Influence of steric and electronic effects of substituents on the molecular structures and conformational flexibility of 1,8-naphthalenedicarboximides

A series of 1,8-naphthalenedicarboximide derivatives containing substituents of different steric and electronic nature were studied by X-ray diffraction analysis.Ab initio quantumchemical calculations in the HF/3–21G approximation demonstrated the high conformational flexibility of the imide tetrahydro ring in the molecules of these compounds. The electronic nature of the substituents has no effect on the geometry and conformational flexibility of naphthalenedicarboximides due to weak conjugation between the imide and naphthalene fragments in the molecules. However, the steric effects of the bulky substituents noticeably affect the equilibrium geometry of the imide ring by increasing its conformational flexibility. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 68–73, January, 2000.     

Effect of electronic interactions between double bonds on the conformational flexibility of 1,4-cyclohexadiene

The electronic structure of 1,4-cyclohexadiene for various angles between the double bond planes has been calculated by the AM1 method. The effects of through-bond and through-space interactions, which result in flattening and unflattening, respectively, are oppositely directed. These effects are specified for various bending angles. In addition to steric factors, electronic factors affect the conformational flexibility of 1,4-cyclohexadiene.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1676–1677, September, 1994.     

Electronic structure and conformational flexibility of 1,4-dihydroazines and their 4-ylide derivatives

The conformational flexibility of 1,4-dihydropyridine, 1,4-dihydropyrimidine, 1,4-dihydropyridazine, 1,4-dihydro-1,3,5-triazine, and their 4-oxo, imino, and methylene derivatives was studied by the semiempirical quantum-chemical AM1 method. It was demonstrated that the replacement of the methylene group in the dihydroazine ring by the exocyclic double bond results only in an increase in the rigidity of the heterocycle rather than leading to a loss of its conformational flexibility. It was suggested that nonplanar conformations of rings in ylide derivatives are stabilized by the nonaromatic cyclic -system. Introduction of the exocyclic double bond does not cause a substantial change in the -electronic structure of the heterocycle. The aromaticity indicesI ₆ andI ₆() were calculated. The correlation between these indices and a change in the energy upon bending of the heterocycle was established.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No 8 pp 1938–1941, August, 1996.     

Molecular and electronic structures and conformational analysis of derivatives of 9-nitroanthracene, anionic σ-complexes

Potassium 10-methoxy-9-nitroanthracenide was studied by X-ray diffraction analysis. The central ring of the anthracene fragment adopts an asymmetrically flattened boat conformation. The bond lengths in the C(Ar)−C(NO₂)−C(Ar) fragment are indicative of the presence of conjugation between the π-systems of the benzene rings and the nitro group owing to a substantial contribution of theaci form to the structure of the nitro group. Quantum-chemical calculations of anionic σ-complexes of 9-nitroanthracene derivatives were performed. In all cases, the central ring adopts two conformations with the pseudoaxial and pseudoequatorial orientations of the substituents at the saturated C(10) atom, respectively. The relative stability of the conformers and the factors determining the stability were considered. The minima on the potential energy surface have a flattened shape in spite of relatively high barriers to the conformational transition (2–4 kcal mol⁻¹). The deviation of the C(Ar)−C(Ar)−C(sp³)−C(Ar) torsion angle from the equilibrium value by ±20° causes an increase in the energy of the anion by less than 1 kcal mol⁻¹. The effect of the substituents on the charge distribution was considered. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 438–443, March, 1998.     

Molecular structures of trinitromethane derivatives

The molecular structures of trinitromethane derivatives XC(NO₂)₃ (X = F, Cl, Br, NC, NF₂, N₃) were studied using the density functional approach. The rules for changing the configurations of substituents in these compounds were revealed. Acceptability of the method employed for the calculations of trinitromethane derivatives is discussed.     

Theoretical investigations on the geometric and electronic structures of phenylene-acetylene macrocycles.

The geometric and electronic structures of a series of conjugated macrocycles (phenylene-acetylene macrocycles, PAMs) have been studied theoretically with ab initio and semiempirical molecular orbital methods. The ab initio calculations at the HF/6-31G* level demonstrate that the model molecules may have a planar conformation. Bigger macrocycles, for example, 7PAM, 8PAM, and 9PAM, result in several energy minima. The boatlike conformation is the most energetically favored form. Based on the conformational analysis, a novel method for analyzing the ring-strain energy was proposed and used. In view of their potential applications as electronic materials, the electronic structures of a series of PAMs are also investigated. The LUMO-HOMO gaps of the planar PAMs show an odd-even difference behavior. In addition, the HOMOs of the planar species 3PAM, 5PAM, 7PAM, and 9PAM are doubly degenerated.     

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).     

Quantum-chemical study of the electronic structure and reactivity of 2-methyl-4H-thieno[3,2-b]pyrrole-5-carboxylic acid methyl ester

We have used the MNDO approximation to carry out a quantum-chemical study showing that the selectivity of acylation of 2-methyl-4H-thieno[3,2-b]pyrrole-5-carboxylic acid methyl ester under Friedel—Crafts reaction conditions in the presence of AlCl₃ depends more on the electron density distribution in the complexes than on the structure parameters. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 291–298, February, 2006.     

Structure and conformational flexibility of hexamethyldiperoxacyclononane

3,3,6,6,9,9-Hexamethyl-1,2,4,5-tetraoxacyclononane, one of the most thermally stable organic peroxides, has been studied by X-ray structural analysis. Possible conformations of this compound have been calculated by the molecular mechanics method.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 110–112, January, 1995.     

Study of the electronic structure of organogermanes with extended coordination sphere of germanium

The spatial and electronic structures of some organogermanes with extended coordination spheres of the metal were calculated using AMPAC and HYPER CHEM 4.0 program packages. Interatomic distances, bond angles, torsion angles, atomic charges, electron densities, bond orders, parameters of localized and canonical molecular orbitals,etc. were determined. The nature of the additional intramolecular O→Ge interaction in the molecules of these compounds was considered. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 383–387, March, 1998.     

The influence of substituents in the quinone dihydrocycle of anthroneylidene molecules on the polymer chain rigidity

The effect of substituents on the conformational rigidity of the six-membered dihydrocycle constituting the repeating unit of heterocyclic polymers was studied by the semiempirical AM1 method and by conformational analysis. The polymer rigidity can be controlled over a wide range by choosing appropriate substituents in the dihydrocycle. An original procedure was proposed for calculating the Kuhn segment of the copolymer taking into account the Boltzmann factor. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 797–801, May, 2000     

A CoMFA analysis with conformational propensity: An attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method

CoMFA analysis, a widely used 3D-QSAR method, has limitations to handle a set of SAR data containing diverse conformational flexibility since it does not explicitly include the conformational entropic effects into the analysis. Here, we present an attempt to incorporate the conformational entropy effects of a molecule into a 3D-QSAR analysis. Our attempt is based on the assumption that the conformational entropic loss of a ligand upon making a ligand-receptor complex is small if the ligand in an unbound state has a conformational propensity to adopt an active conformation in a complex state. For a QSAR analysis, this assumption was interpreted as follows: a potent ligand should have a higher conformational propensity to adopt an `active-conformation'-like structure in an unbound state than an inactive one. The conformational propensity value was defined as the populational ratio, N<sub>active</sub>/N<sub>stable</sub>, of the number of energetically stable conformers, N<sub>stable</sub>, to the number of `active-conformation'-like structures, N_active. The latter number was calculated by counting the number of conformers that satisfied the structural parameters deduced from the active conformation. A set of SAR data of imidazoleglycerol phosphate dehydratase inhibitors containing 20 molecules with different conformational flexibility was used as a training set for developing a 3D structure-activity relationship by a CoMFA analysis with the conformational propensity value. This resulted in a cross-validated squared correlation coefficient of the CoMFA model with the conformational propensity value (R ² _cross = 0.640) higher than that of the standard CoMFA model (R ² _cross = 0.431). Then we evaluated the quality of the CoMFA models by predicting the inhibitory activity for a new molecule.     

A theoretical study on three conformational structures of 2,6‐distyrylpyridine

Ab initio methods at the levels HF/cc‐pVDZ, HF/6‐31G(d,p), MP2/cc‐pVDZ, and MP2/6‐31G(d,p), as well as methods based on density functional theory (DFT) employing the hybrid functional B3LYP with the basis sets cc‐pVDZ and 6‐31G(d,p), have been applied to study the conformers of 2,6‐distyrylpyridine. Bond distances, bond angles, and dihedral angles have been calculated at the B3LYP level. The calculated values were in good agreement with those measured by X‐ray diffraction analysis of 2,6‐distyrylpyridine. The values calculated using the Hartree‐Fock method and second‐order perturbation theory (MP2) were inconsistent. The optimized lowest‐energy geometries were calculated from the reported X‐ray structural data by the B3LYP/cc‐pVDZ method. Three conformations, A, B, and C, were proposed for 2,6‐distyrylpyridine. Calculations at the three levels of theory indicated that conformation A was the most stable structure, with conformations C and B being higher in energy by 1.10 and 2.57 kcal/mol, respectively, using the same method and basis function. The same trend in the relative energies of the three possible conformations was observed at the two levels of theory and with the different basis sets employed. The reported X‐ray data were utilized to optimize total molecular energy of conformation A at the different calculation levels. The bond lengths, bond angles, and dihedral angles were then obtained from the optimized geometries by ab initio methods and by applying DFT using the two basis functions cc‐pVDZ and 6‐31G(d,p). The values were analyzed and compared. The calculated total energies, the relative energies of the molecular orbitals, the gap between them, and the dipole moment for each conformational structure proposed for 2,6‐distyrylpyridine are also reported. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

A molecular mechanics and semiempirical conformational analysis of the herbicide diuron inhibitor of photosystem II

The potential energy surface (PES) for the herbicide diuron (DCMU), a photosystem II inhibitor, has been extensively investigated using the quantum-mechanical semiempirical molecular orbital methods AM1 and PM3 and molecular mechanics method. A detailed conformational search has been carried out which revealed the occurrence of four genuine minimum energy structures. The relative stability of the conformers and rotational barriers to conformational interconversion were evaluated using distinct theoretical approaches. The results showed that thetrans form of the diuron molecule is more stable than thecis form in all methods, and so it may possibly be the biologically active isomer.     

Effect of benzannelation on the conformational flexibility of the rings in oxo, imino, and methylene derivatives of cyclohexa-1,4-diene

The effect of benzannelation on the equilibrium conformation and flexibility of the dihydrocycle in cyclohexa-1,4-dienone,para-quinone, and their imino and methylene analogs was studied by the semiempirical quantum-chemical AM1 method. The equilibrium conformations of the carbonyl derivatives are planar. In the imino- and methylene-substituted analogs, the dihydrocycle adopts a boat conformation due to repulsions between substituted analogs, the dihydrocycle adopts a boat conformation due to repulsions between the hydrogen atoms at the exocyclic double bond and in theperi positions of the benzene rings. Annelation of cyclohexa-2,5-dien-1-one andpara-quinone with benzene rings at the C=C double bonds causes an increase in the conformational flexibility of the partially hydrogenated ring owing to an increase in the bending strain in the first compound and a decrease in the conjugation between the carbonyl groups and the remaining part of the molecule in the second compound. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 388–390, March, 1998.     

Synthesis,molecular and crystal structures,and characteristic features of electronic structures of salicylamide-based B,Si-containing chelates

The reaction of 4-(2-hydroxybenzoyl)-2,2,6,6-tetramethyl-2,6-disilamorpholine with BF₃Et₂O afforded (O-B)-chelate 4-[2-(difluoroboroxy)benzoyl]-2,2,6,6-tetramethyl-2,6-disilamorpholine. Treatment of the latter with BF₃Et₂O or SOCl₂ gave rise to products of the disilamorpholine ring opening, viz., (O-B) chelate 2-(difluoroboroxy)-N,N-bis(dimethylfluorosilylmethyl)benzamide or 2-(difluoroboroxy)-N, N-bis(dimethylchlorosilylmethyl)benzamide, respectively. The structures of the compounds synthesized were confirmed by X-ray diffraction analysis and ¹H, ¹³C, and ²⁹Si NMR spectroscopy. High-precision X-ray diffraction study and quantum-chemical calculations demonstrated that the coordination OSi bond is absent in the two last-mentioned compounds.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1846–1853, September, 2004.     

Structure, thermochemistry, and conformational analysis of peroxides ROOR and hydroperoxides ROOH (R = Me, But, CF3)

The equilibrium structures, total energies, and harmonic frequencies of peroxides ROOR and ROOH (R = Me, Bu^t, CF₃) were calculated using the perturbation theory (MP4//MP2 method) and density functional approach (B3LYP) in the 6-31G(d,p) basis set. The conformational flexibility of peroxides under rotation about the O-O bond was investigated. It was found that the stable conformation of a peroxide molecule is determined by superposition of the destabilizing effects (repulsion between the lone electron pairs, steric hindrances) and the interaction of the nonbonding orbitals of oxygen atoms with the antibonding orbitals of the adjacent polar bonds. The latter effect stabilizes the nonplanar structure of the peroxide molecule. The role of orbital interactions in manifestation of the d-effect (distortion of the tetrahedral configuration of the X₃CO fragment of peroxide molecule) was revealed. The vibrational spectra of peroxides were calculated and compared with the experimental data. The potential energy distribution over normal vibrations was analyzed. The enthalpies of formation and the bond strengths in the molecules of compounds examined were calculated in the framework of the isodesmic reaction approach.     

Conformational analysis and steric effects of substituents in derivatives of 3-oxo-, 3-imino-, and 3-methylenecyclohexene

The equilibrium conformations and the inversion barriers of the rings in 3-oxo-, 3-imino-, 3-methylenecyclohexenes and in their methyl,tert-butyl, and phenyl derivatives were calculated by molecular mechanics. The unsubstituted molecules adopt a sofa conformation. The nonbonded interactions between substituents at positions 2 and 4 and the exocyclic double bond lead to a change in the conformation of the ring to a half-chair. The effect is enhanced as the volume of the substituent increases in the series of the oxo, imino, and methylene derivatives. Substituents at other positions of the ring affect only slightly the equilibrium conformation. The results of calculations were confirmed by X-ray structural analysis of 2-(4-benzoyloxybenzyl)-6-isopropyl-3-methylcyclohex-2-enone. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1995–2000, November, 1997.     

The steric and electronic effects of aliphatic fluoroalkyl groups

Ab initio calculations were performed on 18 fluorinated and unfluorinated alcohols at the B3LYP and HF levels with the 6-311G^∗∗ basis set. Molar volumes of the alcohols were computed at each level and averaged to produce a scale of relative size. From this, various isosteric replacements of potential use in drug design were suggested: ethyl by FCH₂CH₂ or HCF₂CH₂, propyl by CF₃CH₂, isopropyl by CF₃(CH₃)CH or (FCH₂)₂CH, isobutyl or t-butyl by (CF₃)₂CH, and 3-methyl-2-butyl by CF₃(CH₃)₂C. Calculation of the charge on oxygen and the Wiberg index of the CO bond allowed an electronegativity scale to be constructed for the fluoroalkyl groups. Electronegativity decreased in the order: (CF₃)₃C>(CF₃)₂CH>C₂F₅CH₂>CF₃CH₂>CH₃(CF₃)₂C>HCF₂CH₂>CF₃(CH₃)CH>(FCH₂)₂CH>FCH₂CH₂>CF₃(CH₃)₂C. This ranking agreed with literature acid dissociation data for the alcohols studied.     

Substituent steric effects and molecular structure of anionic σ-complexes of 5,7-dinitroquinoline

Molecular structure and conformational flexibility of Meisenheimer complexes of 5,7-dinitroquinoline derivatives are studied experimentally using X-ray diffraction and theoretically by semi-empirical AM1 calculations. The dihydrocycle is found to possess high conformational flexibility in all anionic σ-complexes considered. Substituent steric effects at the saturated carbon atom of the anion significantly influence the equilibrium conformation and deformability of the partially hydrogenated ring. An increase of the bending strain does not cause considerable changes of the conformational characteristics of ring. In the crystal phase, the geometry of the anion depends essentially on the crystal structure and on the cation coordination.