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.     

Quantum-chemical study of supramolecular complexes (DPyEt)n(AgNO3)m

The electronic structures and energies of formation of supramolecular complexes of dipyridylethylene with AgNO₃ were calculated by the semiempirical AM1/d method, at the Hartree—Fock level, and by the density functional theory (B3LYP/6-31G*).     

Alkylhydrazides and their protonated forms: Physical methods andab initio calculations

The basicity of hydrazides of the highest aliphatic carboxylic acids RC(O)NHNH₂ (R = C_nH_2n+1,n = 5-12) has been studied by potentiometric titration, and IR and¹H NMR spectroscopy.Ab initio Hartree-Fork calculations using the 6–31G^* basis set with full optimization of geometry were carried out on the simplest acy1hydrazines and their possible protonated forms. Based on these calculations, and the 1R and¹H NMR spectra, the tautomerism of alkylhydrazides and the structures of their protonated forms are discussed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2645–2649, November, 1996.     

Crystal structure and ab initio calculations of a cyano-carbamimidic acid ethyl ester

The structure of one tautomer (amine form) of cyano-carbamimidic acid ethyl ester or (amino-ethoxy-methylidene)aminoformonitrile (CAS: 13947-84-7) was determined by single crystal X-ray diffraction. Ab initio quantum chemical calculations at the B3LYP, MP2 and G3 levels were performed to investigate the stability and the formation of the different tautomers and conformers. The calculations indicate that the amine form is the more stable tautomer, showing a high degree of electron conjugation. The most stable amine conformer located by the calculations corresponds to the crystallized structure. On the contrary, in the less stable imine form, the conjugation is separated by a N2–C2 single bond.     

Thermodynamic and kinetic parameters of elementary steps in gas-phase hydrolysis of SiF4. Quantum-chemical and FTIR spectroscopic studies

The energies and thermodynamic parameters of elementary steps in the proposed mechanism of silicon tetrafluoride hydrolysis in the gas phase were calculated by the ab initio quantum-chemical method (MP4//MP2/6-311G(2d,2p)) and the density functional theory (B3LYP/6-311G(2d,2p)). The proposed mechanism of gas-phase hydrolysis involves the formation of mono- and dihydroxy derivatives, hexafluorodisiloxane (SiF₃OSiF₃), and linear and cyclic siloxane polymers with the chain length from three to six Si—O and difluorosilanone units. According to the calculations, all reactions considered are endothermic and are characterized by positive Gibbs free energies. The initial hydrolysis steps can be presented with a high accuracy by two parallel processes: formation of trifluorohydroxysilane (SiF₃OH) and SiF₃OSiF₃. These are the most thermodynamically favorable among all reaction channels. The transition states of these elementary steps were found and their kinetic parameters were estimated (G = 132 and 147 kJ mol^–1, respectively). The calculation results were verified using FTIR spectroscopy of a mixture of gas-phase SiF₄ and water vapor. The comparison of the theoretical (absolute) intensities of bands in the IR spectra and integral absorption coefficients in the experimental IR spectrum made it possible to calculate the equilibrium concentrations of the reactants and equilibrium constants of elementary steps of formation of SiF₃OH and SiF₃OSiF₃, which agree with the theoretical values. The role of different derivatives in deep hydrolysis and possibilities of experimental detection of particular intermediates in the gas phase were discussed.     

Pathways of the reaction of nucleophilic addition of ammonia to formaldehyde in the gas phase and in the complex with formic acid:ab initio calculations

The gradient pathways of the reaction of nucleophilic addition of ammonia to formaldehyde were calculated for free molecules and in the NH₃...H₂CO...HC(O)OH complex by theab initio RHF/6-31G^**, MP2(fc)/6-31G^**, and MP2(full)/6-311++G^** methods. Both reactions proceed concertedly. In the first case, the reaction successively passes through two transitional states with an energy barrier exceeding 35 kcal mol⁻¹. In the case of the complex with formic acid, the reaction follows a conventional pathway, although its activation barrier calculated by the RHF/6-31G^** and MP2(fc)/6-31G^** methods decreases to 12.6 and 3.8 kcal mol⁻¹, respectively. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 13–20, January, 1998.     

Quantum-chemical analysis of the nucleophilic substitution of the bromine atom by the cyano group at the sp-hybridized carbon atom in the methylbromoacetylene molecule

This paper reports on our quantum-chemical analysis of the nucleophilic substitution of the bromine atom by the cyano group in the reaction of methylbromoacetylene with copper cyanide. According to calculations, the reaction can form a four-membered ring containing a copper atom.     

DFT(B3LYP) calculations of silatranes and their radical cations. First ionization potentials

DFT(B3LYP) and 2 quantum chemical calculations have been performed for 1-substituted silatranes XSi(OCH₂CH₂)N (X = H, CH₃, CH₂Cl, F), their radical cations, and first ionization potentials (IP₁) of these silatranes. The calculated values of IP₁ agree well with the experiment and make it possible to assign the first band to IP₁ in the photoelectron spectra. Analysis of spin density distribution and electronic charges in the radical cations suggests that ionization occurs mainly due to the lone electron pair of nitrogen, participating in intramolecular coordination. The N → Si interaction is broken, and the N...Si distance increases to 335–340 pm.     

Binary molecular complexes of silicon tetrafluoride with water,methanol, and dimethyl ether. Quantum-chemical study

The molecular structures, the energies of complex formation, and the vibrational spectra of the binary molecular complexes of SiF₄ with water, methanol, and dimethyl ether were calculated by the ab initio MP2 method with the basis sets up to 6-311++G(2d,2p). In the complexes, which have been detected previously by IR spectroscopy in low-temperature (12—15 K) inert matrices, the five-coordinate Si atom is in a distorted trigonal-bipyramidal environment, which is formed through the donor-acceptor interaction of the O atom with the Si atom and is additionally stabilized by the H...F hydrogen bonds.     

Quantum-chemical calculation of a spillover model on a graphite support

The simplest quantum-chemical models of hydrogen spillover over a graphite-like surface as a proton or radical have been considered. The condensed planar C₂₄H₁₂ molecule was used as a model surface. Theab initio calculations of the interaction of hydrogen with the model surface were carried out by the restricted Hartree-Fock (HF) method in the STO-3G and 6-31 G^* basis sets. The radical hydrogen can not bind to such a surface, whereas the proton binds to it with an energy release of 186 kcal mol⁻¹. The activation energy of the transfer of the proton between two neighboring carbon atoms (10 kcal mol⁻¹) has been determined. The simplest model of the hydrogen migration as a proton over the model surface can be used for describing the spillover of hydrogen over the graphite surface. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 428–430, March, 1997.     

Conformational stability of peroxynitric acid molecule and the barriers to internal rotation about the O−O and N−O bonds

The structure of conformers and potential curves of the internal rotation (PCR) about the O?O and N?O bonds in peroxynitric acid (PNA) were calculated by the unrestricted Hartree-Fock-Roothaan method. The standard valence-split 6–31G and 6–31G^* basis sets were used. The presence of two maxima on every curve has been shown. To refine the values of barriers to the internal rotation in the regions of minima and maxima of PCR, calculations taking into account the electron correlation energy have been carried out at the second- and fourth-order Møller-Plesset level of perturbation theory (MP2 and MP4, respectively). At the MP4/6-61G^* level of approximation, the barriers to the rotation about the O?O bond are equal to 8.6 kJ mol^?1 and 14.7 kJ mol^?1, and both barriers to the rotation about the N?O bond are equal to 33.5 kJ mol^?1. The results are compared with those published for PCR in hydrogen peroxide and peroxynitric acid.     

Energy continuity in multi-reference CI calculations

Configuration interaction calculations based on changing numbers of reference configurations at different geometries have a theoretical inconsistency which can affect the continuity of a calculated potential surface. As the number of reference configurations is increased for adjacent points on a potential curve (e.g. to describe molecular dissociation), the CI space can increase by large quantum jumps. Using the MRD-CI method of Buenker and Peyerimhoff and coworkers, we give several criteria which help to ensure energy continuity across these changes in CI space, and demonstrate these criteria for the hydrogen fluoride potential curve.     

Hydration and protonation ofO-vinylacetoxime in the gas phase: anab initio study

Ab initio HF/6–31G^* calculations ofO-vinylacetoxime monohydrates and cations were performed. Each conformer forms two stable H-complexes with participation of N and O atoms. The former have planar heavy-atom skeletons, whereas the water molecule in the latter is located above the plane of the proton-acceptor complex. The complexes stabilized by N...HO and O...HO bonds have different dipole moments and frequencies of the OH stretching vibrations. The most energetically favorable cation is formed by adding a proton to the C_β atom of the vinyl group ofO-vinylacetoxime. Theap,ap-conformer (ap is antiperiplanar) of this cation is 6.5 and 34.9 kcal mol⁻¹ more stable than the onium cations with the NH⁺ and OH⁺ fragments, respectively, and is characterized by polarization and appreciable lengthening of the N−O and C=C bonds. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 597–600, April, 2000.     

Nonempirical calculations of NQR spectrum parameters of azetidine

The components of the¹⁴N electric field gradient (EFG) tensor, the corresponding nuclear quadrupole coupling constant (NQCC) , and the asymmetry parameter of azetidine were calculated using the restricted Hartree-Foek-Roothaan method, The geometry of azetidine was optimized with the 4–31G basis set, and the values of the ring puckering angle () and the angle between the N-H bond and the CNC plane () were refined with the 6–31G^* basis set. The effect of choice of geometry on calculated NQR parameters was studied. To clarify the origin of EFG at the nitrogen atom nucleus, the contributions from individual bond orbitals and lone electron pairs to the EFG tensor componentseq _ii were calculated in the framework of the LMO approach. It was demonstrated that the 4-31G + 6–31G^*//6–31G^* level calculations give NQCC and values of azetidine that are in good agreement with the results of MW spectroscopy.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No, 12, pp. 2886–2889, December, 1996.     

Quantum-chemical investigation of the dependence of pK a on the calculated energy of proton removal for certain derivatives of indole and phenol

The total energies of derivatives of N-hydroxyindole, indole, and phenol, and of their corresponding anions have been estimated with the aid of ab initio calculations on the 3-21G basis. The energies of proton removal were calculated from the difference in total energies of the appropriate anions and molecules. By comparing the calculated energies of proton removal with experimental values of pK_a (acidity characteristic) a practically linear dependence was shown for the acidity characteristic on the energy of proton removal for the series of compounds investigated. An empirical formula has been proposed expressing the dependence of pK_a on the energy of proton removal, which makes it possible to predict pK_a in this series by carrying out calculations of the energy of proton removal (transfer). __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 47–50, January, 2006.     

Structure effects of the protonated lincomycin molecule on the mechanism of its complexation with organic compounds

The mechanism of complexation of the protonated lincomycin molecule with para-substituted nitrobenzenes in the gas phase is analyzed by quantum chemical methods. The regioselectivity of lincomycin protonation is treated in a B3LYP/6-31G(d′, p) approximation; the geometrical structure and conformation of the molecule are analyzed. The lincomycin molecule is protonated at the nitrogen atom of the pyrrolidine cycle. In stable conformers, a pseudovoid is formed and stabilized by intramolecular hydrogen bonding. The cross section of the pseudovoid (1.77–2.62 Å) is too small for the protonated lincomycin molecule to participate in host guest complexation with organic compounds. According to B3LYP/6-31G(d′, p) calculations, complexation of the protonated lincomycin molecule with nitrobenzenes occurs through hydrogen bonding.     

Pathways of the reactions of nucleophilic addition of H2O and HF molecules to formaldehyde in the gas phase and in the complex with formic acid:ab initio calculations

The gradient pathways of the reactions of nucleophilic addition of H₂O and HF molecules to formaldehyde in the gas phase and in the XH…H₂CO…HC(O)OH complex (X=OH, F) were calculated by theab initio RHF/6-31G^**, MP2(fc)/6-31G^**, and MP2(full)/6-311++G^** methods. Both reactions proceed concertedly. The formation of H-bonded bimolecular pre-reaction complexes is the initial stage of the gas-phase reactions; at the same time, no indications of the formation of stable π-complexes were found on the potential energy surfaces of systems under study. The calculated energy barriers to the gasphase reactions exceed 40 kcal mol⁻¹, while those to reactions in the complex XH…H₂CO…HC(O)OH (X=OH, F) become more than halved. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2146–2154, November, 1998.     

Estimation of the Relative Stabilities of the E,Z-Isomers of α,β-Dialkylsubstituted Methyl Vinyl Ethers by Various Computational Methods

The relative thermodynamic stabilities (relative enthalpies) of the E,Z-isomers of ,-dialkylsubstituted methyl vinyl ethers MeOC(R₁)=CHR₂ have been estimated by various computational methods including molecular mechanics, semiempirical, ab initio, and DFT calculations. The best performance, approaching the accuracy of the experimental method of chemical equilibration, is shown by the DFT calculations. Ab initio methods, provided that electron correlation is taken into account, are also satisfactory, but clearly less successful than the DFT calculations. The reliability of the semiempirical methods AM1 and PM3 is considerably less good, and varies in an unpredictable manner from case to case. The poorest general performance is shown by the MM2 and MM3 calculations, which may overestimate the relative stability of the Z isomer by as much as 18 kJ mol^–1.     

Theoretical studies on the conformations of selenamides

Ab initio HF/6-31+G*, MP2/6-31+G*, B3LYP/6-31+G* level calculations have been performed on HSe-NH₂ to estimate the Se-N rotational barriers and N-inversion barriers. Two conformers have been found withsyn andanti arrangement of the NH₂ hydrogens with respect to Se-H bond. The N inversion barriers in selenamide are 1.65, 2.47, 1.93 kcal/mol and the Se-N rotational barriers are 6.58, 6.56 and 6.12 kcal/mol respectively at HF/6-31+G*, MP2/6-31+G* and B3LYP/6-31+G* levels respectively. The n_N →Σ *_Se-H negative hyperconjugation is found to be responsible for the higher rotational barriers.