Conformational analysis of 2-methyl-5-nitro-1,3,2-dioxaborinane

Quantum-chemical methods HF/6-31G(d), HF/6-31+G(d), MP2/6-31G(d)//HF/6-31G(d), and MP2/6-31+G(d)//HF/6-31+G(d) were used to investigate the conformational isomerization of 2-methyl-5-nitro-1,3,2-dioxaborinane. It has been shown that a potential energy surface of this compound includes two minima: an axial form of semi-chair and equatorial sofa together with a transition state belonging to the conformation of 2,5-twist-form. A comparison between experimental NMR ¹H and theoretical vicinal coupling constants was used to determine the quantitative conformational composition of cyclic boric acid ester and a value of ΔG ⁰ for nitro group at the ring carbon atom C⁵ in CCl₄ and C₆D₅NO₂ solutions.     

Special Features of the Geometry of the 2,2,2,4,4,4-Hexachloro-1,3-dimethyl-1,3-diaza-2,4-diphosphetane Molecule and Its Electron Distribution According to Data of ab initio Calculations

The results of a nonempirical calculation of the 2,2,2,4,4,4-hexachloro-1,3-dimethyl-1,3-diaza-2,4-diphosphetane (Cl₃PNCH₃)₂ molecule by the RHF 6-31G(d) method are in agreement with the data of X-ray structural analysis of this compound. Calculated ³⁵Cl NQR frequencies for axial and equatorial chlorine atoms are close to the experimental values. The population of the orbitals of the lone electron pairs and the p orbitals of the equatorial Cl atoms were significantly lower than those of the axial atoms. Among the MO there was no MO corresponding to a three-center bond involving a P atom and axial Cl and N atoms.     

Electronic and Spatial Structure of Piperidine and Its Substituted Derivatives from the Results of ab initio Calculations

The results of non empirical quantum-chemical calculations using the RHF/6-31G(d) and MP2/6-31G(d) methods do not agree with proposals for the axial position of the H atom on the N atom in the piperidine molecule. According to RHF/6-31G(d) calculations for the N-methylpiperidine molecule and its chloro-substituted derivatives an equatorially placed methyl group is energetically more favored than an axial. The axial C-Cl and C-H bonds in these molecules are longer than the equatorial. The ³⁵ Cl NQR frequencies for the axial Cl atoms are lower than the equatorial. The ³⁵ Cl NQR frequency of the axial chlorine atom in 2-chloro-1-methylpiperidine is anomalously low. This is chiefly due to the high population density of its p σ-orbital and this is a result of the polarization of the C-Cl bond via the N atom unshared electron pair directly through the field. The effect of a similar unshared electron pair on the parameters of the C-Cl bond in the ClCH₂NH₂ molecule has been studied by the RHF/6-31(g) method for different angles of rotation of the ClCH₂ group around the C-N bond. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 1044–1052, July, 2005.     

Quantum-chemical study of chlorophosphoranes: I. Structure of the (C<Subscript>6</Subscript>H<Subscript>5</Subscript>)<Subscript>2</Subscript>PCl<Subscript>3</Subscript> molecule in gaseous and crystalline states

The quantum-chemical calculations of the (C₆H₅)₂PCl₃ molecule were performed by the methods RHF/6-31G(d) and MP2/6-31G(d) with complete and partial optimization of its geometry. The results of calculations were used for evaluating the NQR frequencies of ³⁵Cl and the parameters of asymmetry of the of electric field gradient on the ³⁵Cl nuclei of this molecule. According to the results of calculations with the partial optimization of geometry and to the experimental data of ³⁵Cl NQR the bond lengths were found of central atom P in the solid state of this compound. The mutual influence of its axial and equatorial bonds was studied. It is shown that in chlorophosphoranes the ³⁵Cl NQR frequencies of the axial and equatorial chlorine atoms decrease with the decrease in the bond lengths of phosphorus atom.     

Quantum-chemical study of chlorophosphoranes: II. Structure of molecules of (Cl2)aP(ClnX3?n)e series, and mutual influence of axial and equatorial substituents

The quantum-chemical calculations of the (C₆H₅)₂PCl₃ molecule were performed by the methods RHF/6-31G(d) and MP2/6-31G(d) with complete and partial optimization of its geometry. The results of calculations were used for evaluating the NQR frequencies of ³⁵Cl and the parameters of asymmetry of the of electric field gradient on the ³⁵Cl nuclei of this molecule. According to the results of calculations with the partial optimization of geometry and to the experimental data of ³⁵Cl NQR the bond lengths were found of central atom P in the solid state of this compound. The mutual influence of its axial and equatorial bonds was studied. It is shown that in chlorophosphoranes the ³⁵Cl NQR frequencies of the axial and equatorial chlorine atoms decrease with the decrease in the bond lengths of phosphorus atom.     

Conformational analysis of stereoisomers of 2,4-dimethyl-5-isopropyl-1,3,2-dioxaborinane

The investigation of conformation conversions of cis- and trans-isomers of 2,4-dimethyl-5-isopropyl-1,3,2-dioxaborinane using ab initio quantum-chemical approximation HF/6-31G(d) and the hybrid DFT-method PBE/3z showed that the routes of the transformations presuppose an equilibrium between sofa conformers with the different orientation of substituents at the atoms C⁴ and C⁵ of the ring that convert into each other through transition states corresponding to the equatorial and axial conformations of the 2,5-twist form. Based on experimental data of ¹H NMR spectra and calculated vicinal spin-spin coupling constants the quantitative conformational composition of cis- and trans-isomers was established and also the ΔG^o value of the conformation equilibrium was determined.     

Conformational isomerization of 4-methyl-1,3-dioxane

The whole possible course of conformational isomerization of 4-methyl-1,3-dioxane has been established using empirical (MM+) and nonempirical [STO-3G, 3-21G, 6-31G(d) and 6-31G(d,p)] approximations within the limits of the Hartree-Fock method. It was shown that the potential energy surface of this compound contains a principal (equatorial chair conformer) and local minima corresponding to the axial chair conformer and series flexible forms.     

Mutual influence of axial and equatorial P-Cl bonds in the molecular forms of pentachlorophosphorane,their lengths in gaseous and crystalline states

The quantum-chemical calculations by RHF/6-31G(d), MR2/6-31G(d) and MP2/6-31+G(d) methods of molecular forms of pentachlorophosphorane with the complete geometry optimization at the different lengths of P-Cl bonds are performed. The results of the calculations are used for estimation of respective ³⁵Cl NQR frequencies. The lengths of axial (2.05 Å) and equatorial (2.01 Å) P-Cl bonds are found, when the calculated NQR frequencies of Cl atoms practically coincide with the obtained experimentally at 77 K. These bonds are a little shorter than in the gaseous state of the matter. In contrast to the ratio of the lengths of the experimental P-Cl bonds and NQR frequencies of respective Cl atoms, at the use of increased lengths of these bonds in the quantum-chemical calculations of the molecule, the ³⁵Cl NQR frequencies of Cl atoms calculated from the results of these calculations, increase. Therewith, the change in the length of the equatorial P-Cl bonds with unchanged length of axial bonds leads to a significantly greater change in the NQR frequencies of axial chloroine atoms than of the equatorial, and vice versa.     

Conformational analysis of 2,2-dimethyl-5-alkyl-1,3-dioxa-2-silacyclohexanes

Study of conformational isomerization of 2,2-dimethyl-5-alkyl-1,3-dioxa-2-silacyclohexanes using quantum-chemical HF/6-31G(d) and PBE/3z approximations showed that its route involves an equilibrium between the chair conformers with different orientation of substituent at C⁵ ring atom and proceeds through a transition state corresponding to the 2,5-twist conformation. Molecular dynamics method showed that at room temperature this conformation transforms into the equatorial or axial chair conformers through 1,4-twist or sofa forms. Based on the experimental and theoretical values of vicinal ¹H NMR coupling constants we determined quantitative conformational composition of the molecules of these compounds and the values of ??G ⁰ of the conformational equilibrium.     

Nonempirical study on the potential energy surface of 5-methyl-1,3-dioxane

Quantum-chemical study on the potential energy surface of 5-methyl-1,3-dioxane at the nonempirical RHF//STO-3G, RHF//3-21G, RHF//6-31G(d), RHF//6-31G(d,p), and MP2//6-31G(d,p) levels of theory revealed two energy-equivalent paths of conformational transformation of the equatorial and axial chair conformers. Potential barriers to these processes were estimated. The δG° value for the methyl substituent on C⁵ in 1,3-dioxane ring, determined on the basis of the experimental (NMR) and calculated vicinal 1H-1H coupling constants, was very consistent with published data     

Quantum-chemical investigation of conformational characteristics of the complex of 2-methyl-1,3,2-dioxaborinane with dimethyl ether

With the help of the quantum-chemical approximation MP2/6-31G(d)//HF/6-31G(d) conformational characteristics were investigated of donor-acceptor associate of 2-methyl-1,3,2-dioxaborinane with dimethyl ether, 1:1. The character of the conformational isomerization of the adduct differs from that established for the proper cyclic boric ester and involves an interconversion between two conformers nondegenerate by the energy. The stability of the associate under study is comparable with those of the molecular complexes of 2-methyl-1,3,2-dioxaborinane with water and methanol.     

Conformational analysis of 2,4-dialkyl-1,3,2-dioxaborinanes

Computer modeling using the quantum-chemical empirical MM+ method and nonempirical RHF//6-31G(d), MP2//6-31G(d), and, in individual cases, RHF//3-21G methods was employed to study the potential energy surface of 2,4-dialkyl-1,3,2-dioxaborinanes. The optimal geometry and ¹H NMR spectral data gave values for ∆G ⁰ of the methyl and hexyl substituents at C-4 of the heterocyclic ring equal to 0.6 and 1.6 kcal/mol, respectively.     

Cyclic oligothiophenes: novel organic materials and models for polythiophene. A theoretical study

Cyclic oligothiophenes (CnT, n = 6-30, even only) in syn- and anti-conformations are studied theoretically at the B3LYP/6-31G(d) level of theory. Strain energies, ionization potentials, HOMO-LUMO gaps, bond length alternations, NICS values, and IR and Raman spectra have been studied. The properties of anti-conformers change systematically with increasing ring size and were studied in detail in neutral, radical cation, and dication forms. In syn-conformation, the oligomers lose their nearly planar ring shape and bend significantly for n > 14, and thus properties cannot be related to ring size. The HOMO-LUMO gap in C14T-syn is even lower than polythiopehene. IR and Raman spectra calculated at the B3LYP/6-31G(d) level are used to differentiate syn- from anti-conformations. The properties of cyclic oligomers are compared to those of the linear system, and cyclic oligothiophenes are revealed as good models for polythiophene. To assist the experimental study of known cyclic oligomers having dibutyl substituents on alternate thiophene rings, the corresponding dimethyl-substituted oligomers are also studied. The experimentally evaluated HOMO-LUMO gaps for alternately dibutyl-substituted cyclic oligomers match the calculated values; however, they are significantly higher than those of the unsubstituted analogues.     

<Emphasis Type="Italic">Ab Initio</Emphasis> calculations of 3-(trichlorogermyl)propanoylamide structure and nature of its Ge←O coordination bond

Calculations of 3-(trichlorogermyl)propanoylamide molecule containing a Ge←O coordination bond were performed by RHF/6-31G(d) method with full and partial geometry optimization. Its total energy 2.22 kcal mol⁻¹ is lower than that of the molecule with tetracoordinated germanium atoms. Germanium and oxygen atoms initiate the formation of a coordination Ge←O bond in this molecule and are conductors of the electron density transfer from the atoms nearest to the oxygen on the atoms of the germanium coordination polyhedron. No electron density transfer occurs from the oxygen atom to germanium. Upon decrease in the Ge...O distance the axial Ge-Cl bond is polarized much stronger than the equatorial bonds. In the crystalline state of the substance these molecules are fixed in an energetically unfavorable structure.     

Conformation of N‐methyl‐4‐piperidyl 2,4‐dinitrobenzoate

The crystal structure of N‐methyl‐4‐piperidyl 2,4‐di­nitro­benzoate, C₁₃H₁₅N₃O₆, (I), at 130 (2) K reveals that, in the solid state, the mol­ecule exists in the equatorial conformation, (Ieq). Thus, the through‐bond interaction present in the axial conformation, (Iax), is not strong enough to overcome the syn–diaxial interactions between the axial methyl substituent and the axial H atoms on the two piperidyl ring C atoms either side of the ester‐linked ring C atom. The carboxyl­ate group in (I) is orthogonal to the aromatic ring, in contrast with other 2,4‐di­nitro­benzoates, which are coplanar. The piperidyl–ester C—O bond distance is 1.467 (3) Å, which is actually shorter than other equatorial cyclo­hexyl–ester C—O distances. This shorter piperidyl–ester C—O bond distance is due to the reduced electron demand of the orthogonal ester group.     

Conformational analysis of 5-methyl- and 2,2,5-trimethyl-1,3-dithianes

Conformational isomerization of 5-methyl- and 2,2,5-trimethyl-1,3-dithianes was studied using quantum-chemical HF/6-31G(d), HF/pVDZ, and PBE/3z approximations. The potential energy surface of molecules of both compounds is shown to contain the main minimum corresponding to the equatorial chair conformer C-5e. The calculated potential barriers of the conformational isomerization were found. Based on the experimental (¹H NMR) and theoretical vicinal coupling constants the ??G ⁰ values were determined of the methyl group at the ring C⁵ atom. The reasons for the distinctions between the values of this parameter from the ??G ⁰, obtained by energy minimizations of the equatorial and axial chair conformers are discussed.     

Redox potentials of dopamine and its supramolecular complex with aspartic acid

Dopamine (DA) can be oxidized to dopamine quinone (DAquinone) through a one-step, two-electron redox reaction. The electron transfer property of DA and its supramolecular complex with aspartic acid (Asp) has been investigated by the theoretical calculations. We calculated the standard redox potentials (E ^o) of DA/DAquinone at the MP2/6-31G(d,p)//B3LYP/6-31G(d,p), MP2/6-31+G(d,p)//B3LYP/6-31+G(d,p), MP2/6-31G(d,p)//B3LYP/6-311G(d,p), and MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) levels. Comparing the experimental value, the redox potentials of DA/DAquinone obtained at MP2//B3LYP/6-311G(d,p) and MP2//B3LYP/6-311+G(d,p) levels can be considered as the upper and lower estimates. DA can form supramolecular complex (DA-Asp) with Asp through hydrogen bond (H-bond). Therefore, the values of 0.631 and 0.628 V obtained at MP2//B3LYP/6-311G(d,p) and MP2//B3LYP/6-311+G(d,p) levels for DA-Asp/DAquinone-Asp can be proposed as the upper and lower estimates of a probable (about 0.630 V) value of the corresponding redox potential. The calculated E ^o values of DA-Asp/DAquinone-Asp at the four theoretical levels are upper than those of DA/DAquinone, which indicates that the formation of H-bonds weaken the electron-donating ability of DA.     

Ab initio study of force constants and intensities of 1,3,5-trioxane

The structure, vibrational force constants and infrared and Raman intensities have been calculated for 1,3,5-trioxane using a 3-21G basis set. These results have been used to identify some possible inaccuracies in experimental diffraction based structures and in vibrational assignments. It is demonstrated that there is a marked contrast between the trends in the vibrational force constants and in the King's effective atomic charges of the axial and equatorial CH bonds in the series cyclohexane, 1,4-dioxane and 1,3,5-trioxane. The axial CH stretching force constant decreases by 0.04 mdyne Å⁻¹ for each adjacent oxygen atom, whereas that of the equatorial CH bond increases by 0.15 mdyne Å⁻¹ per oxygen. In trioxane the effective atomic charge of the axial hydrogen is twice that of the equatorial. Atomic polar tensors are calculated in a bond oriented frame, and the effect of the oxygens on CH stretching and bending mode intensities discussed. Some properties are also calculated using the 4-31G basis.     

Geminal interaction and “anomeric effect”

Quantum-chemical calculations by the methods of RHF/6-31G(d) and MP2/6-31+G(d) show equal ratio of the lengths of axial and equatorial bonds and electron density on the atoms forming them in cyclohexane and its mono derivatives and in six-membered heterocyclic molecules as well. This feature is due to the interaction of atoms in the chair form of these molecules regardless of the presence in them of a heteroatom. Introducing heteroatom to a cyclohexane ring leads only to increase in the difference between axial and equatorial bonds. This equation excludes the possibility to ascribe the elongation of axial bonds and increase in the electron density on atoms forming them in the heterocyclic molecules to the p,σ*-conjugation of the lone electron pair of the ring heteroatom with the antibonding orbital of the axial bond. Features of molecular geometry defined by the mutual influence of atoms in them, including inductive and non-inductive interaction of geminal atoms in triatomic groups Y-Z-M, result in energetic preference of gauche conformations of these molecules and “anomeric effect” in them.     

Synthesis of thietanyl-substituted pyrimidine-2,4(1H,3H)-dions

Reactions of 6-methylpyrimidine-2,4(1H,3H)-dione or 5-hydroxy-6-methyl-pyrimidine-2,4(1H,3H)-dione with 2-chloromethylthiirane afforded the corresponding substituted 1-(thietan-3-yl)pyrimidine-2,4(1H,3H)-diones. The calculations in the framework of approximations PBE/3z, B3LYP/6-31G++(d,p) and MP2/6-31G++(d,p) showed that the alkylation occurred at the atom N¹ of the pyrimidine ring.