy of computed hyperfine parameters, by comparison with previous calculations based on other self-interaction-free methods, as well as experimental values. We discuss and rationalize the limitations of our approach in computing defect-related excitation energies in low-dielectric-constant insulators.

  15. Ab initio calculation of transport properties between PbSe quantum dots facets with iodide ligands

    Science.gov (United States)

    Wang, B.; Patterson, R.; Chen, W.; Zhang, Z.; Yang, J.; Huang, S.; Shrestha, S.; Conibeer, G.

    2018-01-01

    The transport properties between Lead Selenide (PbSe) quantum dots decorated with iodide ligands has been studied using density functional theory (DFT). Quantum conductance at each selected energy levels has been calculated along with total density of states and projected density of states. The DFT calculation is carried on using a grid-based planar augmented wave (GPAW) code incorporated with the linear combination of atomic orbital (LCAO) mode and Perdew Burke Ernzerhof (PBE) exchange-correlation functional. Three iodide ligand attached low index facets including (001), (011), (111) are investigated in this work. P-orbital of iodide ligand majorly contributes to density of state (DOS) at near top valence band resulting a significant quantum conductance, whereas DOS of Pb p-orbital shows minor influence. Various values of quantum conductance observed along different planes are possibly reasoned from a combined effect electrical field over topmost surface and total distance between adjacent facets. Ligands attached to (001) and (011) planes possess similar bond length whereas it is significantly shortened in (111) plane, whereas transport between (011) has an overall low value due to newly formed electric field. On the other hand, (111) plane with a net surface dipole perpendicular to surface layers leading to stronger electron coupling suggests an apparent increase of transport probability. Apart from previously mentioned, the maximum transport energy levels located several eVs (1 2 eVs) from the edge of valence band top.

  16. FT-IR, RAMAN AND DFT STUDIES ON THE VIBRATIONAL ...

    African Journals Online (AJOL)

    Bis(aminoethoxy)propane, IR spectra, Raman spectra, Molecular structure, DFT. INTRODUCTION. Ketal based linkages have recently been investigated for the development of novel acid- cleavable polymers those are formulated into the ...

  17. Synthesis, spectroscopic and DFT characterization of 4 β -(4- tert ...

    African Journals Online (AJOL)

    Synthesis, spectroscopic and DFT characterization of 4 β -(4-tert-butylphenoxy) phthalocyanine positional isomers for non-linear optical absorption. Denisha Gounden, Grace N. Ngubeni, Marcel S. Louzada, Samson Khene, Jonathan Britton, Nolwazi Nombona ...

  18. Towards the versatile DFT and MP2 computational schemes for 31P NMR chemical shifts taking into account relativistic corrections.

    Science.gov (United States)

    Fedorov, Sergey V; Rusakov, Yury Yu; Krivdin, Leonid B

    2014-11-01

    The main factors affecting the accuracy and computational cost of the calculation of (31)P NMR chemical shifts in the representative series of organophosphorous compounds are examined at the density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2) levels. At the DFT level, the best functionals for the calculation of (31)P NMR chemical shifts are those of Keal and Tozer, KT2 and KT3. Both at the DFT and MP2 levels, the most reliable basis sets are those of Jensen, pcS-2 or larger, and those of Pople, 6-311G(d,p) or larger. The reliable basis sets of Dunning's family are those of at least penta-zeta quality that precludes their practical consideration. An encouraging finding is that basically, the locally dense basis set approach resulting in a dramatic decrease in computational cost is justified in the calculation of (31)P NMR chemical shifts within the 1-2-ppm error. Relativistic corrections to (31)P NMR absolute shielding constants are of major importance reaching about 20-30 ppm (ca 7%) improving (not worsening!) the agreement of calculation with experiment. Further better agreement with the experiment by 1-2 ppm can be obtained by taking into account solvent effects within the integral equation formalism polarizable continuum model solvation scheme. We recommend the GIAO-DFT-KT2/pcS-3//pcS-2 scheme with relativistic corrections and solvent effects taken into account as the most versatile computational scheme for the calculation of (31)P NMR chemical shifts characterized by a mean absolute error of ca 9 ppm in the range of 550 ppm. Copyright © 2014 John Wiley & Sons, Ltd.

  19. DFT and PM3 Computational Studies of the Reaction Mechanism of the Oxidation of L-Tyrosine by Iodine in the Gas Phase

    Directory of Open Access Journals (Sweden)

    Gideon A. Shallangwa

    2014-07-01

    Full Text Available Abstract - The oxidation of L-Tyrosine by molecular iodine was studied using semi-empirical and density functional theory methods. Molecular information such as net charges, values of frontier orbital energies, composition, proportions and bonding contribution were obtained and analyzed. Thus, possible reactive sites were proposed and the reaction mechanism was postulated. The postulated transition states, intermediates and products were also computed using the PM3 and DFT methods. Computed enthalpies of the oxidation reaction at standard conditions for the PM3 and DFT calculation were 216.97 kJ/mol and -36327404.72 kJ/mol respectively. The calculated ΔGo andΔSo, for the transition states according to the DFT model were both large and negative indicating that the processes were exergonic associative substitution reactions.

  20. Synthesis, structural, DFT studies, docking and antibacterial activity of a xanthene based hydrazone ligand

    Science.gov (United States)

    Naseem, Saira; Khalid, Muhammad; Tahir, Muhammad Nawaz; Halim, Mohammad A.; Braga, Ataualpa A. C.; Naseer, Muhammad Moazzam; Shafiq, Zahid

    2017-09-01

    Herein, we present the synthesis of novel xanthene-based hydrazone (1). The chemical structure of 1 was resolved using spectroscopic techniques such as NMR, FT-IR, UV-VIS and X-ray crystallographic approaches. X-ray diffraction analysis shows that the compound (1) crystallizes in triclinic crystal lattice with the Pbar1 space group and diffused to form multi-layered structure due to non-covalent interactions such as intramolecular hydrogen bonding (H.B). In addition to experimental investigation, density functional theory (DFT) calculation with M06-2X/6-31G(d,p) and B3LYP/6-31G(d,p) level of theories was performed on compound (1) to obtain optimized geometry, spectroscopic and electronic properties. DFT optimized geometry shows good agreement with the experimental XRD structure. The hyper conjugative interactions and hydrogen bonding network are responsible for the stability of compound (1) as revealed by natural bond orbital (NBO) calculation. Moreover, hydrogen bonding network in the dimer is confirmed by FT-IR and thermodynamic studies showing excellent agreement with XRD and NBO findings. TD-DFT/UV-VIS analysis provides insight that maximum excitation is found in 1 which shows good agreement with experimental UV-VIS result. The global reactivity parameters are calculated using the energies of frontier molecular orbitals also disclosed that the compound is more stable might be due to hydrogen bonding network. Experimental and molecular docking studies indicated that this compound has anti-bacterial and anti-diabetic properties. The binding affinity of this compound against the multidrug efflux pump subunit AcrB OS=Escherichia coli (strain K12) and Human Pancreatic Alpha-Amylase is -9.2 and -10.00 kcal/mol which are higher than the control drugs. Pi-Pi, Pi-anaion, amide-pi and pi-alkyl bonds play key role in drug-protein complexes.

  1. IR Spectra and Bond Energies Computed Using DFT

    Science.gov (United States)

    Bauschlicher, Charles; Andrews, Lester; Arnold, James (Technical Monitor)

    2000-01-01

    The combination of density functional theory (DFT) frequencies and infrared (IR) intensities and experimental spectra is a very powerful tool in the identification of molecules and ions. The computed and measured isotopic ratios make the identification much more secure than frequencies and intensities alone. This will be illustrated using several examples, such as Mn(CO)n and Mn(CO)n-. The accuracy of DFT metal-ligand bond energies will also be discussed.

  2. Efficient pseudospectral methods for density functional calculations

    International Nuclear Information System (INIS)

    Murphy, R. B.; Cao, Y.; Beachy, M. D.; Ringnalda, M. N.; Friesner, R. A.

    2000-01-01

    Novel improvements of the pseudospectral method for assembling the Coulomb operator are discussed. These improvements consist of a fast atom centered multipole method and a variation of the Head-Gordan J-engine analytic integral evaluation. The details of the methodology are discussed and performance evaluations presented for larger molecules within the context of DFT energy and gradient calculations. (c) 2000 American Institute of Physics

  3. DFT/B3LYP study of tocopherols and chromans antioxidant action energetics

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Erik [Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology, Radlinskeho 9, SK-812 37 Bratislava (Slovakia)], E-mail: erik.klein@stuba.sk; Lukes, Vladimir; Ilcin, Michal [Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology, Radlinskeho 9, SK-812 37 Bratislava (Slovakia)

    2007-07-09

    Gas-phase reaction enthalpies related to the individual steps of three phenolic antioxidants action mechanisms - hydrogen atom transfer (HAT), single-electron transfer-proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET) for four tocopherols and seven chromans - were calculated using DFT/B3LYP method. For {alpha}-tocopherol, one of the chromans and phenol, reaction enthalpies in water were computed. In comparison to gas phase, water causes severe changes in the energetics of studied compounds antioxidant action. From the thermodynamic point of view, entering SPLET mechanism represents the most probable process in water.

  4. DFT molecular modeling and NMR conformational analysis of a new longipinenetriolone diester

    Science.gov (United States)

    Cerda-García-Rojas, Carlos M.; Guerra-Ramírez, Diana; Román-Marín, Luisa U.; Hernández-Hernández, Juan D.; Joseph-Nathan, Pedro

    2006-05-01

    The structure and conformational behavior of the new natural compound (4 R,5 S,7 S,8 R,9 S,10 R,11 R)-longipin-2-en-7,8,9-triol-1-one 7-angelate-9-isovalerate (1) isolated from Stevia eupatoria, were studied by molecular modeling and NMR spectroscopy. A Monte Carlo search followed by DFT calculations at the B3LYP/6-31G* level provided the theoretical conformations of the sesquiterpene framework, which were in full agreement with results derived from the 1H- 1H coupling constant analysis.

  5. A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases.

    Science.gov (United States)

    Gao, Ting; Li, Hongzhi; Li, Wenze; Li, Lin; Fang, Chao; Li, Hui; Hu, LiHong; Lu, Yinghua; Su, Zhong-Min

    2016-01-01

    Non-covalent interactions (NCIs) play critical roles in supramolecular chemistries; however, they are difficult to measure. Currently, reliable computational methods are being pursued to meet this challenge, but the accuracy of calculations based on low levels of theory is not satisfactory and calculations based on high levels of theory are often too costly. Accordingly, to reduce the cost and increase the accuracy of low-level theoretical calculations to describe NCIs, an efficient approach is proposed to correct NCI calculations based on the benchmark databases S22, S66 and X40 (Hobza in Acc Chem Rev 45: 663-672, 2012; Řezáč et al. in J Chem Theory Comput 8:4285, 2012). A novel type of NCI correction is presented for density functional theory (DFT) methods. In this approach, the general regression neural network machine learning method is used to perform the correction for DFT methods on the basis of DFT calculations. Various DFT methods, including M06-2X, B3LYP, B3LYP-D3, PBE, PBE-D3 and ωB97XD, with two small basis sets (i.e., 6-31G* and 6-31+G*) were investigated. Moreover, the conductor-like polarizable continuum model with two types of solvents (i.e., water and pentylamine, which mimics a protein environment with ε = 4.2) were considered in the DFT calculations. With the correction, the root mean square errors of all DFT calculations were improved by at least 70 %. Relative to CCSD(T)/CBS benchmark values (used as experimental NCI values because of its high accuracy), the mean absolute error of the best result was 0.33 kcal/mol, which is comparable to high-level ab initio methods or DFT methods with fairly large basis sets. Notably, this level of accuracy is achieved within a fraction of the time required by other methods. For all of the correction models based on various DFT approaches, the validation parameters according to OECD principles (i.e., the correlation coefficient R (2), the predictive squared correlation coefficient q (2) and [Formula

  6. Are both symmetric and buckled dimers on Si(100) minima? Density functional and multireference perturbation theory calculations

    International Nuclear Information System (INIS)

    Jung, Yousung; Shao, Yihan; Gordon, Mark S.; Doren, Douglas J.; Head-Gordon, Martin

    2003-01-01

    We report a spin-unrestricted density functional theory (DFT) solution at the symmetric dimer structure for cluster models of Si(100). With this solution, it is shown that the symmetric structure is a minimum on the DFT potential energy surface, although higher in energy than the buckled structure. In restricted DFT calculations the symmetric structure is a saddle point connecting the two buckled minima. To further assess the effects of electron correlation on the relative energies of symmetric versus buckled dimers on Si(100), multireference second order perturbation theory (MRMP2) calculations are performed on these DFT optimized minima. The symmetric structure is predicted to be lower in energy than the buckled structure via MRMP2, while the reverse order is found by DFT. The implications for recent experimental interpretations are discussed

  7. DFT study on the second-order nonlinear optical properties of coumarin series molecules with various substituents

    International Nuclear Information System (INIS)

    Liang Xiaorui; Zhang Yong; Liang Chenghong; Li Yin; Zhao Bo

    2011-01-01

    The objective of this investigation was to design a series of coumarin with various substituents which show high nonlinear optical activity. The full geometry optimisations of designed coumarin systems were performed using Density Functional Theory (DFT) method at B3LYP/6-31G level of theory. The calculations of the static second-order NLO polarizabilities (β) of these systems were performed at the same level of theory. Combined with time-dependent density-functional theory (TD-DFT), the molecular electric spectrum was calculated. The results indicate that this series of coumarin have high β values. And series A have better planarity, longer conjugated bridge and larger β tot value than series B. The energy transition of frontier molecular orbitals is the key factor to the second-order NLO response. (authors)

  8. Declination Calculator

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Declination is calculated using the current International Geomagnetic Reference Field (IGRF) model. Declination is calculated using the current World Magnetic Model...

  9. A Solution to the Band Gap and Related Problems in Density Functional Theory (DFT).

    Science.gov (United States)

    Bagayoko, Diola

    This presentation shows that the attainment of self-consistency, with a single basis set, does not allows one to reach results that possess the physical content of density functional theory (DFT). This fact is amply illustrated in the literature where reported DFT eigenvalues appear not to correspond to actual energy levels in materials under study. Our proof includes an understanding of the second Hohenberg-Kohn (HK) theorem that requires the use of successively larger and embedded basis sets to perform completely self-consistent calculations in order to reach the absolute minima of the occupied energies, i.e., the ground state of the system. Embedding here means that, except for the first one, each basis set is obtained by augmenting the one preceding it with one orbital. We also show that arbitrarily large basis sets, by virtue of the first HK theorem, are over-complete for the description of the ground state: This fact explains the well-known underestimation of energy and band gaps by single basis set calculations for the last 50 years. The non-attainment the ground state et the over-completeness of some large basis set explain the inaccuracy of calculated, optical transition energies, effective masses, dielectric functions and of a host of other computational results. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

  10. Study on the structure and vibrational spectra of efavirenz conformers using DFT: Comparison to experimental data

    Science.gov (United States)

    Mishra, Soni; Tandon, Poonam; Ayala, A. P.

    2012-03-01

    Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The infrared and the Raman spectra of the molecule based on DFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule.

  11. Synthesis, spectroscopic and DFT studies of novel 4-(morpholinomethyl)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid

    Science.gov (United States)

    Devi, Poornima; Fatma, Shaheen; Bishnoi, Abha; Srivastava, Krishna; Shukla, Shraddha; Kumar, Roop

    2018-04-01

    A novel 4-(morpholinomethyl)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid has been synthesized and its structural elucidation has been done by UV, FT-IR, 1H and 13C NMR spectroscopy. All quantum chemical calculations were carried out at level of density functional theory (DFT) with B3LYP function using 6-31G (d, p) basis atomic set. AIM approach has been incorporated for the analysis of various intermolecular interactions. Polarizability and hyperpolarizabilities values have been calculated along with the exploration of nonlinear optical properties of the title compound. DFT computed total first static hyperpolarizability (β0 = 0.2747 × 10-30 esu) indicates that title molecule could be an area of interest as an attractive future NLO material. For the analysis of thermal behaviour of title molecule, thermodynamic properties such as heat capacity, entropy and enthalpy change at various temperatures have been calculated. The NBO computations were done for the correlation of possible transitions with the electronic transitions. Electrophilic and nucleophilic regions were identified with the help of MESP plot. Determination of energy gap has been done by using HOMO and LUMO energy values, along with the computation of electronegativity and electrophilicity indices.

  12. Synthesis, characterisation and DFT studies of three Schiff bases derived from histamine

    Science.gov (United States)

    Touafri, Lasnouni; Hellal, Abdelkader; Chafaa, Salah; Khelifa, Abdellah; Kadri, Abdelaziz.

    2017-12-01

    In this paper, we report first, the synthesis and characterisation of three Schiff bases derived from histamine by condensation of histamine with various aldehydes. Then, we present a detailed DFT study based on B3LYP/6-31G(d,p) of geometrical structures and electronic properties of these compounds. The study was extended to the HOMO-LUMO analysis to calculate the energy gap (Δ), Ionisation potential (I), Electron Affinity (A), Global Hardness (η), Chemical Potential (μ), Electrophilicity (ω), Electronegativity (χ) and Polarisability (α). The calculated HOMO and LUMO energy reveals that the charge transfers occurring within the molecule. On the basis of vibration analyses, the thermodynamic properties of the titles compound were also calculated.

  13. Conformational, vibrational spectroscopic and quantum chemical studies on 5-methoxyindole-3-carboxaldehyde: A DFT approach

    Science.gov (United States)

    Jeyaseelan, S. Christopher; Hussain, Shamima; Premkumar, R.; Rekha, T. N.; Benial, A. Milton Franklin

    2018-04-01

    Indole and its derivatives are considered as good ligands for various disease causing proteins in human because of presence of the single nitrogen atom. In the present study, the potential energy surface scan was performed for the most stable molecular structure of the 5-Methoxyindole-3-carboxaldehyde (MICA) molecule. The most stable molecular structure was optimized by DFT/B3LYP method with 6-311G++ (d, p) basis set using Gaussian 09 program package. The vibrational frequencies were calculated and assigned on the basis of potential energy distribution calculations using VEDA 4.0 program. The Frontier molecular orbitals analysis was performed and related molecular propertieswere calculated. The possible electrophilic and nucleophilic reactive sites of the molecule were studied using molecular electrostatic potential analysis, which confirms the bioactivity of the molecule. The natural bond orbital analysis was also performed to confirm the bioactivity of the title molecule.

  14. Crystal structure, spectroscopy, DFT studies and thermal characterization of Cobalt(II) complex with 2-protonated aminopyridinium cation as ligand

    Science.gov (United States)

    Mhadhbi, Noureddine; Saïd, Salem; Elleuch, Slim; Naïli, Houcine

    2016-03-01

    Single crystals of a new organic-inorganic hybrid compound (2-HAMP)2[CoBr4], (2-HAMP = 2-protonated aminopyridinium cation) was synthesized and characterized by X-Ray diffraction at room temperature, DTA-TG measurement, FT-IR and FT-Raman spectroscopies and optical absorption. Its crystal structure is a packing of alternated organic and inorganic layers parallel to (a, b) plane. The different components are connected by a network of N/C-H⋯Br hydrogen bonds and halogen⋯halogen interactions. These hydrogen bonds give notable vibrational effects. Theoretical calculations were performed using density functional theory (DFT) for studying the molecular structure, vibrational spectra and optical properties of the investigated molecule in the ground state. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental UV-Visible spectrum. The results show good consistent with the experiment and confirm the contribution of metal orbital to the HOMO-LUMO boundary. Thermal analysis studies indicate the presence of three phase transitions at 68, 125 and 172 °C, which are confirmed by X-ray powder diffraction as a function of temperature.

  15. Electronic structure and optical spectra of catechol on TiO2 nanoparticles from real time TD-DFT simulations.

    Science.gov (United States)

    Sánchez-de-Armas, R; San-Miguel, M A; Oviedo, J; Márquez, A; Sanz, J F

    2011-01-28

    The electronic structure and the optical response of free catechol, [Ti(cat)(3)](2-) complex, and catechol bound to TiO(2) nanoclusters have been analysed using time dependent density functional theory (TD-DFT) performing calculations both in real time and frequency domains. Both approaches lead to similar results providing the basis sets and functionals are similar. For all cases, the simulated spectra agree well with the experimental ones. For the adsorption systems, the spectra show a band at 4.7 eV associated to intramolecular catechol π→π* transitions, and low energy bands corresponding to transitions from catechol to the cluster with a tail that is red-shifted when the coupling between the dye and the cluster is more effective. Thus, dissociative adsorption modes provide longer tails than the molecular mode. Although the bidentate complex is more stable than the monodentate, the energy difference between both is smaller when the cluster size increases. Small cluster models reproduce the main features of the optical response, however, the (TiO(2))(15) cluster constitutes the minimal size to provide a complete picture. In this case, the conventional TD-DFT (frequency domain) calculations are highly demanding computationally, while real time TD-DFT is more efficient and the calculations become affordable.

  16. A Facile Route to the non-IPR Fullerene Sc3N@C68: Synthesis, Spectroscopic Characterization and DFT Computations

    Czech Academy of Sciences Publication Activity Database

    Yang, S.; Kalbáč, Martin; Popov, A.; Dunsch, L.

    2006-01-01

    Roč. 12, č. 29 (2006), s. 7856-7863 ISSN 0947-6539 Grant - others: Volkswagen Foundation(DE) I-77/855 Institutional research plan: CEZ:AV0Z40400503 Keywords : synthesis * spectroscopy * DFT calculation Subject RIV: CG - Electrochemistry Impact factor: 5.015, year: 2006

  17. Quantum chemical calculations of Cr2O3/SnO2 using density ...

    Indian Academy of Sciences (India)

    The theoretical parameters of the transparent conducting metal oxides were calculated using DFT/B3LYP/LANL2DZ method. The optimised bond parameters such as bond lengths, bond angles and dihedral angles were calculated using the same theory. The non-linear optical property of the title compound was calculated ...

  18. First-principle calculations of the structural, electronic ...

    Indian Academy of Sciences (India)

    Abstract. First-principle calculations were performed to study the structural, electronic, thermodynamic and thermal properties of ZnSxSe1−x ternary alloys using the full potential-linearized augmented plane wave method. (FP-LAPW) within the density functional theory (DFT). In this approach the Wu–Cohen generalized ...

  19. First-principle calculations of the structural, electronic ...

    Indian Academy of Sciences (India)

    First-principle calculations were performed to study the structural, electronic, thermodynamic and thermal properties of ZnSxSe1−x ternary alloys using the full potential-linearized augmented plane wave method (FP-LAPW) within the density functional theory (DFT). In this approach the Wu–Cohen generalized gradient ...

  20. First-principle calculations of structural, electronic, optical, elastic ...

    Indian Academy of Sciences (India)

    S CHEDDADI

    2017-11-28

    Nov 28, 2017 ... Abstract. First-principle calculations on the structural, electronic, optical, elastic and thermal properties of the chalcopyrite MgXAs2 (X = Si, Ge) have been performed within the density functional theory (DFT) using the full- potential linearized augmented plane wave (FP-LAPW) method. The obtained ...

  1. Approximate dynamic fault tree calculations for modelling water supply risks

    International Nuclear Information System (INIS)

    Lindhe, Andreas; Norberg, Tommy; Rosén, Lars

    2012-01-01

    Traditional fault tree analysis is not always sufficient when analysing complex systems. To overcome the limitations dynamic fault tree (DFT) analysis is suggested in the literature as well as different approaches for how to solve DFTs. For added value in fault tree analysis, approximate DFT calculations based on a Markovian approach are presented and evaluated here. The approximate DFT calculations are performed using standard Monte Carlo simulations and do not require simulations of the full Markov models, which simplifies model building and in particular calculations. It is shown how to extend the calculations of the traditional OR- and AND-gates, so that information is available on the failure probability, the failure rate and the mean downtime at all levels in the fault tree. Two additional logic gates are presented that make it possible to model a system's ability to compensate for failures. This work was initiated to enable correct analyses of water supply risks. Drinking water systems are typically complex with an inherent ability to compensate for failures that is not easily modelled using traditional logic gates. The approximate DFT calculations are compared to results from simulations of the corresponding Markov models for three water supply examples. For the traditional OR- and AND-gates, and one gate modelling compensation, the errors in the results are small. For the other gate modelling compensation, the error increases with the number of compensating components. The errors are, however, in most cases acceptable with respect to uncertainties in input data. The approximate DFT calculations improve the capabilities of fault tree analysis of drinking water systems since they provide additional and important information and are simple and practically applicable.

  2. A DFT Study of R-X Bond Dissociation Enthalpies of Relevance to the Initiation Process of Atom Transfer Radical Polymerization

    DEFF Research Database (Denmark)

    Gillies, Malcolm Bjørn; Matyjaszewski, Krzysztof; Norrby, Per-Ola

    2003-01-01

    DFT calculations at the B3P86/6-31G** level have been carried out to derive the bond dissociation energies (BDE) and free energies for a number of R-X systems (X ) Cl, Br, I, N3, and S2-CNMe2) that have been or can potentially be used as initiators for atom transfer radical polymerization (ATRP...... with the equilibrium constants that have been determined from ATRP polymerization rates and from model studies of activation-deactivation-termination processes in the absence of monomer. These comparisons reveal the effectiveness of the DFT-computed BDEs for predicting polymerization rates for new monomers in ATRP...

  3. Mechanistic insights on ethanol dehydrogenation on Pd-Au model catalysts: a combined experimental and DFT study.

    Science.gov (United States)

    Evans, E J; Li, H; Yu, Wen-Yueh; Mullen, G M; Henkelman, G; Mullins, C Buddie

    2017-11-22

    In this study, we have combined ultra-high vacuum (UHV) experiments and density functional theory (DFT) calculations to investigate ethanol (EtOH) dehydrogenation on Pd-Au model catalysts. Using EtOH reactive molecular beam scattering (RMBS), EtOH temperature-programmed desorption (TPD), and DFT calculations, we show how different Pd ensemble sizes on Au(111) can affect the mechanism for EtOH dehydrogenation and H 2 production. The Au(111) surface with an initial coverage of 2 monolayers of Pd (2 ML Pd-Au) had the highest H 2 yield. However, the 1 ML Pd-Au catalyst showed the highest selectivity and stability, yielding appreciable amounts of only H 2 and acetaldehyde. Arrhenius plots of H 2 production confirm that the mechanisms for EtOH dehydrogenation differed between 1 and 2 ML Pd-Au, supporting the perceived difference in selectivity between the two surfaces. DFT calculations support this difference in mechanism, showing a dependence of the initial dehydrogenation selectivity of EtOH on the size of Pd ensemble. DFT binding energies and EtOH TPD confirm that EtOH has increasing surface affinity with increasing Pd ensemble size and Pd coverage, indicating that surfaces with more Pd are more likely to induce an EtOH reaction instead of desorb. Our theoretical results show that the synergistic influence of atomic ensemble and electronic effects on Pd/Au(111) can lead to different H 2 association energies and EtOH dehydrogenation capacities at different Pd ensembles. These results provide mechanistic insights into ethanol's dehydrogenation interactions with different sites on the Pd-Au surface and can potentially aid in bimetallic catalyst design for applications such as fuel cells.

  4. Theoretical, ab initio and DFT, study of the structure and vibrational analysis of Raman, IR and INS spectra of (CH{sub 3}){sub 3}SiNCO

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Liencres, M.P. [Department of Physical and Analytical Chemistry, University of Jaen, 23071 Jaen (Spain)], E-mail: liencres@ujaen.es; Navarro, A. [Department of Physical and Analytical Chemistry, University of Jaen, 23071 Jaen (Spain); Ben Altabef, A. [Instituto de Quimica Fisica, Facultad de Bioquimica, Quimica y Farmacia, Universidad Nacional de Tucuman, San Lorenzo 456, 4000 S.M. de Tucuman (Argentina); Lopez-Gonzalez, J.J. [Department of Physical and Analytical Chemistry, University of Jaen, 23071 Jaen (Spain); Fernandez-Gomez, M. [Department of Physical and Analytical Chemistry, University of Jaen, 23071 Jaen (Spain); Kearley, G.J. [Department of Radiation, Radionuclides and Reactors, Faculty of Applied Sciences, Delft University of Technology, Mekelweg 15, 2629 JB Delft (Netherlands)

    2006-11-08

    The molecular geometry for trimethylsilylisocyanate ((CH{sub 3}){sub 3}SiNCO) has been calculated at MP2 and DFT/B3LYP and DFT/B3PW91 methods, and using the 6-31G*, 6-311G**, 6-311++G**, cc-pVDZ and cc-pVTZ basis sets. The equilibrium structure of the molecule, linear or bent as concerns the -SiNCO moiety, was found to rely on the method employed. The potential energy surface of -SiNC bending has been investigated by quantum mechanical ab initio calculations at MPn (n = 2-4) and QCISD(T) levels of theory with the cc-pVTZ basis set. This large amplitude bending motion (the {upsilon} {sub 24} mode) was determined to be very anharmonic, with a low barrier to linearity of the SiNCO skeleton of {approx}4-25 cm{sup -1}. New vapour and liquid IR, liquid Raman spectra and, for first time, INS spectrum have been recorded, and a complete vibrational assignment has been performed. INS data have allowed to assign two modes at 674 cm{sup -1} and 141 cm{sup -1} which, so far, have been considered as silent, i.e. A{sub 2}, since previous authors have used a frame of C {sub 3v} symmetry for this system. The intermolecular interactions show to have little effect on the torsional region (below 250 cm{sup -1} in INS spectrum) and the isolated-molecule approximation works well in that region. A normal coordinate analysis has been carried out by scaling the force fields calculated at MP2/6-311++G** and B3LYP/cc-pVDZ levels of theory using the scaled quantum mechanical force field (SQMFF) methodology. In order to get the best possible agreement between calculated and observed vibrational wavenumbers, the scale factors were refined by least squares yielding a final r.m.s. of {approx}7 cm{sup -1}.

  5. Two and Three-Dimensional Nonlocal DFT for Inhomogeneous Fluids I: Algorithms and Parallelization

    Energy Technology Data Exchange (ETDEWEB)

    Frink, Laura J. Douglas; Salinger, Andrew

    1999-08-09

    Fluids adsorbed near surfaces, macromolecules, and in porous materials are inhomogeneous, inhibiting spatially varying density distributions. This inhomogeneity in the fluid plays an important role in controlling a wide variety of complex physical phenomena including wetting, self-assembly, corrosion, and molecular recognition. One of the key methods for studying the properties of inhomogeneous fluids in simple geometries has been density functional theory (DFT). However, there has been a conspicuous lack of calculations in complex 2D and 3D geometries. The computational difficulty arises from the need to perform nested integrals that are due to nonlocal terms in the free energy functional These integral equations are expensive both in evaluation time and in memory requirements; however, the expense can be mitigated by intelligent algorithms and the use of parallel computers. This paper details our efforts to develop efficient numerical algorithms so that no local DFT calculations in complex geometries that require two or three dimensions can be performed. The success of this implementation will enable the study of solvation effects at heterogeneous surfaces, in zeolites, in solvated (bio)polymers, and in colloidal suspensions.

  6. Finite-temperature orbital-free DFT molecular dynamics: Coupling PROFESS and QUANTUM ESPRESSO

    Science.gov (United States)

    Karasiev, Valentin V.; Sjostrom, Travis; Trickey, S. B.

    2014-12-01

    Implementation of orbital-free free-energy functionals in the PROFESS code and the coupling of PROFESS with the QUANTUM ESPRESSO code are described. The combination enables orbital-free DFT to drive ab initio molecular dynamics simulations on the same footing (algorithms, thermostats, convergence parameters, etc.) as for Kohn-Sham (KS) DFT. All the non-interacting free-energy functionals implemented are single-point: the local density approximation (LDA; also known as finite-T Thomas-Fermi, ftTF), the second-order gradient approximation (SGA or finite-T gradient-corrected TF), and our recently introduced finite-T generalized gradient approximations (ftGGA). Elimination of the KS orbital bottleneck via orbital-free methodology enables high-T simulations on ordinary computers, whereas those simulations would be costly or even prohibitively time-consuming for KS molecular dynamics (MD) on very high-performance computer systems. Example MD simulations on H over a temperature range 2000 K ≤ T ≤4,000,000 K are reported, with timings on small clusters (16-128 cores) and even laptops. With respect to KS-driven calculations, the orbital-free calculations are between a few times through a few hundreds of times faster.

  7. Phenothiazine-Anthraquinone Donor-Acceptor Molecules: Synthesis, Electronic Properties and DFT-TDDFT Computational Study

    Science.gov (United States)

    Zhang, Wen-Wei; Mao, Wei-Li; Hu, Yun-Xia; Tian, Zi-Qi; Wang, Zhi-Lin; Meng, Qing-Jin

    2009-08-01

    Two donor-acceptor molecules with different π-electron conjugative units, 1-((10-methyl-10H-phenothiazin-3-yl)ethynyl)anthracene-9,10-dione (AqMp) and 1,1'-(10-methyl-10H-phenothiazine-3,7-diyl)bis(ethyne-2,1-diyl)dianthracene-9,10-dione (Aq2Mp), have been synthesized and investigated for their photochemical and electrochemical properties. Density functional theory (DFT) calculations provide insights into their molecular geometry, electronic structures, and properties. These studies satisfactorily explain the electrochemistry of the two compounds and indicate that larger conjugative effect leads to smaller HOMO-LUMO gap (Eg) in Aq2Mp. Both compounds show ICT and π → π* transitions in the UV-visible range in solution, and Aq2Mp has a bathochromic shift and shows higher oscillator strength of the absorption, which has been verified by time-dependent DFT (TDDFT) calculations. The differences between AqMp and Aq2Mp indicate that the structural and conjugative effects have great influence on the electronic properties of the molecules.

  8. NMR J-coupling constants in cisplatin derivatives studied by molecular dynamics and relativistic DFT.

    Science.gov (United States)

    Sutter, Kiplangat; Truflandier, Lionel A; Autschbach, Jochen

    2011-06-06

    Solvent effects on J((195)Pt-(15)N) one-bond nuclear spin-spin coupling constants (J(PtN)) of cisplatin [cis-diamminedichloroplatinum(II)] and three cisplatin derivatives are investigated using a combination of density functional theory (DFT) based ab initio molecular dynamics (aiMD) and all-electron relativistic DFT NMR calculations employing the two-component relativistic zeroth-order regular approximation (ZORA). Good agreement with experiment is obtained when explicit solvent molecules are considered and when the computations are performed with a hybrid functional. Spin-orbit coupling causes only small effects on J(PtN) . Key factors contributing to the magnitude of coupling constants are elucidated, with the most significant being the presence of solvent as well as the quality of the density functional and basis set combination. The solvent effects are of the same magnitude as J(PtN) calculated for gas-phase geometries. However, the trends of J(PtN) among the complexes are already present in the gas phase. Results obtained with a continuum solvent model agree quite well with the aiMD results, provided that the Pt solvent-accessible radius is carefully chosen. The aiMD results support the existence of a partial hydrogen-bond-like inverse-hydration-type interaction affording a weak (1)J(Pt⋅⋅⋅H(w)) coupling between the complexes and the coordinating water molecule. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. A DFT study of phenol adsorption on a low doping Mn-Ce composite oxide model

    Science.gov (United States)

    D´Alessandro, Oriana; Pintos, Delfina García; Juan, Alfredo; Irigoyen, Beatriz; Sambeth, Jorge

    2015-12-01

    Density functional theory calculations (DFT + U) were performed on a low doping Mn-Ce composite oxide prepared from experimental data, including X-ray diffraction (XRD) and temperature-programmed reduction (TPR). We considered a 12.5% Mn-doped CeO2 solid solution with fluorite-type structure, where Mn replaces Ce4+ leading to an oxygen-deficient bulk structure. Then, we modeled the adsorption of phenol on the bare Ce0.875Mn0.125O1.9375(1 1 1) surface. We also studied the effect of water adsorption and dissociation on phenol adsorption on this surface, and compared the predictions of DFT + U calculations with diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) measurements. The experimental results allowed us to both build a realistic model of the low doping Mn-Ce composite oxide and support the prediction that phenol is adsorbed as a phenoxy group with a tilt angle of about 70° with respect to the surface.

  10. Accurate prediction of emission energies with TD-DFT methods for platinum and iridium OLED materials.

    Science.gov (United States)

    Morello, Glenn R

    2017-06-01

    Accurate prediction of triplet excitation energies for transition metal complexes has proven to be a difficult task when confronted with a variety of metal centers and ligand types. Specifically, phosphorescent transition metal light emitters, typically based on iridium or platinum, often give calculated results of varying accuracy when compared to experimentally determined T1 emission values. Developing a computational protocol for reliably calculating OLED emission energies will allow for the prediction of a complex's color prior to synthesis, saving time and resources in the laboratory. A comprehensive investigation into the dependence of the DFT functional, basis set, and solvent model is presented here, with the aim of identifying an accurate method while remaining computationally cost-effective. A protocol that uses TD-DFT excitation energies on ground-state geometries was used to predict triplet emission values of 34 experimentally characterized complexes, using a combination of gas phase B3LYP/LANL2dz for optimization and B3LYP/CEP-31G/PCM(THF) for excitation energies. Results show excellent correlation with experimental emission values of iridium and platinum complexes for a wide range of emission energies. The set of complexes tested includes neutral and charged complexes, as well as a variety of different ligand types.

  11. Bolus calculators.

    Science.gov (United States)

    Schmidt, Signe; Nørgaard, Kirsten

    2014-09-01

    Matching meal insulin to carbohydrate intake, blood glucose, and activity level is recommended in type 1 diabetes management. Calculating an appropriate insulin bolus size several times per day is, however, challenging and resource demanding. Accordingly, there is a need for bolus calculators to support patients in insulin treatment decisions. Currently, bolus calculators are available integrated in insulin pumps, as stand-alone devices and in the form of software applications that can be downloaded to, for example, smartphones. Functionality and complexity of bolus calculators vary greatly, and the few handfuls of published bolus calculator studies are heterogeneous with regard to study design, intervention, duration, and outcome measures. Furthermore, many factors unrelated to the specific device affect outcomes from bolus calculator use and therefore bolus calculator study comparisons should be conducted cautiously. Despite these reservations, there seems to be increasing evidence that bolus calculators may improve glycemic control and treatment satisfaction in patients who use the devices actively and as intended. © 2014 Diabetes Technology Society.

  12. DFT/TD-DFT characterization of conjugational electronic structures and spectral properties of materials based on thieno[3,2-b][1]benzothiophene for organic photovoltaic and solar cell applications

    Directory of Open Access Journals (Sweden)

    Mohamed Bourass

    2017-07-01

    Full Text Available In this work, a theoretical study on five organic π-conjugated molecules based on thieno[3,2-b][1]benzothiophene using together quantum methods, density functional theory (DFT and its derivative time dependent-density functional theory (TD-DFT is reported. Different electron side groups were introduced as a bridge to investigate their effects on the electronic structure; The HOMO, LUMO, chemical hardness (η, chemical potential (μ, electronegativity (χ, electrophilicity power (ω, reorganization energy total (λtotal, open circuit voltage (Voc, the gap energy and NBO analysis of these compounds have been reported and discussed in this paper. Thus, our aim is to explore their electronic and spectroscopic properties on the basis of the DFT quantum chemical calculations, and at the same time, we are interested to make an idea on the parameters influencing the photovoltaic efficiency toward a better understanding of the structure–property relationships. The calculated results of these compounds reveal that C4, C5, with thiophene and thienopyrazine as a bridge group respectively, can be used as a potential donor of electron in organic Bulk Heterojunction solar cells (BHJ, due to its best electronic and optical properties and good photovoltaic parameters. The study of electronic, optical and structural properties of these compounds could help to design more efficient functional photovoltaic organic materials.

  13. Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car–Parrinello molecular dynamics study

    International Nuclear Information System (INIS)

    Dutta, Bipan; De, Rina; Chowdhury, Joydeep

    2015-01-01

    Highlights: • The tautomerism of 4-MTTN molecule in solvent water medium has been investigated. • CPMD presage the possibility of PT reactions through the solvent water medium. • Concerted PT processes in 4-MTTN have been estimated from the DFT and NBO analyses. • Percentage evolution and breaking of the concerned bonds are estimated. - Abstract: The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car–Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

  14. Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car–Parrinello molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Bipan [Department of Physics, Sammilani Mahavidyalaya, E.M. Bypass, Baghajatin Station, Kolkata 700 094 (India); De, Rina [Department of Physics, Raja Rammohun Roy Mahavidyalaya, Nangulpara, Hooghly 712406 (India); Chowdhury, Joydeep, E-mail: joydeep72_c@rediffmail.com [Department of Physics, Sammilani Mahavidyalaya, E.M. Bypass, Baghajatin Station, Kolkata 700 094 (India)

    2015-12-16

    Highlights: • The tautomerism of 4-MTTN molecule in solvent water medium has been investigated. • CPMD presage the possibility of PT reactions through the solvent water medium. • Concerted PT processes in 4-MTTN have been estimated from the DFT and NBO analyses. • Percentage evolution and breaking of the concerned bonds are estimated. - Abstract: The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car–Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

  15. NMR shielding calculations across the periodic table: diamagnetic uranium compounds. 2. Ligand and metal NMR.

    Science.gov (United States)

    Schreckenbach, Georg

    2002-12-16

    In this and a previous article (J. Phys. Chem. A 2000, 104, 8244), the range of application for relativistic density functional theory (DFT) is extended to the calculation of nuclear magnetic resonance (NMR) shieldings and chemical shifts in diamagnetic actinide compounds. Two relativistic DFT methods are used, ZORA ("zeroth-order regular approximation") and the quasirelativistic (QR) method. In the given second paper, NMR shieldings and chemical shifts are calculated and discussed for a wide range of compounds. The molecules studied comprise uranyl complexes, [UO(2)L(n)](+/-)(q); UF(6); inorganic UF(6) derivatives, UF(6-n)Cl(n), n = 0-6; and organometallic UF(6) derivatives, UF(6-n)(OCH(3))(n), n = 0-5. Uranyl complexes include [UO(2)F(4)](2-), [UO(2)Cl(4)](2-), [UO(2)(OH)(4)](2-), [UO(2)(CO(3))(3)](4-), and [UO(2)(H(2)O)(5)](2+). For the ligand NMR, moderate (e.g., (19)F NMR chemical shifts in UF(6-n)Cl(n)) to excellent agreement [e.g., (19)F chemical shift tensor in UF(6) or (1)H NMR in UF(6-n)(OCH(3))(n)] has been found between theory and experiment. The methods have been used to calculate the experimentally unknown (235)U NMR chemical shifts. A large chemical shift range of at least 21,000 ppm has been predicted for the (235)U nucleus. ZORA spin-orbit appears to be the most accurate method for predicting actinide metal chemical shifts. Trends in the (235)U NMR chemical shifts of UF(6-n)L(n) molecules are analyzed and explained in terms of the calculated electronic structure. It is argued that the energy separation and interaction between occupied and virtual orbitals with f-character are the determining factors.

  16. SCC-TB, DFT/B3LYP, MP2, AM1, PM3 and RHF study of ethylene oxide and propylene oxide structures, VA and VCD spectra

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Frimand, Kenneth

    2002-01-01

    -binding method for equilibrium structures, VA and VCD spectra of ethylene oxide and propylene oxide in the gas-phase. Comparison to conventional methods AM1, PM3, MP2, RHF and DFT/B3LYP is carried out. We report results over a wider range of frequencies than previous work. In particular, we find indications...

  17. An efficient ab initio DFT and PCM assessment of the potentiometric selectivity of a salophen type Schiff base.

    Science.gov (United States)

    Demir, Serkan; Yilmaz, Hakan; Dilimulati, Maowulidan; Andaç, Müberra

    2014-06-01

    As a neutral carrier component for the preparation of a potentiometric membrane sensor, the affinity and selectivity of the salophen type Schiff base ligand obtained by 1:2 condensation of 2.3-diaminopyridine with salicylaldehyde toward a series of common cations has been fully examined by DFT/B3LYP and integral equation formalism polarizable continum model (IEF-PCM or only given with PCM as default input in the computations) in combination with the experimental data. Both the potentiometric measurements and DFT calculations have exhibited that the ionophore shows appreciable selectivity for Cu(2+) ion over other cations. Four different approaches where the last three are the modified version of each other have been evaluated and compared with potentiometric data. Based upon the results of comparison among the approaches suggested to verify the selective behavior of ionophore toward Cu(2+), PCM implemented approach having a whole computational groundwork has given well-matched results with the observed data and with the method augmented with experimental hydration energies. The foremost interferences were detected by determining potentiometric selectivity coefficients for each metal ion relative to Cu(2+) and compared to the results obtained by the DFT calculations.

  18. MEMS Calculator

    Science.gov (United States)

    SRD 166 MEMS Calculator (Web, free access)   This MEMS Calculator determines the following thin film properties from data taken with an optical interferometer or comparable instrument: a) residual strain from fixed-fixed beams, b) strain gradient from cantilevers, c) step heights or thicknesses from step-height test structures, and d) in-plane lengths or deflections. Then, residual stress and stress gradient calculations can be made after an optical vibrometer or comparable instrument is used to obtain Young's modulus from resonating cantilevers or fixed-fixed beams. In addition, wafer bond strength is determined from micro-chevron test structures using a material test machine.

  19. Benchmark Calculations of Energetic Properties of Groups 4 and 6 Transition Metal Oxide Nanoclusters Including Comparison to Density Functional Theory

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Zongtang; Both, Johan; Li, Shenggang; Yue, Shuwen; Aprà, Edoardo; Keçeli, Murat; Wagner, Albert F.; Dixon, David A.

    2016-08-09

    The heats of formation and the normalized clustering energies (NCEs) for the group 4 and group 6 transition metal oxide (TMO) trimers and tetramers have been calculated by the Feller-Peterson-Dixon (FPD) method. The heats of formation predicted by the FPD method do not differ much from those previously derived from the NCEs at the CCSD(T)/aT level except for the CrO3 nanoclusters. New and improved heats of formation for Cr3O9 and Cr4O12 were obtained using PW91 orbitals instead of Hartree-Fock (HF) orbitals. Diffuse functions are necessary to predict accurate heats of formation. The fluoride affinities (FAs) are calculated with the CCSD(T) method. The relative energies (REs) of different isomers, NCEs, electron affinities (EAs), and FAs of (MO2)n ( M = Ti, Zr, Hf, n = 1 – 4 ) and (MO3)n ( M = Cr, Mo, W, n = 1 – 3) clusters have been benchmarked with 55 exchange-correlation DFT functionals including both pure and hybrid types. The absolute errors of the DFT results are mostly less than ±10 kcal/mol for the NCEs and the EAs, and less than ±15 kcal/mol for the FAs. Hybrid functionals usually perform better than the pure functionals for the REs and NCEs. The performance of the two types of functionals in predicting EAs and FAs is comparable. The B1B95 and PBE1PBE functionals provide reliable energetic properties for most isomers. Long range corrected pure functionals usually give poor FAs. The standard deviation of the absolute error is always close to the mean errors and the probability distributions of the DFT errors are often not Gaussian (normal). The breadth of the distribution of errors and the maximum probability are dependent on the energy property and the isomer.

  20. Separation of Am3+and Eu3+using hexa-n-octylnitrilo triacetamide (HONTA): complexation, extraction, luminescence, EXAFS and DFT studies.

    Science.gov (United States)

    Bhattacharyya, Arunasis; Egberink, Richard J M; Mohapatra, Prasanta K; Verma, Parveen K; Yadav, Ashok K; Jha, Sambhunath; Bhattacharyya, Dibyendu; Huskens, Jurriaan; Verboom, Willem

    2017-12-21

    This paper reports the solvent extraction of Am 3+ and Eu 3+ using N,N,N',N',N'',N''-hexa-n-octylnitrilotriacetamide (HONTA) as the extractant in n-dodecane. The results are in variance with those reported previously with respect to the nature of the extracted species. The solvent extraction data were entirely different from those reported previously as the extracted species conformed to 1 : 2 (M : L) species for both Am 3+ and Eu 3+ ions. The structure of the extracted complex was determined by EXAFS demonstrating the three amidic 'O' atoms of the HONTA complex with the Eu 3+ ion. In the case of the Am 3+ ion, the pivotal 'N' atom is suggested to bond to the metal ion, which may explain the significantly more favourable extraction of Am 3+ vis-à-vis Eu 3+ . The absence of H 2 O molecules in the inner coordination sphere of the Eu 3+ -HONTA extract was confirmed by luminescence spectroscopic measurements. Complexation studies in MeOH and EtOH indicated the formation of both 1 : 1 and 1 : 2 complexes with Nd 3+ ions. The results are explained on the basis of DFT calculations using HMNTA, the corresponding hexamethyl analogue of HONTA.

  1. Predictions of Physicochemical Properties of Ionic Liquids with DFT

    Directory of Open Access Journals (Sweden)

    Karl Karu

    2016-07-01

    Full Text Available Nowadays, density functional theory (DFT-based high-throughput computational approach is becoming more efficient and, thus, attractive for finding advanced materials for electrochemical applications. In this work, we illustrate how theoretical models, computational methods, and informatics techniques can be put together to form a simple DFT-based throughput computational workflow for predicting physicochemical properties of room-temperature ionic liquids. The developed workflow has been used for screening a set of 48 ionic pairs and for analyzing the gathered data. The predicted relative electrochemical stabilities, ionic charges and dynamic properties of the investigated ionic liquids are discussed in the light of their potential practical applications.

  2. Stationary Conditions of the Electron Density Along the Reaction Path: Connection with Conceptual DFT and Information Theory.

    Science.gov (United States)

    Gonzalez, Carlos A; Squitieri, Emilio; Franco, Hector J; Rincon, Luis C

    2017-01-26

    The Kohn-Sham density functional theory (DFT) formalism has been used to investigate the influence of the stationary behavior of the electron density (ρ(r⃗;s)) along a minimum energy path on the corresponding stationary conditions observed in the total potential energy of the reactive system, information theory measures (Shannon information entropy and Onicescu information energy), and chemical reactivity indexes (the chemical hardness). The theoretical treatment presented in this work, combined with DFT calculations on 3 different test reactions: Ḣ' + H 2 , Ḣ' + CH 4 and H - + CH 4 , suggest that for any reactive system, properties that can be cast as a functional of the electron density, must exhibit stationary points along the IRC path modulated by the corresponding stationary behavior of the electron density.

  3. PdCu alloy nanoparticle-decorated copper nanotubes as enhanced electrocatalysts: DFT prediction validated by experiment

    Science.gov (United States)

    Wu, Dengfeng; Xu, Haoxiang; Cao, Dapeng; Fisher, Adrian; Gao, Yi; Cheng, Daojian

    2016-12-01

    In order to combine the advantages of both 0D and 1D nanostructured materials into a single catalyst, density functional theory (DFT) calculations have been used to study the PdCu alloy NP-decorated Cu nanotubes (PdCu@CuNTs). These present a significant improvement of the electrocatalytic activity of formic acid oxidation (FAO). Motivated by our theoretical work, we adopted the seed-mediated growth method to successfully synthesize the nanostructured PdCu@CuNTs. The new catalysts triple the catalytic activity for FAO, compared with commercial Pd/C. In summary, our work provides a new strategy for the DFT prediction and experimental synthesis of novel metal NP-decorated 1D nanostructures as electrocatalysts for fuel cells.

  4. Spectroscopic data of Labdane Diterpenes: a theoretical analysis via NMR and DFT

    International Nuclear Information System (INIS)

    Souza, Fabrine S. de; Silva, Silvana de O.; Alves, Cláudio N.; Guilhon, Giselle M.S.P.

    2015-01-01

    Labdane diterpenes exhibit important bioactivities such as cardiovascular effects in rats as well as effects in the treatment of autoimmune diseases and Alzheimer syndrome. Recently, the labdane diterpenes ent-13-epi-manoil oxide, ribenone and ribenol were isolated from Croton palanostigma. The computational method DFT/B3LYP/cc-pVDZ was used to optimize the structures of these diterpenes and to calculate infrared data. Chemical shifts (δ H and δ C ) of the minimum energy structures (local minimum) were calculated and compared with the experimental data. Comparison of the NMR data by simple linear regression (SLR) showed satisfactory statistical results with a correlation coefficient (R 2 ) and predictive ability (Q 2 ) of over 98%. The predicted NMR data were used to confirm the δ H values that have not been published. (author)

  5. A DFT study on the catalytic hydrogenation of CO2 to formic acid over Ti-doped graphene nanoflake

    Science.gov (United States)

    Esrafili, Mehdi D.; Dinparast, Leila

    2017-08-01

    The aim of this study is to investigate the potential of Ti-doped graphene nanoflake (Ti-GNF) for the reduction of CO2 to formic acid by H2. To get a deeper insight into the mechanism of this reaction, the reliable DFT calculations are performed. It is found that the large positive charge on the Ti atom can greatly regulate the surface reactivity of GNF. The formation of the formate group is the rate determining step for the reduction of CO2. The calculated activation energies demonstrate that Ti-GNF could be utilized as an efficient catalyst for the reduction of CO2 to formic acid.

  6. Effect of H-vacancy defect on the adsorption of CO and NO on graphane: A DFT study

    Science.gov (United States)

    Zhou, Qingxiao; Ju, Weiwei; Yong, Yongliang; Su, Xiangying; Li, Xiaohong; Fu, Zhibing; Wang, Chaoyang

    2017-10-01

    We investigated the adsorption of CO and NO molecules on hydrogenated graphene (graphane) monolayer using density functional theory (DFT) calculations. The geometry, adsorption stability, and electronic properties of CO and NO molecules absorbed on pure and H-vacancy defected graphane sheet were performed. The calculated results suggested that the small adsorption energy indicated the adsorption of CO and NO molecules on pure graphane were physisorption. However, the presence of H-vacancy improved the reactivity of graphane and the adsorption on H-vacnacy defected graphane changed to chemisorption. The adsorption also induced obvious change into the band gaps, which can be seen as signal to detect the CO and NO gas.

  7. DFT and experimental studies of the structure and vibrational spectra of 2-(tert-buroxycarbonyl (Boc) - amino)-5-bromopyridine

    Science.gov (United States)

    Premkumar, S.; Jawahar, A.; Umadevi, M.; Sathe, V. G.; Asath, R. Mohamed; Franklin Benial, A. Milton

    2014-04-01

    The vibrational frequencies and frontier molecular orbitals of 2-(tert-buroxycarbonyl (Boc) -amino)-5-bromopyridine (BABP) were theoretically calculated by the DFT/B3LYP method with cc-pVTZ basis set using Gaussian 09 program. The vibrational spectra were experimentally recorded by Fourier transform-infrared (FT-IR) and Raman spectrometer. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed vibrational frequencies. Theoretically calculated and experimentally observed vibrational frequencies were compared and assigned. The molecular interaction, stability and intermolecular charge transfer of BABP were studied using frontier molecular orbitals (FMO) analysis.

  8. Raman peak frequencies of fluoromethane molecules measured in clathrate hydrate crystals: experimental investigations and density functional theory calculations.

    Science.gov (United States)

    Uchida, Tsutomu; Ohmura, Ryo; Hori, Akira

    2010-01-14

    Systematic observations of fluoromethane clathrate hydrates were carried out by Raman spectroscopy. The series of fluoromethanes, i.e., methane (CH(4)), fluoromethane (CH(3)F), difluoromethane (CH(2)F(2)), trifluoromethane (CHF(3)), and tetrafluoromethane (CF(4)), were used as standard guest molecules to investigate the vibration modes of the guest molecules in the hydrate phase, since all of these fluoromethanes are included in the same crystal structure and share similar functional groups. In this study, both the C-H and C-F vibration modes of the guest molecules were systematically collected and assigned each peak based on the density functional theory (DFT) calculations. The Raman peak table obtained by the DFT calculations was useful for assigning the Raman peaks measured by the experiments. The assignment of the Raman peaks of the C-H stretching mode of each fluoromethane hydrate coincided well with those estimated both experimentally and theoretically in previous studies. The empirical "loose cage-tight cage" model of the Raman peak shifts allowed us to estimate the unperturbed frequencies of the C-H symmetric stretching mode on CH(3)F molecules in the clathrate structure. Clathrate hydrates formed with deuterated water molecules indicated that the deuterium had little effect on the Raman spectra of the intramolecular vibration modes of the guest molecules within the experimental uncertainties.

  9. Hydrogen storage by BeO nano-cage: A DFT study

    International Nuclear Information System (INIS)

    Beheshtian, Javad; Ravaei, Isa

    2016-01-01

    Graphical abstract: The electrostatic potential contours of Be 12 O 12 cluster with hydrogen molecules adsorbed. - Highlights: • H 2 adsorption on pristine beryllium oxide nano-cage (BeONC) investigated. • We investigated using density functional theory calculations in terms of adsorption energy, gravimetric, and charge transfer of H 2 molecule on BeONC. • We found that H 2 molecule is significantly adsorbed on the pristine BeO nano-cage. • We found that the DFT calculations indicate that gravimetric storage capacity of surface adsorption of hydrogen on BeONC is more than 7.6 wt%. • The H 2 molecule shows significantly adsorbed and gravimetric storage capacity, which our DFT results suggest on providing guidance for material design to better storage materials. - Abstract: First-principles calculations based on density functional theory were performed to study the hydrogen adsorption and H 2 storage on the beryllium oxide nano-cage (BeONC). The adsorption of H 2 molecules on the nano-cage depends on the polarization and charge of the atom surface. The transfer of charge from the Be atom to its neighboring O atoms in the surface of the cluster indicates the ionic character of the Be−O bond, so that Be−O bonds are polarized. The results show that the H 2 molecule is significantly adsorbed on the BeONC surface, so that the H 2 prefers to be adsorbed atop a Be atom as compared to oxygen atoms of the cluster surface. Our calculations also reveal that the gravimetric uptake can overpass the value of 7.6 wt% with an average adsorbed energy (E ads ) of −0.11 eV. These findings have important implications on designing of hydrogen storage materials and significantly broadening the spectrum of strategies for fabricating of new nanostructures to enhance hydrogen storage capacity.

  10. Chemistry of the 5g Elements: Relativistic Calculations on Hexafluorides.

    Science.gov (United States)

    Dognon, Jean-Pierre; Pyykkö, Pekka

    2017-08-14

    A Periodic System was proposed for the elements 1-172 by Pyykkö on the basis of atomic and ionic calculations. In it, the elements 121-138 were nominally assigned to a 5g row. We now perform molecular, relativistic four-component DFT calculations and find that the hexafluorides of the elements 125-129 indeed enjoy occupied 5g states. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Chemistry of the 5g elements. Relativistic calculations on hexafluorides

    Energy Technology Data Exchange (ETDEWEB)

    Dognon, Jean-Pierre [NIMBE, CEA, CNRS, Universite Paris-Saclay, CEA Saclay, Gif-sur-Yvette (France); Pyykkoe, Pekka [Department of Chemistry, University of Helsinki (Finland)

    2017-08-14

    A Periodic System was proposed for the elements 1-172 by Pyykkoe on the basis of atomic and ionic calculations. In it, the elements 121-138 were nominally assigned to a 5g row. We now perform molecular, relativistic four-component DFT calculations and find that the hexafluorides of the elements 125-129 indeed enjoy occupied 5g states. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. On the number of multiplications necessary to compute a length-2 exp n DFT

    Science.gov (United States)

    Heideman, M. T.; Burrus, C. S.

    1986-01-01

    The number of multiplications necessary and sufficient to compute a length-2 exp n DFT is determined. The method of derivation is shown to apply to the multiplicative complexity results of Winograd (1980, 1981) for a length-p exp n DFT, for p an odd prime number. The multiplicative complexity of the one-dimensional DFT is summarized for many possible lengths.

  13. On the Estimation of Complex Speech DFT Coefficients Without Assuming Independent Real and Imaginary Parts

    NARCIS (Netherlands)

    Erkelens, J.S.; Hendriks, R.C.; Heusdens, R.

    2008-01-01

    This letter considers the estimation of speech signals contaminated by additive noise in the discrete Fourier transform (DFT) domain. Existing complex-DFT estimators assume independency of the real and imaginary parts of the speech DFT coefficients, although this is not in line with measurements. In

  14. CHANNEL ESTIMATION FOR ZT DFT-s-OFDM

    DEFF Research Database (Denmark)

    2018-01-01

    A signal modulated according to zero-tail discrete Fourier transform spread orthogonal frequency division multiplexing (ZT DFT-s-OFDM) is received over a channel. The signal is down-sampled into a first sequence comprising N samples, N corresponding to the number of used subcarriers. The first Nh...

  15. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    Sci. Vol. 127, No. 12, December 2015, pp. 2137–2149. c Indian Academy of Sciences. DOI 10.1007/s12039-015-0976-x. Molecular structure and DFT investigations on new cobalt(II) chloride complex with superbase guanidine type ligand. SAIED M SOLIMANa,b,∗, MORSY A M ABU-YOUSSEFb,∗. , JΦRG ALBERINGc and.

  16. DFT analysis of the nucleophilicity of substituted pyridines and ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 4. DFT analysis of the nucleophilicity of substituted pyridines and prediction of new molecules having nucleophilic character stronger than 4-pyrrolidino pyridine. Kaustavmoni Deka Prodeep Phukan. Regular Articles Volume 128 Issue 4 April 2016 pp 633- ...

  17. Abstract: Synthesis, structure and density functional theory (DFT ...

    Indian Academy of Sciences (India)

    Ruthenium Complexes of Chelating Amido-functionalized N-heterocyclic Carbene Ligands: Synthesis, Structure and DFT Studies. Sachin Kumar,† Anantha Narayanan,† Mitta Nageswar Rao,† Mobin M. Shaikh§ and Prasenjit Ghosh*,†. †Department of Chemistry and. §National Single Crystal X-ray Diffraction Facility,.

  18. DFT computations of the lattice constant, stable atomic structure and ...

    African Journals Online (AJOL)

    This paper presents the most stable atomic structure and lattice constant of Fullerenes (C60). FHI-aims DFT code was used to predict the stable structure and the computational lattice constant of C60. These were compared with known experimental structures and lattice constants of C60. The results obtained showed that ...

  19. A DFT study of temperature dependent dissociation mechanism of ...

    Indian Academy of Sciences (India)

    Abstract. We report a Density Functional Theoretical (DFT) study of dissociation of Hydrogen Fluoride (HF) in HF(H2O)7 cluster, using B3LYP functional and empirical exchange correlation functional M06-2X along with 6-31+G(d,p) basis set. Dissociation constant, KRP, of HF dissociation and pKa values of HF in cluster.

  20. DFT-based inhibitor and promoter selection criteria for pentagonal ...

    Indian Academy of Sciences (India)

    Density functional theory (DFT)-based simulations have been performed to provide electronic structure property correlation based reasoning for conceptualizing the effect of encapsulated methane molecule on the formation of methane hydrate cages, the role of methanol and ethylene glycol as inhibitor and the role of ...