Ab initio SCF calculations on low-energy conformers of cyclohexaglycine

Results from ab initio self-consistent field (SCF) calculations with a 3-21G and a double-zeta-plus polarization (DZP) basis set on four low-energy conformations of cyclohexaglycine are reported. In agreement with results from semiempirical and molecular mechanics force field calculations, the lowest-energy conformation found at the DZP level is a conformation forming six C₇ turns. However, the energy difference to the β-turn conformers is significantly smaller at the ab initio DZP level than calculated by the other methods. In contrast to the results obtained with some of the other methods, the present ab initio calculations show that both the double-type-I β turn and the double-type-II β-turn conformer of cyclohexaglycine are stable low-energy structures. © 1995 by John Wiley & Sons, Inc.     

Theoretical investigations on 1,2-ethanediol: The problem of intramolecular hydrogen bonds

The conformational space of 1,2-ethanediol is studied on the basis of ab initio and semiempirical calculations. All possible conformers are treated. The relative energies of the conformers are systematically studied using various basis sets up to 6–311 + G(3df, 3pd) in order to perform calculations as accurate as possible within a reasonable amount of computer time. Electron correlation is included using Møller-Plesset perturbation theory. We propose two methods to evaluate the basis set superposition error associated with the intramolecular hydrogen bond appearing in some of the conformers. The results of semiempirical calculations are compared with these ab initio calculations. © 1996 by John Wiley & Sons, Inc.     

OPLS all-atom force field for carbohydrates

The OPLS all-atom (AA) force field for organic and biomolecular systems has been expanded to include carbohydrates. Starting with reported nonbonded parameters of alcohols, ethers, and diols, torsional parameters were fit to reproduce results from ab initio calculations on the hexopyranoses, α,β-d -glucopyranose, α,β-d -mannopyranose, α,β-d -galactopyranose, methyl α,β-d -glucopyranoside, and methyl α,β-d -mannopyranoside. In all, geometry optimizations were carried out for 144 conformers at the restricted Hartree–Fock (RHF)/6–31G* level. For the conformers with a relative energy within 3 kcal/mol of the global minima, the effects of electron correlation and basis-set extension were considered by performing single-point calculations with density functional theory at the B3LYP/6–311+G** level. The torsional parameters for the OPLS-AA force field were parameterized to reproduce the energies and structures of these 44 conformers. The resultant force field reproduces the ab initio calculated energies with an average unsigned error of 0.41 kcal/mol. The α/β ratios as well as the relative energies between the isomeric hexopyranoses are in good accord with the ab initio results. The predictive abilities of the force field were also tested against RHF/6–31G* results for d -allopyranose with excellent success; a surprising discovery is that the lowest energy conformer of d -allopyranose is a β anomer. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1955–1970, 1997     

The Cyclohexasilanes Si6H11X and Si6Me11X with X=F,Cl, Br and I: A Quantum Chemical and Raman Spectroscopic Investigation of a Multiple Conformer Problem

The conformers of the monohalocyclohexasilanes, Si₆H₁₁X (X=F, Cl, Br or I) and the haloundecamethylcyclohexasilanes, Si₆Me₁₁X (X=F, Cl, Br or I) are investigated by DFT calculations employing the B3LYP density functional and 6‐31+G* basis sets for elements up to the third row, and SDD basis sets for heavier elements. Five minima are found for Si₆H₁₁X—the axial and equatorial chair conformers, with the substituent X either in an axial or equatorial position—and another three twisted structures. The equatorial chair conformer is the global minimum for the X=Cl, Br and I, the axial chair for X=F. The barrier for the ring inversion is ～13 kJ mol^?1 for all four compounds. Five minima closely related to those of Si₆H₁₁X are found for Si₆Me₁₁X. Again, the equatorial chair is the global minimum for X=Cl, Br and I, and the axial chair for X=F. Additionally, two symmetrical boat conformers are found as local minima on the potential energy surfaces for X=F, Cl and Br, but not for X=I. The barrier for the ring inversion is ～14–16 kJ mol^?1 for all compounds. The conformational equilibria for Si₆Me₁₁X in toluene solution are investigated using temperature dependent Raman spectroscopy. The wavenumber range of the stretching vibrations of the heavy atoms X and Si from 270–370 cm^?1 is analyzed. Using the van′t Hoff relationship, the enthalpy differences between axial and equatorial chair conformers (H_ax?H_eq.) are 1.1 kJ mol^?1 for X=F, and 1.8 to 2.8 kJ mol^?1 for X=Cl, Br and I. Due to rapid interconversion, only a single Raman band originating from the “averaged” twist and boat conformers could be observed. Generally, reasonable agreement between the calculated relative energies and the experimentally determined values is found.     

A theoretical study of the relative stability of the isomeric forms of N2O3

The electronic structure, geometrical parameters and relative stability of the isomeric forms of N₂O₃ are analysed by means of ab initio calculations. Total energies of the different isomers are given. The energy difference between the most stable conformers of the symmetric N₂O₃ is 4.31 Kcal mol^–1 as provided by 6–31G basis set. The height of the rotational barrier determined by the ab initio technique is 7.12 kcal mol^–1.Member of the Carrera del Investigador CICPBA, R. Argentina.Member of the Carrera del Investigador CONICET, R. Argentina.Predoctoral fellow of CONICET, R. Argentina.     

Stabilization of nonclassical types of valence bond orientation at the carbon atom in organoboron compounds

The complete topological structure of the potential energy surface (PES) of methane in the inversion region was studied by theab initio CCD(full)/6-311++G^** method. The necessity of taking into account nuclear motions was shown. Penta- and hexacoordination of carbon atoms in boron-containing organic compounds was investigated by theab initio MP2(full)/6-31G^** and MP2(full)/6-311++G^** methods. The CB₄H₄Li₂, CB₆N₂H₂, and CB₆O₂ systems containing hexacoordinated carbon atoms correspond to rather deep minima on the relevant PES and can be the subject of synthetic studies. According to theab initio calculations, pyramidal boron-containing systems with hypercoordinated carbon atoms, which fulfill the “8e rule,” also correspond to rather deep PES minima and can be detected experimentally. Dedicated to Academician V. I. Minkin on the occasion of his 65th birthday. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 786–796, May, 2000     

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

Raman spectra,conformational stability,structural parameters,vibrational assignment,and ab initio calculations for epifluorohydrin

The Raman spectra (3200–100 cm⁻¹) of epifluorohydrin, OCH₂CH(CH₂F), in variable solvents, as well as that of the gas have been recorded and several of the bands due to the two less stable conformers have been identified. The variable solvent studies were inconclusive on the relative conformer stabilities. The conformational energy differences and optimized geometries for all three conformers have been obtained from ab initio calculations with the 3–21G, 4–31G and 6–31G* basis sets. A normal coordinate analysis has also been performed for each conformer with a force field determined from the 3–21G basis set. Assignment of the vibrational fundamentals observed in the Raman spectra of the fluid phases is proposed based on the normal coordinate calculations. In the liquid phase, one of the conformers with a large dipole moment predominates and it appears to be the gauche-I form which is the only one found in the solid. Utilizing the three rotational constants previously reported for each conformer, along with restricted relative distances for several of the structural parameters among the conformers from ab initio calculations, r₀ structural parameters for the heavy atoms have been determined.     

Monte Carlo simulations of solid nitrogen in the isothermal–isobaric ensemble with an ab initioSCF–CI potential

Monte Carlo simulations in the isothermal–isobaric ensemble for the α phase of solid N₂ have been carried out with two different pair potentials obtained from ab initio quantum chemical calculations. Comparison is made with data obtained from empirical potentials as well as with experimental data, and in general, the agreement with experiment is found to be good. It is also found that the differences between experiment and theory can largely be attributed to correlation effects, not considered in the quantum mechanical calculations of the pair potential.     

Ab initio and molecular mechanics (MM2 and MM3) calculations of nonconjugated positively charged nitrogen-containing compounds

High-level ab initio calculations have been performed on N-methyl-N-methyleneammonium and related compounds to obtain accurate rotational barriers, structures, and vibrational frequencies. The 6-31G** basis set has been utilized at the Hartree-Fock level of theory for these calculations because little experimental data are available. The MM2(91) and MM3(94) force fields have been parameterized to include these nonconjugated charged nitrogen-containing compounds. Molecular mechanics geometries and vibrational frequencies compare well with the ab initio results. © 1995 John Wiley & Sons, Inc.     

Joint X-ray spectroscopic and quantum-chemical study of the electronic structure of pentafluorophenylalkyl ethers

The high resolution X-ray emission O-Kα spectra of pentafluorophenylalkyl ethers C₆F₅OR (R=Et, Prⁱ, and Bu^t) exhibit differences related to a change in the electronic structure of the compounds as R is varied. The search for stable conformers was performed by the semiempirical PM3 method. The most probable structures of C₆F₅OR were determined by the comparison of the experimental and theoretical X-ray spectra plotted for each conformer usingab initio calculations in the 6–31 G basis set. Substituent R in pentafluorophenylalkyl ethers is situated outside of the ring plane. The fluorination of the benzene ring changes the energy level of the lone electron pair of oxygen relative to the levels of orbitals of the ring and substituent R and leads to an increase in the efficiency of interactions in the σ-system. Deceased. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2443–2450, December, 1998.     

Molecular mechanics studies (MM4) of sulfides and mercaptans

The MM4 force field has been extended to the title class of compounds. The vibrational spectra, structures, conformational equilibria, and heats of formation have been studied for 47 conformers of 29 compounds. In general, the properties may be calculated with accuracy that is competitive with that for hydrocarbons. The structures are better fit than previously because of the inclusion of a torsion–bend interaction term, which has its origin in the lone pair (Bohlmann) effect. Available experimental data do not suffice to yield detailed torsional potentials, or geometries as a function of torsion angle, and these quantities were determined by ab initio calculations at the MP2/6-31G* level. The rms error in the calculated frequencies of seven representative structures (with a total of 64 experimental and 96 ab initio frequencies) is 25 cm⁻¹. The heats of formation for 23 compounds have a weighted rms error of 0.36 kcal/mol. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1827–1847, 1997     

Conformational analysis,part 43. A theoretical and LIS/NMR investigation of the conformations of substituted benzamides

A refined Lanthanide‐Induced‐Shift Analysis (LISA) is used with molecular mechanics and ab initio calculations to investigate the conformations of benzamide ( 1 ), N‐methylbenzamide ( 2 ), N,N‐dimethylbenzamide ( 3 ) and the conformational equilibria of 2‐fluoro ( 4 ), 2‐chloro ( 5 ) and N‐methyl‐2‐methoxy benzamide ( 6 ). The amino group in 1 is planar in the crystal but is calculated to be pyramidal with the CO/phenyl torsional angle (ω) of 20–25°. The LISA analysis gave acceptable agreement factors (Rcryst ≤ 1%) for the ab initio geometries when ω was decreased to 0°, the other geometries were not as good. In 2 , the N‐methyl is coplanar with the carbonyl group in all the geometries. Good agreement was obtained for the RHF geometries, with ω 25°, the other geometries were only acceptable with increased values of ω. In 3 , good agreement for the RHF and PCModel geometries was found when ω was changed from the calculated values of 40° (RHF) and 90° (PCModel) to ca. 60°, the X‐ray and B3LYP geometries were not as good. The two substituted compounds 4 , 5 and 6 are interconverting between the cis (O,X) and trans (O,X) conformers. The more stable trans conformer is planar in 4 and 6 but the cis form non‐planar. Both the cis and trans conformers of 5 are non‐planar. There is an additional degree of freedom in 6 due to the 2‐methoxy group, which can be either planar or orthogonal to the phenyl ring in both conformers. The conformer ratios were obtained from the LISA analysis to give Ecis‐Etrans in 4 > 2.3 kcal/mol (CDCl₃) and 1.7 kcal/mol (CD₃CN), in 5 0.0 kcal/mol (CD₃CN) and in 6 > 2.5 kcal/mol (CDCl₃) and 2.0 kcal/mol (CD₃CN). These values were used with the observed versus calculated ¹H shifts to determine the conformer ratios and energies in DMSO solvent to give Ecis‐Etrans 1.1, ?0.1 and 1.8 kcal/mol for ( 4 ), ( 5 ) and ( 6 ). Comparison of the observed versus calculated conformer energies show that both the MM and ab initio calculations overestimate the NH..F hydrogen bond in ( 4 ) by ca. 2 kcal/mol. Copyright © 2015 John Wiley & Sons, Ltd.     

Optimizing efficiency of perturbative Monte Carlo method

We introduce error weighting functions into the perturbative Monte Carlo method for use with a hybrid ab initio quantum mechanics/molecular mechanics (QM/MM) potential. The perturbative Monte Carlo approach introduced earlier provides a means to reduce the number of full SCF calculations in simulations using a QM/MM potential by evoking perturbation theory to calculate energy changes due to displacements of an MM molecule. The use of weighting functions, introduced here, allows an optimal number of MM molecule displacements to occur between the performance of the full self-consistent field calculations. This will allow the ab initio QM/MM approach to be applied to systems that require more accurate treatment of the QM and/or MM regions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1632–1638, 1998     

Conformation of 17‐chloro‐16‐formylandrosta‐5,16‐dien‐3β‐yl acetate and 17‐chloroandrosta‐5,16‐dien‐3β‐yl acetate

In the title compounds, C₂₂H₂₉ClO₃, (I), and C₂₁H₂₉ClO₂, (II), respectively, the B rings adopt a half‐chair conformation and the D rings adopt an envelope conformation. A twist of the steroid skeleton of both compounds is observed. There is a positional disorder of the acetoxy group of (II), with the terminal atoms disordered over two positions with near equal occupancy. Quantum‐mechanical ab initio calculations using a molecular orbital Hartree–Fock method were performed for the isolated molecules, thus allowing the distinction within the structural features of these two androstane derivatives of which characteristics are intrinsic to the molecules and which are due to packing effects. The skeletal twisting was found to be innate to the molecules, while the acetoxy disorder is due to packing effects.     

Ab initio studies on polymers. VI. Torsional potential in regular polyethylene chains

Ab initio crystal orbital calculations have been performed on regular polyethylene chains applying basis sets of minimal and double-zeta quality. Relative stabilities of periodic all-trans, all-gauche, and alternating trans–gauche conformers have been evaluated, including extensive geometry optimization. Potential curves for a simultaneous rotation around C? C single bonds from the all-trans to the all-gauche conformation have been computed applying the rigid-rotor approximation, the flexible-rotor approximation, and an additional reoptimization of C? C distances. A rigid-rotor potential curve from the all-trans to the alternating trans-gauche conformation has been computed as well. Results obtained are compared with ab initio calculations on butane and pentane and with semiempirical and empirical force-field studies on polyethylene.     

Dependence of the Interaction Potentials of Ar-HF and N2-HF on HF Bond Length

We explore in detail the nature of the intermolecular interactions in two HF containing complexes, ArHF and N₂ HF, at vibrationally excited HF stretching states using both high overtone spectroscopic and ab initio computational methods. By using an infrared intracavity laser-induced fluorescence technique, second overtone spectra of the two HF complexes have been obtained for the HF stretches and their combination modes with low-frequency van der Waals vibrations. The two complexes show the same trend that both van der Waals bond strength and rotational constant increase smoothly with v of the HF stretch. The investigation of the intermolecular potential above minimum provides a rigorous test of ab initio calculations. In particular for the ab initio calculations using an efficient basis set incorporating bond functions, the technique reproduces reasonably well the anisotropy of the interaction potential of Ar and HF. It is found that the intermolecular potential depends strongly upon the HF bond length only at the linear Ar-H-F geometry.     

Peptide models XXIII. Conformational model for polar side‐chain containing amino acid residues: A comprehensive analysis of RHF,DFT, and MP2 properties of HCO‐L‐SER‐NH2

Geometric and energetic properties of a diamide of serine, HCO‐NH‐L ‐CH(CH₂OH)CO‐NH₂, are investigated by standard methods of computational quantum chemistry. Similarly to other amino acid residues, conformational properties of HCO‐L ‐Ser‐NH₂ can be derived from the analysis of its E=E(ϕ,ψ;χ₁,χ₂) hypersurface. Reoptimization of 44 RHF/3‐21G conformers at the RHF/6‐311++G** level resulted in 36 minima. For all conformers, geometrical properties, including variation of H‐bond parameters and structural shifts in the torsional space, are thoroughly investigated. Results from further single‐point energy calculations at the RHF, DFT, and MP2 levels, performed on the entire conformational data set, form a database of 224 energy values, perhaps the largest set calculated so far for any single amino acid diamide. A comprehensive analysis of this database reveals significant correlation among energies obtained at six levels of ab initio theory. Regression parameters provide an opportunity for extrapolation in order to predict the energy of a conformer at a high level by doing explicit ab initio computations only for a few selected conformers. The computed conformational and relative energy data are compared with structural and occurrence results derived from a nonhomologous protein database incorporating 1135 proteins. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 626–655, 2000     

Crystal structure and reactivity of 2-chloro-3,5-dinitrothiophene and of 2-phenylsulphonyl-3,5-dinitrothiophene with nucleophiles

The geometry obtained by a crystal structure determination of the title compounds, as compared with that of the analogous benzene derivatives, along with results of ab initio calculations, is used to interpret the different S_NAr reactivities in some thiophene and benzene compounds. The smaller rotation of the nitro groups with respect to the aromatic rings observed in thiophene derivatives should be considered a relevant factor in the higher reactivity in the thiophene series.