Ab initio calculations of atomic interaction in the ClCH2OCH3 molecule

Ab initio calculations of both ClCH₂OCH₃ and ClCH₂CH₃ molecules and various ClCH₂OCH₃ structures with fixed angles of rotation of the methoxy group about the C−O bond were performed by the restricted Hartree-Fock method in the valence-split 6–31 G^* basis set with full optimization of the geometry. The populations of the valent p-orbitals of the chlorine atoms in these molecules have been analyzed. The³⁵Cl NQR frequencies and the asymmetry parameters of the electric field gradient (EFG) at the³⁵Cl nuclei have been calculated. Good agreement with experimental NQR frequencies was obtained for the calculations where only the populations of the less diffuse 3p-components of these orbitals were used. The³⁵Cl NQR frequency in ClCH₂OCH₃ is lower than that in ClCH₂CH₃ due to the higher population of the less diffuse component of the p_σ-orbital of the Cl atom in the former molecule. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 431–434, March, 1997.     

Molecular Structure of ortho-Fluoronitrobenzene Studied by Gas Electron Diffraction and Ab Initio MO Calculations

The molecular structure of ortho-fluoronitrobenzene (o-FNB) has been investigated by gas-phase electron diffraction and ab initio MO calculations. The geometrical parameters and force fields of o-FNB were calculated by ab initio and DFT methods. The obtained force fields were used to calculate vibrational amplitudes required as input parameters in an electron diffraction analysis. Within the experimental error limits, the geometrical parameters obtained from the gas-phase electron diffraction analysis are mostly in agreement with the results obtained from the ab initio calculations. The main results are: the molecular geometry of o-FNB is nonplanar with a dihedral angle about C–N of 38(3)°. The r _g (C–F) bond is shortened to 1.307(13) Å in comparison with r _g (C–F) = 1.356(4) Å in C₆H₅F.     

Ab initio calculations of of pyridine and its 2- and 3-chloroderivatives

Ab initio calculations of the C₅H₅N, 2-. and 3-ClC₅H₄N molecules by the RHF method in the valence split 6-31G^* basis set with full optimization of the geometry have been carried out. The alternation of the charges on the atoms of the pyridine ring and of the populations of their p _x -orbitals is in agreement with the noninductive through -the-field interaction of the geminal atoms. The³⁵Cl NQR frequencies and the electric field gradient asymmetry parameters at the³⁵Cl nuclei in 2- and 3-CIC₅H₄N were estimated using the populations of the valentp-orbitals of the Cl atoms and their components. The³⁵Cl NQR frequency for the first compound is lower than that for the second one, mainly due to the higher p-electron population of its Cl atom.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2641–2644, November, 1996.     

Ab initio calculations ofp-Cl2C6H4 molecule and its35Cl NQR parameters

Ab initio calculations ofp-dichlorobenzene molecule were carried out using the Hartree-Fock method in the 6–31 G* valence-split basis set. The molecule was also calculated by the MNDO method in the valence sp-basis set for comparison. The populations of the valent p-orbitals of the C and CI atoms were analyzed. The optimized geometry of the molecule as well as its³⁵Cl NQR frequency and the asymmetry parameter of the electric field gradient at the³⁵CI nuclei calculated using the populations of the less diffuse components of the valent p-orbitals of the Cl atoms are in agreement with the corresponding experimental values for the -modification of 1,4-Cl₂C₆H₄.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 2177–2179, September, 1996.     

Conformational Study of Naringenin in the Isolated and Solvated States by Semiempirical and Ab Initio Methods

Naringenin is a natural widespread flavanone occurring in different foodstuffs that presents several important biological activities. Although its properties are well documented, its mechanisms of action are still controversial. The present article reports a conformational analysis of naringenin, using the semiempirical AM1 and ab initio methods, at the Hartree–Fock level of theory. The 3-21G, 3-21G*, 6-31G, and 6-31G** basis sets were used. The electron correlation effects were included through the Møller–Plesset second-order perturbation theory. The solvation of naringenin has been investigated through the standard SCRF, the supermolecule (SM), and the combined SM/SCRF models. The results have shown that there are two degenerate forms of naringenin, differing mainly by the orientation of a hydroxyl group (C4—OH). The energy barrier for the interconversion between them is ca. 6 kcal.mol^–1, suggesting some conjugation between the -system of the aromatic B ring and the hydroxyl group (C4—OH).     

ArH＋势能曲线的从头计算

ArnH^ 是非常重要而又较简单的簇体系,对于它们的深入研究,有助于人们认识质子在溶液中的溶剂化行为,该簇中最为简单而又重要的存在形式是ArH^ 和ArnH^ 。ArH^ 可以在气相中稳定存在,在所有的ArnH^ 族中被研究得最早,实验数据也最为齐全,人们对ArH^ 体系进行了许多理论计算,但只局限于平衡键长、简正振动频率、解离能等分子参数,计算结果与已知的振动－转动光谱数据基本符合。     

Crystal Structure and Quantum Chemical Ab Initio Calculations of Ibotenic Acid,an Excitatory Amino Acid Receptor Agonist

Ibotenic acid, a constituent of Amanita muscaria, is a potent NMDA receptor agonist. The structure of the ibotenic acid zwitterion monohydrate in the crystalline state has been determined by X-ray crystallography. The crystal structure has two ibotenic acid monohydrate formula units in the asymmetric unit and features an extensive hydrogen bond network. The ibotenic acid zwitter-ions in the crystalline state are compared to the in vacuo structure calculated by quantum chemical ab initio calculations at the HF/6-31+G* level and the effects of the hydrogen bond network on the structures in the solid state are discussed. The calculated potential energy curve with respect to side-chain orientation displays a single energy minimum. The conformations corresponding to the solid-state conformations are calculated to be ca. 2 kcal/mol higher in energy than the minimum-energy conformation in vacuo.     

Cyclohexanone Dimethyl Acetals: A 13C NMR, Thermodynamic, and Ab Initio Study

The spatial structures of a number of mono- and disubstituted 1,1-dimethoxycyclohexanes (cyclohexanone dimethyl acetals) were studied by ¹³C NMR spectroscopy. In the monosubstituted acetals, substituents (Me, Et, i-Pr, and MeO) on C-2 are axially oriented, contrary to their normal, equatorial orientation on C-3 and C-4. Besides the spectroscopic study, the relative thermodynamic stabilities of the cis-trans isomers of a few 2,X-dialkyl (X = 3, 4, 5, or 6) derivatives of the parent cyclohexanone dimethyl acetal were determined by acid-catalyzed chemical equilibration in MeOH solution. In the most stable isomeric form, the 2-substituent is axial and the other equatorial. In the less stable isomer, both substituents are equatorial, excluding the cis-2,6-dimethyl derivative, where the ¹³C NMR shift data point to a predominance of the diaxial form. In general, the enthalpy difference between the isomeric forms is ca. 9 kJ mol^–1, while the entropy term favors the less stable isomer by 4 to 16 J K^–1 mol^–1. In the 2,6-dimethyl derivatives, however, the trans form is favored by only 0.8 kJ mol^–1 in G _m at 298.15 K. The main findings of the experimental work are in good agreement with ab initio calculations.     

Infrared and Raman Spectra,Conformational Stability,Ab Initio Calculations,and Vibrational Assignments for Cyclopropyldifluorosilane

The infrared (3200–30 cm^–1) spectra of gaseous and solid Cyclopropyldifluorosilane, c-C₃H₅SiF₂H, and the Raman spectra (3200–20 cm^–1) of the liquid with quantitative depolarization values and the solid have been recorded. Both the syn (cis) and skew (gauche) conformers have been identified in the fluid phases, but only the syn conformer remains in the solid. Variable temperature (–55 to –100°C) studies of the infrared spectra of the sample dissolved in liquid xenon have been carried out. From these data, the enthalpy difference has been determined to be 73 ± 10 cm^–1 (209 ± 29 cal mol^–1), with the syn conformer being the more stable rotamer, which is at variance with the predictions from ab initio calculations. A complete vibrational assignment is proposed for both conformers based on infared band contours, relative intensities, depolarization values, and group frequencies. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G* calculations. Utilizing the frequencies of the silicon–hydrogen sketch, the rm Si—H bond distances of 1.474 and 1.472 Å have been obtained for the syn and skew conformers, respectively. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing the 6-31G* and 6-311 +G** basis sets at levels of restricted Hartree-Fock (RHF) and/or Moller–Plesset (MP) to second order. The potential energy terms for the conformer interconversion have been obtained from the MP2/6-31G* calculation. The results are discussed and compared to those obtained for some similar molecules.     

An Ab Initio Study of the Relative Stabilities and Molecular Structures of 3-Substituted 2,5-Dihydrofurans and 4-Substituted 2,3-Dihydrofurans

The geometry optimized structures and total energies of 3-substituted (R) 2,5-dihydrofurans (a) and their isomers, 4-substituted 2,3-dihydrofurans (b), have been determined by ab initio calculations at the MP2/6-31G^*//HF/6-31G^* level. The nature of the moiety R has a marked effect on the relative total energies of the isomeric forms: at the calculation level cited, the reaction enthalpies for the a b isomerization range from +4.7 kJ mol^–1 for R = MeO to –30.5 kJ mol^–1 for both R = COOMe and R = NO₂. The reaction enthalpies appear to be controlled by the electronic effect of R on the strength of p- conjugation in b. The a isomer has a planar ring, independent of R (excluding NH₂), whereas the planarity of b depends on the electronic nature of R: the 2,3-dihydrofuran ring is planar for both R = COOMe and R = NO₂, but nonplanar for less conjugation-enhancing substituents.     

Ab initio calculations ofo- andm-Cl2C6H4 molecules and their35CI NQR parameters

The MNDO andab initio (Hartree—Fock method, split 6-31G^* basis set, full optimization of geometry) calculations for theo- andm-dichlorobenzene molecules have been performed. The populations of the valent p-orbitals of the carbon and chlorine atoms have been analyzed. Estimations of the³⁵Cl NQR frequencies and the asymmetry parameters of the electric field gradient at the³⁵CI nuclei have been made. It was confirmed that these values are not determined by the contribution of the whole valent p-shell, but only by its less diffuse component.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 2180–2183, September, 1996.     

Molecular Structure of 1-Substituted Bicyclo[2.2.0]hexanes: A Combined X-Ray Structural and Ab Initio Study

The synthesis and X-ray crystal structure of the p-bromoanilide derivative of bicyclo[2.2.0]hexane-l-carboxylic acid (1), N-(4-bromophenyl)-bicyclo[2.2.0]hexane-l-carboxamide (2), is reported. N-(4-Bromophenyl)-bicyclo[2.2.0]hexane-l-carboxamide is synthesized in good yield via the DCC coupling of bicyclo[2.2.0]hexane-l-carboxylic acid (1) with p-bromoaniline. Low-temperature X-ray analysis of 2 reveals that the bonds of the bicyclo[2.2.0]hexane skeleton vicinal to the amide group show a slight lengthening due to conjugative interaction with the -accepting amide group. Ab initio calculations at the 6-31G* level of theory on bicyclo[2.2.0]hexane-l-carboxamide, a model for 2, and for other 1-substituted bicyclo[2.2.0]hexanes are also reported.     

Molecular Conformation of 2,2'-Dinitrodiphenylamine According to Dielectric Studies and Ab Initio Quantum Chemical Calculations

According to the results of ab initio calculations employing the HF/6-31G* approach, the isolated 2,2'-dinitrodiphenylamine molecule exists as an sc, sc conformer stabilized by a symmetric intramolecular bifurcated (three-center) hydrogen bond. In protophilic solvents (1,4-dioxane), the conformational equilibrium is also shifted in the direction of this rotational isomer.     

Molecular Structures and Thermodynamic Stabilities of Cycloalkadienes and Their Methoxy Derivatives: An Ab Initio and DFT Study

The geometry-optimized molecular structures and total energies of 4- to 6-membered cycloalkadienes, and of a number of their monoand dimethoxy derivatives, have been calculated by ab initio (HF/6-31G^*, MP2/6-31G^*//HF/6-31G^*) and DFT (B3LYP/6-31G^*) methods. By comparison with available experimental data, the reliability of these computational methods for an estimation of the relative stabilities (enthalpies) of the isomeric forms of the title compounds was tested. The experimental enthalpies of isomerization proved to agree best with the respective theoretical data based on the mean of the HF/6-31G^* and B3LYP/6-31G^* energies. The theoretical calculations were then extended to several isomeric methoxy-substituted cycloalkadienes, for which no previous thermodynamic data exist. Some structural features of the title dienes were also discussed.     

Spectra and Structure of Silicon-Containing Compounds. XXV. Raman and Infrared Spectra,r 0 Structural Parameters,Vibrational Assignment,and Ab Initio Calculations of Ethyl Chlorosilane-Si-d2

The infrared (3200 to 400 cm^–1) spectra of gaseous and solid and Raman (3200 to 20 cm^–1) spectra of liquid and solid ethyl chlorosilane-Si-d₂, CH₃CH₂SiD₂Cl, have been recorded. Both the gauche and trans conformers have been identified in the fluid phases, but only the gauche conformer remains in the solid phase. Variable temperature (–105 to –150°C) studies of the infrared spectra of CH₃CH₂SiH₂Cl dissolved in liquid krypton have been carried out. From these data, the enthalpy difference has been determined to be 78±11 cm^–1 (0.93±0.13 kJ/mol), with the gauche conformer the more stable form. Utilizing the frequencies of the silicon-hydrogen stretches, from the chlorosilane-Si-d isotopomer, Si—H bond distances of 1.481 and 1.480 Å have been obtained for the gauche conformer and 1.481 Å for the trans conformer. Complete vibrational assignments are proposed for both isotopomers which are consistent with the predicted frequencies utilizing the force constants from ab initio MP2/6-31G(d) calculations. Both the infrared intensities and the Raman activities and depolarization values have been obtained from the ab initio calculations. Complete equilibrium geometries have been determined by ab initio calculations employing the 6-31(d), 6-311++G(d,p), and 6-311+G(2d,2p) basis sets with full electron correlation by the Moller–Plesset (MP) perturbation method to second order. Continuing the previously reported rotational constants from five different isotopomers and the ab initio predicted structural parameters, adjusted r ₀ parameters have been calculated, which are compared to the corresponding r _s parameters. The results are discussed and the theoretical values are compared to the experimental values when appropriate.Taken in part from the dissertation of Y. E. Nashed, which will be submitted to the Department of Chemistry in partial fulfillment of the Ph.D. degree     

The Molecular Structure and the Puckering Potential Function of Octamethylcyclotetrasilane,Si4Me8, Determined by Gas Electron Diffraction and Relaxation Constraints from Ab Initio Calculations

Gas electron diffraction data are applied to determine the geometrical parameters of the octamethylcyclotetrasilane molecule using a dynamic model in which the ring puckering is treated as a large amplitude motion. The structural parameters and parameters of the potential function were refined, taking into account the relaxation of the molecular geometry estimated from ab initio calculations at the Hartree–Fock level of theory using a 6-311G** basis set. The potential function has been described as V() = V ₀[(/ _e )² – 1]² with V ₀ = 1.0 ± 0.5 kcal/mol and _e = 28.3 ± 1.9°, where is the puckering angle of the ring. The geometric parameters at the minimum of V() (r _a in Å, in degrees and errors given as three times the standard deviations including a scale error) are as follows: r(Si—C)_av = 1.894(3), r(Si—Si) = 2.363(3), r(C—H) = 1.104(3), CSiC = 109.5(6), SiSiSi = 88.2(2), SiCH = 111.7(6), C = 4.1, where the tilt C was estimated from ab initio constraints. The structural parameters are compared with those obtained for related compounds.     

MNDO refinement of the Townes-Dailey theory. Calculation of NQR frequencies of chloro-containing compounds

Corrections accounting for the effect of the differences in p-electron energies on the electric field gradient are suggested and justified in the framework of Townes-Dailey theory. MNDO calculations of 31 chloro-containing molecules with full geometry optimization were used to evaluate the³⁵Cl NQR frequencies. The correlational relationships between experimental and calculated NQR frequencies are compared.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 38–42, January, 1995.This work was supported by the Russian Foundation for Basic Research (Project No. 93-03-5201).     

Ab initio calculations of methionines and their protonated forms

Ab initio calculations of molecular and electronic structures of neutral molecules and protonated forms of methionine and its derivatives in the gaseous phase were carried out by the Hartree-Fock method using the 6–31G^* basis set with full geometry optimization. Proton affinities of methionine (1), methionine sulfoxide (2), and methionine sulfone (3) were calculated for different modes of coordination of the proton. The results of calculations demonstrated that in protonated forms of 1 and 3, bonding between the proton and the N atom is most favorable, while in protonated form of 2, bonding between the proton and the O atom of the SO group is most favorable. The proton affinities of the amino acids are as follows: 223.2 (1), 241.2 (2), and 221.5 (3) kcal mol⁻¹,i.e., methionine sulfoxide 2 exhibits the highest proton affinity in the series of the amino acids under consideration. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1487–1490, August, 1998.     

Ab Initio Study of the Nonequivalence of Adsorption of D- and L-Peptides on Clay Mineral Surfaces

Ab initio geometry optimizations were performed of the structures of the L and D enantiomers of the model dipeptide, N-formyl alanine amide (L-Ala and D-Ala, respectively) adsorbed on the mineral surface in the interlayer space of the 2:1 clay, nontronite. Density functional procedures were used as implemented in the ab initio program CASTEP, in fully periodic calculations in which the properties of a model unit cell are determined by including the effects of its neighboring cells in an infinite crystal. Geometry optimization included the atomic positions of the mineral and the adsorbates within the unit cell, in addition to unit cell lengths and angles, achieving full optimization of the entire crystal system. In agreement with previous studies of the adsorption of organic compounds on clay mineral surfaces, in the most stable arrangement of L-Ala and D-Ala found here, the two molecules reside flat on the mineral basal plane, forming a parallel monolayer. The resulting L-Ala/mineral cocrystal is more stable, by 6 kcal/mol, than D-Ala. A characteristic structural difference exists for the enantiomers in that, in the optimized structure of L-Ala, the C()–C() bond is directed away from one of the mineral basal planes toward the dioctahedral cavity of the other, while the side group of D-Ala is parallel to the mineral basal plane and pointing to the nearest neighbor in an adjacent unit cell. As expected, the reverse results are obtained for the adsorption of L-Ala and D-Ala on a nontronite surface that is the enantiomer of the one used above. The geometry optimizations illustrate the structural compatibility of clay mineral lattices with peptide structures. That is, balance of adsorption energies and peptide interaction energies, and mineral lattice structure and periodicity allow for adsorption structures, which involve the entire backbone of a single peptide molecule and can, at the same time, immobilize the adsorbates in such a way that stabilizing intermolecular interactions occur across unit cell boundaries. Compatibility of the repeat distances on the clay surface with repeat distances of peptides should be an important property when clay minerals serve as templates for protein synthesis.