Complete sets of fragment compositions of structures for ir spectrum interpretation using a database. 4. Forming the most probable hypothesis about the structure of the unknown

This paper offers a new approach to forming hypotheses about the structure of organic compounds. The approach uses the fragment compositions of the structures selected by seeking analogs of the IR spectrum of the compound in the database. Even with “noise” fragments, the whole set of revealed fragments may be used for generating the possible structures of the unknown due to the variety of intersecting fragments in the selected structures. Forming the most plausible hypothesis about the structure of the compound is treated in detail, and the results are shown on particular examples. Translated fromZhumal Strukturnoi Khimii, Vol. 38, No. 4, pp. 785–794, July–August, 1997.     

Interpretation of IR spectra using complete sets of structure fragment compositions and an IR search system. 3. Analysis of large fragments

The results of identification of five-, six-, and seven-node fragments by the IR spectra of compounds are characterized by quantitative parameters: probability, reliability, and types of fragments. This analysis is carried out using the database containing more than 11,000 complete IR spectra and structures of organic compounds. It is analyzed how the fractions of correct fragments in the search result depend on the threshold occurrence and nonrandomness of fragment selection. Examples of statistical reliability of the revealed fragments are given. Translated fromZhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 369–379, March–April, 1997.     

Evaluation of the relationship between spectral and structural similarity in IR spectroscopy

Representation of a structural formula of a compound as a complete set of nonisomorphic k-vertex (2 ≤k≤7) connected fragments is used to evaluate the structural similarity of compounds. The spectra and structures of spectrally or structurally alike compounds are compared statistically using a database containing 32,000 IR spectra and structures. This study reveals some tendencies typical for both full IR spectra and their abbreviated versions represented by sets of most characteristic peaks. Applicability of IR databases to spectrum simulation for compounds with a specified structure is justified statistically. A method is proposed for evaluating the efficiency of a search algorithm selecting structural analogs of the compound from an IR database according to the query spectrum. Translated fromZhurnal Strukturnoi Khimii, Vol. 41, No. 2, pp. 379–390, March–April, 2000.     

Interpretation of IR spectra using complete sets of fragment compositions and an ir search system. 2. Determination of microfragment compositions of organic compounds

Identification of fragments of organic compounds by the IR spectra of the latter using complete sets of fragments and an IR database of more than 11,000 complete spectra and structures of organic compounds is treated. Probability and reliability of identification are estimated, and types of revealed fragments are examined. For many fragments, automatic identification is possible. The influence of the threshold and nonrandom occurrences of the fragment in the resulting list of structures on the efficiency of identification are considered. The reliability of identification is justified statistically. Translated fromZhurnal Struktumoi Khimii, Vol. 38, No. 1, pp. 155–166, January–February, 1997.     

Rotational isomerism of vinyl ethers of azines based on the data of IR spectroscopy and quantum-chemical AM1 calculations

The IR spectra of vinyl ethers of azines have two C=C stretching vibration bands of the vinyl group at 1620 and 1640 cm⁻¹, which correspond to thes-cis and nonplanars-trans conformers, respectively. According to the results of AM1 calculations, the hetaryl fragment and the vinyl group in thes-trans conformers of all the ethers under study are twisted out of the C−O−C plane by ∼30°. In thes-cis conformation, the angle of rotation of the heterocycle with respect to the vinyloxy group varies from 45 to 90°. The character of the change in the intensity of the v(C=C) absorption bands of the doublet under changes of the temperature indicates that thes-trans conformer is energetically favorable. The exception is 5-vinyloxyacridine for which thes-cis conformation is more favorable. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2439–2442, December, 1998.     

Fragmentary analysis of crystal structures of the Al,Ca-ferrite phase (Fe,Ca)4(Fe,Al)2CaFe(Al,Fe)2O14

The crystal structure of a somatic compound, Ca_7.12Fe_24.7Al_8.18O₅₆, is investigated by isolating spinel (Fe₃O₄) and pyroxene [Ca(Fe, Ca)(Al, Si)₂O₆] parent structures (fragments) from the homogeneous region of the Al, Ca-ferrite (CFA) phase. Crystal chemical factors leading to formation of these fragments and conditions for their conjugation are revealed. Polytypic modifications and structural homologs of the CFA phase are considered. It is suggested that somatic (fragmentary) structures be analyzed by determining an n-dimensional periodic fragment of the parent structure, isolating a subset of fragmentary structures from modular ones, and establishing common features of parent structure fragments in derivative fragmentary structures. Admissible chemical compositions of the CFA phase are analyzed; the role of the Si impurity in stabilizing structural homologs of the CFA phase is discussed. Baikov Institute of Metallurgy, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 5, pp. 84–96, September–October, 1994. Translated by L. Smolina     

Crystal and molecular structure of (1S,2S,4aS, 8aS)-N-(N-allyldiaminomethanethione)-1-(2-hydroxy-2,5,5,8a-tetramethyldecahydronaphthalenyl) acetamide

Crystal and molecular structure of a new homodrimanic compound (1S,2S,4aS, 8aS)-N-(N-allyldiaminomethanethione)-1-(2-hydroxy-2,5,5,8a-tetramethyldecahydronaphthalenyl) acetamide has been determined by X-ray diffraction analysis. The crystal is monoclinic, unit cell parameters are: a = 9.577(2) Å, b = 7.414(1) Å, c = 16.856(3) Å; β = 94.83(3)°, space group P2₁, Z = 2, of composition C₂₀H₃₅N₃O₂S. Two cyclohexan fragments have ordinary structure and chair-configuration typical of this compound class in homodrimanic skeleton. Ethanol molecule is located in the outer sphere. The withdrawal of carbon atoms from planar fragments of cyclohexan rings varies within the limits from 0.722(5) Å to − 0.634(5) Å. A dihedral angle between the mean-square planes of the latter equals 16.0(2)°, torsion angle (5)-(5)-(10)-(16) 171.0(1)° indicates their trans-joint. In the side non linear chain allyl group is connected to terminal nitrogen atom of thiosemicarbazide molecule. Intermolecular hydrogen bonds between carbonyl atom of acetamide fragment, ethanol molecule, and donor-acceptor groups of thiosemicarbazide moiety play the main part in crystal structure organization. Original Russian Text Copyright ? 2005 by E. P. Styngach, S. T. Malinovskii, L. P. Bets, L. A. Vlad, M. Gdanets, and F. Z. Makaev __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 46, No. 4, pp.785–789, July–August, 2005.     

Fragment calculation of electronic structures of polyatomic molecules in the ground state. II. A method of delocalized states of fragments

A fragment method is proposed to calculate the electronic structures of polyatomic molecules in the ground state. Localization and delocalization of the electronic states of molecular fragments are calculated simultaneously. The compact formulation of the method allows algorithmically efficient calculations of the electronic structures of interacting molecular fragments as well as of the whole molecules. V. I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Translated fromZhurnal Struktumoi Khimii, Vol. 36, No. 3, pp. 395–400, May–June, 1995. Translated by I. Izvekova     

Experimental and theoretical investigation of the electronic absorption spectra of 2-H(methyl, methylthio, phenyl)-3,4-dihydro-4-quinazolinylidenecyanoacetic ester

The effect of substituents (Me, SMe, Ph) in position 2 has been studied on the nature of the absorption bands of 2-H-3,4-dihydro-4-quinazolinylidenecyanoacetic esters and a very high sensitivity on the substituent has been detected for the short wave maxima. On the basis of data calculated by the ZINDO/S method the featureless long-wave absorption band was assigned to an electronic transition from HOMO to LUMO caused by charge transfer from fragments of the benzene ring and the N=C—N bond to the >C=C—C=O fragment. Dedicated to Professor L. I. Belen’kii on his 75th birthday. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 227–232, February, 2006.     

Quantum chemical investigation of the electronic structure of poly(2,4-dioxocyclobuta-1,3-diylidene)

The electronic structure of poly(2,4-dioxocyclobuta-1,3-diylidene) molecule is calculated by the semiempirical CNDO/S3 method. The calculated Wiberg indices and the additive occupancies of interatomic bonds determine the structural formula, which includes the C=C and C=O conjugated double bonds and corresponds to the name of the compound. Polarization of C=O bonds and πelectron conjugation do not lead to a zwitterionic structure with positive aromatic fourmembered cycles. The indices and occupancies of carboncarbon bonds 1– 3 and 2– 4 are σelectronic, negative, and negligibly small. The band structure corresponds to strong electronaccepting properties of the polymer; the MO of the bottom of the lowlying vacant band contains 2pπorbitals of all atoms of the compound. The occupied π-electronic bands do not overlap, and their widths are relatively small. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 5, pp. 781–786, September–October, 1998.     

Molecular architecture and conformation of macromolecules of novel polysilanes

Molecular-weight parameters of new silane homo- and copolymers were analyzed. For all polymers, theM _w values are close ((6.0–8.6)·10⁴), the curves of molecular weight distribution are unimodal, andM _w/M _n=2−2.5. Cyclic fragments or those containing the −C=C− groups make the major contribution to the polysilane chain rigidity. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2430–2433, December, 1998.     

Quantum-Chemical Study of Yb@C 60 , Yb@B 2 C 58 , and Gd@B 3 C 57 Molecules

Using the DFT PBE0/SDD method, the structural parameters of the Yb@η2-C60, Yb@η6-C60, Yb@η6-B2C58, and Gd@η6-B3C57 molecules, of corresponding anions (1,4-B2C58)2–, (1,3,5-B3C57)3–, and free radicals BkC60–k were calculated. Ytterbium is coordinated by the degraded C=C bond in the Yb@η2-C60 molecule and by the 1,4-diboratacyclohexa-1,3,5-triene fragment, in Yb@η6-B2C58. Symmetric substitution of three atoms of the cyclohexa-1,3,5-triene fragment leads to the formation of cyclopropane fragment, three 1,4-diboratacycloocta-1,3,5,7-tetraene fragments, and three boratacyclobutane fragments. The dipole moment μ(Yb@C60) is directed from the cavity center to Yb; the dipole moment μ(Gd@η6-B3C57) is greater and has the opposite direction (from B3 to Gd). The populations of the 4f-shells of the Yb and Gd atoms are conserved. The binding energy of the endoatom in Ln@BkC60–k is significantly higher than that in Yb@C60.     

A study of the interaction of dimethylcadmium and diethylcadmium with the Aerosil surface by IR spectroscopy and mass spectrometry

Dimethyl- and diethylcadmium interact with both free hydroxyl and siloxane groups of the Aerosil surface to form ≡Si-O-Cd-C≡ and ≡Si-H fragments. At 200 °C these structures undergo β-elimination to form surface ≡Si-O-Cd-H groups. It has been established that on heating to 600 °C, these groups decompose to afford metallic cadmium with the regeneration of the ≡Si-OH surface groups. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1717–1720, October, 1993.     

μ-Acyl Os3 clusters containing metallocenyl substituents and products of their protonation

Previously unknown μ-acyl osmium clusters containing simultaneously permethyl-metallocenyl and Os₃ cluster fragments were synthesized. The IR, UV, NMR (¹H and¹³C), and FAB-MS spectra were examined. Protonation of the clusters proceeds at the metal atom of the metallocenyl fragment. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 180–183, January, 1999.     

Effect of molecular and crystal structure ofN-naphthylurethanes (carbamates) on their IR spectra

A comparative analysis of the IR spectra in the region of 3000–400 cm⁻¹ of four urethanes (methyl-(N-(1-naphthyl) carbamate, ethyl-N-(1-naphthyl) carbamate, dimethyl-N,N′-(1,5-naphthylene) dicarbamate, and diethyl-N,N′-(1,5-naphthylene) dicarbamate) with known molecular and crystal structures was carried out. The assignment of the bands related to the vibrations of the urethane and naphthyl fragments was refined on the basis of the study of the crystalline samples, melts, solutions, and deuterated analogs. The effect of the degree of conjugation of the urethane group with the naphthalene ring on the Amide II vibration frequency in the crystals was shown. It was suggested that the stretching vibrations of the C(Ar)−N bond in naphthylurethanes (unlike aliphatic derivatives) make a considerable contribution to the Amide II vibration, while the planar deformation vibration of the N−H bond was proved to be more significant for Amide III than for Amide II. In addition, strong nonspecific intermolecular interactions in the crystal can weaken valent bonds. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 300–303, February, 1998.     

Methods and algorithms for predicting the properties of chemical compounds by common fragments of molecular graphs

Methods and algorithms for predicting the properties of chemical compounds by common fragments of their molecular graphs are described. The prediction algorithms are based on determination of a measure of structural proximity (distance) between molecular graphs, which depends on the size of their common fragment. The prediction procedure involves the following steps: partitioning the property classes of the training sample compounds into subclasses of structurally similar compounds; seeking structurally typical compounds and their fragments in each subclass; classifying control compounds according to their distances from the training sample compounds or fragments of classes; forming a set of essential fragments of samples potentially responsible for the properties exhibited by the compounds. The algorithms were successfully tested in the BACC system for analyzing and classifying biologically active compounds designed at the Institute of Mathematics, Siberian Branch, Russian Academy of Sciences. S. L. Sobolev Institute of Mathematics, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 1, pp. 113–125, January–February, 1998.     

Semiempirical andab initio study of the structure of the alumophenylsiloxane complex and its fragments

The structures, spectra, and electron density distributions of the alumophenylsiloxane (APS) complex and its fragments have been calculated using semiempirical (AM1) and ab initio (SCF/3-21G and SCF/6-31G^*) quantum chemical approximations. It has been shown that the local properties of the central fragment of alumophenylsiloxane, which is a slightly distorted tetrahedron AlO₄, are described with the (LiO)₂AlOBe(OH) cluster. M. V. Lomonosov Moscow State University. I. M. Gubkin State Academy of Oil and Gas. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 3, pp. 410–417, May–June, 1995. Translated by I. Izvekova     

6,6′-Bis(1,5-diazabicyclo[3.1.0]hexane)

The interaction of 1,3-diaminopropane with glyoxal and NaOCl in water at pH 9.5–10.5 afforded the previously unknown 6,6′-bis(1,5-diazabicyclo[3.1.0]hexane). According to X-ray diffraction data, both bicyclic fragments of the title compound adopt a boat conformation. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 623–625, March, 1999.     

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