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.     

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.     

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.     

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.     

Geometry of intramolecular silicon complexes: an ab initio estimation of the sensitivity to the effect of medium. (Aroyloxymethyl)trifluorosilanes

The effect of medium on the geometry of the (benzoyloxymethyl)trifluorosilane (1) molecule was studied by the HF and MP2 methods with the 6-31G(d), 6-311G(d), and 6-311+G(d,p) basis sets, as well as using the Onsager SCRF model, the PCM approach, and the data of X-ray diffraction study. Molecule 1 has a low complexation energy (5.4 kcal mol^–1 according to MP2(Full)/6-31G(d)+ZPE calculations and 6.8 kcal mol^–1 according to IR spectroscopy data), while its geometric parameters are the least sensitive to the effects of medium among all hypervalent silicon compounds studied to date. Nevertheless, the results obtained revealed a pronounced deformation of the SiO coordination bond in 1 on going from the gas phase to the polar solution and crystal. This serves as a theoretical substantiation of the hypothesis that substantial changes in the IR and NMR spectral characteristics of the (O—Si)-chelate (aroyloxymethyl)trifluorosilanes upon variation of external factors are due to geometric reasons. Analysis of the electron density distribution according to Bader indicates that the SiO bond in molecule 1 can be treated as a covalent bond of high polarity.     

Comparison of the capacity of nitrogen, oxygen, sulfur, and selenium atoms to exist in onium states. quantum-chemical investigation of isomeric model systems with two heteroatoms

HF, B3LYP, and MP2 calculations with the 6-31+G(d) basis set with correction to the energy of zero-point vibrations were carried out to determine the energy characteristics of model molecules containing two heteroatoms in the sp ³- and sp ²-hybrid states; different combinations of N, O, S, and Se atoms were studied. The stability of the onium states of the nitrogen atom was found to be greater than for its chalcogen analogs and the relative stability of onium states of the chalcogen analogs was found to depend on the hybridization of these atoms. Analysis of these results permitted us to construct a stability series of onium derivatives and to interpret the positional selectivity in electrophilic substitution reactions of five-membered heterocyclic compounds with one heteroatom. To J. Stradins, an outstanding and tireless scientist, with our deep respect and sincere affection. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1801–1808, December, 2008.     

Structure and isomerization of heterapentalene compounds containing hypervalent bonds with central nitrogen,phosphorus, or arsenic atom

The possibility for a specific type of isomerization (electromorphism) to occur in conjugated bicyclic organic compounds containing Group V elements was studied by the ab initio (RHF/6-31G**, MP2(full)/6-31G**), and DFT (B3LYP/6-31G**) methods. Compounds 2 (X = N, P, As) were found to exist in a monocyclic planar form with intramolecular donor-acceptor N...O coordination (X = N) and as aromatic heterapentalene structures with hypervalent O--X--O bonds (X = P, As). According to calculations, no isomerization of planar heteroaromatic structures into pyramidal ones occurs. The strength of the O--X--O hypervalent bond and the aromaticity of heterapentalene structures 2 with ten -electrons increase on going from X = N to X = P. Correct estimation of these effects requires the inclusion of electron correlation.     

Molecular structure,conformational mobility,vibrational spectra,and thermochemistry of peroxyacetic acid: an ab initio and density functional study

The structure of the peroxyacetic acid (PAA) molecule and its conformational mobility under rotation about the peroxide bond was studied by ab initio and density functional methods. The free rotation is hindered by the trans-barrier of height 22.3 kJ mol^–1. The equilibrium molecular structure of AcOOH (C _s symmetry) is a result of intramolecular hydrogen bond. The high energy of hydrogen bonding (46 kJ mol^–1 according to natural bonding orbital analysis) hampers formation of intermolecular associates of AcOOH in the gas and liquid phases. The standard enthalpies of formation for AcOOH (–353.2 kJ mol^–1) and products of radical decomposition of the peroxide — AcO^· (–190.2 kJ mol^–1) and AcOO^· (–153.4 kJ mol^–1) — were determined by the G2 and G2(MP2) composite methods. The O—H and O—O bonds in the PAA molecule (bond energies are 417.8 and 202.3 kJ mol^–1, respectively) are much stronger than in alkyl hydroperoxide molecules. This provides an explanation for substantial contribution of non-radical channels of the decomposition of peroxyacetic acid. The electron density distribution and gas-phase acidity of PAA were determined. The transition states of the ethylene and cyclohexene epoxidation reactions were located (E _a = 71.7 and 50.9 kJ mol^–1 respectively).     

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.     

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.     

Ab initio calculations of activation energy of the reaction of hydrogen exchange on strongly acidic centers

Ab initio calculations of fragments of the potential energy surfaces of hydrogen exchange reactions between H₂, CH₄, and alanine molecules and the H₃O⁺ ion were performed by the restricted Hartree-Fock method, at the second-order Møller-Plesset level of perturbation theory, and by the method of coupled clusters using the 6–31G^* and aug-cc-pVDZ basis sets. The one-center synchronous mechanism of hydrogen exchange reaction was studied and the activation energies and structures of transition states were determined. It was found that the geometric parameters of the H₂ and CH₄ molecules in the transition states are close to those of the H₃ ⁺ and CH₅ ⁺ ions. The higher the proton affinity of the reacting molecule in the reaction studied the lower the activiation energy of hydrogen exchange. The one-center mechanism studied can be used to describe the high-temperature solid-state catalytic isotope exchange (HSCIE) reaction. The results ofab initio calculations of synchronous hydrogen exchange between the H₃O⁺ ion and hydrogen atoms in different positions of the alanine molecule are in good agreement with experimental data on the regioselectivity and stereoselectivity of the HSCIE reaction with spillover-tritium.     

Matrix IR-spectroscopic and quantum-chemical study of difluorostannylene complexation with dinitrogen

Complexes of difluorostannylene with dinitrogen of composition 1∶1 and 1∶2 were stabilized in Ar matrix (12 K) and characterized by IR spectra. The bands at 588, 565, and 583, 557 cm⁻¹, respectively, were assigned to these complexes. Potential energy surfaces of the systems SnF₂+N₂ and SnF₂+2N₂ were studied by theab initio MP2/3-21G(d2)//HF/3-21G(d2) method using the basis set including polarization functions at Sn, F, and N atoms. Equilibrium structures of the complexes haveC _s andC _2v symmetry and correspond to coordination of lone electron pairs of nitrogen molecules with vacant p-AO of the carbenic center. The calculated complexation energies are equal to 4.6 and 8.9 kcal mol⁻¹, respectively. Based on results of quantum-chemical calculations an interpretation of the IR spectra of the complexes was given and it was shown that cycloaddition of SnF₂ to a triple N≡N bond with formation ofcyclo-SnF₂N₂ is energetically unfavorable. The absorption band belonging to SiF₄·N₂ complex in Ar matrix was detected and assigned. Dedicated to the memory of Academician M. E. Vol'pin timed to his 75th birthday. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1087–1093, June, 1998.     

Anab initio MO study on the direct and migratory reaction mechanism for the formation of HF in H + CIF system

Anab initio MO method has been used to calculate the potential energy surface for the formation of HF when H reacts with C1F. The various transition states possibly related to forming HF were optimized. An IRC calculation starting from the collinear F-centered transition state was performed and energies of a series of points with bending configurations were also calculated to determine the direct reaction path leading to HF product. Another IRC calculation starting from the H-centered transition state was run to determine the migratory path to forming HF. By doing so, the Polanyi’s assumption that it would involve the direct and a migratory mechanisms for the formation of HF when H reacts with CIF has been verified theoretically. Project supported by the National Natural Science Foundation of China.     

Structure,stability, and disproportionation mechanisms of organic interhalides of the cholinium series: an experimental and theoretical study

The stability constants of acetylcholinium, carbamoylcholinium, and cholinium diiodochlorides and diiodobromides in chloroform solutions were determined and the kinetics of disproportionation of these systems in 1 : 9 CHCl₃—MeOH (MeCN) mixtures were studied by UV spectroscopy. A possible mechanism of mutual transformations of the polyhalides is proposed and an interrelation between the nature of the iodine-coordinating solvent and the extent of reversibility of the process is established. The electronic structures and relative stabilities of acetylcholinium iodohalides and charge-transfer complexes S·XI₂ ^– and S·I₂ (S = MeOH, MeCN, CHCl₃; X = Cl, Br, I) were studied by ab initio RHF and MP2(full) methods in the HW+(3d) and 6-31G++(d,p) basis sets. It was found that all the solvents studied favor the decomposition of the iodohalide anions to liberate molecular iodine; however, disproportionation of I₂ is possible only for the S·I₂ complexes with a high extent of charge transfer.     

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.     

Anab initio theoretical study of the binding of ZnII with biologically significant ligands: CO2, H2O,OH−, imidazole,and imidazolate

Zinc is one of the most important biological metals involved in the catalytic site of many enzymes. SCFab initio computations with good quality basis sets are reported for monoadducts of Zn^II with various biologically significant ligands, and the fundamental features of the binding are characterized, using in particular energy decomposition scheme, population analysis and difference density curves. A test of the possibility of using pseudopotentials in this domain is also reported.     

Effect of intramolecular interaction between polar and polarizable bonds on13C shielding constants in different conformations of 2-methoxy- and 2-vinyloxynaphthalene molecules: Anab initio study

Shielding constants of¹³C nuclei calculated for different conformations of 2-methoxynaphthalene and 2-vinyloxynaphthalene molecules by the GIAOab initio method in the D95^** basis set indicate a strong shielding effect of the intramolecular interaction between the polar O−C bond of the substituent and the polarizable π-bond of the naphthyl moiety on the C atom incis-position. The results obtained are in agreement with the experimentally found trends of changes in the chemical shifts of¹³C nuclei and are in reasonable quantitative agreement with experimental data. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1066–1069, June, 1999.     

Chemical bonding in isolated molecules and crystals of zwitterionic pentacoordinate silicon chelates

The electronic structures of a number of zwitterionic pentacoordinate silicon chelates were investigated using the results of X-ray diffraction studies and quantum-chemical calculatoins by the MPW1PW91/6-311G(d) method. The topological analysis of the electron density distribution function and the study in the framework of the natural bond orbital partitioning scheme showed that the character of chemical bonding in the axial fragments of the molecules under consideration changes from dative to three-center, four-electron as the silicon atom assumes a trigonal-bipyramidal coordination.     

Planar or quasi-planar octa- and ennea-coordinate aluminum and gallium in boron rings

An ab initio theoretical investigation has been performed on planar or quasi-planar octa-and ennea-coordinate Al and Ga centered in X@B8- and X@B9 (X=Al, Ga). These high symmetry molecular wheels all turned out to be true minima of the systems and σ+π double aromatic in nature, similar to the previously characterized D8h B@B8- both electronically and geometrically. Adiabatic and vertical detachment energies of the anions and the ionization potentials of the neutrals have been calculated to aid their eventua...     

Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si)

To obtain a set of consistent benchmark potential energy surfaces (PES) for the two archetypal nucleophilic substitution reactions of the chloride anion at carbon in chloromethane (S(N)2@C) and at silicon in chlorosilane (S(N)2@Si), we have explored these PESes using a hierarchical series of ab initio methods [HF, MP2, MP4SDQ, CCSD, CCSD(T)] in combination with a hierarchical series of six Gaussian-type basis sets, up to g polarization. Relative energies of stationary points are converged to within 0.01 to 0.56 kcal/mol as a function of the basis-set size. Our best estimate, at CCSD(T)/aug-cc-pVQZ, for the relative energies of the [Cl(-), CH(3)Cl] reactant complex, the [Cl-CH(3)-Cl](-) transition state and the stable [Cl-SiH(3)-Cl](-) transition complex is -10.42, +2.52, and -27.10 kcal/mol, respectively. Furthermore, we have investigated the performance for these reactions of four popular density functionals, namely, BP86, BLYP, B3LYP, and OLYP, in combination with a large doubly polarized Slater-type basis set of triple-zeta quality (TZ2P). Best overall agreement with our CCSD(T)/aug-cc-pVQZ benchmark is obtained with OLYP and B3LYP. However, OLYP performs better for the S(N)2@C overall and central barriers, which it underestimates by 2.65 and 4.05 kcal/mol, respectively. The other DFT approaches underestimate these barriers by some 4.8 (B3LYP) to 9.0 kcal/mol (BLYP).