Intramolecular nucleophilicS N 2 substitution at the tetrahedral carbon atom: Anab initio study

Pentacoordination of carbon atom in bicyclic organic compounds of the pentalene type was studied by theab initio RHF/6-31G^** and MP2(full)/6-31G^** methods. It was shown that intramolecularS _N 2 reactions with energy barriers within the energy scale of NMR spectroscopy can occur in systems in which a linear orientation of the attacking and leaving groups is realized. The barrier to the intramolecular nucleophilic substitution reaction in 2,3-dihydro-3-formylmethylenefuran is 36.9 (RHF) and 27.7 kcal mol⁻¹ (MP2) and decreases to 16.4 and 19.4 kcal mol⁻¹, respectively, in the case of diprotonation at the O atoms in this system. For model pentalene type compounds containing electron-deficient B atoms in the ring, theab initio calculations predict a further decrease in the barrier height (down to less than 10 kcal mol⁻¹). Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 7, pp. 1246–1256, July, 1999.     

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.     

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.     

Pentacoordination of boron, carbon, aluminum, and silicon atoms in organic compounds: Anab initio study

Pentacoordination of boron, carbon, aluminum, and silicon atoms in bicyclic organic compounds of the pentalene type was studied using theab initio RHF/6-31G^** and MP2(full)/6-31G^** methods. It was shown that the ability of the atom to form pentacoordinate structures increases on going from B to Al and from C to Si atom,i.e. as the number of the element of Groups IIIA and IVA of the periodic system increases. At the same time, the reverse tendencies are observed in the 2nd and 3rd periods of the periodic system,viz., the ability of the atom to form pentacoordinate structures increases on going from C to B and from Al to Si atom. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1238–1245, July, 1999.     

A quest for triplet silylenes XHSi3 at ab initio and DFT levels (X = H, F, Cl and Br)

Four ground state triplet silylenes are found among 30 possible silylenic XHSi₃ structures (X = H, F, Cl and Br), at seven ab initio and DFT levels including: B3LYP/6-311++G^∗∗, HF/6-311++G^∗∗, MP3/6-311G^∗, MP2/6-311+G^∗∗, MP4(SDTQ)/6-311++G^∗∗, QCISD(T)/6-311++G^∗∗ and CCSD(T)/6-311++G^∗∗. The latter six methods indicate that the triplet states of 3-flouro-1,2,3-trisilapropadienylidene, 1-chloro-1,2,3-trisilapropargylene and 3-chloro-1,2,3-trisilapropargylene are energy minima. These triplets appear more stable than their corresponding singlet states which cannot even exist for showing negative force constants. Also, triplet state of 1-flouro-1,2,3-trisilapropargylene is possibly accessible for being an energy minimum, since its corresponding singlet state is not a real isomer. Some discrepancies are observed between energetic and/or structural results of DFT vs. ab initio data.     

Inversion of Pyramidal Configuration of Pnictogenic Center in Diazapnictolenes

The possibility of pyramidal inversion in diazapnictolenes was investigated by methods ab initio MP2(full)/6-31G^** and density functional theory B3LYP/6-31G^**. The inversion of tricoordinate phosphorus in 2-fluoro-1,3,2-diazaphospholene and of arsenic in 2-fluoro-1,3,2-diazaarsolene requires low activation barriers (<15 kcal mol^-1) corresponding to the time scale of the NMR method.     

Intramolecular Hypervalent X←X Interaction in Mono- and Bicyclic Heteroelement Compounds Containing Se and Te Atoms

Chalcogen-containing heterapentalene and quasimonocyclic compounds having SeÄSeÄSe and TeÄTeÄTe triads or SeÄSe and TeÄTe diads were studied by the ab initio [MP2(full)/6-31G**, MP2(fc)/6-31+G**, and MP2(fc)/LANL2DZ] and DFT methods (B3LYP/6-31G^**, B3LYP/6-31+G^**, and B3LYP/LANL2DZ). Heterapentalene compounds were found to be stable as planar bicyclic structures having a C _2v symmetry. The stability of quasimonocycic -chalcogenovinyl aldehydes increases with increase in the electron-acceptor power of the substituent at the X atom.     

Carbon,nitrogen, and oxygen hypercoordination in half-sandwich and sandwich structures

The structures and stabilities of a number of neutral and charged half-sandwich (pyramidal) and sandwich compounds, which obey the “electron octet” rule and contain hypercoordinate carbon, nitrogen, and oxygen atoms, were studied by ab initio MP2(full)/6-311+G** and density functional B3LYP/6-311+G** methods. Introduction of lithium counterions or bridging hydrogen atoms can provide an additional stabilization of non-classical systems with hypercoordinate centers.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 527–540, March, 2005.     

Mechanisms of inversion of bond configuration at the tetrahedral boron atom in five-membered chelate cycles

Mechanisms of inversion of the bond configuration at the tetrahedral boron center in five-membered chelate cycles of the 1,3,2-oxazaborolidine and 1,3,2-oxazaborolidene molecules were studied by theab initio MP2(full)/6-31G^** method. It was shown that enantiotopomerization occurs by a dissociative mechanism with the cleavage of the B←N bond and the formation of acyclic intermediates with tricoordinate planar boron atom. The calculated energy barriers to inversion of tetrahedral bond configurations at boron centers in the two chelate complexes are equal to 13.1 and 15.4 kcal mol⁻¹, respectively. In contrast to 1,3,2-oxazaborolidine, internal rotation about the B−O bond in its unsaturated analog makes an appreciable contribution to the reaction coordinate. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 250–255 February, 1999.     

Anab initio quantum-chemical study of proton addition to F-, Ch3-, and CF3-substituted ethylene derivatives

Protonated forms of the molecules of ethylene derivatives with the general formula C₂X₂Y₂ (X=Y=H) (1), F (2), CH₃ (3) CH₃ (4); X=F, Y=H:cis-(5)trans- (6)) were calculated by theab initio MP2/6-31 G^* method with full geometry optimization. The minima and saddle points located on the potential energy surface (PES) of the protonated ethylene molecule correspond to the stationary states and transition states of proton migration, respectively. The stationary states are characterized by a nonclassical geometry of carbocations similar to that of π-complexes, whereas the transition states have a classical structure. Unlike1, the carbocations of molecules2–6 have the classical structure. The saddle points on the PES of the ethylene derivatives correspond to the structures of the π-complex type, which are the transition states of proton migration between the C atoms of the ethylene bond. The barrier to rotation about, the C−C bond depends essentially on the substituent nature. Published inIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1333–1337, August, 2000.     

Ab initio Mechanism Study on the Reaction of Chlorine Atom with Formic Acid

The potential energy surface(PES) for the reaction of Cl atom with HCOOH is predicted using ab initio molecular orbital calculation methods at UQCIDS(T,full)6-311 G(3df,2p)//UMP2(full)/6-311 G(d,P) level of theory with zero-point vibrational energy (ZPVE) correction.The calculated results show that the reaction mechanism of Cl atom with formic acid is a C-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom with a 3.73kJ/mol reaction barrier height,leading to the formation of cis-HOCO radical which will reacts with Cl atom or other molecules in such a reaction system.Because the reaction barrier height of O-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom which leads to the formation of HCO2 radical is 67.95kJ/mol,it is a secondary reaction channel in experiment,This is in good agreement with the prediction based on the previous experiments.     

Molecular structures of acetylene derivatives of tin

The geometry and force fields of the bis(trimethylstannyl)acetylene molecule (a conformer withD _3d symmetry corresponding to a minimum of the total energy of the molecule) were calculated by the RHF and MP2(fc) methods. The effective core potential in SBK form with the optimized 31G^* valence basis set was employed in the case of Sn atoms. The 6–31G^** and 6–311G^** basis sets were used for carbon and hydrogen atoms. Vibrational spectra of the light and perdeuterated isotopomers of bis(trimethylstannyl)acetylene were interpreted using the procedure of scaling the quantum-chemical force fields. For Part 5, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 616–626, April, 2000.     

Molecular and electronic structures of anionic σ-complexes of 9-nitroanthracene and its derivatives studied byab initio HF/6-31G** calculations

The molecular structures of anionic σ-complexes of 9-nitroanthracene and its 10-methoxy and 10-acetonyl derivatives were calculated by theab initio quantum-chemical HF/6-31G^** method. The central ring of the anthracene fragment adopts a boat conformation. The values of the bond lengths and bond orders in the compounds under study indicate that the contribution of theaci-resonance form to the structure of the nitro group is substantially larger than that estimated for 2,4,6-trinitrobenzene derivatives. The substituents have no substantial effect on the geometry of the anion. The negative charge is localized mainly on the oxygen atoms of the nitro group and of the substituents. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2142–2145, November, 1998.     

Structure and stability of closo-hexaboranes and their heteroanalogs

The molecular and electronic structures of closo-hexaboranes B₆H₆ ^2–, B₆H₇ ^–, and B₆H₈ and closo-heterohexaboranes XYB₄H₄ (X = Y = CH, N; X = BH, Y = CH^–, N^–, NH, O) were studed by the ab initio (MP2(full)/6-311+G**) and density functional (B3LYP/6-311+G**) methods. The bridging H atoms in closo-hexaboranes B₆H₇ ^– and B₆H₈ can undergo facile low-barrier migrations around the boron cage (the barrier heights are about 10—15 kcal mol^–1). All heteroboranes having octahedron-like structures with hypercoordinated N and O atoms are rather stable and can be the subject of synthetic research efforts.     

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise‐corrected second‐order Møller‐Plesset (MP2) perturbation theory. Single‐point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6‐311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc‐pVXZ and aug‐cc‐pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon–carbon separation was sampled in a step 0.1 Å for a range of 3–9 Å, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well‐established analytical extrapolation schemes. A 4‐site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen–hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom‐wise radial distribution functions and the self‐diffusion coefficients over a wide range of experimental conditions. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Ab. initio calculations of Cl2SO ·nAICl3 complexes (n = 1, 2)

Fragments' of the potential energy surfaces (PES) for the SOCl₂ ·nAICl₃ (n = 1, 2) complexes were calculated by theab initio MO LCAO method using the RHF approximation for the STO-3G basis set and adding a 3d-AO for the S atom, as well as by the semiempirical MNDO method. Two local minima, assigned to the donor-acceptor complex Cl₂SO+AlCl₃ (la) and to Cl₃SOAlCl₂ (1b) were located on the PES atn = 1. Two local minima corresponding to two donor-acceptor complexes Cl₂SOAl₂Cl₆ and, were also located on the PES atn = 2. An analysis of the enthalpies of cation formation in the SOC1₂ +nAICl₃ (n = 1-3) systems calculated by theab initio method shows that the enthalpy of formation of the SOCl₊ cation atn = 2 is 17 kcal mol^–1 less than that atn = 1; the structure of the Cl₂SOAlCl₂ ⁺ cation with two strong electrophilic centers at the Al and S atoms becomes more favorable energetically atn = 3. The results of calculations for Cl₂SO ·nAICl₃ complexes by the MNDO method are in agreement with those obtained by theab initio method except for the geometry of complexes containing the Cl₃SO fragment and the charge values on the S atoms.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1116–1120, May, 1996.     

A study of methanetetraol dehydration to carbonic acid

Two alternative dehydration reactions C(OH)₄ → (HO)₂CO + H₂O and C(OH)₄ + H₂O → (HO)₂CO + 2H₂O are studied by ab initio Becke3LYP/6–311 + G^** and MP2/6–31G^** methods. Calculated energy and geometry characteristics of intermediates and transition states predict a catalytic effect of one water molecule and the exothermism of the transformations. Relevant HF/6–311 + G^**, HF/6–31G^**, HF/6–31G, and HF/3–21G calculations were performed for comparison. © 1997 John Wiley & Sons, Inc.     

Computational Exploration of Conformations of Glycine-Arginine and a Deduced Model on Global Minimum Configurations of Dipeptides in Gas Phase

An extensive computational study on the conformations of gaseous dipeptide glycinearginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface (PES) of GlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G^*, BHandHLYP/6-31G^*, and BHandHLYP/6-311++G^** in order to reliably find the low energy conformations. The conformational energies were finally determined with the methods of BHandHLYP, camB3LYP, B97D, and MP2 using the basis set of 6-311++G(3df,3pd). The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.     

Hydrogen Bonding Properties of the Complexes of Formaldehyde and its Derivatives with HF and HCl

Summary.  The complexes of formaldehyde and some of its derivatives with HF and HCl were investigated at HF/6-311 + +G^** and MP2/6-311 + +G^** levels of theory. Interaction energies were corrected for the basis set superposition error (BSSE). The full optimizations of dimers and monomers were performed during calculations. The Bader theory of atoms-in-molecules (AIM) was also applied for the localization of bond critical points (BCP) and for the calculation the electron densities and their Laplacians at these points. The relationships between H-bond energy and parameters obtained from calculations were also studied. Received June 29, 2001. Accepted (revised) October 29, 2001     

Stabilization of octacoordinate carbon center in metal-containing derivatives of orthocarbonic acid

The electronic and spatial structures of alkali metal compounds CO₃M₂, CO₃M₃ ⁺, and CO₄M₄ (M = Li, Na, K) were investigated by the ab initio (MP2(full)/6-311+G**) and density functional (B3LYP/6-311+G**) methods. The calculated energies of formation decrease in the order E ^Li > E ^Na > E ^K for all structural types, being determined by steric and orbital interactions. Stable structures with octacoordinate carbon are formed in the case of CO₄M₄ salts. Dedicated to Academicians A. L. Buchachenko and N. S. Zefirov on the occasions of their 70th birthdays. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1929–1938, September, 2005.