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.     

An ab initio evaluation of the role of p,π interaction: II. Molecules of the CH3COX series

The RHF/6-311G(d) and MP2/6-311G(d) calculations with full geometry optimization were performed for CH₃COX molecules (X = F, Cl, Br, CH₃). Variations in the populations of the p _y orbitals of their halogen and carbon atoms (orbitals whose symmetry axes are perpendicular to the molecular plane) from X = F to X = Cl, Br, and CH₃ are not associated with variations in the extent of the p,π conjugation between the lone electron pair of the halogen atom and the π-electron system of the carbonyl group. The bonding molecular orbitals formed by these atomic p _y orbitals are not determined by this interaction. The RHF/6-311G(d) and MP2/6-311G(d) calculations give similar results.     

An ab initio evaluation of the role of p,π interaction: I. Ethylene derivatives

The RHF/6-311G(d) and MP2/6-311G(d) calculations with full geometry optimization were performed for XCH=CH₂ molecules (X = F, Cl, Br, CH₃, CH₂CH₃, CH₂F, CHO). The p _y electron density distribution in these molecules and the bonding molecular orbitals formed by the p _y orbitals of atoms of the planar fragment of these molecule (atomic orbitals whose symmetry axes are perpendicular to this plane) are not determined by the p,π conjugation between the lone electron pair of the heteroatom in substituent X and π electrons of the C=C bond. Changes in the population of the p _y orbitals of the halogen and carbon atoms in going from X = F to X = Cl and Br are not associated with changes in the extent of this p,π interaction. Taking into account the electon correlation in the MP2 method does not noticeably alter the features of the electron density distribution in these molecules estimated by restricted Hartree-Fock calculations.     

Structure of N-chloromethyllactams and features of the interaction of atoms in them as a result of ab initio calculations

Quantum-chemical calculations have been carried out by the RHF/6-31G(d) and MP2/6-31+G(d) methods of molecules of N-chloromethylpyrrolidone, N-chloromethylcaprolactam, N-chloromethyl-succinimide, and N-chloromethylphthalimide with full optimization of their geometry, and also N-chloromethylpyrrolidone molecule by the RHF/6-31G(d) method at various angles of rotation of the CH₂Cl group around the C―N bond. It was shown that the lower frequencies of the ³⁵Cl NQR of the first two molecules in comparison with the later are mainly determined by the high populations of the p _σ -orbitals of their Cl atoms. The population of the orbitals of the unshared electron pair of the N atom is practically unchanged on rotating the CH₂Cl group, but the N atom polarizes the C―Cl bond in the indicated molecule. This does not confirm the supposed p,σ*-conjugation in the Cl―C―N grouping. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1537–1544, October, 2008.     

The intermolecular interactions in the aminonitromethylbenzenes

The intermolecular non-covalent interactions in aminonitromethylbenzenes namely 2-methyl-4-nitroaniline, 4-methyl-3-nitroaniline, 2-methyl-6-nitroaniline, 4-amino-2,6-dinitrotoluene, 2-methyl-5-nitroaniline, 4-methyl-2-nitroaniline, 2,3-dimethyl-6-nitroaniline, 4,5-dimethyl-2-nitroaniline and 2-methyl-3,5-dinitroaniline were studied by quantum mechanical calculations at RHF/311++G(3df,2p) and B3LYP/311++G(3df,2p) level of theory. The calculations prove that solely geometrical study of hydrogen bonding can be very misleading because not all short distances (classified as hydrogen bonds on the basis of interaction geometry) are bonding in character. For studied compounds interaction energy ranges from 0.23 kcal mol⁻¹ to 5.59 kcal mol⁻¹. The creation of intermolecular hydrogen bonds leads to charge redistribution in donors and acceptors. The Natural Bonding Orbitals analysis shows that hydrogen bonds are created by transfer of electron density from the lone pair orbitals of the H-bond acceptor to the antibonding molecular orbitals of the H-bond donor and Rydberg orbitals of the hydrogen atom. The stacking interactions are the interactions of delocalized molecular π-orbitals of the one molecule with delocalized antibonding molecular π-orbitals and the antibonding molecular σ-orbital created between the carbon atoms of the second aromatic ring and vice versa.      

Quantum chemical and experimental studies on the structure and vibrational spectra of substituted 2-pyranones

A systematic study on the structural characteristics of the 2-pyranone ring containing molecules with bromine, nitrile, and amide substituents at the C-3 position in the ring is conducted in the electronic ground (S ₀) state by DFT calculations using the B3LYP/6-311++G** method. The geometrical structure of the bromine substituted compound, which shows potent hepatoprotective activity, is studied both in the ground (S ₀) and first excited singlet (S ₁) states using RHF/6-311++G** and CIS/6-311++G** methods respectively. The molecules are found to exist in two isomeric forms gauche and trans that have the enthalpy difference of less than 3.32 kcal/mol; the latter is the preferred orientation in the gaseous phase. The S ₁ state is a ¹(π,π*) state that arises π-electron transfer from the region of a double bond in the pyranone ring to the region of the internuclear bond connecting the 2-pyranone and benzene rings. A complete vibrational analysis is conducted for the 3-bromo-6-(4-chlorophenyl)-4-thiomethyl-2H-pyran-2-one molecule based on the experimental infrared spectra in the 50–4000 cm⁻¹ region and DFT/6- 311++G** computations of vibrational frequencies for the gauche and trans isomeric forms. Spectral assignments based on the potential energy distribution along the internal coordinates confirm the nonplanar structure of the molecule.     

Synthesis,characterization, and quantum chemical calculational studies on 3-<Emphasis Type="Italic">p</Emphasis>-methylphenyl-4-amino- 1, 2, 4-triazole-5-thione

The title compound of 3-p-methylphenyl-4-amino-1, 2, 4-triazole-5-thione was synthesized and characterized by elemental analysis, IR, electronic spectra, and X-ray single crystal diffraction. Quantum chemical calculations of the structure, natural bond orbital, and thermodynamic functions of the title compound were performed by using B3LYP/6-311G** and HF-6-311G** methods. Both the methods can well simulate the molecular structure. Vibrational frequencies were predicted, assigned and compared with the experimental values, and B3LYP/6-311G** method is superior to HF/6-311G** method to predict the vibrational frequencies. Electronic absorption spectra calculated by B3LYP/6-311G** method have some red shifts compared with the experimental ones and natural bond orbitals analyses indicate that the two absorption bands are mainly derived from the contribution of n → π^* and π → π^* transitions. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between C ⁰ _p,m , S ⁰ _m , H ⁰ _m , and temperatures.     

An ab initio study of the p,π interaction: III. Interaction of an ether oxygen atom with a double bond

RHF/6-311G(d) calculations were performed for the H₂C=CHOCH₃ and H₂C=CClOCH₃ molecules with full geometry optimization and at varied angles of rotation of the methoxy group about the C-O bond, with all the other geometric parameters optimized. The first molecule has one energy minimum and one transition state, and the second molecule, two minima. Changes in the populations of the p _y orbitals of the olefinic carbon and oxygen atoms (orbitals whose symmetry axes are perpendicular to the molecular plane) and in the fractional charges on these carbon atoms, occurring upon rotation of the methoxy groups about the C-O bonds, cannot be attributed to changes in the extent of the p,π conjugation between the lone electron pairs of the oxygen atoms and π electrons of the C=C bonds.     

Influence of the water molecules (n?=?1–6) on the interaction between Li+, Na+, K+ cations and indole molecule as tryptophan amino acid residue

Influence of the addition of water molecules (n = 1–6) on the interaction energy between Li⁺, Na⁺, K⁺ cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation–π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation–π interaction indicates that there is a correlation between the electron density (ρ(r)) in the cage critical points generated upon complexation and the distance between metal cation and centroid of phenyl ring in indole molecule.     

Electronegativity and resonance parameters from the geometry of monosubstituted benzene rings

Reference values of the structural substituent parameters, S _E and S _R, measuring the electronegativity and resonance effects, respectively, of functional groups (Campanelli et al. J Phys Chem A 107:6429–6440, 2003) have been determined from the benzene ring geometries of 100 Ph–X species, including different conformations of the same molecule. Geometries have been obtained by quantum chemical calculations at the HF/6-31G*, HF/6-311++G**, and B3LYP/6-311++G** levels of theory. The substituent parameters from HF/6-311++G** calculations are in close agreement with those determined at the HF/6-31G* level. Using the B3LYP density functional yields S _E and S _R values which—in general—correlate well with the corresponding HF values. Exceptions occur with some charged groups, and, in the case of S _E, with a few dipolar groups having very high or low electronegativities. S _R values from B3LYP calculations are about 22% smaller than the corresponding HF values. The variations of the benzene ring geometry caused by electronegativity, resonance, and steric effects are illustrated in some detail.     

Structural and electronic effects involving pyridine rings in 4-methylpyridine Cu4OX6L4 complexes. II. Correlations based on molecular structure of the Cu4OCl6(4-Mepy)4 complex

Correlations involving bond lengths and bond angles in the molecular structure of the Cu₄OCl₆(4-Mepy)₄ complex (4-Mepy = 4-methylpyridine) with four symmetrically independent molecules present in the unit cell showed that the donor-acceptor behavior involving the π-back donation into the pyridine rings of the 4-Mepy ligands is most effectively stimulated by a suitable orientation of the pyridine rings in the trigonal bipyramidal geometry. The pyridine ring planes are almost in parallel orientation with one of the three Cu-Cl bonds. The bond lengths of these Cu-Cl bonds are in a significant linear correlation with the Cu-N bond lengths and the bonds lengths of the pyridine rings. The pyridine rings orientation is affected by distortion of the trigonal bipyramidal geometry to tetragonal pyramidal coordination, by out-of plane pyridine rings deviation and in-plane pyridine rings tilting, by puckering of the pyridine rings and by the effects of the methyl groups. The pyridine rings in at least seven of the sixteen trigonal bipyramidal coordinations exhibit an orientation supporting the π-back bonding between the Cu(II) atoms and the pyridine rings.     

Quantum chemical analysis of the structure and spectroscopic properties of aryl vinyl ethers

A series of aromatic vinyl ethers and some compounds close to them in structure are studied by DFT (B3LYP/6-311+G(2d,p)) and MP2(full)/6-311+G(2d,p) methods. Measurements of Raman spectra are also used. The calculation of vibrational spectra of aryl vinyl ether (AVE) isomers shows that stretching vibrations ν(C=C) are most conformation sensitive. The calculated value of I(C=C) for vinyl phenyl ether more than twice exceeds the corresponding value for vinyl methyl ether. The calculated and experimental values of I(C=C) are consistent with the hypothesis about the presence of a common conjugated π-system in the molecules of substituted AVEs. Here the bridging oxygen atom provides the π,p,π-interaction.     

Electronic structure of monosubstituted benzenes and X-ray emission spectroscopy

The electronic structure of fluorobenzene was investigated by X-ray emission spectroscopy (using the F−Kα- and C−Kα-spectra) and quantum-chemical MNDO calculations. Molecular orbitals of fluorobenzene were compared with those of benzene and hydrogen fluoride. The P_π−p_π-interaction between the phenyl ring and the fluorine atom in the fluorobenzene molecule is weak for both the outer and inner π levels. For Part 2, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1454–1460, August, 1997.     

On the protonation of partially quaternized poly-4-vinylpyridines in aqueous solution

The ionic equilibria for free pyridine rings in water-soluble macromolecules of poly-4-vinylpyridine (PVP), partially quaternized with either benzylchloride (PP_yBz) or bromoacetone (PP_yAc), were studied by potentiometry and spectrophotometry. Peculiarities of protonation in aqueous solution were observed for the pyridine rings of these polymers compared with the analogue 4-ethylpyridine (EtP_y). The values of intrinsic pK₀ in the absence of protonated pyridine residues for PP_yBz and PP_yAc were found to be 2·4–3·3, and are abnormally low compared with pK_a of EtP_y (6·1). The pK₀ depends insignificantly on the degree of quaternization in PVP but more markedly on ionic strength. However, increase of NaCl concentration (from 0 to 0·1 M) does not cause pK₀ to rise to pK_a of the analogue. The titration data of the base group and keto-enol tautomerism of acetomethylene fragments in PP_yAc allow one to assume the effect of positively charged atoms in α-position of the ring on the proton binding to nitrogen atom of the same ring, thereby decreasing the value of pK₀. The intensification of electrostatic interactions between these charges in the polymer pyridine compared with that of the analogue is likely to be due to partial dehydration of the microregion near to nitrogen atom (microenvironmental effect).     

Density functional calculations of the pseudorotational flexibility of tetrahydrofuran

The flexibility of the five-membered ring in tetrahydrofuran was investigated using quantum mechanical methods involving density functional, Hartree-Fock, and many-body perturbation theory (MP2, MP4) calculations. We found that motion along the pseudorotational path of tetrahydrofuran is nearly free. The 0.1 kcal/mol energy barrier for pseudorotation, calculated at the highest MP4(SDQ)/6-311++G(2d,p)//MP2/6-311++G(2d,p) level of theory, agrees well with the experimental value of 0.16±0.03 kcal/mol. Similar results were obtained with the S-VWN, B3-LYP and B-LYP density functional calculations using the 6-31G(d) set of atomic orbitals. Also the density functional dipole moments and geometries were in good agreement with both the MP2 and experimental benchmarks. However, all density functional methods that utilized the default integration grid in the Gaussian 94 program were found to provide false stationary points of the C ₁ symmetry near the pseudorotational angle of 100°. These stationary points disappeared when a denser spherical-product grid was used. Overall, the hybrid B3-LYP functional was found to be the most promising quantum mechanical method for the modeling of biomolecules containing the furanose ring. Received: 17 June 1997 / Accepted: 20 November 1997     

Conformation dependence of pKa’s of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins

Two members of the green fluorescent protein family, the purple asFP595 and yellow zFP538 proteins, are perspective fluorescent markers for use in multicolor imaging and resonance energy-transfer applications. We report the results of quantum based calculations of the solution pK_a values for selected protonation sites of the denatured asFP595 and zFP538 chromophores in the trans- and cis-conformations in order to add in the interpretation of photo-physical properties of these proteins. The pK_a values were determined from the theromodynamic cycle based on B3LYP/6-311++G(2df, 2p) calculations of the gas phase free energies of the molecules and the B3LYP/6-311++G(d, p) calculations of solvation energies. The results show that the pK_a’s of the protonation sites of the chromophore from asFP595 noticeably depend on the isomer conformation (cis- or trans-), while those of zFP538 are much less sensitive to isomerization.     

Ab initio MO LCAO SCF simulation of molecular and electronic structure of η5-π-C60H5XCp (X=Fe, Si) complexes

The problem of existence of η⁵-π-complexes of unsubstituted fullereneI _h -C₆₀ and its cyclopentadienyl type derivative C₆₀H₅ ^. is discussed.Ab initio MO LCAO SCF calculations of hypothetical sandwich systems η⁵-π-C₆₀H₅XCp (X=Fe (1a), Si (1b)), the cationic complex C₆₀FeCp⁺ of unsubstituted C₆₀, and the C₆₀H₅ ^. radical were performed in the STO-3G and 3-21G basis sets. In the1a, 1b, and C₆₀H₅ ^. systems, hydrogen atoms are attached to carbon atoms of fullerenei _h -C₆₀ at α-positions relative to the same pentagonal face (pent ^*). In η⁵-complexes, XCp species are also coordinated to this face. According to calculations in the 3-21G basis set, the Fe-pent ^* bond energy in complex1a is much higher than those of similar bonds in1b and in the η⁵-π-C₆₀FECp⁺ cation (117 kcal mol⁻¹ vs. 37 and 64 kcal mol⁻¹, respectively) and is 7 kcal mol⁻¹ higher than the Fe−Cp bond energy in the classical sandwich system FeCp₂. The Fe…C _pent* and Fe…C_Cp distances in complex1a are slightly shorter than the Fe…C distance in the ferrocene molecule. The spin populations in the C₆₀H₅ ^. radical are almost completely localized on the atoms of thepent ^* face, which must favor the formation of η⁵-π-complexes of this radical. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1657–1662, September, 1999.     

Theoretical analysis of the internal rotation in aminoborane and borylphosphine

Using a recently proposed orbital deletion procedure and the block-localized wavefunction method, the rotational barriers in H₂BNH₂ and H₂BPH₂ are analyzed in terms of conjugation, hyperconjugation, steric effect and pyramidalization. With the zero-point energy corrections, the π-binding strengths in the planar H₂BNH₂ and H₂BPH₂ are both around 20 kcal/mol at the HF level using the 6-311+G** basis set. With the deactivation of the π atomic orbitals on the boron atom and the evolution from a planar structure to a 90°-twisted structure, the steric repulsion between the B‐H and the N‐H or P‐H is relieved and moreover, the negative hyperconjugation from the lone electron pair or pairs on the nitrogen or phosphorus atoms to the antibonding orbital ^χ* _B H ₂ of the BH₂ group stabilizes the twisted structure by 7.4(8.8) or 4.0(5.0) kcal/mol at the HF/6-31G*(6-311+G**) level. However, the repulsive interaction between the lone pair(s) and the two BH σ bonds is so prominent that the overall steric effect contributes 20.3(22.9) and 19.3(19.8) kcal/mol to the rotational barriers in H₂BNH₂ and H₂BPH₂ with the 6-31G*(6-311+G**) basis set. The present techniques and analyses may also give some clues to justify the parameterization in the empirical molecular mechanics methods. Received: 17 April 1998 / Accepted: 17 September 1998 / Published online: 1 February 1999     

Hypercoordinate atoms of second-row elements in dodecahedrane endohedral complexes

The energy characteristics and geometric parameters of the dodecahedrane endohedral complexes X@C₂₀H₂₀ (X = C⁴⁻, N³⁻, O²⁻, F⁻, Ne) were studied by the density functional theory B3LYP method with the 6-311G(d,p), 6-311+G(d,p), and 6-311G(df,p)) basis sets. In all structures the central atoms X are characterized by a coordination number of 20. The energy of formation of the complexes decreases in the order X = C⁴⁻, N³⁻, O²⁻, F⁻, Ne. The coordination number of the central atom remains unchanged upon adding Li⁺ counterions to anionic systems. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 824–830, May, 2007.     

Lithium 5-(2-diphenylphosphinoethyl)-1,2,3,4-tetramethylcyclopentadienide: Regioselectivity of alkylation of the tetramethylcyclopentadienide anion

Treatment of a mixture of isomeric (2-chloroethyl)-1,2,3,4-tetramethylcyclopentadienes with lithium diphenylphosphide leads to novel 4,5,6,7-tetramethylspiro[2,4]hepta-4,6-diene among the reaction products. The reaction of spiroheptadiene obtained with excess LiPPh₂ at elevated temperature affords lithium 5-(2-diphenylphosphinoethyl)-1,2,3,4-tetramethylcyclopentadienide in almost quantitative yield. the regioselectivity of alkylation of the tetramethylcyclopentadienide anion is estimated from quantum-chemical calculations performedab initio for C₅Mc₄H⁻. The full charges on the ring carbon atoms are determined within the framework of Bader's theory of atomic fragments in molecules. Translated fromIzvestiya Akademii Nauk. Seriya, Khimicheskaya, No. 5, pp. 986–989, may, 1998.