Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction

A systematic analysis of the molecular electrostatic potential (MEP) is presented. This study has been performed with a twofold purpose: first, to study the MEP dependence with regard to the quality of the basis set used to compute the ab initio SCF wavefunction and second, to develop and to assess a new strategy for computing isoelectrostatic potential maps using the semiempirical MNDO wavefunction. The only differences between this procedure and the ab initio SCF MEP computation lie in the freezing of the inner electrons and in the origin of the first-order density matrix. The statistical analysis of MEPs computed for a large number of molecules from MNDO wavefunction and ab initio SCF wavefunctions obtained using STO-3G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** basis sets points out the ability of any wavefunction to reproduce the general topological characteristics of the MEP surfaces. Nevertheless, split-valence basis sets including polarization functions are necessary to obtain accurate MEP minimum energy values. MNDO wavefunction tends to overestimate the MEP minima depth by a constant factor and shows an excellent ability to reflect the relative variation of MEP minima energies derived from a rather sophisticated (6-31G*) basis set, lacking of the shortcomings detected in the semiempirical CNDO approximation.     

The vibrational spectra, assignments and ab initio/DFT analysis for 3-chloro, 4-chloro and 5-chloro-2-methylphenyl isocyanates

The Raman (3500-50 cm(-1)) and infrared (4000-200 cm(-1)) spectra of 3-chloro, 4-chloro and 5-chloro-2-methylphenyl isocyanates have been measured. Ab initio and density functional theory calculations, at the levels of RHF/6-311G* and B3LYP/6-311G*, have been performed: energies, optimized geometrical parameters, vibrational frequencies, infrared intensities, Raman activities, depolarization ratios and nuclear displacements are obtained. Potential energy distributions (PEDs) and normal modes, for the spectral data computed at B3LYP/6-311G*, have also been obtained from a force-field calculations. A complete vibrational assignments of the observed spectra have been proposed. The force-field calculations have shown that, several of the normal modes are coupled, as is the case with large molecular systems possessing very low or no symmetry, such as investigated in the present study. Further, the investigation of the internal rotation of the isocyanate, NCO, by B3LYP/6-31G* level of theory has shown that the moiety maintains nearly the same orientation in all the three compounds (approximately 140-145 degrees tilt to the para-position) as in phenyl isocyanate. Two conformers, cis and trans forms, with respect to the substituents, NCO and CH(3), have been determined: the cis form lies above trans form by less than a kilocalorie per mole for each compound.     

苯乙烯基吡啶类化合物几何结构与光谱的理论研究

采用量子化学密度泛函理论(DFT)方法分别在B3LYP/6-31G*, 6-31G**, 6-31＋G*水平上对苯乙烯基吡啶类化合物进行计算研究. 通过在相同水平下的振动频率分析发现苯乙烯基吡啶类化合物具有C₁对称性, 酯基的碳氧原子与苯环形成不同的离域大π键, 空间位阻和共轭效应使得两苯环处于两个不同平面, 二面角在60°与62°之间. 使用含时密度泛函理论(TD-DFT)方法计算第一激发态的电子垂直跃迁能, 得到最大吸收波长λ_max. 计算结果表明末端烷基链的长度对该类化合物的几何结构与振动光谱、电子光谱无影响.     

一种天然产物Wangzaozin A的细胞毒活性

从总序香茶菜Isodon racemosa (Hemsl) Hara植物中分离得到一个对人类肿瘤细胞Bel-7402和HD-8910具有毒活性的对映-贝壳衫烷型二萜Wangzaozin A化合物(1). 应用密度泛函理论(DFT)B3LYP方法, 对该分子的几何构型进行优化, 结果表明用B3LYP/6-31G(d)优化的几何参数与它的X射线衍射结构参数基本一致. 在优化的几何构型基础上, 采用规范不变原子轨道(GIAO)法, 在B3LYP理论水平分别用6-31G(d), 6-31G(d,p), 6-31+G(d,p)和6-31++G(d,p)基组进行核磁共振(NMR)化学位移值计算, 预测的1H和13CNMR化学位移值与实验值吻合; 统计误差分析表明, 用B3LYP/6-31G(d)优化的分子构型接近实际的分子构型. 因此, DFT方法适用这一类型化合物的构型和NMR参数进行预测. 在几何优化的基础上, 在B3LYP/6-31G(d)水平上, 对Wangzaozin A分子的静电位(MEP)进行理论计算. MEP三维图表明, 在Wangzaozin A分子中α-亚甲基环戊酮的羰基和羟基附近出现富电子区域(负电位), 起着供电子作用, 与受体的正电子区域结合. 这些结果从理论上支持了α-亚甲基环戊酮结构是一种抗肿瘤活性中心的看法.     

Conformational study of the structure of 12-crown-4-alkali metal cation complexes

A conformational search was performed for the 12-crown-4 (12c4)-alkali metal cation complexes using two different methods, one of them is the CONFLEX method, whereby eight conformations were predicted. Computations were performed for the eight predicted conformations at the HF/6-31+G*, MP2/6-31+G*//HF/6-31+G*, B3LYP/6-31+G*, MP2/6-31+G*//B3LYP/6-31+G*, and MP2/6-31+G* levels. The calculated energies predict a C4 conformation for the 12c4-Na+, -K+, -Rb+, and -Cs+ complexes and a C(s) conformation for the 12c4-Li+ complex to be the lowest energy conformations. For most of the conformations considered, the relative energies, with respect to the C4 conformation, at the MP2/6-31+G*//B3LYP/6-31+G* are overestimated, compared to those at the MP2/6-31+G* level, the highest level of theory considerd in this report, by 0.2 kcal/mol. Larger relative energy differences are attributed to larger differences between the B3LYP and MP2 optimized geomtries. Binding enthalpies (BEs) were calculated at the above-mentioned levels for the eight conformations. The agreement between the calculated and experimental BEs is discussed.     

FT-IR, FT-Raman and quantum chemical calculations of (E)-N-carbamimidoyl-4-((3,4-dimethoxybenzylidene) amino) benzenesulfonamide

FT-IR and FT-Raman spectra of (E)-N-carbamimidoyl-4-((3,4-dimethoxybenzylidene) amino) benzenesulfonamide were recorded and analyzed. The vibrational wavenumbers were computed using HF/6-31G*, B3PW91/6-31G* and B3LYP/6-31G* basis. The data obtained from vibrational wavenumber calculations are used to assign vibrational bands obtained experimentally. The results indicate that the B3LYP method is able to provide satisfactory results for predicting vibrational frequencies and structural parameters. The calculated first hyperpolarizability is comparable with the reported values of similar derivatives and is an attractive object for future studies of non-linear optics. The geometrical parameters of the title compound are in agreement with that of similar derivatives.     

Reliability of MEP and MEP-derived properties computed from DFT methods for molecules containing P, S and CL

We present a systematic study on the reliability of different theoretical methods to represent the molecular electrostatic potential (MEP), and MEP-derived properties of prototypical compounds containing phosphorus, sulfur and chlorine. Calculations at the Hartree-Fock and M?ller-Plesset up to fourth-order level of theory, as well as local, non-local and hybrid density functional computations were performed for a representative set of neutral molecules. The study was carried out using different basis sets ranging from the medium-sized 6-31G(d ) to the large 6-31G(2d,2p) basis set, but in some test calculations more extended basis sets were also considered. The analysis of the results was performed discussing separately the effect of the basis set and of the level of theory used to determine the molecular wavefunction on the reliability of the MEP and MEP-derived properties. Received: 4 March 1997 / Accepted: 27 June 1997     

Proton affinities of molecules containing nitrogen and oxygen: comparing ab initio and semiempirical results to experiments

We report a comparison of theoretical and experimental proton affinities at nitrogen and oxygen sites within a series of small molecules. The calculated proton affinities are determined using the semiempirical methods AM 1, MNDO , and PM 3; the ab initio Hartree–Fock method at the following basis levels: 3-21G //3-21G , 3-21+G //3-21G , 6-31G *//6-31G *, and 6-31+G (d, p)//6-31G *; and Møller–Plesset perturbation calculations: MP 2/6-31G *//6-31G *, MP 3/6-31G *//6-31G *, MP 2/6-31G +(d, p)//6-31G *, MP 3/6-31G +(d, p)//6-31G *, and MP 4(SDTQ )/6-31G +G (d, p)//6-31G *. The semiempirical methods have more nonsystematic scatter from the experimental values, compared to even the minimal 3-21G level ab initio calculations. The thermodynamically corrected 6-31G *//6-31G * proton affinities provide acceptable results compared to experiment, and we see no significant improvement over 6-31G *//6-31G * in the proton affinities with any of the higher-level calculations. © 1992 John Wiley & Sons, Inc.     

Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods

Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*.     

Gas-phase structures of acetyl peroxynitrate and trifluoroacetyl peroxynitrate

The molecular structures and conformational properties of acetyl peroxynitrate (PAN, CH3C(O)OONO2) and trifluoroacetyl peroxynitrate (FPAN, CF3C(O)OONO2) were investigated in the gas phase by electron diffraction (GED), microwave spectroscopy (MW), and quantum chemical methods (HF/3-21G, HF/6-31G*, MP2/6-31G*, B3PW91/6-31G*, and B3PW91/6-311+G*). All experimental and theoretical methods show the syn conformer (C=O bond of acetyl group syn to O-O bond) to be strongly predominant relative to the anti conformer. The O-NO2 bonds are extremely long, 1.492(7) A in PAN and 1.526(10) A in FPAN, which correlates with their low bond energy and the easy formation of CX3C(O)OO* and *NO2 radicals in the atmosphere. The O-O bonds (1.418(12) A in PAN and 1.408(8) A in FPAN) are shorter than that in hydrogen peroxide (1.464 A). In both compounds the C-O-O-N dihedral angle is close to 85 degrees.     

Photocyclization of iminyl radicals: theoretical study and photochemical aspects

The irradiation of acyloximes was studied by theoretical methods. CASPT2/6-31G*//CASSCF/6-31G* calculations, using an active space of 14 electrons in 11 orbitals, indicate that S2 should be the spectroscopic state, and its relaxation leads directly to N-O bond breakage due to coupling between the imine pi* and the sigma* N-O orbitals. Subsequent calculations at the B3PW91/6-31+G* level suggest that the resulting iminyl radicals are able to cyclize to the five- or six-membered ring, depending on the presence of a phenyl group as a spacer, a process that has been verified experimentally. The photochemical aspects of the more common five-membered ring formation, such as excited-state quenching, quantum yield, excited-state sensitizers, laser flash photolysis experiments, Stern-Volmer plot, and luminescence measurements, were investigated. These studies indicate that singlet and triplet excited states undergo the same reaction. Emission lifetimes of ca. tau = 10.6 micros for compound 11 are suggestive of triplet parentage, while no fluorescence was detected, in agreement with the computed MEP energy profile.     

硝酸甲与硝酸乙酯的结构、振动频率和热力学性质的密度函数 理论(DFT)研究

用密度函数理论(DFT)的BLYP和B3LYP方法,取6-31G,6-31G^*,6-31G^*^*,6-311G,6-311G^*和6-311G^*^*六种基组,对硝酸甲酯和硝酸乙酯的几何构型和红外振动频率进行了计算研究.结果表明,B3LYP方法在采用极化基组(6-31G^*,6-31G^*^*,6-311G^*和6-311G^*^*)时计算得到的结果均较好,适用于硝酸酯类化合物的研究.而BLYP方法无论采用何种基组均不适用;运用校正后的B3LYP/6-31G^*频率(校正因子0.975)计算得到的热力学性质(C^o~p,H^o和S^o)与实验结果较吻合。     

Selection of a quantum-chemical method and basis set for optimization of the complex ion Cu(H2O)+

Calculations of the open-shell van der Waals complex Cu(H₂O)⁺ were carried out at 15 theoretical levels basing on the DFT theory in its variants B3LYP and BLYP. Five types of basis function were used (3-21G*, 3-21G**, 6-31G(d,p), 6-311G(d,p) and CEP-4G) each combined with one (+) or two (++) diffuse functions. The aim of the research was to find out the most accurate combination of method and basis set which predicts structural, energetic and vibration parameters closest to the experimentally found ones. Several experimental parameters were used as reference values.     

Inclusion complexes of ortho-anisidine and β-cyclodextrin: A quantum mechanical calculation

The structural aspects for the complexation of ortho-anisidine (O-AN)/β-cyclodextrin were explored by using PM6, density function theory B3LYP/6-31G*, M05-2X/6-31G*, B3PW91/6-31G*, MPW1PW91/6-31G*, HF/6-31G* methods and several combinations of ONIOM2 hybrid calculations. Calculations were performed upon the inclusion complexation of β-cyclodextrin (β-CD) with neutral (O-AN1) and cationic (O-AN2) species of ortho-anisidine. The obtained results with PM6 method clearly indicate that the formed complexes are energetically favored, the complex of O-AN2/β-CD in B orientation is significantly more favorable than the others energetically. The structures show the presence of several intermolecular hydrogen bond interactions that were studied on the basis of natural bonding orbital (NBO) analysis, employed to quantify the donor–acceptor interactions between ortho-anisidine and β-CD.     

Electronic, optical, and charge transfer properties of donor–bridge–acceptor hydrazone sensitizers

The ground state geometries have been computed by using density functional theory (DFT) at B3LYP/6-31G*, B3LYP/6-31G**, and PCM-B3LYP/6-31G* level of theories. The highest occupied molecular orbitals (HOMOs) are delocalized on whole of the molecule and the lowest unoccupied molecular orbitals (LUMOs) are localized on the tricarbonitrile. The lowest HOMO and LUMO energies have been observed for Dye1 while highest for Dye4. The LUMO energies of Dye1–Dye4 are above the conduction band of TiO₂ and HOMOs are below the redox couple. The absorption spectra have been computed in solvent (methanol) and without solvent by using time-dependant DFT at TD-B3LYP/6-31G*, TD-B3LYP/6-31G**, and PCM-TD-B3LYP/6-31G* level of theories. The calculated maximum absorption wavelengths of the spectra in methanol are in good agreement with experimental evidences. The maximum absorption wavelengths of new designed sensitizers are red shifted compared to parent molecule. The electronic coupling constant and electron injection have been computed by first principle investigations. The improved electronic coupling constant and electron injection revealed that new modeled systems would be efficient sensitizers.     

电场作用下分子导线的理论研究

摘要利用从头计算法分别在HF/6-31G, HF/6-31G*, HF/6-31G**, HF/6-31+G, HF/6-31++G, HF/6-31+G*, HF/6-31+G**, HF/D95+*, B3LYP/6-31G*和B3LYP/6-31+G*水平上计算了5个单体的聚乙炔分子导线, 从几何构型、 SCF能量和分子轨道能级三个方面讨论了外电场对分子导线的影响, 给出了聚乙炔分子导线性质与外电场变化的定量关系.     

Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid

2-(4-Fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid (4-FT) was synthesized through the reaction of 4-fluorobenzaldehyde and l-tyrosine in refluxing EtOH. The structure of 4-FT was verified by measuring 1H NMR, FTIR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains. The vibrational wavenumbers of 4-FT were calculated at same levels. The scaled spectra using B3LYP methods, which are in a good agreement with the measured spectra, are superior to those calculated using HF methods.     

Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-mercaptopropanoic acid

2-(4-Fluorobenzylideneamino)-3-mercaptopropanoic acid (4-FC) was synthesized through the reaction of 4-fluorobenzaldehyde and l-cysteine in refluxing EtOH. Its structure was verified by (1)H NMR, FT-IR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains, respectively. The vibrational wavenumbers of 4-FC were calculated at same level. The scaled theoretical spectra using B3LYP methods, which are in a good agreement with the experimental ones, are superior to those using HF methods.     

Absolute configuration of C76 from optical rotatory dispersion.

The absolute configuration of C76 has been determined as (+)589-(fC)-C76 , for the first time, by comparing the experimental and predicted optical rotatory dispersion (ORD) patterns. The experimental ORD pattern was derived from the experimental electronic circular dichroism (ECD) spectrum using the Kramers-Kronig (KK) transform. The theoretical ORD spectra were calculated in the resonant region using linear response theory, and also using the KK transform of the theoretical ECD spectrum, at different theoretical levels, namely BHLYP/6-31G*, B3LYP/6-31G*, BLYP/6-31G*, and HF/6-31G*. Good agreement noted between experimental and predicted spectra allows for an unambiguous determination of the absolute configuration.