Fragment calculation of electronic structures of polyatomic molecules in the ground state. I. A method of intermediate fragment

A method is proposed for fragment calculation of electronic structures of polyatomic molecules in the ground state. The wave function of a molecule in the ground state in single-determinantal representation of a closed shell is employed. The concise formulation allows efficient calculation of the electronic structures of polyatomic molecules taking into account possible charge transfer between interacting molecular fragments. V.I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Translated fromZhurnal Struktumoi Khimii, Vol. 36, No. 3, pp. 387–394, May–June, 1995. Translated by I. Izvekova     

Quantitative prediction of absorption maxima in the electronic spectra of unsaturated compounds: Extrapolation from fragments to molecules in quantum chemical calculations

The possibility of quantitative prediction of maxima in the electronic absorption spectra of unsaturated organic compounds is studied by the Pariser-Parr-Pople method with fitted parameters. The quantum chemical methods are classified according to the type of extrapolation: from elementary particles (physical constants) to molecules, from atoms to molecules, and from fragments to molecules. N. G. Chernyshevskii Saratov State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 6, pp. 1016–1022, November–December, 1996. Translated by I. Izvekova     

Experimental structural and conformational studies of carbonyl molecules in the ground and lower excited states

Experimental data (obtained by the authors and taken from the literature) on the structure and conformations of carbonyl molecules in the ground and lower excited electronic states are presented. The structure of carbonyl fragments, the orientation of substituent groups, the energy of the molecules in excited states, and the potential functions of the internal rotation and inversion are considered. The structural similarities of the molecules are discussed. M. V. Lomonosov Moscow State University, Chemical Faculty. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 269–285, March–April, 1995. Translated by I. Izvekova     

Algorithm for determination of the local similarity of molecules

An algorithm for seeking common structural fragments in compounds of different classes is developed. The algorithm allows for the molecular geometry and atomic characteristics, It may be used for recognition of compounds with properties associated with the local similarity of molecules such as ligand complementarity to a receptor. An example of seeking common structural elements for nondrug analgesics (para-acetamidophenol, acetylsalicylic acid, and amidopyrine) is given. I. I. Polzunov Altai State Technical University. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 6, pp. 1083–1087, November–December, 1995. Translated by L. Smolina     

Parametric method in the theory of vibronic spectra of complex molecules. Excited state structure and fluorescence spectrum of stilbene

The parameters of the adiabatic model of the stilbene molecule in the excited state and the vibrational structure of the fluorescence spectrum are calculated by the parametric method of the theory of vibronic spectra of complex molecules. The first and second orders of theory are used. The molecular models are constructed by the fragment method. Satisfactory agreement with experiment is obtained. The parameters of molecular fragments are shown to be highly transferable. The model and the spectrum max be refined in the second order of theory using only one additional parameter for CCC angles (optimal values were obtained). The parametric method under discussion makes it possible to predict variations of structural parameters due to excitation and to calculate the vibrational structure of the electronic spectra of complex molecules, including characteristic variations of the spectra in series of related molecules (stilbene-di-phenylpolyenes). This method surpasses all previous procedures (in particular, the correlation method) in completeness and accuracy of results. Translated fromZhurnal Strukturnoi Khinii, Vol. 41, No. 2, pp. 369–378, March–April, 2000.     

Parametric method for computing the structure of the excited states and the vibronic spectra of complex molecules. Absorption and fluorescence spectra of perylene

The structures of the perylene molecule in the first excited 1¹ 0B_2u state and the band shape (vibrational structure) of its fluorescence and absorption spectra are computed by the parametric method. A fragmentary approach and the molecular fragments H/1C= with the parameters obtained for acenes and polyenes are used to form molecular models in the excited state. It is shown that a model that corresponds to the choice of fragments with the parameters of acenes is the most optimal. The theoretical spectra satisfactorily reproduce both qualitatively and quantitatively, the basic specific features of the vibrational structure of the experimental spectra. Calculation results show high degree of transfer of the parameters of the method in a series of related molecules not only for acenes with “linear” arrangement of the rings (benzene, naphthalene, anthracene, etc.) but also for more complex structures (perylene). It is shown that the parametric method developed is efficient for predicting the vibronic spectra and the structure of the excited states of complex molecules. Translated fromZhurnal Struktumoi Khimii, Vol.40, No. 2, pp. 242–250, March–April, 1999.     

Phase transitions,conformational lability,and intermolecular interactions in alkoxycyanobiphenyls

Vibrational spectroscopy methods (IR absorption, Raman scattering, calculations) were used to study changes in molecular structures of alkoxycyanobiphenyls during phase transitions. The spectra were measured in the 33–3500 cm⁻¹ region at temperatures of 100–450 K. The temperature dependences of the IR bands that correspond to the noncharacteristic vibrations of molecular fragments between the phenyl rings and the alkyl radicals point to the conformational polymorphism of these molecules. An analysis of the Raman bands corresponding to the characteristic vibrations of the C−H bonds of alkyl radicals [q(CH)], the C−H and C−C bonds of phenyl rings [q(CH) and Q(CC)], and the CN bonds of the cyano groups [Q(CN)] suggests significant intermolecular interactions. The conformational lability and intermolecular interactions are associated with differences in molecular packing in the substances of this homologous series. Saratov State University. Institute of Solid State Physics, Rostov State University. Institute of Physics, Uzbekistan Academy of Sciences. Samarkand State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 5, pp. 814–822, September–October, 1995. Translated by I. Izvekova     

Analysis of molecular chirality using the lattice model of spatial structure

A lattice model of the spatial structure of a molecule is suggested. A broken line is constructed to characterize atoms and molecular fragments. The line is a spiral (left or right) embracing the whole lattice containing the molecule. The mutual arrangement of molecular fragments along the broken line is described by a molecular code. The code contains all the necessary information about molecular conformation and configuration in compressed form. Comparing the codes makes it possible to evaluate the structural similarity and dissimilarity of molecules. For example, one can easily estimate the chirality level for enantiomers. Using this approach is demonstrated on various model structures. A. V. Bogatskii Physicochemical Institute, Ukrainian Academy of Sciences. Odessa State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 3, pp. 541–546, May–June, 1998. This work was supported by INTAS grant INTAS-UA 95-0060.     

Force fields of halide-substituted methane derivatives

The paper describes methods for determining the force fields of large sets of molecules which share the common property that in their constituent groups of molecules the equivalent force constants always change monotonically with the properties of substituent atoms belonging to the same subgroup of the periodic table. The force fields of the CH_4−nX_n (n=0–4, X=F, Cl, Br, I) molecules of the methane series are obtained. The applications of these force fields are discussed. In particular, they can serve as a basis for a data bank of the force fields of fragments suitable for constructing the force fields of more complex molecules. Russian Scientific Center “Applied Chemistry”, St. Petersburg. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 250–256, March–April, 1996. Translated by I. Izvekova     

Matrix method of conformational optimization. Application to cyclic and polyhedral water clusters

A matrix method for conformational optimization of quasi-one-dimensional molecular structures is suggested. The method is used to determine cyclic and polyhedral configurations of water clusters with the maximal number of stable trans-conformations of molecular pairs forming hydrogen bonds. Institute of Earth Cryosphere, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 1, pp. 107–115, January–February, 1996 Translated by L. Smolina     

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.     

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.     

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.     

Data selection for structure generation in structure elucidation systems using molecular spectroscopy databases

Data selection techniques are considered for structure generation in structure elucidation systems using molecular spectroscopy databases. The starting data are sets of microfragments and connected structural fragments obtained from computer-aided analysis of mass, IR, and NMR spectra. Selection of fragments that do not isomorphically fit in larger fragments mostly leads to correct results with fewer output structures anddemands less computer time. Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 2, pp. 46–53, March–April, 1994. Translated by L. Smolina     

Energy characteristics of structures in aqueous solutions of sucrose

Structures arising in sucrose solutions of various concentrations are modeled. A computer simulation by the molecular mechanics method proves the existence of three aqueous sucrose structures, which depends on the ratio between water and sucrose molecules. The calculated data are in good agreement with the experimental results obtained by different methods. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 5, pp. 864–871, September–October, 1998.     

Adiabatic theory of the vibronic states of the topological isomers of polyatomic molecules. Calculation of optimal conditions for optical stimulation of isomeric rearrangements

The problem of calculating the probability of optical transitions between the topological isomers of polyatomic molecules is considered. It is shown that the adiabatic approximation can be extended to this case. It is suggested that under certain conditions an “unoccupied” isomeric state can be populated or light-stimulated accumulation of one isomer can be achieved. This opens up prospects for designing molecular elements for computer memory. V. I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 6, pp. 994–1005, November–December, 1996. Translated by I. Izvekova     

Semiempirical parametric method in the theory of vibronic spectra of polyatomic molecules

A semiempirical parametric method for calculating the vibrational structure of the electronic spectra of polyatomic molecules is developed; the method is based on the adiabatic molecular model and uses a single parametric system for all excited states. Within the model approach, simplified analytical expressions for potential surface variation during molecular excitation are derived; the expressions include the principal terms according to the order of magnitude. The first and second derivatives of Coulomb and resonance one-electron integrals with respect to natural coordinates in a basis set of hybrid atomic orbitals are used as parameters. It is shown that the parameters possess distinct locality, are transferable in molecular series, and may be easily ranked according to absolute values; describing a molecular model requires few most significant parameters. Excitation-induced variations of potential surfaces and absorption spectra of some molecules (butadiene, hexatriene, octatetraene) are calculated using only two parameters, which are the same for all molecules. The results of calculations are in good agreement with the experimental data. Supported by RFFR grant No. 95-03-08808. V.I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Translated fromZhumal Struckturnoi Khimii, Vol. 37, No. 3, pp. 419–431, May–June, 1996.     

Electronic absorption spectrum of pyridine N-oxide in the gas phase. General characterization

The full electronic absorption spectrum of pyridine N-oxide vapor in the near ultraviolet region has been obtained. The vibronic structure has been analyzed in detail. The four absorption bands, which are observed at 341, 290, 228, and 217 nm, correspond to four 0–0 vibronic transitions. The spectrum is interpreted in terms of the CNDO/S method. The symmetry of the vibrations that exhibit activity due to the Herzberg-Teller effect in different electronic states has been studied. N. G. Chernyshevskii Saratov State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 345–349, March–April, 1995. Translated by I. Izvekova     

Ordinary organic crystal chemistry. Interpretation of the most probable homomolecular structures

For homomolecular organic crystals, most characteristic types of molecular arrangement corresponding to most widespread structural classes and subclasses are named and interpreted. These characteristic structural variants cover about 70% of crystal substances consisting of chemically identical molecules. Examples of crystal structures are cited to illustrate the structural laws of organic crystals; the structures are given as easily perceptible representations taken from the album “Structure of Organic Crystals.” An important structural feature of ordinary molecular crystals is coexistence of molecules with four or two different orientations (64 and 28%, respectively). Basic notions and approaches of modern organic crystal chemistry are briefly defined. M. V. Lomonosov Moscow State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 1, pp. 126–152, January–February, 1998. This work was supported by RFFR grant No. 96-03-32455.     

MNDO study of the electronic structure and potential energy surface of fluorinated singlet cyclopentadienyl and methylcyclopentadienyl cations

The electronic structure and geometry of some symmetric fluorinated singlet cyclopentadienyl and methylcyclopentadienyl cations are studied by the MNDO method. The structure of the potential energy surface (PES), which is a pseudorotation surface, is investigated. Extreme points of the PES, determining the PES barrier, correspond to structures with inverted frontier molecular orbitals. (Anti)aromaticity of fluorinated methylcyclopentadienyl cations is estimated using the Dewar-Breslow criterion. Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 6, pp. 1023–1030, November–December, 1996. Translated by L. Smolina