Lill, Sten O Nilsson
2010-09-01
An evaluation of a dispersion-corrected density functional theory method (B3LYP-DCP) [I.D. Mackie, G.A. DiLabio, Interactions in large, polyaromatic hydrocarbon dimers: application of density functional theory with dispersion corrections, J. Phys. Chem. A 112 (2008) 10968-10976] for three systems of biochemical interest is presented. Firstly, structures and energies of isomers of the tripeptide Phe-Gly-Phe have been compared with CCSD(T)/CBS//RI-MP2/cc-pVTZ literature values. In the system aromatic interactions compete with XH-pi (X=C, N) interactions and hydrogen bonds which makes it a reliable model for proteins. The resulting mean absolute deviation between B3LYP-DCP and CCSD(T)/CBS relative energies is found to be 0.50 kcal mol(-1). Secondly, a phenylalanine derivative featuring a CH-pi interaction has been investigated. A comparison between the optimized geometry and X-ray crystal data shows that B3LYP-DCP accurately predicts the interaction between the two aromatic rings. Thirdly, the dipeptide Ac-Phe-Phe-NH(2) which contains an edge-to-face interaction between two aromatic rings has been studied. The study demonstrates the general applicability of the B3LYP-DCP method on systems which features interactions typically present in biochemical compounds.
Legler, C R; Brown, N R; Dunbar, R A; Harness, M D; Nguyen, K; Oyewole, O; Collier, W B
2015-06-15
The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.
Indian Academy of Sciences (India)
M Talebian; E Talebian; A Abdi
2012-05-01
We obtained an approximation of the force ﬁeld of -quartz crystal using a new idea of applying density functional theory [J Purton, R Jones, C R A Catlow and M Leslie, Phys. Chem. Minerals 19, 392 (1993)]. Our calculations were based on B3LYP Hamiltonian [A N Lazarev and A P Mirgorodsky, Phys. Chem. Minerals 18, 231 (1991)] in 6−311+G(2d) basis set for H16Si7O6 cluster and included a unit cell of the lattice. The advantage of our method is the increase in the speed of calculations and the better adaption of simulation results with the experimental data.
Maschio, L.; Ferrabone, M.; Meyer, A.; Garza, J.; Dovesi, R.
2011-01-01
The performance of five different density functionals (LDA, PBE, PBESOL, B3LYP and PBE0) in describing the infrared spectrum of a crystalline periodic system with a large unit cell (spessartine, 80 atoms in the primitive cell) is studied by using the periodic ab initio CRYSTAL09 code and an all electron basis set. The transverse (TO) and longitudinal (LO) optical branches of the 17 IR active modes are evaluated together with the oscillator strengths and the high frequency dielectric tensor ɛ∞ . These ingredients permit to compute the dielectric function ɛ (ν) , and then the reflectance spectrum R (ν) , which is compared with experiment.
De la Pierre, M; Orlando, R; Maschio, L; Doll, K; Ugliengo, P; Dovesi, R
2011-07-15
The performance of six different density functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in describing the infrared spectrum of forsterite, a crystalline periodic system with orthorhombic unit cell (28 atoms in the primitive cell, Pbmn space group), is investigated by using the periodic ab initio CRYSTAL09 code and an all-electron Gaussian-type basis set. The transverse optical (TO) branches of the 35 IR active modes are evaluated at the equilibrium geometry together with the oscillator strengths and the high-frequency dielectric tensor ϵ(∞) . These quantities are essential to compute the dielectric function ϵ(ν), and then the reflectance spectrum R(ν), which is compared with experiment. It turns out that hybrid functionals perform better than LDA and GGA, in general; that B3LYP overperforms WC1LYP and, in turn, PBE0; that PBESOL is better than PBE; that LDA is the worst performing functional among the six under study.
Abkari, A.; Chaabane, I.; Guidara, K.
2016-07-01
The organic-inorganic salt, bis(4-acetylanilinium) tetrachlorocuprate(II), was synthesized and characterized by means of FT-IR (4000-400 cm-1) and Raman (3500-50 cm-1) in solid phase. The structure of [C8H10NO]2CuCl4 compound which was optimized by density functional theory (DFT) using B3LYP method showed that the calculated values obtained by B3LYP with LanL2DZ and 6311G+(d,p) basis sets are in better agreement with the experimental data. The computed vibrational frequencies were scaled by different scale factors to yield a good agreement with the experimental vibrational frequencies. The latter have been discussed on the basis of quantum chemical DFT calculations using the B3LYP/6311G+(d,p) and B3LYP/LanL2DZ method approach in gas phase. Besides, the effects due to the substitutions and the intermolecular interactions were investigated. The comparative analysis of the Raman spectra of the title compound with that of the free ligand was also discussed. The geometries and normal modes of the vibrations obtained from B3LYP/6311G+(d,p) calculation are found to be in good agreement with the experimentally observed data. The complete vibrational assignments and analysis of the observed fundamental bands of molecule were carried out.
Bleken, Francesca; Svelle, Stian; Lillerud, Karl Petter; Olsbye, Unni; Arstad, Bjørnar; Swang, Ole
2010-07-15
The methylation of ethene by methyl chloride and methanol in the microporous materials SAPO-34 and SSZ-13 has been studied using different periodic atomistic modeling approaches based on density functional theory. The RPBE functional, which earlier has been used successfully in studies of surface reactions on metals, fails to yield a qualitatively correct description of the transition states under study. Employing B3LYP as functional gives results in line with experimental data: (1) Methanol is adsorbed more strongly than methyl chloride to the acid site. (2) The activation energies for the methylation of ethene are slightly lower for SSZ-13. Furthermore, the B3LYP activation energies are lower for methyl chloride than for methanol.
Tarchouna, S.; Chaabane, I.; Rahaiem, A. Ben
2016-09-01
4-acetylanilinium was used as a ligand for the synthesis of the organic/inorganic compound bis (4-acetylanilinium) hexachlorostannate. Vibrational study in the solid state was performed by FT-Raman of the free 4-acetylanilinium ligand C8H9ON+ and by FT-IR and FT-Raman spectroscopies of the [C8H10NO]2 SnCl6 compound. The comparative analysis of the Raman spectra of the title compound with that of the free ligand was discussed. The structure of the [C8H10NO]2SnCl6 was optimized by density functional theory (DFT) using B3LYP method and shows that the calculated values obtained by B3LYP/LanL2DZ basis are in a better agreement with the experimental data reported by Song et al. (2011) [1] than those obtained by B3LYP/LanL2MB basis. The vibrational frequencies are calculated using density functional theory (DFT) with the B3LYP/LanL2DZ basis, and scaled by various factors. Root mean square (RMS) value was calculated and the small difference between experimental and calculated modes has been interpreted by intermolecular interactions in the crystal.
Theoretical insight into hydrogen adsorption onto graphene: a first-principles B3LYP-D3 study.
Darvish Ganji, M; Hosseini-Khah, S M; Amini-Tabar, Z
2015-01-28
This work investigates hydrogen adsorption onto various graphene flakes such as coronene and coronene-like as suitable models of graphene within the framework of the DFT-B3LYP method. The non-local van der Waals (vdW) density functional (B3LYP-D3) method is used for both structural geometry optimization and total energy estimations. Calculations were carried out for a hydrogen molecule above a coronene surface with both conventional and vdW corrected DFT to investigate how these approaches perform in the case of hydrogen adsorption on a graphene surface. Our first-principles results within the B3LYP-D3/def2-TZVPP model show that hydrogen physisorbs on a coronene surface with an adsorption energy of -5.013 (kJ mol(-1)) which is in good agreement with the experimental value. The influence of the basis set and graphene flake size were also evaluated and the results indicate that these slightly affect the adsorption properties. We found also that it is crucial to use non-local dispersion interactions to get accurate results for hydrogen adsorption on a graphene surface. Furthermore, the co-adsorption of H2 molecules onto the graphene surface was investigated. The results obtained at the B3LYP-D3/def2-TZVP level show that H2 molecules can be physisorbed on both sides of the graphene layer with adsorption properties similar to those for a single surface. Finally, we showed that H2 molecules might be bound to the graphene surface via a bilayer adsorption scheme with weak adsorption energy. Charge population and electron density analysis confirm the weak binding nature of the system under consideration.
B3LYP, BLYP and PBE DFT band structures of the nucleotide base stacks
Szekeres, Zs; Bogár, F.; Ladik, J.
DFT crystal orbital (band structure) calculations have been performed for the nucleotide base stacks of cytosine, thymine, adenine, and guanine arranged in DNA B geometry. The band structures obtained with PBE, BLYP, and B3LYP functionals are presented and compared to other related experimental and theoretical results. The influence of the quality of the basis set on the fundamental gap values was also investigated using Clementi's double ζ, 6-31G and 6-31G* basis sets.
DiLabio, Gino A; Torres, Edmanuel
2013-01-01
We recently showed that dispersion-correcting potentials (DCPs), atom-centered Gaussian-type functions developed for use with B3LYP (J. Phys. Chem. Lett. 2012, 3, 1738-1744) greatly improved the ability of the underlying functional to predict non-covalent interactions. However, the application of B3LYP-DCP for the {\\beta}-scission of the cumyloxyl radical led a calculated barrier height that was over-estimated by ca. 8 kcal/mol. We show in the present work that the source of this error arises from the previously developed carbon atom DCPs, which erroneously alters the electron density in the C-C covalent-bonding region. In this work, we present a new C-DCP with a form that was expected to influence the electron density farther from the nucleus. Tests of the new C-DCP, with previously published H-, N- and O-DCPs, with B3LYP-DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of non-covalently interacting dimers showed that it is one of the most accurate methods available for treating intermolecular i...
Chemistry by Way of Density Functional Theory
Bauschlicher, Charles W., Jr.; Ricca, Alessandra; Partridge, Harry; Langohff, Stephen R.; Arnold, James O. (Technical Monitor)
1996-01-01
In this work we demonstrate that density functional theory (DFT) methods make an important contribution to understanding chemical systems and are an important additional method for the computational chemist. We report calibration calculations obtained with different functionals for the 55 G2 molecules to justify our selection of the B3LYP functional. We show that accurate geometries and vibrational frequencies obtained at the B3LYP level can be combined with traditional methods to simplify the calculation of accurate heats of formation. We illustrate the application of the B3LYP approach to a variety of chemical problems from the vibrational frequencies of polycyclic aromatic hydrocarbons to transition metal systems. We show that the B3LYP method typically performs better than the MP2 method at a significantly lower computational cost. Thus the B3LYP method allows us to extend our studies to much larger systems while maintaining a high degree of accuracy. We show that for transition metal systems, the B3LYP bond energies are typically of sufficient accuracy that they can be used to explain experimental trends and even differentiate between different experimental values. We show that for boron clusters the B3LYP energetics are not as good as for many of the other systems presented, but even in this case the B3LYP approach is able to help understand the experimental trends.
Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.
Bielecki, Jakub; Lipiec, Ewelina
2016-02-01
Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople's basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.
Study of cyclic quaternary ammonium bromides by B3LYP calculations, NMR and FTIR spectroscopies.
Brycki, Bogumił; Szulc, Adrianna; Kowalczyk, Iwona
2010-08-16
N,N-dioctyl-azepanium, -piperidinium and -pyrrolidinium bromides 1-3, have been obtained and characterized by FTIR and NMR spectroscopy. DFT calculations have also been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p) approach have been presented. Both FTIR and Raman spectra of 1-3 are consistent with the calculated structures in the gas phase. The screening constants for 13C and 1H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between the experimental 1H and 13C chemical shifts and the computed screening constants confirm the optimized geometry.
Study of Cyclic Quaternary Ammonium Bromides by B3LYP Calculations, NMR and FTIR Spectroscopies
Directory of Open Access Journals (Sweden)
Iwona Kowalczyk
2010-08-01
Full Text Available N,N-dioctyl-azepanium, -piperidinium and -pyrrolidinium bromides 1-3, have been obtained and characterized by FTIR and NMR spectroscopy. DFT calculations have also been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p approach have been presented. Both FTIR and Raman spectra of 1-3 are consistent with the calculated structures in the gas phase. The screening constants for 13C and 1H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p approach and analyzed. Linear correlations between the experimental 1H and 13C chemical shifts and the computed screening constants confirm the optimized geometry.
Wang, Ting; Brudvig, Gary; Batista, Victor S
2010-01-29
The capabilities and limitations of the Becke-3-Lee-Yang-Parr (B3LYP) density functional theory (DFT) for modeling proton coupled electron transfer (PCET) in the mixed-valence oxomanganese complex 1 [(bpy)(2)Mn(III)(mu-O)(2)Mn(IV)(bpy)(2)](3+) (bpy = 2,2'-bipyridyl) are analyzed. Complex 1 serves as a prototypical synthetic model for studies of redox processes analogous to those responsible for water oxidation in the oxygen-evolving complex (OEC) of photosystem II (PSII). DFT B3LYP free energy calculations of redox potentials and pKa's are obtained according to the thermodynamic cycle formalism applied in conjunction with a continuum solvation model. We find that the pKa's of the oxo-ligands depend strongly on the oxidation states of the complex, changing by approximately 10 pH units (i.e., from pH~2 to pH~12) upon III,IV-->III,III reduction of complex 1. These computational results are consistent with the experimental pKa's determined by solution magnetic susceptibility and near-IR spectroscopy as well as with the pH dependence of the redox potential reported by cyclic voltammogram measurements, suggesting that the III,IV-->III,III reduction of complex 1 is coupled to protonation of the di-mu-oxo bridge as follows: [(bpy)(2)Mn(III)(mu-O)(2) Mn(IV)(bpy)(2)](3+)+H(+)+e(-)-->[(bpy)(2)Mn(III)(mu-O)(mu-OH)Mn(III)(bpy)(2)](3+). It is thus natural to expect that analogous redox processes might strongly modulate the pKa's of oxo and hydroxo/water ligands in the OEC of PSII, leading to deprotonation of the OEC upon oxidation state transitions.
Bahgat, Khaled; EL-Emary, Talaat
2013-02-01
FT Raman and IR spectra of the crystallized biologically active molecule, 5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (5-APHC, C11H11N3O) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of 5-APHC have been investigated with the help of B3LYP density functional theory (DFT) method with 6-31G(d) and 6-311+G(d,p) as basis set. The calculated molecular geometry has been compared with the experimental data. 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 (SQM) technique. The optimized geometry shows the co-planarity of the aldehyde group with pyrazole ring. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G(d,p) basis set. The red shifting of NH2 stretching wavenumber indicates the formation of N-H⋯O hydrogen bonding. 1H and 13C NMR spectra were recorded and 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-Vis spectrum of the compound was recorded in the region 200-400 nm and the electronic properties HOMO and LUMO energies were calculated by time-dependent TD-DFT approach. Mulliken charges of the 5-APHC molecule was also calculated and interpreted.
Density functional theory study on the molecular structure of loganin
Pandey, Anoop Kumar; Siddiqui, Shamoon Ahmad; Dwivedi, Apoorva; Raj, Kanwal; Misra, Neeraj
2011-01-01
The computational Quantum Chemistry (QC) has been used for different types of problems, for example: structural biology, surface phenomena and liquid phase. In this paper we have employed the density functional method for the study of molecular structure of loganin. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by B3LYP/6-311G (d, p) method and basis set combinations. It was found that the optimized parameters obtained by the DFT/B3LYP met...
THz spectroscopic investigation of chlorotoluron by solid-state density functional theory
Wang, Qiang; Wang, H. L.
2012-05-01
The terahertz time-domain spectrum (THz-TDS) of chlorotoluron has been simulated and assigned with solid-state density functional theory (DFT) in the range of 0.5-2.2 THz. The calculations based on the hybrid density functionals B3LYP and PW91 are performed to analyze the origins of observed spectral features in chlorotoluron THz spectra of solid-state forms using the software package CRYSTAL09. The computed THz spectrum of the B3LYP provides better agreements with observed THz spectral characters. Moreover, all the experimental THz absorption peaks are assigned utilizing the B3LYP method.
Xin, Dongyue; Sader, C Avery; Chaudhary, Om; Jones, Paul-James; Wagner, Klaus; Tautermann, Christofer S; Yang, Zheng; Busacca, Carl A; Saraceno, Reginaldo A; Fandrick, Keith R; Gonnella, Nina C; Horspool, Keith; Hansen, Gordon; Senanayake, Chris H
2017-05-19
An accurate and efficient procedure was developed for performing (13)C NMR chemical shift calculations employing density functional theory with the gauge invariant atomic orbitals (DFT-GIAO). Benchmarking analysis was carried out, incorporating several density functionals and basis sets commonly used for prediction of (13)C NMR chemical shifts, from which the B3LYP/cc-pVDZ level of theory was found to provide accurate results at low computational cost. Statistical analyses from a large data set of (13)C NMR chemical shifts in DMSO are presented with TMS as the calculated reference and with empirical scaling parameters obtained from a linear regression analysis. Systematic errors were observed locally for key functional groups and carbon types, and correction factors were determined. The application of this process and associated correction factors enabled assignment of the correct structures of therapeutically relevant compounds in cases where experimental data yielded inconclusive or ambiguous results. Overall, the use of B3LYP/cc-pVDZ with linear scaling and correction terms affords a powerful and efficient tool for structure elucidation.
Ganji, M. Darvish; Tajbakhsh, M.; Kariminasab, M.; Alinezhad, H.
2016-07-01
The efficiency of polymer solar cells can be essentially enhanced by improving the performance of electron acceptor materials especially by increasing its lowest unoccupied molecular orbital (LUMO) level. To this aim, the electronic properties of an extremely π-extended system, graphene flake and functionalized graphene flake with phenyl-C-butyric methyl ester (PCBM) group, were investigated and compared with those of C60 ones. Several properties of phenyl-C61-butyric methyl ester ([C60]PCBM) derivatives have been calculated and compared against the experimental and other theoretical results. All geometrical and electronic structures calculations were carried out by using the density functional theory (DFT) method at the B3LYP level of theory. The results show that the phenyl ring of [C60]PCBM was substituted with the methoxy groups to increase the LUMO level of the respective system which is in agreement with other studies. We found that graphene flake functionalized by methoxy-PCBM group offer significant increase in the value of the LUMO energy level in comparison with C60 counterpart. Furthermore, the electrophilicity of this compound is lower than that of the other counterparts, which results in higher open circuit voltage (Voc) value in the photovoltaic device. These findings could provide fundamental insights in improving the Voc value as well as raising the LUMO levels of electron acceptor materials and may also serve as an alternative strategy to increase open circuit voltage in polymer solar cells.
Mazurek, A. P.; Sadlej-Sosnowska, N.
2000-11-01
A comparison of the ab initio quantum chemical methods: Hartree-Fock (HF) and hybrid density functional theory (DFT)/B3LYP for the treatment of tautomeric equilibria both in the gas phase and in the solution is made. The solvent effects were investigated in terms of the self-consistent reaction field (SCRF). Ionization potentials (IP), calculated by DFT/B3LYP, are also compared with those calculated previously within the HF frame.
Orlando, Roberto; Lacivita, Valentina; Bast, Radovan; Ruud, Kenneth
2010-06-01
The computational scheme for the evaluation of the second-order electric susceptibility tensor in periodic systems, recently implemented in the CRYSTAL code within the coupled perturbed Hartree-Fock (HF) scheme, has been extended to local-density, gradient-corrected, and hybrid density functionals (coupled-perturbed Kohn-Sham) and applied to a set of cubic and hexagonal semiconductors. The method is based on the use of local basis sets and analytical calculation of derivatives. The high-frequency dielectric tensor (ɛ∞) and second-harmonic generation susceptibility (d) have been calculated with hybrid functionals (PBE0 and B3LYP) and the HF approximation. Results are compared with the values of ɛ∞ and d obtained from previous plane-wave local density approximation or generalized gradient approximation calculations and from experiment. The agreement is in general good, although comparison with experiment is affected by a certain degree of uncertainty implicit in the experimental techniques.
Orlando, Roberto; Lacivita, Valentina; Bast, Radovan; Ruud, Kenneth
2010-06-28
The computational scheme for the evaluation of the second-order electric susceptibility tensor in periodic systems, recently implemented in the CRYSTAL code within the coupled perturbed Hartree-Fock (HF) scheme, has been extended to local-density, gradient-corrected, and hybrid density functionals (coupled-perturbed Kohn-Sham) and applied to a set of cubic and hexagonal semiconductors. The method is based on the use of local basis sets and analytical calculation of derivatives. The high-frequency dielectric tensor (epsilon(infinity)) and second-harmonic generation susceptibility (d) have been calculated with hybrid functionals (PBE0 and B3LYP) and the HF approximation. Results are compared with the values of epsilon(infinity) and d obtained from previous plane-wave local density approximation or generalized gradient approximation calculations and from experiment. The agreement is in general good, although comparison with experiment is affected by a certain degree of uncertainty implicit in the experimental techniques.
Analytic cubic and quartic force fields using density-functional theory
Energy Technology Data Exchange (ETDEWEB)
Ringholm, Magnus; Gao, Bin; Thorvaldsen, Andreas J.; Ruud, Kenneth [Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); Jonsson, Dan [Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); High Performance Computing Group, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); Bast, Radovan [Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, S-10691 Stockholm, Sweden and PDC Center for High Performance Computing, Royal Institute of Technology, S-10044 Stockholm (Sweden); Ekström, Ulf; Helgaker, Trygve [Center for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo (Norway)
2014-01-21
We present the first analytic implementation of cubic and quartic force constants at the level of Kohn–Sham density-functional theory. The implementation is based on an open-ended formalism for the evaluation of energy derivatives in an atomic-orbital basis. The implementation relies on the availability of open-ended codes for evaluation of one- and two-electron integrals differentiated with respect to nuclear displacements as well as automatic differentiation of the exchange–correlation kernels. We use generalized second-order vibrational perturbation theory to calculate the fundamental frequencies of methane, ethane, benzene, and aniline, comparing B3LYP, BLYP, and Hartree–Fock results. The Hartree–Fock anharmonic corrections agree well with the B3LYP corrections when calculated at the B3LYP geometry and from B3LYP normal coordinates, suggesting that the inclusion of electron correlation is not essential for the reliable calculation of cubic and quartic force constants.
Mohamed, Tarek A.; Hassan, Ali M.; Soliman, Usama A.; Zoghaib, Wajdi M.; Husband, John; Abdelall, Mahmoud M.
2011-01-01
The Raman and infrared spectra of solid 5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbothioamide (AMPC, C 6H 7N 5S 2) were measured in the spectral range of 3700-100 cm -1 and 4000-200 cm -1 with a resolution of 4 and 0.5 cm -1, respectively. Aided by normal coordinate analysis and potential energy distributions, a confident vibrational assignment of all fundamentals is proposed herein. As a result of internal rotation around C sbnd N and/or C sbnd S bonds, 32 rotational isomers are suggested for AMPC (C s symmetry). RHF and DFT/B3LYP quantum mechanical calculations including polarization and diffusion functions up to 6-311++G(d,p) basis sets, predict that after complete relaxation of the 32 possible isomers, four structures lie within 1500 cm -1 of the lowest energy conformer. However, vibrational analysis reveals the lowest energy conformer to be the only structure giving all real frequencies. Thus, the only stable conformer of AMPC is shown to have a fully planar skeleton with the NH 2 groups trans to one another. The recorded IR and Raman spectral measurements favor the calculated structural parameters which are further supported by spectral simulation. Additional support is given by 1H and 13C NMR spectra recorded with the sample dissolved in DMSO-d 6 and by predicted chemical shifts at the B3LYP/6-311+G(2d,p) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). Finally, CH 3, CH 3S, and NH 2 torsional barriers to internal rotation have been investigated using the optimized structural parameters from the B3LYP method with the 6-31G(d) basis set. The results are discussed herein and compared with similar molecules whenever appropriate.
Energy Technology Data Exchange (ETDEWEB)
Blanco, Raquel; Orts, Jose Manuel [Departamento de Quimica Fisica e Instituto Universitario de Electroquimica, Universidad de Alicante, Apartado 99, E-03080 Alicante (Spain)
2008-11-01
A density functional theory (DFT) study of the adsorption of a water molecule on Pt(1 1 1), Pt(1 0 0) and Pt(1 1 0) surfaces has been carried out using cluster models, at the B3LYP/LANL2DZ,6-311++G(d,p) level. The water molecule binds preferentially at the top site on Pt(1 1 1) and Pt(1 0 0) with adsorption energy around -27 kJ mol{sup -1}, and is oriented with the molecular plane nearly parallel to the metal surface and the H atoms pointing away from it. On Pt(1 1 0) a hollow site is preferred, with adsorption energy of -32 kJ mol{sup -1}. Potential energy barriers for the rotation around an axis normal to the surface have been estimated to be below 1 kJ mol{sup -1} for Pt(1 1 1) and Pt(1 0 0) when water is adsorbed on top. Upon application of an external electric field (inducing positive charge density on the metal) adsorbed water is additionally stabilized on the three surfaces, especially at the top adsorption site, and adsorption on Pt(1 1 1) and Pt(1 0 0) becomes more favoured than on Pt(1 1 0). Good agreement has been found between harmonic vibrational frequencies calculated at the B3LYP/LANL2DZ,6-311++G(d,p) level and experimental frequencies for adsorbed water monomers on Pt(h k l) surfaces. (author)
Bushnell, Eric A C; Gauld, James W
2013-01-15
The performance of a range density functional theory functionals combined in a quantum mechanical (QM)/molecular mechanical (MM) approach was investigated in their ability to reliably provide geometries, electronic distributions, and relative energies of a multicentered open-shell mechanistic intermediate in the mechanism 8R-Lipoxygenase. With the use of large QM/MM active site chemical models, the smallest average differences in geometries between the catalytically relevant quartet and sextet complexes were obtained with the B3LYP(*) functional. Moreover, in the case of the relative energies between (4) II and (6) II, the use of the B3LYP(*) functional provided a difference of 0.0 kcal mol(-1). However, B3LYP(±) and B3LYP also predicted differences in energies of less than 1 kcal mol(-1). In the case of describing the electronic distribution (i.e., spin density), the B3LYP(*), B3LYP, or M06-L functionals appeared to be the most suitable. Overall, the results obtained suggest that for systems with multiple centers having unpaired electrons, the B3LYP(*) appears most well rounded to provide reliable geometries, electronic structures, and relative energies. Copyright © 2012 Wiley Periodicals, Inc.
Density functional theory studies of etoricoxib
Sachdeva, Ritika; Kaur, Prabhjot; Singh, V. P.; Saini, G. S. S.
2016-05-01
Etoricoxib is a COX-2 selective inhibitor drug with molecular formula C18H15ClN2O2S. It is primarily used for the treatment of arthritis(rheumatoid, psoriatic, osteoarthritis), ankylosing spondylitis, gout and chronic low back pain. Theoretical studies of the molecule including geometry optimization and vibrational frequency calculations were carried out with the help of density functional theory calculations using 6-311++ g (d, p) basis set and B3LYP functional.
Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A
2008-12-07
This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.
Sternheimer shieldings and EFG polarizabilities: a density-functional theory study
Rizzo, Antonio; Ruud, Kenneth; Helgaker, Trygve; Sałek, Paweł; Ågren, Hans; Vahtras, Olav
2003-04-01
The electric field gradient (EFG) at the nucleus, the generalized Sternheimer shielding constants, and the EFG hyperpolarizabilities of a set of reference molecules are computed using analytic density-functional (up to quadratic) response theory. At the three-parameter Becke-Lee-Yang-Parr (B3LYP) level, density functional theory (DFT) underestimates correlation effects compared with other approaches such as coupled-cluster and multiconfigurational self-consistent field. For the prediction of EFG properties of hydrogen nuclei and electron-rich atoms such as halides, DFT/B3LYP provides results even less reliable than Hartree-Fock theory.
Zeffiro, Alberto; Lazzaroni, Simone; Merli, Daniele; Profumo, Antonella; Buttafava, Armando; Serpone, Nick; Dondi, Daniele
2016-06-01
Despite its importance in the prebiotic and biochemical fields, a complete theoretical study of the formation of hexamethylenetetramine (HMT) starting from its precursors ammonia and formaldehyde has not received due considerations in the literature with regard to the thermodynamic feasibility of many of the mechanistically proposed intermediates in its formation. Most of the studies in this area have been mostly concerned with the initial steps of the reaction between formaldehyde and ammonia, while poor attention is dedicated to successive steps. In this article, different results from published literature were critically considered and the most probable hypothesis regarding the mechanism of HMT formation is discussed on the basis of B3LYP calculations of free energies.
Zeffiro, Alberto; Lazzaroni, Simone; Merli, Daniele; Profumo, Antonella; Buttafava, Armando; Serpone, Nick; Dondi, Daniele
2016-06-01
Despite its importance in the prebiotic and biochemical fields, a complete theoretical study of the formation of hexamethylenetetramine (HMT) starting from its precursors ammonia and formaldehyde has not received due considerations in the literature with regard to the thermodynamic feasibility of many of the mechanistically proposed intermediates in its formation. Most of the studies in this area have been mostly concerned with the initial steps of the reaction between formaldehyde and ammonia, while poor attention is dedicated to successive steps. In this article, different results from published literature were critically considered and the most probable hypothesis regarding the mechanism of HMT formation is discussed on the basis of B3LYP calculations of free energies.
Using Density Functional Theory (DFT) for the Calculation of Atomization Energies
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.
Sert, Yusuf; Miroslaw, Barbara; Çırak, Çağrı; Doğan, Hatice; Szulczyk, Daniel; Struga, Marta
2014-07-15
In this study, the experimental and theoretical vibrational spectral analysis of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone have been carried out. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) have been recorded for the solid state samples. The theoretical vibrational frequencies and the optimized geometric parameters (bond lengths and angles) have been calculated for gas phase using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set. The diversity in molecular geometry of fluorophenyl substituted thiosemicarbazones has been discussed based on the X-ray crystal structure reports and theoretical calculation results from the literature. The assignments of the vibrational frequencies have been done on the basis of potential energy distribution (PED) analysis by using VEDA4 software. A good correlation was found between the computed and experimental geometric and vibrational data. In addition, the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbital energy levels and other related molecular energy values of the compound have been determined using the same level of theoretical calculations.
Density functional theory/B3LYP has been employed to optimize the conformations of selected 4-arylflavan-3-ols and their phenolic methyl ether 3-O-acetates. The electronic circular dichroism spectra of the major conformers have been calculated using time-dependent density functional theory to valida...
The disaccharide, alpha/beta-maltose, has been studied using constant energy ab initio molecular dynamics at the B3LYP/6-31+G* COSMO (solvent) level of theory. Maltose is of particular interest as the variation in glycosidic dihedral angles is dependent upon the starting hydroxyl conformation. Tha...
Several mono- and disaccharides have been studied by performing constant energy molecular dynamics at the B3LYP/6-31+G* + COSMO (solvation) level of theory, alpha-maltose is of particular interest as the variation in glycosidic dihedral angles is dependent upon the starting hydroxyl conformation. T...
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...
Calculations of Optical Rotation from Density Functional Theory
Institute of Scientific and Technical Information of China (English)
António Canal Neto; Francisco Elias Jorge
2007-01-01
Density function theory calculations of frequency-dependent optical rotations [α]ω for three rigid chiral molecules are reported. Calculations have been carried out at the sodium D line frequency, using the ADZP basis set and a wide variety of functionals. Gauge-invariant atomic orbitals are used to guarantee origin-independent values of [α]D. In addition, study of geometry dependence of [α]D. Is reported. Using the geometries optimized at the B3LYP/ADZP level, the mean absolute deviation of B3LYP/ADZP and experimental [α]D values yields 60.1°/(dm g/cm3). According to our knowledge, this value has not been achieved until now with any other model.
DEFF Research Database (Denmark)
Frimand, Kenneth; Bohr, Henrik; Jalkanen, Karl J.;
2000-01-01
at the density functional theory level using the B3LYP functional with the 6-31G* basis set. The Hessians and atomic polar tensors and atomic axial tensors were all calculated at the B3LYP/6-31G* level of theory. An important result is the method of treating solvent effects by both adding explicit water....... The calculated VA and VCD spectra of this conformer are in better agreement with experimentally measured VA and VCD spectra previously reported. (C) 2000 Elsevier Science B.V. All rights reserved....
Institute of Scientific and Technical Information of China (English)
YUAN Qing-Hui; ZHOU Li-Xin
2007-01-01
In the present work, the hydrolysis process of non-classical transplatin(Ⅱ) with two same planar heterocycle amines has been studied using hybrid density functional theory (B3LYP) and IEF-PCM solvation models. Optimizations were performed at the B3LYP level using a combined basis set of (LanL2DZ+6-31+G(d,p)) with single-point energy evaluations using the B3LYP/6-31++G(3df,2pd) approach in vacuo and in aqueous solution. For the obtained structures of reactants, intermediates, transition states, and products, both thermodynamic (reaction energies and Gibbs energies) and kinetic (reaction barriers) characteristics were estimated. In comparison with cisplatin, decreased activation energies were obtained. The result implies that the non-classical transplatin with two same planar heterocycle amines increases the equatorial steric effect and lowers reaction barriers, which may assist in designing novel Pt-based anticancer drugs.
Jensen, Lasse; Govind, Niranjan
2009-09-10
In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.
Luzon, Javier; Castro, Miguel; Vertelman, Esther J.M.; Gengler, Régis Y.N.; van Koningsbruggen, Petra J.; Molodtsova, Olga; Knupfer, Martin; Rudolf, Petra; Loosdrecht, Paul H.M. van; Broer, Ria
2008-01-01
A periodic density functional theory method using the B3LYP hybrid exchange-correlation potential is applied to the Prussian blue analogue RbMn[Fe(CN)(6)] to evaluate the suitability of the method for studying, and predicting, the photomagnetic behavior of Prussian blue analogues and related materia
Ben Gzaiel, M.; Oueslati, A.; Chaabane, I.; Gargouri, M.
2016-10-01
The molecular structure and vibrational spectra of bis-tetrapropyl-ammonium hexachloro-dizincate in the ground state have been investigated by density functional method (DFT) using the B3LYP method with the LanL2DZ and LanL2MB basis set. Infrared and Raman spectroscopes of the [N(C3H7)4]2Zn2Cl6 compound have been measured at room temperature in the frequencies range (3500-400 cm-1) and (3500-100 cm-1), respectively. The optimized geometric shows that the calculated values obtained by B3LYP/LanL2DZ basis are in much better agreement with the experimental data than those obtained by B3LYP/LanL2MB. Actually the theoretical vibrational spectra (B3LYP/LanL2DZ) of the title compound have been interpreted by means of potential energy distribution (PED) which is in good agreement with the experimental data. The comparison of the infrared spectrum of the tetrapropyl-ammonium chloride ligand with those of the bis-tetrapropyl-ammonium hexachloro-dizincate compound confirms an increase of the wavenumber in the [N(C3H7)4]2Zn2Cl6 compound. This can be explained by an increase of the electrostatic interactions of the [N(C3H7)4]Cl ligand.
Performance of density functional theory methods to describe intramolecular hydrogen shifts
Indian Academy of Sciences (India)
Nelly González-Rivas; Andrés Cedillo
2005-09-01
The performance of three exchange and correlation density functionals, LDA, BLYP and B3LYP, with four basis sets is tested in three intramolecular hydrogen shift reactions. The best reaction and activation energies come from the hybrid functional B3LYP with triple- basis sets, when they are compared with high-level post-Hartree-Fock results from the literature. For a fixed molecular geometry, the electrophilic Fukui function is computed from a finite difference approximation. Fukui function shows a small dependence with both the exchange and correlation functional and the basis set. Evolution of the Fukui function along the reaction path describes important changes in the basic sites of the corresponding molecules. These results are in agreement with the chemical behavior of those species.
Institute of Scientific and Technical Information of China (English)
HE Xiang; WANG Fan
2006-01-01
@@ Thioaldehydes and thioketones are candidates of new photoluminescence materials. The time-dependent density functional theory is applied to calculate the absorption and emission wavelengths of ten thiocarbonyl compounds using both B3LYP and PBE0 functionals. The theoretical results are in agreement with the measurable ones.Furthermore, it is found that the maximum absorption and emission wavelengths are linearly correlated to the C-S bond lengths.
The accuracy of geometries for iron porphyrin complexes from density functional theory
DEFF Research Database (Denmark)
Rydberg, Patrik Åke Anders; Olsen, Lars
2009-01-01
Iron porphyrin complexes are cofactors in many important proteins such as cytochromes P450, hemoglobin, heme peroxidases, etc. Many computational studies on these systems have been done over the past decade. In this study, the performance of some of the most commonly used density functional theory...... functionals is evaluated with regard to how they reproduce experimental structures. Seven different functionals (BP86, PBE, PBE0, TPSS, TPSSH, B3LYP, and B97-D) are used to study eight different iron porphyrin complexes. The results show that the TPSSH, PBE0, and TPSS functionals give the best results...... (absolute bond distance deviations of 0.015-0.016 A), but the geometries are well-reproduced by all functionals except B3LYP. We also test four different basis sets of double-zeta quality, and we find that a combination of double-zeta basis set of Schafer et al. on the iron atom and the 6-31G* basis set...
Density functional theory investigations of radical scavenging activity of 3′-Methyl-quercetin
Directory of Open Access Journals (Sweden)
Abdullah G. Al-Sehemi
2016-09-01
Full Text Available The possible eight rotamers of 3′-Methyl-quercetin have been optimized by using density functional theory (DFT at B3LYP/6-31G∗ level of theory. The molecular structure and molecular properties of the most stable rotamers have been investigated at the same level of theory. We have computed the descriptors; electronegativity (χ, hardness (η, electrophilicity (ω, softness (S and electrophilicity index (ωi by DFT approach. We have shed light on the structure–property relationship. The absorption spectrum has been computed by time dependent density functional theory (TD-DFT at TD-B3LYP/6-31G∗ level of theory. Radical scavenging activity has been explained on the basis of bond dissociation enthalpy (BDE and the adiabatic ionization potential (IP. Two mechanisms have been explained for the radical scavenging processes, i.e., hydrogen atom transfer and one-electron transfer.
Spin-orbit Coupling and Intersystem Crossing in 4H-Pyran-4-thione: CASSCF//TD-B3LYP Study
Institute of Scientific and Technical Information of China (English)
L(U), Ling-Ling; LIU, Xin-Wen; YUAN, Kun; WANG, Yong-Cheng; WANG, Han-Qing
2007-01-01
The intersystem crossing channels of gaseous 4H-pyran-4-thione were investigated using the CASSCF//TD-B3LYP methods and group theory. Using the effective one-electron spin-orbit Hamiltonian, the strengths of spin-orbit coupling were estimated, which plays an essential role in the spin transitions between different spin states. Calculated results show that phosphorescence and non-radiative decay via intersystem crossing to the S0 state are concurrent processes occurring at the T1 state. A rapid depletion of the S1 state via intersystem crossing to the T1 state can be mediated by the T2 state, if spin relaxation is fast within the triplet levels. Our calculated results are in close agreement with experimental observations.
Hole trapping at Al impurities in silica: A challenge for density functional theories
DEFF Research Database (Denmark)
Lægsgaard, Jesper; Stokbro, Kurt
2001-01-01
The atomic geometry and electronic structure around a neutral substitutional Al impurity in silica is investigated using either the unrestricted Hartree-Fock (UHF) approximation, or Beckes three-parameter hybrid functional (B3LYP). It is found that the B3LYP functional fails to describe the struc...
Guido, Ciro A; Knecht, Stefan; Kongsted, Jacob; Mennucci, Benedetta
2013-05-14
We analyze potentials and limits of the Time-Dependent Density Functional Theory (TD-DFT) approach for the determination of excited-state geometries of organic molecules in gas-phase and in solution. Three very popular DFT exchange-correlation functionals, two hybrids (B3LYP and PBE0) and one long-range corrected (CAM-B3LYP), are here investigated, and the results are compared to the correlated RI-CC2 wave function approach. Solvent effects are further analyzed by means of a polarizable continuum model. A total of 15 organic chromophores (including both small molecules and larger push-pull systems) are considered as prototypes of n → π* and π → π* singlet excitations. Our analysis allows to point out specific correlations between the accuracy of the various functionals and the type of excitation and/or the type of chemical bonds involved. We find that while the best ground-state geometries are obtained with PBE0 and B3LYP, CAM-B3LYP yields the most accurate description of electronic and geometrical characteristics of excited states, both in gas-phase and in solution.
Lutnaes, Ola B; Ruden, Torgeir A; Helgaker, Trygve
2004-10-01
Density functional theory, in particular, with the Becke-3-parameter-Lee-Yang-Parr (B3LYP) hybrid functional, has been shown to be a promising method for the calculation of indirect nuclear spin-spin coupling constants. However, no systematic investigation has so far been undertaken to evaluate the capability of B3LYP to calculate these coupling constants accurately, taking properly into account the vibrational contributions. In this work, vibrationally corrected indirect spin-spin coupling constants were calculated using the B3LYP functional for 10 rigid unsubstituted and substituted hydrocarbons: ethyne, ethene, allene, cyclopropene, cyclopropane, cyclobutene, pyrrole, furan, thiophene and benzene. The resulting spin-spin constants were compared with the available experimental values. The basis sets in these calculations give indirect nuclear spin-spin coupling constants of ethyne that are almost converged to the basis-set limit, making the intrinsic error of the computational method and the error in equilibrium geometry the main sources of error. On average, the B3LYP functional overestimates the indirect nuclear spin-spin coupling constants in hydrocarbons by 10%.
Dispersion corrections to density functionals for water aromatic interactions.
Zimmerli, Urs; Parrinello, Michele; Koumoutsakos, Petros
2004-02-08
We investigate recently published methods for extending density functional theory to the description of long-range dispersive interactions. In all schemes an empirical correction consisting of a C6r(-6) term is introduced that is damped at short range. The coefficient C6 is calculated either from average molecular or atomic polarizabilities. We calculate geometry-dependent interaction energy profiles for the water benzene cluster and compare the results with second-order Møller-Plesset calculations. Our results indicate that the use of the B3LYP functional in combination with an appropriate mixing rule and damping function is recommended for the interaction of water with aromatics.
Density functional theory study on the ionic liquid pyridinium hydrogen sulfate
Tankov, Ivaylo; Yankova, Rumyana; Genieva, Svetlana; Mitkova, Magdalena; Stratiev, Dicho
2017-07-01
The geometry, electronic structure and chemical reactivity of a pyridinium-based ionic liquid, pyridinium hydrogen sulfate ([H-Pyr]+[HSO4]-), have been discussed on the basis of quantum chemical density functional theory calculations using B3LYP/6-311+G(d,p) and B3LYP/6-311++G(2d,2p) approaches. The calculations indicated that [H-Pyr]+[HSO4]- exists in the form of an ion pair. A large electropositive potential was found on the pyridinium ring, while the regions of a negative electrostatic potential is linked with the lone pair of electronegative oxygen atoms in hydrogen sulfate anion ([HSO4]-). Electron transfer both within the anion, and between the anion and cation of an ion pair were described using natural bond orbital theory. The energy values of -7.1375 and -2.8801 eV were related to HOMO and LUMO orbitals, respectively.
Directory of Open Access Journals (Sweden)
Giorgio Molteni
2017-01-01
Full Text Available Conventional frontier molecular orbital theory is not able to satisfactorily explain the regioselectivity outcome of the nitrilimine–alkene cycloaddition. We considered that conceptual density functional theory (DFT could be an effective theoretical framework to rationalize the regioselectivity of the title reaction. Several nitrilimine–alkene cycloadditions were analyzed, for which we could find regioselectivity data in the literature. We computed DFT reactivity indices at the B3LYP/6-311G(2d,p//B3LYP/6-31G(d,p and employed the grand potential stabilization criterion to calculate the preferred regioisomer. Experimental and calculated regioselectivity agree in the vast majority of cases. It was concluded that predominance of a single regioisomer can be obtained by maximizing (i the chemical potential difference between nitrilimine and alkene and (ii the local softness difference between the reactive atomic sites within each reactant. Such maximization can be achieved by carefully selecting the substituents on both reactants.
DEFF Research Database (Denmark)
Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.;
2008-01-01
Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole...... moments are computed using the same geometries (MP2/6-31G*) and basis set (TZVP) as in our previous ab initio benchmark study on electronically excited states. The results from TD-DFT (with the functionals BP86, B3LYP, and BHLYP) and from DFT/MRCI are compared against the previous high-level ab initio...
Diaconu, C V; Doll, J D; Freeman, D L; Diaconu, Cristian V.; Cho, Art E.; Freeman, David L.
2004-01-01
In the present work we investigate the adequacy of broken-symmetry (BS) unrestricted (U) density functional theory (DFT) for constructing the potential energy curve of nickel dimer and nickel hydride, as model for larger bare and hydrogenated nickel cluster calculations. We use three hybrid functionals: B3LYP, Becke98, and FSLYP (50% Hartree-Fock and 50% Slater exchange and LYP correlation functional) with two basis sets: all-electron (AE) Wachters+f basis set and Stuttgart RSC effective core potential (ECP) and basis set. We find that, overall, B3LYP functional with Wachters+f AE basis set performs best, with only 1.3% root-mean-square (RMS) deviation from experiment, followed by Becke98/AE and B3LYP/ECP, with RMS deviation from experimental value of 2.5% and 2.7%, respectively. We also find that for Ni dimer, the spin-projection for the broken-symmetry unrestricted singlet states changes the ordering of the states, but the splittings are less than 10 meV. All our calculations predict a (delta)(delta)-hole g...
Zehe, Michael J.; Jaffe, Richard L.
2010-01-01
High-level ab initio calculations have been performed on the exo and endo isomers of gas-phase tetrahydrodicyclopentadiene (THDCPD), a principal component of the jet fuel JP10, using the Gaussian Gx and Gx(MPx) composite methods, as well as the CBS-QB3 method, and using a variety of isodesmic and homodesmotic reaction schemes. The impetus for this work is to help resolve large discrepancies existing between literature measurements of the formation enthalpy Delta (sub f)H deg (298) for exo-THDCPD. We find that use of the isodesmic bond separation reaction C10H16 + 14CH4 yields 12C2H6 yields results for the exo isomer (JP10) in between the two experimentally accepted values, for the composite methods G3(MP2), G3(MP2)//B3LYP, and CBS-QB3. Application of this same isodesmic bond separation scheme to gas-phase adamantane yields a value for Delta (sub f)H deg (298) within 5 kJ/mol of experiment. Isodesmic bond separation calculations for the endo isomer give a heat of formation in excellent agreement with the experimental measurement. Combining our calculated values for the gas-phase heat of formation with recent measurements of the heat of vaporization yields recommended values for Delta (sub f)H deg (298)liq of -126.4 and -114.7 kJ/mol for the exo and endo isomers, respectively.
Quiroga, Diego; Becerra, Lili Dahiana; Sadat-Bernal, John; Vargas, Nathalia; Coy-Barrera, Ericsson
2016-10-11
An efficient methodology to obtain novel antifungal analogs of brassinin 1 is described. Starting from l-tryptophan 2, N,N'-dialkylthiourea 4, 4-[(1H-indol-3-yl)methylene]-2-sulfanylidene-1,3-thiazolidin-5-one 5 and alkyl (2S)-3-(1H-indol-3-yl)-2-{[(alkylsulfanyl)carbonothioyl]amino}propanoate 6 type compounds were obtained as main products in different ratios depending on the reaction conditions via a tandem dithiocarbamate formation and Michael addition reaction. In order to understand the dependence of the reaction conditions on the mechanism pathway, a DFT/B3LYP study was performed. The results suggested the existence of competitive mechanistic routes which involve the presence of an ionic dithiocarbamate intermediate 9. Antifungal activities of all products were then evaluated against Fusarium oxysporum through mycelial growth inhibition using a microscale amended-medium assay. IC50 values were thus determined for each compound. These results showed that 6-related compounds can be considered as promissory antifungal agents.
Navarro-Ruiz, Javier; Ugliengo, Piero; Rimola, Albert; Sodupe, Mariona
2014-08-07
B3LYP periodic simulations have been carried out to study some physicochemical properties of the bulk structures and the corresponding nonpolar (010) surfaces of Mg-pure and Fe-containing olivine systems; i.e., Mg2SiO4 (Fo) and Mg1.5Fe0.5SiO4 (Fo75). A detailed structural analysis of the (010) Fo and Fo75 surface models shows the presence of coordinatively unsaturated metal cations (Mg(2+) and Fe(2+), respectively) with shorter metal-O distances compared to the bulk ones. Energetic analysis devoted to the Fe(2+) electronic spin configuration and to the ion position in the surfaces reveals that Fe(2+) in its quintet state and placed at the outermost positions of the slab constitutes the most stable Fe-containing surface, which is related to the higher stability of high spin states when Fe(2+) is coordinatively unsaturated. Comparison of the simulated IR and the corresponding reflectance spectra indicates that Fe(2+) substitution induces an overall bathochromic shift of the spectra due to the larger mass of Fe compared to Mg cation. In contrast, the IR spectra of the surfaces are shifted to upper values and exhibit more bands compared to the corresponding bulk systems due to the shorter metal-O distances given in the coordinatively unsaturated metals and to symmetry reduction which brings nonequivalent motions between the outermost and the internal modes, respectively.
Preparation of TiO2/SnO2 thin films by sol-gel method and periodic B3LYP simulations.
Floriano, Emerson A; Scalvi, Luis V A; Saeki, Margarida J; Sambrano, Julio R
2014-08-07
Titanium dioxide (TiO2) thin films are grown by the sol-gel dip-coating technique, in conjunction with SnO2 in the form of a heterostructure. It was found that the crystalline structure of the most internal layer (TiO2) depends on the thermal annealing temperature and the substrate type. Films deposited on glass substrate submitted to thermal annealing until 550 °C present anatase structure, whereas films deposited on quartz substrate transform to rutile structure at much higher temperatures, close to 1000 °C, unlike powder samples where the phase transition takes place at about 780 °C. When structured as rutile, the oxide semiconductors TiO2/SnO2 have very close lattice parameters, making the heterostructure assembling easier. The SnO2 and TiO2 have their electronic properties evaluated by first-principles calculations by means of DFT/B3LYP. Taking into account the calculated band structure diagram of these materials, the TiO2/SnO2 heterostructure is qualitatively investigated and proposed to increase the detection efficiency as gas sensors. This efficiency can be further improved by doping the SnO2 layer with Sb atoms. This assembly may be also useful in photoelectrocatalysis processes.
Directory of Open Access Journals (Sweden)
Diego Quiroga
2016-10-01
Full Text Available An efficient methodology to obtain novel antifungal analogs of brassinin 1 is described. Starting from l-tryptophan 2, N,N′-dialkylthiourea 4, 4-[(1H-indol-3-ylmethylene]-2-sulfanylidene-1,3-thiazolidin-5-one 5 and alkyl (2S-3-(1H-indol-3-yl-2-{[(alkylsulfanylcarbonothioyl]amino}propanoate 6 type compounds were obtained as main products in different ratios depending on the reaction conditions via a tandem dithiocarbamate formation and Michael addition reaction. In order to understand the dependence of the reaction conditions on the mechanism pathway, a DFT/B3LYP study was performed. The results suggested the existence of competitive mechanistic routes which involve the presence of an ionic dithiocarbamate intermediate 9. Antifungal activities of all products were then evaluated against Fusarium oxysporum through mycelial growth inhibition using a microscale amended-medium assay. IC50 values were thus determined for each compound. These results showed that 6-related compounds can be considered as promissory antifungal agents.
Tulub, Alexander A
2006-05-14
A molecular dynamics DFT:B3LYP (6-31G(**) basis set) study is used to elucidate the mechanism of guanosinetriphosphate (GTP) conversion into guanosinemonophosphate (GMP) upon the action of Mg(2+) (magnesium cofactor). The computations are carried out at 310 K in a volume of 178 water molecules, which surround the Mg(2+)-GTP complex and imitate the effect of solution. Over 5 ps, Mg(2+)-GTP appears to be fully decomposed, yielding five final products: two hydrated molecules of inorganic phosphate Pi, a hydrated Mg(2+), atomic oxygen (which in the course of a couple of subsequent reactions gains two hydrogens and converts into a water molecule) and a highly active *GMP radical. The radical production is linked to presence of Mg(2+), which initiates a radical mechanism of GTP cleavage. At the initial stage, Mg(2+) undergoes reduction to Mg(+), accompanied by the formation of an ion-radical pair with GTP, (+)Mg*-*GTP(3-). Without Mg(2+), an inert form of GMP (the ionic mechanism of GTP hydrolytic cleavage) rather than GMP is produced. *GMP production, which is similar to that of *AMP (adenosinemonophosphate), *CMP (cytidinemonophosphate), TMP (thymidinemonophosphate) and *UMP (uridinemonophosphate), plays a crucial role in DNA and RNA single chain synthesis.
Haghdani, Shokouh; Åstrand, Per-Olof; Koch, Henrik
2016-02-01
We have calculated the electronic optical rotation of seven molecules using coupled cluster singles-doubles (CCSD) and the second-order approximation (CC2) employing the aug-cc-pVXZ (X = D, T, or Q) basis sets. We have also compared to time-dependent density functional theory (TDDFT) by utilizing two functionals B3LYP and CAM-B3LYP and the same basis sets. Using relative and absolute error schemes, our calculations demonstrate that the CAM-B3LYP functional predicts optical rotation with the minimum deviations compared to CCSD at λ = 355 and 589.3 nm. Furthermore, our results illustrate that the aug-cc-pVDZ basis set provides the optical rotation in good agreement with the larger basis sets for molecules not possessing small-angle optical rotation at λ = 589.3 nm. We have also performed several two-point inverse power extrapolations for the basis set convergence, i.e., OR(∞) + AX(-n), using the CC2 model at λ = 355 and 589.3 nm. Our results reveal that a two-point inverse power extrapolation with the aug-cc-pVTZ and aug-cc-pVQZ basis sets at n = 5 provides optical rotation deviations similar to those of aug-cc-pV5Z with respect to the basis limit.
Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.
2016-10-01
The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.
Comparative Studies of 1,4-Bis[ 2-(4-Pyridyl) ethenyl ]-benzene Using Density Functional Theory
Institute of Scientific and Technical Information of China (English)
CHENG Jian-bo; L(U) Jia-ping; GONG Bao-an; LI Wen-zuo
2007-01-01
The optimized molecular structure and harmonic vibrational frequencies of a 1,4-bis [ 2-( 4-pyridyl ) ethenyl ] -benzene(BPENB) molecule were calculated via five popular density functional theory(DFT) methods. On the basis of the comparison between calculated and experimental results, it is concluded that the B3PW91 and B3LYP methods are superior to the others in optimizing structures, and the BPW91 method reproduces the observed fundamental frequencies most satisfactorily.
Density functional theory predictions of isotropic hyperfine coupling constants.
Hermosilla, L; Calle, P; García de la Vega, J M; Sieiro, C
2005-02-17
The reliability of density functional theory (DFT) in the determination of the isotropic hyperfine coupling constants (hfccs) of the ground electronic states of organic and inorganic radicals is examined. Predictions using several DFT methods and 6-31G, TZVP, EPR-III and cc-pVQZ basis sets are made and compared to experimental values. The set of 75 radicals here studied was selected using a wide range of criteria. The systems studied are neutral, cationic, anionic; doublet, triplet, quartet; localized, and conjugated radicals, containing 1H, 9Be, 11B, 13C, 14N, 17O, 19F, 23Na, 25Mg, 27Al, 29Si, 31P, 33S, and 35Cl nuclei. The considered radicals provide 241 theoretical hfcc values, which are compared with 174 available experimental ones. The geometries of the studied systems are obtained by theoretical optimization using the same functional and basis set with which the hfccs were calculated. Regression analysis is used as a basic and appropriate methodology for this kind of comparative study. From this analysis, we conclude that DFT predictions of the hfccs are reliable for B3LYP/TZVP and B3LYP/EPR-III combinations. Both functional/basis set scheme are the more useful theoretical tools for predicting hfccs if compared to other much more expensive methods.
Institute of Scientific and Technical Information of China (English)
Zheng Guo Huang; Li Zhou; En Cui Yang
2008-01-01
Density functional theoretical calculations have been made on the electronic structure of (CH)n(BCO)6-n(n=0-6) at B3LYP/6-311 + G(d) level.The nuclear-independent chemical shifts (NICS) values calculated using the gauge-including atomic orbitals (GIAO) method were used to assess on the aromaticities of these molecules.The results shows that (CH)n(BCO)6-n(n=0-6)species are aromatic.
Balachandran, V.; Parimala, K.
This study is a comparative analysis of FT-IR and FT-Raman spectra of vanillin (3-methoxy-4-hydroxybenzaldehyde) and isovanillin (3-hydroxy-4-methoxybenzaldehyde). The molecular structure, vibrational wavenumbers, infrared intensities, Raman scattering activities were calculated for both molecules using the B3LYP density functional theory (DFT) with the standard 6-311++G∗∗ basis set. The computed values of frequencies are scaled using multiple scaling factors to yield good coherence with the observed values. The calculated harmonic vibrational frequencies are compared with experimental FT-IR and FT-Raman spectra. The geometrical parameters and total energies of vanillin and isovanillin were obtained for all the eight conformers (a-h) from DFT/B3LYP method with 6-311++G∗∗ basis set. The computational results identified the most stable conformer of vanillin and isovanillin as in the "a" form. Non-linear properties such as electric dipole moment (μ), polarizability (α), and hyperpolarizability (β) values of the investigated molecules have been computed using B3LYP quantum chemical calculation. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules.
Energy Technology Data Exchange (ETDEWEB)
Carrasquilla, Rafael J; Neira, Oscar L, E-mail: rjcarrasquilla@yahoo.com [Grupo de Espectroscopia Optica y Laser, Universidad Popular del Cesar, Valledupar (Colombia)
2011-01-01
Time dependent density functional (TD-DFT) calculations were performed on 1,3-benzoxazole and substituted benzoxazoles using the B3LYP functional and the 6-31+G(d) basis sets. The geometry of the S{sub 0} and S{sub 1} singlet ground and excited states were optimized in gas phase, toluene and methanol using B3LYP/6-31+G(d) y CIS/6-31+G(d) methods, respectively, and the vertical {pi} {yields} {pi}{sup *} absorption largest wavelength transitions were determined. Several global molecular descriptors were considered such as the hardness, chemical potential, electronegativity and the dipole moment for each molecule and was determined the influence that has, about the values of these descriptors, the alteration of the main molecular chain of an initial structure (1,3 not substituted Benzoxazole). Generally, the predicted spectra are in agreement with the experimental data.
Paranthaman, Selvarengan; Hong, Kiryong; Kim, Joonghan; Kim, Dong Eon; Kim, Tae Kyu
2013-09-26
We report the results of a benchmarking study on hybrid, hybrid-meta, long-range-corrected, meta-generalized gradient approximation (meta-GGA), and GGA density functional theory (DFT) methods for aluminum (Al) clusters. A range of DFT functionals, such as B3LYP, B1B95, PBE0, mPW1PW91, M06, M06-2X, ωB97X, ωB97XD, TPSSh, BLYP, PBE, mPWPW91, M06-L, and TPSS, have been used to optimize the molecular structures and calculate the vibrational frequencies and four energetic parameters for neutral and anionic Al(n) (n = 2-10) clusters. The performances of these functionals are assessed systematically by calculating the vertical ionization energy for neutral Al clusters and the vertical electron detachment energy for anionic Al clusters, along with the cohesive energy and dissociation energy. The results are compared with the available experimental and high-level ab initio calculated results. The calculated results showed that the PBE0 and mPW1PW91 functionals generally provide better results than the other functionals studied. TPSS can be a good choice for the calculations of very large Al clusters. On the other hand, the B3LYP, BLYP, and M06-L functionals are in poor agreement with the available experimental and theoretical results. The calculated results suggest that the hybrid DFT functionals like B3LYP do not always provide better performance than GGA functionals.
Wang, Ying; Qian, Hu-Jun; Morokuma, Keiji; Irle, Stephan
2012-07-05
Ab initio coupled cluster and density functional theory studies of atomic hydrogen addition to the central region of pyrene and coronene as molecular models for graphene hydrogenation were performed. Fully relaxed potential energy curves (PECs) were computed at the spin-unrestricted B3LYP/cc-pVDZ level of theory for the atomic hydrogen attack of a center carbon atom (site A), the midpoint of a neighboring carbon bond (site B), and the center of a central hexagon (site C). Using the B3LYP/cc-pVDZ PEC geometries, we evaluated energies at the PBE density functional, as well as ab initio restricted open-shell ROMP2, ROCCSD, and ROCCSD(T) levels of theory, employing cc-pVDZ and cc-pVTZ basis sets, and performed a G2MS extrapolation to the ROCCSD(T)/cc-pVTZ level of theory. In agreement with earlier studies, we find that only site A attack leads to chemisorption. The G2MS entrance channel barrier heights, binding energies, and PEC profiles are found to agree well with a recent ab initio multireference wave function theory study (Bonfanti et al. J. Chem. Phys.2011, 135, 164701), indicating that single-reference open-shell methods including B3LYP are sufficient for the theoretical treatment of the interaction of graphene with a single hydrogen atom.
甲基苯丙胺光谱性质的密度泛函分析与指认%Density Functional Analysis and Spectral Identification of Methamphetamine
Institute of Scientific and Technical Information of China (English)
陈凯浩; 钟爱国
2014-01-01
采用密度泛函理论的DFT/B3LYP/6-311+G(d,p)方法和基组,对甲基苯丙胺的UV-Vis光谱，IR光谱,1HNMR光谱和荧光光谱进行了理论模拟和指认。自然电荷计算表明，胺基N和H原子很可能是其发挥药理活性的亲电和亲核反应中心。%Using density functional theory DFT/B3LYP/6-311+G (d, p) method and basis set, UV-Vis spectroscopy, IR spectroscopy, 1HNMR spectrum and fluorescence spectroscopy of methamphetamine were studied by the theoretical simulation and identification. Natural charge calculation shows that N and H atoms of amine may be electrophilic and nucleophilic reaction center to play the pharmacological activity.
Institute of Scientific and Technical Information of China (English)
LIU Hongfei; JIA Tiekun; MIN Xinmin
2014-01-01
Density functional theory calculations were carried out to explore the potential energy surface (PES) associated with the gas-phase reaction of NiL2(L=SO3CH3) with acetone. The geometries and energies of the reactants, intermediates, products and transition states of the triplet ground potential energy surfaces of [Ni, O, C2, H4] were obtained at the B3LYP/6-311++G(d,p) levels in C,H,O atoms and B3LYP/Lanl2dz in Ni atom. It was found through our calculations that the decabonylation of acetaldehyde contains four steps including encounter complexation, C-C activation, aldehyde H-shift and nonreactive dissociation. The results revealed that C-C activation induced by NiL2(L=SO3CH3) led to the decarbonylation of acetaldehyde.
Directory of Open Access Journals (Sweden)
Toh Pek–Lan
2015-01-01
Full Text Available We have employed first principle Density Functional Theory (DFT investigations to study the physical and electronic properties of 4–Azidomethyl–6–isopropyl–2H–chromen–2–one, C13H13N3O2. Complete geometry optimization calculations were carried out to find local energy minimum of the molecular system using the B3LYP approach with a variety of basis sets. The optimized geometries were then used to determine the HOMO–LUMO gaps, Mulliken atomic charges, and others. Our calculation results show that the computed geometrical properties of C13H13N3O2 cluster model are in good agreement with the corresponding measured experimental value. The calculated energies obtained are close to each other using the B3LYP density functional method combined with a variety of basis sets. Furthermore, using B3LYP/6–31G** method, the oxygen–attached carbon, C2 atom has the highest positively charge, with the corresponding value of +0.59. For both oxygen atoms (O1 and O2, the calculated charge values obtained are about –0.52 and –0.46, respectively.
Kumar, N V Suresh; Priyakumar, U Deva; Singh, Harjinder; Roy, Saumya; Chakraborty, Tushar Kanti
2012-07-01
Density functional B3LYP method was used to investigate the preference of intra- and inter-molecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction, and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory-based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.
An improved theoretical approach to the empirical corrections of density functional theory
Lii, Jenn-Huei; Hu, Ching-Han
2012-02-01
An empirical correction to density functional theory (DFT) has been developed in this study. The approach, called correlation corrected atomization-dispersion (CCAZD), involves short- and long-range terms. Short-range correction consists of bond ( 1,2-) and angle ( 1,3-) interactions, which remedies the deficiency of DFT in describing the proto-branching stabilization effects. Long-range correction includes a Buckingham potential function aiming to account for the dispersion interactions. The empirical corrections of DFT were parameterized to reproduce reported Δ H f values of the training set containing alkane, alcohol and ether molecules. The Δ H f of the training set molecules predicted by the CCAZD method combined with two different DFT methods, B3LYP and MPWB1K, with a 6-31G* basis set agreed well with the experimental data. For 106 alkane, alcohol and ether compounds, the average absolute deviations (AADs) in Δ H f were 0.45 and 0.51 kcal/mol for B3LYP- and MPWB1K-CCAZD, respectively. Calculations of isomerization energies, rotational barriers and conformational energies further validated the CCAZD approach. The isomerization energies improved significantly with the CCAZD treatment. The AADs for 22 energies of isomerization reactions were decreased from 3.55 and 2.44 to 0.55 and 0.82 kcal/mol for B3LYP and MPWB1K, respectively. This study also provided predictions of MM4, G3, CBS-QB3 and B2PLYP-D for comparison. The final test of the CCAZD approach on the calculation of the cellobiose analog potential surface also showed promising results. This study demonstrated that DFT calculations with CCAZD empirical corrections achieved very good agreement with reported values for various chemical reactions with a small basis set as 6-31G*.
Ramalingam, S; Periandy, S
2011-03-01
In the present study, the FT-IR and FT-Raman spectra of 4-chloro-2-methylaniline (4CH2MA) have been recorded in the range of 4000-100 cm(-1). The fundamental modes of vibrational frequencies of 4CH2MA are assigned. All the geometrical parameters have been calculated by HF and DFT (LSDA, B3LYP and B3PW91) methods with 6-31G (d, p) and 6-311G (d, p) basis sets. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values for aniline and some substituted aniline. The harmonic and anharmonic vibrational wavenumbers, IR intensities and Raman activities are calculated at the same theory levels used in geometry optimization. The calculated frequencies are scaled and compared with experimental values. The scaled vibrational frequencies at LSDA/B3LYP/6-311G (d, p) seem to coincide with the experimentally observed values with acceptable deviations. The impact of substitutions on the benzene structure is investigated. The molecular interactions between the substitutions (Cl, CH(3) and NH(2)) are also analyzed.
Svozil, Daniel; Jungwirth, Pavel
2006-07-27
In the present study, the performance of six popular density functionals (B3LYP, PBE0, BLYP, BP86, PBE, and SVWN) for the description of the autoionization process in the water octamer was studied. As a benchmark, MP2 energies with complete basis sets limit extrapolation and CCSD(T) correction were used. At this level, the autoionized structure lies 28.5 kcal.mol(-1) above the neutral water octamer. Accounting for zero-point energy lowers this value by 3.0 kcal.mol(-1). The transition state of the proton transfer reaction, lying only 0.7 kcal.mol(-1) above the energy of the ionized system, was identified at the MP2/aug-cc-pVDZ level of theory. Different density functionals describe the reactant and product with varying accuracy, while they all fail to characterize the transition state. We find improved results with hybrid functionals compared to the gradient-corrected ones. In particular, B3LYP describes the reaction energetics within 2.5 kcal.mol(-1) of the benchmark value. Therefore, this functional is suggested to be preferably used both for Carr-Parinello molecular dynamics and for quantum mechanics/molecular mechanics (QM/MM) simulations of autoionization of water.
Electrostatic potential of several small molecules from density functional theory
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
A number of density functional theory (DFT) methods were used to calculate the electrostatic potential for the series of molecules N2, F2, NH3, H2O, CHF3, CHCl3, C6H6, TiF4, CO(NH2)2 and C4H5N3O compared with QCISD (quadratic configuration interaction method including single and double substitutions) results. Comparisons were made between the DFT computed results and the QCISD ab initio ones and MP2 ab initio ones, compared with the root-mean-square deviation and electrostatic potential difference contours figures. It was found that the hybrid DFT method B3LYP, yields electrostatic potential in good agreement with the QCISD results. It is suggest this is a useful approach, especially for large molecules that are difficult to study by ab initio methods.
Density Functionals with Broad Applicability in Chemistry
Energy Technology Data Exchange (ETDEWEB)
Zhao, Yan; Truhlar, Donald G.
2008-02-01
The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Although density functional theory is widely used in the computational chemistry community, the most popular density functional, B3LYP, has some serious shortcomings: (i) it is better for main-group chemistry than for transition metals; (ii) it systematically underestimates reaction barrier heights; (iii) it is inaccurate for interactions dominated by mediumrange correlation energy, such as van der Waals attraction, aromatic-aromatic stacking, and alkane isomerization energies. We have developed a variety of databases for testing and designing new density functionals. We used these data to design new density functionals, called M06-class (and, earlier, M05-class) functionals, for which we enforced some fundamental exact constraints such as the uniform-electron-gas limit and the absence of self-correlation energy. Our M06-class functionals depend on spin-up and spin-down electron densities (i.e., spin densities), spin density gradients, spin kinetic energy densities, and, for nonlocal (also called hybrid) functionals, Hartree-Fock exchange. We have developed four new functionals that overcome the above-mentioned difficulties: (a) M06, a hybrid meta functional, is a functional with good accuracy “across-theboard” for transition metals, main group thermochemistry, medium-range correlation energy, and barrier heights; (b) M06- 2X, another hybrid meta functional, is not good for transition metals but has excellent performance for main group chemistry, predicts accurate valence and Rydberg electronic excitation energies, and is an excellent functional for aromatic-aromatic stacking interactions; (c) M06-L is not as accurate as M06 for barrier heights but is the most accurate
Density Functional Study on the Mechanism of Collision Reaction among Protons,N2 and Water Vapor
Institute of Scientific and Technical Information of China (English)
SUN,Hao(孙昊); PAN,Xiu-Mei(潘秀梅); ZHAO,Min(赵岷); LIU,Peng-Jun(刘朋军); SU,Zhong-Min(苏忠民); WANG,Rong-Shun(王荣顺)
2004-01-01
The mechanism of collision reaction among protons, N2 and water vapor was theoretically studied using Density Functional Theory. The geometries of reactants, transition states, intermediates and products were optimized at the B3LYP/6-311 + G** level by the BERNY gradient analysis method. Transition states and intermediates have been identified by vibrational frequency analysis. The relationship among reactants, intermediates, transition states and products was affirmed by IRC calculation. The variations of energy and geometry along the IRC-determined reaction paths were described. The possible reaction pathways were represented and the optimal one was decided from the viewpoint of energy.
Dutton, Andrew S; Fukuto, Jon M; Houk, K N
2004-02-09
The mechanism of decomposition of dialkylamino diazeniumdiolate salts, R(2)N[NONO](-)M(+), to form nitric oxide, NO, was explored using theoretical methods. B3LYP/6-311+G(d) density functional theory calculations gave the optimized geometries, and energetics were further evaluated with the high accuracy CBS-QB3 method, when feasible. Relative pK(a) values were estimated using the PCM model for aqueous solvation. The terminal oxygen is the most basic site, followed closely by the internal oxygen. Protonation of these sites does not lead to decomposition. However, protonation of the weakly basic amino nitrogen leads to very rapid decomposition and NO generation.
Directory of Open Access Journals (Sweden)
Ramzan Ullah
2013-01-01
Full Text Available We present terahertz time domain spectra of acrylamide in the frequency range from 0.2 to 2 THz with nearly constant refractive index having an average value of 1.33 and an absorption coefficient. Raman (95–3000 cm−1 and FTIR (450–4000 cm−1 spectra also show good agreement with density functional theory (DFT B3LYP 6-311G++ (3df 3pd calculations except C-H and N-H stretching frequencies even after scaling with scale factor of 0.9679. We use MOLVIB to rescale such frequencies to match experimental values.
Directory of Open Access Journals (Sweden)
Özgür Alver
2013-01-01
Full Text Available FT-IR and Raman spectra of methacrylamidoantipyrine (MAAP have been reported in the region of 4000–10 cm−1 and 4000–100 cm−1, respectively. The optimized geometric parameters, conformational analysis, normal mode frequencies, and corresponding vibrational assignments of MAAP (C15H17N3O2 have been examined by means of density functional theory (DFT method using the Becke-3-Lee-Yang-Parr (B3LYP exchange-correlation functional and the 6-31G++(d,p basis sets. Vibrational assignments have been made on the basis of potential energy distribution (PED and the thermodynamics functions, and the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO of MAAP have been predicted. Calculations are carried out with the possible seven (amide-1–5 and imide-1-2 conformational isomers of MAAP. Comparison between the experimental and theoretical results indicates that the B3LYP method provides satisfactory evidence for the prediction of vibrational wavenumbers, and the amide-1 conformational isomer is supposed to be the most stable form of MAAP.
Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R
2015-02-25
A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.
Institute of Scientific and Technical Information of China (English)
Shao Ju-Xiang; Cheng Xin-Lu; Ynag Xiang-Dong; He Bi
2006-01-01
By using the density functional theory (B3LYP) and four highly accurate complete basis set (CBS-Q, CBS-QB3, CBS-Lq, and CBS-4M) ab initio methods, the X(C, N, O)-NO2 bond dissociation energies (BDEs) for ChsNO2, C2H3NO2) C2H5NO2, HONO2, CH3ONO2, C2H5ONO2, NH2NO2 (CH3)2NNO2 are computed. By comparing the computed BDEs and experimental results, it is found that the B3LYP method is unable to predict satisfactorily the results of bond dissociation energy (BDE); however, all four CBS models are generally able to give reliable predication of the X(C, N, O)-NO2 BDEs for these nitro compounds. Moreover, the CBS-4M calculation is the least computationally demanding among the four CBS methods considered. Therefore, we recommend CBS-4M method as a reliable method of computing the BDEs for this nitro compound system.
Rahman, Adhip; Ali, Mohammad Tuhin; Shawan, Mohammad Mahfuz Ali Khan; Sarwar, Mohammed Golam; Khan, Mohammad A K; Halim, Mohammad A
2016-01-01
A series of halogen-directed donepezil drugs has been designed to inhibit acetyl cholinesterase (AChE). Density Functional theory (DFT) has been employed to optimize the chair as well as boat conformers of the parent drug and modified ligands at B3LYP/MidiX and B3LYP/6-311G + (d,p) level of theories. Charge distribution, dipole moment, enthalpy, free energy and molecular orbitals of these ligands are also investigated to understand how the halogen-directed modifications impact the ligand structure and govern the non-bonding interactions with the receptors. Molecular docking calculation has been performed to understand the similarities and differences between the binding modes of unmodified and halogenated chair-formed ligands. Molecular docking indicated donepezil and modified ligands had non-covalent interactions with hydrophobic gorges and anionic subsites of AChE. The -CF3-directed ligand possessed the most negative binding affinity. Non-covalent interactions within the ligand-receptor systems were found to be mostly hydrophobic and π- stacking type. F, Cl and -CF3 containing ligands emerge as effective and selective AChE inhibitors, which can strongly interact with the two active sites of AChE. In addition, we have also investigated selected pharmacokinetic parameters of the parent and modified ligands.
Indian Academy of Sciences (India)
Andrea Alparone
2014-05-01
Structural, energetic, spectroscopic, linear and nonlinear optical (NLO) properties of the environmental mutagens 1- and 3-nitro-6-azabenzo[]pyrene -oxides were characterized by means of Hartree-Fock as well as B3LYP and CAM-B3LYP density functional theory computations. The NLO investigations were performed for the second harmonic generation (SHG) and electro-optical Pockels effect (EOPE) at the incident wavelength of 1064 nm. The results show that, the predicted structures, vibrational spectra, nucleus independent chemical shifts, ionization energy, electron affinity as well as electronic polarizabilities are little influenced by the position of the nitro substituent. Differently, the dipole moment () and the first-order hyperpolarizabilities () are significantly dependent on the isomerization. The rather different mutagenic activity of the investigated isomers could be related to their diverse polarity. At the CAM-B3LYP level, when passing from the 1- to the 3-nitro-6-azabenzo[a]pyrene -oxide isomer, the datum increases by about 5 D (a factor of three), whereas the static and dynamic values decrease by ca. 50%. Dipole moment measurement and SHG and EOPE NLO techniques are potentially useful to distinguish these important environmental mutagens.
Saravanan, S. P.; Sankar, A.; Parimala, K.
2017-01-01
The complete structural and vibrational analysis of the 2,5-Difluoronitrobenzene (DNB) was carried out by Hartree-Fock (HF) and density functional theory (DFT) method (B3LYP) with 6-311++G (d,p) basis set. The fundamental vibrations are assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. Using the time-dependent density functional theory (TD-DFT) method, electronic absorption spectra of the title compound have been predicted and a good agreement with the experimental ones is determined. 13C and 1H NMR spectra were recorded and chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The hyperconjugative interaction energy (E(2)) and electron densities of donor (i) and acceptor (j) bonds were calculated using natural bond orbital (NBO) analysis. In addition, molecular electrostatic potential (MEP) and atomic charges were calculated using B3LYP/6-311++G (d,p) level of theory. Moreover, thermodynamic properties (heat capacities, entropy, enthalpy and Gibb's free energy) of the title compound at different temperatures were calculated.
Shukla, Manoj K.; Leszczynski, Jerzy
2010-11-01
A comprehensive analysis of the performance of the TD-DFT method using different density functionals including recently developed medium and long-range correlation corrected density functionals have been carried out for lower-lying electronic singlet valence transitions of nucleic acid bases and the Watson-Crick base pairs in the gas phase and in the water solution. The standard 6-311++G(d,p) basis set was used. Ground state geometries of bases and base pairs were optimized at the M05-2X/6-311++G(d,p) level. The nature of potential energy surfaces (PES) was ascertained through the harmonic vibrational frequency analysis; all geometries were found to be minima at the respective PES. Electronic singlet vertical transition energies were also computed at the CC2/def2-TZVP level in the gas phase. The effect of state-specific water solvation on TD-DFT computed transition energies was considered using the PCM model. For the isolated bases the performance of the B3LYP functional was generally found to be superior among all functionals, but it measurably fails for charge-transfer states in the base pairs. The CC2/def2-TZVP computed transition energies were also revealed to be inferior compared with B3LYP results for the isolated bases. The performance of the ωB97XD, CAM-B3LYP and BMK functionals were found to be similar and comparable with the CC2 results for the isolated bases. However, for the Watson-Crick adenine-thymine and guanine-cytosine base pairs the performance of the ωB97XD functional was found to be the best among all the studied functionals in the present work in predicting the locally excited transitions as well as charge transfer states.
Labat, Frédéric; Baranek, Philippe; Domain, Christophe; Minot, Christian; Adamo, Carlo
2007-04-21
The two polymorphs of TiO2, rutile and anatase, have been investigated at the ab initio level using different Hamiltonians with all-electron Gaussian and projector augmented plane wave basis sets. Their equilibrium lattice parameters, relative stabilities, binding energies, and band structures have been evaluated. The calculations have been performed at the Hartree-Fock, density functional theory (DFT), and hybrid (B3LYP and PBE0) levels. As regards DFT, the local density and generalized gradient (PBE) approximations have been used. Our results show an excellent agreement with the experimental band structures and binding energies for the B3LYP and PBE0 functionals, while the best structural descriptions are obtained at the PBE0 level. However, no matter which Hamiltonian and method are used, anatase is found more stable than rutile, in contrast with recent experimental reports, although the relative stabilities of the two phases are very close to each other. Nevertheless, based on the overall results, the hybrid PBE0 functional appears as a good compromise to obtain an accurate description of both structural and electronic properties of solids.
Ahmad, Faheem; Parveen, Mehtab; Alam, Mahboob; Azaz, Shaista; Malla, Ali Mohammed; Alam, Mohammad Jane; Lee, Dong-Ung; Ahmad, Shabbir
2016-07-01
The present study reports the synthesis of 7-Hydroximinocholest-5-en-3-ol acetate (syn. 3β-acetoxycholest-5-en-7-one oxime; in general, steroidal oxime). The identity of steroidal molecule was confirmed by NMR, FT-IR, MS, CHN microanalysis and X-ray crystallography. DFT calculations on the titled molecule have been performed. The molecular structure and spectra interpreted by Gaussian hybrid computational analysis theory (B3LYP) are found to be in good correlation with the experimental data obtained from the various spectrophotometric techniques. The vibrational bands appearing in the FTIR are assigned with great accuracy using harmonic frequencies along with intensities and animated modes. Molecular properties like HOMO-LUMO analysis, chemical reactivity descriptors, MEP mapping, dipole moment and natural atomic charges have been presented at the same level of theory. Moreover, the Hirshfeld analysis was carried out to ascertain the secondary interactions and associated 2D fingerprint plots. The percentages of various interactions are pictorialized by fingerprint plots of Hirshfeld surface. Steroidal oxime exhibited promising inhibitory activity against acetylcholinesterase (AChE) as compared to the reference drug, tacrine. Molecular docking was performed to introduce steroidal molecules into the X-ray crystal structures of acetylcholinesterase at the active site to find out the probable binding mode. The results of molecular docking admitted that steroidal oxime may exhibit enzyme inhibitor activity.
Téllez Soto, Claudio Alberto; Pereira, Liliane; dos Santos, Laurita; Rajasekaran, Ramu; Fávero, Priscila; Martin, Airton Abrahão
2016-12-01
In the confocal Raman spectra of skin dermis, the band area in the spectral region of proline and hydroxyproline varies according to the age and health condition of the volunteers, classified as healthy young women, healthy elderly women, and diabetic elderly women. Another observation refers to the intensity variation and negative Raman shift of the amide I band. To understand these effects, we adopted a model system using the DFT/B3LYP:3-21G procedure, considering the amino acid chain formed by glycine, hydroxyproline, proline, and alanine, which interacts with two and six water molecules. Through these systems, polarizability variations were analyzed to correlate its values with the observed Raman intensities of the three groups of volunteers and to assign the vibrational spectra of the skin dermis. As a way to correlate other experimental trends, we propose a model of chemical reaction of water interchange between the bonding amino acids, in which water molecules are attached with glucose by hydrogen bonds. The theoretical results are in accordance with the observed experimental trends.
Energy Technology Data Exchange (ETDEWEB)
Marana, Naiara L. [Modeling and Molecular Simulations Group, São Paulo State University, UNESP, 17033-360 Bauru, SP (Brazil); Albuquerque, Anderson R. [Federal Institute of Education, Science and Technology of Sertão Pernambucano, 56400-000 Floresta, PE (Brazil); La Porta, Felipe A. [Chemistry Department, Federal Technological University of Paraná, 86036-370 Londrina, PR (Brazil); Longo, Elson [São Paulo State University, Chemistry Institute, UNESP, 14801-907 Araraquara, SP (Brazil); Sambrano, Julio R. [Modeling and Molecular Simulations Group, São Paulo State University, UNESP, 17033-360 Bauru, SP (Brazil)
2016-05-15
Periodic density functional theory calculations with the B3LYP hybrid functional and all-electron Gaussian basis set were performed to simulate the structural and electronic properties as well as the strain and formation energies of single-walled ZnO nanotubes (SWZnONTs) and Carbon nanotubes (SWCNTs) with different chiralities as functions of their diameters. For all SWZnONTs, the band gap, strain energy, and formation energy converge to ~4.5 eV, 0.0 eV/atom, and 0.40 eV/atom, respectively. This result suggests that the nanotubes are formed more easily from the surface than from the bulk. For SWCNTs, the strain energy is always positive, while the formation energy is negative for armchair and zigzag nanotubes, therefore suggesting that these types of nanotubes can be preferentially formed from the bulk. The electronic properties of SWCNTs depend on the chirality; all armchair nanotubes are metallic, while zigzag and chiral nanotubes can be metallic or semiconducting, depending on the n and m vectors. - Graphical abstract: DFT/B3LYP were performed to simulate the structural and electronic properties as well as the strain and formation energies of SWZnONTs and SWCNTs with different chiralities as functions of their diameters. - Highlights: • The energies of SWZnONTs converge for chirality with diameters up 20 Å. • SWCNTs electronic properties depend on the chirality. • The properties of SWZnONTs are very similar to those of monolayer surface.
Directory of Open Access Journals (Sweden)
*B. Semire
2012-12-01
Full Text Available Theoretical calculations using Density Functional Theory (DFT were performed on 2,5-bis[4-N,N-diethylaminostyryl]thiophene and its furan and pyrrole derivatives The energy band gaps calculated at B3LYP/6-31G(d level for thiophene derivatives are lower than that of furan and pyrrole analogues. The absorption λmax calculated using DFT was shifted to longer wavelength by replacement of R = CH3 by C2H5 for all studied molecules. The geometries and electronic properties of the compounds were also studied.
Liu, Xing; Wang, Xuefeng; Wang, Qiang; Andrews, Lester
2012-07-02
Infrared spectra of the matrix isolated OMS, OM(η(2)-SO), and OM(η(2)-SO)(η(2)-SO(2)) (M = Ti, Zr, Hf) molecules were observed following laser-ablated metal atom reactions with SO(2) during condensation in solid argon and neon. The assignments for the major vibrational modes were confirmed by appropriate S(18)O(2) and (34)SO(2) isotopic shifts, and density functional vibrational frequency calculations (B3LYP and BPW91). Bonding in the initial OM(η(2)-SO) reaction products and in the OM(η(2)-SO)(η(2)-SO(2)) adduct molecules with unusual chiral structures is discussed.
Singh, Gurpreet; Dogra, Sukh Dev; Kaur, Sarvpreet; Tripathi, S K; Prakash, Satya; Rai, Bimal; Saini, G S S
2015-01-01
The vibrational properties of glutathione have been investigated by infrared absorption and Raman spectroscopic techniques, and density functional theory calculations at the B3LYP/6-31+G(d,p) level. Assignments of all the experimentally observed vibrational bands have been done with the help of simulated vibrational spectra and potential energy distribution calculations of glutathione water cluster, which includes the effect of hydrogen bonding. Optimized molecular parameters of energy minimized structure have been compared with the available experimental values. Calculated molecular parameters of glutathione-water cluster match well with the experimental values. Some of the calculated molecular parameters and vibrational frequencies of vapor phase glutathione-water cluster suggest participation of some atoms of glutathione in hydrogen bonding. Experimentally observed UV-Visible absorption spectrum of glutathione has also been reported. Observed band at 203 nm has been assigned to electronic transitions calculated with time dependent density functional theory. Copyright © 2015 Elsevier B.V. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Ringholm, Magnus; Ruud, Kenneth [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø – The Arctic University of Norway, 9037 Tromsø (Norway); Bast, Radovan [Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, S-10691 Stockholm (Sweden); PDC Center for High Performance Computing, Royal Institute of Technology, S-10044 Stockholm (Sweden); Oggioni, Luca [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø – The Arctic University of Norway, 9037 Tromsø (Norway); Department of Physics G. Occhialini, University of Milano Bicocca, Piazza della scienza 3, 20126 Milan (Italy); Ekström, Ulf [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo (Norway)
2014-10-07
We present the first analytic calculations of the geometrical gradients of the first hyperpolarizability tensors at the density-functional theory (DFT) level. We use the analytically calculated hyperpolarizability gradients to explore the importance of electron correlation effects, as described by DFT, on hyper-Raman spectra. In particular, we calculate the hyper-Raman spectra of the all-trans and 11-cis isomers of retinal at the Hartree-Fock (HF) and density-functional levels of theory, also allowing us to explore the sensitivity of the hyper-Raman spectra on the geometrical characteristics of these structurally related molecules. We show that the HF results, using B3LYP-calculated vibrational frequencies and force fields, reproduce the experimental data for all-trans-retinal well, and that electron correlation effects are of minor importance for the hyper-Raman intensities.
Ringholm, Magnus; Bast, Radovan; Oggioni, Luca; Ekström, Ulf; Ruud, Kenneth
2014-10-01
We present the first analytic calculations of the geometrical gradients of the first hyperpolarizability tensors at the density-functional theory (DFT) level. We use the analytically calculated hyperpolarizability gradients to explore the importance of electron correlation effects, as described by DFT, on hyper-Raman spectra. In particular, we calculate the hyper-Raman spectra of the all-trans and 11-cis isomers of retinal at the Hartree-Fock (HF) and density-functional levels of theory, also allowing us to explore the sensitivity of the hyper-Raman spectra on the geometrical characteristics of these structurally related molecules. We show that the HF results, using B3LYP-calculated vibrational frequencies and force fields, reproduce the experimental data for all-trans-retinal well, and that electron correlation effects are of minor importance for the hyper-Raman intensities.
Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib
2015-04-15
Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases.
Tounsi, Amal; Hamdi, Besma; Zouari, Ridha; Ben Salah, Abdelhamid
2016-10-01
A new organic-inorganic material [C6H10(NH3)2]CoCl4·H2O was reported. The title compound was synthesized at room temperature by slow evaporation and then characterized by a single X-ray diffraction, spectroscopic measurements, thermal analysis and dielectric technique. It crystallizes in the non-centrosymmetric space group Pna21 with the following unit cell parameters: a=12.5328(1) Å, b=9.0908(1) Å, c=11.7440(1) and α=β=γ=90°. The structure can be described by the alternation of two different cationic-anionic layers. It consists of isolated H2O, isolated [CoCl4]2- tetrahedral anions and diammoniumcyclohexane [C6H10(NH3)2]2+ cations, which are connected via N-H…Cl, N-H…O and O-H…N hydrogen bonds. The Hirshfeld surface analysis was conducted to investigate intermolecular interactions and associated 2D fingerprint plots, revealing the relative contribution of these interactions in the crystal structure quantitatively. Theoretical calculations were performed using DFT/B3LYP/LanL2DZ method for studying the molecular structure and vibrational spectra and especially to examine the non-linear optical behavior of the compound. Solid state 13C NMR spectrum shows three signals correspond to three different carbon environments. Thermal analysis discloses a phase transition at the temperature 315 K and the evaporation of water molecule at 327 K. A detailed dielectric study was reported and shows a good agreement with thermal measurements.
Elsässer, Brigitta; Fels, Gregor; Weare, John H
2014-01-22
The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN + DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10(11) difference in rate strongly supporting the less accepted triester mechanism.
Energy Technology Data Exchange (ETDEWEB)
Elsasser, Brigitta M.; Fels, Gregor; Weare, John H.
2014-01-22
The mechanism of the backbone cleavage transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report QM/MM free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2? oxygen on the neighboring diester phosphate bond and both reach the same product state (PS) (a O3??O2? cyclic phosphate and a O5? hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition state (TS) general acid (His 119)/base (His 12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2? migrates to the non-bridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN+DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 1011 difference in rate strongly supporting the less accepted triester mechanism.
Rajavel, A.; Aditya Prasad, A.; Jeyakumar, T.
2017-02-01
The structural features of conformational isomerism in 4-isopropylbenzylidine thiophene-2-carbohydrazide (ITC) polymorphs have been investigated to conquer distinguishable strong Nsbnd H⋯O and weak Csbnd H⋯S hydrogen bond interactions. The single crystals were grown at constant temperature and have characterized by density functional theory computations using B3LYP method by 3-21G basis set. The conformational isomers of ITC were compared and spectroscopically characterized by FT-IR and Raman spectroscopy. The bulk phases were studied by the powder X-ray diffraction patterns. External morphology of ITC was discussed using scanning electron microscopic and transmission electron microscopic studies. Comparisons between various types of intermolecular interactions in the two polymorphic forms have been quantified via Fingerprint and Hirshfeld surface analysis. DFT computations were used to illustrate molecular electrostatic potential, HOMO-LUMO, mulliken atomic charges and electron density of states.
Edwin, Bismi; Hubert Joe, I
2012-11-01
Vibrational spectral analysis and quantum chemical computations based on density functional theory have been performed on the anti-neuro-degenerative drug Orphenadrine hydrochloride. The geometry, intermolecular hydrogen bond, and harmonic vibrational frequencies of the title molecule have been investigated with the help of B3LYP method. The calculated molecular geometry has been compared with the experimental data. The various intramolecular interactions have been exposed by natural bond orbital analysis. The distribution of Mulliken atomic charges and bending of natural hybrid orbitals also reflect the presence of intramolecular hydrogen bonding. The analysis of the electron density of HOMO and LUMO gives an idea of the delocalization and low value of energy gap indicates electron transport in the molecule and thereby bioactivity. Effective docking of the drug molecule with NMDA receptor subunit 3A also enhances its bioactive nature. Copyright © 2012 Elsevier B.V. All rights reserved.
Ovchinnikov, Vasily A; Sundholm, Dage
2014-04-21
The 0-0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations. Excitation energies have also been calculated at the linear-response time-dependent density functional theory (TDDFT) level using the B3LYP functional. Large basis sets have been employed for ensuring that the obtained excitation energies are close to the basis-set limit. Zero-point vibrational energy corrections have been calculated at the B3LYP and CC2 levels for the ground and excited states rendering direct comparisons with high-precision spectroscopy measurements feasible. The obtained excitation energies for the 0-0 transitions of the first excited states of guanine tautomers are in good agreement with experimental values confirming the experimental assignment of the energetic order of the tautomers of the DNA bases. For the experimentally detected guanine tautomers, the first excited state corresponds to a π→π* transition, whereas for the tautomers of adenine, thymine, and the lowest tautomer of cytosine the transition to the first excited state has n →π* character. The calculations suggest that the 0-0 transitions of adenine, thymine, and cytosine are not observed in the absorption spectrum due to the weak oscillator strength of the formally symmetry-forbidden transitions, while 0-0 transitions of thymine have been detected in fluorescence excitation spectra.
Indian Academy of Sciences (India)
Vijayanand Kalamse; Sanjay Gaikwad; Ajay Chaudhari
2010-06-01
5-metal mononitrides and monoborides viz. X–N and X–B (X = La, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg) are studied using density functional method based B3LYP functional with LANL2DZ and SDD basis set. The lowest spin state, electron affinities, ionization potentials and binding energies for mononitrides and monoborides are obtained. The electronic state and electronic configuration of mononitrides and monoborides are discussed. Orbitals involved in bond formation are identified. The properties of mononitrides and monoborides are compared. It is found that 5-metal atoms form stronger bond with nitrogen atom than the boron atom. The range of binding energy, electron affinity and ionization potential is wider for mononitrides than that for monoborides. The properties of 5-metal mononitrides and 3-metal mononitrides are also compared. The binding energies for the former are lower than those for the latter.
Enhanced NLO response in BODIPY-coumarin hybrids: density functional theory approach
Indian Academy of Sciences (India)
YOGESH ERANDE; NAGAIYAN SEKAR
2017-09-01
We have thoroughly investigated the first, second and third polarizability characteristics of four hybrid chromophores by spectroscopic and computational methods. B3LYP, CAMB3LYP and BHandHLYP functionals in combination with 6-311+G(d,p) basis set were used to evaluate the polarizability and hyperpolarizability characteristics of these chromophores. Generalized Mulliken Hush analysis and frontier molecular orbital electronic distribution images of chromophores obtained from Density functional theory computation has established the charge transfer characteristics of these hybrid chromophores. On the basis of charge transfer characteristic, these red absorbing and NIR emissive chromophores possess high nonlinear optical response. Comparison of isolated units with their analogous hybrid chromophores shows that fusion ofcoumarin with BODIPY enhances the nonlinear optical response.
LuChunHai; Liao Jun Sheng; Sun Ying; WangXiaoLin
2002-01-01
The density functional theory method using B3' exchange and Lee-Yang-Parr's correlation function (B3LYP) with 6-31G** basis set were used to study and optimize equilibrium structure and fundamental vibrational frequencies in the equilibrium for CH4, CH3D, CH2D2, CHD3 and CD4. The relative result error from 1.1% to 6.3% were obtained between the calculation and the observation values of fundamental vibrational frequencies. After scaled, the relative result error is between 0.1% and - 2.9%. This method is used to study period properties of methane that some hydrogen atoms are replaced by tritium atoms. Following deuterium or tritium atom number rising in methane, entropy increases, but zero-point vibrational energy, heat capacity and enthalpy reduces
Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F-
Directory of Open Access Journals (Sweden)
Wei Li
2009-07-01
Full Text Available The structures, electron affinities and bond dissociation energies of BrO4F/BrO4F− species have been investigated with five density functional theory (DFT methods with DZP++ basis sets. The planar F-Br…O2…O2 complexes possess 3A' electronic state for neutral molecule and 4A' state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EAad, the vertical electron affinity (EAvert, and the vertical detachment energy (VDE. The EAad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies De (BrO4F → BrO4-mF + Om (m = 1-4 and De- (BrO4F- → BrO4-mF- + Om and BrO4F- → BrO4-mF + Om- are predicted. The adiabatic electron affinities (EAad were predicted to be 4.52 eV for F-Br…O2…O2 (3A'← 4A' (B3LYP method.
Alpaslan, Gökhan; Macit, Mustafa
2014-03-01
The Schiff base compound (E)-1-((3-methoxyphenylimino)methyl)naphthalen-2-ol was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 3-methoxyaniline. The structural properties of the compound has been characterized by using FT-IR, UV-vis and X-ray single-crystal methods. According to X-ray diffraction result, the title compound exists in the phenol-imine tautomeric form. The molecular geometry, vibrational frequencies of the compound in the ground state have been calculated using the density functional theory (DFT/B3LYP) method with the 6-311++G(d,p) basis set, and compared with the experimental data. The obtained results show that the optimized molecular geometry is well reproduce the crystal structure. The theoretical vibrational frequencies are in good agreement with the experimental values. The calculations of electronic absorption spectra of tautomeric forms of the compound were performed by using TD-DFT calculations both in the gas phase and ethanol solvent. To investigate the tautomeric stability, optimization calculations at the B3LYP/6-311++G(d,p) level were performed for the phenol-imine and keto-amine forms of the compound. According to calculated results, the OH form is more stable than NH form. In addition, molecular electrostatic potential (MEP), frontier molecular orbital analysis (HOMO-LUMO), thermodynamic and, non-linear optical (NLO) properties of the compound were investigated using same theoretical calculations.
Jone Pradeepa, S; Sundaraganesan, N
2014-05-05
In this present investigation, the collective experimental and theoretical study on molecular structure, vibrational analysis and NBO analysis has been reported for 2-aminofluorene. FT-IR spectrum was recorded in the range 4000-400 cm(-1). FT-Raman spectrum was recorded in the range 4000-50 cm(-1). The molecular geometry, vibrational spectra, and natural bond orbital analysis (NBO) were calculated for 2-aminofluorene using Density Functional Theory (DFT) based on B3LYP/6-31G(d,p) model chemistry. (13)C and (1)H NMR chemical shifts of 2-aminofluorene were calculated using GIAO method. The computed vibrational and NMR spectra were compared with the experimental results. The total energy distribution (TED) was derived to deepen the understanding of different modes of vibrations contributed by respective wavenumber. The experimental UV-Vis spectra was recorded in the region of 400-200 nm and correlated with simulated spectra by suitably solvated B3LYP/6-31G(d,p) model. The HOMO-LUMO energies were measured with time dependent DFT approach. The nonlinearity of the title compound was confirmed by hyperpolarizabilty examination. Using theoretical calculation Molecular Electrostatic Potential (MEP) was investigated.
Saravanan, S; Balachandran, V
2015-03-05
The experimental and theoretical study on the structures and vibrations of 4-hexylacetophenone (abbreviated as 4HAP) are presented. The FT-IR and FT-Raman spectra of the title compound have been recorded in the region 4000-400cm(-1) and 3500-100cm(-1) respectively. The molecular structures, vibrational wavenumbers, infrared intensities and Raman activities were calculated using DFT (B3LYP and LSDA) method with 6-311++G(d,p) basis set. The most stable conformer of 4HAP is identified from the computational results. The assignments of the vibrational spectra have been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMEF). The linear polarizability (α) and the first hyperpolarizability (βtot) values of the investigated molecule have been computed using B3LYP and LSDA with 6-311++G(d,p) basis set. Stability of the molecule arising from hyper conjugative interaction and charge transfer delocalization has been analyzed using natural bond orbital (NBO) analysis. The molecule orbital contributions are studied by density of energy states (DOSs). UV-Vis spectrum and effects of solvents have been discussed effects of solvents have been discussed and the electronic properties such as HOMO and LUMO energies were determined by time-dependent TD-DFT approach. Fukui function and Mulliken analysis on atomic charges of the title compound have been calculated. Finally, electrophilic and nucleophilic descriptors of the title molecule have been calculated.
Energy Technology Data Exchange (ETDEWEB)
Silverstein, Daniel W.; Govind, Niranjan; van Dam, Hubertus J. J.; Jensen, Lasse
2013-12-10
A parallel implementation of analytical time-dependent density functional theory gradients is presented for the quantum chemistry program NWChem. The implementation is based on the Lagrangian approach developed by Furche and Ahlrichs. To validate our implementation, we first calculate the Stokes shifts for a range of organic dye molecules using a diverse set of exchange-correlation functionals (traditional density functionals, global hybrids, and range-separated hybrids) followed by simulations of the one-photon absorption and resonance Raman scattering spectrum of the phenoxyl radical, the well-studied dye molecule rhodamine 6G, and a molecular host–guest complex (TTFcCBPQT^{4+}). The study of organic dye molecules illustrates that B3LYP and CAM-B3LYP generally give the best agreement with experimentally determined Stokes shifts unless the excited state is a charge transfer state. Absorption, resonance Raman, and fluorescence simulations for the phenoxyl radical indicate that explicit solvation may be required for accurate characterization. For the host–guest complex and rhodamine 6G, it is demonstrated that absorption spectra can be simulated in good agreement with experimental data for most exchange-correlation functionals. Finally, however, because one-photon absorption spectra generally lack well-resolved vibrational features, resonance Raman simulations are necessary to evaluate the accuracy of the exchange-correlation functional for describing a potential energy surface.
Chan, Bun; Radom, Leo
2016-08-09
In the present study, we have obtained geometries and frequency scale factors for a number of double-hybrid density functional theory (DH-DFT) procedures. We have evaluated their performance for obtaining thermochemical quantities [zero-point vibrational energies (ZPVE) and thermal corrections for 298 K enthalpies (ΔH298) and 298 K entropies (S298)] to be used within high-level composite protocols (using the W2X procedure as a probe). We find that, in comparison with the previously prescribed protocol for optimization and frequency calculations (B3-LYP/cc-pVTZ+d), the use of contemporary DH-DFT methods such as DuT-D3 and DSD-type procedures leads to a slight overall improved performance compared with B3-LYP. A major strength of this approach, however, lies in the better robustness of the DH-DFT methods in that the largest deviations are notably smaller than those for B3-LYP. In general, the specific choices of the DH-DFT procedure and the associated basis set do not drastically change the performance. Nonetheless, we find that the DSD-PBE-P86/aug'-cc-pVTZ+d combination has a very slight edge over the others that we have examined, and we recommend its general use for geometry optimization and vibrational frequency calculations, in particular within high-level composite methods such as the higher-level members of the WnX series of protocols. The scale factors determined for DSD-PBE-P86/aug'-cc-pVTZ+d are 0.9830 (ZPVE), 0.9876 (ΔH298), and 0.9923 (S298).
Molecular orbital ab initio and density functional theoretical study on reaction between PH2 and NO
Institute of Scientific and Technical Information of China (English)
HU; Zhengfa(胡正发); WANG; Zhenya(王振亚); LI; Haiyang(李海洋); ZHOU; Shikang(周士康)
2002-01-01
The theoretical study of reaction between PH2 and NO on the ground state potential energy surface is reported by using molecular orbital ab initio calculation and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energies and zero point energies of all species during reaction are computed by HF, MP2 (full) and B3LYP theory levels with the medium basis set 6-31G*. Theoretical results indicate that intermediate IM1(H2PNO) is firstly formed by overcoming a small energy barrier TS1, and then two four-membered ring transient states TS2 and TS5, with energy barriers 103.3 and 102.6 kJ/mol respectively,then H-migration and isomerization are completed and the products PN and H2O are formed. The reaction is exothermic one with -189.6 k J/mol released.
On the binding mode of urease active site inhibitors: A density functional study
Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M.
The way with which boric acid, a rapid reversible competitive inhibitor, binds the urease active site was explored at density functional B3LYP level of theory. The catalytic core of the enzyme was simulated by two models of different size. In both cases, amino acid residues belonging to the inner and to the outer coordination spheres of nickel ions were replaced by smaller molecular species. Contrary to the experimental indication that attributes the inhibitory ability of this acid to the lack of a nucleophilic attack by the enzyme to the boron atom, we instead found that another possibility exists based on the presence of a strong covalent sigma bond between boron and urease that we think can be hardly broken to allow any course of the reaction.
Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: A density functional study
DEFF Research Database (Denmark)
Hemmingsen, Lars Bo Stegeager; Olsen, L.; Antony, J.
2003-01-01
. For most studied systems, the tetrahedral structure is a stable intermediate. Moreover, the C-N bond in the lactam ring is intact in this intermediate, as well as in the following transition state-its cleavage is induced by proton transfer to the nitrogen atom in the lactam ring. However, for the model...... with Asp as a proton shuttle, attack of the zinc-bond hydroxide ion seems to be concerted with the proton transfer. We have also studied the effect of replacing one of the histidine ligands by an asparagine or glutamine residue, giving a zinc site representative of other subclasses of metallo......Two central steps in the hydrolysis of lactam antibiotics catalyzed by mononuclear metallo-beta-lactamases, formation of the tetrahedral intermediate and its breakdown by proton transfer, are studied for model systems using the density functional B3LYP method. Metallo-beta-lactamases have two metal...
Density Functional Theory Study of the Interaction between Thymine and Luteolin
Institute of Scientific and Technical Information of China (English)
王晓岚; 蔡皖飞; 郑妍; 李来才; 田安民
2012-01-01
The density function B3LYP method has been used to optimize the geometries of the luteolin, thymine and lute- olin-thymine complexes at 6-31＋G＊ basis. The vibrational frequencies have been studied at the same level to ana- lyze these seventeen complexes, respectively. Theories of atoms in molecules （AIM） and natural bond orbital （NBO） have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of the complexes corrected by basis set superposition error are between -93.00-76.69 kJ/mol. The calculating results indicate that strong hydrogen bonding interactions have been found in the luteolin-thymine complexes.
Density Functional Investigations into the Adsorption of Methanol on Isomorphously Substituted ZSM-5
Institute of Scientific and Technical Information of China (English)
Shuping Yuan; Jianguo Wang; Yongwang Li; Haijun Jiao
2003-01-01
The adsorption of methanol in the acid sites of zeolites has attracted a great deal of attention because of its relevance to the industrial methanol to gasoline conversion process. In this work, the B3LYP hybrid density functional method was used to investigate the adsorption behavior of methanol on Bronsted acid sites in B, Al, Ga and Fe isomorphously substituted ZSM-5 zeolites. The optimized structures reveal a physisorbed methanol interacting with the zeolite framework through two hydrogen bonds. The order of the computed adsorption energy correlates with the acid strength of the isomorphously substituted ZSM-5:B-ZSM-5《Fe-ZSM-5＜Ga-ZSM-5＜Al-ZSM-5. The adsorption difference between methanol and ammonia is compared.
Energy Technology Data Exchange (ETDEWEB)
Wang Xiaowei; Wang Qiang, E-mail: qiangwang@cjlu.edu.cn [Department of Quality and Safety Engineering, China Jiliang University, Hangzhou, 310018 (China)
2011-02-01
In the room temperature and nitrogen conditions, we presented well-resolved absorption spectra and indexes of refraction of bactericide molecules in the far infrared radiation (FIR) spectral region recorded by terahertz time-domain spectroscopy (THz-TDS). As illustrative examples we discussed the absorption spectra of captan and folpet in THz region. The absorption coefficient and index of refraction of them were obtained. Meanwhile, density functional theory (DFT) with software package Gaussian 03 using B3LYP theory was employed for optimization and vibration analysis. With the help of Gaussian View 3.09, the distinct absorption peaks of those molecules were assigned with reliable accuracy. They were caused by intermolecular hydrogen-bonding, molecular torsion or vibration modes, absorption of water molecules, etc. As the absorption spectra are highly sensitive to the overall structure and configuration of the molecules, the THz-TDS procedure can provide a direct fingerprint of the molecular structure or conformational state of a compound.
Density functional theory study of neutral AlSn(n = 2-9) clusters
Institute of Scientific and Technical Information of China (English)
Li Ting-Xin; Wang Lin; Wang Fei; Chen Jun; Jiang Zhen-Yi; Li Li-Sha
2011-01-01
This paper investigates the geometrical structures and relative stabilities of neutral AlSn(n = 2-9) using the density functional theory. Structural optimisation and frequency analysis are performed at the B3LYP/6-311G(d) level. The ground state structures of the AlSn show that the sulfur atoms prefer not only to evenly distribute on both sides of the aluminum atom but also to form stable structures in AlSn clusters. The structures of pure Sn are fundamentally changed due to the doping of the Al atom. The fragmentation energies and the second-order energy differences are calculated and discussed. Among neutral AlSn(n = 2-9) clusters, AlS4 and AlS6 are the most stable.
Infrared and density functional theory studies of formic acid hydrate clusters in noble gas matrices
Ito, Fumiyuki
2016-08-01
Infrared absorption spectra of formic acid hydrate clusters (HCOOH)m(H2O)n have been measured in noble gas matrices (Ar and Kr). The concentration dependence of the spectra and the comparison with a previous experimental study on HCOOH(H2O) and HCOOH(H2O)2 [Geoge et al., Spectrochim. Acta, Part A 60 (2004) 3225] led to the identification of large clusters. Density functional theory calculations at the B3LYP-DCP/6-31+G(2d,2p) level were carried out to determine the anharmonic vibrational properties of the clusters, enabling a consistent assignment of the observed vibrational peaks to specific clusters.
Institute of Scientific and Technical Information of China (English)
LI; Ming; ZHENG; Wenxu
2006-01-01
The enantioselective reduction of keto oxime ether with borane catalyzed by oxazaborolidine is discussed by the density functional theory (DFT) method. The main intermediates and transition states for this reaction are optimized completely at the B3LYP/6-31g(d) level, and the transition states are verified by vibrational modes. As shown, the chirality-controlled steps for this reaction are the hydride transfer from borane to carbonyl carbon and oxime carbon of keto oxime ether, and the chirality for the reduced products is determined in these two reaction steps. In all examined reaction paths, the first hydride is transferred via a six-membered ring and the second hydride via a five-membered ring or a four-membered ring.
Daramola, Damilola A; Muthuvel, Madhivanan; Botte, Gerardine G
2010-07-29
Geometry and vibration properties for monoclinic zirconium oxide were studied using Gaussian basis sets and LDA, GGA, and B3LYP functionals. Bond angles, bond lengths, lattice parameters, and Raman frequencies were calculated and compared to experimental values. Bond angles and lengths were found to agree within experimental standard deviations. The B3LYP gave the best performance of all three functionals with a percent error of 1.35% for the lattice parameters while the average difference between experimental and calculated Raman frequency values was -3 cm(-1). The B3LYP functional was then used to assign the atomic vibrations causing each frequency mode using isotopic substitution of (93.40)Zr for (91.22)Zr and (18.00)O for (16.00)O. This resulted in seven modes assigned to the Zr atom, ten modes to the O atom, and one mode being a mixture of both.
Asath, R. Mohamed; Rekha, T. N.; Premkumar, S.; Mathavan, T.; Benial, A. Milton Franklin
2016-12-01
Conformational analysis was carried out for N-(5-aminopyridin-2-yl)acetamide (APA) molecule. The most stable, optimized structure was predicted by the density functional theory calculations using the B3LYP functional with cc-pVQZ basis set. The optimized structural parameters and vibrational frequencies were calculated. The experimental and theoretical vibrational frequencies were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed, which reveals that the higher molecular reactivity and stability of the APA molecule and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the APA molecule. Antidiabetic activity was studied based on the molecular docking analysis and the APA molecule was identified that it can act as a good inhibitor against diabetic nephropathy.
Liakos, Dimitrios G; Neese, Frank
2015-09-08
The recently developed domain-based local pair natural orbital coupled cluster theory with single, double, and perturbative triple excitations (DLPNO-CCSD(T)) delivers results that are closely approaching those of the parent canonical coupled cluster method at a small fraction of the computational cost. A recent extended benchmark study established that, depending on the three main truncation thresholds, it is possible to approach the canonical CCSD(T) results within 1 kJ (default setting, TightPNO), 1 kcal/mol (default setting, NormalPNO), and 2-3 kcal (default setting, LoosePNO). Although thresholds for calculations with TightPNO are 2-4 times slower than those based on NormalPNO thresholds, they are still many orders of magnitude faster than canonical CCSD(T) calculations, even for small and medium sized molecules where there is little locality. The computational effort for the coupled cluster step scales nearly linearly with system size. Since, in many instances, the coupled cluster step in DLPNO-CCSD(T) is cheaper or at least not much more expensive than the preceding Hartree-Fock calculation, it is useful to compare the method against modern density functional theory (DFT), which requires an effort comparable to that of Hartree-Fock theory (at least if Hartree-Fock exchange is part of the functional definition). Double hybrid density functionals (DHDF's) even require a MP2-like step. The purpose of this article is to evaluate the cost vs accuracy ratio of DLPNO-CCSD(T) against modern DFT (including the PBE, B3LYP, M06-2X, B2PLYP, and B2GP-PLYP functionals and, where applicable, their van der Waals corrected counterparts). To eliminate any possible bias in favor of DLPNO-CCSD(T), we have chosen established benchmark sets that were specifically proposed for evaluating DFT functionals. It is demonstrated that DLPNO-CCSD(T) with any of the three default thresholds is more accurate than any of the DFT functionals. Furthermore, using the aug-cc-pVTZ basis set and
Energy Technology Data Exchange (ETDEWEB)
Lee, Sang Uck [Univ. of Ulsan, Ulsan (Korea, Republic of)
2013-08-15
The accurate prediction of vertical excitation energies is very important for the development of new materials in the dye and pigment industry. A time-dependent density functional theory (TD-DFT) approach coupled with 22 different exchange-correlation functionals was used for the prediction of vertical excitation energies in the halogenated copper phthalocyanine molecules in order to find the most appropriate functional and to determine the accuracy of the prediction of the absorption wavelength and observed spectral shifts. Among the tested functional, B3LYP functional provides much more accurate vertical excitation energies and UV-vis spectra. Our results clearly provide a benchmark calibration of the TD-DFT method for phthalocyanine based dyes and pigments used in industry.
Zheng, Xiaoyan; Wang, Xueye; Shen, Keqi; Miao, Yuan; Ouyang, Dan
2011-10-01
Theoretical studies of an unsymmetrical calix[4]-crown-5-N-azacrown-5 (1) in a fixed 1,3-alternate conformation and the complexes 1·K(+)(a), 1·K(+)(b), 1·K(+)(c) and 1·K(+)K(+) were performed using density functional theory (DFT) at the B3LYP/6-31G level. The fully optimized geometric structures of the free macroligand and its 1:1 and 1:2 complexes, as obtained from DFT calculations, were used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal-ligand and cation-π interactions were investigated. NBO analysis indicated that the stabilization interaction energies (E (2)) for O…K(+) and N…K(+) are larger than the other intermolecular interactions in each complex. The significant increase in electron density in the RY or LP orbitals of K(+) results in strong host-guest interactions. In addition, the intermolecular interaction thermal energies (ΔE, ΔH, ΔG) were calculated by frequency analysis at the B3LYP/6-31G level. For all structures, the most pronounced changes in the geometric parameters upon interaction are observed in the calix[4]arene molecule. The results indicate that both the intermolecular electrostatic interactions and the cation-π interactions between the metal ion and π orbitals of the two pairs that face the inverted benzene rings play a significant role.
Malik, Magdalena; Wysokiński, Rafał; Zierkiewicz, Wiktor; Helios, Katarzyna; Michalska, Danuta
2014-08-28
Picoplatin, cis-[PtCl2(NH3)(2-picoline)], is a new promising anticancer agent undergoing clinical trials, which reveals high efficacy against many tumors and greatly reduced toxicity, in comparison to cisplatin. In this work, we present for the first time the Fourier-transform Raman and infrared spectra of picoplatin, in the region of 3500-50 cm(-1). The comprehensive theoretical studies on the molecular structure, the nature of Pt-ligand bonding, vibrational frequencies, and intensities were performed by employing different DFT methods, including hybrid (PBE0, mPW1PW, and B3LYP) and long-range-corrected hybrid density functionals (LC-ωPBE, CAM-B3LYP). Various effective core potentials (ECP) and basis sets have been used. In the prediction of the molecular structure of picoplatin, the best results have been obtained by LC-ωPBE, followed by PBE0, mPW1PW, and CAM-B3LYP density functionals, while the least accurate is B3LYP. The use of the LanL2TZ(f) ECP/basis set for Pt, in conjunction with all tested DFT methods, improves the calculated geometry of the title complex. The PBE0, mPW1PW, and CAM-B3LYP methods have shown the best performance in the calculations of the frequencies of Pt-ligand vibrations. A clear-cut assignment of all the bands in the IR and Raman spectra have been made on the basis of the calculated potential energy distribution (PED). The nature of the "vibrational signatures" of picoplatin have been determined. These results are indispensable for further investigation on drug-target interactions using vibrational spectroscopy.
Rahman, Taj Ur; Uddin, Ghias; Nisa, Riffat Un; Ludwig, Ralf; Liaqat, Wajiha; Mahmood, Tariq; Mohammad, Ghulam; Choudhary, M Iqbal; Ayub, Khurshid
2015-09-05
A new isoflavone 7-hydroxy 3'-methoxyisoflavone (1) is isolated from the seeds of Indigofera heterantha. The structure of this new compound was established using spectroscopic techniques such as ID, 2D NMR, and mass spectrometry. Density functional theory calculations are carried out for the first time for geometric, electronic and spectroscopic properties of 1 (isoflavone). DFT calculations have been performed at B3LYP/6-311G(d,p) level of theory for obtaining geometric and spectroscopic properties of compound 1. The simulated vibrational spectrum of compound 1 at B3LYP/6-311G(d,p) shows nice correlation with the experimental IR spectrum after a scaling factor of 0.973. (1)H and (13)C NMR chemical shifts were calculated using Cramer's re-parameterized function WP04 at 6-311G(d,p) basis set, and show nice correlation with the experimental data. Four conformers were considered for NMR chemical shift calculations. Electronic properties such as band gap, Ionization potential and electron affinities were also simulated for the first time; however, no comparison could be made with the experiment.
Density functional theory study of BnC clusters.
Liu, Chunhui; Han, Peilin; Tang, Mingsheng
2011-05-15
B(n)C clusters (n = 3-10) were studied at the density functional theory (DFT) (B3LYP)/6-311G** level of theory. The calculations predicted that the most stable configurations of the B(n) C clusters are the (n + 1)-membered cyclic structures. For boron-carbon clusters, the configurations containing greater numbers of three-membered boron rings are more favorable, except for the B(7)C and B(9)C clusters. Through molecular orbital analysis of these B(n)C clusters, we have concluded that π-electron delocalization plays a crucial role in the stability of n + 1-membered cyclic structures. In this paper, the relative stability of each cluster is discussed based on their single atomic-binding energies. The capability of clusters to obtain or lose an electron was also discussed, based on their vertical electron detachment energies (VDEs), adiabatic electron detachment energies (ADEs), vertical electron affinities (VEAs) and adiabatic electron affinities (AEAs). Copyright © 2011 John Wiley & Sons, Ltd.
Wungu, T. D. K.; Marsha, S. E.; Widayani; Suprijadi
2017-07-01
In order to find an alternative biosensor material which enables to detect the glucose level, therefore in this study, the interaction between Methacrylic Acid (MAA) based Molecularly Imprinted Polymer (MIP) with D-Glucose is investigated using the Density Functional Theory (DFT). The aim of this study is to determine whether a molecule of the MAA can be functioned as a bio-sensing of glucose. In this calculation, the Gaussian 09 with B3LYP and 631+G(d) basis sets is used to calculate all electronic properties. It is found that the interaction between a molecule of MAA and a molecule of D-Glucose was observed through the shortened distance between the two molecules. The binding energy of MAA/D-glucose and the Mulliken population analysis are investigated for checking possible interaction. From analysis, the MAA based MIP can be used as a bio-sensing material.
The Variety of Carbon-Metal Bonds inside Cu-ZSM-5 Zeolites: A Density Functional Theory Study
Directory of Open Access Journals (Sweden)
Takashi Yumura
2010-04-01
Full Text Available Large-scale density functional theory calculations (DFT found various types of binding of an unsaturated hydrocarbon (C2H2 and C2H4 to a ZSM-5 zeolite extraframework copper cation. We employed the DFT calculations based on the B3LYP functional to obtain local minima of an unsaturated hydrocarbon adsorbed on one or two copper cations embedded inside ZSM-5, and then compared their stabilization energies. The DFT results show that the stabilization energies are strongly dependent on the copper coordination environment as well as configurations of two copper cations. Consequently, the inner copper-carbon bonds are influenced substantially by a nanometer-scale cavity of ZSM-5.
Directory of Open Access Journals (Sweden)
Imanelakehal
2016-05-01
Full Text Available Complex of cerium (III with (E-N-benzylidene-4-methoxyaniline is synthesized through a one-pot three-componentreaction from aromatical dehyde, aromatic amine and the CeCl3· 7 H2O, as an efficient catalyst. This cerium(IIIcom- plexis characterized by IR, 1H, and 13 CNMR-spectros copy and mass-spectraldata. Molecular structure, Mullikan charges, thermodynamic parameters; vibrational frequencies and intensities were calculated by Density Functional theory methods (B3LYP,B3PW91,mPW1PW91 and PBEPBE using the SDD basis set. The comparison between the calculated and experimental data inorder to attain the best quality and to predict the structure, the best perfor-mance in the vibration spectra perfected of the title compound,we have found that the harmonic vibration computed are in a good agreement with the observed in IRspectrum, for closest match we calculated optimal scaling factors can recommend for the IR spectral future predictions for unknown compounds of this class. In order to better comparison, we also root meansqu are values of the experimental and calculated IR bands are 16.64,16.64,17.45,17.66 and the mean absolute percentage error values are1.33,1.39,1.40, and 1.5forB3LYP, B3PW91,mPW1PW91, and PBEPBE methods respectively
Directory of Open Access Journals (Sweden)
Loay A. Elalfy
2013-01-01
Full Text Available Density functional theory calculations using B3LYP/3-21G level of theory have been implemented on 6 carbon nanotubes (CNTs structures (3 zigzag and 3 armchair CNTs to study the energetics of the reverse osmosis during water desalination process. Calculations of the band gap, interaction energy, highest occupied molecular orbital, lowest unoccupied molecular orbital, electronegativity, hardness, and pressure of the system are discussed. The calculations showed that the water molecule that exists inside the CNT is about 2-3 Å away from its wall. The calculations have proven that the zigzag CNTs are more efficient for reverse osmosis water desalination process than armchair CNTs as the reverse osmosis process requires pressure of approximately 200 MPa for armchair CNTs, which is consistent with the values used in molecular dynamics simulations, while that needed when using zigzag CNTs was in the order of 60 MPa.
Institute of Scientific and Technical Information of China (English)
Wang Yan-Li; Zhang Jun-Ping; Su Ke-He; Wang Xin; Liu Yan; Sun Xu
2012-01-01
Armchair (n,n) single walled boron nitride nanotubes with n=2-17 are studied by the density functional theory at the B3LYP/3-21G(d) level combined with the periodic boundary conditions for simulating the ultra long model.The results show that the structure parameters and the formation energies bear a strong relationship to n.The fitted analytical equations are developed with correlation coefficients larger than 0.999.The energy gaps of (2,2) and (3,3)tubes are indirect gaps,and the larger tubes (n=4-17) have direct energy gaps.Results show that the armchair boron nitride nanotubes (n=2-17) are insulators with wide energy gaps of between 5.93 eV and 6.23 eV.
Indian Academy of Sciences (India)
G SUBHAPRIYA; S KALYANARAMAN; S GANDHIMATHI; N SURUMBARKUZHALI; V KRISHNAKUMAR
2017-02-01
An extensive theoretical study on the molecular structure and vibrational analysis of 3-amino-4-methoxy benzamide (3A4MBA) was undertaken using density functional theoretical (DFT) method. The possibility of formation of intramolecular hydrogen bonding was identified from structural parameter analysis andconfirmed with the natural bond orbital (NBO), molecular electrostatic potential (MEP) and natural charge analysis. The harmonic oscillator model of aromaticity (HOMA) index elucidated the impact of hydrogen bonding in the ring. Intramolecular hydrogen bonding energy has been calculated from topological study. The lowwavenumber vibrational modes obtained from experimental FT-Raman spectrum also supported the presence of hydrogen bonding. Bands are assigned for vibrational frequencies using DFT/B3LYP/6-311++G** level of theory.
Indian Academy of Sciences (India)
G SUBHAPRIYA; S KALYANARAMAN; S GANDHIMATHI; N SURUMBARKUZHALI; V KRISHNAKUMAR
2017-02-01
An extensive theoretical study on the molecular structure and vibrational analysis of 3-amino-4- methoxy benzamide (3A4MBA) was undertaken using density functional theoretical (DFT) method. The possibility of formation of intramolecular hydrogen bonding was identified from structural parameter analysis and confirmed with the natural bond orbital (NBO), molecular electrostatic potential (MEP) and natural charge analysis. The harmonic oscillator model of aromaticity (HOMA) index elucidated the impact of hydrogen bonding in the ring. Intramolecular hydrogen bonding energy has been calculated from topological study. The lowwavenumber vibrational modes obtained from experimental FT-Raman spectrum also supported the presence of hydrogen bonding. Bands are assigned for vibrational frequencies using DFT/B3LYP/6-311++G** level of theory.
Reda, S M; Soliman, K A
2016-02-01
This work presents an experimental and theoretical study of cyanidin natural dye as a sensitizer for ZnO dye-sensitized solar cells. ZnO nanoparticles were prepared using ammonia and oxalic acid as a capping agent. The calculated average size of the synthesized ZnO with different capping agents was found to be 32.1 nm. Electronic properties of cyanidin and delphinidin dye were studied using density functional theory (DFT) and time-dependent DFT with a B3LYP/6-31G(d,p) level. By comparing the theoretical results with the experimental data, the cyanidin dye can be used as a sensitizer in dye-sensitized solar cells. An efficiency of 0.006% under an AM-1.5 illumination at 100 mW/cm(2) was attained. The influence of dye adsorption time on the solar cell performance is discussed.
Padmaja, L.; Amalanathan, M.; Ravikumar, C.; Hubert Joe, I.
2009-10-01
Vibrational analysis of the 2,6-bis(p-methyl benzylidene cyclohexanone) [PMBC] compound was carried out by using NIR FT-Raman and FT-IR spectroscopic techniques. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of PMBC have been investigated with the help of B3LYP/6-31G(d) density functional theory method. The optimized geometry clearly demonstrates cyclohexanone ring chair conformation is changed into half-chair conformation. The shortening of C-H bond length and blue shifting of the CH stretching wavenumber suggest the existence of improper weak C-H⋯O hydrogen bonding, which is confirmed by the natural bond orbital analysis. The Mulliken population analysis on atomic charges and the HOMO-LUMO energy are also calculated.
Institute of Scientific and Technical Information of China (English)
Chen Yuan-Zheng; Li Shuo; Zhou Mi; Li Zuo-Wei; Sun Cheng-Lin
2013-01-01
We report on a temperature-dependent resonance Raman spectral characterization of the polyene chain of canthaxanthin.It is observed that all vibrational intensities of the polyene chain are inversely proportional to temperature,which is analyzed by the resonance Raman effect and the coherent weakly damped electron/lattice vibrations.The increase in intensity of the CC overtone/combination relative to the fundamental with temperature decreasing is detected and discussed in terms of electron/phonon coupling and the activation energy Uop.Moreover,the polyene chain studies using the density functional theory B3LYP/6-31G* level reveal a prominent peak at 1525 cm-1 consisting of two closely spaced modes that are both dominated by C=C stretching coordinates of the polyene chain.
Liaw, Chih-Chuang; Chang, Jia-Lin; Chen, Shou-Fong; Huang, Jhih-Hong; Sie, Jyun-Fu; Cheng, Yung-Yi
2011-11-01
We present the first theoretical study on a pair of diterpene enantiomers of formula C 21H 34O 5, which were newly isolated from plants and identified as 3β,5β-dihydroxy-16 α/ β-methoxyhalima-13(14)-en-15,16-olide. The equilibrium geometries and harmonic vibrational frequencies of their low-lying conformers were obtained by using the AM1 and B3LYP/6-31+G(d) methods. At the optimized geometries, rotatory strengths of six excited states of each conformer were computed by the time-dependent density functional theory. The electronic circular dichroism spectra were simulated by taking Boltzmann averaging and considering the solvent effect, from which the absolute configurations of the enantiomers were determined. Their vibrational circular dichroism spectra were also predicted.
Institute of Scientific and Technical Information of China (English)
LI Xiao-Hong; TANG Zheng-Xin; Abraham F.Jalbout; ZHANG Xian-Zhou; CHENG Xin-Lu
2008-01-01
The N-NO2 bond dissociation energies (BDEs) for 7 energetic materials were computed by means of accurate density functional theory (B3LYP, B3PW91 and B3P86) with 6-31G** and 6-311G** basis sets. By comparing the computed energies and experimental results, we find that the B3P86/6-311G** method can give good results of BDE, which has the mean absolute deviation of 1.30 kcal/mol. In addition, substituent effects were also taken into account. It is noted that the Hammett constants of substituent groups are related to the BDEs of the N-NO2 bond and the bond dissociation energies of the energetic materials studied decrease when increasing the number of NO2 group.
Villamena, Frederick A; Hadad, Christopher M; Zweier, Jay L
2004-02-18
The hydroxyl radical (*OH) is an important mediator of biological oxidative stress, and this has stimulated interest in its detection. 5,5-Dimethyl-1-pyrroline N-oxide (DMPO) and its alkoxycarbonyl and alkoxyphosphoryl analogues have been employed as spin traps for electron paramagnetic resonance (EPR) spectroscopic radical detection. Energies of optimized geometries of nitrones and their corresponding *OH adducts were calculated using density functional theory (DFT) at the B3LYP/6-31+G//B3LYP/6-31G level. Calculations predict that the trans adduct formation is favored in alkoxycarbonyl nitrones, while cis adducts with intramolecular H-bonding is favored for alkoxyphosphoryl nitrones. Addition of *OH to a phosphoryl-substituted nitrone is more exoergic than the carbonylated nitrones. Charge and spin densities on the nitrone spin traps were correlated with their rates of addition with *OH, and results show that the charge density on the nitronyl C, the site of *OH addition, is more positive in phosphorylated nitrones compared to DMPO and the alkoxycarbonyl nitrones. The dihedral angle between the beta-H and nitroxyl O bonds is smaller in phosphorylated nitrones, and that aspect appears to account for the longer half-lives of the spin adducts compared to those in DMPO and alkoxycarbonyl nitrones. Structures of nitrones with trifluoromethyl-, trifluoromethylcarbonyl-, methylsulfonyl-, trifluoromethylsulfonyl-, amido-, spiropentyl-, and spiroester substituents were optimized and their energies compared. Amido and spiroester nitrones were predicted to be the most suitable nitrones for spin trapping of *OH due to the similarity of their thermodynamic and electronic properties to those of alkoxyphosphoryl nitrones. Moreover, dimethoxyphosphoryl substitution at C-5 was found to be the most efficient substitution site for spin trapping of *OH, and their spin adducts are predicted to be the most stable of all of the isomeric forms.
Shahidha, R; Muthu, S; Elamurugu Porchelvi, E; Govindarajan, M
2014-11-11
Vibrational spectral analysis of 5-methyl-N-[4-(trifluoromethyl) phenyl]-isoxazole-4-carboxamide is (5MN4TPI4C) molecule was carried out using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry, harmonic vibrational wavenumbers, various bonding features have been computed using density functional B3LYP method with 6-311G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFFM). Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The non-linear optical (NLO) behavior of 5MN4TPI4C has been studied by determination of the electric dipole moment (μ) and hyperpolarizability (β) by using B3LYP/6-311G(d,p) method. The molecular orbital compositions and their contributions to the chemical bonding are studied by Total density of energy states (TDOS), sum of α and β electron (αβDOS) density of states. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are calculated.
Li, Ji-Lai; Mata, Ricardo A; Ryde, Ulf
2013-03-12
The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated. Basis sets of at least triple-ζ quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD(T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBE0, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.
Cao, Yixiang; Hughes, Thomas; Giesen, Dave; Halls, Mathew D; Goldberg, Alexander; Vadicherla, Tati Reddy; Sastry, Madhavi; Patel, Bhargav; Sherman, Woody; Weisman, Andrew L; Friesner, Richard A
2016-06-15
We have developed and implemented pseudospectral time-dependent density-functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm-Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time-dependent density-functional theory with full linear response (PS-FLR-TDDFT) and within the Tamm-Dancoff approximation (PS-TDA-TDDFT) for G2 set molecules using B3LYP/6-31G*(*) show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS-FLR-TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS-FLR-TDDFT and best estimations demonstrate that the accuracy of both PS-FLR-TDDFT and PS-TDA-TDDFT. Calculations for a set of medium-sized molecules, including Cn fullerenes and nanotubes, using the B3LYP functional and 6-31G(**) basis set show PS-TDA-TDDFT provides 19- to 34-fold speedups for Cn fullerenes with 450-1470 basis functions, 11- to 32-fold speedups for nanotubes with 660-3180 basis functions, and 9- to 16-fold speedups for organic molecules with 540-1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46-residue crambin protein, fullerenes up to C540 and nanotubes up to 14×(6,6), using the B3LYP functional and 6-31G
Karamanis, Panaghiotis; Marchal, Remi; Carbonniére, Philippe; Pouchan, Claude
2011-07-28
in this work, (B3LYP, B3PW91, BhandHLYP, PBE0, CAM-B3LYP, LC-BLYP, LC-BPW91) only B3PW91 and PBE0 out of the seven provided a consistent quantitative performance for both polarizabilities and hyperpolarizabilities with respect to the ab initio methods utilized here. On the other hand, the long range corrected functionals LC-(U)BLYP and LC-(U)BPW91 (μ = 0.47) failed to supply quantitatively accurate hyperpolarizability results in all the studied clusters while the CAM-(U)B3LYP functional performs satisfactory only in the case of the Na and K doped systems. © 2011 American Institute of Physics
A generalized exchange-correlation functional: the Neural-Networks approach
Zheng, X; Wang, X J; Chen, G H; Zheng, Xiao; Hu, LiHong; Wang, XiuJun; Chen, GuanHua
2003-01-01
A Neural-Networks-based approach is proposed to construct a new type of exchange-correlation functional for density functional theory. It is applied to improve B3LYP functional by taking into account of high-order contributions to the exchange-correlation functional. The improved B3LYP functional is based on a neural network whose structure and synaptic weights are determined from 116 known experimental atomization energies, ionization potentials, proton affinities or total atomic energies which were used by Becke in his pioneer work on the hybrid functionals [J. Chem. Phys. ${\\bf 98}$, 5648 (1993)]. It leads to better agreement between the first-principles calculation results and these 116 experimental data. The new B3LYP functional is further tested by applying it to calculate the ionization potentials of 24 molecules of the G2 test set. The 6-311+G(3{\\it df},2{\\it p}) basis set is employed in the calculation, and the resulting root-mean-square error is reduced to 2.2 kcal$\\cdot$mol$^{-1}$ in comparison to ...
McWilliams, Sean F; Brennan-Wydra, Emma; MacLeod, K Cory; Holland, Patrick L
2017-06-30
The relative ease of Mössbauer spectroscopy and of density functional theory (DFT) calculations encourages the use of Mössbauer parameters as a validation method for calculations, and the use of calculations as a double check on crystallographic structures. A number of studies have proposed correlations between the computationally determined electron density at the iron nucleus and the observed isomer shift, but deviations from these correlations in low-valent iron β-diketiminate complexes encouraged us to determine a new correlation for these compounds. The use of B3LYP/def2-TZVP in the ORCA platform provides an excellent balance of accuracy and speed. We provide here not only this new correlation and a clear guide to its use but also a systematic analysis of the limitations of this approach. We also highlight the impact of crystallographic inaccuracies, DFT model truncation, and spin states, with intent to assist experimentalists to use Mössbauer spectroscopy and calculations together.
Directory of Open Access Journals (Sweden)
Mnaza Noreen
2015-11-01
Full Text Available A variety of novel 5-aryl thiophenes 4a–g containing sulphonylacetamide (sulfacetamide groups were synthesized in appreciable yields via Pd[0] Suzuki cross coupling reactions. The structures of these newly synthesized compounds were determined using spectral data and elemental analysis. Density functional theory (DFT studies were performed using the B3LYP/6-31G (d, p basis set to gain insight into their structural properties. Frontier molecular orbital (FMOs analysis of all compounds 4a–g was computed at the same level of theory to get an idea about their kinetic stability. The molecular electrostatic potential (MEP mapping over the entire stabilized geometries of the molecules indicated the reactive sites. First hyperpolarizability analysis (nonlinear optical response were simulated at the B3LYP/6-31G (d, p level of theory as well. The compounds were further evaluated for their promising antibacterial and anti-urease activities. In this case, the antibacterial activities were estimated by the agar well diffusion method, whereas the anti-urease activities of these compounds were determined using the indophenol method by quantifying the evolved ammonia produced. The results revealed that all the sulfacetamide derivatives displayed antibacterial activity against Bacillus subtiles, Escherichia coli, Staphylococcus aureus, Shigella dysenteriae, Salmonella typhae, Pseudomonas aeruginosa at various concentrations. Furthermore, the compound 4g N-((5-(4-chlorophenylthiophen-2-ylsulfonyl acetamide showed excellent urease inhibition with percentage inhibition activity ~46.23 ± 0.11 at 15 µg/mL with IC50 17.1 µg/mL. Moreover, some other compounds 4a–f also exhibited very good inhibition against urease enzyme.
Noreen, Mnaza; Rasool, Nasir; Gull, Yasmeen; Zubair, Muhammad; Mahmood, Tariq; Ayub, Khurshid; Nasim, Faiz-Ul-Hassan; Yaqoob, Asma; Zia-Ul-Haq, Muhammad; de Feo, Vincenzo
2015-11-05
A variety of novel 5-aryl thiophenes 4a-g containing sulphonylacetamide (sulfacetamide) groups were synthesized in appreciable yields via Pd[0] Suzuki cross coupling reactions. The structures of these newly synthesized compounds were determined using spectral data and elemental analysis. Density functional theory (DFT) studies were performed using the B3LYP/6-31G (d, p) basis set to gain insight into their structural properties. Frontier molecular orbital (FMOs) analysis of all compounds 4a-g was computed at the same level of theory to get an idea about their kinetic stability. The molecular electrostatic potential (MEP) mapping over the entire stabilized geometries of the molecules indicated the reactive sites. First hyperpolarizability analysis (nonlinear optical response) were simulated at the B3LYP/6-31G (d, p) level of theory as well. The compounds were further evaluated for their promising antibacterial and anti-urease activities. In this case, the antibacterial activities were estimated by the agar well diffusion method, whereas the anti-urease activities of these compounds were determined using the indophenol method by quantifying the evolved ammonia produced. The results revealed that all the sulfacetamide derivatives displayed antibacterial activity against Bacillus subtiles, Escherichia coli, Staphylococcus aureus, Shigella dysenteriae, Salmonella typhae, Pseudomonas aeruginosa at various concentrations. Furthermore, the compound 4g N-((5-(4-chlorophenyl)thiophen-2-yl)sulfonyl) acetamide showed excellent urease inhibition with percentage inhibition activity ~46.23 ± 0.11 at 15 µg/mL with IC50 17.1 µg/mL. Moreover, some other compounds 4a-f also exhibited very good inhibition against urease enzyme.
Energy Technology Data Exchange (ETDEWEB)
Ulian, Gianfranco; Valdrè, Giovanni, E-mail: giovanni.valdre@unibo.it [Dipartimento di Scienze Biologiche e Geologico-Ambientali, Centro di Ricerca Interdisciplinare di Biomineralogia, Cristallografia e Biomateriali, Università di Bologna “Alma Mater Studiorum” Piazza di Porta San Donato 1, 40126 Bologna (Italy); Tosoni, Sergio [Departament de Química Física and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/ Martí i Franquès 1, E-08028 Barcelona (Spain)
2013-11-28
The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.
Bjornsson, Ragnar; Bühl, Michael
2010-06-14
Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C(6)H(6))(CO)(3), MnO(3)F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omegaPBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters.
Ramalingam, S; Jayaprakash, A; Mohan, S; Karabacak, M
2011-11-01
FT-IR and FT-Raman (4000-100 cm(-1)) spectral measurements of 3-methyl-1,2-butadiene (3M12B) have been attempted in the present work. Ab-initio HF and DFT (LSDA/B3LYP/B3PW91) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, IR intensities and Raman activities. Complete vibrational assignments on the observed spectra are made with vibrational frequencies obtained by HF and DFT (LSDA/B3LYP/B3PW91) at 6-31G(d,p) and 6-311G(d,p) basis sets. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The potential energy distribution (PED) corresponding to each of the observed frequencies are calculated which confirms the reliability and precision of the assignment and analysis of the vibrational fundamentals modes. The oscillation of vibrational frequencies of butadiene due to the couple of methyl group is also discussed. A study on the electronic properties such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The thermodynamic properties of the title compound at different temperatures reveal the correlations between standard heat capacities (C) standard entropies (S), and standard enthalpy changes (H).
Todde, Guido; Hovmöller, Sven; Laaksonen, Aatto
2016-03-01
Four mutated hemoglobin (Hb) variants and wild type hemoglobin as a reference have been investigated using density functional theory methods focusing on oxygen binding. Dispersion-corrected B3LYP functional is used and found to provide reliable oxygen binding energies. It also correctly reproduces the spin distribution of both bound and free heme groups as well as provides correct geometries at their close vicinity. Mutations in hemoglobin are not only an intrigued biological problem and it is also highly important to understand their effects from a clinical point of view. This study clearly shows how even small structural differences close to the heme group can have a significant effect in reducing the oxygen binding of mutated hemoglobins and consequently affecting the health condition of the patient suffering from the mutations. All of the studied mutated Hb variants did exhibit much weaker binding of molecular oxygen compared to the wild type of hemoglobin.
Tsuchimochi, Takashi; Kobayashi, Masato; Nakata, Ayako; Imamura, Yutaka; Nakai, Hiromi
2008-11-15
The Sakurai-Sugiura projection (SS) method was implemented and numerically assessed for diagonalization of the Hamiltonian in time-dependent density functional theory (TDDFT). Since the SS method can be used to specify the range in which the eigenvalues are computed, it may be an efficient tool for use with eigenvalues in a particular range. In this article, the SS method is applied to core excited calculations for which the eigenvalues are located within a particular range, since the eigenvalues are unique to atomic species in molecules. The numerical assessment of formaldehyde molecule by TDDFT with core-valence Becke's three-parameter exchange (B3) plus Lee-Yang-Parr (LYP) correlation (CV-B3LYP) functional demonstrates that the SS method can be used to selectively obtain highly accurate eigenvalues and eigenvectors. Thus, the SS method is a new and powerful alternative for calculating core-excitation energies without high computation costs.
Huang, Lulu; Matta, Chérif F; Massa, Lou
2011-11-17
We investigate anew the possible equilibrium geometries of ion induced dipole clusters of hydrogen molecular ions, of molecular formula H(n)(-) (3 ≤ n-odd ≤ 13). Our previous publications [Sapse, A. M.; et al. Nature 1979, 278, 332; Rayez, J. C.; et al., J. Chem. Phys. 1981, 75, 5393] indicated these molecules would have a shallow minimum and adopt symmetrical geometries that accord with the valence shell electron pair repulsion (VSEPR) rules for geometries defined by electron pairs surrounding a central point of attraction. These earlier calculations were all based upon Hartree-Fock (HF) calculations with a fairly small basis of atomic functions, except for the H3(-) ion for which configuration interaction (CI) calculations were carried out. A related paper [Hirao, K.; et al., Chem. Phys. 1983, 80, 237] carried out similar calculations on the same clusters, finding geometries similar to our earlier calculations. However, although that paper argued that the stabilization energy of negative ion clusters H(n)(-) is small, vibration frequencies for the whole set of clusters was not reported, and so a definitive assertion of a true equilibrium was not present. In this paper we recalculate the energetics of the ion induced dipole clusters using density function theory (DFT) B3LYP method calculations in a basis of functions (6-311++G(d,p)). By calculating the vibration frequencies of the VSEPR geometries, we prove that in general they are not true minima because not all the resulting frequencies correspond to real values. By searching the energy surface of the B3LYP calculations, we find the true minimum geometries, which are surprising configurations and are perhaps counterintuitive. We calculate the total energy and binding energy of the new geometries. We also calculate the bond paths associated with the quantum theory of atoms in molecules (QTAIM). The B3LYP/6-311++G(d,p) results, for each molecule, deliver bond paths that radiate between each polarized H2
Shamsipur, Mojtaba; Allahyari, Leila; Fasihi, Javad; Taherpour, Avat (Arman); Asfari, Zuhair; Valinejad, Azizollah
2016-03-01
Complexation of two 1,3-alternate calix[4]crown ligands with alkali metals (K+, Rb+ and Cs+) has been investigated by electrospray ionization mass spectrometry (ESI-MS) and density functional theory calculations. The binding selectivities of the ligands and the binding constants of their complexes in solution have been determined using the obtained mass spectra. Also the percentage of each formed complex species in the mixture of each ligand and alkali metal has been experimentally evaluated. For both calix[4]crown-5 and calix[4]crown-6 ligands the experimental and theoretical selectivity of their alkali metal complexes found to follow the trend K+ > Rb+ > Cs+. The structures of ligands were optimized by DFT-B3LYP/6-31G method and the structures of complexes were obtained by QM-SCF-MO/PM6 method and discussed in the text.
Behzadi, Hadi; Hadipour, Nasser L; Mirzaei, Mahmoud
2007-01-01
A density functional theory (DFT) study was carried out to calculate (17)O, (14)N and (2)H electric field gradient (EFG) tensors in accurate neutron diffraction structures of alpha-glycine at 288 and 427 K. B3LYP is the used method and 6-311+G(*) and 6-311++G(**) are the basis sets in the calculations of EFG tensors at the sites of (17)O, (14)N and (2)H nuclei in the monomer and the octameric cluster of alpha-glycine at two temperatures. Quadrupole coupling constants and asymmetry parameters are the converted parameters of calculated EFG tensors to experimentally measurable ones. The calculated results of monomer and the target molecule in octameric cluster reveal that hydrogen-bonding interactions play an important role in the crystalline structure of alpha-glycine where the results of the target molecule in octameric cluster are in good agreement with the experiments.
Ucun, Fatih; Sağlam, Adnan; Güçlü, Vesile
2007-06-01
The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.
Öner, Nazmiye; Tamer, Ömer; Başoǧlu, Adil; Avcı, Davut; Atalay, Yusuf
2017-02-01
In this paper, quantum chemical calculations of (2e)-3-(3-Bromo-4-methoxyphenyl) -1-(pyridin-2-yl)prop-2-en-1-one were performed by using B3LYP and CAMB3LYP levels of density functional theory (DFT) with 6-311++G(d, p) basis set. Geometric parameters of the title molecule in the ground state were found to be in good agreement with experimental data. 13C and 1H NMR chemical shifts were calculated within GIAO approach which is one of the most common approaches. The frontier molecular orbitals (HOMO and LUMO) were simulated by the same levels. Nonlinear optical parameters (NLO) were also evaluated by determining of dipole moment, polarizability and first hyperpolarizability. All of calculations were carried out Gaussian 09 package program.
Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha
2011-11-01
Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.
Institute of Scientific and Technical Information of China (English)
ZHANG Ding-lin; WEI Xi-wen; WANG Xiang-zhi
2007-01-01
The activities of dimethyl carbonate and dimethyl sulfate as a methylation reagent were studied by density- functional theory (DFT). B3LYP/6-31G(d, p) methods were used to optimize the structures of dimethyl carbonate and dimethyl sulfate and calculate theirs charge densities. Dimethyl sulfate is easier than dimethyl carbonate to react with a nucleophilic reagent. In dimethyl sulfate, the alkoxy carbons are the only reactive atomic nucleus because of steric hindrance. A nucleophilic reagent is more likely to react with carbonyl carbons than alkoxy carbons of dimethyl carbonate; in the presence of a Lewis acid, the phenyl nucleophilic reagent reacts with the Lewis acid first. Lewis acid increases the negative charge density of a nucleophilic reagent in polar solvent, and also incurs an accretion of steric hindrance. Polar solvent avails to ionize dimethyl carbonate and thus enables the reaction of methylation. The frequencies of transition state calculated by Gaussion 03 confirm the inferred reaction mechanism. The harvest rates of 4-methoxyphenol in the experiments of methylation reactions of hydroquinone with respectively dimethyl carbonate and dimethyl sulfate support the foregoing theortical conclusions.
Coumarin Dyes for Dye-Sensitized Solar Cells - A Long-Range-Corrected Density Functional Study
Wong, Bryan M; 10.1063/1.3025924
2010-01-01
The excited-state properties in a series of coumarin solar cell dyes are investigated with a long-range-corrected (LC) functional which asymptotically incorporates Hartree-Fock exchange. Using time-dependent density functional theory (TDDFT), we calculate excitation energies, oscillator strengths, and excited-state dipole moments in each of the dyes as a function of the range-separation paramenter, mu. To investigate the acceptable range of mu and assess the quality of the LC-TDDFT formalism, an extensive comparison is made between LC-BLYP excitation energies and approximate coupled cluster singles and doubles (CC2) calculations. When using a properly-optimized value of mu, we find that the LC technique provides a consistent picture of charge-transfer excitations as a function of molecular size. In contrast, we find that the widely-used B3LYP hybrid functional severely overestimates excited-state dipole moments and underestimates vertical excitations energies, especially for larger dye molecules. The results ...
Vibrational analysis of ferrocyanide complex ion based on density functional force field
Energy Technology Data Exchange (ETDEWEB)
Park, Sun Kyung; Lee, Choong Keun; Lee, Nam Soo [Chungbuk National Univ., Cheongju (Korea, Republic of); Lee, Sang Ho [The University of Michigan, Ann Arbor (United States)
2002-02-01
Vibrational properties of ferrocyanide complex ion, [Fe(CN){sub 6}]{sup 4-}, have been studied based on the force constants obtained from the density functional calculations at B3LYP/6-31G level by means of the normal mode analysis using new bond angle and linear angle internal coordinates recently developed. Vibrations of ferrocyanide were manipulated by twenty-three symmetry force constants. The angled bending deformations of C-Fe-C, the linear bending deformations of Fe-C{identical_to}N and the stretching vibrations of Fe-C have been quantitatively assigned to the calculated frequencies. The force constants in the internal coordinates employed in the modified Urey-Bradley type potential were evaluated on the density functional force field applied, and better interaction force constants in the internal coordinates have been proposed. The valence force constants in the general quadratic valence force field were also given. The stretch-stretch interaction and stretch-bending interaction constants are not sensitive to the geometrical displacement in the valence force field.
Birke, Ronald L; Znamenskiy, Vasiliy; Lombardi, John R
2010-06-07
Vibrational frequency calculations were made for a Ag(10)-pyridine vertex complex with density functional theory (DFT) for static simulated spectra and with time-dependent DFT (TD-DFT) for preresonance and resonance simulated spectra using both B3LYP/LANL2DZ and BP86/TZP methodologies. In addition, 40 excited states of the complex were calculated and assigned symmetry based on a C(2v) symmetry of the optimized complex found with B3LYP/LANL2DZ. Molecular orbital isosurfaces show that the excited states involve both Ag(10) intercluster excitations and charge-transfer (CT) excitations between the Ag nanocluster and the pyridine molecule. An excitation around 500 nm involving CT from the Ag cluster to pyridine was found in both calculations. For free pyridine, the relative average deviations between unscaled calculated and experimental results were 1.5 cm(-1) for BP86 and 3.1 cm(-1) for the B3LYP calculations. For the complex, simulated spectra at a variety of excitation wavelengths were calculated. In the case of 514 nm excitation, the simulated Raman cross section from the TD-DFT calculations (near the CT resonance) was plotted versus Raman shift frequency and compared with an experimental surface enhanced Raman scattering (SERS) spectrum obtained on an oxidation-reduction cycle, ORC roughened Ag electrode. The BP86 TD-DFT calculation with finite damping term showed a better fit to experimental spectrum with respect to both relative intensities and frequencies. The average deviation of the unscaled BP86 calculations for 16 bands in the experimental spectrum was 13.0 cm(-1). The calculated spectrum in both cases shows many contributions from nontotally symmetric as well as totally symmetric modes, indicating the contribution of Herzberg-Teller (HT) scattering. The simulated intensities of the Raman modes of different symmetry from Ag(10)-pyridine can be correlated with HT intensity borrowing from excited states of given symmetry and decent oscillator strength. These
Fekete, Attila; Komáromi, István
2016-12-07
A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to
Laury, Marie L; Carlson, Matthew J; Wilson, Angela K
2012-11-15
Calculated harmonic vibrational frequencies systematically deviate from experimental vibrational frequencies. The observed deviation can be corrected by applying a scale factor. Scale factors for: (i) harmonic vibrational frequencies [categorized into low (1000 cm(-1))], (ii) vibrational contributions to enthalpy and entropy, and (iii) zero-point vibrational energies (ZPVEs) have been determined for widely used density functionals in combination with polarization consistent basis sets (pc-n, n = 0,1,2,3,4). The density functionals include pure functionals (BP86, BPW91, BLYP, HCTH93, PBEPBE), hybrid functionals with Hartree-Fock exchange (B3LYP, B3P86, B3PW91, PBE1PBE, mPW1K, BH&HLYP), hybrid meta functionals with the kinetic energy density gradient (M05, M06, M05-2X, M06-2X), a double hybrid functional with Møller-Plesset correlation (B2GP-PLYP), and a dispersion corrected functional (B97-D). The experimental frequencies for calibration were from 41 organic molecules and the ZPVEs for comparison were from 24 small molecules (diatomics, triatomics). For this family of basis sets, the scale factors for each property are more dependent on the functional selection than on basis set level, and thus allow for a suggested scale factor for each density functional when employing polarization consistent basis sets (pc-n, n = 1,2,3,4). A separate scale factor is recommended when the un-polarized basis set, pc-0, is used in combination with the density functionals.
Synthesis and density functional theoretical study of steroidal spiro-triazolidinone.
Sharma, Kamlesh; Lal, Bhajan
2008-06-01
The reaction of 3beta-chloro-5alpha-cholestan-6-one semicarbazone 1 with hydrogen peroxide at 0 degrees C gives 3beta-chloro-5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one 2 as a product. The structural assignment of the product was confirmed on the basis of its elemental, analytical and spectral data. The ab initio calculations were performed by using density functional theory (DFT) at B3LYP/6-31G* basis set in order to describe a free radical reaction mechanism. The reaction proceeds through two radical intermediates formation. The mechanism of the reaction was explained by using frontier molecular orbital (FMO), spin electronic density map, encoded electrostatic potential map and atomic charges. It was found that the localization of frontier orbitals and the flow of atomic charges of all the calculated structures support the present reaction mechanism. The molecular properties like total energy, dipole moment and hardness of each optimized structure, were also explained. Stability of all the optimized structures in this study was supported by their respective fundamental frequencies and energy minima.
Mir, Jan Mohammad; Jain, N; Jaget, P S; Maurya, R C
2017-07-22
Photodynamic therapy (PDT) is a treatment that uses photosensitizing agents to kill cancer cells. Scientific community has been eager for decades in enduring curiosity to design an efficient PDT drug. Under such purview, the current report deals with the computational photodynamic behavior of ruthenium(II) nitrosyl complex containing N, N'-salicyldehyde-ethylenediimine (SalenH2), the synthesis and X-ray crystallography of which is already known [Ref. 36]. Gaussian 09W software package was employed to carry out the density functional (DFT) studies. DFT calculations with Becke-3-Lee-Yang-Parr (B3LYP)/Los Alamos National Laboratory 2 Double Z (LanL2DZ) specified for Ru atom and B3LYP/6-31G(d,p) combination for all other atoms were used using effective core potential method. Both, the ground and excited states of the complex were evolved. Some known photosensitizers were compared with the target complex. Pthalocyanine and porphyrin derivatives were the compounds selected for the respective comparative study. It is suggested that effective photoactivity was found due to the presence of ruthenium core in the model complex. In addition to the evaluation of theoretical aspects in vitro anticancer aspects against COLO-205 human cancer cells have also been carried out with regard to the complex. More emphasis was laid to extrapolate DFT to depict the chemical power of the target compound to release nitric oxide. A promising visible light triggered nitric oxide releasing power of the compound has been inferred. In vitro antiproliferative studies of [RuCl3(PPh3)3] and [Ru(NO)(Salen)(Cl)] have revealed the model complex as an excellent anticancer agent. From IC50 values of 40.031mg/mL in former and of 9.74mg/mL in latter, it is established that latter bears more anticancer potentiality. From overall study the DFT based structural elucidation and the efficiency of NO, Ru and Salen co-ligands has shown promising drug delivery property and a good candidacy for both chemotherapy as
Density Functional Theory Study of Cyanoetheneselenol: A Molecule of Astrobiological Interest
Surajbali, P.; Ramanah, D. Kodi; Rhyman, L.; Alswaidan, I. A.; Fun, H.-K.; Somanah, R.; Ramasami, P.
2015-12-01
The interstellar medium has a rich chemistry which involves a wide variety of molecules. Of particular interest are molecules that have a link to prebiotic chemistry which hold the key to understanding of our origins. On the basis of suggestions that selenium may have been involved in the origin and evolution of life, we have studied the selenium analogue of cyanoethenethiol, namely the novel cyanoetheneselenol. Cyanoetheneselenol exhibits conformational and geometrical isomerism. This theoretical work deals with the study of four forms of cyanoetheneselenol in terms of their structural, spectroscopic and thermodynamic parameters. All computations were performed using density functional theory method with the B3LYP functional and the Pople basis set, 6-311 + G(d,p), for all atoms. The relative stability of the four isomers of cyanoetheneselenol was obtained and interpreted. The infrared spectra were generated and assignment of the normal modes of vibration was performed. Probable regions of detection, proposed on the basis of parameters obtained from this study for the four isomers, include comets, the molecular cloud: Sagittarius B2(N), and planetary atmospheres. The molecular and spectroscopic parameters should be useful for future identification of the astrobiological molecule cyanoetheneselenol and the development of the Square Kilometre Array.
Takahashi, Ohgi; Kirikoshi, Ryota
2014-01-01
Aspartic acid (Asp) residues in peptides and proteins (l-Asp) are known to undergo spontaneous nonenzymatic reactions to form l-β-Asp, d-Asp, and d-β-Asp residues. The formation of these abnormal Asp residues in proteins may affect their three-dimensional structures and hence their properties and functions. Indeed, the reactions have been thought to contribute to aging and pathologies. Most of the above reactions of the l-Asp residues proceed via a cyclic succinimide intermediate. In this paper, a novel three-water-assisted mechanism is proposed for cyclization of an Asp residue (forming a gem-diol precursor of the succinimide) by the B3LYP/6-31 + G(d,p) density functional theory calculations carried out for an Asp-containing model compound (Ace-Asp-Nme, where Ace = acetyl and Nme = NHCH3). The three water molecules act as catalysts by mediating ‘long-range’ proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form (iminolization). Then, reorientation of a water molecule and a conformational change occur successively, followed by the nucleophilic attack of the iminol nitrogen on the carboxyl carbon of the Asp side chain to form the gem-diol species. A satisfactory agreement was obtained between the calculated and experimental energetics.
Understanding Rubredoxin Redox Sites by Density Functional Theory Studies of Analogues
Energy Technology Data Exchange (ETDEWEB)
Luo, Yan; Niu, Shuqiang; Ichiye, Toshiko
2012-09-06
Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH3)4]0/1-/2-, [Fe(S2-o-xyl)2]0/1-/2-, and Na+[Fe(S2-oxyl) 2]1-/2- in different conformations. In particular, the study of Na+[Fe(S2-o-xyl)2]1-/2- is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ~0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.
Vibrational circular dichroism and IR absorption spectra of amino acids: a density functional study.
Ji, Zhi; Santamaria, Rubén; Garzón, Ignacio L
2010-03-18
With density functional theory, vibrational circular dichroism (VCD) and infrared absorption (IR) spectra are obtained at the B3LYP/CC-pVTZ level of theory for 20 alpha-amino acids. The contribution of different vibration modes to the IR and VCD spectra is analyzed. Overall agreement between calculated results for amino acids in gas phase with the available experimental VCD data for matrix-assisted amino acid films is found. The analysis of the calculated IR and VCD spectra indicates that the functional groups in the backbones and side chains of amino acids contribute differently to the spectra line shape. It is obtained that molecular torsions are the characteristic vibrations of the amino acids at the low-frequency regime, whereas the bending of bond angles, the out-of-plane wagging of individual atoms, and some stretching modes dominate the intermediate frequency range. Specific modes like NH(2) scissoring, CO bond stretching, and the (symmetric and asymmetric) stretching of the hydrogen atoms in the NH(2) and OH groups characterize the high-frequency regime. A general trend emerging from these calculations indicates that the rho(OH) rocking and nu(C=O) stretching modes have the highest intensity in the VCD spectra of most amino acids.
Density Functional Study on the Reaction Mechanism for the Reaction of Ni+ with Ethane
Institute of Scientific and Technical Information of China (English)
ZHANG,Dong-Ju(张冬菊); LIU,Cheng-Bu(刘成卜); LIU,Yong-Jun(刘永军); HU,Hai-Quan(胡海泉)
2002-01-01
The mechanism of the reaction of Ni+ (2D) with ethane in the gas-phase was studied by using density functional theory. Both the B3LYP and BLYP functionals with standard all-electron basis sets are used to give the detailed information of the potential energy surface (PES) of [Ni, C2, H6 ] +. Tne mechanisms forming the products CH4 and H2 in the reaction of Ni+with ethane are proposed. The reductive eliminations of CH4and H2 are typical addition-elimination reactions. Each of the two reactions consists of two elementary steps: C-C or CH bond activations to form inserted species followed by isomerizations to form product-like intermediate. The rate determining steps for the elimination reatcions of forming CH4 and H2 are the isomerizations of the inserted species rather than C-C or C-H bond activations. The elimination reaction of forming H2 was found to be thermodynamically favored compared to that of CH4.
Density Functional Theory Study of Cyanoetheneselenol: A Molecule of Astrobiological Interest.
Surajbali, P; Ramanah, D Kodi; Rhyman, L; Alswaidan, I A; Fun, H-K; Somanah, R; Ramasami, P
2015-12-01
The interstellar medium has a rich chemistry which involves a wide variety of molecules. Of particular interest are molecules that have a link to prebiotic chemistry which hold the key to understanding of our origins. On the basis of suggestions that selenium may have been involved in the origin and evolution of life, we have studied the selenium analogue of cyanoethenethiol, namely the novel cyanoetheneselenol. Cyanoetheneselenol exhibits conformational and geometrical isomerism. This theoretical work deals with the study of four forms of cyanoetheneselenol in terms of their structural, spectroscopic and thermodynamic parameters. All computations were performed using density functional theory method with the B3LYP functional and the Pople basis set, 6-311 + G(d,p), for all atoms. The relative stability of the four isomers of cyanoetheneselenol was obtained and interpreted. The infrared spectra were generated and assignment of the normal modes of vibration was performed. Probable regions of detection, proposed on the basis of parameters obtained from this study for the four isomers, include comets, the molecular cloud: Sagittarius B2(N), and planetary atmospheres. The molecular and spectroscopic parameters should be useful for future identification of the astrobiological molecule cyanoetheneselenol and the development of the Square Kilometre Array. Graphical Abstract E and Z isomers of cyanoetheneselenol.
Ensling, David; Thissen, Andreas; Laubach, Stefan; Schmidt, Peter C.; Jaegermann, Wolfram
2010-11-01
The electronic properties of LiCoO2 have been studied by theoretical band-structure calculations (using density functional theory) and experimental methods (photoemission). Synchrotron-induced photoelectron spectroscopy, resonant photoemission spectroscopy (ResPES), and soft x-ray absorption (XAS) have been applied to investigate the electronic structure of both occupied and unoccupied states. High-quality PES spectra were obtained from stoichiometric and highly crystalline LiCoO2 thin films deposited “in situ” by rf magnetron sputtering. An experimental approach of separating oxygen- and cobalt-derived (final) states by ResPES in the valence-band region is presented. The procedure takes advantage of an antiresonant behavior of cobalt-derived states at the 3p-3d excitation threshold. Information about the unoccupied density of states has been obtained by OK XAS. The structure of the CoL absorption edge is compared to semiempirical charge-transfer multiplet calculations. The experimental results are furthermore compared with band-structure calculations considering three different exchange potentials [generalized gradient approximation (GGA), using a nonlocal Hubbard U (GGA+U) and using a hybrid functional (Becke, three-parameter, Lee-Yang-Parr [B3LYP])]. For these different approaches total density of states and partial valence-band density of states have been investigated. The best qualitative agreement with experimental results has been obtained by using a GGA+U functional with U=2.9eV .
Laboratory Density Functionals
Giraud, B. G.
2007-01-01
We compare several definitions of the density of a self-bound system, such as a nucleus, in relation with its center-of-mass zero-point motion. A trivial deconvolution relates the internal density to the density defined in the laboratory frame. This result is useful for the practical definition of density functionals.
Laboratory Density Functionals
Giraud, B G
2007-01-01
We compare several definitions of the density of a self-bound system, such as a nucleus, in relation with its center-of-mass zero-point motion. A trivial deconvolution relates the internal density to the density defined in the laboratory frame. This result is useful for the practical definition of density functionals.
帕拉米韦分子的密度泛函理论研究%Density Functional Theory Study on Peramivir
Institute of Scientific and Technical Information of China (English)
焉炳飞; 肖翠平; 李文佐; 程建波
2015-01-01
The peramivir molecule is investigated using density functional theory (DFT) method at B3LYP/6-311+G( d, p) level. The stable geometric configuration of peramivir molecule is obtained. The geometric parameters, such as molecular bond lengths, bond angles, and dihedral angles, are calculated. NBO charge analysis and fron-tier molecular orbital analysis are also performed. The solvent effect of the steric structure of peramivir molecule is investigated using H2 O as solvent. In addition, the infrared spectroscopy of peramivir molecule both in gas and in water is simulated. The present results provide theoretical information for further experimental studies.%采用密度泛函理论(DFT)方法,在B3LYP/6-311+G(d, p)水平上对抗流感药物帕拉米韦进行了计算研究。优化得到了帕拉米韦分子的稳定几何构型,计算了分子的键长、键角、二面角等参数,并对其进行了自然电荷分析和前线轨道分析。以H2 O为溶剂研究了溶剂效应对帕拉米韦分子空间结构的影响。理论模拟了帕拉米韦分子在气相和水溶液中的红外光谱,为进一步实验工作提供了理论信息。
Energy Technology Data Exchange (ETDEWEB)
Kullie, Ossama, E-mail: kullie@uni-kassel.de [Institute de Chimie de Strasbourg, CNRS et Université de Strasbourg, Laboratoire de Chimie Quantique, 4 rue Blaise Pascal, 67070 Strasbourg (France); Theoretical Physics, Institute for Physics, Department of Mathematics and Natural Science, University of Kassel (Germany)
2013-03-29
Highlights: ► The achievement of CAMB3LYP functional for excited states in framework of TD-DFT. ► Relativistic 4-components calculations for the excited states of the Cd{sub 2} dimer. ► Relativistic Spin-Free calculations for the excited states of Cd{sub 2} dimer. ► A comparison of the achievements of different types of DFT approximations upon Cd{sub 2}. - Abstract: In this paper we present a time-dependent density functional study for the ground-state as well the 20-lowest laying excited states of the cadmium dimer Cd{sub 2}, we analyze its spectrum obtained from all electrons calculations performed with time-depended density functional for the relativistic Dirac-Coulomb- and relativistic spin-free-Hamiltonian as implemented in DIRAC-PACKAGE. The calculations were obtained with different density functional approximations, and a comparison with the literature is given as far as available. Our result is very encouraging, especially for the lowest excited states of this dimer, and is expected to be enlightened for similar systems. The result shows that only long-range corrected functionals such as CAMB3LYP, gives the correct asymptotic behavior for the higher states. A comparable but less satisfactory results were obtained with B3LYP and PBE0 functionals. Spin-free-Hamiltonian is shown to be very efficient for systems containing heavy elements such as Cd{sub 2} in frameworks of (time-dependent) density functional without introducing large errors.
Density functional studies of endosulphan and its interaction with glycine and GABA
Indian Academy of Sciences (India)
C N Ramachandran; Brijesh Kumar Mishra; Ashwani Kumar Tiwari
2012-01-01
Density functional theoretic (DFT) methods are employed to study the interactions between endosulphan and two amino acids, namely glycine and -aminobutyric acid (GABA). Two conformers of each isomer - and -endosulphan are considered in the study. The DFT methods B3LYP, M05, M05-2X, M06 and M06-2X in conjunction with the basis set 6-31++G∗∗ are used. The complexes of - and -endosulphan with amino acids are stabilized by a strong hydrogen bond. In addition, there are several weak C-H…O interactions present between the two moieties. Among the DFT methods used, M06-2X method shows the highest stabilization energy for all the complexes. The M06-2X/6-31++G∗∗ method predicts that among the four conformers of endosulphan, the conformer in which the S=O points up, forms the most stable complex with both glycine and GABA, with stabilization energies −15.24 kcal/mol and −14.39 kcal/mol, respectively. The conformer in which the S=O points down, forms the least stable complex with both amino acids with stabilization energies −7.14 and −7.85 kcal/mol, respectively.
Oligomeric synthesis and density functional theory of leucoemeraldine base form of polyaniline
Ullah, Rizwan; Ullah, Habib; Shah, Anwar-ul-Haq Ali; Bilal, Salma; Ali, Khurshid
2017-01-01
Oligomeric synthesis of phenyl-end-capped oligoaniline (4PANI LB) has been carried out through a weak oxidizing agent, CuCl2, using chemical oxidative polymerization protocol. The sample was characterized by mass spectrometry, UV-vis, IR, and CHN elemental analysis. The experimental results are counterchecked with the aid of Quantum mechanical calculations such as density functional theory (DFT). DFT at B3LYP/6-31 G (d) level of theory was used for the geometric and electronic properties simulations which also confirm the existence of 4PANI LB. Excellent correlation is observed between the experiment and theory, particularly in the UV-vis spectra which conclude the formation of tetramer (fully reduced form) 4PANI LB (C24H20.06N4.07). Electronic properties such as Ionization Potential (I.P), Electron Affinities (E.A), the coefficient of highest occupied molecular orbital (HOMO), the coefficient of lowest unoccupied molecular orbital (LUMO) of 4PANI LB were evaluated at the above-mentioned level of theory.
Adsorption of parent nitrosamine on the nanocrystaline M-ZSM-5 zeolite: A density functional study
Indian Academy of Sciences (India)
Hossein Roohi; Mahjoubeh Jahantab
2013-11-01
The adsorption of parent nitrosamine (NA) on the Brønsted acid sites of M-ZSM-5 (M = H, Li and Na) zeolites have been investigated via the utilization of 10T cluster model by density functional calculations, at the B3LYP/6-311++G(d,p) level. Two A and B complexes with two types O(N)…M and NH…OZ interactions were predicted from adsorption of nitrosamine on the M-zeolite clusters. The comparison of interaction energies shows that the order of energies for adsorption of NA on the Brønsted acid site of M-ZSM-5 is Na Li < H for the A complexes and Li < H for the B complexes. The calculated adsorption enthalpy of NA on the Brønsted acid site of 10T cluster of M-ZSM-5 catalyst ranges from −14.41 to −52.95 kJ/mol. The acid strength of H-ZSM-5 was found to exceed those of the corresponding to the alkali metal ion-exchanged zeolites. The results reveal that the interaction between hydrogen of NA and OZ of framework is weaker than O(N)…M one. The NH…OZ and O(N)…HZ hydrogen bonds in these complexes are electrostatic and partially covalent in nature, respectively. The results of natural bond orbital (NBO) analysis showed that charge transfer occurs from NA to M-zeolite cluster.
Hydrogen atom addition to the surface of graphene nanoflakes: A density functional theory study
Tachikawa, Hiroto
2017-02-01
Polycyclic aromatic hydrocarbons (PAHs) provide a 2-dimensional (2D) reaction surface in 3-dimensional (3D) interstellar space and have been utilized as a model of graphene surfaces. In the present study, the reaction of PAHs with atomic hydrogen was investigated by means of density functional theory (DFT) to systematically elucidate the binding nature of atomic hydrogen to graphene nanoflakes. PAHs with n = 4-37 were chosen, where n indicates the number of benzene rings. Activation energies of hydrogen addition to the graphene surface were calculated to be 5.2-7.0 kcal/mol at the CAM-B3LYP/6-311G(d,p) level, which is almost constant for all PAHs. The binding energies of hydrogen atom were slightly dependent on the size (n): 14.8-28.5 kcal/mol. The absorption spectra showed that a long tail is generated at the low-energy region after hydrogen addition to the graphene surface. The electronic states of hydrogenated graphenes were discussed on the basis of theoretical results.
Sensato, Fabrício R; Custodio, Rogério; Longo, E; Safont, Vicent S; Andres, Juan
2003-07-25
The molecular mechanism for the oxidation of sulfides to sulfoxides and subsequent oxidation to sulfones by diperoxo, MoO(O(2))(2)(OPH(3)) (I), and monoperoxo, MoO(2)(O(2))(OPH(3)) (II), complexes of molybdenum was studied using density functional calculations at the b3lyp level and the transition state theory. Complexes I and II were both found to be active species. Sulfide oxidation by I or II shows similar activation free energy values of 18.5 and 20.9 kcal/mol, respectively, whereas sulfoxides are oxidized by I (deltaG = 20.6 kcal/mol) rather than by II (deltaG = 30.3 kcal/mol). Calculated kinetic and thermodynamic parameters account for the spontaneous overoxidation of sulfides to sulfones as has been experimentally observed. The charge decomposition analysis (CDA) of the calculated transition structures of sulfide and sulfoxide oxidations revealed that I and II are stronger electrophilic oxidants toward sulfides than they are toward sulfoxides.
Density Functional Theory Study of Atomic Layer Deposition of Zinc Oxide on Graphene.
Ali, Amgad Ahmed; Hashim, Abdul Manaf
2015-12-01
The dissociation of zinc ions (Zn(2+)) from vapor-phase zinc acetylacetonate, Zn(C5H7O2)2, or Zn(acac)2 and its adsorption onto graphene oxide via atomic layer deposition (ALD) were studied using a quantum mechanics approach. Density functional theory (DFT) was used to obtain an approximate solution to the Schrödinger equation. The graphene oxide cluster model was used to represent the surface of the graphene film after pre-oxidation. In this study, the geometries of reactants, transition states, and products were optimized using the B3LYB/6-31G** level of theory or higher. Furthermore, the relative energies of the various intermediates and products in the gas-phase radical mechanism were calculated at the B3LYP/6-311++G** and MP2/6-311 + G(2df,2p) levels of theory. Additionally, a molecular orbital (MO) analysis was performed for the products of the decomposition of the Zn(acac)2 complex to investigate the dissociation of Zn(2+) and the subsequent adsorption of H atoms on the C5H7O2 cluster to form acetylacetonate enol. The reaction energies were calculated, and the reaction mechanism was accordingly proposed. A simulation of infrared (IR) properties was performed using the same approach to support the proposed mechanism via a complete explanation of bond forming and breaking during each reaction step.
Density Functional Theory Study of Red-shifted Hydrogen Bonds of 4-Pyridinemethanol with Water
Institute of Scientific and Technical Information of China (English)
LI Quan; CAI Jing; CHEN Jun-Rong; ZHAO Ke-Qing
2008-01-01
The hydrogen bonds of 1∶1 and 1∶2 complexes formed between 4-pyridinemethanol and water have been investigated using a density functional theory (DFT) method and 6-311++G** basis set, and three and eight stable geometries have been obtained for 1∶1 and 1∶2 complexes, respectively.The interaction energy is -20.536 and -44.256 kJ/mol for the most stable 1∶1 and 1∶2 complexes, respectively, after the basis set superposition error and zero-point corrections.The formation of O-H…N(O) hydrogen bonds makes O-H symmetric stretching modes in the complexes red-shifted relative to those of the monomer.The natural bond orbit analysis indicates that the intermolecular charge transfer between 4-pyridinemethanol and water is 0.02642 e and 0.03813 e for the most stable 1∶1 and 1∶2 complexes, respectively.In addition, TD-B3LYP/6-311++G** calculations show that formation of water-OH…N and water-OH…OH hydrogen bonds makes maximum absorbance wavelength λmax blue-shifted 8-16 nm and red-shifted 4-11 nm compared to that of 4-pyridinemethanol monomer molecule, respectively.
Hartley, Madeline K; Vine, Seanna; Walsh, Elizabeth; Avrantinis, Sara; Daub, G William; Cave, Robert J
2016-03-03
We investigate several representative density functional theory approaches for the calculation of relative activation energies and free energies of a set of model pericyclic reactions, some of which have been studied experimentally. In particular, we use a standard hybrid functional (B3LYP), the same hybrid functional augmented with a basis set superposition error and dispersion correction, a meta-hybrid functional developed to treat transition states and weak interactions (M06-2X), and the recently implemented random phase approximation (RPA) based on Kohn-Sham orbitals from conventional density functional theory by Furche and co-workers. We apply these methods to calculate relative activation energies and estimated free energies for the amide acetal Claisen rearrangement. We focus on relative activation energies to assess the effects of steric and weak interactions in the various methods and compare with experiment where possible. We also discuss the advantages of using this set of reactions as a test bed for the comparison of treatments of weak interactions. We conclude that all methods yield similar trends in relative reactivity, but the RPA yields results in best agreement with the experimental values.
El-Nahas, Ahmed M.; Simmie, John M.; Mangood, Ahmed H.; Hirao, Kimihiko; Song, Jong-Won; Watson, Mark A.; Taketsugu, Tetsuya; Koga, Nobuaki
2015-07-01
The enthalpies of formation for some selected oxygenates have been calculated by the atomisation energy approach using B3LYP, BHandHLYP, MPW3LYP, MPW1K, MPWB1K, BB1K, MPW1B95, BMK, and long-range corrected (LC-ωPBE, LC-BOP, LCgau-BOP, LC-BOP12, LCgau-B97) density functionals, as well as the composite CBS-QB3 method. Compared with experiment, BMK, LC-ωPBE, LCgau-BOP, LC-BOP12, LCgau-B97, MPW195, MPW3LYP functionals and CBS-QB3 give root mean square errors (RMSE) in enthalpies of formation no greater than 4 kcal/mol, whilst MPW1K and BHandHLYP show much worse performance (RMSE of 20-40 kcal/mol). The B3LYP, MPWB1K, and BB1K results fall between the two extremes. Energy barriers for the dominant paths in the unimolecular decomposition of simple esters (HCO2CH3, C2H5CO2C2H5), C1-C3 acids, and 1-butanol are reproduced well by CBS-QB3, BMK, BB1K, LCgau-B97, and PW1B95 (RMSE = 1-2 kcal/mol), while other LC methods (LC-ωPBE, LC-BOP, LCgau-BOP, and LC-BOP12) show a deviation of up to 4 kcal/mol. For the ionisation potentials, calculated from Koopman's theorem, all of the investigated LC-methods give good results compared with other density functional theory functionals with a maximum deviation of 0.4 eV, except for LCgau-B97, which has an RMSE of 0.7 eV.
Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman
2008-04-24
We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results
Ghadar, Yasaman; Clark, Aurora E
2012-02-07
The interaction potentials between immiscible polar and non-polar solvents are a major driving force behind the formation of liquid:liquid interfaces. In this work, the interaction energy of water-pentane dimer has been determined using coupled-cluster theory with single double (triple) excitations [CCSD(T)], 2nd order Möller Plesset perturbation theory (MP2), density fitted local MP2 (DF-LMP2), as well as density functional theory using a wide variety of density functionals and several different basis sets. The M05-2X exchange correlation functionals exhibit excellent agreement with CCSD(T) and DF-LMP2 after taking into account basis set superposition error. The gas phase water-pentane interaction energy is found to be quite sensitive to the specific pentane isomer (2,2-dimethylpropane vs. n-pentane) and relative orientation of the monomeric constituents. Subsequent solution phase cluster calculations of 2,2-dimethylpropane and n-pentane solvated by water indicate a positive free energy of solvation that is in good agreement with available experimental data. Structural parameters are quite sensitive to the density functional employed and reflect differences in the two-body interaction energy calculated by each method. In contrast, cluster calculations of pentane solvation of H(2)O solute are found to be inadequate for describing the organic solvent, likely due to limitations associated with the functionals employed (B3LYP, BHandH, and M05-2X).
Dutton, Andrew S; Suhrada, Christopher P; Miranda, Katrina M; Wink, David A; Fukuto, Jon M; Houk, K N
2006-03-20
Isopropylamine diazeniumdiolate, IPA/NO, the product of the reaction of isopropylamine and nitric oxide, NO, decomposes in a pH-dependent manner to afford nitroxyl, HNO, in the pH range of 13 to above 5, and NO below pH 7. Theoretical studies using B3LYP/6-311+G(d) density functional theory, the polarizable continuum and conductor-like polarizable continuum solvation models, and the high-accuracy CBS-QB3 method on the simplified model compound methylamine diazeniumdiolate predict a mechanism involving HNO production via decomposition of the unstable tautomer MeNN+(O-)NHO-. The production of NO at lower pH is predicted to result from fragmentation of the amide/NO adduct upon protonation of the amine nitrogen.
Dutton, Andrew S.; Suhrada, Christopher P.; Miranda, Katrina M.; Wink, David A.; Fukuto, Jon M.; Houk, K. N.
2011-01-01
Isopropylamine diazeniumdiolate, IPA/NO, the product of the reaction of isopropylamine and nitric oxide, NO, decomposes in a pH dependent manner to afford nitroxyl, HNO, in the pH range of 13 to above 5 and NO below pH 7. Theoretical studies using B3LYP/6-311+G(d) density functional theory, the PCM and CPCM solvation models and the high accuracy CBS-QB3 method on the simplified model compound, methylamine diazeniumdiolate, predict a mechanism involving HNO production via decomposition of the unstable tautomer MeNN+(O−)NHO−. The production of NO at lower pH is predicted to result from fragmentation of the amide/NO adduct upon protonation of the amine nitrogen. PMID:16529464
Engel, J
2006-01-01
The Hohenberg-Kohn theorem and Kohn-Sham procedure are extended to functionals of the localized intrinsic density of a self-bound system such as a nucleus. After defining the intrinsic-density functional, we modify the usual Kohn-Sham procedure slightly to evaluate the mean-field approximation to the functional, and carefully describe the construction of the leading corrections for a system of fermions in one dimension with a spin-degeneracy equal to the number of particles N. Despite the fact that the corrections are complicated and nonlocal, we are able to construct a local Skyrme-like intrinsic-density functional that, while different from the exact functional, shares with it a minimum value equal to the exact ground-state energy at the exact ground-state intrinsic density, to next-to-leading order in 1/N. We briefly discuss implications for real Skyrme functionals.
Directory of Open Access Journals (Sweden)
Sérgio Ricardo de Lázaro
2005-02-01
Full Text Available Calculations based on density functional theory at the B3LYP hybrid functional level applied to periodic models have been performed to characterize the structural and electronic properties of PbTiO3. Two different slab terminations (PbO and TiO2 have been considered to obtain and discuss the results of band structure, density of states, charge distribution on bulk and surface relaxation. It is observed that the relaxation processes are most prominent for the Ti and Pb surface atoms. The electron density maps confirm the partial covalent character of the Ti-O bonds. The calculated optical band gap and other results are in agreement with experimental data.
Ulian, Gianfranco; Valdrè, Giovanni
2015-02-01
The knowledge of the P, T behavior of talc is very important in mineralogical-petrological and geophysical research fields because talc can be considered a hydrous phase that can recycle water into the Earth's mantle and also an important mineral in both industrial and technological applications. However, very few works have been presented to fully characterize the thermodynamic properties of this mineral, especially at atomic scale. In a previous work, we modeled the structural and mechanical properties of talc using the B3LYP-D* hybrid density functional, which included a correction for the dispersive forces and all-electron Gaussian-type orbital basis sets. The results were in good agreement with single-crystal X-ray and neutron diffraction experimental data. Here, we extend the investigation to the thermochemical and thermophysical properties of talc using the same density functional approach and the quasi-harmonic approximation, providing the thermal equation of state, the heat capacity and the entropy of the mineral at different P, T conditions.
Vélez, Ederley; Alberola, Antonio; Polo, Víctor
2009-12-17
The magnetic exchange coupling constants between two Mn(II) centers for a set of five inverse crown structures have been investigated by means of a methodology based on broken-symmetry unrestricted density functional theory. These novel and highly unstable compounds present superexchange interactions between two Mn centers, each one with S = 5/2 through anionic "guests" such as oxygen, benzene, or hydrides or through the cationic ring formed by amide ligands and alkali metals (Na, Li). Magnetic exchange couplings calculated at B3LYP/6-31G(d,p) level yield strong antiferromagnetic couplings for compounds linked via an oxygen atom or hydride and very small antiferromagnetic couplings for those linked via a benzene molecule, deprotonated in either 1,4- or 1,3- positions. Analysis of the magnetic orbitals and spin polarization maps provide an understanding of the exchange mechanism between the Mn centers. The dependence of J with respect to 10 different density functional theory potentials employed and the basis set has been analyzed.
Yildirim, G; Senol, S D; Dogruer, M; Ozturk, O; Senol, A; Tasci, A T; Terzioglu, C
2012-01-01
This study reports the optimized molecular structures, vibrational frequencies including Infrared intensities and Raman activities, corresponding vibrational assignments, (1)H and (13)C NMR chemical shifts, the magnitudes of the JCH and JCC coupling constants, Ultraviolet-visible (UV-vis) spectra, thermodynamic properties and atomic charges of the title compounds, α,α,α-trifluoro-3, -p and o-nitrotoluene, in the ground state by means of the density functional theory (DFT) with the standard B3LYP/6-311++G(d,p) method and basis set combination for the first time. Theoretical vibrational spectra were interpreted by normal coordinate analysis based on scaled density functional force field. The results show that the vibrational frequencies and chemical shifts calculated were obtained to be in good agreement with the experimental data. Based on the comparison between experimental results and theoretical data, the calculation level chosen is powerful approach for understanding the identification of all the molecules studied. In addition, not only were frontier molecular orbitals (HOMO and LUMO), molecular electrostatic potential (MEP) and electrostatic potential (ESP) simulated but also the dipole moment, softness, electronegativity, chemical hardness, electrophilicity index, transition state and energy band gap values were predicted. According to the investigations, all compounds were found to be useful to bond metallically and interact intermolecularly; however, the thermodynamic properties confirm that the α,α,α-trifluoro-p-nitrotoluene was more reactive and more polar than the others.
Yildirim, G.; Senol, S. D.; Dogruer, M.; Ozturk, O.; Senol, A.; Tasci, A. T.; Terzioglu, C.
2012-01-01
This study reports the optimized molecular structures, vibrational frequencies including Infrared intensities and Raman activities, corresponding vibrational assignments, 1H and 13C NMR chemical shifts, the magnitudes of the JCH and JCC coupling constants, Ultraviolet-visible (UV-vis) spectra, thermodynamic properties and atomic charges of the title compounds, α,α,α-trifluoro-3, -p and o-nitrotoluene, in the ground state by means of the density functional theory (DFT) with the standard B3LYP/6-311++G(d,p) method and basis set combination for the first time. Theoretical vibrational spectra were interpreted by normal coordinate analysis based on scaled density functional force field. The results show that the vibrational frequencies and chemical shifts calculated were obtained to be in good agreement with the experimental data. Based on the comparison between experimental results and theoretical data, the calculation level chosen is powerful approach for understanding the identification of all the molecules studied. In addition, not only were frontier molecular orbitals (HOMO and LUMO), molecular electrostatic potential (MEP) and electrostatic potential (ESP) simulated but also the dipole moment, softness, electronegativity, chemical hardness, electrophilicity index, transition state and energy band gap values were predicted. According to the investigations, all compounds were found to be useful to bond metallically and interact intermolecularly; however, the thermodynamic properties confirm that the α,α,α-trifluoro-p-nitrotoluene was more reactive and more polar than the others.
DFT study on the covalent adsorption of drug carvedilol onto COOH functionalized carbon nanotubes
Directory of Open Access Journals (Sweden)
M. Rahbar
2015-09-01
Full Text Available In this work, using quantum mechanics, the interaction of drug carvedilol with (5, 5 COOH functionalized single wall carbon nanotubes (SWNT have been studied. All of the calculations have been performed using a hybrid density functional method (B3LYP in gas and solution phases. Two possible modes of covalent interaction of carvedilol onto COOH functionalized SWNT were investigated. Quantum molecular descriptors and frontier orbital analysis in the drug-nanotube systems were studied. It was found that bonding of carvedilol to COOH functionalized carbon nanotubes through hydroxyl group is stronger than amino group.
Water cluster anions studied by the long-range corrected density functional theory.
Yagi, Kiyoshi; Okano, Yuko; Sato, Takeshi; Kawashima, Yukio; Tsuneda, Takao; Hirao, Kimihiko
2008-10-09
Long-range corrected density functional theory (LC-DFT) is applied to a series of small water cluster anions(n= 2-6) to compute their vertical detachment energies (VDEs). The LC scheme is shown to eliminate an unphysical overestimation of the electron-water attraction in the hybrid functional by properly accounting for the long-range exchange repulsions. It is shown that a correct correlation energy behavior for a rapidly varying density is also important for describing a spatially extent, excess electron. The one-parameter progressive (OP) correlation functional, which satisfies this condition, leads to a remarkable improvement in the calculated VDE over the conventional one. The LC-BOP method produces highly accurate VDEs with a mean absolute deviation of 13.8 meV from the reference CCSD(T) results, reducing the error of B3LYP by more than 15 times. LC-BOP is found to be more accurate than MP2 which yields an excess electron underbound by 43.6 meV. The effect of basis sets on the calculated VDE is also examined. The aug-cc-pVDZ basis set with an extra diffuse function is found to be more accurate and reliable than the extended Pople-type basis sets used in the previous works. The extrapolation of the calculated VDE of different electron binding motifs is compared with the VDEs of experimentally observed three isomers (Verlet, J. R. R.; Bragg,A. E.; Kammrath, A.; Cheshnovsky, O.; Neumark, D. M. Science 2005, 307, 93).
Energy Technology Data Exchange (ETDEWEB)
Nishimura, Yoshifumi [Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China); Lee, Yuan-Pern [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan (China); Irle, Stephan [Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Witek, Henryk A., E-mail: hwitek@mail.nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China)
2014-09-07
Vibrational infrared (IR) spectra of gas-phase O–H⋅⋅⋅O methanol clusters up to pentamer are simulated using self-consistent-charge density functional tight-binding method using two distinct methodologies: standard normal mode analysis and Fourier transform of the dipole time-correlation function. The twofold simulations aim at the direct critical assignment of the C–H stretching region of the recently recorded experimental spectra [H.-L. Han, C. Camacho, H. A. Witek, and Y.-P. Lee, J. Chem. Phys. 134, 144309 (2011)]. Both approaches confirm the previous assignment (ibid.) of the C–H stretching bands based on the B3LYP/ANO1 harmonic frequencies, showing that ν{sub 3}, ν{sub 9}, and ν{sub 2} C–H stretching modes of the proton-accepting (PA) and proton-donating (PD) methanol monomers experience only small splittings upon the cluster formation. This finding is in sharp discord with the assignment based on anharmonic B3LYP/VPT2/ANO1 vibrational frequencies (ibid.), suggesting that some procedural faults, likely related to the breakdown of the perturbational vibrational treatment, led the anharmonic calculations astray. The IR spectra based on the Fourier transform of the dipole time-correlation function include new, previously unaccounted for physical factors such as non-zero temperature of the system and large amplitude motions of the clusters. The elevation of temperature results in a considerable non-homogeneous broadening of the observed IR signals, while the presence of large-amplitude motions (methyl group rotations and PA-PD flipping), somewhat surprisingly, does not introduce any new features in the spectrum.
Modelling excited states of weakly bound complexes with density functional theory.
Briggs, Edward A; Besley, Nicholas A
2014-07-28
The binding within the ethene-argon and formaldehyde-methane complexes in the ground and electronically excited states is studied with equation of motion coupled cluster theory (EOM-CCSD), second-order Møller-Plesset perturbation theory (MP2) and density functional theory with dispersion corrections (DFT-D). Electronically excited states are studied within MP2 and Kohn-Sham DFT formalisms by exploiting a procedure called the maximum overlap method that allows convergence of the relevant self-consistent field equations to higher energy (or excited state) solutions. Potential energy curves computed using MP2 are in good agreement with the EOM-CCSD calculations for both the valence and Rydberg excited states studied. For the DFT-D approach, B3LYP-D3/aug-cc-pVTZ calculations are found to be in agreement with EOM-CCSD for the ground and valence excited states. However, for the π3s Rydberg state of ethene-argon and the n3s Rydberg state of formaldehyde-methane significant deviation is observed, and this disagreement with EOM-CCSD is present for a variety of DFT-D based approaches. Variation of the parameters within the D2 dispersion correction results in closer agreement with EOM-CCSD for the Rydberg states but demonstrates that a different parameterisation from the ground state is required for these states. This indicates that time-dependent density functional theory calculations based upon a DFT-D reference may be satisfactory for excitations to valence states, but will potentially be inaccurate for excitations to Rydberg states, or more generally states where the nature of the electron density is significantly different from the ground state.
Directory of Open Access Journals (Sweden)
Shahla Hamedani
2015-03-01
Full Text Available In this study, we studied the adsorption behavior of folic acid on the (5,0 zigzag and (5,5 armchair single-walled carbon nanotube (SWCNT by Density Functional Theory (DFT. Geometry optimizations were carried out at the B3LYP/6-31 G* level of theory using the Gaussian 09 suite of programs. The adsorption energies, the quantum molecular descriptors analysis and the structural changes at the adsorption site are indicative of chemisorption (adsorption energy -31.673 kcal/mol on the zigzag SWCNT surface, while the adsorption is physical (adsorption energy -9.70 kcal/mol in nature on the armchair SWCNT surface. The density of the states (DOS Plots, Natural bond orbital (NBO analysis, and HOMO and LUMO are witness to the substantial changes in the electronic properties of the SWCNT systems after the attachment adsorbed species with the tube surface. These results are extremely relevant in order to diagnosis the potential applications of carbon nanotubes as drug delivery systems.
Institute of Scientific and Technical Information of China (English)
2008-01-01
Ionic dissociation of chlorosulfonic acid (HSO3Cl) in the molecular clusters HSO3Cl-(H2O)n (n = 1-4) and HSO3Cl-NH3-(H2O)n (n = 0-3) was investigated by density functional theory and ab initio molecular orbital theory. The equilibrium structures, binding energies, and thermodynamic properties, such as relative enthalpy and relative Gibbs free energy, and were calculated using the hybrid density func- tional (B3LYP) method and the second order M?ller-Plesset approximation (MP2) method with the 6-311++G** basis set. Chlorosulfonic acid was found to require a minimum of three water molecules for ionization to occur and at least one water molecule to protonate ammonia. The corresponding clusters with fewer water molecules were found to be strongly hydrogen-bonded. The related properties and acid strength of chlorosulfonic acid were discussed and compared to the acid strengths of perchloric acid and sulfuric acid in the context of clusters with ammonia and water. The relative stabilities of these clusters were also investigated.
Fonseca, Matheus C.; Nascimento, Clebio S.; Borges, Keyller B.
2016-02-01
The purpose of this Letter was to study for the first time the interaction process of tramadol (TRM) with distinct functional monomers (FM) in the formation of molecular imprinted polymer (MIP), using density functional theory (DFT) calculations at B3LYP/6-31G(d,p). As result we were able to establish that the best MIP synthesis conditions are obtained with acrylic acid as FM in 1:3 molar ratio and with chloroform as solvent. This condition presented the lowest stabilization energy for the pre-polymerization complexes. Besides, the intermolecular hydrogen bonds found between the template molecule and functional monomers play a primary role to the complex stability.
Sproviero, Eduardo M
2017-02-20
We present a theoretical study of the reaction pathway for dioxygen molecular formation catalyzed by the [(terpy)(H2O)Mn(III)(O)2Mn(IV)(OH2) (terpy)](NO3)3 (terpy=2,2':6',2″-terpyridine) complex based on DFT-B3LYP calculations. In the initial state of the reaction, a partial oxido radical (0.44 spins) is formed ligated to Mn. This radical is involved in a nucleophylic attack by bulk water in the OO bond reaction formation step, in which the oxido fractional unpaired electron is delocalized toward the outermost Mn of the μ-oxo bridge, instead of the ligated Mn center. The reaction then follows with a series of proton-coupled electron transfer steps, in which the oxidation state, as well as the bond strength of the OO moiety increase, while the OOMn(1) bond gets weaker until O2 is released. In this model, basic acetate ions from the buffer solution capture protons in the proton-transfer steps. In each step there is reduction of the OOMn(1) binding strength, with concomitant increase of the OO bond strength, which culminates with the release of O2 in the last step. This last step is entropy driven, while formation of hydroperoxide and superoxide moieties is enthalpy driven. According with experiments, the rate-limiting step is the double oxidation of Mn(IV,III) or peroxymonosulfate binding, which occur prior to the OO bond formation step. This supports our findings that the barriers of all intermediate steps are below the experimental barrier of 19-21kcal/mol. The implications of these findings for understanding photosynthetic water-splitting catalysis are also discussed.
Weber, Valéry; Tymczak, Christopher J; Challacombe, Matt
2006-06-14
The application of theoretical methods based on density-functional theory is known to provide atomic and cell parameters in very good agreement with experimental values. Recently, construction of the exact Hartree-Fock exchange gradients with respect to atomic positions and cell parameters within the Gamma-point approximation has been introduced. In this article, the formalism is extended to the evaluation of analytical Gamma-point density-functional atomic and cell gradients. The infinite Coulomb summation is solved with an effective periodic summation of multipole tensors. While the evaluation of Coulomb and exchange-correlation gradients with respect to atomic positions are similar to those in the gas phase limit, the gradients with respect to cell parameters needs to be treated with some care. The derivative of the periodic multipole interaction tensor needs to be carefully handled in both direct and reciprocal space and the exchange-correlation energy derivative leads to a surface term that has its origin in derivatives of the integration limits that depend on the cell. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm to optimize one-dimensional and three-dimensional periodic systems at the density-functional theory and hybrid Hartree-Fock/density-functional theory levels. We also report the full relaxation of forsterite supercells at the B3LYP level of theory.
Shi, Haifeng; Lan, Benyue; Zhang, Chengliang; Ye, Enjia; Nie, Yanguang; Bian, Baoan
2016-10-01
The influences of a series of anion doping on the electronic structures of sodium niobate (NaNbO3) have been systematically investigated by density functional theory (DFT) calculations with the hybrid B3LYP functional. As for B(C,P)-doped NaNbO3, the isolated B 2p (C 2p, P 3p) states were formed above the valence band maximum (VBM) of NaNbO3, which were too weak to mix with O 2p states and thus produced band gap narrowing. While the band gap of NaNbO3 was slightly narrowed after F doping. As for S-doped NaNbO3, the S 3p states mixed with O 2p states well and thus reduced the band gap energy. According to the calculation results, we tentatively put forward that S doping would be appropriate for single anion doping NaNbO3, while the B(C,P) elements would be suitable candidates for co-doping NaNbO3.
Energy Technology Data Exchange (ETDEWEB)
Dimakis, N; Mion, T [Department of Physics and Geology, University of Texas-Pan American, Edinburg, TX 78539 (United States); Bunker, G, E-mail: dimakis@utpa.ed [Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616 (United States)
2009-11-15
We present an accurate and efficient technique for calculating thermal X-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) applicable to crystalline materials. Using Density Functional Theory on a 3x3x3 supercell pattern of MnO structure, under the nonlocal hybrid B3LYP functional paired with Gaussian local basis sets, we obtain the normal mode eigenfrequencies and eigenvectors; these parameters are in turn used to calculate single and multiple scattering XAFS DWFs. The DWFs obtained via this technique are temperature dependent expressions and can be used to substantially reduce the number of fitting parameters, when experimental spectra are fitted with a hypothetical structure. The size of the supercell size limits the R-space range that these parameters could be used. Therefore corresponding DWFs for paths outside of this range are calculated using the correlated Debye model. Our method is compared with prior cluster calculations and with corresponding values obtained from fitting experimental XAFS spectra on manganosite with simulated spectra.
Espinosa-Torres, Néstor D; la Luz, David Hernández-de; Flores-Gracia, José Francisco J; Luna-López, José A; Martínez-Juárez, Javier; Vázquez-Valerdi, Diana E
2014-01-01
In systems in atomic scale and nanoscale such as clusters or agglomerates constituted by particles from a few to less than 100 atoms, quantum confinement effects are very important. Their optical and electronic properties are often dependent on the size of the systems and the way in which the atoms in these clusters are bonded. Generally, these nanostructures display optical and electronic properties significantly different to those found in corresponding bulk materials. Silicon agglomerates embedded in silicon rich oxide (SRO) films have optical properties, which have been reported to be directly dependent on silicon nanocrystal size. Furthermore, the room temperature photoluminescence (PL) of SRO has repeatedly generated a huge interest due to its possible applications in optoelectronic devices. However, a plausible emission mechanism has not been widely accepted in the scientific community. In this work, we present a short review about the experimental results on silicon nanoclusters in SRO considering different techniques of growth. We focus mainly on their size, Raman spectra, and photoluminescence spectra. With this as background, we employed the density functional theory with a functional B3LYP and a basis set 6-31G* to calculate the optical and electronic properties of clusters of silicon (constituted by 15 to 20 silicon atoms). With the theoretical calculation of the structural and optical properties of silicon clusters, it is possible to evaluate the contribution of silicon agglomerates in the luminescent emission mechanism, experimentally found in thin SRO films.
Thicoipe, Sandrine; Carbonniere, Philippe; Pouchan, Claude
2013-08-15
This study presents structural properties of microhydrated nucleic acid bases (NABs) - uracil (U), thymine (T), guanine (G), adenine (A), and cytosine (C) - investigated by theoretical computations at the B3LYP level of theory. To obtain the different representations of these microhydrated species, we applied the GSAM procedure: the most stable conformers labeled X,nH2O (X = U, T, G, A and n = 1...5) for which the Boltzmann population is higher than 2% at 298K are calculated at the B3LYP and B3LYP-D levels of theory. At the B3LYP level, our calculated geometries are compared with those obtained in the literature. New physically relevant isomers are found with the GSAM algorithm, especially for the tetra- and pentahydrated species. The use of DFT-D functional does not strongly modify the relative energies of the isomers for the monohydrated species. When the number of water molecules increases, the results become extremely sensitive to the consideration of dispersion contributions.
[The Study on Infrared Spectra of 7-Hydroxycoumarin by Density Functional Theory].
Jia, Fei-yun; Su, Yu; Ran, Ming; Zhu, Jiang; Zhang, Bo
2016-01-01
Infrared spectroscopy is an important source of information for the identification of the compounds structure and it is great significant for biological activity research of natural and organic drug molecules. With the theoretical calculation method is more reasonable and calculation accuracy continues to improve, Theoretical calculate advantage is more obvious in the infrared spectrum simulation and vibration modes attributable identified. And it has important reference value for experimental study of infrared spectral analysis. Using density functional theory, geometry optimizations and frequencies calculation of 7-Hydroxycoumarin were performed at the level of B3LYP/6-311G(d, p), the stable structure and all vibration modes of 7-Hydroxycoumarin were attained. The results show that the infrared absorption peak of 7-hydroxycoumarin is mainly distributed in the several regions in wave number of 3 700-3 500, 3 150-3 000, 1 750-1 400, 1 400-1 000, 1 000-50 cm(-1). In addition to the vibration in a wave number range of 3 700-3 500, 3 150-3 000 cm(-1) is relatively independent, and were attributed to OH stretching vibration and benzene ring CH stretching vibration, the other several vibration regions are more complex, the different degree of spectral peaks is composed of multiple vibration modes. Finally, based on the theoretical analysis of the vibration mode, the vibration modes of 7-Hydroxycoumarin molecule were assigned, and in order to discuss the reliability of theoretical calculation method, the correlation diagram of the main absorption peak of 7-hydroxyl group was drawn from the theoretical value of X axis and the experimental value of Y axis, the correlation between experimental IR data and calculated IR data of 7-Hydroxycoumarin was analyzed through the linear regression method. Results show that they have good correlation, correlation coefficient values "r" equals 0.998 5, and the theory calculation of 7-Hydroxycoumarin IR by density functional theory at
Institute of Scientific and Technical Information of China (English)
苏现想; 刘成虎; 吴振
2012-01-01
The stable geometries of room temperature ionic liquid l-ethyl-3-methyl-imidazole tetrafluoroborate { [Emim] BF4} and its composite with water { [Emim]BF4-H2O} as well as the interaction energies between [Emiin]BF4 and H2O were investigated by density functional theory (DFT) at the B3LYP/6-31 +G(d, p) level. The infrared (IR) spectra for the most stable [Emirn]BF4 and its complex with H2O were obtained through analyzing the vibrational frequency. The computed results indicate that the interaction between water and anion has more obviJ ous influence on the structure of the ionic liquid than the interaction between water with cation. In the meantime, the experimentally measured IR spectrum of []EmimJ BF4 ionic liquid well conforms to the computed one.%采用量子化学计算中的密度泛函理论(DFT),在B3LYP/6-31+ G(d,p)计算水平上研究了离子液体1-乙基-3-甲基咪唑四氟硼酸盐([Emim]BF4)及其与水分子形成的复合物的稳定构型和相互作用能；经振动频率分析得到了[Emim]BF4及其与水的复合物的红外光谱.计算结果表明,相对于水分子与阳离子的作用而言,水 分子与阴离子的作用对离子液体结构的影响更大.与此同时,实验测得的[Emim]BF4的红外光谱与计算结果吻合.
Nemykin, Victor N; Hadt, Ryan G
2006-10-01
Influence of molecular geometry, type of exchange-correlation functional, and contraction scheme of basis set applied at the iron nuclei have been tested in the calculation of 57Fe Mössbauer isomer shifts and quadrupole splittings for a wide range of ligand types, as well as oxidation and spin states, in inorganic and organometallic systems. It has been found that uncontraction of the s-part of Wachter's full-electron basis set at the iron nuclei does not appreciably improve the calculated isomer shifts. The observed correlations for all tested sets of geometries are close to each other and predominantly depend on the employed exchange-correlation functional with B3LYP functional being slightly better as compared to BPW91. Both hybrid (B3LYP) and pure (BPW91) exchange-correlation functionals are suitable for the calculation of isomer shifts in organometallic compounds. Surprisingly, it has been found that the hybrid B3LYP exchange-correlation functional completely fails in accurate prediction of quadrupole splittings in ferrocenes, while performance of the pure BPW91 functional for the same systems was excellent. This observation has been explained on the basis of relationship between the amount of Hartree-Fock exchange involved in the applied exchange-correlation functional and the calculated HOMO-LUMO energy gap in ferrocenes. On the basis of this explanation, use of only pure exchange-correlation functionals has been suggested for accurate prediction of Mössbauer spectra parameters in ferrocenes.
Partition density functional theory
Nafziger, Jonathan
Partition density functional theory (PDFT) is a method for dividing a molecular electronic structure calculation into fragment calculations. The molecular density and energy corresponding to Kohn Sham density-functional theory (KS-DFT) may be exactly recovered from these fragments. Each fragment acts as an isolated system except for the influence of a global one-body 'partition' potential which deforms the fragment densities. In this work, the developments of PDFT are put into the context of other fragment-based density functional methods. We developed three numerical implementations of PDFT: One within the NWChem computational chemistry package using basis sets, and the other two developed from scratch using real-space grids. It is shown that all three of these programs can exactly reproduce a KS-DFT calculation via fragment calculations. The first of our in-house codes handles non-interacting electrons in arbitrary one-dimensional potentials with any number of fragments. This code is used to explore how the exact partition potential changes for different partitionings of the same system and also to study features which determine which systems yield non-integer PDFT occupations and which systems are locked into integer PDFT occupations. The second in-house code, CADMium, performs real-space calculations of diatomic molecules. Features of the exact partition potential are studied for a variety of cases and an analytical formula determining singularities in the partition potential is derived. We introduce an approximation for the non-additive kinetic energy and show how this quantity can be computed exactly. Finally a PDFT functional is developed to address the issues of static correlation and delocalization errors in approximations within DFT. The functional is applied to the dissociation of H2 + and H2.
Density Functional Method Studies of X-H (X=C, N, O, Si, P, S) Bond Dissociation Energies
Institute of Scientific and Technical Information of China (English)
FU Yao; DONG Xiao-Yu; WANG Yi-Min; LIU Lei; GUO Qing-Xiang
2005-01-01
The performances of the density functional theory (DFT) methods in calculating X-H bond dissociation energies (BDE, X=C, N, O, Si, P, S) were evaluated. It was found that most DFT methods including B3LYP, B3PW91,G96LYP, PBE1PBE and BH&HLYP significantly underestimated the X-H BDE by as much as 13-24 kJ/mol.The underestimation is not due to the use of finite basis set, because the DFT methods still significantly underestimate the X-H BDE with the complete basis set. Therefore, these DFT methods can not be used to calculate the BDE directly. Nevertheless, the B3P86 method shows very small underestimation for the X-H BDE. Further analysis suggests that there be no advantage for using the restricted open-shell DFT methods. The unrestricted DFT methods actually perform slightly better than the restricted open-shell DFT methods in most cases. Finally, it was found that the underestimation by the DFT methods was largely systematic. The use of the calibrated UDFT/6-311+ + G(d, p) method was recommended to calculate the X-H BDE.
Baker, Alexander B; Samet, Cindy; Lyon, Jonathan T; Andrews, Lester
2005-09-22
Hydrogen-bonded complexes of pentachlorocyclopropane with the bases acetonitrile, ammonia, monomethylamine, and dimethylamine have been isolated and characterized for the first time in argon matrices at 16 K. Coordination of the proton of pentachlorocyclopropane (Pccp) to the electron donor (N) of the base was evidenced by red shifts of the CH stretching mode. These shifts, which range from 22 to 170 cm(-1), increase in the order CH3CN, NH3, (CH3)NH2, and (CH3)2NH. Density functional theory (DFT) calculations at the B3LYP level agree well with experiment and support the formation of 1:1 complexes of Pccp/base. Distinct changes were observed in ring modes as well as CCl and CCl2 modes. The hydrogen bond energy of the complexes varies from 2.95 to 4.22 kcal/mol and is stronger than our previously studied bromocyclopropane-ammonia complex (2.35 kcal/mol, MP2).
Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama
2013-12-01
Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.
Institute of Scientific and Technical Information of China (English)
刘伟龙; 王志刚; 郑植仁; 蒋礼林; 杨延强; 赵连城; 苏文辉
2012-01-01
The molecular structural and Raman spectroscopic characteristics of fl-carotene and lycopene are investigated by density functional calculations. The effects of molecular structure and solvent environment on the Raman spectra are analyzed by comparing the calculated and measured results. It is found that the B3LYP/6-31G(d) method can predict the reasonable result for β-carotene, but the vl Raman activities of lycopene overflow at all the used theo- retical methods because of the longer conjugation length in β-carotene impedes the delocalization of ~r-electrons The calculated results indicate that the rotation of β-rings shortens the effective conjugation length, and results in higher frequency and lower activity of the vl mode in /q-carotene than lycopene. The measured vl bands of β-carotene and lycopene shift respectively to higher and lower frequencies in solution compared with that in crystals since the crystal packing forces can lead to different conformational variations in the carotenoids molecules. The polarized continuum model theoretical analysis suggests that solvent has slight (significant) effects on the Raman frequencies (intensities) of both carotenoids.
Indian Academy of Sciences (India)
Shamoon Ahmad Siddiqui; Tabish Rasheed; Nadir Bouarissa
2013-08-01
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 6.95 eV for RuF6. Its stability and reactivity were also examined by using HOMO–LUMO gap, molecular orbital analysis and binding energy of these clusters. It is found that energy required for dissociation of F2 molecules are higher than energy required for dissociation of F atoms. The unusual properties are attributed to the involvement of inner shell 4-electrons, which not only allow RuF clusters to belong to the class of superhalogens but also show that its valence can exceed the nominal value of 1. The interaction of RuF4 superhalogen with an alkali atom lithium (Li) were also studied which suggests that a new class of salt can be synthesized by reacting RuF4 with Li.
Islam, Nasarul; Niaz, Saba; Manzoor, Taniya; Pandith, Altaf Hussain
2014-10-01
The density functional theoretical (DFT) computations were performed at the B3LYP/6-311G++(d, p) level to calculate the equilibrium geometry, vibrational wave numbers, intensities, and various other molecular properties of brucine and strychnine, which were found in satisfactory agreement with the experimental data. The out-of-phase stretching modes of aromatic rings and carbonyl stretching modes in combination with CH stretching modes at stereogenic centers generate VCD signals, which are remarkably efficient configuration markers for these chiral molecular systems. NBOs analysis reveals that the large values of second order perturbation energy (47.24 kcal/mol for brucine and 46.93 kcal/mol for strychnine) confirms strong hyperconjugative interaction between the orbital containing the lone pair of electron of nitrogen and the neighboring Cdbnd O antibonding orbital. The molecular electrostatic potential map of strychnine molecule, with no polar groups other than the lone keto group, shows less polarization, which accounts for its lower susceptibility towards electrophilic attack as compared to brucine.
Islam, Nasarul; Niaz, Saba; Manzoor, Taniya; Pandith, Altaf Hussain
2014-10-15
The density functional theoretical (DFT) computations were performed at the B3LYP/6-311G++(d, p) level to calculate the equilibrium geometry, vibrational wave numbers, intensities, and various other molecular properties of brucine and strychnine, which were found in satisfactory agreement with the experimental data. The out-of-phase stretching modes of aromatic rings and carbonyl stretching modes in combination with CH stretching modes at stereogenic centers generate VCD signals, which are remarkably efficient configuration markers for these chiral molecular systems. NBOs analysis reveals that the large values of second order perturbation energy (47.24kcal/mol for brucine and 46.93kcal/mol for strychnine) confirms strong hyperconjugative interaction between the orbital containing the lone pair of electron of nitrogen and the neighboring CO antibonding orbital. The molecular electrostatic potential map of strychnine molecule, with no polar groups other than the lone keto group, shows less polarization, which accounts for its lower susceptibility towards electrophilic attack as compared to brucine.
Wang, Yi-Siang; Chao, Sheng D
2011-03-10
We have calculated the structural and energetic properties of neutral and ionic (singly charged anionic and cationic) semiconductor binary silicon-germanium clusters Si(m)Ge(n) for s = m + n ≤ 12 using the density functional theory (DFT-B3LYP) and coupled cluster [CCSD(T)] methods with Pople's 6-311++G(3df, 3pd) basis set. Neutral and anionic clusters share similar ground state structures for s = 3-7, independent of the stoichiometry and atom locations, but start to deviate at s = 8. The relative energetic stability of the calculated ground state structures among possible isomers has been analyzed through a bond strength propensity model where the pair interactions of Si-Si, Si-Ge, and Ge-Ge are competing. Electron affinities, ionization potentials, energy gaps between the highest and lowest occupied molecular orbitals (HOMO-LUMO gaps), and cluster mixing energies were calculated and analyzed. Overall, for a fixed s, the vertical ionization potential increases as the number of silicon atoms m increases, while the vertical electron affinity shows a dip at m = 2. As s increases, the ionization potentials increase from s = 2 to s = 3 and then decrease slowly to s = 8. The mixing energies for neutral and ionic clusters are all negative, indicating that the binary clusters are more stable than pure elemental clusters. Except for s = 4 and 8, cationic clusters are more stable than anionic ones and, thus, are more likely to be observed in experiments.
Yu-Chol, Jong; Yun-Hui, Ju; Kye-Ryong, Sin
2016-01-01
In this paper, carried out were the investigations on the synthetic reaction mechanisms of 3,4-epoxybutyric acid (EBA) from 3-hydroxy-{\\gamma}-butyrolactone (HBL) with two different activating agents, methanesulfonyl chloride (MC) or acetic acid (AA), respectively, and on the convertion of EBA to L-carnitine by density functional theory (DFT/B3LYP). The theoretical calculations showed that the two reaction mechanisms of EBA synthesis with MC or AA as an activating agent were nearly the same. If activated HBL is hydrolysed, not only ring cleavage reaction, but also reverse reaction to HBL can take place. In the case of AA as the activating agent, the activation energy ( energy barrier ) for EBA synthesis is 1.8 times larger than that with MC. It means that the synthesis of EBA with AA may make more by-products with less yield of EBA than that with MC, that can be one reason why AA gave the less yield than MC in EBA synthesis, as reported in the previous experimental study.
Holland, Jason P; Vasdev, Neil
2014-07-14
The reaction of [(89)Zr(C2O4)4](4-) with the tris-hydroxamate ligand desferrioxamine B (DFO) provides the basis of radiolabelling biological vectors such as antibodies and proteins with the radionuclide (89)Zr for positron emission tomography imaging. In this work, density functional theory methods were used to investigate the mechanism of reaction from [Zr(C2O4)4](4-) to Zr(MeAHA)4 by ligand substitution with N-methyl acetohydroxamate (MeAHA). Calculations were performed under simulated basic and acidic conditions. Ligand substitution under basic conditions was found to be thermodynamically feasible with an overall calculated change in solvation free energy, ΔGsol = -97 kJ mol(-1) using the B3LYP/DGDZVP methodology and a water continuum solvation model. In contrast, an acid-mediated mechanism of ligand substitution was found to be thermodynamically non-feasible. Molecular orbital analysis provides a rationale for the difference in thermodynamic stability between [Zr(C2O4)4](4-) and Zr(MeAHA)4. Overall, the DFT calculations are consistent with observed experimental (89)Zr-radiolabelling reactions and suggest that computational methods may prove useful in designing novel chelates for increasing the thermodynamic and kinetic stability of (89)Zr-complexes in vivo.
Quantal density functional theory
Sahni, Viraht
2016-01-01
This book deals with quantal density functional theory (QDFT) which is a time-dependent local effective potential theory of the electronic structure of matter. The treated time-independent QDFT constitutes a special case. In the 2nd edition, the theory is extended to include the presence of external magnetostatic fields. The theory is a description of matter based on the ‘quantal Newtonian’ first and second laws which is in terms of “classical” fields that pervade all space, and their quantal sources. The fields, which are explicitly defined, are separately representative of electron correlations due to the Pauli exclusion principle, Coulomb repulsion, correlation-kinetic, correlation-current-density, and correlation-magnetic effects. The book further describes Schrödinger theory from the new physical perspective of fields and quantal sources. It also describes traditional Hohenberg-Kohn-Sham DFT, and explains via QDFT the physics underlying the various energy functionals and functional derivatives o...
Weymuth, Thomas; Chen, Peter; Reiher, Markus
2014-01-01
We present the WCCR10 data set of ten ligand dissociation energies of large cationic transition metal complexes for the assessment of approximate exchange--correlation functionals. We analyze nine popular functionals, namely BP86, BP86-D3, B3LYP, B3LYP-D3, B97-D-D2, PBE, TPSS, PBE0, and TPSSh by mutual comparison and by comparison to experimental gas-phase data measured with well-known precision. The comparison of all calculated data reveals a large, system-dependent scattering of results with nonnegligible consequences for computational chemistry studies on transition metal compounds. Considering further the comparison with experiment, the non-empirical functionals PBE and TPSS turn out to be among the best functionals for our reference data set. The deviation can be lowered further by including Hartree--Fock exchange. Accordingly, PBE0 and TPSSh are the two most accurate functionals for our test set, but also these functionals exhibit deviations from experiment by up to 50 kJ/mol for individual reactions. A...
Bokareva, O S; Al-Marri, M J; Pullerits, T; Kühn, O
2016-01-01
The reliable prediction of optical and fundamental gaps of finite size systems using density functional theory requires to account for the potential self-interaction error, which is notorious for degrading the description of charge transfer transitions. One solution is provided by parameterized long-range corrected functionals such as LC-BLYP, which can be tuned such as to describe certain properties of the particular system at hand. Here, bare and 3-mercaptoprotionic acid covered \\ce{Cd33Se33} quantum dots are investigated using the optimally tuned LC-BLYP functional. The range separation parameter, which determines the switching on of the exact exchange contribution is found to be 0.12 bohr$^{-1}$ and 0.09 bohr$^{-1}$ for the bare and covered quantum dot, respectively. It is shown that density functional optimization indeed yields optical and fundamental gaps and thus exciton binding energies, considerably different compared with standard functionals such as the popular PBE and B3LYP ones. This holds true, ...
DFT STUDY OF THE HYDROLYSIS OF SOME S-TRIAZINES
The acid-catalyzed hydrolysis of atrazine and related 2-chloro-s-triazines to the corresponding 2-hydroxy-s-triazines was investigated using the B3LYP hybrid density functional theory method. Gas-phase calculations were performed at the B3LYP/6-311++G(d,p)//B3LYP/6-31G* level of ...
Ulian, Gianfranco; Valdrè, Giovanni
2015-07-01
Pyrophyllite has a significant role in both geophysics as a hydrous phase, which can recycle water into the Earth's mantle, and many industrial applications, such as petroleum and civil engineering. However, very few works have been proposed to fully characterize the thermodynamic properties of this mineral, especially at atomic scale. In the present work, we report structural, vibrational, thermochemical and thermophysical properties of pyrophyllite, calculated at the density functional theory level with the hybrid B3LYP functional, all-electron Gaussian-type orbitals and taking into account a correction to include dispersive forces. V( P, T) data at 300 K fit with isothermal third-order Birch-Murnaghan equations of state and yield K T 0 = 46.57 GPa, K' = 10.51 and V 0 = 213.67 Å3, where K T 0 is the thermal bulk modulus at 0 GPa, K' is the first derivative and V 0 is the volume at zero pressure, in very good agreement with recent experimental results obtained by in situ single-crystal synchrotron XRD. The compressional behaviour is highly anisotropic, with axial compressibility in ratio β( a):β( b):β( c) = 1.218:1.000:4.188. Pyrophyllite bulk modulus, thermal expansion coefficients and heat capacity at different P- T conditions are provided. The results of this kind of analysis can be useful in both geophysical and technological applications of the mineral and expand the high-temperature and high-pressure knowledge of this phase at physical conditions that are still difficult to obtain by experimental means. The simulated vibrational spectrum can also be used as a guideline by other authors in their experimental investigation of pyrophyllite.
Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin
2016-05-01
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.
Witte, Jonathon; Neaton, Jeffrey B; Head-Gordon, Martin
2016-05-21
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions-noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms-with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.
Density Functional Investigation of Methanethiol and Dimethyl Sulfide Adsorption on Zeolite
Institute of Scientific and Technical Information of China (English)
Renqing Lü; Guangmin Qiu; Chenguang Liu
2006-01-01
The density functional theory and cluster model methods have been employed to investigate the interactions between methanethiol, dimethyl sulfide and zeolites. The molecular complexes formed by adsorption of methanethiol or dimethyl sulfide on silanol H3SiOSi(OH)2OSiH3 with five coordination forms or four coordination forms, and complexes formed by interactions of Br(o)nsted acid sites of bridging hydroxyl H3Si(OH)Al(OH)2OSiH3 with methanethiol or dimethyl sulfide have been investigated. Full optimization and frequency analysis of all cluster models have been carried out using the B3LYP hybrid method at 6-31+G (d,p) basis set level for hydrogen, silicon, aluminum, oxygen,carbon, and sulfur atoms. The structures and energy changes of different coordination forms between methanethiol and H3Si(OH)Al(OH)2OSiH3, dimethyl sulfide and H3Si(OH)Al(OH)2OSiH3, methanethiol and H3SiOSi(OH)2OSiH3, dimethyl sulfide and H3SiOSi(OH)2OSiH3 complexes have been comparatively studied. The calculated results showed the nature of interactions that led to the formation of all complexes was van der Waals force confirmed by an insignificant change of geometric structures and properties. The conclusions that methanethiol and dimethyl sulfide molecules were adsorbed on bridging hydroxyl group prior to silanol group were obtained on the basis of adsorption heat, the most stable adsorption models of a 6 ring structure for interaction between bridging hydroxyl and methanethiol, and a 7 ring structure for interaction between bridging hydroxyl and dimethyl sulfide.
Timón, V; Praveen, C S; Escamilla-Roa, E; Valant, M
2013-07-01
A hybrid density functional based study of a phyllosilicate (PS) is presented here for the first time. Using all-electron electronic structure calculations with the B3LYP hybrid functional, we have investigated the electronic and structural properties of a series of trioctahedral 1M-polytype K-bearing micas starting from phlogopite (the Mg-end member), ending with the annite (the Fe-end member), and passing through the biotite (a solid solution of the end members). Electronic band gap is calculated for all the compositions and nature of the electronic transition is discussed with the aid of band structure and density of states plots. An excellent agreement with the available experimental data has been observed. An insulator to semiconductor transition is explained on the basis of orbital hybridization. A further comparison is made using the pure GGA functional. For the completeness of the study, the dielectric properties of phlogopite are calculated using the coupled perturbed Kohn-Sham scheme, as implemented within the CRYSTAL09 code.
Institute of Scientific and Technical Information of China (English)
WANG Han-Lu; WANG Xue-Ye; WANG Ling; WANG Heng-Liang; LIU Ai-Hong
2007-01-01
Electronic properties, such as HOMO and LUMO energies, band gaps, ionization potential (IP) and electron affinity (EA) of 2,7- and 3,6-linked carbazole trimers, two conjugated oligomers with different linkages of carbazole, were studied by the density functional theory with Becke-Lee-Young-Parr composite exchange correlation functional (B3LYP). The absorption spectra of these compounds were also investigated by time-dependent density functional theory (TD-DFT) with 6-31G* basis set. The calculated results indicated that the HOMO and LUMO of the 2,7- and 3,6-linked carbazole trimers are both slightly destabilized on going from methyl substitution to sec-butyl substitution. Both IP and EA exhibit their good hole-transporting but poor electron-accepting ability. The presence of alkyl groups on the nitrogen atoms does not affect the intra-chain electronic delocalization along the molecular frame. Thus no significant effect on the band gap and absorption spectra of compounds has been found.
Hybrid density functional theory study of Cu(In1−xGaxSe2 band structure for solar cell application
Directory of Open Access Journals (Sweden)
Xu-Dong Chen
2014-08-01
Full Text Available Cu(In1−xGaxSe2 (CIGS alloy based thin film photovoltaic solar cells have attracted more and more attention due to its large optical absorption coefficient, long term stability, low cost and high efficiency. However, the previous theoretical investigation of this material with first principle calculation cannot fulfill the requirement of experimental development, especially the accurate description of band structure and density of states. In this work, we use first principle calculation based on hybrid density functional theory to investigate the feature of CIGS, with B3LYP applied in the CuIn1−xGaxSe2 stimulation of the band structure and density of states. We report the simulation of the lattice parameter, band gap and chemical composition. The band gaps of CuGaSe2, CuIn0.25Ga0.75Se2, CuIn0.5Ga0.5Se2, CuIn0.75Ga0.25Se2 and CuInSe2 are obtained as 1.568 eV, 1.445 eV, 1.416 eV, 1.275 eV and 1.205 eV according to our calculation, which agree well with the available experimental values. The band structure of CIGS is also in accordance with the current theory.
Kornobis, Karina; Wong, Bryan M; Lodowski, Piotr; Jaworska, Maria; Andruniów, Tadeusz; Rudd, Kenneth; Kozlowski, Pawel M; 10.1021/jp110914y
2011-01-01
Time-dependent density functional theory (TD-DFT) and correlated ab initio methods have been applied to the electronically excited states of vitamin B12 (cyanocobalamin or CNCbl). Different experimental techniques have been used to probe the excited states of CNCbl, revealing many issues that remain poorly understood from an electronic structure point of view. Due to its efficient scaling with size, TD-DFT emerges as one of the most practical tools that can be used to predict the electronic properties of these fairly complex molecules. However, the description of excited states is strongly dependent on the type of functional used in the calculations. In the present contribution, the choice of a proper functional for vitamin B12 was evaluated in terms of its agreement with both experimental results and correlated ab initio calculations. Three different functionals, i.e. B3LYP, BP86, and LC-BLYP, were tested. In addition, the effect of relative contributions of DFT and HF to the exchange-correlation functional ...
Potential Function and Thermodynamic Property of UO
Institute of Scientific and Technical Information of China (English)
Xiu-lin Zeng; Si-yu Xu; Xue-hai Ju
2013-01-01
Potential energy scan for uranium oxide (UO) was performed by ab initio configuration interaction (CI) method and density functional theory methods at the PBE1 and the B3LYP levels in combination with the (ECP80MWB_AVQZ+2f) basis set for uranium and 6-311+G* for oxygen.The dissociation energies of UO,after being corrected for the zero-point vibrational energy,are 2.38,3.76,and 3.31 eV at the CI,PBE1,and B3LYP levels,respectively.The calculated energy was fitted to potential functions of Morse,Lennard-Jones,and Rydberg.Only the Morse function is eligible for the potential.The anharmonicity constant is 0.00425.The anharmonic frequency is 540.95 cm-1 deduced from the PBE1 results.Thermodynamic properties of entropy and heat capacity at 298.2-1500 K were calculated using DFT-UPBE1 results and Morse parameters.The relationship between entropy and temperature was established.
Denis, Pablo A
2005-09-01
We have investigated the SX (X = first- or second-row atom), SO2, and SO3 molecules employing the correlation-consistent (cc), the recently developed polarization-consistent (pc), and three Pople-type basis sets, in conjunction with the B3LYP functional. The results confirmed that the aug-pc basis sets represent a great contribution in terms of cost-benefits. In the case of the B3LYP functional, when employing the aug-pc-3 and aug-pc-4 basis sets, it is possible to obtain results that are of aug-cc-pV(5+d)Z and aug-cc-pV(6+d)Z quality, respectively, at a much lower cost. The estimations obtained employing smaller members of the family are of nearly double-ζ quality and do not provide reliable results. There is no basis set of quadruple-ζ quality among the polarized-consistent basis sets, although in terms of composition, the aug-pc-3 basis set is a QZ basis set. A precise estimation of the Kohn-Sham complete basis set (CBS) limit with the aug-pc-X basis sets is too difficult for the B3LYP functional because the ∞(aug-pc-4, aug-pc-3, aug-pc-2) extrapolation gives the same results as those of the aug-pc-4 basis set. This is in contrast with the results observed for ab initio methodologies for which the largest basis sets provided the best estimation of the CBS limit. In our opinion, the closest results to the B3LYP/CBS limit are expected to be those obtained with a two-point extrapolation employing the aug-cc-pV(X+d)Z (X = 5, 6) basis sets. The results obtained with this extrapolation are very close to those predicted by the ∞(aug-pc-3, aug-pc-2, aug-pc-1) extrapolation, and that provides a cheaper but more inaccurate alternative to estimate the CBS limit. Minor problems were found for the aug-pc-X basis sets and the B3LYP functional for molecules in which sulfur is bound to a very electronegative element, such as SO, SF, SO2, and SO3. For these molecules, the cc basis sets were demonstrated to be more useful. The importance of tight d functions was observed
Zhao, Guo-zheng; Lu, Ming
2013-01-01
The B3LYP/6-31G (d) method of density functional theory (DFT) was used to study molecular geometry, electronic structure, infrared spectrum (IR) and thermodynamic properties. The heat of formation (HOF) and calculated density were estimated to evaluate the detonation properties using Kamlet-Jacobs equations. Thermal stability of 3,5,7,10,12,14,15,16-octanitro- 3,5,7,10,12,14,15,16-octaaza-heptacyclo[7.5.1.1(2,8).0(1,11).0(2,6).0(4,13).0(6,11)]hexadecane (cage-tetranitrotetraazabicyclooctane) was investigated by calculating the bond dissociation energy (BDE) at unrestricted B3LYP/6-31G (d) level. The calculated results show that the N-NO2 bond is a trigger bond during thermolysis initiation process. The crystal structure obtained by molecular mechanics (MM) methods belongs to Pna2(1) space group, with cell parameters a=12.840 Å, b=9.129 Å, c=14.346 Å, Z=6 and ρ=2.292 g·cm(-3). Both the detonation velocity of 9.96 km·s(-1) and the detonation pressure of 47.47 GPa are better than those of CL-20. According to the quantitative standard of energetics and stability, as a high energy density compound (HEDC), cage-tetranitrotetraazabicyclooctane essentially satisfies this requirement.
Hansen, Jared A; Ehara, Masahiro; Piecuch, Piotr
2013-10-10
The left-eigenstate completely renormalized coupled-cluster (CC) method with singles, doubles, and noniterative triples [CR-CC(2,3)] and a few representative density functional theory (DFT) approaches have been applied to methanol oxidation to formic acid on a Au8(-) cluster, which is a model for aerobic oxidations on gold nanoparticles. It is demonstrated that CR-CC(2,3) supports the previous exothermic reaction mechanism, placing the initial rate-determining transition state, which corresponds to hydrogen transfer from the methoxy species to the molecular oxygen, at about 20 kcal/mol above the reactants, less than 40 kcal/mol above the O2 and CH3O(-) species coadsorbed on Au8(-), and considerably above the remaining two transition states along the reaction pathway. The DFT calculations using the previously exploited M06 hybrid functional show reasonable agreement with CR-CC(2,3), but B3LYP offers additional improvements in the description of the relevant activation energies. Pure functionals, including M06-L, BP86, and TPSS, do not work well, significantly underestimating the activation barriers, but dispersion corrections, as in B97-D, bring the results closer to the M06 accuracy level.
Thimm, Wulf; Gradert, Christian; Broda, Henning; Wennmohs, Frank; Neese, Frank; Tuczek, Felix
2015-10-05
A series of density functional theory (DFT) calculations on the full [Mo(HIPT)N3N] catalyst are performed to obtain an energy profile of the Schrock cycle. This is a continuation of our earlier investigation of this cycle in which the bulky hexaisopropyterphenyl (HIPT) substituents of the ligand were replaced by hydrogen atoms (Angew. Chem., Int. Ed. 2005, 44, 5639). In an effort to provide a treatment that is as converged as possible from a quantum-chemical point of view, the present study now fully takes the HIPT moieties into account. Moreover, structures and energies are calculated with a near-saturated basis set, leading to models with 280 atoms and 4850 basis functions. Solvent and scalar relativistic effects have been treated using the conductor-like screening model and zeroth-order regular approximation, respectively. Free reaction enthalpies are evaluated using the PBE and B3LYP functionals. A comparison to the available experimental data reveals much better agreement with the experiment than preceding DFT treatments of the Schrock cycle. In particular, free reaction enthalpies of reduction steps and NH3/N2 exchange are now excellently reproduced.
Semiclassics in Density Functional Theory
Lee, Donghyung; Cangi, Attila; Elliott, Peter; Burke, Kieron
2009-03-01
Recently, we published an article [1] about the semiclassical origin of density functional theory. We showed that the density and the kinetic energy density of one dimensional finite systems with hard walls can be expressed in terms of the external potential using the semiclassical Green's function method. Here, we show a uniformization scheme for the semiclassical density and the kinetic energy density for turning-point problems.[1] P. Elliott, D. Lee, A. Cangi, and K. Burke, Phys. Rev. Lett. 100, 256406 (2008).
Energy Technology Data Exchange (ETDEWEB)
Zarycz, M. Natalia C., E-mail: mnzarycz@gmail.com; Provasi, Patricio F., E-mail: patricio@unne.edu.ar [Department of Physics, University of Northeastern - CONICET, Av. Libertad 5500, Corrientes W3404AAS (Argentina); Sauer, Stephan P. A., E-mail: sauer@kiku.dk [Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø (Denmark)
2015-12-28
It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH{sub 4}, NH{sub 3}, H{sub 2}O, SiH{sub 4}, PH{sub 3}, SH{sub 2}, C{sub 2}H{sub 2}, C{sub 2}H{sub 4}, and C{sub 2}H{sub 6}. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.
Tiwari, Manish K
2015-01-01
Structures and minimum molecular electrostatic potential (MEP) distributions in anacardic acid and some of its derivatives have been studied by full geometry optimization at the M06-2X/6-31G(d,p), WB97XD/6-31G(d,p) and B3LYP/6-31G(d,p) levels of density functional theory (DFT) in gas phase as well as in DMSO and aqueous solutions. Solvent effect was treated employing the integral equation formalism of the polarizable continuum model. Effects of modifications of the C1-side chain on the minimum MEP values in various regions were studied. Minimum MEP values near the oxygen atoms of the C2-OH group, oxygen or sulfur atoms of the C1-attached urea or thiourea groups and above or below the ring plane considered to be involved in interaction with the receptor were used to perform multiple linear regression. Experimentally observed anti-bacterial activities of these molecules against S. aureus are thus shown to be related to minimum MEP values in the above mentioned regions. Among the three DFT functionals used in th...
Zarycz, M Natalia C; Provasi, Patricio F; Sauer, Stephan P A
2015-12-28
It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH4, NH3, H2O, SiH4, PH3, SH2, C2H2, C2H4, and C2H6. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.
Gao, Aifang; Du, Hongli; Li, Aiguo; Pei, Huiyi
2013-06-01
The equilibrium geometries and electron affinities of the R-SS/R-SS(-)(R=CH₃, C₂H₅, n-C₃H7, i-C₃H₇, n-C₄H₉, t-C₄H₉, n-C₅H₁₁) species have been studied using the higher level of the Gaussian-3(G3) theory and 21 carefully calibrated pure and hybrid density functionals (five generalized gradient approximation (GGA) methods, seven hybrid GGAs, three meta GGA methods, and six hybrid meta GGAs) in conjunction with diffuse function augmented double-ζ plus polarization (DZP++) basis sets. The geometries are fully optimized with each method and discussed. The reliable adiabatic electron affinity has been presented by means of the high level of G3 technique. With the DZP++ DFT method, three measures of neutral/anion energy differences reported in this work are the adiabatic electron affinity, the vertical electron affinity, and the vertical detachment energy. The adiabatic electron affinities, obtained at the BP86, M05-2X, B3LYP, M06, B98, M06-2X, mPW1PW91, HCTH, B97-1, M05, PBE1PBE, and VSXC methods, are in agreement with the G3 results. These methods perform better for EA prediction and are considered to be reliable.
Wang, Bing; Wang, Dandan; Zhao, Shan; Huang, Xiaobin; Zhang, Jianbin; Lv, Yan; Liu, Xiaocen; Lv, Guojun; Ma, Xiaojun
2017-01-01
In this study, we used density functional theory (DFT) to predict polymer-drug interactions, and then evaluated the ability of poly (vinyl pyrrolidone) (PVP) to inhibit crystallization of amorphous solid dispersions by experimental-verification. Solid dispersions of PVP/resveratrol (Res) and PVP/griseofulvin (Gri) were adopted for evaluating the ability of PVP to inhibit crystallization. The density functional theory (DFT) with the B3LYP was used to calculate polymer-drug and drug-drug interactions. Fourier transform infrared spectroscopy (FTIR) was used to confirm hydrogen bonding interactions. Polymer-drug miscibility and drug crystallinity were characterized by the modulated differential scanning calorimetry (MDSC) and X-ray powder diffraction (XRD). The release profiles were studied to investigate the dissolution advantage. DFT results indicated that EPVP-Res>ERes-Res (E: represents hydrogen bonding energy). A strong interaction was formed between PVP and Res. In addition, Fourier transform infrared spectroscopy (FTIR) analysis showed hydrogen bonding formed between PVP and Res, but not between PVP and Gri. MDSC and XRD results suggested that 70-90wt% PVP/Res and PVP/Gri solid dispersions formed amorphous solid dispersions (ASDs). Under the accelerated testing condition, PVP/Res dispersions with higher miscibility quantified as 90/10wt% were more stable than PVP/Gri dispersions. The cumulative dissolution rate of 90wt% PVP/Res dispersions still kept high after 90days storage due to the strong interaction. However, the cumulative dissolution rate of PVP/Gri solid dispersions significantly dropped because of the recrystallization of Gri. Copyright © 2016 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Guozheng Zhao
2013-01-01
Full Text Available The B3LYP/6-31G (d density functional theory (DFT method was used to study molecular geometry, electronic structure, infrared spectrum (IR and thermodynamic properties. Heat of formation (HOF and calculated density were estimated to evaluate detonation properties using Kamlet-Jacobs equations. Thermal stability of 3,6,7,8-tetranitro-3,6,7,8-tetraaza-tricyclo [3.1.1.1(2,4]octane (TTTO was investigated by calculating bond dissociation energy (BDE at the unrestricted B3LYP/6-31G(d level. Results showed the N-NO2 bond is a trigger bond during the thermolysis initiation process. The crystal structure obtained by molecular mechanics (MM methods belongs to P2(1/C space group, with cell parameters a = 8.239 Å, b = 8.079 Å, c = 16.860 Å, Z = 4 and r = 1.922 g cm-3. Both detonation velocity of 9.79 km s-1 and detonation pressure of 44.22 GPa performed similarly to CL-20. According to the quantitative standards of energetics and stability, TTTO essentially satisfies this requirement as a high energy density compound (HEDC.
Institute of Scientific and Technical Information of China (English)
JIN,Chen(金晨); ZHANG,Lin(张琳); HONG,Jin(洪瑾); YANG,Gao-Sheng(杨高升); ZHU,Long-Gen(朱龙根)
2004-01-01
The structure of dipepide AcMet-Gly was determined by X-ray crystallographic analysis. It possesses monoclinic, space group P21 (No. 4), with cell dimensions of a=0.8571(2) nm, b=0.5871(2) nm, c= 1.197(3) nm,β=99.290(10)°, V=0.5944(15) nm3, Z=2, .μ=2.74 cm-1. Mononuclear chelates, described as [Pd(X)(S,N,O-AcMet-Gly)] +, in which Pd(II) is coordinated by thioether, deprotonated amide nitrogen, carbonyl oxygen of methionine and X (AcMetGly or other ligands present in aqueous solution or in mobile phase solution), were detected 5 min after mixing AcMet-Gly with [Pd(H2O)4]2- at room temperature using electrospray ionization mass spectrometry. The geometry of [Pd(H2O)(S,N,O-AcMet-Gly)]+ is optimized at density functional B3LYP/LanL2DZ level. The fused five- and six-membered chelate is responsible for cleavage of Met-Gly bond. This is the first time to provide a direct evidence for Pd(II)-mediated cleavage of dipeptides via external solvent attack.
Rasool, Nasir; Kanwal, Aqsa; Rasheed, Tehmina; Ain, Quratulain; Mahmood, Tariq; Ayub, Khurshid; Zubair, Muhammad; Khan, Khalid Mohammed; Arshad, Muhammad Nadeem; M Asiri, Abdullah; Zia-Ul-Haq, Muhammad; Jaafar, Hawa Z E
2016-06-28
Synthesis of 2,5-bisarylthiophenes was accomplished by sequential Suzuki cross coupling reaction of 2-bromo-5-chloro thiophenes. Density functional theory (DFT) studies were carried out at the B3LYP/6-31G(d, p) level of theory to compare the geometric parameters of 2,5-bisarylthiophenes with those from X-ray diffraction results. The synthesized compounds are screened for in vitro bacteria scavenging abilities. At the concentration of 50 and 100 μg/mL, compounds 2b, 2c, 2d, 3c, and 3f with IC50-values of 51.4, 52.10, 58.0, 56.2, and 56.5 μg/mL respectively, were found most potent against E. coli. Among all the synthesized compounds 2a, 2d, 3c, and 3e with the least values of IC50 77, 76.26, 79.13 μg/mL respectively showed significant antioxidant activities. Almost all of the compounds showed good antibacterial activity against Escherichia coli, whereas 2-chloro-5-(4-methoxyphenyl) thiophene (2b) was found most active among all synthesized compound with an IC50 value of 51.4 μg/mL. All of the synthesized compounds were screened for nitric oxide scavenging activity as well. Frontier molecular orbitals (FMOs) and molecular electrostatic potentials of the target compounds were also studied theoretically to account for their relative reactivity.
Leininger, J-Philippe; Minot, Christian; Lorant, François; Behar, Françoise
2007-04-26
Density functional B3LYP and BH&HLYP calculations with the 6-31G** basis set have been performed to investigate elementary reactions playing an important role in the pyrolysis of 1-methylnaphthalene. The pathways describing the destiny of the main radicals, H, methyl, hydromethylnaphthyl and methylnaphthyl, have been studied. At low temperature, addition of H atoms on the aromatic ring is favored over hydrogen abstraction. Except at low temperature (below 400 K), the hydromethylnaphthyl radical undergoes preferentially a loss of hydrogen rather than a bimolecular hydrogen transfer with methylnaphthalene or addition reaction on methylnaphthalene forming a hydrogenated dimer. In the range 400-750 K, the formation of methane by hydrogen abstraction of methyl radical on methylnaphthalene is predominant compared to the formation of hydrodimethylnaphthalenes by addition reaction. Rate constants of reactions describing the formation of heavy products like methyldinaphthylmethanes or dimethylbinaphthalenes have been calculated and discussed. They are also compared to recombination reactions from the literature. Rate constants of these reactions have been computed using transition state theory and can be integrated in kinetic radical schemes of methylated polyaromatic compounds pyrolysis from geological to laboratory conditions.
Khoshkholgh, Mehri Javan; Marsusi, Farah; Abolhassani, Mohammad Reza
2015-02-05
PTBs polymers with thieno[3,4-b]thiophene [TT] and benzodithiophene [BDT] units have particular properties, which demonstrate it as one of the best group of donor materials in organic solar cells. In the present work, density functional theory (DFT) is applied to investigate the optimized structure, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), band gap and dihedral angle of PTB7 at B3LYP/6-31G(d). Two different approaches are applied to carry out these investigations: Oligomer extrapolation technique and periodic boundary condition (PBC) method. The results obtained from PBC-DFT method are in fair agreement with experiments. Based on these reliable outcomes; the investigations continued to perform some derivatives of PTB7. In this study, sulfur is substituted by nitrogen, oxygen, silicon, phosphor or selenium atoms in pristine PTB7. Due to the shift of HOMO and LUMO levels, smaller band gaps are predicted to appear in some derivatives in comparison with PTB7. Maximum theoretical efficiencies, η, of the mentioned derivatives as well as local difference of dipole moments between the ground and excited states (Δμge) are computed. The results indicate that substitution of sulfur by nitrogen or oxygen in BDT unit, and silicon or phosphor in TT unit of pristine PTB7 leads to a higher η as well as Δμge.
Govindarasu, K; Kavitha, E
2014-12-10
The Fourier transform infrared (4000-400cm(-1)) and Fourier transform Raman (3500-50cm(-1)) spectra of 4-Chloro-dl-phenylalanine (4CLPA) were recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational wavenumbers were investigated with the help of density functional theory (DFT) method using B3LYP/6-31G(d,p) as basis set. The observed vibrational wavenumbers were compared with the calculated results. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Predicted electronic absorption spectra from TD-DFT calculation have been analyzed comparing with the UV-Vis (200-800nm) spectrum. The effects of chlorine and ethylene group substituent in benzene ring in the vibrational wavenumbers have been analyzed. The HOMO-LUMO energy gap explains the charge interaction taking place within the molecule. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 4CLPA were calculated. The Chemical reactivity and chemical potential of 4CLPA is calculated. In addition, molecular electrostatic potential (MEP), frontier molecular orbital (FMO) analysis were investigated using theoretical calculations. Published by Elsevier B.V.
Energy Technology Data Exchange (ETDEWEB)
Wu, Jing-He; Liu, Chang-Xin [Henan Institute of Education, Zhengzhou (China). Dept. of Physics; Wang, Ping; Zhang, Shuai; Lu, Cheng [Nanyang Normal Univ (China). Dept. of Physics; Yang, Gui [Anyang Normal Univ. (China). Dept. of Physics and Electrical Engineering
2015-07-01
Ab initio methods based on density functional theory at B3LYP level have been applied in investigating the equilibrium geometries, growth patterns, relative stabilities, and electronic properties of Zr{sub 2}-doped Si{sub n} clusters. The optimisation results shown that the lowest-energy configurations for Zr{sub 2}Si{sub n} clusters do not keep the corresponding silicon framework unchanged, which reflects that the doped Zr atoms dramatically affect the most stable structures of the Si{sub n} clusters. By analysing the relative stabilities, it is found that the doping of zirconium atoms reduces the chemical stabilities of silicon host. The Zr{sub 2}Si{sub 4} and Zr{sub 2}Si{sub 7} clusters are the magic numbers. The natural population and natural electronic configuration analyses indicated that the Zr atoms possess positive charge for n=1-6 and negative charge for n=7-11. In addition, the chemical hardness, chemical potential, infrared, and Raman spectra are also discussed.
Govindarasu, K.; Kavitha, E.
2014-12-01
The Fourier transform infrared (4000-400 cm-1) and Fourier transform Raman (3500-50 cm-1) spectra of 4-Chloro-DL-phenylalanine (4CLPA) were recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational wavenumbers were investigated with the help of density functional theory (DFT) method using B3LYP/6-31G(d,p) as basis set. The observed vibrational wavenumbers were compared with the calculated results. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Predicted electronic absorption spectra from TD-DFT calculation have been analyzed comparing with the UV-Vis (200-800 nm) spectrum. The effects of chlorine and ethylene group substituent in benzene ring in the vibrational wavenumbers have been analyzed. The HOMO-LUMO energy gap explains the charge interaction taking place within the molecule. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 4CLPA were calculated. The Chemical reactivity and chemical potential of 4CLPA is calculated. In addition, molecular electrostatic potential (MEP), frontier molecular orbital (FMO) analysis were investigated using theoretical calculations.
Anitha, K; Balachandran, V
2015-07-05
Vibrational spectral analysis and quantum chemical computations based on density functional theory have been performed on the N-(2-cyanoethyl)-N-butylaniline. The geometry, structural properties, intermolecular hydrogen bond, and harmonic vibrational frequencies of the title molecule have been investigated with the help of DFT (B3LYP) and LC-DFT (CAM-B3LYP) method. Molecular electrostatic potential (MEP) have been performed. The various intramolecular interactions have been exposed by natural bond orbital analysis. The distribution of atomic charges and bending of natural hybrid orbitals also reflect the presence of intramolecular hydrogen bonding. Global reactivity and local reactivity descriptors of the title molecule have been calculated. The analysis of the electron density of HOMO and LUMO gives an idea of the delocalization and low value of energy gap indicated the electron transport in the molecule and thereby NLO activity. The effect of solvent on second-order NLO properties has been studied using polarized continuum model (PCM) in the tetrahydrofuran (THF) solution. The solvent leads to a slight enhancement of the NLO responses for the studied complexes relevant to their NLO responses in gas phase. The electronic absorption spectra were investigated by the TDDFT methods. The frequency-dependent first hyperpolarizabilities of the N-(2-cyanoethyl)-N-butylaniline were also evaluated. The (1)H and (13)C NMR chemical shifts have been calculated by gauge-indepedent atomic orbital (GIAO) method with B3LYP/6-311++G(d, p) approach. Copyright © 2015 Elsevier B.V. All rights reserved.
Hybrid density functional calculations of the defect properties of ZnO:Rh and ZnO:Ir
Energy Technology Data Exchange (ETDEWEB)
Muñoz Ramo, David, E-mail: dm586@cam.ac.uk; Bristowe, Paul D., E-mail: pdb1000@cam.ac.uk
2014-03-31
We report density functional calculations of the atomic and electronic structure of the spinel phases ZnRh{sub 2}O{sub 4} and ZnIr{sub 2}O{sub 4} as well as crystalline ZnO lightly doped (1 at.%) with Rh and Ir ions using the B3LYP hybrid functional. Calculations for the spinels show band gaps (∼ 3 eV) and lattice parameters (∼ 2% difference) in reasonable agreement with experimental data. Incorporation of the transition metals into ZnO induces local distortions in the lattice and the appearance of metal d levels in the low gap region and near the conduction band minimum, with a d–d splitting of about 2 eV, which reduces the effective transparency of the material. Addition of a hole to the simulation cell of both spinels and doped ZnO leads to charge localization in the neighbourhood of Rh/Ir accompanied by local lattice deformations to form a small polaron which may lead to low hole mobility. We calculate polaron diffusion barriers in the spinels and obtain values around 0.02–0.03 eV. These very low barrier energies suggest that at high Rh/Ir concentrations polaron hopping is not going to be detected at room temperature. - Highlights: • Rh/Ir incorporation into ZnO at low doping induces local distortions in the lattice. • Localized levels appear in the gap of ZnO:Rh/ZnO:Ir near band edges. • Hole trapping is found in ZnO:Rh/ZnO:Ir and in the ZnRh{sub 2}O{sub 4}/ZnIr{sub 2}O{sub 4} spinels. • Hole diffusion barriers in the spinels are very small.
Brandenburg, Jan Gerit; Alessio, Maristella; Civalleri, Bartolomeo; Peintinger, Michael F; Bredow, Thomas; Grimme, Stefan
2013-09-26
We extend the previously developed geometrical correction for the inter- and intramolecular basis set superposition error (gCP) to periodic density functional theory (DFT) calculations. We report gCP results compared to those from the standard Boys-Bernardi counterpoise correction scheme and large basis set calculations. The applicability of the method to molecular crystals as the main target is tested for the benchmark set X23. It consists of 23 noncovalently bound crystals as introduced by Johnson et al. (J. Chem. Phys. 2012, 137, 054103) and refined by Tkatchenko et al. (J. Chem. Phys. 2013, 139, 024705). In order to accurately describe long-range electron correlation effects, we use the standard atom-pairwise dispersion correction scheme DFT-D3. We show that a combination of DFT energies with small atom-centered basis sets, the D3 dispersion correction, and the gCP correction can accurately describe van der Waals and hydrogen-bonded crystals. Mean absolute deviations of the X23 sublimation energies can be reduced by more than 70% and 80% for the standard functionals PBE and B3LYP, respectively, to small residual mean absolute deviations of about 2 kcal/mol (corresponding to 13% of the average sublimation energy). As a further test, we compute the interlayer interaction of graphite for varying distances and obtain a good equilibrium distance and interaction energy of 6.75 Å and -43.0 meV/atom at the PBE-D3-gCP/SVP level. We fit the gCP scheme for a recently developed pob-TZVP solid-state basis set and obtain reasonable results for the X23 benchmark set and the potential energy curve for water adsorption on a nickel (110) surface.
Neese, Frank
2007-10-28
The zero-field splitting (ZFS) (expressed in terms of the D tensor) is the leading spin-Hamiltonian parameter for systems with a ground state spin S>12. To first order in perturbation theory, the ZFS arises from the direct spin-spin dipole-dipole interaction. To second order, contributions arise from spin-orbit coupling (SOC). The latter contributions are difficult to treat since the SOC mixes states of different multiplicities. This is an aspect of dominant importance for the correct prediction of the D tensor. In this work, the theory of the D tensor is discussed from the point of view of analytic derivative theory. Starting from a general earlier perturbation treatment [F. Neese and E. I. Soloman, Inorg. Chem. 37, 6568 (1998)], straightforward response equations are derived that are readily transferred to the self-consistent field (SCF) Hartree-Fock (HF) or density functional theory (DFT) framework. The main additional effort in such calculations arises from the solution of nine sets of nonstandard coupled-perturbed SCF equations. These equations have been implemented together with the spin-orbit mean-field representation of the SOC operator and a mean-field treatment of the direct spin-spin interaction into the ORCA electronic structure program. A series of test calculations on diatomic molecules with accurately known zero-field splittings shows that the new approach corrects most of the shortcomings of previous DFT based methods and, on average, leads to predictions within 10% of the experimental values. The slope of the correlation line is essentially unity for the B3LYP and BLYP functionals compared to approximately 0.5 in previous treatments.
Grimme, Stefan; Steinmetz, Marc
2013-10-14
A benchmark set of 25 rotational constants measured in the gas phase for nine molecules (termed ROT25) was compiled from available experimental data. The medium-sized molecules with 18-35 atoms cover common (bio)organic structure motifs including hydrogen bonding and flexible side chains. They were each considered in a single conformation. The experimental B0 values were back-corrected to reference equilibrium rotational constants (Be) by computation of the vibrational corrections ΔBvib. Various density functional theory (DFT) methods and Hartree-Fock with and without dispersion corrections as well as MP2 type methods and semi-empirical quantum chemical approaches are investigated. The ROT25 benchmark tests their ability to describe covalent bond lengths, longer inter-atomic distances, and the relative orientation of functional groups (intramolecular non-covalent interactions). In general, dispersion corrections to DFT and HF increase Be values (shrink molecular size) significantly by about 0.5-1.5% thereby in general improving agreement with the reference data. Regarding DFT methods, the overall accuracy of the optimized structures roughly follows the 'Jacobs ladder' classification scheme, i.e., it decreases in the series double-hybrid > (meta)hybrid > (meta)GGA > LDA. With B2PLYP-D3, SCS-MP2, B3LYP-D3/NL, or PW6B95-D3 methods and extended QZVP (def2-TZVP) AO basis sets, Be values, accurate to about 0.3-0.6 (0.5-1)% on average, can be computed routinely. The accuracy of B2PLYP-D3/QZVP with a mean deviation of only 3 MHz and a standard deviation of 0.24% is exceptional and we recommend this method when highly accurate structures are required or for problematic conformer assignments. The correlation effects for three inter-atomic distance regimes (covalent, medium-range, long) and the performance of minimal basis set (semi-empirical) methods are discussed.
LANL2DZ basis sets recontracted in the framework of density functional theory.
Chiodo, S; Russo, N; Sicilia, E
2006-09-14
In this paper we report recontracted LANL2DZ basis sets for first-row transition metals. The valence-electron shell basis functions were recontracted using the PWP86 generalized gradient approximation functional and the hybrid B3LYP one. Starting from the original LANL2DZ basis sets a cyclic method was used in order to optimize variationally the contraction coefficients, while the contraction scheme was held fixed at the original one of the LANL2DZ basis functions. The performance of the recontracted basis sets was analyzed by direct comparison between calculated and experimental excitation and ionization energies. Results reported here compared with those obtained using the original basis sets show clearly an improvement in the reproduction of the corresponding experimental gaps.
Institute of Scientific and Technical Information of China (English)
朱佳平; 刘胜楠; 李永祥; 王建龙; 曹端林; 任君
2011-01-01
运用B3LYP/6-311+G**密度泛函理论(Density Functional Theory,DFT)方法对CL-14,NNHT,ANPZ-i,DNMT的结构进行了全优化.几何优化结果表明:所有化合物均无虚频,为势能面上的稳定结构.采用Monte-Carlo方法理论估算了4种化合物的密度,并设计等键等电子反应计算了其生成焓;基于统计热力学,求得部分标题化合物100～1 200 K温度范围内的热力学性质;运用Kamlet-Jacobs方程预测了爆速、爆压,其爆速在7.83～8.44 km·s-1之间.研究结果表明:苯并呋咱环、三嗪环、吡嗪环和三唑环具有一定的芳香性,使得分子能稳定存在,所设计的标题化合物能量较高,是有潜力的含能材料候选物.%Four compounds, CL-14, NNHT, ANPZ-i and DNMT were investigated with density functional theory. Their optimized geometries and electronic structures were calculated at the B3LYP/6311 + G** level. Optimized geometries of these compounds showed that there were no imaginary frequencies, so they were stable on the potential energy surface. The heat capacities and enthalpies of some representative compounds at different temperatures form 100 K to 1 200 K were obtained by statistic thermodynamics. In order to calculate standard enthalpies of formation, isodesmic reactions were designed. The average molar volume and theoretical density were estimated by using the MonteCarlo method. Furthermore, the detonation velocity and pressure of the derivatives were estimated by the Kamlet-Jacbos equation. The results showed that the ring of benzofuroxan, triazine, pyrazine and triazole are of aromaticity and the detonation velocities of these compounds were between 7. 83～8. 44 km·s-1. Detonation performance suggests that these title compounds are good candidates for energetic materials.
Milko, Petr; Iron, Mark A
2014-01-14
The electronic structures of a number of iron, cobalt, vanadium, and titanium complexes with the 2,2'-bipyridine (bpy) ligand were considered using the multireference CASSCF and NEVPT2 methods. Many of these systems have been studied in the past using B3LYP and were then found to contain the bpy ligand as a radical anion. For many of the cases, this is contradicted by our multireference calculations. While there are instances where the ligand is indeed a radical anion, in many cases it remains neutral and is involved in backbonding from the metal center. For those cases where CASSCF is too costly, a number of DFT functionals, including the newer double-hybrid functionals, were evaluated against the CASSCF data. It was found that nonhybrid functionals, especially those containing the kinetic energy density τ, were the best at predicting the electronic nature of the complexes. The τ-HCTH and HCTH functionals were the top performers, correctly predicting eleven out of eleven test cases and with the lowest mean unsigned errors (MUE, 7.6 and 7.8 kcal·mol(-1), respectively); the M06-L, N12, BLYP, PBE, and TPSS functionals also did well, while B3LYP had significant problems.
Dyke, John; Levason, William; Light, Mark E; Pugh, David; Reid, Gillian; Bhakhoa, Hanusha; Ramasami, Ponnadurai; Rhyman, Lydia
2015-08-21
The Group 1 complexes, [M(Me6[18]aneN6)][BAr(F)] (M = Li-Cs; Me6[18]aneN6 = 1,4,7,10,13,16-hexamethyl-1,4,7,10,13,16-hexaazacyclooctadecane; BAr(F) = tetrakis{3,5-bis(trifluoromethyl)-phenyl}borate), are obtained in high yield by reaction of the macrocycle with M[BAr(F)] in anhydrous CH2Cl2 solution, and characterised spectroscopically ((1)H, (13)C{(1)H}, (7)Li, (23)Na, and (133)Cs NMR), by microanalysis and, for M = Li, K, and Rb, by single crystal X-ray analysis. The structures show N6-coordination to the metal ion; the small ionic radius for Li(+) leads to a puckered conformation. In contrast, the K(+) ion fits well into the N6 plane, with the [BAr(F)](-) anions above and below, leading to two K(+) species in the asymmetric unit (a hexagonal planar [K(Me6[18]aneN6)](+) cation and a '[K(Me6[18]aneN6)(κ(1)-BAr(F))2](-) anion', with long axial KF interactions). The Rb(+) ion sits above the N6 plane, with two long axial RbF interactions in one cation and two long, mutually cis RbF interactions in the other. The unusual sandwich cations, [M(Me3tacn)2](+) (M = Na, K; distorted octahedral, N6 donor set) and half-sandwich cations [Li(Me3tacn)(thf)](+) (distorted tetrahedron, N3O donor set), [Li(Me4cyclen)(OH2)](+), and [Na(Me4cyclen)(thf)](+) (both distorted square pyramids with N4O donor sets) were also prepared (Me3tacn = 1,4,7-trimethyl-1,4,7-triazacyclononane, Me4cyclen = 1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane). Density functional theory (DFT) calculations, using the BP86 and B3LYP functionals, show that the accessibility of the [M(Me3tacn)2](+) sandwich cations depends strongly on the M(+) ionic radius, such that it is sufficiently large to avoid steric clashing between the Me groups of the two rings, and small enough to avoid very acute N-M-N chelate angles. The calculations also show that coordination to the Group 1 cation involves significant donation of electron density from the p-orbitals on the N atoms of the macrocycle, rather than purely
Karabacak, M.; Kose, E.; Atac, A.; Sas, E. B.; Asiri, A. M.; Kurt, M.
2014-11-01
Structurally, boronic acids are trivalent boron-containing organic compounds that possess one alkyl substituent (i.e., C-Br bond) and two hydroxyl groups to fill the remaining valences on the boron atom. We studied 3-bromophenylboronic acid (3BrPBA); a derivative of boronic acid. This study includes the experimental (FT-IR, FT-Raman, 1H and 13C NMR, UV-Vis) techniques and theoretical (DFT-density functional theory) calculations. The experimental data are recorded, FT-IR (4000-400 cm-1) and FT-Raman spectra (3500-10 cm-1) in the solid phase. 1H and 13C NMR spectra are recorded in DMSO solution. UV-Vis spectrum is recorded in the range of 200-400 nm for each solution (in ethanol and water). The theoretical calculations are computed DFT/B3LYP/6-311++G(d,p) basis set. The optimum geometry is also obtained from inside for possible four conformers using according to position of hydrogen atoms after the scan coordinate of these structures. 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 parallel quantum solutions (PQS) program. 1H and 13C NMR chemical shifts are racked on by using the gauge-invariant atomic orbital (GIAO) method. The time-dependent density functional theory (TD-DFT) is used to find HOMO and LUMO energies, excitation energies, oscillator strengths. The density of state of the studied molecule is investigated as total and partial density of state (TDOS and PDOS) and overlap population density of state (OPDOS or COOP) diagrams have been presented. Besides, frontier molecular orbitals (FMOs), molecular electrostatic potential surface (MEPs) and thermodynamic properties are performed. At the end of this work, the results are ensured beneficial for the literature contribution.
Institute of Scientific and Technical Information of China (English)
陈铁旦; 王卷刚
2011-01-01
采用B3LYP/6-311++G**方法对26种硝基吡嗪类衍生物体系进行了全优化,几何优化结果表明所有优化后的化合物结构均无虚频,为势能面上的稳定结构；采用Monte-Carlo方法理论估算了26种化合物的密度,随着硝基数目的增加,密度增加;并设计等键等电子反应计算了其生成焓及其热力学性质,硝基数目逐渐增加时,Cp、Sm、Hm值都逐渐增大；运用Kamlet-Jacobs预测了爆速、爆压,其爆速在(6.52～9.72)km.s-1之间.结果表明:吡嗪环上有一定的芳香性,所设计的系列硝基吡嗪类化合物能量较高,是有潜力的含能材料候选物.%Twenty-six nitropyrazine compounds and its derivatives have been calculated by density functional theory. Their optimized geometries and electronic structures were computed at the B3LYP/6-311++G(d, p) level. Optimized geometries of these compounds show that they have no inmaginary frequencies, and they are stable on the potential energy surface. The heat capacity and enthalpy of some representative compounds at different temperatures were obtained by statistic thermodynamics. In order to calculate standard enthalpies of formation for the derivatives of nitrotriazole, isodesmic reactions were designed. The average molar volume and theoretical density were estimated using the Monte-Carlo method based on 0.001 ebohr-3 density space. Furthermore, the detonation velocity and pressure of the derivatives were estimated by the Kamlet-Jacbos equation. The results show that the ring of triazole has some aromaticity and the detonation velocities of these compounds are between 6.52 and 9.72 km·s-1. Detonation performance shows that these compounds are very good candidates for energetic materials.
Institute of Scientific and Technical Information of China (English)
冯艳萍; 田磊; 董玉慧
2014-01-01
以并3-6苯环为氢化石墨烯片层模型，采用量子化学密度泛函理论方法(DFT)在B3LYP/6-31G (d, p)水平上进行了几何结构全优化，讨论了分子结构、能量、前线分子轨道等性质的变化规律。在得到化合物基态稳定构型的基础上，运用含时密度泛函理论(TD-DFT)计算了电子吸收光谱的性质。计算结果显示边缘氢化石墨烯片层均为平面结构，线型扶手椅型结构能量最低，结构最稳定。随着石墨烯片层环数的增加HOMO轨道能量增加，LUMO轨道能量降低，能隙能量降低，最大吸收波长明显红移。%Theoretical studies on the edge hydrogenated graphene sheet models formed by combining 3-6 benzene rings were carried out by using the Density Functional Theory (DFT) at B3LYP/6-31G (d, p) level to obtain the optimized equilibrium structures. The molecular geometric structures, energies, frontier molecular orbitals were investigated in detail. On this basis, the electronic transition energy of the excited state was calculated by using Time-Dependent Density Functional Theory (TD-DFT). The calculation results indicated that the edge hydrogenated graphene sheets were planar, and the linear armchair structure was the most stable one. HOMO energy increased and LUMO energy decreased with the number of benzene rings increasing which leaded to the energy gap decreasing and the maximum absorption spectra red shifted significantly.
Indian Academy of Sciences (India)
Zhang Rui-Zhou; Li Xiao-Hong; Zhang Xian-Zhou
2012-09-01
Density functional theory calculations at B3LYP/6-31G∗∗ and B3P86/6-31G∗∗ levels were performed to predict the densities (), detonation velocities (D), pressures (P) and the thermal stabilities for a series of 1,2,4-triazole derivatives for looking high energy density compounds (HEDCs). The heats of formation (HOFs) are also calculated via designed isodesmic reactions. The calculations on the bond dissociation energies (BDEs) indicate that the position of the subsitutent group has great effect on the BDE and the BDEs of the initial scission step are between 31 and 65 kcal/mol. In addition, the condensed phase heats of formation are also calculated for the title compounds. These results would provide basic information for further studies of HEDCs.
Directory of Open Access Journals (Sweden)
Georges Dive
2004-11-01
Full Text Available Abstract: Vertical ionization energies (IE as a function of the conformation are determined at the quantum chemistry level for eighteen ÃŽÂ±-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT framework using the hybrid method B3LYP and the 6-31G**(5d basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO can change a lot as a function of the nuclear structure.
Ochoa-Calle, A J; Zicovich-Wilson, C M; Hernández-Lamoneda, R; Ramírez-Solís, A
2015-03-10
The experimentally characterized ε and ζ phases of solid oxygen are studied by periodic Hartree-Fock (HF) and Density Functional Theory calculations at pressures from 10 to 160 GPa using different types of exchange-correlation functionals with Gaussian atomic basis sets. Full geometry optimizations of the monoclinic C2/m (O2)4 unit cell were done to study the evolution of the structural and electronic properties with pressure. Vibrational calculations were performed at each pressure. While periodic HF does not predict the ε-ζ phase transition in the considered range, Local Density approximation and Generalized Gradient approximation methods predict too low transition pressures. The performance of hybrid functional methods is dependent on the amount of non-local HF exchange. PBE0, M06, B3PW91, and B3LYP approaches correctly predict the structural and electronic changes associated with the phase transition. GGA and hybrid functionals predict a pressure range where both phases coexist, but only the latter type of methods yield results in agreement with experiment. Using the optimized (O2)4 unit cell at each pressure we show, through CASSCF(8,8) calculations, that the greater accuracy of the optimized geometrical parameters with increasing pressure is due to a decreasing multireference character of the unit cell wave function. The mechanism of the transition from the non-conducting to the conducting ζ phase is explained through the Electron Pair Localization Function, which clearly reveals chemical bonding between O2 molecules in the ab crystal planes belonging to different unit cells due to much shorter intercell O2-O2 distances.
Reis, H; Rasulev, B; Papadopoulos, M G; Leszczynski, J
2015-01-01
Fullerene and its derivatives are currently one of the most intensively investigated species in the area of nanomedicine and nanochemistry. Various unique properties of fullerenes are responsible for their wide range applications in industry, biology and medicine. A large pool of functionalized C60 and C70 fullerenes is investigated theoretically at different levels of quantum-mechanical theory. The semiempirial PM6 method, density functional theory with the B3LYP functional, and correlated ab initio MP2 method are employed to compute the optimized structures, and an array of properties for the considered species. In addition to the calculations for isolated molecules, the results of solution calculations are also reported at the DFT level, using the polarizable continuum model (PCM). Ionization potentials (IPs) and electron affinities (EAs) are computed by means of Koopmans' theorem as well as with the more accurate but computationally expensive ΔSCF method. Both procedures yield comparable values, while comparison of IPs and EAs computed with different quantum-mechanical methods shows surprisingly large differences. Harmonic vibrational frequencies are computed at the PM6 and B3LYP levels of theory and compared with each other. A possible application of the frequencies as 3D descriptors in the EVA (EigenVAlues) method is shown. All the computed data are made available, and may be used to replace experimental data in routine applications where large amounts of data are required, e.g. in structure-activity relationship studies of the toxicity of fullerene derivatives.
Subramanian, N.; Sundaraganesan, N.; Jayabharathi, J.
2010-07-01
Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of 1,2-bis(3-methoxy-4-hydroxybenzylidene)hydrazine [vanillin azine (VA)] were carried out by using density functional (DFT/B3LYP) method with 6-31G(d) as basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from solid phase FT-IR and FT-Raman spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with calculated values. The electric dipole moment ( μ) and the first hyperpolarizability ( β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the VA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of VA was also reported. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The theoretical NMR chemical shifts complement with experimentally measured ones.
Venkata Prasad, K; Samatha, K; Jagadeeswara Rao, D; Santhamma, C; Muthu, S; Mark Heron, B
2015-01-01
The vibrational frequencies of 3,4-dichlorobenzophenone (DCLBP) were obtained from the FT-IR and Raman spectral data, and evaluated based on the Density Functional Theory using the standard method B3LYP with 6-311+G(d,p) as the basis set. On the basis of potential energy distribution together with the normal-co-ordinate analysis and following the scaled quantum mechanical force methodology, the assignments for the various frequencies were described. The values of the electric dipole moment (μ) and the first-order hyperpolarizability (β) of the molecule were computed. The UV-absorption spectrum was also recorded to study the electronic transitions. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The NBO analysis, to study the intramolecular hyperconjugative interactions, was carried out. Mulliken's net charges were evaluated. The MEP and thermodynamic properties were also calculated. The electron density-based local reactivity descriptor, such as Fukui functions, was calculated to explain the chemical selectivity or reactivity site in 3,4-dichlorobenzophenone. Copyright © 2015 Elsevier B.V. All rights reserved.
Density functionals from deep learning
McMahon, Jeffrey M
2016-01-01
Density-functional theory is a formally exact description of a many-body quantum system in terms of its density; in practice, however, approximations to the universal density functional are required. In this work, a model based on deep learning is developed to approximate this functional. Deep learning allows computational models that are capable of naturally discovering intricate structure in large and/or high-dimensional data sets, with multiple levels of abstraction. As no assumptions are made as to the form of this structure, this approach is much more powerful and flexible than traditional approaches. As an example application, the model is shown to perform well on approximating the kinetic-energy density functional for noninteracting electrons. The model is analyzed in detail, and its advantages over conventional machine learning are discussed.
Rajalakshmi, Gnanasekaran; Hathwar, Venkatesha R; Kumaradhas, Poomani
2014-06-01
An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max = 1.1 Å(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H...N and N-H...O hydrogen bonds, in which the N3-H3B...N1 and N3-H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.
Arun Sasi, B. S.; Twinkle, A. R.; James, C.
2017-08-01
The density functional theoretical (DFT) calculations have been carried out at the B3LYP/6-311G(d,p) level of theory for nitroxoline monomer and dimer molecule. The dimer molecule formed between two nitroxoline subunits has the largest stability, and is held together by two Osbnd H⋯N hydrogen bonds. Stability of the molecule arising from hyperconjugative interaction and intra/inter molecular charge transfer has been analyzed using natural bond orbital (NBO) analysis. The topological analysis of electron localization function (ELF) provides effect of delocalization. Quantum theory of atoms in molecule (QTAIM) has been applied to gain deep understanding to the existence of intra- and inter-molecular interaction.
Donzello, Maria Pia; Ercolani, Claudio; Cai, Xiaohui; Kadish, Karl M; Ricciardi, Giampaolo; Rosa, Angela
2009-10-19
Following previous cyclic voltammetric studies of tetrakis(thiadiazole)porphyrazines [TTDPzM] where M = Zn(II), Mg(II)(H(2)O), Cu(II), or 2H(I) in nonaqueous media, a thin-layer spectroelectrochemical investigation was carried out in pyridine to characterize each stepwise one-electron reduction of the electrogenerated [TTDPzM](n-) complexes where n = 1-4. A similar UV-visible spectrum was observed for each form of the anion, independent of the central metal ion and detailed theoretical calculations by density functional theory (DFT) and time-dependent DFT (TDDFT) methods were applied to interpret the spectral features of [TTDPzZn](n-) (n = 1-4) which was selected as representative for describing the ground and excited-state electronic structures of the entire [TTDPzM](n-) series. The use of two exchange-correlation functionals, the pure, asymptotically correct statistical average of orbital potentials (SAOP) and the hybrid B3LYP functionals, proved to be essential for attaining a correct assignment of the key spectral features. The nature and intensity of the main spectral features are highlighted and interpreted on the basis of the ground-state electronic structure of the complexes.
Density Functionals of Chemical Bonding
Directory of Open Access Journals (Sweden)
Mihai V. Putz
2008-06-01
Full Text Available The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and authorÃ¢Â€Â™s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR analysis for basic atomic and molecular systems.
Sharma, Divya; Paterson, Martin J
2014-11-01
DFT and MP2 calculations are performed to obtain optimized ground state geometries and binding energies of the cage and the prism conformers of water W6 clusters and Bz-W6 clusters using the aug-cc-pVDZ basis set. The cage conformer of Bz-W6 system is found to be more stable than prism conformer for all range of DFT functionals and MP2. Time dependent-DFT is then used to study UV spectroscopy of Bz, water W6 clusters and Bz-W6 clusters at both the MP2 and wB97XD optimized ground state geometries using the B3LYP, CAM-B3LYP and M06-2X functionals with 6-31++G(d,p) and aug-cc-pVTZ basis sets. Our results predict minor differences in the UV spectroscopy of cage and prism conformers W6 and Bz-W6 clusters that may be observable with high-resolution spectroscopy. The M06-2X and CAM-B3LYP functionals perform consistently with each other. Benzene-mediated excitations of the water W6 cluster towards longer wavelengths above 170 nm are noticed in both the cage and prism geometries of Bz-W6. Benzene is found to be influenced after interacting with the cage and prism W6 geometries, and is seen to undergo a red shift in the main π→π* electronic transition, in which the degeneracy is slightly broken. Charge transfer (CT) states and diffuse Rydberg-type states are also found to play an important role in the spectroscopy of such systems.
Institute of Scientific and Technical Information of China (English)
陈艳; 陈善俊; 易早; 罗江山; 易有根; 唐永建
2012-01-01
采用密度泛函理论(density functional theory,DFT),在B3LYP/6-31+G** (C,H,O)/LANL2DZ(Ag)水平上,对糠醛(furfural,FUR)分子进行了几何结构优化,并计算了FUR分子的常规拉曼散射(normal Raman scattering,NRS)光谱和FUR与Ag原子以及Ag2和Ag4团簇吸附的表面增强拉曼散射(surface-enhanced Raman scattering,SERS)光谱.结果表明,理论值与已有的实验值符合得较好,采用FUR-Ag4吸附构型的计算结果比FUR-Ag和FUR-Ag2吸附构型的计算结果更符合已有实验值.最后,通过Gauss View可视化软件,对FUR分子的振动频率进行了更为全面地归属.通过FUR分子SERS与NRS的比较,可得出FUR分子与Ag原子发生了相互作用,且被吸附的糠醛分子的杂五环是与银表面垂直的.%In the present paper, DFT method at the B3LYP/6-31+G" * (C, H, O)/LANL2DZ(Ag) level was used to optimize molecular configurations of furfural. Based on the optimized structure, the normal Raman spectrum (NRS) of FUR and the surface-enhanced Raman spectrum (SERS) of FUR adsorbed on Ag, Ag2 and Ag4 were all calculated, which were compared with the experimental values. The calculation results indicated that a good conformity was found between the computed and the experimental results. The results of furfural adsorbed on Ag4 were more approximate to the ever reported experimental date than those of furfural adsorbed on Ag and Ag2. At the end, detailed analysis of the Raman spectrum and more comprehensive assignments of the vibration mode for furfural were studied by the software of Gauss View. The data of the SERS by comparing with the one of NRS show that furfural molecule and Ag atoms interact with each other. And we suppose that the molecular plane with the ring of adsorbed furfural molecule is vertically orientated to the silver surface. The work in this paper offers a theory evidence for detection and trace analysis of drinks containing furfural.
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculation were adopted to study the structures and properties of metal-free and magnesium tetrathieno[2,3-b]porphyrazine (TTPPzH2 and TTPPzMg) using B3LYP method with the 6-31G(d) basis set.A comparison of the geometrical structures,atomic charges,molecular orbitals,UV-vis spectra and infrared (IR) spectra among tetrathieno[2,3-b]porphyrazine (TTPPzH2),phthalocyanine (H2Pc) and porphyrazine (H2Pz) compounds was performed.The substituent effect of the thiophene heterocycle for electron-donating on the structures and properties of these compounds has been discussed.Compared with other atoms,the charge distribution of Cβ atoms adjacent to the sulfur atom is significantly influenced by the thiophene heterocycle substituents.The enlargement of the HOMO-LUMO gaps from H2Pc and MgPc to TTPPzH2 and TTPPzMg is at the origin of the observed blue shift of the Q band when moving from H2Pc to TTPPzH2 compounds.Special emphasis has been devoted to the strongest B bands for TTPPzH2 compounds which show red shift due to the large destabilization of the lower lying occupied orbitals compared with the corresponding B bands of H2Pc compounds.With the assistance of animated pictures produced on the basis of the normal coordinates,the significant peaks and vibration modes in the IR spectra of all the compounds were assigned and analyzed.
Quantal Density Functional Theory II
Sahni, Viraht
2009-01-01
Discusses approximation methods and applications of Quantal Density Functional Theory (QDFT), a local effective-potential-energy theory of electronic structure. This book describes approximations methods based on the incorporation of different electron correlations, as well as a many-body perturbation theory within the context of QDFT
Cembran, Alessandro; Song, Lingchun; Mo, Yirong; Gao, Jiali
2009-10-13
A multistate density functional theory in the framework of the valence bond model is described. The method is based on a block-localized density functional theory (BLDFT) for the construction of valence-bond-like diabatic electronic states and is suitable for the study of electron transfer reactions and for the representation of reactive potential energy surfaces. The method is equivalent to a valence bond theory with the treatment of the localized configurations by using density functional theory (VBDFT). In VBDFT, the electron densities and energies of the valence bond states are determined by BLDFT. A functional estimate of the off-diagonal matrix elements of the VB Hamiltonian is proposed, making use of the overlap integral between Kohn-Sham determinants and the exchange-correlation functional for the ground state substituted with the transition (exchange) density. In addition, we describe an approximate approach, in which the off-diagonal matrix element is computed by wave function theory using block-localized Kohn-Sham orbitals. The key feature is that the electron density of the adiabatic ground state is not directly computed nor used to obtain the ground-state energy; the energy is determined by diagonalization of the multistate valence bond Hamiltonian. This represents a departure from the standard single-determinant Kohn-Sham density functional theory. The multistate VBDFT method is illustrated by the bond dissociation of H2+ and a set of three nucleophilic substitution reactions in the DBH24 database. In the dissociation of H2+, the VBDFT method yields the correct asymptotic behavior as the two protons stretch to infinity, whereas approximate functionals fail badly. For the S(N)2 nucleophilic substitution reactions, the hybrid functional B3LYP severely underestimates the barrier heights, while the approximate two-state VBDFT method overcomes the self-interaction error, and overestimates the barrier heights. Inclusion of the ionic state in a three
Indian Academy of Sciences (India)
Amit S Tiwary; Asok K Mukherjee
2013-07-01
The inductive effect of methyl group has been quantified by expressing highest occupied molecular orbital (HOMO) and HOMO-1 energies of indole and a series of methylated indoles using a combination of graph theory (GT) and the Coulson-Longuett-Higgins perturbation method. By correlating these expressions with the corresponding Kohn-Sham orbital energies of the indoles obtained by density functional theory (DFT) calculation at the B3LYP/6-31++G(d,p) and M06-2X/6-31++G(d,p) levels of theory, the inductive effect parameter ℎ has been estimated; the Coulomb integral of -conjugated carbon atom also comes out from the analysis. A correlation of the GT results with the HOMO and HOMO-1 energies obtained by the HF/STO-3G method yield almost the same values of ℎ and . Finally, when these estimated ℎ and are used to calculate the vertical ionization potentials of the methylated indoles in the series, an excellent correlation with experimental charge transfer transition energies of their molecular complexes with tetracyanoethylene is obtained which complies with Mulliken’s theory of charge transfer.
Mirzaei, Mahmoud; Hadipour, Nasser L
2006-04-13
Hydrogen-bonding effects in the real crystalline structure of 9-methyladenine, 9-MA, were studied using calculated electric field gradient, EFG, and chemical shielding, CS, tensors for nitrogen and hydrogen nuclei via density functional theory. The calculations were carried out at the B3LYP and B3PW91 levels with the 6-311++G basis set via the Gaussian 98 package. Nuclear quadrupole coupling constants, C(Q), and asymmetry parameters, eta(Q), are reported for (14)N and (2)H. The chemical shielding anisotropy, Deltasigma, and chemical shielding isotropy, sigma(iso), are also reported for (15)N and (1)H. The difference between the calculated parameters of the monomer and heptameric layer-like cluster 9-MA shows how much H-bonding interactions affect the EFG and CS tensors of each nucleus. This result indicates that N(10) (imino nitrogen) has a major role in H-bonding interactions, whereas that of N(9) is negligible. There is good agreement between the present calculated parameters and reported experimental data. Although some discrepancies were observed, this could be attributed to the different conditions which were applied for calculation and the experiments.
Gladis Anitha, E; Joseph Vedhagiri, S; Parimala, K
2015-02-05
The molecular structure, geometry optimization, vibrational frequencies of organic dye sensitizer 2,6-Diamino-4-chloropyrimidine (DACP) were studied based on Hartree-Fock (HF) and density functional theory (DFT) using B3LYP methods with 6-311++G(d,p) basis set. Ultraviolet-Visible (UV-Vis) spectrum was investigated by time dependent DFT (TD-DFT). Features of the electronic absorption spectrum in the UV-Visible regions were assigned based on TD-DFT calculation. The absorption bands are assigned to transitions. The interfacial electron transfer between semiconductor TiO2 electrode and dye sensitizer DACP is due to an electron injection process from excited dye to the semiconductor's conduction band. The observed and the calculated frequencies are found to be in good agreement. The energies of the frontier molecular orbitals (FMOS) have also been determined. The chemical shielding anisotropic (CSA) parameters are calculated from the NMR analysis, Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Copyright © 2014 Elsevier B.V. All rights reserved.
Liu, Jie; Li, Xinyong; Zhao, Qidong; Hao, Ce; Zhang, Dongke
2013-05-07
The mechanism of selective catalytic reduction of NOx by propene (C3H6-SCR) over the Cu/Ti0.7Zr0.3O2 catalyst was studied by in situ Fourier transform infrared (FTIR) spectroscopy and density functional theory (DFT) calculations. Especially, the formation and transformation of cyanide (-CN species) during the reaction was discussed. According to FTIR results, the excellent performance of the Cu/Ti0.7Zr0.3O2 catalyst in C3H6-SCR was attributed to the coexistence of two parallel pathways to produce N2 by the isocyanate (-NCO species) and -CN species intermediates. Besides the hydrolysis of the -NCO species, the reaction between the -CN species and nitrates and/or NO2 was also a crucial pathway for the NO reduction. On the basis of the DFT calculations on the energy of possible intermediates and transition states at the B3LYP/6-311 G (d, p) level of theory, the reaction channel of -CN species in the SCR reaction was identified and the role of -CN species as a crucial intermediate to generate N2 was also confirmed from the thermodynamics view. In combination of the FTIR and DFT results, a modified mechanism with two parallel pathways to produce N2 by the reaction of -NCO and -CN species over the Cu/Ti0.7Zr0.3O2 catalyst was proposed.
Wang, Fen; Meng, Qingxi; Li, Ming
Density functional theory has been used to study the Fe-catalyzed cyclopropanation of Fe-carbene complexes with ethene. All the intermediates and transition states were optimized completely at the B3LYP/6-31+G(d,p) level. Calculation results confirm that the cyclopropanation of Fe-carbene complexes with ethene involves the two reaction paths I and II. In the reaction path I, the double bond of ethene attacks directly on the carbene carbon of Fe-carbene complexes to generate the cyclopropane. In the reaction path II, ethene substitution for PMe3 or CO in the Fe-carbene complexes leads to the complexes M2; and the attack of one carbon of ethene on the carbene carbon results in the complexes M3 with a Fe bond C bond C bond C four-membered ring, and then generates the cyclopropane via the elimination reaction. For Fe-carbene complexes A, C, D, E, and H, the main reaction mode is the reaction path I; for Fe-carbene complexes B, F, and G, the main reaction mode is the reaction path II.0
Plumley, Joshua A; Tsai, Midas I-Hsien; Dannenberg, J J
2011-02-17
We compare the energies and enthalpies of inter-action of three- and seven-stranded capped polyglycine aggregates in both the pleated and rippled antiparallel and parallel β-sheet structures as well as the collagenic (three-strand) or polyglycine II-like (seven-strand) forms using density functional theory at the B3LYP/D95(d,p) level. We present the overall interaction energies as broken down into pure H-bonding between the strands at the geometries they assume in the aggregates and the distortion energies required to achieve those geometries starting from the fully relaxed single strands. While the antiparallel sheets represent the most stable structures for both the three- and seven-strand structures, the pure H-bonding interactions are the smallest for these structures. The overall interaction energies are dominated by the energy required to distort the relaxed polyglycine strands rather than the H-bonding energies. The antiparallel β-sheet constrained to C(s) symmetry has a lower enthalpy, but higher energy, of interaction than the fully optimized structure.
Chaitanya, K
2012-02-01
The FT-IR (4000-450 cm(-1)) and FT-Raman spectra (3500-100 cm(-1)) of benzophenone 2,4-dicarboxylic acid (2,4-BDA) have been recorded in the condensed state. Density functional theory calculation with B3LYP/6-31G(d,p) basis set have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman activities and bonding features of the title compounds. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 2,4-BDA is calculated using HF/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charges is also calculated. Because of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-vis spectra and electronic absorption properties were explained and illustrated from the frontier molecular orbitals.
Carneiro, José Walkimar de M; Cruz, Maurício T de M
2008-09-25
B3LYP/LANL2DZ and B3LYP/6-31G(d)-restricted and -unrestricted calculations are employed to calculate energies and adsorption forms of formaldehyde adsorbed on planar and on tetrahedral Pd4 clusters and on a Pd4 cluster supported on Al10O15. Formaldehyde adsorbs on planar Pd4 in the eta(2)(C,O)-di-sigma adsorption mode, while on tetrahedral Pd4, it adsorbs in the eta(2)(C,O)-pi adsorption mode. The adsorption energy on planar Pd4 is -21.4 kcal x mol(-1), whereas for the tetrahedral Pd4 cluster, the adsorption energy is -13.2 kcal x mol(-1). The latter value is close to experimental findings (-12 to -14 kcal x mol(-1)). Adsorption of formaldehyde on Pd4 supported on an Al10O15 cluster leads essentially to the same result as that found for adsorption on the tetrahedral Pd4 cluster. Charge density analysis for the interaction between formaldehyde and the Pd4 clusters indicates strong backdonation in the eta(2) adsorption mode, leading to positive charge on the Pd4 cluster. NBO analysis shows that the highly coordinated octahedral aluminum atoms of Al10O15 donate electron density to the supported Pd4 cluster, while tetrahedral aluminum atoms with lower coordination number have acidic nature and therefore act as electron acceptors.
Energy Technology Data Exchange (ETDEWEB)
Van Kuiken, Benjamin E.; Valiev, Marat; Daifuku, Stephanie L.; Bannan, Caitlin; Strader, Matthew L.; Cho, Hana; Huse, N.; Schoenlein, R. W.; Govind, Niranjan; Khalil, Munira
2013-05-01
Ruthenium L2,3-edge X-ray absorption (XA) spectroscopy probes transitions from core 2p orbitals to the 4d levels of the atom and is a powerful tool for interrogating the local electronic and molecular structure around the metal atom. However, a molecular-level interpretation of the Ru L2,3-edge spectral lineshapes is often complicated by spin–orbit coupling (SOC) and multiplet effects. In this study, we develop spin-free time-dependent density functional theory (TDDFT) as a viable and predictive tool to simulate the Ru L3-edge spectra. We successfully simulate and analyze the ground state Ru L3-edge XA spectra of a series of RuII and RuIII complexes: [Ru(NH3)6]2+/3+, [Ru(CN)6]4-/3-, [RuCl6]4-/3-, and the ground (1A1) and photoexcited (3MLCT) transient states of [Ru(bpy)3]2+ and Ru(dcbpy)2(NCS)2 (termed N3). The TDDFT simulations reproduce all the experimentally observed features in Ru L3-edge XA spectra. The advantage of using TDDFT to assign complicated Ru L3-edge spectra is illustrated by its ability to identify ligand specific charge transfer features in complex molecules. We conclude that the B3LYP functional is the most reliable functional for accurately predicting the location of charge transfer features in these spectra. Experimental and simulated Ru L3-edge XA spectra are presented for the transition metal mixed-valence dimers [(NC)5MII-CN-RuIII(NH3)5]- (where M = Fe or Ru) dissolved in water. We explore the spectral signatures of electron delocalization in Ru L3-edge XA spectroscopy and our simulations reveal that the inclusion of explicit solvent molecules is crucial for reproducing the experimentally determined valencies, highlighting the importance of the role of the solvent in transition metal charge transfer chemistry.
DEFF Research Database (Denmark)
Kuhlman, Thomas Scheby; Mikkelsen, Kurt V.; Møller, Klaus Braagaard;
2009-01-01
We present a study on the excited states of an ethylene dimer as to investigate the presence of and perturbation from low-lying charge-resonance states calculated by linear response density functional theory (DFT) using the B3LYP and CAM-B3LYP functionals. The calculations are compared to a refer......We present a study on the excited states of an ethylene dimer as to investigate the presence of and perturbation from low-lying charge-resonance states calculated by linear response density functional theory (DFT) using the B3LYP and CAM-B3LYP functionals. The calculations are compared...
Density functional theory: Foundations reviewed
Energy Technology Data Exchange (ETDEWEB)
Kryachko, Eugene S., E-mail: eugene.kryachko@ulg.ac.be [Bogolyubov Institute for Theoretical Physics, Kiev, 03680 (Ukraine); Ludeña, Eduardo V., E-mail: popluabe@yahoo.es [Centro de Química, Instituto Venezolano de Investigaciones Científicas, IVIC, Apartado 21827, Caracas 1020-A (Venezuela, Bolivarian Republic of); Prometheus Program, Senescyt (Ecuador); Grupo Ecuatoriano para el Estudio Experimental y Teórico de Nanosistemas, GETNano, USFQ, N104-E, Quito (Ecuador); Escuela Politécnica Superior del Litoral, ESPOL, Guayaquil (Ecuador)
2014-11-10
Guided by the above motto (quotation), we review a broad range of issues lying at the foundations of Density Functional Theory, DFT, a theory which is currently omnipresent in our everyday computational study of atoms and molecules, solids and nano-materials, and which lies at the heart of modern many-body computational technologies. The key goal is to demonstrate that there are definitely the ways to improve DFT. We start by considering DFT in the larger context provided by reduced density matrix theory (RDMT) and natural orbital functional theory (NOFT), and examine the implications that N-representability conditions on the second-order reduced density matrix (2-RDM) have not only on RDMT and NOFT but, also, by extension, on the functionals of DFT. This examination is timely in view of the fact that necessary and sufficient N-representability conditions on the 2-RDM have recently been attained. In the second place, we review some problems appearing in the original formulation of the first Hohenberg–Kohn theorem which is still a subject of some controversy. In this vein we recall Lieb’s comment on this proof and the extension to this proof given by Pino et al. (2009), and in this context examine the conditions that must be met in order that the one-to-one correspondence between ground-state densities and external potentials remains valid for finite subspaces (namely, the subspaces where all Kohn–Sham solutions are obtained in practical applications). We also consider the issue of whether the Kohn–Sham equations can be derived from basic principles or whether they are postulated. We examine this problem in relation to ab initio DFT. The possibility of postulating arbitrary Kohn–Sham-type equations, where the effective potential is by definition some arbitrary mixture of local and non-local terms, is discussed. We also deal with the issue of whether there exists a universal functional, or whether one should advocate instead the construction of problem
Koohi, M.; Soleimani Amiri, S.; Shariati, M.
2017-01-01
Density functional theory (DFT) calculations are applied to compare and contrast silicon atom substitution doped C20-nSin heterofullerene analogous with n = 1-10, at B3LYP/AUG-cc-pVTZ. Vibrational frequency analysis confirms that all studied systems are true minima. Isolating the dopants is an applicable strategy for obtaining highly doped stable heterofullerenes, since it avoids weak silicon―silicon single bonds. Comparing and contrasting the optimized geometries shows that except C11Si9 and C10Si10 species (with deformed cages of segregated analogous), all eight fullerenic cages are the complete isolated-pentagon analogous. Hence, the dopants must be completely isolated from each other by means of strong Cdbnd C double bonds. Isolable or extractable fullerene isomers must be not only thermodynamically but also stable against electronic excitations. We then predicted that these isomers must have not only relatively large heats of atomization per carbon as a criterion of thermodynamic stability but also relatively large HOMO-LUMO energy separation against electronic excitations. The calculated the highest binding energy (6.52 eV/atom), heat of atomization per carbon (3193.2 kcal mol-1), band gap (2.86 eV) and nucleus independent chemical shift at the cage center (-50.00 ppm) for C18Si2 reveals it as the most stable heterofullerene. It has Ci symmetry and contains two silicon atoms in equatorial. High charge transfer on the surfaces of our scrutinized heterofullerenes provokes further investigations on their possible application for hydrogen storage. We hope that the present study will stimulate new experiments.
Altun, Ahmet; Swesi, O. A. A.; Alhatab, B. S. S.
2017-01-01
The molecular structures, vibrational spectra (IR and Raman), electronic spectra (UV-Vis and DOS), and NMR spectra (13C and 1H) of p-anisaldehyde, m-anisaldehyde, and o-anisaldehyde have been studied by using the B3LYP density functional and the 6-311++G** basis set. While p-anisaldehyde has been found to contain two stable conformers at room temperature, m-anisaldehyde and o-anisaldehyde contain four stable conformers. In agreement with the calculated ground-state energetics and small transition barriers, the comparison of the experimental and calculated spectra of the anisaldehydes indicates equilibrium between all conformers at room temperature. However, the two conformers of o-anisaldehyde, in which the methoxy group lies out of the ring plane, are too rare at the equilibrium. The equilibrium conditions of the conformers of the anisaldehyde isomers have been shown readily accessible through UV-Vis and 13C NMR spectral studies but requiring very detailed vibrational analyses. The effect of the solvent has been found to red-shift the electronic absorption bands and to make the anisaldehydes more reactive and soft. Molecular electrostatic potential maps of the anisaldehydes show that their oxygen atoms are the sites for nucleophilic reactivity. Compared with the most sophisticated NBO method, ESP charges have been found mostly reliable while Mulliken charges fail badly with the present large 6-311++G** basis set. The present calculations reproduce not only the experimental spectral characteristics of the anisaldehydes but also reveal their several structural features.
Jeilani, Yassin A; Duncan, Kameron A; Newallo, Domnique S; Thompson, Albert N; Bose, Nripendra K
2015-05-15
Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is an explosive compound that finds a wide range of military and civilian applications. RDX has been a target in environmental matrices by gas chromatography/tandem mass spectrometry (GC/MS/MS). MS/MS in negative chemical ionization (NCI) mode of RDX provides important fragmentation patterns that are useful for structural elucidation. The fragmentation patterns are needed for proper identification of precursor and product ions in analytical methods that depend on MS/MS approaches for a reliable identification of RDX. This study focuses on the MS fragmentation mechanisms of RDX in NCI mode using both MS/MS and density functional theory (DFT). The DFT studies were performed at the B3LYP/6-311G(d,p) level of theory. The DFT results showed that NCI of RDX leads to the formation of an anion-molecule complex that was energetically more stable than the RDX anion. The fragmentation proceeds through two pathways, leading to the loss of NO(2) and NO(3). The loss of NO(3) takes place in an anion-molecule complex leading to the formation of characteristic nitroso group fragment ions. Using the fragmentation schemes, important ion structures are proposed including structures for m/z 160, 129, 102, and 86. The results demonstrate the importance of both charge-induced and charge-remote dissociations in RDX pathways. The ion structures identified along the pathways could be used as targets in analytical methods for reliable identification purposes. Copyright © 2015 John Wiley & Sons, Ltd.
Choubey, Sanjay K.; Mariadasse, Richard; Rajendran, Santhosh; Jeyaraman, Jeyakanthan
2016-12-01
Overexpression of HDAC1, a member of Class I histone deacetylase is reported to be implicated in breast cancer. Epigenetic alteration in carcinogenesis has been the thrust of research for few decades. Increased deacetylation leads to accelerated cell proliferation, cell migration, angiogenesis and invasion. HDAC1 is pronounced as the potential drug target towards the treatment of breast cancer. In this study, the biochemical potential of 6-aminonicotinamide derivatives was rationalized. Five point pharmacophore model with one hydrogen-bond acceptor (A3), two hydrogen-bond donors (D5, D6), one ring (R12) and one hydrophobic group (H8) was developed using 6-aminonicotinamide derivatives. The pharmacophore hypothesis yielded a 3D-QSAR model with correlation-coefficient (r2 = 0.977, q2 = 0.801) and it was externally validated with (r2pred = 0.929, r2cv = 0.850 and r2m = 0.856) which reveals the statistical significance of the model having high predictive power. The model was then employed as 3D search query for virtual screening against compound libraries (Zinc, Maybridge, Enamine, Asinex, Toslab, LifeChem and Specs) in order to identify novel scaffolds which can be experimentally validated to design future drug molecule. Density Functional Theory (DFT) at B3LYP/6-31G* level was employed to explore the electronic features of the ligands involved in charge transfer reaction during receptor ligand interaction. Binding free energy (ΔGbind) calculation was done using MM/GBSA which defines the affinity of ligands towards the receptor.
Minaeva, V A; Minaev, B F; Hovorun, D M
2008-01-01
The structure of estrogen receptors and their interaction with 17beta-estradiol and estriol are of particular interest today because the treatment of breast cancer and the cause of the disease are intricately linked to the activity of the estrogen receptor and the normal blood serum level of these hormones. Molecular geometry and vibration frequencies of these steroid hormones are calculated by density functional theory with the B3LYP/ 6-31G** approximation. Intensities of infrared absorption and Raman spectra for estradiol are in an agreement with the experiment data. The assignments of all vibrational bands in the spectra of these hormones are presented on the basis of quantum chemical calculations of frequencies and normal modes. For the large number of bands such an assignment is made for the first time. The analysis of infrared spectra of both hormones indicates some nontrivial structure-spectra correlations. A series of specific vibrations is predicted in the low-frequency region of the IR spectra; their role in hormone-receptor interaction and in energy transfer processes are discussed. The search of the optimized geometrical structure by minimization of the total energy gradient is accompanied by the second derivatives calculation; diagonalization of the Hessian matrix leads finally to solution of vibration problem. The 17beta-estradiol molecule consists of 44 atoms and has 126 normal modes of internal vibrations. All these normal modes are presented together with their analysis and comparison with experimental data. From this comparison we have obtained an assignment of all absorption IR bands of 17beta-estradiol recorded earlier in KBr. For all stretching vibrations our assignment is in agreement with the previous one, obtained on the basis of the empirical rules. Direct DFT calculation of vibrational frequencies cannot provide a 100% agreement with the experimental IR spectra and scaling factors in the range of 0.95-0.97 are used in order to fit
Sharma, Ashwani; Ohanessian, Gilles; Clavaguéra, Carine
2014-09-01
The performances of quantum chemistry methods (i.e., DFT and ab initio) in calculating the structural and vibrational properties of phosphates and phosphorylated compounds have been evaluated. Diethyl-phosphate, phosphonic acid, dihydrogen phosphate anion, phosphoric acid dimer and protonated glycylphosphotyrosine dipeptide were selected for our study. Geometry and harmonic frequency deviations were investigated, pointing out the contribution of dispersion interactions on diethyl-phosphate, [Gly-pTyr+H](+) and the phosphoric acid dimer. The B3LYP-D functional, followed by CC2 and MP2 methods, revealed significant accuracy for frequency calculations of the majority of the phosphorylated compounds in comparison with available experimental data. These investigations provide a guide to the accurate computation of phosphorylated biological compounds.
Directory of Open Access Journals (Sweden)
Omar Bin Shawkataly
Full Text Available A series of complexes of the type LAuCl where L = tris(p-tolylarsane, tris(m-tolylarsane, bis(diphenylarsanoethane, and tris(naphthylarsane have been synthesized. All of the new complexes, 1-4, have been fully characterized by means of ¹H NMR and ¹³C NMR spectroscopy and single crystal X-ray crystallography. The structures of complexes 1-4 have been determined from X-ray diffraction data. The linear molecules have an average bond distance between gold-arsenic and gold-chlorine of 2.3390Å and 2.2846Å, respectively. Aurophilic interaction was prominent in complex 1 and 3, whereas complex 2 and 4 do not show any such interaction. The intermolecular gold interaction bond length was affected by the electronegativity of the molecule. The computed values calculated at DFT level using B3LYP function are in good agreement with the experimental results.
Scaled density functional theory correlation functionals.
Ghouri, Mohammed M; Singh, Saurabh; Ramachandran, B
2007-10-18
We show that a simple one-parameter scaling of the dynamical correlation energy estimated by the density functional theory (DFT) correlation functionals helps increase the overall accuracy for several local and nonlocal functionals. The approach taken here has been described as the "scaled dynamical correlation" (SDC) method [Ramachandran, J. Phys. Chem. A 2006, 110, 396], and its justification is the same as that of the scaled external correlation (SEC) method of Brown and Truhlar. We examine five local and five nonlocal (hybrid) DFT functionals, the latter group including three functionals developed specifically for kinetics by the Truhlar group. The optimum scale factors are obtained by use of a set of 98 data values consisting of molecules, ions, and transition states. The optimum scale factors, found with a linear regression relationship, are found to differ from unity with a high degree of correlation in nearly every case, indicating that the deviation of calculated results from the experimental values are systematic and proportional to the dynamic correlation energy. As a consequence, the SDC scaling of dynamical correlation decreases the mean errors (signed and unsigned) by significant amounts in an overwhelming majority of cases. These results indicate that there are gains to be realized from further parametrization of several popular exchange-correlation functionals.
Di Valentin, Cristiana; Pacchioni, Gianfranco
2014-11-18
, for a more accurate description of the oxide band gap and of the electron localization of the impurity states associated with dopants or defects, we resorted to the use of hybrid functionals (B3LYP), where a portion of exact exchange in the exchange-correlation functional partly corrects for the self-interaction error inherent in DFT. In many cases, the self-interaction correction is very important, and these results can lead to a completely different physical picture than that obtained using local or semilocal functionals. We analyzed the electronic transitions in terms of their transition energy levels, which provided a more accurate comparison with experimental spectroscopic data than Kohn-Sham eigenvalues. The effects of N-doping were similar among the three oxides that we considered. The nature of the impurity state is always localized at the dopant site, which may limit their application in photocatalytic processes. Photocatalytic systems require highly delocalized photoexcited carriers within the material to effectively trigger redox processes at the surface. The nature of the electronic states associated with the oxygen deficiency differed widely in the three investigated oxides. In ZnO1-x and WO3-x the electronic states resemble the typical F-centers in insulating oxides or halides, with the excess electron density localized at the vacancy site. However, TiO2 acts as a reducible oxide, and the removal of neutral oxygen atoms reduced Ti(4+) to Ti(3+).
Energy Technology Data Exchange (ETDEWEB)
Valdes, Haydee; Pluhackova, Kristyna; Pitonak, Michal; Rezac, Jan; Hobza, Pavel
2008-03-13
A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A)—where F and W are of aromatic character—is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone–aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a ‘-D’ symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals—not covering this energy—fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.
Berski, Slawomir; Gordon, Agnieszka J
2011-09-07
In this paper, the electronic structures of cis- and trans-ClONO and BrONO are studied at the CCSD∕aug-cc-pVTZ, CASSCF(14,12)/aug-cc-pVTZ, and B3LYP/aug-cc-pVTZ computational levels. For the Cl-O bond, topological analysis of the electron density field, ρ(r), shows the prevalence of the shared-electron type bond (∇(2)ρ((3,-1)) 0). Topological analysis of the electron localization function, η(r), and electron localizability indicator (ELI-D), (D) (σ)(r), shows that the electronic structure of the central N-O bond is very sensitive to both electron correlation improvements (coupled-cluster single double (CCSD), CASSCF, density functional theory (DFT)) and bond length alteration. Depending on the method used, the N-O bond can be characterized as a "normal" N-O bond with a disynaptic V(N,O) basin (DFT); a protocovalent N-O bond with two monosynaptic, V(N) and V(O), basins (CCSD, CASSCF); or a new type, first discovered for FONO, characterized by a single monosynaptic, V(N) basin (CCSD, DFT). The total basin population oscillates between 0.46-0.96 e (CCSD) and 0.86-1.02 e (CASSCF). The X-O bond is described by the single disynaptic basin, V(X,O), with a basin population between 0.76 and 0.81 e (CCSD) or 0.77 and 0.85 e (CASSCF). Analysis of the localized electron detector distribution for the cis-Cl-O1-N=O2 shows a manifold in the Cl···O2 region, associated with decreased electron density. © 2011 American Institute of Physics
Jin, Xiaoyan; Yan, Yu; Shi, Wenjing; Bi, Shuping
2011-12-01
The structures and water-exchange reactions of aqueous aluminum-oxalate complexes are investigated using density functional theory. The present work includes (1) The structures of Al(C(2)O(4))(H(2)O)(4)(+) and Al(C(2)O(4))(2)(H(2)O)(2)(-) were optimized at the level of B3LYP/6-311+G(d,p). The geometries obtained suggest that the Al-OH(2) bond lengths trans to C(2)O(4)(2-) ligand in Al(C(2)O(4))(H(2)O)(4)(+) are much longer than the Al-OH(2) bond lengths cis to C(2)O(4)(2-). For Al(C(2)O(4))(2)(H(2)O)(2)(-), the close energies between cis and trans isomers imply the coexistence in aqueous solution. The (27)Al NMR and (13)C NMR chemical shifts computed with the consideration of sufficient solvent effect using HF GIAO method and 6-311+G(d,p) basis set are in agreement with the experimental values available, indicating the appropriateness of the applied models; (2) The water-exchange reactions of Al(III)-oxalate complexes were simulated at the same computational level. The results show that water exchange proceeds via dissociative pathway and the activation energy barriers are sensitive to the solvent effect. The energy barriers obtained indicate that the coordinated H(2)O cis to C(2)O(4)(2-) in Al(C(2)O(4))(H(2)O)(4)(+) is more labile than trans H(2)O. The water-exchange rate constants (k(ex)) of trans- and cis-Al(C(2)O(4))(2)(H(2)O)(2)(-) were estimated by four methods and their respective characteristics were explored; (3) The significance of the study on the aqueous aluminum-oxalate complexes to environmental chemistry is discussed. The influences of ubiquitous organic ligands in environment on aluminum chemistry behavior can be elucidated by extending this study to a series of Al(III)-organic system.
Directory of Open Access Journals (Sweden)
Man Wu
2009-08-01
Full Text Available In the present study, a theoretical study of 1,1-diaminohexaazidocyclo-tetraphophazene (DAHA and its isomers has been performed, using quantum computational density functional theory (B3LYP and B3PW91 methods with 6-31G* and 6-31G** basis sets implemented in Gaussian 03 program suite. Molecular structure and bonding, vibrational frequencies, Milliken population analysis, and natural bond orbit (NBO have been studied. The heats of formation from atomization energies have also been calculated based on the optimized geometry. The obtained heats of formation data are compared with their homologous cyclophosphazene in order to demonstrate the accuracy of the methods, which indicate that the studied compounds might be potentially used as high energetic materials. In addition, the relative stability of five isomers have been deduced based on the total energy and the gap of frontier orbital energies.
Multiconfiguration Pair-Density Functional Theory.
Li Manni, Giovanni; Carlson, Rebecca K; Luo, Sijie; Ma, Dongxia; Olsen, Jeppe; Truhlar, Donald G; Gagliardi, Laura
2014-09-09
We present a new theoretical framework, called Multiconfiguration Pair-Density Functional Theory (MC-PDFT), which combines multiconfigurational wave functions with a generalization of density functional theory (DFT). A multiconfigurational self-consistent-field (MCSCF) wave function with correct spin and space symmetry is used to compute the total electronic density, its gradient, the on-top pair density, and the kinetic and Coulomb contributions to the total electronic energy. We then use a functional of the total density, its gradient, and the on-top pair density to calculate the remaining part of the energy, which we call the on-top-density-functional energy in contrast to the exchange-correlation energy of Kohn-Sham DFT. Because the on-top pair density is an element of the two-particle density matrix, this goes beyond the Hohenberg-Kohn theorem that refers only to the one-particle density. To illustrate the theory, we obtain first approximations to the required new type of density functionals by translating conventional density functionals of the spin densities using a simple prescription, and we perform post-SCF density functional calculations using the total density, density gradient, and on-top pair density from the MCSCF calculations. Double counting of dynamic correlation or exchange does not occur because the MCSCF energy is not used. The theory is illustrated by applications to the bond energies and potential energy curves of H2, N2, F2, CaO, Cr2, and NiCl and the electronic excitation energies of Be, C, N, N(+), O, O(+), Sc(+), Mn, Co, Mo, Ru, N2, HCHO, C4H6, c-C5H6, and pyrazine. The method presented has a computational cost and scaling similar to MCSCF, but a quantitative accuracy, even with the present first approximations to the new types of density functionals, that is comparable to much more expensive multireference perturbation theory methods.
Functionalization of SBA-15 mesoporous silica by Cu-phosphonate units: Probing of synthesis route
Laskowski, Lukasz; Laskowska, Magdalena
2014-12-01
Mesoporous silica SBA-15 containing propyl-copper phosphonate units was investigated. The structure of mesoporous samples was tested by N2 isothermal sorption (BET and BHJ analysis), TEM microscopy and X-Ray scattering. Quantitative analysis EDX has given information about proportions between component atoms in the sample. Quantitative elemental analysis has been carried out to support EDX. To examine bounding between copper atoms and phosphonic units the Raman spectroscopy was carried out. As a support of Raman scattering, the theoretical calculations were made based on density functional theory, with the B3LYP method. By comparison of the calculated vibrational spectra of the molecule with experimental results, distribution of the active units inside silica matrix has been determined.
Gedanken Densities and Exact Constraints in Density Functional Theory
Perdew, John P; Sun, Jianwei; Burke, Kieron
2014-01-01
Approximations to the exact density functional for the exchange-correlation energy of a many-electron ground state can be constructed by satisfying constraints that are universal, i.e., valid for all electron densities. Gedanken densities are designed for the purpose of this construction, but need not be realistic. The uniform electron gas is an old gedanken density. Here, we propose a spherical two-electron gedanken density in which the dimensionless density gradient can be an arbitrary positive constant wherever the density is non-zero. The Lieb-Oxford lower bound on the exchange energy can be satisfied within a generalized gradient approximation (GGA) by bounding its enhancement factor or simplest GGA exchange-energy density. This enhancement-factor bound is well known to be sufficient, but our gedanken density shows that it is also necessary. The conventional exact exchange-energy density satisfies no such local bound, but energy densities are not unique, and the simplest GGA exchange-energy density is no...
Theoretical Study on the High Energy Density Compound Hexanitrohexaazatricyclotetradecanedifuroxan
Institute of Scientific and Technical Information of China (English)
QIU Ling; XIAO He-Ming; ZHU Wei-Hua; JU Xue-Hai; GONG Xue-Dong
2006-01-01
Density functional theory (DFT) has been employed to study the molecular geometries, electronic structures,infrared (IR) spectra, and thermodynamic properties of the high energy density compound hexanitrohexaazatricyclotetradecanedifuroxan (HHTTD) at the B3LYP/6-31G** level of theory. The calculated results showthattherearefourconformationalisomers (a, β, γ and δ) for HHTTD, and the relative stabilities of four conformers were assessed based on the calculated total energies and the energy-gaps between the frontier molecular orbitals. The computed harmonic vibrational frequencies are in reasonable agreement with the available experimental data. Thermodynamic properties derived from the IR spectra on the basis of statistical thermodynamic principles are linearly correlated with the temperature. Detonation performances were evaluated by using the Kamlet-Jacobsequationsbasedonthecalculated densities and heats of formation. It was found that four HHTTD isomers with the predicted densities of ca. 2 g·cm-3, detonation velocities near 10 km·s-1, and detonation pressures over 45 Gpa, may be novel potential candidates of high energy density materials (HEDM). These results may provide basic information for the molecular designof HEDM.
Bell Inequalities and Pseudo-functional densities
Geurdes, J F
2001-01-01
A local hidden variable model with pseudo-functional density function restricted to a binary probability event space is demonstrated to be able to reproduce the quantum correlation in an Einstein Podolsky Rosen Bohm and Aharonov type of experiment. In the density function use is made of Hadamard's finite part which disables the possibility to derive Bell's inequality from models with such a type of density function.
SOME QUANTUM CHEMICAL STUDY ON THE STRUCTURAL ...
African Journals Online (AJOL)
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Formula. Formula weight. (gmol-1) ... Quantum chemical calculations (Density Functional Theory, B3LYP/6-31G (d)) were used to purposed the ... correlation functional [B3LYP/6-31G(d)]) calculations were done by using Gaussian 03 program ...
Density functional theory calculations on dipeptide gallic acid interaction
Madhan, B.; Parthasarathi, R.; Subramanian, V.; Raghava Rao, J.; Nair, Balachandran Unni; Ramasami, T.
2003-02-01
In the present investigation, an attempt has been made to study the interaction of dipeptides with gallic acid, using Becke3 parameter Lee Yang Parr (B3LYP) method employing 3-21G*, 6-31G* and 6-31+G* basis sets. The interaction energies of the dipeptide-gallic acid complexes are in the range of -5 to -18 kcal/mol depending on the mode of intermolecular complexation. Calculated molecular electrostatic potential (MESP) for the various intermolecular complexes revealed the electrostatic nature of the interaction. Qualitative estimations based on chemical hardness and chemical potential demonstrated fractional electron transfer from dipeptide to gallic acid.
Density functional theory study of proton transfer in carbonic anhydrase
Institute of Scientific and Technical Information of China (English)
ZHANG Lidong; XIE Daiqian
2005-01-01
Proton transfer in carbonic anhydrase II has been studied at the B3LYP/6-31G(D) level. The active site model consists of the zinc ion, four histidine residues, two threonine residues, and three water molecules. Our calculations showed that the proton of the zinc-bound water molecule could be transferred to the nearest water molecule and an intermediate containing H3O+ is then formed. The intermediate is only 1.3 kJ·mol-1 above the reactant complex, whereas the barrier height for the proton transfer is about 8.1 kJ·mol-1.
Dove, P. M.; Wallace, A. F.; Gibbs, G. V.
2007-12-01
The dissolution of amorphous and crystalline varieties of SiO2 is an integral part of the global biogeochemical cycle of silicon. Nanoparticulate biogenic silica produced by marine phytoplankton and terrestrial plants are of particular interest because their enhanced reactivity and abundance make them important sources and sinks of dissolved silicon in natural environments. Recent experimental results on (100) surfaces of quartz show that the dominant dissolution mechanism in simple H2O solutions is by retreat of Q2 groups along step edges. In the presence of electrolytes, rates are accelerated by up to 100X in the presence by a crossover in the dominant dissolution mechanism to nucleation of vacancy islands at Q3 terminated species (Dove et al., PNAS, 2005). While the control of surface coordination in reactivity is clear, the molecular pathway by which electrolytes induce dissolution by a nucleated process remains poorly understood. The results of previous ab initio investigations of Si-O bond hydrolysis by water have demonstrated that the reaction proceeds through the dissociative adsorption of H2O at the silica surface, resulting in the formation of a pentacoordinated Si transition state, followed by the transfer of one of the water bound hydrogen atoms to a bridging oxygen in the SiO2 bonded network, and breakage of the Si-O bond. Assuming a similar reaction path, the specific effects of hydrated group II metal cations (Mg2+, Ca2+, Sr2+, Ba2+) on the energetics of Si-O bond hydrolysis have been investigated with density functional methods (B3LYP) and a relatively large neutral silica cluster (H8Si6O16). Reactant, product, and transition states for Q3 to Q2 hydrolysis in the presence and absence of the afore-mentioned cations have been determined with all electron (6-31G(d)) and effective core potential (SDDALL) Gaussian basis sets. The free energy of activation for Q3 to Q2 Si-O bond hydrolysis was determined to be approximately 5 kJ/mol lower for Ca2+ than Mg
A Density Functional Theory Study
Lim, XiaoZhi
2011-12-11
Complexes with pincer ligand moieties have garnered much attention in the past few decades. They have been shown to be highly active catalysts in several known transition metal-catalyzed organic reactions as well as some unprecedented organic transformations. At the same time, the use of computational organometallic chemistry to aid in the understanding of the mechanisms in organometallic catalysis for the development of improved catalysts is on the rise. While it was common in earlier studies to reduce computational cost by truncating donor group substituents on complexes such as tertbutyl or isopropyl groups to hydrogen or methyl groups, recent advancements in the processing capabilities of computer clusters and codes have streamlined the time required for calculations. As the full modeling of complexes become increasingly popular, a commonly overlooked aspect, especially in the case of complexes bearing isopropyl substituents, is the conformational analysis of complexes. Isopropyl groups generate a different conformer with each 120 ° rotation (rotamer), and it has been found that each rotamer typically resides in its own potential energy well in density functional theory studies. As a result, it can be challenging to select the most appropriate structure for a theoretical study, as the adjustment of isopropyl substituents from a higher-energy rotamer to the lowest-energy rotamer usually does not occur during structure optimization. In this report, the influence of the arrangement of isopropyl substituents in pincer complexes on calculated complex structure energies as well as a case study on the mechanism of the isomerization of an iPrPCP-Fe complex is covered. It was found that as many as 324 rotamers can be generated for a single complex, as in the case of an iPrPCP-Ni formato complex, with the energy difference between the global minimum and the highest local minimum being as large as 16.5 kcalmol-1. In the isomerization of a iPrPCP-Fe complex, it was found
Gupta, Mayuri; da Silva, Eirik F; Hartono, Ardi; Svendsen, Hallvard F
2013-08-15
Temperature dependent correlations for enthalpy of deprotonation, carbamate formation, and heat of absorption of the overall reaction between aqueous MEA and MDEA and gaseous CO2 are calculated on the basis of computational chemistry based ln K values input to the Gibbs-Helmholtz equation. Temperature dependency of reaction equilibrium constants for deprotonation and carbamate formation reactions is calculated with the SM8T continuum solvation model coupled with density functional theoretical calculations at the B3LYP/6-311++G(d,p) level of theory. Calculated reaction equilibrium constants and enthalpies of individual reactions and overall heat of absorption are compared against experimental data in the temperature range 273.15-373 K. Temperature dependent correlations for different reaction equilibrium constants and enthalpies of reactions are given. These correlated results can be used in thermodynamic models such as UNIQUAC and NRTL for better understanding of post-combustion CO2 capture solvent chemistry.
Energy Technology Data Exchange (ETDEWEB)
Van Kuiken, Benjamin E.; Valiev, Marat; Daifuku, Stephanie L.; Bannan, Caitlin; Strader, Matthew L.; Cho, Hana; Huse, Nils; Schoenlein, Robert W.; Govind, Niranjan; Khalil, Munira
2013-05-30
Ruthenium L3-edge X-ray absorption (XA) spectroscopy probes unoccupied 4d orbitals of the metal atom and is increasingly being used to investigate the local electronic structure in ground and excited electronic states of Ru complexes. The simultaneous development of computational tools for simulating Ru L3-edge spectra is crucial for interpreting the spectral features at a molecular level. This study demonstrates that time-dependent density functional theory (TDDFT) is a viable and predictive tool for simulating ruthenium L3-edge XA spectroscopy. We systematically investigate the effects of exchange correlation functional and implicit and explicit solvent interactions on a series of RuII and RuIII complexes in their ground and electronic excited states. The TDDFT simulations reproduce all of the experimentally observed features in Ru L3-edge XA spectra within the experimental resolution (0.4 eV). Our simulations identify ligand-specific charge transfer features in complicated Ru L3-edge spectra of [Ru(CN)6]4- and RuII polypyridyl complexes illustrating the advantage of using TDDFT in complex systems. We conclude that the B3LYP functional most accurately predicts the transition energies of charge transfer features in these systems. We use our TDDFT approach to simulate experimental Ru L3-edge XA spectra of transition metal mixed-valence dimers of the form [(NC)5MII-CN-RuIII(NH3)5] (where M = Fe or Ru) dissolved in water. Our study determines the spectral signatures of electron delocalization in Ru L3-edge XA spectra. We find that the inclusion of explicit solvent molecules is necessary for reproducing the spectral features and the experimentally determined valencies in these mixed-valence complexes. This study validates the use of TDDFT for simulating Ru 2p excitations using popular quantum chemistry codes and providing a powerful interpretive tool for equilibrium and ultrafast Ru L3-edge XA spectroscopy.
Joubert, Daniel P.
2012-03-01
It is shown that the density-functional-theory exchange and correlation functionals satisfy 0=γEhx[ρN]+2Ecγ[ρN]-γEhx[ρN-1γ]-2Ecγ[ρN-1γ]+2∫d3r'[ρN-10(r)-ρN-1γ(r)]v0([ρN];r)+∫d3r'[ρN-10(r)-ρN-1γ(r)]r·∇v0([ρN];r)+∫d3r'ρN(r)r·∇vcγ([ρN];r)-∫d3r'ρN-1γ(r)r·∇vcγ([ρN-1γ];r)-∫d3r'fγ(r)r·∇vhxcγ([ρN];r)-2∫d3r'fγ(r)vhxcγ([ρN];r). In the derivation of this equation the adiabatic connection formulation is used, where the ground-state density of an N-electron system ρN is kept constant independent of the electron-electron coupling strength γ. Here Ehx[ρ] is the Hartree plus exchange energy, Ecγ[ρ] is the correlation energy, vhxcγ[ρ] is the Hartree plus exchange-correlation potential, vc[ρ] is the correlation potential, and v0[ρ]is the Kohn-Sham potential. The charge densities ρN and ρN-1γ are the N- and (N-1)-electron ground-state densities of the same Hamiltonian at electron-electron coupling strength γ. fγ(r)=ρN(r)-ρN-1γ(r) is the Fukui function. This equation can be useful in testing the internal self-consistency of approximations to the exchange and correlation functionals. As an example the identity is tested on the analytical Hooke's atom charge density for some frequently used approximate functionals.
Kandasamy, M; Velraj, G; Kalaichelvan, S; Mariappan, G
2015-01-05
In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and natural bond orbital (NBO) analysis of 1,5-dimethoxynaphthalene. The optimized molecular structure, atomic charges, vibrational frequencies and natural bond orbital analysis of 1,5-dimethoxynaphthalene have been studied by performing DFT/B3LYP/6-31G(d,p) level of theory. The FTIR, FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The scaled wavenumbers are compared with the experimental values. The difference between the observed and scaled wavenumber values of the most fundamentals is very small. The formation of hydrogen bond was investigated in terms of the charge density by the NBO analysis. Natural Population Analysis (NPA) was used for charge determination in the title molecule. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations.
Oliveira, Leonardo B. A.; Fonseca, Tertius L.; Coutinho, Kaline; Canuto, Sylvio
2011-10-01
Solvatochromic shifts of the π-π∗ and n-π∗ transitions for the pyridinium-N-phenoxide [2-(pyridinium-1-yl)phenolate] betaine changing from vacuum to water, have been investigated using Monte Carlo simulations and time-dependent density functional theory schemes using standard and long-range corrected functionals. The classical Boltzmann distribution of the interring twist angle obtained from the calculated free energy agrees with a Car-Parrinello distribution. For the calculated spectral shifts BHandHLYP/6-311+G(2d,p) performs better than the CAM-B3LYP/6-311+G(2d,p) or LC-ωPBE/6-311+G(2d,p) model but the experimental shift is very well reproduced only after the inclusion of solute polarization and proper consideration of the twist geometry relaxation associated with the intramolecular charge transfer.
Density functional theory in quantum chemistry
Tsuneda, Takao
2014-01-01
This book examines density functional theory based on the foundation of quantum chemistry. Unconventional in approach, it reviews basic concepts, then describes the physical meanings of state-of-the-art exchange-correlation functionals and their corrections.
DEFF Research Database (Denmark)
List, Nanna Holmgaard; Olsen, Jógvan Magnus Haugaard; Rocha-Rinza, Tomás
2012-01-01
are found to give the overall best performance. The Coulomb-attenuated CAM-B3LYP functional systematically overestimates the excitation energies of the charged states; however, its error has the attractive feature of being size-independent and almost identical for the considered anionic and cationic systems...
A multiconfigurational hybrid density-functional theory
DEFF Research Database (Denmark)
Sharkas, Kamal; Savin, Andreas; Jensen, Hans Jørgen Aagaard
2012-01-01
We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension ...
A multiconfigurational hybrid density-functional theory
DEFF Research Database (Denmark)
Sharkas, Kamal; Savin, Andreas; Jensen, Hans Jørgen Aagaard
2012-01-01
We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension ...
Diwaker
2015-02-05
The geometric parameters, chemical shifts, FTIR, NMR and orbital overlap population along with DOS (density of states) to know different kinds of interactions for binding of copper atom with (E)-4-(2-(4-nitrophenyl) diazenyl)-N, N bis ((pyridin-2-yl) methyl) benzamine to form its copper complex has been reported by DFT methods. The theoretically predicted values for structural parameters are in agreement with the experimentally reported values. NMR chemical shifts calculated using B3LYP/DFT/GIAO level of theory gives information about binding of copper atom with three nitrogen atoms namely N (3, 8 and 11). Orbital overlap population analysis using DFT/B3LYP/SDD level of theory is used to study the kind of interactions involved in binding of copper with the three nitrogen atoms. DOS studies are done to know about the contribution of alpha, beta electrons to the valence and conduction band. IR spectroscopy investigations gave the absorption bands for the formation of title compound. Electronic spectrum along with HOMO-LUMO energies of the title compound has been investigated using Time-dependent (TD-DFT) approach.
Institute of Scientific and Technical Information of China (English)
廉鹏; 来蔚鹏; 常海波; 李亚南; 李辉; 杨威; 王友兵; 王伯周; 薛永强
2012-01-01
The structures and the stabilities of polynitrogen compounds N＋5Y^- [Y=B（CF3）4, BF4, PF6, and B（N3）4], as the potential high energy density compounds, have been investigated at the B3LYP/6-31G（d,p） and B3LYP/6-311 ＋G（d,p） levels. On the basis of our geometry optimization calculations, the structural properties of the N＋5Y^- compounds are discussed, and it is found that the combination of the N＋ cation and the Y- anions leads to dis- tortion of the structures of the Y anions. Based on the TS calculations for the N2-10ss dissociations of the N＋Y- compounds, the stabilities of these compounds are discussed, and the following conclusion can be drawn that among the four compounds, N＋B（CF3）4 is the most stable one and N＋B（N3）7 is the most unstable, and the relative stability of these compounds is always consistent using different basis sets. From these discussions, it is re- vealed that there are close correlations between the stuctrual distortions of the Y-anions and the stabilities of the N＋Y- compounds, and between the nitrogen content in the compounds and the stabilities of the N＋5Y^- compounds.
Magnetic fields and density functional theory
Energy Technology Data Exchange (ETDEWEB)
Salsbury Jr., Freddie [Univ. of California, Berkeley, CA (United States)
1999-02-01
A major focus of this dissertation is the development of functionals for the magnetic susceptibility and the chemical shielding within the context of magnetic field density functional theory (BDFT). These functionals depend on the electron density in the absence of the field, which is unlike any other treatment of these responses. There have been several advances made within this theory. The first of which is the development of local density functionals for chemical shieldings and magnetic susceptibilities. There are the first such functionals ever proposed. These parameters have been studied by constructing functionals for the current density and then using the Biot-Savart equations to obtain the responses. In order to examine the advantages and disadvantages of the local functionals, they were tested numerically on some small molecules.
Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Cech, Petr; Otyepka, Michal; Banáš, Pavel; Zgarbová, Marie; Jurečka, Petr; Sponer, Jiří
2013-05-21
The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by ΔCCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important families of DNA backbone conformations and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar-phosphate-sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-ζ basis set, which is, however, computationally very demanding. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as
A Tryst With Density: Walter Kohn and Density Functional Theory
Indian Academy of Sciences (India)
Shobhana Narasimhan
2017-08-01
Walter Kohn transformed theoretical chemistry and solid statephysics with his development of density functional theory, forwhich he was awarded the Nobel Prize. This article tries toexplain, in simple terms, why this was an important advancein the field, and to describe precisely what it was that he (togetherwith his collaborators Pierre Hohenberg and Lu JeuSham) achieved.
Multicomponent density functional theory embedding formulation.
Culpitt, Tanner; Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon
2016-07-28
Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF(-) molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.
Multicomponent density functional theory embedding formulation
Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.; Hammes-Schiffer, Sharon
2016-07-01
Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF- molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.
Locality of correlation in density functional theory.
Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano
2016-08-07
The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.
Density-functional theory of thermoelectric phenomena.
Eich, F G; Di Ventra, M; Vignale, G
2014-05-16
We introduce a nonequilibrium density-functional theory of local temperature and associated local energy density that is suited for the study of thermoelectric phenomena. The theory rests on a local temperature field coupled to the energy-density operator. We identify the excess-energy density, in addition to the particle density, as the basic variable, which is reproduced by an effective noninteracting Kohn-Sham system. A novel Kohn-Sham equation emerges featuring a time-dependent and spatially varying mass which represents local temperature variations. The adiabatic contribution to the Kohn-Sham potentials is related to the entropy viewed as a functional of the particle and energy density. Dissipation can be taken into account by employing linear response theory and the thermoelectric transport coefficients of the electron gas.
Directory of Open Access Journals (Sweden)
Bahjat A. Saeed
2010-01-01
Full Text Available Problem statement: QSAR techniques increase the probability of success and reduce time and coast in drug discovery process. The study presented QSAR investigation on 32 bioactive aziridinylbenzoquinones that have activity against lymphoid leukemia. Approach: Molecular descriptors, molecular weight, total energy, hardness, chemical potential, electrophilicity index, HOMO and LUMO energies were calculated. Initial geometry optimizations were carried out with the AM1 Hamiltonian. The lowest energy conformations were subjected to single point calculations by the DFT method by employing Beck's Three-Parameter hybrid functional (B3LYP and pvDZ basis set. Several models for the prediction of biological activity have been drawn up by using the multiple regression technique. Results: A model with hapta parametric linear equation with R2 value of 0.886 was presented. Conclusion: The biological activity of the studied compounds can be modeled with quantum chemical molecular descriptors.
Relativistic density functional for nuclear structure
2016-01-01
This book aims to provide a detailed introduction to the state-of-the-art covariant density functional theory, which follows the Lorentz invariance from the very beginning and is able to describe nuclear many-body quantum systems microscopically and self-consistently. Covariant density functional theory was introduced in nuclear physics in the 1970s and has since been developed and used to describe the diversity of nuclear properties and phenomena with great success. In order to provide an advanced and updated textbook of covariant density functional theory for graduate students and nuclear physics researchers, this book summarizes the enormous amount of material that has accumulated in the field of covariant density functional theory over the last few decades as well as the latest developments in this area. Moreover, the book contains enough details for readers to follow the formalism and theoretical results, and provides exhaustive references to explore the research literature.
Nuclear Energy Density Functional for KIDS
Gil, Hana; Hyun, Chang Ho; Park, Tae-Sun; Oh, Yongseok
2016-01-01
The density functional theory (DFT) is based on the existence and uniqueness of a universal functional $E[\\rho]$, which determines the dependence of the total energy on single-particle density distributions. However, DFT says nothing about the form of the functional. Our strategy is to first look at what we know, from independent considerations, about the analytical density dependence of the energy of nuclear matter and then, for practical applications, to obtain an appropriate density-dependent effective interaction by reverse engineering. In a previous work on homogeneous matter, we identified the most essential terms to include in our "KIDS" functional, named after the early-stage participating institutes. We now present first results for finite nuclei, namely the energies and radii of $^{16,28}$O, $^{40,60}$Ca.
A multiconfigurational hybrid density-functional theory
Sharkas, Kamal; Jensen, Hans Jørgen Aa; Toulouse, Julien; 10.1063/1.4733672
2012-01-01
We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension of the usual hybrid approximations by essentially adding a fraction \\lambda of exact static correlation in addition to the fraction \\lambda of exact exchange. Test calculations on the cycloaddition reactions of ozone with ethylene or acetylene and the dissociation of diatomic molecules with the Perdew-Burke-Ernzerhof (PBE) and Becke-Lee-Yang-Parr (BLYP) density functionals show that a good value of \\lambda is 0.25, as in the usual hybrid approximations. The results suggest that the proposed multiconfigurational hybrid approximations can improve over usual density-functional calculations for situations with strong static correlation effects.
Kumar, Amit; Deval, Vipin; Tandon, Poonam; Gupta, Archana; Deepak D'silva, E
2014-09-15
A combined experimental and theoretical investigation on FT-IR, FT-Raman, NMR, UV-vis spectra of a chalcone derivative (2E)-3-[4-(methylsulfanyl) phenyl]-1-(4-nitrophenyl) prop-2-en-1-one (4N4MSP) has been reported. 4N4MSP has two planar rings connected through conjugated double bond and it provides a necessary configuration to show non-linear optical (NLO) response. 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 density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set combination. The analysis of the fundamental modes was made with the help of potential energy distribution (PED). Molecular electrostatic potential (MEP) surface was plotted over the geometry primarily for predicting sites and relative reactivities towards electrophilic and nucleophilic attack. The delocalization of electron density of various constituents of the molecule has been discussed with the aid of NBO analysis. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were calculated by time-dependent density functional theory (TD-DFT) and the results complement the experimental findings. The recorded and calculated 1H chemical shifts in gas phase and MeOD solution are gathered for reliable calculations of magnetic properties. Thermodynamic properties like heat capacity (C°p,m), entropy (S°m), enthalpy (H°m) have been calculated for the molecule at the different temperatures. Based on the finite-field approach, the non-linear optical (NLO) parameters such as dipole moment, mean polarizability, anisotropy of polarizability and first order hyperpolarizability of 4N4MSP molecule are calculated. The predicted first hyperpolarizability shows that the molecule has a reasonably good nonlinear optical (NLO) behavior.
Development of New Density Functional Approximations
Su, Neil Qiang; Xu, Xin
2017-05-01
Kohn-Sham density functional theory has become the leading electronic structure method for atoms, molecules, and extended systems. It is in principle exact, but any practical application must rely on density functional approximations (DFAs) for the exchange-correlation energy. Here we emphasize four aspects of the subject: (a) philosophies and strategies for developing DFAs; (b) classification of DFAs; (c) major sources of error in existing DFAs; and (d) some recent developments and future directions.
Indian Academy of Sciences (India)
Heidar Raissi; Mehdi Yoosefian; Effat Moshfeghi; Farzaneh Farzad
2012-05-01
The characteristics of the intramolecular hydrogen bonding for a series of 19 different derivatives of -aminoacroleine have been systematically analysed at the B3LYP/6-31G∗∗ level of theory. The topological properties of the electron density distributions for N-H$\\cdots$O intramolecular bridges have been analysed by the Bader theory of atoms in molecules. The electron density () and Laplacian (∇2 ρ) properties at critical points of the relevant bonds, estimated by AIM calculations, showed that N-H$\\cdots$O have low and positive character (∇2 ρ > 0), consistent with electrostatic character of the hydrogen bond. The vibrational study of the hydrogen bonded systems showed negative (red) shifts for the (N−H) stretching mode. The -electron delocalization parameter () as a geometrical indicator of a local aromaticity and the geometry-based HOMA have also been calculated. Furthermore, the analysis of hydrogen bond in this molecule and its derivatives by natural bond orbital (NBO) methods support the DFT results. The results of AIM and NBO analysis as well as (N−H) were further used for estimation of the hydrogen bonding interactions and the forces driving their formation. The various correlations were found between geometrical, energetic and topological parameters. The substituent effect was also analysed and it was found that the strongest hydrogen bonds exist for N+(CH3)3 and Cl substituents while the weakest ones for COOCH3.
Calculations of Molar Fractions of the IPR C78 Fullerenes
Uhlík, Filip; Slanina, Zdeněk
2002-10-01
There are five isolated-pentagon-rule (IPR) satisfying isomers of C78. In contradiction to theoretical predictions, only three isomers were observed in experiments and the fourth one was not identified until very recently. In this work we calculate structural and energetic data of the five IPR C78 fullerenes, namely we optimized their geometries with the B3LYP density-functional method using the standard 4-31G basis set (B3LYP/4-31G), calculated separation energies at the B3LYP/6-311G* level (B3LYP/6-311G*//B3LYP/4-31G), estimated energies of low lying electronic states with the ZINDO semiempirical method and calculated harmonic vibrational frequencies with the semiempirical SAM1 method. From the obtained data we constructed chirality respecting isomeric partition functions and evaluated molar fractions in the equilibrium isomeric mixture for a wide temperature interval.
Whitenack, Daniel L; Wasserman, Adam
2012-04-28
Aspects of density functional resonance theory (DFRT) [D. L. Whitenack and A. Wasserman, Phys. Rev. Lett. 107, 163002 (2011)], a recently developed complex-scaled version of ground-state density functional theory (DFT), are studied in detail. The asymptotic behavior of the complex density function is related to the complex resonance energy and system's threshold energy, and the function's local oscillatory behavior is connected with preferential directions of electron decay. Practical considerations for implementation of the theory are addressed including sensitivity to the complex-scaling parameter, θ. In Kohn-Sham DFRT, it is shown that almost all θ-dependence in the calculated energies and lifetimes can be extinguished via use of a proper basis set or fine grid. The highest occupied Kohn-Sham orbital energy and lifetime are related to physical affinity and width, and the threshold energy of the Kohn-Sham system is shown to be equal to the threshold energy of the interacting system shifted by a well-defined functional. Finally, various complex-scaling conditions are derived which relate the functionals of ground-state DFT to those of DFRT via proper scaling factors and a non-Hermitian coupling-constant system.
Heuser, Johannes; Höfener, Sebastian
2017-10-15
We report the derivation and implementation of analytical nuclear gradients for excited states using time-dependent density functional theory using the Tamm-Dancoff approximation combined with uncoupled frozen-density embedding using density fitting. Explicit equations are presented and discussed. The implementation is able to treat singlet as well as triplet states and functionals using the local density approximation, the generalized gradient approximation, combinations with Hartree-Fock exchange (hybrids), and range-separated functionals such as CAM-B3LYP. The new method is benchmarked against supermolecule calculations in two case studies: The solvatochromic shift of the (vertical) fluorescence energy of 4-aminophthalimide on solvation, and the first local excitation of the benzonitrile dimer. Whereas for the 4-aminophthalimide-water complex deviations of about 0.2 eV are obtained to supermolecular calculations, for the benzonitrile dimer the maximum error for adiabatic excitation energies is below 0.01 eV due to a weak coupling of the subsystems. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Functional responses modified by predator density
Kratina, P.; Vos, M.; Bateman, A.W.; Anholt, B.R.
2009-01-01
Realistic functional responses are required for accurate model predictions at the community level. However, controversy remains regarding which types of dependencies need to be included in functional response models. Several studies have shown an effect of very high predator densities on per capita
Particle conservation in dynamical density functional theory.
de Las Heras, Daniel; Brader, Joseph M; Fortini, Andrea; Schmidt, Matthias
2016-06-22
We present the exact adiabatic theory for the dynamics of the inhomogeneous density distribution of a classical fluid. Erroneous particle number fluctuations of dynamical density functional theory are absent, both for canonical and grand canonical initial conditions. We obtain the canonical free energy functional, which yields the adiabatic interparticle forces of overdamped Brownian motion. Using an exact and one of the most advanced approximate hard core free energy functionals, we obtain excellent agreement with simulations. The theory applies to finite systems in and out of equilibrium.
Versatile Density Functionals for Computational Surface Science
DEFF Research Database (Denmark)
Wellendorff, Jess
Density functional theory (DFT) emerged almost 50 years ago. Since then DFT has established itself as the central electronic structure methodology for simulating atomicscale systems from a few atoms to a few hundred atoms. This success of DFT is due to a very favorable accuracy-to-computational c......Density functional theory (DFT) emerged almost 50 years ago. Since then DFT has established itself as the central electronic structure methodology for simulating atomicscale systems from a few atoms to a few hundred atoms. This success of DFT is due to a very favorable accuracy...... resampling techniques, thereby systematically avoiding problems with overfitting. The first ever density functional presenting both reliable accuracy and convincing error estimation is generated. The methodology is general enough to be applied to more complex functional forms with higher-dimensional fitting...
Integer Discontinuity of Density Functional Theory
Mosquera, Martin A
2014-01-01
Density functional approximations to the exchange-correlation energy of Kohn-Sham theory, such as the local density approximation and generalized gradient approximations, lack the well-known integer discontinuity, a feature that is critical to describe molecular dissociation correctly. Moreover, standard approximations to the exchange-correlation energy also fail to yield the correct linear dependence of the ground-state energy on the number of electrons when this is a non-integer number obtained from the grand canonical ensemble statistics. We present a formal framework to restore the integer discontinuity of any density functional approximation. Our formalism derives from a formula for the exact energy functional and a new constrained search functional that recovers the linear dependence of the energy on the number of electrons.
Density functional theory and multiscale materials modeling
Indian Academy of Sciences (India)
Swapan K Ghosh
2003-01-01
One of the vital ingredients in the theoretical tools useful in materials modeling at all the length scales of interest is the concept of density. In the microscopic length scale, it is the electron density that has played a major role in providing a deeper understanding of chemical binding in atoms, molecules and solids. In the intermediate mesoscopic length scale, an appropriate picture of the equilibrium and dynamical processes has been obtained through the single particle number density of the constituent atoms or molecules. A wide class of problems involving nanomaterials, interfacial science and soft condensed matter has been addressed using the density based theoretical formalism as well as atomistic simulation in this regime. In the macroscopic length scale, however, matter is usually treated as a continuous medium and a description using local mass density, energy density and other related density functions has been found to be quite appropriate. A unique single unified theoretical framework that emerges through the density concept at these diverse length scales and is applicable to both quantum and classical systems is the so called density functional theory (DFT) which essentially provides a vehicle to project the many-particle picture to a single particle one. Thus, the central equation for quantum DFT is a one-particle Schrödinger-like Kohn–Sham equation, while the same for classical DFT consists of Boltzmann type distributions, both corresponding to a system of noninteracting particles in the field of a density-dependent effective potential. Selected illustrative applications of quantum DFT to microscopic modeling of intermolecular interaction and that of classical DFT to a mesoscopic modeling of soft condensed matter systems are presented.
Noncovalent Interactions in Density-Functional Theory
DiLabio, Gino A
2014-01-01
Non-covalent interactions are essential in the description of soft matter, including materials of technological importance and biological molecules. In density-functional theory, common approaches fail to describe dispersion forces, an essential component in noncovalent binding interactions. In the last decade, great progress has been made in the development of accurate and computationally-efficient methods to describe noncovalently bound systems within the framework of density-functional theory. In this review, we give an account of the field from a chemical and didactic perspective, describing different approaches to the calculation of dispersion energies and comparing their accuracy, complexity, popularity, and general availability. This review should be useful to the newcomer who wants to learn more about noncovalent interactions and the different methods available at present to describe them using density-functional theory.
Connection formula for thermal density functional theory
Pribram-Jones, Aurora
2015-01-01
The adiabatic connection formula of ground-state density functional theory relates the correlation energy to a coupling-constant integral over a purely potential contribution, and is widely used to understand and improve approximations. The corresponding formula for thermal density functional theory is cast as an integral over temperatures instead, ranging upwards from the system's physical temperature to infinite temperatures. Several formulas yield one component of the thermal correlation free energy in terms of another, many of which can be expressed either in terms of temperature- or coupling-constant integration. We illustrate with the uniform electron gas.
Density functional calculations of nanoscale conductance
Energy Technology Data Exchange (ETDEWEB)
Koentopp, Max; Chang, Connie [Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854 (United States); Burke, Kieron [Department of Chemistry, UC Irvine, 1102 Natural Sciences 2, Irvine, CA 92697 (United States); Car, Roberto [Department of Chemistry and Princeton Institute for the Science and Technology of Materials (PRISM), Princeton University, Princeton, NJ 08544 (United States)
2008-02-27
Density functional calculations for the electronic conductance of single molecules are now common. We examine the methodology from a rigorous point of view, discussing where it can be expected to work, and where it should fail. When molecules are weakly coupled to leads, local and gradient-corrected approximations fail, as the Kohn-Sham levels are misaligned. In the weak bias regime, exchange-correlation corrections to the current are missed by the standard methodology. For finite bias, a new methodology for performing calculations can be rigorously derived using an extension of time-dependent current density functional theory from the Schroedinger equation to a master equation. (topical review)
Institute of Scientific and Technical Information of China (English)
YANG,En-Cui(杨恩翠); ZHAO,Xiao-Jun(赵小军); TIAN,Peng(田鹏); HAO,Jin-Ku(郝金库)
2004-01-01
The two possible reaction paths of producing ethane on coupling reaction of methane through plasma were theoretically investigated by B3LYP and MP2 methods with 6-311G* respectively and further compared with the previous results calculated from B3LYP/6-31G*.The new investigated results consistently confirmed the previous conclusion.And the influences of the calculation methods and basis sets on the calculated results were also discussed.
Molecular Density Functional Theory of Water
Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel; 10.1021/jz301956b
2013-01-01
Three dimensional implementations of liquid state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical) molecular density functional theory (MDFT) of water that is derived from first principles and is based on two classical density fields, a scalar one, the particle density, and a vectorial one, the multipolar polarization density. Its implementation requires as input the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the k-dependent longitudinal and transverse dielectric constants. It has to be complemented by a solute-solvent three-body term that reinforces tetrahedral order at short range. The approach is shown to provide the correct three-dimensional microscopic solvation profile around various molecular solutes, possibly possessing H-bonding sites, at a computer cost two-three orders of magnitude lower tha...
Density Functional Simulation of a Breaking Nanowire
DEFF Research Database (Denmark)
Nakamura, A.; Brandbyge, Mads; Hansen, Lars Bruno
1999-01-01
We study the deformation and breaking of an atomic-sized sodium wire using density functional simulations. The wire deforms through sudden atomic rearrangements and smoother atomic displacements. The conductance of the wire exhibits plateaus at integer values in units of 2e(2)/h corresponding...
Density functional and neural network analysis
DEFF Research Database (Denmark)
Jalkanen, K. J.; Bohr, Henrik
1997-01-01
Density functional theory (DFT) calculations have been carried out for hydrated L-alanine, L-alanyl-L-alanine and N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA) and vibrational circular...
Density functional theory with quantum nuclei
Requist, Ryan
2016-01-01
It is proved that the ground state energy of an electron-nuclear system is a variational functional of the conditional electronic density n_R(r), the nuclear wavefunction \\chi(R) and the quantum geometric tensor of the conditional electronic wavefunction $T_{\\mu\
Current Developments in Nuclear Density Functional Methods
Dobaczewski, J
2010-01-01
Density functional theory (DFT) became a universal approach to compute ground-state and excited configurations of many-electron systems held together by an external one-body potential in condensed-matter, atomic, and molecular physics. At present, the DFT strategy is also intensely studied and applied in the area of nuclear structure. The nuclear DFT, a natural extension of the self-consistent mean-field theory, is a tool of choice for computations of ground-state properties and low-lying excitations of medium-mass and heavy nuclei. Over the past thirty-odd years, a lot of experience was accumulated in implementing, adjusting, and using the density-functional methods in nuclei. This research direction is still extremely actively pursued. In particular, current developments concentrate on (i) attempts to improve the performance and precision delivered by the nuclear density-functional methods, (ii) derivations of density functionals from first principles rooted in the low-energy chromodynamics and effective th...
Density functional theory: Fixing Jacob's ladder
Car, Roberto
2016-09-01
Density functional theory calculations can be carried out with different levels of accuracy, forming a hierarchy that is often represented by the rungs of a ladder. Now a new method has been developed that significantly improves the accuracy of the 'third rung' when calculating the properties of diversely bonded systems.
Spin in Density-Functional Theory
Jacob, Christoph R; 10.1002/qua.24309
2012-01-01
The accurate description of open-shell molecules, in particular of transition metal complexes and clusters, is still an important challenge for quantum chemistry. While density-functional theory (DFT) is widely applied in this area, the sometimes severe limitations of its currently available approximate realizations often preclude its application as a predictive theory. Here, we review the foundations of DFT applied to open-shell systems, both within the nonrelativistic and the relativistic framework. In particular, we provide an in-depth discussion of the exact theory, with a focus on the role of the spin density and possibilities for targeting specific spin states. It turns out that different options exist for setting up Kohn-Sham DFT schemes for open-shell systems, which imply different definitions of the exchange-correlation energy functional and lead to different exact conditions on this functional. Finally, we suggest some possible directions for future developments.
Khan, Muntazir S; Krupadam, Reddithota J
2013-11-01
Molecular imprinting is an interesting technique for preparation of molecular recognition materials with discriminating similar molecules from complex systems. In particular, imprinting more than one molecule has immense application in remediation of industrial waste. Major difficulty in molecular imprinting is the selection of suitable polymer precursors. In this article, authors have proposed a new computational approach for combinatorial screening of polymer precursor library to select appropriate polymer precursors to prepare imprinted polymer capable of selectively binding carcinogenic polycyclic aromatic hydrocarbons (PAHs). Molecular Dynamics (MD) and Quantum Mechanics (QM) models were used to compute interaction energy scores between polymer precursors and PAHs in a simulated solvent box. A self-designed virtual library of functional monomers has been prepared, and then used for MD simulations to screen the best functional monomers. Initially, molecules used in the study were geometrically optimized and then interaction energies were computed using density functional theory (DFT) in Becke 3-Parameter Exchange Correlation Function (B3LYP) level with 6-31G*basis set on Gaussian 4.1 Ver. software. Complimentary to theoretical predictions, selected polymers were prepared in laboratory and compared theoretically computed binding score with the binding capacity of the polymer on spectrofluorimetry. The computer simulations used in this research paper are rapid and reliable for the combinatorial screening of polymer precursors in experimental-free way to design of multi-template imprinted polymers.
Hughes, Thomas F; Friesner, Richard A
2011-07-28
The mechanism of water oxidation by a single site ruthenium oxygen evolving complex is investigated using fully unrestricted pseudospectral B3LYP with the effective core potential LACV3P in continuum solvent with some quantum mechanical waters. Guess wave functions have been used that allow greater flexibility in sampling different electronic configurations of the complex. Systematic comparison with experiment is improved using these guesses because they provide a complete analysis of the low energy manifold and help to alleviate the formal disconnect between theory and experiment in assigning Lewis structures for transition metal complexes. In agreement with results from the literature, the challenging 4e(-)and 4H(+) oxidation of water is accomplished using a mechanism that features three proton coupled electron transfers, one electron transfer, one atom proton transfer (APT), and one ligand exchange (LE). Calculations on a large database of ruthenium complexes allows us to benchmark the computation of reduction half potentials and free energies of activation and to investigate systematic ligand variations and their effect on the reaction mechanism. Mean unsigned errors of reduction half potentials in comparison to experiment are generally small (100-200 mV). The APT and LE steps are found to be rate limiting with free energy barriers of 19.27 and 19.53 kcal/mol respectively, which is in excellent agreement with the ∼20 kcal/mol barrier obtained from experimental rate constants using classical transition state theory.
Wang, Nick X; Wilson, Angela K
2005-08-18
The HSO and HOS isomers have been revisited using the DFT functionals, B3LYP, B3PW91, and PBE, in combination with tight d-augmented correlation consistent basis sets, cc-pV(x+d)Z and aug-cc-pV(x+d)Z for second-row atoms. Structures, vibrationally averaged structures, relative energies, harmonic and anharmonic frequencies, enthalpies of formation of HSO and HOS, and the barrier for the HSO/HOS isomerization have been determined. These results were compared with results from previous DFT and ab initio studies in which the standard correlation consistent basis sets were used. The relative energies of the two isomers converge more rapidly and smoothly with respect to increasing basis set size for the tight d-augmented sets than for the standard basis sets. Our best calculations, B3PW91/aug-cc-pV(5+d)Z, for the relative energy of the isomers are in excellent agreement with previous CCSD(T) results given by Wilson and Dunning.
Adiabatic density-functional perturbation theory
Gonze, Xavier
1995-08-01
The treatment of adiabatic perturbations within density-functional theory is examined, at arbitrary order of the perturbation expansion. Due to the extremal property of the energy functional, standard variation-perturbation theorems can be used. The different methods (Sternheimer equation, extremal principle, Green's function, and sum over state) for obtaining the perturbation expansion of the wave functions are presented. The invariance of the Hilbert space of occupied wave functions with respect to a unitary transformation leads to the definition of a ``parallel-transport-gauge'' and a ``diagonal-gauge'' perturbation expansion. Then, the general expressions are specialized for the second, third, and fourth derivative of the energy, with an example of application of the method up to third order.
National Research Council Canada - National Science Library
Lee, Richmond; Tan, Davin; Liu, Chaoli; Li, Huaifeng; Guo, Hao; Shyue, Jing-Jong; Huang, Kuo-Wei
2017-01-01
Mechanistic insights into the selective C–H terminal activation of n-pentane with tungsten allyl nitrosyl complex reported by Legzdins were gained by employing density functional theory with B3LYP hybrid functional. Using...
Density functional theory on phase space
Blanchard, Philippe; Várilly, Joseph C
2010-01-01
Forty-five years after the point de d\\'epart [1] of density functional theory, its applications in chemistry and the study of electronic structures keep steadily growing. However, the precise form of the "divine" energy functional in terms of the electron density [2] still eludes us --and possibly will do so forever [3]. In what follows we examine a formulation in the same spirit with phase-space variables. The validity of Hohenberg-Kohn-Levy-type theorems on phase space is recalled. We study the representability problem for reduced Wigner functions, and proceed to analyze properties of the new functional. Along the way, new results on states in the phase-space formalism of quantum mechanics are established. Natural Wigner orbital theory is developed in depth, with the final aim of constructing accurate correlation-exchange functionals on phase space. A new proof of the overbinding property of the Mueller functional is given. This exact theory supplies its home at long last to that illustrious ancestor, the T...
Pressure Correction in Density Functional Theory Calculations
Lee, S H
2008-01-01
First-principles calculations based on density functional theory have been widely used in studies of the structural, thermoelastic, rheological, and electronic properties of earth-forming materials. The exchange-correlation term, however, is implemented based on various approximations, and this is believed to be the main reason for discrepancies between experiments and theoretical predictions. In this work, by using periclase MgO as a prototype system we examine the discrepancies in pressure and Kohn-Sham energy that are due to the choice of the exchange-correlation functional. For instance, we choose local density approximation and generalized gradient approximation. We perform extensive first-principles calculations at various temperatures and volumes and find that the exchange-correlation-based discrepancies in Kohn-Sham energy and pressure should be independent of temperature. This implies that the physical quantities, such as the equation of states, heat capacity, and the Gr\\"{u}neisen parameter, estimat...
Density functional theory a practical introduction
Sholl, David
2009-01-01
Demonstrates how anyone in math, science, and engineering can master DFT calculations Density functional theory (DFT) is one of the most frequently used computational tools for studying and predicting the properties of isolated molecules, bulk solids, and material interfaces, including surfaces. Although the theoretical underpinnings of DFT are quite complicated, this book demonstrates that the basic concepts underlying the calculations are simple enough to be understood by anyone with a background in chemistry, physics, engineering, or mathematics. The authors show how the widespread availability of powerful DFT codes makes it possible for students and researchers to apply this important computational technique to a broad range of fundamental and applied problems. Density Functional Theory: A Practical Introduction offers a concise, easy-to-follow introduction to the key concepts and practical applications of DFT, focusing on plane-wave DFT. The authors have many years of experience introducing DFT to studen...
Teaching Density Functional Theory Through Experiential Learning
Narasimhan, Shobhana
2015-09-01
Today, quantum mechanical density functional theory is often the method of choice for performing accurate calculations on atomic, molecular and condensed matter systems. Here, I share some of my experiences in teaching the necessary basics of solid state physics, as well as the theory and practice of density functional theory, in a number of workshops held in developing countries over the past two decades. I discuss the advantages of supplementing the usual mathematically formal teaching methods, characteristic of graduate courses, with the use of visual imagery and analogies. I also describe a successful experiment we carried out, which resulted in a joint publication co-authored by 67 lecturers and students participating in a summer school.
Pribram-Jones, Aurora
Warm dense matter (WDM) is a high energy phase between solids and plasmas, with characteristics of both. It is present in the centers of giant planets, within the earth's core, and on the path to ignition of inertial confinement fusion. The high temperatures and pressures of warm dense matter lead to complications in its simulation, as both classical and quantum effects must be included. One of the most successful simulation methods is density functional theory-molecular dynamics (DFT-MD). Despite great success in a diverse array of applications, DFT-MD remains computationally expensive and it neglects the explicit temperature dependence of electron-electron interactions known to exist within exact DFT. Finite-temperature density functional theory (FT DFT) is an extension of the wildly successful ground-state DFT formalism via thermal ensembles, broadening its quantum mechanical treatment of electrons to include systems at non-zero temperatures. Exact mathematical conditions have been used to predict the behavior of approximations in limiting conditions and to connect FT DFT to the ground-state theory. An introduction to FT DFT is given within the context of ensemble DFT and the larger field of DFT is discussed for context. Ensemble DFT is used to describe ensembles of ground-state and excited systems. Exact conditions in ensemble DFT and the performance of approximations depend on ensemble weights. Using an inversion method, exact Kohn-Sham ensemble potentials are found and compared to approximations. The symmetry eigenstate Hartree-exchange approximation is in good agreement with exact calculations because of its inclusion of an ensemble derivative discontinuity. Since ensemble weights in FT DFT are temperature-dependent Fermi weights, this insight may help develop approximations well-suited to both ground-state and FT DFT. A novel, highly efficient approach to free energy calculations, finite-temperature potential functional theory, is derived, which has the
General degeneracy in density functional perturbation theory
Palenik, Mark C
2016-01-01
Degenerate perturbation theory from quantum mechanics is inadequate in density functional theory (DFT) because of nonlinearity in the Kohn-Sham potential. We develop the fully general degenerate perturbation theory for DFT without assuming that the degeneracy is required by symmetry. The resulting methodology is applied to the iron atom ground state in order to demonstrate the effects of degeneracy that appears both due to symmetry requirements and accidentally, between different representations of the symmetry group.
Density Functional Theory Study on the Addition Reactions of 4-methyl-benzaldoximes with Propene
Institute of Scientific and Technical Information of China (English)
张健; 马金广
2009-01-01
The Michael addition reactions of Z and E 4-methyl-benzaldoximes with propene were investigated theoretically by DFT method at B3LYP/6-31G* level. The calculation results show that both addition reactions are concerted processes accompanied by the migration of hydrogen from the atom oxygen to carbon. Both products Z and E nitrones have dipolar charge distributions and activities. Z isomer is more favorable in the reaction due to the barrier is lower.
Institute of Scientific and Technical Information of China (English)
刘红飞
2015-01-01
There was a large number of O-H�X(X=N、O、S) hydrogen in thick oil which resulted the poor flowability, high vis-cosity and large intermolecular force. Using a transition metal compound as a catalyst to weaken the hydrogen bond was the primary method of reducing the intermolecular forces. CrCl3 attacking the O-H�X(X=N、O、S) hydrogen to weaken hydrogen was cal-culated with GAUSSIAN 03 package. The density functional method in its hybrid B3LYP functional was used in the calculations. The results showed that the hydrogen bond length was increased, the charge of N, O and S atom transfer, the system front energy gap drop. The hydrogen bonds were effectively weaken by CrCl3.%稠油分子间大量O-H�X(X=N、O、S)氢键，造成其分子间作用力、黏度较大，使用过渡金属化合物作为催化剂削弱氢键是降低分子间作用力的主要方法。采用密度泛函理论B3LYP方法，使用Gaussian 03程序，CrCl3作为催化剂，对稠油间CrCl3-O-H�X(X=N、O、S)氢键的攻击削弱情况进行了计算。结果表明，CrCl3不仅增加了氢键的键长，N、O、S的电荷发生了转移，同时还使得系统的前线能隙下降，有效地削弱了氢键。
Computing dispersion interactions in density functional theory
Cooper, V. R.; Kong, L.; Langreth, D. C.
2010-02-01
In this article techniques for including dispersion interactions within density functional theory are examined. In particular comparisons are made between four popular methods: dispersion corrected DFT, pseudopotential correction schemes, symmetry adapted perturbation theory, and a non-local density functional - the so called Rutgers-Chalmers van der Waals density functional (vdW-DF). The S22 benchmark data set is used to evaluate the relative accuracy of these methods and factors such as scalability and transferability are also discussed. We demonstrate that vdW-DF presents an excellent compromise between computational speed and accuracy and lends most easily to full scale application in solid materials. This claim is supported through a brief discussion of a recent large scale application to H2 in a prototype metal organic framework material (MOF), Zn2BDC2TED. The vdW-DF shows overwhelming promise for first-principles studies of physisorbed molecules in porous extended systems; thereby having broad applicability for studies as diverse as molecular adsorption and storage, battery technology, catalysis and gas separations.
Extended screened exchange functional derived from transcorrelated density functional theory
Umezawa, Naoto
2017-09-01
We propose a new formulation of the correlation energy functional derived from the transcorrelated method in use in density functional theory (TC-DFT). An effective Hamiltonian, HTC, is introduced by a similarity transformation of a many-body Hamiltonian, H , with respect to a complex function F: HTC=1/F H F . It is proved that an expectation value of HTC for a normalized single Slater determinant, Dn, corresponds to the total energy: E [n ] = ⟨Ψn|H |Ψn ⟩ /⟨Ψn|Ψn ⟩ = ⟨Dn|HTC|Dn ⟩ under the two assumptions: (1) The electron density n (r ) associated with a trial wave function Ψn = DnF is v -representable and (2) Ψn and Dn give rise to the same electron density n (r ). This formulation, therefore, provides an alternative expression of the total energy that is useful for the development of novel correlation energy functionals. By substituting a specific function for F, we successfully derived a model correlation energy functional, which resembles the functional form of the screened exchange method. The proposed functional, named the extended screened exchange (ESX) functional, is described within two-body integrals and is parametrized for a numerically exact correlation energy of the homogeneous electron gas. The ESX functional does not contain any ingredients of (semi-)local functionals and thus is totally free from self-interactions. The computational cost for solving the self-consistent-field equation is comparable to that of the Hartree-Fock method. We apply the ESX functional to electronic structure calculations for a solid silicon, H- ion, and small atoms. The results demonstrate that the TC-DFT formulation is promising for the systematic improvement of the correlation energy functional.
Density Functional Theory An Advanced Course
Dreizler, Reiner M
2011-01-01
Density Functional Theory (DFT) has firmly established itself as the workhorse for the atomic-level simulation of condensed matter phases, pure or composite materials and quantum chemical systems. The present book is a rigorous and detailed introduction to the foundations up to and including such advanced topics as orbital-dependent functionals and both time-dependent and relativistic DFT. Given the many ramifications of contemporary DFT, this text concentrates on the self-contained presentation of the basics of the most widely used DFT variants. This implies a thorough discussion of the corresponding existence theorems and effective single particle equations, as well as of key approximations utilized in implementations. The formal results are complemented by selected quantitative results, which primarily aim at illustrating strengths and weaknesses of a particular approach or functional. DFT for superconducting or nuclear and hadronic systems are not addressed in this work. The structure and material contain...
Splitting of the Ti-3d bands of TiSe2 in the charge-density wave phase
Ghafari, A.; Petaccia, L.; Janowitz, C.
2017-02-01
Very high resolution angular resolved photoemission (ARPES) spectra on TiSe2 in two distinct polarization geometries (vertical and horizontal) at temperatures between 300 K and 22 K enabled the observation of details of bands near the Fermi level not reported so far. Calculations of the electronic band structure based on density functional theory (DFT) using B3LYP hybrid functional and MBJ potential (with and without spin-orbit coupling) were performed to obtain the orbital symmetry and dispersion. Two degenerate conduction bands (CB's) were observed at the Γ-point, a weak CB- emission at the A-point, and two non degenerate CB's (i.e. splitting of CB) at the M/L-point of the Brillouin Zone (BZ). The splitting was detected at L for both polarizations, while at M remarkably only for horizontal polarization. These results cannot be fully accounted for by current theories for the charge density wave (CDW) and point to a reduced symmetry of the electronic states, possibly due to the chiral CDW.
Covariant density functional theory for nuclear matter
Energy Technology Data Exchange (ETDEWEB)
Badarch, U.
2007-07-01
The present thesis is organized as follows. In Chapter 2 we study the Nucleon-Nucleon (NN) interaction in Dirac-Brueckner (DB) approach. We start by considering the NN interaction in free-space in terms of the Bethe-Salpeter (BS) equation to the meson exchange potential model. Then we present the DB approach for nuclear matter by extending the BS equation for the in-medium NN interaction. From the solution of the three-dimensional in-medium BS equation, we derive the DB self-energies and total binding energy which are the main results of the DB approach, which we later incorporate in the field theoretical calculation of the nuclear equation of state. In Chapter 3, we introduce the basic concepts of density functional theory in the context of Quantum Hadrodynamics (QHD-I). We reach the main point of this work in Chapter 4 where we introduce the DDRH approach. In the DDRH theory, the medium dependence of the meson-nucleon vertices is expressed as functionals of the baryon field operators. Because of the complexities of the operator-valued functionals we decide to use the mean-field approximation. In Chapter 5, we contrast microscopic and phenomenological approaches to extracting density dependent meson-baryon vertices. Chapter 6 gives the results of our studies of the EOS of infinite nuclear matter in detail. Using formulas derived in Chapters 4 and 5 we calculate the properties of symmetric and asymmetric nuclear matter and pure neutron matter. (orig.)
Density Functional Approach Based on Numerically Obtained Bridge Functional
Institute of Scientific and Technical Information of China (English)
ZHOUShi－Qi
2002-01-01
The ornstein-zenike equation is solved with the Rogers-Young approximation for bulk hard sphere fluid and Lennard-Jones fluid for several state points.Then the resulted bulk fluid radial distribution function combined with the test particle method is employed to determine numerically the function relationship of bridge functional as a function of indirect correlation function.It is found that all of the calculated points from different phase space state points for a same type of fluid collapse onto a same smooth curve.Then the numerically obtained curve is used to substitute the analytic expression of the bridge functional as a function of indirect correlation function required in the methodology [J.Chem.Phys,112(2000)8079] to determine the density distribution of non-uniform hard sphere fluid and Lennard-Jones fluid.The good agreement of theoretical predictions with the computer simulation data is obtained.The present numerical procedure incroporates the knowledge of bulk fluid radial distribution function into the constructing of the density functional approximation and makes the original methodology more accurate and more filexible for various interaction potential fluid.
Insight and progress in density functional theory
Yang, Weitao; Mori-Sanchez, Paula; Cohen, Aron J.
2012-12-01
Density functional theory of electronic structure is widely and successfully applied in simulations throughout engineering and sciences. However, there are spectacular failures for many predicted properties. The errors include underestimation of the barriers of chemical reactions, the band gaps of materials, the energies of dissociating molecular ions and charge transfer excitation energies. Typical DFT calculations also fail to describe degenerate or near degenerate systems, as arise in the breaking of chemical bonds, and strongly correlated materials. These errors can all be characterized and understood through the perspective of fractional charges and fractional spins introduced recently.
Density functional and neural network analysis
DEFF Research Database (Denmark)
Jalkanen, K. J.; Bohr, Henrik
1997-01-01
Density functional theory (DFT) calculations have been carried out for hydrated L-alanine, L-alanyl-L-alanine and N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA) and vibrational circular...... dichroism (VCD) intensities. The large changes due to hydration on the structures, relative stability of conformers, and in the VA and VCD spectra observed experimentally are reproduced by the DFT calculations. Furthermore a neural network was constructed for reproducing the inverse scattering data (infer...
Modulation Based on Probability Density Functions
Williams, Glenn L.
2009-01-01
A proposed method of modulating a sinusoidal carrier signal to convey digital information involves the use of histograms representing probability density functions (PDFs) that characterize samples of the signal waveform. The method is based partly on the observation that when a waveform is sampled (whether by analog or digital means) over a time interval at least as long as one half cycle of the waveform, the samples can be sorted by frequency of occurrence, thereby constructing a histogram representing a PDF of the waveform during that time interval.
Energy Technology Data Exchange (ETDEWEB)
Mattsson, Ann Elisabet; Modine, Normand Arthur; Desjarlais, Michael Paul; Muller, Richard Partain; Sears, Mark P.; Wright, Alan Francis
2006-11-01
A finite temperature version of 'exact-exchange' density functional theory (EXX) has been implemented in Sandia's Socorro code. The method uses the optimized effective potential (OEP) formalism and an efficient gradient-based iterative minimization of the energy. The derivation of the gradient is based on the density matrix, simplifying the extension to finite temperatures. A stand-alone all-electron exact-exchange capability has been developed for testing exact exchange and compatible correlation functionals on small systems. Calculations of eigenvalues for the helium atom, beryllium atom, and the hydrogen molecule are reported, showing excellent agreement with highly converged quantumMonte Carlo calculations. Several approaches to the generation of pseudopotentials for use in EXX calculations have been examined and are discussed. The difficult problem of finding a correlation functional compatible with EXX has been studied and some initial findings are reported.
Directory of Open Access Journals (Sweden)
F.Z. MIMOUNI
2013-03-01
Full Text Available The isolation of the pair atropisomers of the both iminothiazoline derivatives and the spectroscopic analytical of the compound have been computed using B3LYP/6-31G(d,p level to derive the equilibrium geometry, conformational stability, molecular orbital energies and vibrational frequencies was studied in this paper.
Density Functional Approach Based on Numerically Obtained Bridge Functional
Institute of Scientific and Technical Information of China (English)
ZHOU Shi-Qi
2002-01-01
The Ornstein Zernike equation is solved with the Rogers Young approximation for bulk hard sphere fluidand Lennard-Jones fluid for several state points. Then the resulted bulk fluid radial distribution function combinedwith the test particle method is employed to determine numerically the function relationship of bridge functional as afunction of indirect correlation function. It is found that all of the calculated points from different phase space statepoints for a same type of fluid collapse onto a same smooth curve. Then the numerically obtained curve is used tosubstitute the analytic expression of the bridge functional as a function of indirect correlation function required in themethodology [J. Chem. Phys. 112 (2000) 8079] to deterrnine the density distribution of non-uniform hard spherefluid and Lennard Jones fluid. The good agreement of theoretical predictions with the computer simulation data isobtained. The present numerical procedure incorporates the knowledge of bulk fluid radial distribution function intothe constructing of the density functional approximation and makes the original methodology more accurate and moreflexible for various interaction potential fluid.
Interpretation of van der Waal density functionals
Hyldgaard, Per; Schröder, Elsebeth
2014-01-01
The nonlocal correlation energy in the van der Waals density functional (vdW-DF) method [Phys. Rev. Lett. 92, 246401 (2004); Phys. Rev. B 76, 125112 (2007); Phys. Rev. B 89, 035412 (2014)] can be interpreted in terms of a coupling of zero-point energies of characteristic modes of semilocal exchange-correlation (xc) holes. These xc holes reflect the internal functional in the framework of the vdW-DF method [Phys. Rev. B 82, 081101(2010)]. We explore the internal xc hole components, showing that they share properties with those of the generalized-gradient approximation. We use these results to illustrate the nonlocality in the vdW-DF description and analyze the vdW-DF formulation of nonlocal correlation.
Quantal density functional theory. 2. ed.
Energy Technology Data Exchange (ETDEWEB)
Sahni, Viraht
2016-07-01
This book is on quantal density functional theory (QDFT) which is a time-dependent local effective potential theory of the electronic structure of matter. The time-independent QDFT constitutes a special case. The 2{sup nd} edition describes the further development of the theory, and extends it to include the presence of an external magnetostatic field. The theory is based on the 'quantal Newtonian' second and first laws for the individual electron. These laws are in terms of 'classical' fields that pervade all space, and their quantal sources. The fields are separately representative of the electron correlations that must be accounted for in local potential theory. Recent developments show that irrespective of the type of external field the electrons are subject to, the only correlations beyond those due to the Pauli exclusion principle and Coulomb repulsion that need be considered are solely of the correlation-kinetic effects. Foundational to QDFT, the book describes Schroedinger theory from the new perspective of the single electron in terms of the 'quantal Newtonian' laws. Hohenberg-Kohn density functional theory (DFT), new understandings of the theory and its extension to the presence of an external uniform magnetostatic field are described. The physical interpretation via QDFT, in terms of electron correlations, of Kohn-Sham DFT, approximations to it and Slater theory are provided.
Rahman, Taj Ur; Arfan, Mohammad; Mahmood, Tariq; Liaqat, Wajiha; Gilani, Mazhar Amjad; Uddin, Ghias; Ludwig, Ralf; Zaman, Khair; Choudhary, M. Iqbal; Khattak, Khanzadi Fatima; Ayub, Khurshid
2015-07-01
The phytochemical examination of chloroform soluble fraction (FX2) of methanolic extract of bark of Millettia ovalifolia yielded a new flavonoid; 7-(4-methoxyphenyl)-9H-furo [2,3-f]chromen-9-one (1). Compound 1 is characterized by spectroscopic analytical techniques such as UV, IR, 1D, 2D NMR spectroscopy, and mass spectrometry. A theoretical model is also developed for obtaining geometric, electronic and spectroscopic properties of 1. The geometry optimization and harmonic vibration simulations have been carried out at B3LYP/6-31G(d,p). The vibrational spectrum of compound 1 shows nice correlation with the experimental IR spectrum, through a scaling factor of 0.9613. 1H and 13C NMR chemical shifts are simulated using Cramer's re-parameterized function WP04 at 6-31G(d,p) basis set, and correlate nicely with the experimental chemical shifts.
Universality principle and the development of classical density functional theory
Institute of Scientific and Technical Information of China (English)
周世琦; 张晓琪
2002-01-01
The universality principle of the free energy density functional and the ‘test particle' trick by Percus are combined to construct the approximate free energy density functional or its functional derivative. Information about the bulk fluid ralial distribution function is integrated into the density functional approximation directly for the first time in the present methodology. The physical foundation of the present methodology also applies to the quantum density functional theory.
Wang, Fang; Du, Hongchen; Zhang, Jianying; Gong, Xuedong
2011-10-27
Studies have suggested that octanitrocubane (ONC) is one of the most powerful non-nuclear high energy density material (HEDM) currently known. 2,4,6,8-Tetranitro-1,3,5,7-tetraazacubane (TNTAC) studied in this work may also be a novel HEDM due to its high nitrogen content and crystal density. Density functional theory and molecular mechanics methods have been employed to study the crystal structure, IR spectrum, electronic structure, thermodynamic properties, gas-phase and condensed-phase heat of formation, detonation performance, and pyrolysis mechanism of TNTAC. The TNTAC has a predicted density of about 2.12 g/cm(3), and its detonation velocity (10.42 km/s) and detonation pressure (52.82 GPa) are higher than that of ONC. The crystalline packing is P2(1)2(1)2(1), and the corresponding cell parameters are Z = 4, a = 8.87 Å, b = 8.87 Å, and c = 11.47 Å. Both the density of states of the predicted crystal and the bond dissociation energy of the molecule in gas phase show that the cage C-N bond is the trigger bond during thermolysis. The activation energy of the pyrolysis initiation reaction obtained from the B3LYP/6-311++G(2df,2p) level is 125.98 kJ/mol, which indicates that TNTAC meets the thermal stability request as an exploitable HEDM.
Nitrogenase structure and function relationships by density functional theory.
Harris, Travis V; Szilagyi, Robert K
2011-01-01
Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we provide a review with extensive practical details of the compilation and evaluation of experimental data for an unbiased and systematic density functional theory analysis that can lead to remarkable new insights about the structure-function relationships of the iron-sulfur clusters of nitrogenase.
Comparison of density estimators. [Estimation of probability density functions
Energy Technology Data Exchange (ETDEWEB)
Kao, S.; Monahan, J.F.
1977-09-01
Recent work in the field of probability density estimation has included the introduction of some new methods, such as the polynomial and spline methods and the nearest neighbor method, and the study of asymptotic properties in depth. This earlier work is summarized here. In addition, the computational complexity of the various algorithms is analyzed, as are some simulations. The object is to compare the performance of the various methods in small samples and their sensitivity to change in their parameters, and to attempt to discover at what point a sample is so small that density estimation can no longer be worthwhile. (RWR)
Zhang, Jian-ying; Du, Hong-chen; Wang, Fang; Gong, Xue-dong; Huang, Yin-sheng
2011-06-23
Polynitro cage compound 4-trinitroethyl-2,6,8,10,12-pentanitrohexaazaisowurtzitane has the same framework with but higher stability than CL-20 and is a potential new high energy density compound (HEDC). In this paper, the B3LYP/6-31G(d,p) method of density functional theory (DFT) has been used to study its heat of formation, IR spectrum, and thermodynamic properties. The stability of the compound was evaluated by the bond dissociation energies. The calculated results show that the first step of pyrolysis is the rupture of the N-NO(2) bond in the side chain and verify the experimental observation that the title compound has better stability than CL-20. The crystal structure obtained by molecular mechanics belongs to the P2(1)2(1)2(1) space group, with lattice parameters a = 12.59 Å, b = 10.52 Å, c = 12.89 Å, Z = 4, and ρ = 2.165 g·cm(-3). Both the detonation velocity of 9.767 km·s(-1) and the detonation pressure of 45.191 GPa estimated using the Kamlet-Jacobs equation are better than those of CL-20. Considering that this cage compound has a better detonation performance and stability than CL-20, it may be a superior HEDC.
Directory of Open Access Journals (Sweden)
Jiguang Du
2016-04-01
Full Text Available The interaction natures between Pu and different ligands in several plutonyl (VI complexes are investigated by performing topological analyses of electron density. The geometrical structures in both gaseous and aqueous phases are obtained with B3LYP functional, and are generally in agreement with available theoretical and experimental results when combined with all-electron segmented all-electron relativistic contracted (SARC basis set. The Pu– O y l bond orders show significant linear dependence on bond length and the charge of oxygen atoms in plutonyl moiety. The closed-shell interactions were identified for Pu-Ligand bonds in most complexes with quantum theory of atoms in molecules (QTAIM analyses. Meanwhile, we found that some Pu–Ligand bonds, like Pu–OH−, show weak covalent. The interactive nature of Pu–ligand bonds were revealed based on the interaction quantum atom (IQA energy decomposition approach, and our results indicate that all Pu–Ligand interactions is dominated by the electrostatic attraction interaction as expected. Meanwhile it is also important to note that the quantum mechanical exchange-correlation contributions can not be ignored. By means of the non-covalent interaction (NCI approach it has been found that some weak and repulsion interactions existed in plutonyl(VI complexes, which can not be distinguished by QTAIM, can be successfully identified.
Gandhimathi, S.; Balakrishnan, C.; Theetharappan, M.; Neelakantan, M. A.; Venkataraman, R.
2017-03-01
Two Schiff bases were prepared by the condensation of o-allyl substituted 2,4-dihydroxy acetophenone with 1,2-diaminopropane (L1) and ethanediamine (L2) and characterized by elemental analysis, and ESI-MS, IR, UV-Vis, 1H and 13C NMR spectral techniques. The effect of solvents with respect to different polarities on UV-Vis and emission spectra of L1 and L2 was investigated at room temperature show that the compounds exist in keto and enol forms in solution and may be attributed to the intramolecular proton transfer in the ground state. The solute-solvent interactions, change in dipole moment and solvatochromic properties of the compounds were studied based on the solvent polarity parameters. For L1 and L2, the ground and excited state electronic structure calculations were carried out by DFT and TD-DFT at B3LYP/6-311G (d,p) level, respectively. The IR, NMR and electronic absorption spectra computed were compared with the experimental observations. The intramolecular charge transfer within the molecule is evidenced from the HOMO and LUMO energy levels and surface analysis. The noncovalent interactions like hydrogen bonding and van der Waals interactions were identified from the molecular geometry and electron localization function. These interactions in molecules have been studied by using reduced density gradient and graphed by Multiwfn.
Energy Technology Data Exchange (ETDEWEB)
Kapoor, Varun; Brics, Martins; Bauer, Dieter [Institut fuer Physik, Universitaet Rostock, 18051 Rostock (Germany)
2013-07-01
Autoionizing states are inaccessible to time-dependent density functional theory (TDDFT) using known, adiabatic Kohn-Sham (KS) potentials. We determine the exact KS potential for a numerically exactly solvable model Helium atom interacting with a laser field that is populating an autoionizing state. The exact single-particle density of the population in the autoionizing state corresponds to that of the energetically lowest quasi-stationary state in the exact KS potential. We describe how this exact potential controls the decay by a barrier whose height and width allows for the density to tunnel out and decay with the same rate as in the ab initio time-dependent Schroedinger calculation. However, devising a useful exchange-correlation potential that is capable of governing such a scenario in general and in more complex systems is hopeless. As an improvement over TDDFT, time-dependent reduced density matrix functional theory has been proposed. We are able to obtain for the above described autoionization process the exact time-dependent natural orbitals (i.e., the eigenfunctions of the exact, time-dependent one-body reduced density matrix) and study the potentials that appear in the equations of motion for the natural orbitals and the structure of the two-body density matrix expanded in them.
General degeneracy in density functional perturbation theory
Palenik, Mark C.; Dunlap, Brett I.
2017-07-01
Degenerate perturbation theory from quantum mechanics is inadequate in density functional theory (DFT) because of nonlinearity in the Kohn-Sham potential. Herein, we develop the fully general perturbation theory for open-shell, degenerate systems in Kohn-Sham DFT, without assuming the presence of symmetry or equal occupation of degenerate orbitals. To demonstrate the resulting methodology, we apply it to the iron atom in the central field approximation, perturbed by an electric quadrupole. This system was chosen because it displays both symmetry required degeneracy, between the five 3 d orbitals, as well as accidental degeneracy, between the 3 d and 4 s orbitals. The quadrupole potential couples the degenerate 3 d and 4 s states, serving as an example of the most general perturbation.
Phases of Polonium via Density Functional Theory
Verstraete, Matthieu J.
2010-01-01
The thermodynamical properties of the main phases of metallic polonium are examined using density functional theory. The exceptional nature of the solid-solid phase transition of α to β Po is underlined: it induces a lowering in symmetry, from cubic to rhombohedral, with increasing temperature. This is explained as the result of a delicate balance between bonding and entropic effects. Overall agreement with existing experimental data is good by state-of-the-art standards. The phonons of Po present Kohn anomalies, and it is shown that the effect of spin-orbit interactions is the inverse of that in normal metals: due to the nonspherical nature of the Fermi Surface, spin-orbit effects reduce nesting and harden most phonon frequencies.
Effective potential in density matrix functional theory.
Nagy, A; Amovilli, C
2004-10-01
In the previous paper it was shown that in the ground state the diagonal of the spin independent second-order density matrix n can be determined by solving a single auxiliary equation of a two-particle problem. Thus the problem of an arbitrary system with even electrons can be reduced to a two-particle problem. The effective potential of the two-particle equation contains a term v(p) of completely kinetic origin. Virial theorem and hierarchy of equations are derived for v(p) and simple approximations are proposed. A relationship between the effective potential u(p) of the shape function equation and the potential v(p) is established.
Khanniche, Sarah; Louis, Florent; Cantrel, Laurent; Černušák, Ivan
2016-03-17
To get an insight into the possible reactivity between iodine oxides and CO, a first step was to study the thermochemical properties and kinetic parameters of the reaction between IO and CO using theoretical chemistry tools. All stationary points involved were optimized using the Becke's three-parameter hybrid exchange functional coupled with the Lee-Yang-Parr nonlocal correlation functional (B3LYP) and the Møller-Plesset second-order perturbation theory (MP2). Single-point energy calculations were performed using the coupled cluster theory with the iterative inclusion of singles and doubles and the perturbative estimation for triple excitations (CCSD(T)) and the aug-cc-pVnZ (n = T, Q, and 5) basis sets on geometries previously optimized at the aug-cc-pVTZ level. The energetics was then recalculated using the one-component DK-CCSD(T) approach with the relativistic ANO basis sets. The spin-orbit coupling for the iodine containing species was calculated a posteriori using the restricted active space state interaction method in conjunction with the multiconfigurational perturbation theory (CASPT2/RASSI) employing the complete active space (CASSCF) wave function as the reference. The CCSD(T) energies were also corrected for BSSE for molecular complexes and refined with the extrapolation to CBS limit while the DK-CCSD(T) values were refined with the extrapolation to FCI. The exploration of the potential energy surface revealed a two-steps mechanism with a trans and a cis pathway. The rate constants for the direct and complex mechanism were computed as a function of temperature (250-2500 K) using the canonical transition state theory. The three-parameter Arrhenius expressions obtained for the direct and indirect mechanism at the DK-CCSD(T)-cf level of theory is 1.49 × 10(-17) × T(1.77) exp(-47.4 (kJ mol(-1))/RT).
Kolev, Stefan K; St Petkov, Petko; Rangelov, Miroslav A; Vayssilov, Georgi N
2011-12-08
Various hydrogen-bonded complexes of methanol with different proton accepting and proton donating molecules containing Cl, F, NH(2), OH, OR, and COOH functional groups have been modeled using DFT with hybrid B3LYP and M05-2X functionals. The latter functional was found to provide more accurate estimates of the structural and thermodynamic parameters of the complexes of halides, amines, and alcohols. The characteristics of these complexes are influenced not only by the principle hydrogen bond of the methanol OH with the proton acceptor heteroatom, but also by additional hydrogen bonds of a C-H moiety with methanol oxygen as a proton acceptor. The contribution of the former hydrogen bond in the total binding enthalpy increases in the order chlorides contribution of the second type of hydrogen bond increases in the reverse order. A general correlation was found between the binding enthalpy of the complex and the electrostatic potential at the hydrogen center participating in the formation of the hydrogen bond. The calculated binding enthalpies of different complexes were used to clarify which functional groups can potentially form a hydrogen bond to the 2'-OH hydroxyl group in ribose, which is strong enough to block it from participation in the intramolecular catalytic activation of the peptide bond synthesis. Such blocking could result in inhibition of the protein biosynthesis in the living cell if the corresponding group is delivered as a part of a drug molecule in the vicinity of the active site in the ribosome. According to our results, such activity can be accomplished by secondary or tertiary amines, alkoxy groups, deprotonated carboxyl groups, and aliphatic fluorides, but not by the other modeled functional groups.
DEFF Research Database (Denmark)
Aidas, Kestutis; Møgelhøj, Andreas; Nilsson, Elna Johanna Kristina
2008-01-01
The performance of the Hartree–Fock method and the three density functionals B3LYP, PBE0, and CAM-B3LYP is compared to results based on the coupled cluster singles and doubles model in predictions of the solvatochromic effects on the vertical n¿* and ¿* electronic excitation energies of acrolein...... of acrolein in vapor phase and aqueous solution. The gas-to-aqueous solution shift of the n¿* excitation energy is well reproduced by using all density functional methods considered. However, the B3LYP and PBE0 functionals completely fail to describe the ¿* electronic transition in solution, whereas...... the recent CAM-B3LYP functional performs well also in this case. The ¿* excitation energy of acrolein in water solution is found to be very dependent on intermolecular induction and nonelectrostatic interactions. The computed excitation energies of acrolein in vacuum and solution compare well to experimental...
Theory Study on Structures and Vibrational Frequencies of Pyruvic acid
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
Density functional theory BLYP (using Becke's and Lee-Yang-Parr's correlation functionals ), ab initio Hartree-Fock (HF) and hybrid DFT/HF B3LYP calculations were carried out to study the structure and vibrational spectra of pyruvic acid. The scaled B3LYP/6-31G* frequencies correspond well with available experimental assignment of the functional vibrational modes and the mean absolut devation is only 12.3cm-1.
Building a Universal Nuclear Energy Density Functional
Energy Technology Data Exchange (ETDEWEB)
Carlson, Joe A. [Michigan State Univ., East Lansing, MI (United States); Furnstahl, Dick; Horoi, Mihai; Lust, Rusty; Nazaewicc, Witek; Ng, Esmond; Thompson, Ian; Vary, James
2012-12-30
During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.
Building a Universal Nuclear Energy Density Functional
Energy Technology Data Exchange (ETDEWEB)
Carlson, Joe A. [Michigan State University; Furnstahl, Dick; Horoi, Mihai; Lust, Rusty; Nazaewicc, Witek; Ng, Esmond; Thompson, Ian; Vary, James
2012-12-30
During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.
Wang, Tianyi; Zheng, Chunmei; Yang, Junqing; Zhang, Xueli; Gong, Xuedong; Xia, Mingzhu
2014-06-01
The derivatives of 1,2,3,4-tetrazine may be promising candidates for high-energy density compounds and are receiving more and more attentions. In this study, a new derivative 6-amino-7-nitropyrazino[2,3-e][1,2,3,4]tetrazine 1,3,5-trioxide (ANPTTO) has been designed. The geometrical structure and IR spectrum in the gas phase were studied at the B3LYP/6-31G* level of density functional theory (DFT). The crystal structure was predicted by molecular mechanics method and refined by the GGA/BOP function of periodic DFT with the basis set of TNP. The gas phase enthalpy of formation was calculated by the homodesmotic reaction method. The enthalpy of sublimation and solid phase enthalpy of formation were also predicted. The detonation properties were estimated with the Kamlet-Jacobs equations based on the predicted density and enthalpy of formation in solid state. The available free space in the lattice and resonance energy were calculated to evaluate its stability. ANPTTO has a high stability and is a promising high energetic component with the density >2 g · cm(-3), detonation velocity >9000 m · s(-1), and detonation pressure >40 GPa. A synthetic route was proposed to provide a consideration for further study.
Marković, Zoran S.; Mentus, Slavko V.; Dimitrić Marković, Jasmina M.
2009-12-01
Antioxidative properties of naturally occurring flavon-3-ol, fisetin, were examined by both cyclic voltammetry and quantum-chemical based calculations. The three voltametrically detectable consecutive steps, reflected the fisetin molecular structure, catecholic structural unit in the ring B, C3-OH, and C7-OH groups in the rings C and A. Oxidation potential values, used as quantitative parameter in determining its oxidation capability, indicated good antioxidative properties found with this molecule. Oxidation of the C3'C4' dixydroxy moiety at the B ring occurred first at the lowest positive potentials. The first oxidation step induced fast intramolecular transformations in which the C3 hydroxy group disappeared and the product of this transformation participated in the second oxidation step. The highest potential of oxidation was attributed to the oxidation of C7 hydroxy group. The structural and electronic features of fisetin were investigated at the B3LYP/6-311++G** level of theory. Particularly, the interest was focused on the C3' and C4'-OH sites in the B ring and on C3-OH site in the C ring. The calculated bond dissociation enthalpy values for all OH sites of fisetin clearly indicated the importance of the B ring and C3' and C4'-OH group. The importance of keto-enol tautomerism has also been considered. The analysis also included the Mulliken spin density distribution for the radicals formed after H removal on each OH site. The results showed the higher values of the BDE on the C7-OH and C3-OH sites.
Lan, Yu; Zou, Lufeng; Cao, Yang; Houk, K N
2011-12-01
Theoretical calculations were performed on the 1,3-dipolar cycloaddition reactions of 24 1,3-dipoles with ethylene and acetylene. The 24 1,3-dipoles are of the formula X≡Y(+)-Z(-) (where X is HC or N, Y is N, and Z is CH(2), NH, or O) or X═Y(+)-Z(-) (where X and Z are CH(2), NH, or O and Y is NH, O, or S). The high-accuracy G3B3 method was employed as the reference. CBS-QB3, CCSD(T)//B3LYP, SCS-MP2//B3LYP, B3LYP, M06-2X, and B97-D methods were benchmarked to assess their accuracies and to determine an accurate method that is practical for large systems. Several basis sets were also evaluated. Compared to the G3B3 method, CBS-QB3 and CCSD(T)/maug-cc-pV(T+d)Z//B3LYP methods give similar results for both activation and reaction enthalpies (mean average deviation, MAD, < 1.5 kcal/mol). SCS-MP2//B3LYP and M06-2X give small errors for the activation enthalpies (MAD < 1.5 kcal/mol), while B3LYP has MAD = 2.3 kcal/mol. SCS-MP2//B3LYP and B3LYP give the reasonable reaction enthalpies (MAD < 5.0 kcal/mol). The B3LYP functional also gives good results for most 1,3-dipoles (MAD = 1.9 kcal/mol for 17 common 1,3-dipoles), but the activation and reaction enthalpies for ozone and sulfur dioxide are difficult to calculate by any of the density functional methods.
Reduced density-matrix functionals from many-particle theory
Schade, Robert; Kamil, Ebad; Blöchl, Peter
2017-07-01
In materials with strong electron correlation the proper treatment of local atomic physics described by orbital occupations is crucial. Reduced density-matrix functional theory is a natural extension of density functional theory for systems that are dominated by orbital physics. We review the current state of reduced density-matrix functional theory (RDMFT). For atomic structure relaxations or ab-initio molecular dynamics the combination of density functional theory (DFT) and dynamical mean-field theory (DMFT) possesses a number of disadvantages, like the cumbersome evaluation of forces. We therefore describe a method, DFT+RDMFT, that combines many-particle effects based on reduced density-matrix functional theory with a density functional-like framework. A recent development is the construction of density-matrix functionals directly from many-particle theory such as methods from quantum chemistry or many-particle Green's functions. We present the underlying exact theorems and describe current progress towards quantitative functionals.
Orbital functionals in density-matrix- and current-density-functional theory
Energy Technology Data Exchange (ETDEWEB)
Helbig, N.
2006-05-15
Density-Functional Theory (DFT), although widely used and very successful in the calculation of several observables, fails to correctly describe strongly correlated materials. In the first part of this work we, therefore, introduce reduced-densitymatrix- functional theory (RDMFT) which is one possible way to treat electron correlation beyond DFT. Within this theory the one-body reduced density matrix (1- RDM) is used as the basic variable. Our main interest is the calculation of the fundamental gap which proves very problematic within DFT. In order to calculate the fundamental gap we generalize RDMFT to fractional particle numbers M by describing the system as an ensemble of an N and an N+1 particle system (with N{<=}M{<=}N+1). For each fixed particle number, M, the total energy is minimized with respect to the natural orbitals and their occupation numbers. This leads to the total energy as a function of M. The derivative of this function with respect to the particle number has a discontinuity at integer particle number which is identical to the gap. In addition, we investigate the necessary and sufficient conditions for the 1- RDM of a system with fractional particle number to be N-representable. Numerical results are presented for alkali atoms, small molecules, and periodic systems. Another problem within DFT is the description of non-relativistic many-electron systems in the presence of magnetic fields. It requires the paramagnetic current density and the spin magnetization to be used as basic variables besides the electron density. However, electron-gas-based functionals of current-spin-density-functional Theory (CSDFT) exhibit derivative discontinuities as a function of the magnetic field whenever a new Landau level is occupied, which makes them difficult to use in practice. Since the appearance of Landau levels is, intrinsically, an orbital effect it is appealing to use orbital-dependent functionals. We have developed a CSDFT version of the optimized
Density functional theory in the solid state.
Hasnip, Philip J; Refson, Keith; Probert, Matt I J; Yates, Jonathan R; Clark, Stewart J; Pickard, Chris J
2014-03-13
Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure-property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program.
Combining Molecular Dynamics and Density Functional Theory
Kaxiras, Efthimios
2015-03-01
The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.
Bone mineral density, adiposity and cognitive functions
Directory of Open Access Journals (Sweden)
Hamid R Sohrabi
2015-02-01
Full Text Available Cognitive decline and dementia due to Alzheimer’s disease have been associated with genetic, lifestyle, and environmental factors. A number of potentially modifiable risk factors should be taken into account when preventive or ameliorative interventions targeting dementia and its preclinical stages are investigated. Bone mineral density (BMD and body composition are two such potentially modifiable risk factors, and their association with cognitive decline was investigated in this study. 164 participants, aged 34 to 87 years old (62.78±9.27, were recruited for this longitudinal study and underwent cognitive and clinical examinations at baseline and after three years. Blood samples were collected for apolipoprotein E (APOE genotyping and dual energy x-ray absorptiometry (DXA was conducted at the same day as cognitive assessment. Using hierarchical regression analysis, we found that BMD and lean body mass, as measured using DXA were significant predictors of episodic memory. Age, gender, APOE status and premorbid IQ were controlled for. Specifically, the List A learning from California Verbal Learning Test was significantly associated with BMD and lean mass both at baseline and at follow up assessment. Our findings indicate that there is a significant association between BMD and lean body mass and episodic verbal learning. While the involvement of modifiable lifestyle factors in human cognitive function has been examined in different studies, there is a need for further research to understand the potential underlying mechanisms.
Institute of Scientific and Technical Information of China (English)
Zhou Shi-Qi
2007-01-01
A universal theoretical approach is proposed which enables all hard sphere density functional approximations(DFAs) applicable to van der Waals fluids. The resultant DFA obtained by combining the universal theoretical approach with any hard sphere DFAs only needs as input a second-order direct correlation function (DCF) of a coexistence bulk fluid, and is applicable in both supercritical and subcritical temperature regions. The associated effective hard sphere density can be specified by a hard wall sum rule. It is indicated that the value of the effective hard sphere density so determined can be universal, i.e. can be applied to any external potentials different from the single hard wall. As an illustrating example, the universal theoretical approach is combined with a hard sphere bridge DFA to predict the density profile of a hard core attractive Yukawa model fluid influenced by diverse external fields; agreement between the present formalism's predictions and the corresponding simulation data is good or at least comparable to several previous DFT approaches. The primary advantage of the present theoretical approach combined with other hard sphere DFAs is discussed.
Youcef, Megrouss; Nadia, Benhalima; Rawia, Bahoussi; Nouredine, Boukabcha; Abdelkader, Chouaih; Fodil, Hamzaoui
2015-10-01
This work is devoted to the experimental determination of the electrostatic properties of the molecular 4-methyl-7-(salicylidene amino) coumarin (C17H13NC3) using high resolution x-ray diffraction data. The experimental results are compared with those obtained theoretically from calculation type ab initio. The experimental investigation is carried out using the molecular electron charge density distribution based on the multipolar model of Hansen and Coppens. However the theoretical calculations are conducted by using the molecular orbital B3LYP method and the Hartree-Fock (HF) approximation with the basis set 6-31G (d,p) implemented in the Gaussian program. In addition to the structural analysis, the thermal agitation is also analyzed in terms of rigid blocks to ensure a better precision of the results. Subsequently, the electrostatic atomic and molecular properties such as the net charges, the molecular dipolar moment to highlight the nature of charge transfer existing within the molecule studied are derived. Moreover, the obtained electrostatic potential enables the localization of the electropositive and the electronegative parts of the investigated molecule. The present work reports in detail the obtained electrostatic properties of this biologically important molecule.
Institute of Scientific and Technical Information of China (English)
Youcef Megrouss; Nadia Benhalima; Rawia Bahoussi; Nouredine Boukabcha; Abdelkader Chouaih; Fodil Hamzaoui
2015-01-01
This work is devoted to the experimental determination of the electrostatic properties of the molecular 4-methyl-7-(salicylidene amino) coumarin (C17H13NC3) using high resolution x-ray diffraction data. The experimental results are compared with those obtained theoretically from calculation type ab initio. The experimental investigation is carried out using the molecular electron charge density distribution based on the multipolar model of Hansen and Coppens. However the theoretical calculations are conducted by using the molecular orbital B3LYP method and the Hartree–Fock (HF) ap-proximation with the basis set 6-31G (d,p) implemented in the Gaussian program. In addition to the structural analysis, the thermal agitation is also analyzed in terms of rigid blocks to ensure a better precision of the results. Subsequently, the electrostatic atomic and molecular properties such as the net charges, the molecular dipolar moment to highlight the nature of charge transfer existing within the molecule studied are derived. Moreover, the obtained electrostatic potential enables the localization of the electropositive and the electronegative parts of the investigated molecule. The present work reports in detail the obtained electrostatic properties of this biologically important molecule.
Brorsen, Kurt R; Yang, Yang; Pak, Michael V; Hammes-Schiffer, Sharon
2017-05-04
The development of approximate exchange-correlation functionals is critical for modern density functional theory. A recent analysis of atomic systems suggested that some modern functionals are straying from the path toward the exact functional because electron densities are becoming less accurate while energies are becoming more accurate since the year 2000. To investigate this trend for more chemically relevant systems, the electron densities in the bonding regions and the atomization energies are analyzed for a series of diatomic molecules with 90 different functionals. For hybrid generalized gradient approximation functionals developed since the year 2000, the errors in densities and atomization energies are decoupled; the accuracy of the energies remains relatively consistent while the accuracy of the densities varies significantly. Such decoupling is not observed for generalized gradient and meta-generalized gradient approximation functionals. Analysis of electron densities in bonding regions is found to be important for the evaluation of functionals for chemical systems.
Ions in solution: density corrected density functional theory (DC-DFT).
Kim, Min-Cheol; Sim, Eunji; Burke, Kieron
2014-05-14
Standard density functional approximations often give questionable results for odd-electron radical complexes, with the error typically attributed to self-interaction. In density corrected density functional theory (DC-DFT), certain classes of density functional theory calculations are significantly improved by using densities more accurate than the self-consistent densities. We discuss how to identify such cases, and how DC-DFT applies more generally. To illustrate, we calculate potential energy surfaces of HO·Cl(-) and HO·H2O complexes using various common approximate functionals, with and without this density correction. Commonly used approximations yield wrongly shaped surfaces and/or incorrect minima when calculated self consistently, while yielding almost identical shapes and minima when density corrected. This improvement is retained even in the presence of implicit solvent.
Ions in solution: Density Corrected Density Functional Theory (DC-DFT)
Kim, Min-Cheol; Burke, Kieron
2014-01-01
Standard density functional approximations often give questionable results for odd-electron radical complexes, with the error typically attributed to self-interaction. In density corrected density functional theory (DC-DFT), certain classes of density functional theory calculations are significantly improved by using densities more accurate than the self-consistent densities. We discuss how to identify such cases, and how DC-DFT applies more generally. To illustrate, we calculate potential energy surfaces of HO$\\cdot$Cl$^-$ and HO$\\cdot$H$_2$O complexes using various common approximate functionals, with and without this density correction. Commonly used approximations yield wrongly shaped surfaces and/or incorrect minima when calculated self consistently, while yielding almost identical shapes and minima when density corrected. This improvement is retained even in the presence of implicit solvent.
Graphene on metals: A van der Waals density functional study
DEFF Research Database (Denmark)
Vanin, Marco; Mortensen, Jens Jørgen; Kelkkanen, Kari André;
2010-01-01
We use density functional theory (DFT) with a recently developed van der Waals density functional (vdW-DF) to study the adsorption of graphene on Co, Ni, Pd, Ag, Au, Cu, Pt, and Al(111) surfaces. In contrast to the local-density approximation (LDA) which predicts relatively strong binding for Ni...
Energy density functional for nuclei and neutron stars
Erler, J; Nazarewicz, W; Rafalski, M; Reinhard, P -G
2012-01-01
We aim to develop a nuclear energy density functional that can be simultaneously applied to finite nuclei and neutron stars. We use the self-consistent nuclear density functional theory (DFT) with Skyrme energy density functionals and covariance analysis to assess correlations between observables for finite nuclei and neutron stars. In a first step two energy functionals -- a high density energy functional giving reasonable neutron properties, and a low density functional fitted to nuclear properties -- are matched. In a second step, we optimize a new functional using exactly the same protocol as in earlier studies pertaining to nuclei but now including neutron star data. This allows direct comparisons of performance of the new functional relative to the standard one. The new functional TOV-min yields results for nuclear bulk properties (energy, r.m.s. radius, diffraction radius, surface thickness) that are of the same quality as those obtained with the established Skyrme functionals, including SV-min. When c...
Structure and Properties of Semiconductor Microclusters GanPn(n=1-4):A First Principle Study
Institute of Scientific and Technical Information of China (English)
ZHANG Cai-rong; CHEN Hong-shan; WANG Guang-hou
2004-01-01
The possible geometrical structures and relative stabilities of semiconductor microclusters GanPn(n= 1-4) were studied by virtue of density functional calculations with generalized gradient approximation (B3LYP).For the most stable isomers of GanPn(n= 1-4) clusters, the electronic structure, vibrational properties,dipole moment, polarizability and ionization potential were analyzed by means of HF, MP2, CISD and B3LYP methods with different basis sets.
Directory of Open Access Journals (Sweden)
Yujie Huang
2015-01-01
Full Text Available This paper theoretically investigates interactions between a template and functional monomer required for synthesizing an efficient molecularly imprinted polymer (MIP. We employed density functional theory (DFT to compute geometry, single-point energy, and binding energy (ΔE of an MIP system, where spermidine (SPD and methacrylic acid (MAA were selected as template and functional monomer, respectively. The geometry was calculated by using B3LYP method with 6-31+(d basis set. Furthermore, 6-311++(d, p basis set was used to compute the single-point energy of the above geometry. The optimized geometries at different template to functional monomer molar ratios, mode of bonding between template and functional monomer, changes in charge on natural bond orbital (NBO, and binding energy were analyzed. The simulation results show that SPD and MAA form a stable complex via hydrogen bonding. At 1 : 5 SPD to MAA ratio, the binding energy is minimum, while the amount of transferred charge between the molecules is maximum; SPD and MAA form a stable complex at 1 : 5 molar ratio through six hydrogen bonds. Optimizing structure of template-functional monomer complex, through computational modeling prior synthesis, significantly contributes towards choosing a suitable pair of template-functional monomer that yields an efficient MIP with high specificity and selectivity.
Matsui, Toru; Kitagawa, Yasutaka; Shigeta, Yasuteru; Okumura, Mitsutaka
2013-07-09
We propose an accurate scheme to evaluate the redox potential of a wide variety of transition metal complexes by adding a charge-dependent correction term for a counterion around the charged complexes, which is based on Generalized Born theory, to the solvation energy. The mean absolute error (MAE) toward experimental redox potentials of charged complexes is considerably reduced from 0.81 V (maximum error 1.22 V) to 0.22 V (maximum error 0.50 V). We found a remarkable exchange-correlation functional dependence on the results rather than the basis set ones. The combination of Wachters+f (for metal) and 6-31++G(d,p) (for other atoms) with the B3LYP functional gives the least MAE 0.15 V for the test complexes. This scheme is applicable to other solvents, and heavier transition metal complexes such as M1(CO)5(pycn) (M1 = Cr, Mo, W), M2(mnt)2 (M2 = Ni, Pd, Pt), and M3(bpy)3 (M3 = Fe, Ru, Os) with the same quality.
Kesharwani, Manoj K; Brauer, Brina; Martin, Jan M L
2015-03-05
We have obtained uniform frequency scaling factors λ(harm) (for harmonic frequencies), λ(fund) (for fundamentals), and λ(ZPVE) (for zero-point vibrational energies (ZPVEs)) for the Weigend-Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10-12 cm(-1) for def2-TZVP and larger basis sets, compared to 5 cm(-1) at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is clearly inadequate.
Parveen, Firdaus; Patra, Tanmoy; Upadhyayula, Sreedevi
2016-01-01
Cellulose conversion to platform chemicals is required to meet the demands of increasing population and modernization of the world. Hydrolysis of microcrystalline cellulose was studied with SO3H, COOH and OH functionalized imidazole based ionic liquid using 1-butyl-3-methylimidazolium chloride [BMIM]Cl as a solvent. The influence of temperature, time, acidity of ionic liquids and catalyst loading was studied on hydrolysis reaction. The maximum %TRS yield 85%, was obtained at 100°C and 90min with 0.2g of SO3H functionalized ionic liquid. UV-vis spectroscopy using 4-nitro aniline as an indicator was performed to find out the Hammett function of ionic liquid and acidity trends are as follows: SO3H>COOH>OH. Density functional theory (DFT) calculations were performed to optimize the ionic liquid and their conjugate bases at B3LYP 6-311G++ (d, p) level using Gaussian 09 program. Theoretical findings are in agreement with the experimental results. Copyright © 2015 Elsevier Ltd. All rights reserved.
Bioinorganic Chemistry Modeled with the TPSSh Density Functional
DEFF Research Database (Denmark)
Kepp, Kasper Planeta
2008-01-01
In this work, the TPSSh density functional has been benchmarked against a test set of experimental structures and bond energies for 80 transition-metal-containing diatomics. It is found that the TPSSh functional gives structures of the same quality as other commonly used hybrid and nonhybrid func...... promising density functional for use and further development within the field of bioinorganic chemistry....
Energy Technology Data Exchange (ETDEWEB)
Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)
2012-02-15
The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Petsalakis, I D; Georgiadou, D G; Vasilopoulou, M; Pistolis, G; Dimotikali, D; Argitis, P; Theodorakopoulos, G
2010-05-06
A theoretical investigation on the electronic structure of 4-dimethylamino-4'-nitrostilbene (DANS), 4-(dicyanomethylene)-2-methyl-6-p-(dimethylamino) styryl-4H-pyran (DCM), and their protonated forms is presented in an effort to rationalize recent experimental results on the tuning of the emitted color of organic light-emitting diodes through photochemically induced protonation. Density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations have been carried out on the neutral and protonated forms of DANS and DCM, employing both the B3LYP and the CAM-B3LYP functionals. It was found that the CAM-B3LYP functional leads to better agreement than the B3LYP of the calculated with the experimental absorption lambda(max) for DANS, whereas B3LYP is more appropriate than CAM-B3LYP for DCM. The results of the calculations aid in a rationalization of the observed differences of the spectra of DANS and DCM upon protonation, and in particular those differences that make DANS a more attractive system for absorbance and emission tuning.
Multicomponent density-functional theory for time-dependent systems
Butriy, O.; Ebadi, H.; de Boeij, P. L.; van Leeuwen, R.; Gross, E. K. U.
2007-01-01
We derive the basic formalism of density functional theory for time-dependent electron-nuclear systems. The basic variables of this theory are the electron density in body-fixed frame coordinates and the diagonal of the nuclear N-body density matrix. The body-fixed frame transformation is carried ou
Many-body Expanded Analytical Potential Energy Function for Ground State PuOH Molecule
Institute of Scientific and Technical Information of China (English)
LI Yue-Xun; GAO Tao; ZHU Zheng-He
2006-01-01
Using the density functional method B3LYP with relativistic effective core potential (RECP) for Pu atom, the low-lying excited states (4∑+, 6∑+, 8∑+) for three structures of PuOH molecule were optimized. The results show that the ground state is X6∑+of the linear Pu-O-H (C∞v), its corresponding equilibrium geometry and dissociation energy are RPu-O=0.20595 nm, RO-H=0.09581 nm and -8.68 eV, respectively. At the same time, two other metastable structures [PuOH (Cs) and H-Pu-O (C∞v)] were found. The analytical potential energy function has also been derived for whole range using the many-body expansion method. This potential energy function represents the considerable topographical features of PuOH molecule in detail, which is adequately accurate in the whole potential surface and can be used for the molecular reaction dynamics research.
Indian Academy of Sciences (India)
Paul W Ayers; Mel Levy
2005-09-01
Using the constrained search and Legendre-transform formalisms, one can derive ``generalized” density-functional theories, in which the fundamental variable is either the electron pair density or the second-order reduced density matrix. In both approaches, the -representability problem is solved by the functional, and the variational principle is with respect to all pair densities (density matrices) that are nonnegative and appropriately normalized. The Legendre-transform formulation provides a lower bound on the constrained-search functional. Noting that experience in density-functional and density-matrix theories suggests that it is easier to approximate functionals than it is to approximate the set of -representable densities sheds some light on the significance of this work.
Energy Technology Data Exchange (ETDEWEB)
Appell, Michael, E-mail: michael.appell@ars.usda.gov [Bacterial Foodborne Pathogens and Mycology Research USDA, ARS, National Center for Agricultural Utilization Research 1815 N. University St., Peoria, IL 61604 (United States); Bosma, Wayne B., E-mail: bosma@bumail.bradley.edu [Mund-Lagowski Department of Chemistry and Biochemistry Bradley University 1501 W. Bradley Ave., Peoria, IL 61625 (United States)
2015-05-15
Highlights: • Quantum-based properties of type A and B trichothecenes are related to toxicity. • Deoxynivalenol and nivalenol exhibit complex hydrogen bonding schemes. • QSAR models explain trichothecene toxicity and immunochemical detection. • False-positive detection is associated with spatial autocorrelation indices. - Abstract: A comprehensive quantum chemical study was carried out on 35 type A and B trichothecenes and biosynthetic precursors, including selected derivatives of deoxynivalenol and T-2 toxin. Quantum chemical properties, Natural Bond Orbital (NBO) analysis, and molecular parameters were calculated on structures geometry optimized at the B3LYP/6-311+G** level. Type B trichothecenes possessed significantly larger electrophilicity index compared to the type A trichothecenes studied. Certain hydroxyl groups of deoxynivalenol, nivalenol, and T-2 toxin exhibited considerable rotation during molecular dynamics simulations (5 ps) at the B3LYP/6-31G** level in implicit aqueous solvent. Quantitative structure activity relationship (QSAR) models were developed to evaluate toxicity and detection using genetic algorithm, principal component, and multilinear analyses. The models suggest electronegativity and several 2-dimensional topological descriptors contain important information related to trichothecene cytotoxicity, phytotoxicity, immunochemical detection, and cross-reactivity.
Exact conditions on the temperature dependence of density functionals
Burke, Kieron; Grabowski, Paul E; Pribram-Jones, Aurora
2015-01-01
Universal exact conditions guided the construction of most ground-state density functional approximations in use today. We derive the relation between the entropy and Mermin free energy density functionals for thermal density functional theory. Both the entropy and sum of kinetic and electron-electron repulsion functionals are shown to be monotonically increasing with temperature, while the Mermin functional is concave downwards. Analogous relations are found for both exchange and correlation. The importance of these conditions is illustrated in two extremes: the Hubbard dimer and the uniform gas.
Exact conditions on the temperature dependence of density functionals
Burke, K.; Smith, J. C.; Grabowski, P. E.; Pribram-Jones, A.
2016-05-01
Universal exact conditions guided the construction of most ground-state density functional approximations in use today. We derive the relation between the entropy and Mermin free energy density functionals for thermal density functional theory. Both the entropy and sum of kinetic and electron-electron repulsion functionals are shown to be monotonically increasing with temperature, while the Mermin functional is concave downwards. Analogous relations are found for both exchange and correlation. The importance of these conditions is illustrated in two extremes: the Hubbard dimer and the uniform gas.
Directory of Open Access Journals (Sweden)
Humberto J. SoscÃƒÂºn Machado
2004-09-01
Full Text Available We report high quality B3LYP Ab Initio studies of the electric dipole polarizability of three related series of molecules: para-XC6H4Y, XC6H4CH=CHC6H4Y and XC6H4N=NC6H4Y, where X and Y represent H together with the six various activating through deactivating groups NH2, OH, OCH3, CHO, CN and NO2. Molecules for which X is activating and Y deactivating all show an enhancement to the mean polarizability compared to the unsubstituted molecule, in accord with the order given above. A number of representative Ab Initio calculations at different levels of theory are discussed for azoarene; all subsequent Ab Initio polarizability calculations were done at the B3LYP/6-311G(2d,1p//B3LYP/6-311++G(2d,1p level of theory. We also consider semi-empirical polarizability and molecular volume calculations at the AM1 level of theory together with QSAR-quality empirical polarizability calculations using MillerÃ¢Â€Â™s scheme. Least-squares correlations between the various sets of results show that these less costly procedures are reliable predictors of for the first series of molecules, but less reliable for the larger molecules.
A density functional for sparse matter
DEFF Research Database (Denmark)
Langreth, D.C.; Lundqvist, Bengt; Chakarova-Kack, S.D.;
2009-01-01
forces in molecules, to adsorbed molecules, like benzene, naphthalene, phenol and adenine on graphite, alumina and metals, to polymer and carbon nanotube (CNT) crystals, and hydrogen storage in graphite and metal-organic frameworks (MOFs), and to the structure of DNA and of DNA with intercalators......Sparse matter is abundant and has both strong local bonds and weak nonbonding forces, in particular nonlocal van der Waals (vdW) forces between atoms separated by empty space. It encompasses a broad spectrum of systems, like soft matter, adsorption systems and biostructures. Density...
Xu, Yi-Jun; Zhang, Yong-Fan; Li, Jun-Qian
2006-02-23
By means of density functional theory (B3LYP/6-31G*) coupled with effective cluster models, we predict that the well-known cycloaddition reactions of carbenes and nitrenes to alkenes in organic chemistry can be employed as a new type of surface reaction to organically functionalize the Si (100) and Ge (100) surfaces at low temperature. The well-established abundance of carbenes and nitrenes addition chemistry in organic chemistry provides versatile flexibility of functionalizing the surfaces of Si (100) and Ge (100), which can potentially impart new organic functionalities to the semiconductors surface for novel applications in a diversity of fields. Our predictions strongly advance the concept of using organic reactions to modify the solid surface in a controlled manner and quite intriguing chemistry can lie in the material featuring the analogous bonding motif. In further perspective, implications for other theoretical work, regarding disilenes, digermenes, silenes, and germenes that all feature the bonding motif similar to alkenes, are also discussed.
Exact Maps in Density Functional Theory for Lattice Models
Dimitrov, Tanja; Fuks, Johanna I; Rubio, Angel
2015-01-01
In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and for the first time the exact density-to-wavefunction map that underly the Hohenberg-Kohn theorem in density functional theory. Having the explicit wavefunction-to- density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragmen...
Introduction to Classical Density Functional Theory by a Computational Experiment
Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel
2014-01-01
We propose an in silico experiment to introduce the classical density functional theory (cDFT). Density functional theories, whether quantum or classical, rely on abstract concepts that are nonintuitive; however, they are at the heart of powerful tools and active fields of research in both physics and chemistry. They led to the 1998 Nobel Prize in…
Molecular density functional theory of water including density-polarization coupling.
Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel
2016-06-22
We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.
Molecular density functional theory of water including density-polarization coupling
Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel
2016-01-01
We present a three-dimensional molecular density functional theory (MDFT) of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: ($i$) a scalar density and a vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and ($ii$) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.
Muthu, S; Ramachandran, G
2014-01-01
The Fourier transform infrared (FT-IR) and FT-Raman of (1R)-N-(Prop-2-yn-1-yl)-2,3-dihydro-1H-inden-1-amine (1RNPDA) were recorded in the regions 4000-400 cm(-1) and 4000-100 cm(-1) respectively. A complete assignment and analysis of the fundamental vibrational modes of the molecule were carried out. The observed fundamental modes have been compared with the harmonic vibrational frequencies computed using HF method by employing 6-31G(d,p) basis set and DFT(B3LYP) method by employing 6-31G(d,p) basis set. The vibrational studies were interpreted in terms of Potential Energy Distribution (PED). The complete vibrational frequency assignments were made by Normal Co-ordinate Analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The first order hyper polarizability (β0) of this molecular system and related properties (α, μ, and Δα) are calculated using B3LYP/6-31G(d,p) method based on the finite-field approach. The thermodynamic functions of the title compound were also performed at the above methods and basis set. A detailed interpretation of the infrared and Raman spectra of 1RNPDA is reported. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated using the GIAO method confirms with the experimental values. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using Natural Bond Orbital (NBO) analysis. UV-vis spectrum of the compound was recorded and electronic properties such as excitation energies, oscillator strength and wavelength were performed by TD-DFT/B3LYP using 6-31G(d,p) basis set. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The observed and calculated wave numbers are formed to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectra. Copyright © 2013 Elsevier B.V. All rights reserved.
Spin constraints on nuclear energy density functionals
Robledo, L M; Bertsch, G F
2013-01-01
The Gallagher-Moszkowski rule in the spectroscopy of odd-odd nuclei imposes a new spin constraint on the energy functionals for self-consistent mean field theory. The commonly used parameterization of the effective three-body interaction in the Gogny and Skyrme families of energy functionals is ill-suited to satisfy the spin constraint. In particular, the Gogny parameterization of the three-body interaction has the opposite spin dependence to that required by the observed spectra. The two-body part has a correct sign, but in combination the rule is violated as often as not. We conclude that a new functional form is needed for the effective three-body interaction that can take into better account the different spin-isospin channels of the interaction.
Analytical Potential Energy Function for the Ground State X1∑+ of Lanthanum Monofluoride
Institute of Scientific and Technical Information of China (English)
CHEN Lin-Hong; SHANG Ren-Cheng
2003-01-01
The equilibrium geometry, harmonic frequency and bond dissociation energy of lanthanum monofluoride have been calculated using Density-Functional Theory (DFT), post-HF methods MP2 and CCSD(T) with the energyconsistent relativistic effective core potentials. The possible electronic state and reasonable dissociation limit of the ground state of LaF are determined based on atomic and molecular reaction statics. Potential energy curve scans for the ground state X 1∑+ have been performed at B3LYP and CCSD(T) levels, due to their better results of harmonic frequency and bond dissociation energy. We find that the potential energy calculated with CCSD(T) is about 0.6 eV larger than the bond dissociation energy, when the internuclear distance is as large as 0.8 nm. The problem that single-reference ab initio methods do not meet dissociation limit during calculations of lanthanide heavy-metal elements is analyzed. We propose the calculation scheme to derive the analytical Murrell-Sorbie potential energy function. Vibrotational spectroscopic constants Be, ωe, ωeχe, αe, βe, De and He obtained by the standard Dunham treatment coincide well with the results of rotational analyses on spectroscopic experiments.
Rana, Meenakshi; Singla, Nidhi; Chatterjee, Amrita; Shukla, Abhishek; Chowdhury, Papia
2016-12-01
Nonlinear Optical (NLO) properties of amine functionalized tetraphenylethylene (TPE-NH2) have been recorded and analyzed. The structural geometry, bonding features, harmonic vibrational frequencies (FTIR and Raman) of TPE-NH2 have been investigated by B3LYP density functional theory (DFT). Charge (Mulliken and natural) analysis, natural bond orbital (NBO) analysis, frontier molecular orbitals (FMOs), 13C and 1H nuclear magnetic resonance (NMR) and molecular electrostatic potential (MEP) indicate the delocalization of charges over the donor-acceptor region by the increase of C-N bond length. The vibrational analysis on the basis of potential energy distribution (PED) confirms the charge transfer interaction between donor and acceptor groups, and that in turn validates the presence of the larger dipole moment (μ), polarizability and hyperpolarizabilities (α, β and γ) in TPE-NH2. Higher value of ionization potential (IP), electronegativity (χ), hardness (η), chemical potential (CP) and smaller HOMO-LUMO energy gap (Δε) validate TPE-NH2's strong candidature to be used as an NLO active material.
Functionalization of SBA-15 mesoporous silica by Cu-phosphonate units: Probing of synthesis route
Energy Technology Data Exchange (ETDEWEB)
Laskowski, Lukasz, E-mail: lukasz.laskowski@kik.pcz.pl [Czestochowa University of Technology, Institute of Computational Intelligence, Al. Armii Krajowej 36, 42-201 Czestochowa (Poland); Czestochowa University of Technology, Institute of Physics, Al. Armii Krajowej 19, 42-201 Czestochowa (Poland); Laskowska, Magdalena, E-mail: magdalena.laskowska@onet.pl [Czestochowa University of Technology, Institute of Physics, Al. Armii Krajowej 19, 42-201 Czestochowa (Poland)
2014-12-15
Mesoporous silica SBA-15 containing propyl-copper phosphonate units was investigated. The structure of mesoporous samples was tested by N{sub 2} isothermal sorption (BET and BHJ analysis), TEM microscopy and X-Ray scattering. Quantitative analysis EDX has given information about proportions between component atoms in the sample. Quantitative elemental analysis has been carried out to support EDX. To examine bounding between copper atoms and phosphonic units the Raman spectroscopy was carried out. As a support of Raman scattering, the theoretical calculations were made based on density functional theory, with the B3LYP method. By comparison of the calculated vibrational spectra of the molecule with experimental results, distribution of the active units inside silica matrix has been determined. - Graphical abstract: The present study is devoted to mesoporous silica SBA-15 containing propyl-copper phosphonate units. The species were investigated to confirm of synthesis procedure correctness by the micro-Raman technique combined with DFT numerical simulations. Complementary research was carried out to test the structure of mesoporous samples. - Highlights: • SBA-15 silica functionalized with propyl-copper phosphonate units was synthesized. • Synthesis efficiency probed by Raman study supported with DFT simulations. • Homogenous distribution of active units was proved. • Synthesis route enables precise control of distance between copper ions.
Analytical potential energy function for the ground state（1A1） of hydrogen isotopic D2O molecule
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
The present work is to construct the potential energy function of isotopic molecules. The so-called molecular potential energy function is the electronic energy function under Born-Oppenheimer approximation,in which the nuclear motions(translational,rotational and vibration motions) are not included,therefore,its nuclear vibration motion and isotopic effect need to be considered. Based on group theory and atomic and molecular reactive statics(AMRS),the reasonable dissociation limits of D2O(1A1)are determined,its equilibrium geometry and dissociation energy are calculated by density-functional theory(DFT) B3lyp,and then,using the many-body expansion method the potential energy function of D2O(1A1) is obtained for the first time. The potential contours are drawn,in which it is found that the reactive channel D + OD→D2O has no threshold energy,so it is a free radical reaction. But the reactive channel O + DD→D2O has a saddle point. The study of collision for D2O(1A1) is under way.
The benchmark of gutzwiller density functional theory in hydrogen systems
Energy Technology Data Exchange (ETDEWEB)
Yao, Y.; Wang, Cai-Zhuang; Ho, Kai-Ming
2012-02-23
We propose an approximate form of the exchange-correlation energy functional for the Gutzwiller density functional theory. It satisfies certain physical constraints in both weak and strong electron correlation limits. We benchmark the Gutzwiller density functional approximation in the hydrogen systems, where the static correlation error is shown to be negligible. The good transferability is demonstrated by applications to the hydrogen molecule and some crystal structures.
The Benchmark of Gutzwiller Density Functional Theory in Hydrogen Systems
Energy Technology Data Exchange (ETDEWEB)
Yao, Yongxin; Wang, Cai-Zhuang; Ho, Kai-Ming
2011-01-13
We propose an approximate form of the exchange-correlation energy functional for the Gutzwiller density functional theory. It satisfies certain physical constraints in both weak and strong electron correlation limits. We benchmark the Gutzwiller density functional approximation in the hydrogen systems, where the static correlation error is shown to be negligible. The good transferability is demonstrated by applications to the hydrogen molecule and some crystal structures. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Li, Ran; Mao, Zhu; Chen, Lei; Lv, Haiming; Cheng, Jianbo; Zhao, Bing
2015-01-25
In this work, the structural parameters of the title molecule (MTT) have been obtained at the B3LYP/6-311++G(**) level of theory. The two phenyl rings and the two heterocyclic rings are found in four different planes. The tetrazolium ring was connected with other three rings and their distances are also different in decrease order of 1.461 Å (from tetrazolium ring to carbon connected phenyl)>1.445 Å (from tetrazolium ring to nitrogen connected phenyl)>1.425 Å (from tetrazolium ring to thiazolyl ring). Fourier transform infrared (FTIR) and Raman spectra of the compound were obtained experimentally. All FTIR and Raman bands of the compound obtained experimentally were assigned based on the modeling results obtained at the B3LYP/6-311++G(**) level. The calculated vibrational frequencies were in good agreement with the experimental values. In addition, the UV-Vis spectra were obtained experimentally and theoretically. Considering the effect of the PCM modelling error, the calculated absorbance peaks obtained at the B3LYP/6-311++G(**) level were also in good agreement with the experimental values. The HOMO-LUMO gap was predicted to be 1.83 eV at the B3LYP/6-311++G(**) level.
Ivanov, Petko
2016-03-01
The balances of interactions were studied by computational methods in the translational isomers of a solvent switchable fullerene-stoppered [2]rotaxane (1) manifesting unexpected behavior, namely that due to favorable dispersion interactions the fullerene stopper becomes the second station upon change of the solvent. For comparison, another system, a pH switchable molecular shuttle (2), was also examined as an example of prevailing electrostatic interactions. Tested for 1 were five global hybrid Generalized Gradient Approximation functionals (B3LYP, B3LYP-D3, B3LYP-D3BJ, PBEh1PBE and APFD), one long-range corrected, range-separated functional with D2 empirical dispersion correction, ωB97XD, the Zhao-Truhlar's hybrid meta-GGA functional M06 with double the amount of nonlocal exchange (2X), and a pure functional, B97, with the Grimme's D3BJ dispersion (B97D3). The molecular mechanics method qualitatively correctly reproduced the behavior of the [2]rotaxanes, whereas the DFT models, except for M06-2X to some extent, failed in the case of significant dispersion interactions with participation of the fulleropyrrolidine stopper (rotaxane 1). Unexpectedly, the benzylic amide macrocycle tends to adopt preferentially 'boat'-like conformation in most of the cases. Four hydrogen bonds interconnect the axle with the wheel for the translational isomer with the macroring at the succinamide station (station II), whereas the number of hydrogen bonds vary for the isomer with the macroring at the fulleropyrrolidine stopper (station I) depending of the computational model used. The B3LYP and the PBEh1PBE results show strong preference of station II in the gas phase and in the model solvent DMSO. After including empirical dispersion correction, the translational isomer with the macroring at station I has the lower energy with B3LYP, both in the gas phase and in DMSO. The same result, but with higher preference of station I, was estimated with APFD, ωB97XD and B97D3. Only M06-2X
Exact maps in density functional theory for lattice models
Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel
2016-08-01
In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg-Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.
Density functional calculations on hydrocarbon isodesmic reactions
Fortunelli, Alessandro; Selmi, Massimo
1994-06-01
Hartree—Fock, Hartree—Fock-plus-correlation and self-consistent Kohn—Sham calculations are performed on a set of hydrocarbon isodesmic reactions, i.e. reactions among hydrocarbons in which the number and type of carbon—carbon and carbon—hydrogen bonds is conserved. It is found that neither Hartree—Fock nor Kohn—Sham methods correctly predict standard enthalpies, Δ Hr(298 K), of these reactions, even though — for reactions involving molecules containing strained double bonds — the agreement between the theoretical estimates and the experimental values of Δ Hr seems to be improved by the self-consistent solution of the Kohn—Sham equations. The remaining discrepancies are attributed to intramolecular dispersion effects, that are not described by ordinary exchange—correlation functionals, and are eliminated by introducing corrections based on a simple semi-empirical model.
Energy Technology Data Exchange (ETDEWEB)
Gudmundsdóttir, Hildur [Science Institute and Faculty of Physical Sciences VR-III, University of Iceland, 107 Reykjavík (Iceland); Zhang, Yao; Weber, Peter M. [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States); Jónsson, Hannes [Science Institute and Faculty of Physical Sciences VR-III, University of Iceland, 107 Reykjavík (Iceland); Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States)
2014-12-21
Theoretical calculations of Rydberg excited states of molecular clusters consisting of N,N-dimethylisopropylamine molecules using a Perdew-Zunger self-interaction corrected energy functional are presented and compared with results of resonant multiphoton ionization measurements. The binding energy of the Rydberg electron in the monomer is calculated to be 2.79 eV and 2.27 eV in the 3s and 3p state, respectively, which compares well with measured values of 2.88 eV and 2.21 eV. Three different stable configurations of the dimer in the ground state were found using an energy functional that includes van der Waals interaction. The lowest ground state energy conformation has the two N-atoms widely separated, by 6.2 Å, while the Rydberg state energy is lowest for a configuration where the N-atoms of the two molecules come close together, separated by 3.7 Å. This conformational change is found to lower the Rydberg electron binding energy by 0.2 eV. The self-interaction corrected functional gives a highly localized hole on one of the two molecules, unlike results obtained using the PBE functional or the hybrid B3LYP functional which give a delocalized hole. For the trimer, the self-interaction corrected calculation gives a Rydberg electron binding energy lowered further by 0.13 eV as compared with the dimer. The calculated results compare well with trends observed in experimental measurements. The reduction of the Rydberg electron binding energy with cluster size can be ascribed to an effective delocalization of the positive charge of the hole by the induced and permanent dipole moments of the neighboring molecules. A further decrease observed to occur on a time scale of tens of ps can be ascribed to a structural rearrangement of the clusters in the Rydberg state where molecules rotate to orient their dipoles in response to the formation of the localized hole.
A Joint Density Function in the Renewal Risk Model
Institute of Scientific and Technical Information of China (English)
XU HUAI; TANG LING; Wang De-hui
2013-01-01
In this paper,we consider a general expression for (Φ)(u,x,y),the joint density function of the surplus prior to ruin and the deficit at ruin when the initial surplus is u.In the renewal risk model,this density function is expressed in terms of the corresponding density function when the initial surplus is 0.In the compound Poisson risk process with phase-type claim size,we derive an explicit expression for (Φ)(u,x,y).Finally,we give a numerical example to illustrate the application of these results.
Hilbert Space of Probability Density Functions Based on Aitchison Geometry
Institute of Scientific and Technical Information of China (English)
J. J. EGOZCUE; J. L. D(I)AZ-BARRERO; V. PAWLOWSKY-GLAHN
2006-01-01
The set of probability functions is a convex subset of L1 and it does not have a linear space structure when using ordinary sum and multiplication by real constants. Moreover, difficulties arise when dealing with distances between densities. The crucial point is that usual distances are not invariant under relevant transformations of densities. To overcome these limitations, Aitchison's ideas on compositional data analysis are used, generalizing perturbation and power transformation, as well as the Aitchison inner product, to operations on probability density functions with support on a finite interval. With these operations at hand, it is shown that the set of bounded probability density functions on finite intervals is a pre-Hilbert space. A Hilbert space of densities, whose logarithm is square-integrable, is obtained as the natural completion of the pre-Hilbert space.
A molecular density functional theory to study solvation in water
Jeanmairet, Guillaume
2014-01-01
A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation functions. Those functions can be computed by using molecular simulations such as molecular dynamic or Monte Carlo. It is also possible to use functions that have been determined experimentally. The functional minimization gives access to the solvation free energy and to the equilibrium solvent density. Some correction to the functional are also proposed to get the proper tetrahedral order of solvent molecules around a charged solute and to reproduce the correct long range hydrophobic behavior of big apolar solutes. To proceed the numerical minimization of the functional, the theory has been discretized on two tridimensional grids, one for the space coordinates, the other for the angular coordinates, in a functional minimization code written in modern Fortran, mdft. This program i...
Energy Density Functional for Nuclei and Neutron Stars
Energy Technology Data Exchange (ETDEWEB)
Erler, J. [UTK/ORNL/German Cancer Research Center-Heidelberg; Horowitz, C. J. [UTK/ORNL/Indiana University; Nazarewicz, Witold [UTK/ORNL/University of Warsaw; Rafalski, M. [UTK/ORNL; Reinhard, P.-G. [Universitat Erlangen, Germany
2013-01-01
Background: Recent observational data on neutron star masses and radii provide stringent constraints on the equation of state of neutron rich matter [ Annu. Rev. Nucl. Part. Sci. 62 485 (2012)]. Purpose: We aim to develop a nuclear energy density functional that can be simultaneously applied to finite nuclei and neutron stars. Methods: We use the self-consistent nuclear density functional theory (DFT) with Skyrme energy density functionals and covariance analysis to assess correlations between observables for finite nuclei and neutron stars. In a first step two energy functionals a high density energy functional giving reasonable neutron properties, and a low density functional fitted to nuclear properties are matched. In a second step, we optimize a new functional using exactly the same protocol as in earlier studies pertaining to nuclei but now including neutron star data. This allows direct comparisons of performance of the new functional relative to the standard one. Results: The new functional TOV-min yields results for nuclear bulk properties (energy, rms radius, diffraction radius, and surface thickness) that are of the same quality as those obtained with the established Skyrme functionals, including SV-min. When comparing SV-min and TOV-min, isoscalar nuclear matter indicators vary slightly while isovector properties are changed considerably. We discuss neutron skins, dipole polarizability, separation energies of the heaviest elements, and proton and neutron drip lines. We confirm a correlation between the neutron skin of 208Pb and the neutron star radius. Conclusions: We demonstrate that standard energy density functionals optimized to nuclear data do not carry information on the expected maximum neutron star mass, and that predictions can only be made within an extremely broad uncertainty band. For atomic nuclei, the new functional TOV-min performs at least as well as the standard nuclear functionals, but it also reproduces expected neutron star data
Density functional theory of the crystal field in dioxides
Diviš, M.; Kuriplach, J.; Richter, M.; Steinbeck, L.
1996-04-01
Presented are the results of ab-initio density functional calculations for PrO2 and UO2 using the general potential LAPW and optimized LCAO method in the local density approximation. The crystal field splitting of ionic Pr4+ and U4+ ground states was calculated and compared with predictions of a superposition model.
Charge and spin fluctuations in the density functional theory
Energy Technology Data Exchange (ETDEWEB)
Gyoerffy, B.L.; Barbieri, A. (Bristol Univ. (UK). H.H. Wills Physics Lab.); Staunton, J.B. (Warwick Univ., Coventry (UK). Dept. of Physics); Shelton, W.A.; Stocks, G.M. (Oak Ridge National Lab., TN (USA))
1990-01-01
We introduce a conceptual framework which allow us to treat charge and spin fluctuations about the Local density Approximation (LDA) to the Density Functional Theory (DFT). We illustrate the approach by explicit study of the Disordered Local Moment (DLM) state in Fe above the Curie Temperature {Tc} and the Mott insulating state in MnO. 27 refs., 6 figs.
Excitation Spectra of Nucleobases with Multiconfigurational Density Functional Theory
DEFF Research Database (Denmark)
Hubert, Mickaël; Jensen, Hans Jørgen Aa; Hedegård, Erik D.
2016-01-01
Range-separated hybrid methods between wave function theory and density functional theory (DFT) can provide high-accuracy results, while correcting some of the inherent flaws of both the underlying wave function theory and DFT. We here assess the accuracy for excitation energies of the nucleobases...
Applications and validations of the Minnesota density functionals
Zhao, Yan; Truhlar, Donald G.
2011-01-01
We discuss and review selected recent applications and validations of the Minnesota density functionals, especially the M06 family, emphasizing nanochemistry, organic, inorganic, and biological chemistry, and catalysis and highlighting the broad accuracy of these functionals as compared to previous popular functionals for thermochemistry, kinetics, and noncovalent interactions.
Density Functional Calculations for the Neutron Star Matter at Subnormal Density
Kashiwaba, Yu; Nakatsukasa, Takashi
The pasta phases of nuclear matter, whose existence is suggested at low density, may influence observable properties of neutron stars. In order to investigate properties of the neutron star matter, we calculate self-consistent solutions for the ground states of slab-like phase using the microscopic density functional theory with Bloch wave functions. The calculations are performed at each point of fixed average density and proton fraction (\\bar{ρ },Yp), varying the lattice constant of the unit cell. For small Yp values, the dripped neutrons emerge in the ground state, while the protons constitute the slab (crystallized) structure. The shell effect of protons affects the thickness of the slab nuclei.
Reflection-asymmetric nuclear deformations within the Density Functional Theory
Olsen, E; Nazarewicz, W; Stoitsov, M; 10.1088/1742-6596/402/1/012034
2013-01-01
Within the nuclear density functional theory (DFT) we study the effect of reflection-asymmetric shapes on ground-state binding energies and binding energy differences. To this end, we developed the new DFT solver AxialHFB that uses an approximate second-order gradient to solve the Hartree-Fock-Bogoliubov equations of superconducting DFT with the quasi-local Skyrme energy density functionals. Illustrative calculations are carried out for even-even isotopes of radium and thorium.
Density Functional Theory with Dissipation: Transport through Single Molecules
Energy Technology Data Exchange (ETDEWEB)
Kieron Burke
2012-04-30
A huge amount of fundamental research was performed on this grant. Most of it focussed on fundamental issues of electronic structure calculations of transport through single molecules, using density functional theory. Achievements were: (1) First density functional theory with dissipation; (2) Pseudopotential plane wave calculations with master equation; (3) Weak bias limit; (4) Long-chain conductance; and (5) Self-interaction effects in tunneling.
Impact of ATLAS Data on Parton Density Functions
Newman, PR; The ATLAS collaboration
2014-01-01
Various measurements provided by the ATLAS collaboration have significant impact on parton density functions. The production of W and Z bosons inclusively or in association with charm-quark have are found to constraint the strange-quark density at medium and low Bjorken-x. Multi-Jet and photon production processes show impact on the gluon density. Off-resonance Drell Yan production at large lepton pair masses may be used to constrain anti-quark density at high x. A qualitative comparison of the ATLAS measurements to predictions based on different PDFs is presented.
Basis convergence of range-separated density-functional theory
Franck, Odile; Luppi, Eleonora; Toulouse, Julien
2014-01-01
Range-separated density-functional theory is an alternative approach to Kohn-Sham density-functional theory. The strategy of range-separated density-functional theory consists in separating the Coulomb electron-electron interaction into long-range and short-range components, and treating the long-range part by an explicit many-body wave-function method and the short-range part by a density-functional approximation. Among the advantages of using many-body methods for the long-range part of the electron-electron interaction is that they are much less sensitive to the one-electron atomic basis compared to the case of the standard Coulomb interaction. Here, we provide a detailed study of the basis convergence of range-separated density-functional theory. We study the convergence of the partial-wave expansion of the long-range wave function near the electron-electron coalescence. We show that the rate of convergence is exponential with respect to the maximal angular momentum L for the long-range wave function, whe...
Density functional theory for polymeric systems in 2D.
Słyk, Edyta; Roth, Roland; Bryk, Paweł
2016-06-22
We propose density functional theory for polymeric fluids in two dimensions. The approach is based on Wertheim's first order thermodynamic perturbation theory (TPT) and closely follows density functional theory for polymers proposed by Yu and Wu (2002 J. Chem. Phys. 117 2368). As a simple application we evaluate the density profiles of tangent hard-disk polymers at hard walls. The theoretical predictions are compared against the results of the Monte Carlo simulations. We find that for short chain lengths the theoretical density profiles are in an excellent agreement with the Monte Carlo data. The agreement is less satisfactory for longer chains. The performance of the theory can be improved by recasting the approach using the self-consistent field theory formalism. When the self-avoiding chain statistics is used, the theory yields a marked improvement in the low density limit. Further improvements for long chains could be reached by going beyond the first order of TPT.
Linear response of homogeneous nuclear matter with energy density functionals
Energy Technology Data Exchange (ETDEWEB)
Pastore, A. [Institut d’Astronomie et d’Astrophysique, CP 226, Université Libre de Bruxelles, B-1050 Bruxelles (Belgium); Davesne, D., E-mail: davesne@ipnl.in2p3.fr [Institut de Physique Nucléaire de Lyon, CNRS-IN2P3, UMR 5822, Université Lyon 1, F-69622 Villeurbanne (France); Navarro, J. [IFIC (CSIC University of Valencia), Apdo. Postal 22085, E-46071 Valencia (Spain)
2015-03-01
Response functions of infinite nuclear matter with arbitrary isospin asymmetry are studied in the framework of the random phase approximation. The residual interaction is derived from a general nuclear Skyrme energy density functional. Besides the usual central, spin–orbit and tensor terms it could also include other components as new density-dependent terms or three-body terms. Algebraic expressions for the response functions are obtained from the Bethe–Salpeter equation for the particle–hole propagator. Applications to symmetric nuclear matter, pure neutron matter and asymmetric nuclear matter are presented and discussed. Spin–isospin strength functions are analyzed for varying conditions of density, momentum transfer, isospin asymmetry, and temperature for some representative Skyrme functionals. Particular attention is paid to the discussion of instabilities, either real or unphysical, which could manifest in finite nuclei.
Inclusion of Dispersion Effects in Density Functional Theory
DEFF Research Database (Denmark)
Møgelhøj, Andreas
In this thesis, applications and development will be presented within the field of van der Waals interactions in density functional theory. The thesis is based on the three projects: i) van der Waals interactions effect on the structure of liquid water at ambient conditions, ii) development...... and benchmarking of a new van der Waals density functional, and iii) the application of the newly developed functional to CO desorption from Ru(0001). The effect of van der Waals interactions in water was studied by performing ab initio molecular dynamics simulations using PBE and the two recent van der Waals...... density functionals optPBE-vdW and vdW-DF2 with identical computational setup. The two van der Waals functionals have been found to give excellent descriptions of the constituents of water (e.g., water dimers and hexamers). Including van der Waals interactions gives a softer water structure as seen from...
Introduction to Classical Density Functional Theory by Computational Experiment
Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel
2014-01-01
We present here an introductory practical course to classical density functional theory (cDFT). Density functional theories, whether quantum or classical, rely largely on nonintuitive abstract concepts and applied mathematics. They are nevertheless a powerful tool and an active field of research in physics and chemistry that led to the 1998 Nobel prize in chemistry. We here illustrate the DFT in its most mathematically simple and yet physically relevant form: the classical density functional theory of an ideal fluid in an external field, as applied to the prediction of the structure of liquid neon at the molecular scale. This introductory course is built around the production of a cDFT code written by students using the Mathematica language. In this way, they are brought to deal with (i) the cDFT theory itself, (ii) some basic concepts around the statistical mechanics of simple fluids, (iii) the underlying mathematical and numerical problem of functional minimization, and (iv) a functional programming languag...
Sloppy nuclear energy density functionals: effective model reduction
Niksic, Tamara
2016-01-01
Concepts from information geometry are used to analyse parameter sensitivity for a nuclear energy density functional, representative of a class of semi-empirical functionals that start from a microscopically motivated ansatz for the density dependence of the energy of a system of protons and neutrons. It is shown that such functionals are sloppy, characterized by an exponential range of sensitivity to parameter variations. Responsive to only a few stiff parameter combinations, they exhibit an exponential decrease of sensitivity to variations of the remaining soft parameters. By interpreting the space of model predictions as a manifold embedded in the data space, with the parameters of the functional as coordinates on the manifold, it is also shown that the exponential distribution of model manifold widths corresponds to the distribution of parameter sensitivity. Using the Manifold Boundary Approximation Method, we illustrate how to systematically construct effective nuclear density functionals of successively...
Density functionals and dimensional renormalization for an exactly solvable model
Kais, S.; Herschbach, D. R.; Handy, N. C.; Murray, C. W.; Laming, G. J.
1993-07-01
We treat an analytically solvable version of the ``Hooke's Law'' model for a two-electron atom, in which the electron-electron repulsion is Coulombic but the electron-nucleus attraction is replaced by a harmonic oscillator potential. Exact expressions are obtained for the ground-state wave function and electron density, the Hartree-Fock solution, the correlation energy, the Kohn-Sham orbital, and, by inversion, the exchange and correlation functionals. These functionals pertain to the ``intermediate'' density regime (rs≥1.4) for an electron gas. As a test of customary approximations employed in density functional theory, we compare our exact density, exchange, and correlation potentials and energies with results from two approximations. These use Becke's exchange functional and either the Lee-Yang-Parr or the Perdew correlation functional. Both approximations yield rather good results for the density and the exchange and correlation energies, but both deviate markedly from the exact exchange and correlation potentials. We also compare properties of the Hooke's Law model with those of two-electron atoms, including the large dimension limit. A renormalization procedure applied to this very simple limit yields correlation energies as good as those obtained from the approximate functionals, for both the model and actual atoms.
The Role of the Basis Set: Assessing Density Functional Theory
Boese, A D; Handy, N C; Martin, Jan M. L.; Handy, Nicholas C.
2003-01-01
When developing and assessing density functional theory methods, a finite basis set is usually employed. In most cases, however, the issue of basis set dependency is neglected. Here, we assess several basis sets and functionals. In addition, the dependency of the semiempirical fits to a given basis set for a generalised gradient approximation and a hybrid functional is investigated. The resulting functionals are then tested for other basis sets, evaluating their errors and transferability.
Nucleation for Lennard-Jones Fluid by Density Functional Theory
Institute of Scientific and Technical Information of China (English)
FU Dong
2005-01-01
@@ A non-mean field density functional theory is employed to investigate the vapour-liquid nucleation. The excess Helmholtz free energy functional is formulated in terms of a local density approximation for short ranged repulsion and a density-gradient expansion for long-ranged attractions. An analytical expression for the direct correlation function of a Lennard-Jones fluid is utilized to take into account the effect of long-ranged attractions on intermolecular correlations. With the predicted bulk properties and surface tension as input, the nucleation properties including density profile, work of formation and number of particles at the reduced temperatures T* = 0.694 and 0.741 are inuestigated. The obtained number of particles in the critical nucleus agrees well with the simulation data.
Specification of Density Functional Approximation by Radial Distribution Function of Bulk Fluid
Institute of Scientific and Technical Information of China (English)
ZHOUShi－Qi
2002-01-01
A systematic methodology is proposed to deal with the weighted density approximation version of classical density functional theory by employing the knowledge of radial distribution function of bulk fluid.The present methodology results from the concept of universality of the free energy density functional combined with the test particle method.It is shown that the new method is very accurate for the predictions of density distribution of a hard sphere fluid at different confining geometries.The physical foundation of the present methodology is also applied to the quantum density functional theory.
Basis convergence of range-separated density-functional theory.
Franck, Odile; Mussard, Bastien; Luppi, Eleonora; Toulouse, Julien
2015-02-21
Range-separated density-functional theory (DFT) is an alternative approach to Kohn-Sham density-functional theory. The strategy of range-separated density-functional theory consists in separating the Coulomb electron-electron interaction into long-range and short-range components and treating the long-range part by an explicit many-body wave-function method and the short-range part by a density-functional approximation. Among the advantages of using many-body methods for the long-range part of the electron-electron interaction is that they are much less sensitive to the one-electron atomic basis compared to the case of the standard Coulomb interaction. Here, we provide a detailed study of the basis convergence of range-separated density-functional theory. We study the convergence of the partial-wave expansion of the long-range wave function near the electron-electron coalescence. We show that the rate of convergence is exponential with respect to the maximal angular momentum L for the long-range wave function, whereas it is polynomial for the case of the Coulomb interaction. We also study the convergence of the long-range second-order Møller-Plesset correlation energy of four systems (He, Ne, N2, and H2O) with cardinal number X of the Dunning basis sets cc - p(C)V XZ and find that the error in the correlation energy is best fitted by an exponential in X. This leads us to propose a three-point complete-basis-set extrapolation scheme for range-separated density-functional theory based on an exponential formula.
A real-space stochastic density matrix approach for density functional electronic structure.
Beck, Thomas L
2015-12-21
The recent development of real-space grid methods has led to more efficient, accurate, and adaptable approaches for large-scale electrostatics and density functional electronic structure modeling. With the incorporation of multiscale techniques, linear-scaling real-space solvers are possible for density functional problems if localized orbitals are used to represent the Kohn-Sham energy functional. These methods still suffer from high computational and storage overheads, however, due to extensive matrix operations related to the underlying wave function grid representation. In this paper, an alternative stochastic method is outlined that aims to solve directly for the one-electron density matrix in real space. In order to illustrate aspects of the method, model calculations are performed for simple one-dimensional problems that display some features of the more general problem, such as spatial nodes in the density matrix. This orbital-free approach may prove helpful considering a future involving increasingly parallel computing architectures. Its primary advantage is the near-locality of the random walks, allowing for simultaneous updates of the density matrix in different regions of space partitioned across the processors. In addition, it allows for testing and enforcement of the particle number and idempotency constraints through stabilization of a Feynman-Kac functional integral as opposed to the extensive matrix operations in traditional approaches.
Higher-accuracy van der Waals density functional
DEFF Research Database (Denmark)
Lee, Kyuho; Murray, Éamonn D.; Kong, Lingzhu
2010-01-01
We propose a second version of the van der Waals density functional of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)], employing a more accurate semilocal exchange functional and the use of a large-N asymptote gradient correction in determining the vdW kernel. The predicted binding energy...
Wigner Function of Density Operator for Negative Binomial Distribution
Institute of Scientific and Technical Information of China (English)
HE Min-Hua; XU Xing-Lei; ZHANG Duan-Ming; LI Hong-Qi; PAN Gui-Jun; YIN Yan-Ping; CHEN Zhi-Yuan
2008-01-01
By using the technique of integration within an ordered product (IWOP) of operator we derive Wigner function of density operator for negative binomial distribution of radiation field in the mixed state case, then we derive the Wigner function of squeezed number state, which yields negative binomial distribution by virtue of the entangled state representation and the entangled Wigner operator.
Density-functional perturbation theory goes time-dependent
Gebauer, Ralph; Rocca, Dario; Baroni, Stefano
2009-01-01
The scope of time-dependent density-functional theory (TDDFT) is limited to the lowest portion of the spectrum of rather small systems (a few tens of atoms at most). In the static regime, density-functional perturbation theory (DFPT) allows one to calculate response functions of systems as large as currently dealt with in ground-state simulations. In this paper we present an effective way of combining DFPT with TDDFT. The dynamical polarizability is first expressed as an off-diagonal matrix e...
Density Functional Theory for General Hard-Core Lattice Gases
Lafuente, Luis; Cuesta, José A.
2004-09-01
We put forward a general procedure to obtain an approximate free-energy density functional for any hard-core lattice gas, regardless of the shape of the particles, the underlying lattice, or the dimension of the system. The procedure is conceptually very simple and recovers effortlessly previous results for some particular systems. Also, the obtained density functionals belong to the class of fundamental measure functionals and, therefore, are always consistent through dimensional reduction. We discuss possible extensions of this method to account for attractive lattice models.
Density Functional Theory and Materials Modeling at Atomistic Length Scales
Directory of Open Access Journals (Sweden)
Swapan K. Ghosh
2002-04-01
Full Text Available Abstract: We discuss the basic concepts of density functional theory (DFT as applied to materials modeling in the microscopic, mesoscopic and macroscopic length scales. The picture that emerges is that of a single unified framework for the study of both quantum and classical systems. While for quantum DFT, the central equation is a one-particle Schrodinger-like Kohn-Sham equation, the classical DFT consists of Boltzmann type distributions, both corresponding to a system of noninteracting particles in the field of a density-dependent effective potential, the exact functional form of which is unknown. One therefore approximates the exchange-correlation potential for quantum systems and the excess free energy density functional or the direct correlation functions for classical systems. Illustrative applications of quantum DFT to microscopic modeling of molecular interaction and that of classical DFT to a mesoscopic modeling of soft condensed matter systems are highlighted.
Density functional for ternary non-additive hard sphere mixtures.
Schmidt, Matthias
2011-10-19
Based on fundamental measure theory, a Helmholtz free energy density functional for three-component mixtures of hard spheres with general, non-additive interaction distances is constructed. The functional constitutes a generalization of the previously given theory for binary non-additive mixtures. The diagrammatic structure of the spatial integrals in both functionals is of star-like (or tree-like) topology. The ternary diagrams possess a higher degree of complexity than the binary diagrams. Results for partial pair correlation functions, obtained via the Ornstein-Zernike route from the second functional derivatives of the excess free energy functional, agree well with Monte Carlo simulation data. © 2011 IOP Publishing Ltd
Directory of Open Access Journals (Sweden)
Đurović Igor B.
2015-01-01
Full Text Available Aromatic hydroxy acids, the compounds of large industrial importance, can be prepared in the Kolbe-Schmitt reaction, i.e. a carboxylation reaction of alkali metal phenoxides (MOPh and naphthoxides (MONaph. On the basis of the experimental results two contradictory reaction mechanisms have been proposed: the one of direct carboxylation, and the other involving initial formation of the MOPh-CO2 or MONaph-CO2 complex. Previous theoretical investigations of the carboxylation reaction of sodium 2-naphthoxide, performed by means of the B3LYP method, confirmed the initial formation of the NaONaph-CO2 complex, and showed that the carbon of the CO2 moiety performs an electrophilic attack at C1 of the ring, leading to the formation of sodium 2-hydroxy-1-naphthoate (E1. Surprisingly, transition states for possible electrophilic attacks at C3 and C6 were not revealed, and the formation of other two products (E3 and E6 was explained by a number of consecutive rearrangements. In addition, this mechanism includes a reaction step with rather high activation energy. Since more sophisticated functionals are today available, the aim of this work is to reinvestigate the mechanism of the Kolbe-Schmitt reaction of NaONaph in all three positions (1, 3, and 6. Our investigations with the M062X method demonstrated that CO2 and NaONaph can spontaneously build two complexes: B (the one previously reported and C. While B cannot be further transformed to yield the reaction products, the CO2 moiety in C takes perfect position for electrophilic attacks at all three sites of the ring. These attacks are realized via the transition states TS1, which lead to the formation of the new C-C bonds, and corresponding intermediates D. In the next, bimolecular reaction step two D intermediates exchange the protons adjacent to the CO2 groups. These intermolecular reaction steps require significantly lower activation energies in comparison to the intramolecular proton shift from C to O
Quattrociocchi, Daniel Garcez S; Meuser, Marcos Vinicius Monsores; Ferreira, Glaucio Braga; de M Carneiro, José Walkimar; Stoyanov, Stanislav R; da Costa, Leonardo Moreira
2017-02-01
Calcium complexes with bidentate carbonyl ligands are important in biological systems, medicine and industry, where the concentration of Ca(2+) is controlled using chelating ligands. The exchange of two water molecules of [Ca(H2O)6](2+) for one bidentate monosubstituted and homo disubstituted dicarbonyl ligand was investigated using the B3LYP/6-311++G(d,p) method. The ligand substituents NH2, OCH3, OH, CH3, H, F, Cl, CN and NO2 are functional groups with distinct electron-donating and -withdrawing effects that bond directly to the sp(2) C atom of the carbonyl group. The geometry, charge and energy characteristics of the complexes were analyzed to help understand the effects of substituents, spacer length and chelation. Coordination strength was quantified in terms of the enthalpy and free energy of the exchange reaction. The most negative enthalpies were calculated for the coordination of bidentate ligands containing three to five methylene group spacers between carbonyls. The chelate effect contribution was analyzed based on the thermochemistry. The electronic character of the substituent modulates the strength of binding to the metal cation, as ligands containing electron-donor substituents coordinate stronger than those with electron-acceptor substituents. This is reflected in the geometric (bond length and chelating angle), electronic (atomic charges) and energetic (components of the total interacting energy) characteristics of the complexes. Energy decomposition analysis (EDA)-an approach for partitioning of the energy into its chemical origins-shows that the electrostatic component of the coordination is predominant, and yields relevant contribution of the covalent term, especially for the electron-withdrawing substituted ligands. The chelate effect of the bidentate ligands was noticeable when compared with substitution by two monodentate ligands. Graphical abstract The affinity of 18 bidentate carbonyl ligands toward the [Ca(H2O)4](2+) cation is evaluated in
Abraham, Christina Susan; Prasana, Johanan Christian; Muthu, S.
2017-06-01
Experimental and theoretical investigations on the molecular structure, electronic and vibrational characteristics of 2-Amino-3-bromo-5-nitropyridine are presented. The vibrational frequencies were obtained by DFT/B3LYP calculations employing 6-311 ++ G (d, p) basis set. This was compared with experimental FT-IR and FT-Raman spectral data. Simulated FT-IR (4000-400 cm- 1) and FT-Raman spectra (4000-100 cm- 1) showed good agreement with the observed spectra. The molecular equilibrium geometry of the title compound was fully optimized. Quantum chemical calculations of the equilibrium geometry and the complete vibrational assignments of wavenumbers using potential energy distribution (PED) were calculated with scaled quantum mechanics. HOMO-LUMO energies, energy gap (ΔE), electronegativity (χ), chemical potential (μ), global hardness (η), softness (S) and the Fukui function were calculated for the title molecule. The title compound has a low softness value (0.239) and the calculated value of electrophilicity index (5.905) describes the biological activity. The stability and charge delocalization of the title molecule were studied by Natural Bond Orbital (NBO) analysis, Non-Linear Optical (NLO) behaviour in terms of first order hyperpolarizability, dipole moment and anisotropy of polarizability and Molecular Electrostatic Potential (MEP) were accounted. The computed values of μ, α and β for the title molecule are 1.851 Debye, 1.723 × 10- 23 esu and 7.428 × 10- 30 esu respectively. The high β value and non-zero value of μ indicate that the title compound might be a good candidate for NLO material. Thermodynamic properties of the title molecule were studied for different temperatures thereby revealing the correlations between heat capacity (C), entropy (S) and enthalpy changes (H) with temperatures. Docking studies of the title compound were scrutinized to predict the preferred binding orientation, affinity and activity of the given compound. The title