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  • 1
    Keywords: DENSITY-FUNCTIONAL-THEORY ; Germany ; DNA adducts ; BASE ; NUCLEIC-ACIDS ; TIGHT-BINDING SCHEME ; CARCINOGENS ; AROMATIC-HYDROCARBONS ; carcinogen,benzo(a)pyrene,anti- and syn-diol epoxide,anti- and syn-triol carbocation,intercalation ; DIOL EPOXIDES ; MODIFIED DEOXYGUANOSINE ; NONEMPIRICAL AB-INITIO ; SOLUTION CONFORMATION ; STACKING INTERACTIONS
    Type of Publication: Journal article published
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  • 2
    Keywords: AB-INITIO ; FREQUENCY ; DIFFERENCE ; basis set superposition error ; chemical Hamiltonian approach ; FREE SCF ALGORITHM ; INTERACTION ENERGIES ; PERTURBATION-THEORY ; SAMPLE CALCULATIONS ; SET SUPERPOSITION ERROR ; DISSOCIATION ; CLUSTERS ; CONSTANTS ; harmonic vibrational frequencies ; HYDROGEN-BONDED COMPLEXES ; INFRARED DOUBLE-RESONANCE ; INTERACTING SYSTEMS ; intermolecular interactions
    Abstract: The influence of basis set superposition error (BSSE) in optimized geometries, force constants and intermolecular harmonic vibrational frequencies of the ammonia-ammonia dimer have been studied both at the Hartree-Fock and correlated (second-order Moller-Plesset perturbation theory) levels of theory using several different basis sets as (6-31G, 6-311G, 6-31 + +G, 6-311 + +G, 6-31G(d,p), 6-311G(d,p), 6-31 + +G(d,p) 6-311 + +G(d,p) and 6-311 + +G(2d,2p)). The widely used a posteriori Boys-Bernardi "counterpoise" (CP) correction scheme has been compared with the a priori method utilizing the chemical Hamiltonian approach (CHA). The results show that practically there is no difference between these two methods, so the a priori CHA scheme can be considered as an ultimate solution of the BSSE problem. It is also concluded that the BSSE influence is very significant, so removing this effect is very important. (C) 2004 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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  • 3
    Keywords: DENSITY-FUNCTIONAL-THEORY ; ENERGIES ; CONSTRUCTION ; ENSEMBLES ; excitation energies ; EXCITATION-ENERGIES ; FORMALISM ; FRACTIONALLY OCCUPIED STATES ; KOHN ; OPTIMIZED POTENTIAL METHOD ; RIGOROUS FORMULATION ; SHAM THEORY ; SPECIAL SYMMETRIES ; spin- indexed exchange correlation potential ; subspace density functional theory ; subspace von Barth- Hedin potential
    Abstract: Applicability of the subspace density functional theory (SDFT) for calculation of excitation energies of atoms is Studied. In the SDFT the subspace construction gives the opportunity to perform calculations with the standard ground-state potentials or make a distinction between the subspaces with different quantum numbers (L and S), using special potentials depending on the quantum numbers. Theophiliou and Papaconstantinou gave a spin-indexed version of the local von Barth-Hedin potential to treat singlet and triplet states. In this article we 1,study the same spin-indexed potential for atoms having multiplet structure and compare the results with the values obtained in calculations using the ground-state version of the von Barth-I Win potential. (C) 2003 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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  • 4
    Keywords: AB-INITIO ; ENERGIES ; SCC-DFTB ; X-RAY-DIFFRACTION ; DENSITY ; DNA ; BASE ; ENERGY ; PERTURBATION-THEORY ; TIGHT-BINDING SCHEME ; PARAMETERS ; STABILITY ; ORIENTATION ; ENERGETICS ; 2 '-deoxyribonucleosides ; ABINITIO ; chemical hardness ; chemical potential ; conformational analysis ; LMP2 ; NUCLEOSIDES ; PSEUDOROTATION ; RIBONUCLEOSIDES
    Abstract: The molecular structure of free canonical 2'-deoxyribonucleosides have been studied by applying the electron-correlated local second-order Moller-Plesset perturbation theory (LMP2) and self-consistent-charge density-functional tight-binding (SCC-DFTB) methods. The variation of structural parameters for C2, C3 endo and exo conformations, and anti, syn orientation of the base unit with furanose ring have been discussed. The relative energies have been calculated for the anti and syn conformations of dT, dC, dG, and dA. Conformational analysis has been performed using the results of the LMP2 and SCC-DFTB methods. Chemical hardness and chemical potential have been used to study the conformational stability of the conformers. The maximum hardness principle is obeyed for the furanose ring conformations and not for the nucleosides. (C) 2004 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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  • 5
    Keywords: DENSITY-FUNCTIONAL-THEORY ; DFT ; AGENTS ; Germany ; MODEL ; DENSITY ; EXPOSURE ; MOLECULES ; MICE ; COMPLEX ; COMPLEXES ; MECHANISM ; CARCINOGENESIS ; mechanisms ; BINDING ; FIELD ; MOLECULE ; REPAIR ; STABILITY ; mutagenesis ; F344 RATS ; RE ; CARCINOGEN ; LEVEL ; PHASE ; O-6-methylguanine ; carcinogenic ; GEOMETRY ; DNA-METHYLATION ; mutagen ; ADAPTIVE RESPONSE ; ALKYLATION DAMAGE ; methyl bromide ; methyl chloride ; O(6)-METHYLGUANINE ; O6-methylguanine
    Abstract: Density functional theory (DFT) at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels was employed to study O6-methylation of guanine due to its reactions with methyl chloride and methyl bromide and to obtain explanation as to why the methyl halides cause genotoxicity and possess mutagenic and carcinogenic properties. Geometries of the various isolated species involved in the reactions, reactant complexes (RCs), and product complexes (PCs) were optimized in gas phase. Transition states connecting the reactant complexes with the product complexes were also optimized in gas phase at the same levels of theory. The reactant complexes, product complexes, and transition states were solvated in aqueous media using the polarizable continuum model (PCM) of the selfconsistent reaction field theory. Zero-point energy (ZPE) correction to total energy and the corresponding thermal energy correction to enthalpy were made in each case. The reactant complexes of the keto form of guanine with methyl chloride and methyl bromide in water are appreciably more stable than the corresponding complexes involving the enol form of guanine. The nature of binding in the product complexes was found to be of the charge transfer type (O6mG(+) center dot X-, X=Cl, Br). Binding of HCl, HBr, and H2O molecules to the PCs obtained with the keto form of guanine did not alter the positions of the halide anions in the PCs, and the charge transfer character of the PCs was also not modified due to this binding. Further, the complexes obtained due to the binding of HCl, HBr, and H2O molecules to the PCs had greater stability than the isolated PCs. The reaction barriers involved in the formation of PCs were found to be quite high (similar to 50 kcal/mol). Mechanisms of genotoxicity, mutagenesis and carcinogenesis caused by the methyl halides appear to involve charge transfer-type complex formation. Thus the mechanisms of these processes involving the methyl halides appear to be quite different from those that involve the other strongly carcinogenic methylating agents. (c) 2006 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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  • 6
    Keywords: DENSITY-FUNCTIONAL-THEORY ; DFT ; SIMULATIONS ; SPECTRA ; COMBINATION ; MODEL ; MOLECULES ; SIMULATION ; treatment ; DERIVATIVES ; US ; FORCE-FIELD ; AB-INITIO CALCULATION ; ATOMIC AXIAL TENSORS ; EXPLICIT WATER-MOLECULES ; FREQUENCY-DEPENDENT HYPERPOLARIZABILITIES ; GAUGE DEPENDENCE ; L-alanyl-L-alanine ; QM/MM METHODS ; Raman ; Raman optical activity (ROA) ; ROA SPECTRA ; ROTATIONAL STRENGTHS ; vibrational absorption ; vibrational circular dichroism (VCD)
    Abstract: In a recent work (Knapp-Mohammady, M.; Jalkanen, K. J.; Nardi, F.; Wade, R. C.; Suhai, S. Chem Phys 1999, 240, 63-77) the structures of the zwitterionic species Of L-alanyI-L-alanine (LALA) in aqueous solution using a combination of molecular mechanics (MM) and density functional theory (DFT) have been reported. Subsequently, the vibrational absorption (VA) and vibrational circular dichroism (VCD) and the Raman and Raman Optical Activity (ROA) spectra have been reported. In this work an analysis of the aqueous solution VA, VCD, Raman, and ROA spectra for various isotopomers of LALA are reported. DFT Becke3LYP/6-31G* theory has been used to determine the geometry, Hessian, atomic polar tensors (APT), and atomic axial tensors (AAT), and the electric dipole-electric dipole polarizability derivatives (EDEDPD), which are required for us to simulate the VA, VCD, and Raman spectra. The electric dipole-magnetic dipole polarizability derivatives (EDMDPD) and tile electric dipole-electric cluadrapole polarizability derivatives (EDEQPD) have been calculated at the RHF/6-31G* level of theory, The VA, VCD, Raman, and ROA spectral simulations for the various isotoporners are compared with the experimentally measured spectra. With the DFT, explicit water molecules, and a continuum solvent model we are better able to reproduce the vibrational absorption and Raman spectra than previously reported. The AAT have been implemented at the DFT level, although not within the continuum treatment. The VCD sign pattern could be reproduced with the DIFT atomic axial tensors calculated for the LALA plus explicit water molecules. The continuum treatment of the solvent for the calculation of these tensors appeirs to be a secondary effect. The ROA spectra are not well reproduced due to the failure to take into account electron correlation via DFT and the continuum treatment of the solvent for the EDMDPD and EDEQPD, We look forward to reporting ROA simulations utilizing more accurate tensors in the near future. Oc 2003 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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  • 7
    Keywords: ENERGIES ; SYSTEM ; SYSTEMS ; COMPLEX ; COMPLEXES ; DONOR ; BINDING ; PROTON ; ENERGY ; basis set superposition error ; chemical Hamiltonian approach ; FREE SCF ALGORITHM ; SAMPLE CALCULATIONS ; SERIES ; HYDROGEN-BONDED COMPLEXES ; INTERACTING SYSTEMS ; intermolecular interactions ; interaction ; CHA ; INTERMOLECULAR PERTURBATION-THEORY ; MOLLER-PLESSET ; BSSE-FREE DESCRIPTION ; CHARGE ; FORMAMIDE ; HYDROGEN ; intermolecular perturbation theory ; MOLECULAR-STRUCTURE ; SET-SUPERPOSITION-ERROR
    Abstract: The equilibrium structures, the binding energies, and the second-order energy components of a series of hydrogen-bonded complexes involving acetylene are studied. The strength of the binding energy of the selected systems (HF...HCCH, HCl...HCCH, HCN...HCCH, and HCCH...HCCH) was different, ranging from a very weak interaction to a strong interaction. Calculations have been carried out at both the Hartree-Fock and correlated (second-order Moller-Plesset perturbation theory) levels of theory, using several different basis sets [6-31G(d,p), 6-311G(d,p), 631G++(d,p), 6-311G++(d,p), 6-31++G(2d,2p) and 6-311++G(2d,2p)]. The widely used a posteriori Boys-Bernardi counterpoise (CP) correction scheme has been compared with the a priori CHA/CE, CHA-MP2, and CHA-PT2 methods, using the chemical Hamiltonian approach (CHA). The results show that at both levels the CP and the appropriate CHA results are very close to each other. Only the monomer-based CHAPT2 theory gives slightly overcorrected results, reflecting that the charge transfer and polarization effects are not taken into account in this method up to second order. We have also applied our earlier developed energy decomposition scheme in order to decompose the second-order energy contribution into different physically meaningful components. The results show that at large and intermediate intermolecular distances, the second-order intermolecular contribution is almost equal to the sum of different physically meaningful components (e.g., polarization, charge transfer, dispersion), while at shorter distances the slightly strong overlap effects fairly disturb this simple additivity. (C) 2004 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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  • 8
    Keywords: AB-INITIO ; DENSITY ; TIME ; FREE SCF ALGORITHM ; SAMPLE CALCULATIONS ; SET SUPERPOSITION ERROR ; PARAMETERS ; HYDROGEN-BONDED COMPLEXES ; INTERACTING SYSTEMS ; RE ; interaction ; anharmonic frequency ; BSSE ; CHA ; FORCE-CONSTANTS ; formamide dimer ; formamide-water ; INTERMOLECULAR PERTURBATION-THEORY ; MOLLER-PLESSET
    Abstract: The basis set superposition error (BSSE) influence in the geometry structure, interaction energies, and intermolecular harmonic and anharmonic vibrational frequencies of cyclic formamide-formamide and formamide-water dimers have been studied using different basis sets (6-31G, 6-31G**, 6-31++G**, D95V, D95V**, and D95V++**). The a posteriori "counterpoise" (CP) correction scheme has been compared with the a priori "chemical Hamiltonian approach" (CHA) both at the Hartree-Fock (HF) and second-order Moller-Plesset many-body perturbation (MP2) levels of theory. The effect of BSSE on geometrical parameters, interaction energies, and intermolecular harmonic vibrational frequencies are discussed and compared with the existing experimental data. As expected, the BSSE-free CP and CHA interaction energies usually show less deep minima than those obtained from the uncorrected methods at both the ET and MP2 levels. Focusing on the correlated level, the amount of BSSE in the intermolecular interaction energies is much larger than that at the HT level, and this effect is also conserved in the values of the force constants and harmonic vibrational frequencies. All these results clearly indicate the importance of the proper BSSE-free correlation treatment with the well-defined basis functions. At the same time, the results show a good agreement between the a priori CRA and a posteriori CP correction scheme; this agreement is remarkable in the case of large and well-balanced basis sets. The anharmonic frequency correction values also show an important BSSE dependence, especially for hydrogen bond stretching and for low frequencies belonging to the intermolecular normal modes. (C) 2005 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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  • 9
    Keywords: AB-INITIO ; DENSITY-FUNCTIONAL-THEORY ; ENERGIES ; OPTIMIZATION ; COMBINATION ; Germany ; MODEL ; DENSITY ; MOLECULES ; COMPLEX ; MOLECULE ; ENERGY ; STATES ; GAS-PHASE ; molecular ; GLYCINE ; LEVEL ; PHASE ; MOLECULAR-STRUCTURE ; USA ; AGREEMENT ; MEDIA ; amino acids ; CONTINUUM MODEL ; ZWITTERION ; ALPHA-GLYCINE ; GASEOUS GLYCINE ; INTRAMOLECULAR PROTON-TRANSFER ; MILLIMETER WAVE SPECTRUM ; reaction barrier ; solvent effect ; tautomerization ; VIBRATIONAL ANALYSIS
    Abstract: Geometries of the normal (N) and zwitterionic (Z) forms of glycine (gly) and their complexes gly.(H2O)(n), n = 0-2, were fully optimized in gas phase and aqueous media, and transition states located between the corresponding N and Z forms. The geometry was also optimized and vibrational spectra calculated for the gly.(H2O)(3) complex of Z glycine. Density functional theory at the B3LYP/AUG-cc-pVDZ level was employed for the geometry optimization calculations in gas phase and aqueous media while single point energy calculations were performed at the MP2/AUG-cc-pVDZ level in each case. Solvation in bulk water was treated using the polarizable continuum model (PCM). Zero-point energy correction to total energy and thermal energy correction to enthalpy were obtained at the B3LYP/AUG-cc-pVDZ level of theory in both gas phase and bulk aqueous media and these corrections were also considered to be valid for the corresponding single point energy calculations performed at the MP2/ AUG-cc-pVDZ level of theory. When geometries of the complexes of glycine with water molecules are optimized in aqueous media, the calculated properties are found to be appreciably modified with respect to those obtained by gas phase geometry optimization followed by solvation in aqueous media. For several vibrational frequencies, the agreement between the calculated and experimentally observed results is improved appreciably when both the specific and bulk solvent effects are considered in combination with full geometry optimization in aqueous media. For certain vibrational frequencies, mode assignments have also been modified. (c) 2007 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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  • 10
    Keywords: SYSTEMS ; MOLECULES ; FREQUENCY ; basis set ; basis set superposition error ; BONDED COMPLEXES ; chemical Hamiltonian approach ; force constants ; FREE SCF ALGORITHM ; H2O dimer ; HF dimer ; INTERACTION ENERGIES ; PERTURBATION-THEORY ; SAMPLE CALCULATIONS ; SET SUPERPOSITION ERROR ; TIGHT-BINDING SCHEME ; VIBRATIONAL-SPECTRA
    Abstract: Theoretical studies have been performed to Calculate the force constants and harmonic vibrational frequencies in the hydrogen fluoride and water dimers. The calculations have been undertaken both at the Hartree-Fock and correlated (second- order Moller-Plesset perturbation theory) levels of theory using several different basis sets ranging from the weak to the intermediate. The basis set superposition error (BSSE) has been excluded by using the chemical Hamiltonian approach. The results show that the BSSE influence is significant in the force constants and harmonic vibrational frequencies even if electron correlation is accounted for, so removing the BSSE is important. The results are compared with those obtained by the basis independent density-functional tight-binding method. (C) 2003 Wiley Periodicals, Inc
    Type of Publication: Journal article published
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