Complete sets of structure fragments for interpreting IR spectra using IR databases

This paper studies the possibility of revealing various fragments (not given beforehand) in a structure by analyzing the structures selected from the database as a result of a retrieval by the IR spectrum of the compound; the fragments range from those with two nodes (e.g., C=O, C=C) to those with some limited number of connected nodes. It is shown that complete fragment sets reflecting the composition of the selected compound (fragment compositions) contain the information about the set of bonded fragments of the compound. Various factors affecting analysis of the compiled list of fragments are considered using a particular example. Different techniques for revealing structural information are discussed. Scientific and Technical Center of Chemical Informatics, Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 368–378, March–April, 1996. Translated by L. Smolina     

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.     

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.     

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.     

Polyfused nitrogen-containing heterocycles 18. 2′-Amino-5-methyl-1,2,3,4,4′,5′-hexahydrospiro[quinoxaline-2,4′-thiazol]-3-ones. Synthesis,structure, and recyclization

Bis-3-(α-bromoethyl)quinoxalin-2-ones with 3-oxapentane or 3,6-dioxaoctane spacer binding two heterocyclic fragments react with thiourea to give the corresponding bis-spirothiazoloquinoxalines, which upon treatment with acetic anhydride can be converted to podands with terminal thiazoloannulated quinoxaline fragments. X-Ray data for 2′-amino-4-ethyl-5-methyl-1,2,3,4,4′,5′-hexahydrospiro[quinoxaline-2,4′-thiazol]-3-one indicate for this compound a potentiality to form clathrate structures with various solvate molecules. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2386–2393, December, 2007.     

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     

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     

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.     

Spectroscopic Evidence for an Oxazolone Structure in Anionic <Emphasis Type="BoldItalic">b</Emphasis>-Type Peptide Fragments

Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b₂ fragments of deprotonated AlaAlaAla and AlaTyrAla have been recorded over the 800–1800 cm^–1 spectral range by multiple-photon dissociation (MPD) spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Structural characterization of the b-type fragments is accomplished by comparison with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. Although diketopiperazine structures represent the energetically lowest isomers, the IR spectra suggest an oxazolone structure for the b₂ fragments of both peptides. Deprotonation is shown to occur on the oxazolone α-carbon, which leads to a conjugated structure in which the negative charge is practically delocalized over the entire oxazolone ring, providing enhanced gas-phase stability.     

Calculation of the hydrogen binding energies of complexes between formamide and adenine-thymine pair

The hydrogen bonding of complexes formed between formamide and adenine-thymine base pair has been completely investigated in the present study. In order to gain deeper insight into structure, charge distribution, and energies of complexes, we have investigated them using density functional theory at 6–311++G(d, p), 6–31G, 6–31+G(d), and 6–31++G(d, p) level. Seven stable cyclic structures (ATF1–ATF7) being involved in the interaction has been found on the potential energy surface. In addition, for further correction of interaction energies between adenine—thymine and formamide, the basis set superposition error associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported.     

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     

Syntheses based on norfluorocurarine. 3. Structures of (−)-norfluorocurarine, (±)-norfluorocurarine,and fluorocurarine

Structures of the alkaloids (−)-norfluorocurarine, its racemate (±)-norfluorocurarine from Vinca erecta, and fluorocurarine obtained by N(β)-methylation of (−)-norfluorocurarine were established by x-ray crystal structure analyses. The alkaloid crystallized with two molecules in the asymmetric unit for the first two crystals. The asymmetric unit of (±)-norfluorocurarine crystal consisted of two antipods. The asymmetric unit in the crystal of the last compound consisted of the N(β)-methylated cation and a hydroxide anion. The formation of bimolecular associates through intermolecular N–H…O H-bonds was typical of these crystal- line structures. An associate in the crystal structure of fluorocurarine involved two hydroxide anions.     

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.     

Photochromic dihetarylethenes

The structures of two hetarylethene photochromes,viz., 1,2-bis(2-ethyl-5-ethylsulfonylthien-3-yl)perfluorocyclopentene and 1,2-bis[5-(benzoxazol-2-yl)-2-methylthien-3-yl]perfluorocyclopentene, were established by X-ray diffraction analysis. The conformational parameters of the title compounds are considered. The cyclopentene ring in the former compound is planar and this ring in the latter compound adopts an envelope conformation. There are no overall conjugated systems in the molecules under study. In both structures, the dihetaryl fragments are rotated with respect to the perfluorocyclopentene fragments by ∼55°. The thiophene and benzoxazole rings in 1,2-bis[5-(benzoxazol-2-yl)-2-methylthien-3-yl]perfluorocyclopentene are coplanar. For Part 3, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 74–77, January, 2000.     

Photochromic dihetarylethenes

The structures of two hetarylethene photochromes,viz., 1,2-bis(2-ethyl-5-ethylsulfonylthien-3-yl)perfluorocyclopentene and 1,2-bis[5-(benzoxazol-2-yl)-2-methylthien-3-yl]perfluorocyclopentene, were established by X-ray diffraction analysis. The conformational parameters of the title compounds are considered. The cyclopentene ring in the former compound is planar and this ring in the latter compound adopts an envelope conformation. There are no overall conjugated systems in the molecules under study. In both structures, the dihetaryl fragments are rotated with respect to the perfluorocyclopentene fragments by ∼55°. The thiophene and benzoxazole rings in 1,2-bis[5-(benzoxazol-2-yl)-2-methylthien-3-yl]perfluorocyclopentene are coplanar. For Part 3, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 74–77, January, 2000.     

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     

Fragmentation methods on the balance: unambiguous top–down mass spectrometric characterization of oxaliplatin–ubiquitin binding sites

The interaction between oxaliplatin and the model protein ubiquitin (Ub) was investigated in a top–down approach by means of high-resolution electrospray ionization mass spectrometry (ESI-MS) using diverse tandem mass spectrometric (MS/MS) techniques, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD). To the best of our knowledge, this is the first time that metallodrug–protein adducts were analyzed for the metal-binding site by ETD-MS/MS, which outperformed both CID and HCD in terms of number of identified metallated peptide fragments in the mass spectra and the localization of the binding sites. Only ETD allowed the simultaneous and exact determination of Met1 and His68 residues as binding partners for oxaliplatin. CID-MS/MS experiments were carried out on orbitrap and ion cyclotron resonance (ICR)-FT mass spectrometers and both instruments yielded similar results with respect to number of metallated fragments and the localization of the binding sites. A comparison of the protein secondary structure with the intensities of peptide fragments generated by collisional activation of the [Ub + Pt-(chxn)] adduct [chxn = (1R,2R)-cyclohexanediamine] revealed a correlation with cleavages in solution phase random coil areas, indicating that the N-terminal β-hairpin and α-helix structures are retained in the gas phase.     

X-ray crystal structures of <Emphasis Type="Italic">p</Emphasis>-halogenated 6,6-diphenylfulvenes

Crystal structures of a series of p-halogenated 6,6-diphenylfulvenes 2–5 are reported and comparatively discussed including the known structure of the non-halogenate parent compound 1. The molecular structures show twisted conformations of the plane aryl and fulvene subunits against each other, rather unaffected by the different halogen substituents. The packing structures exclusively involve C–H···X (X = F, Cl, π) contacts while Hal···Hal and π-stacking interactions do not occur.     

New sterically hindered di-o-quinones of the biphenyl series

New di-o-quinones of the biphenyl series, namely, 2,2′-dialkyl-5,5′-di-tert-butylbiphenyl-3,4,3′,4′-diquinones, were synthesized. Their structures were established by IR and NMR spectroscopy. The molecular structure of 2,2′-dimethyl-5,5′-di-tert-butylbiphenyl-3,4,3′,4′-diquinone was established by X-ray structural analysis. The structure is characterized by orthogonal (the torsion angle is 82.9°) mutual arrangement ofo-benzoquinone fragments. ESR studies demonstrated that chemical reduction of diquinone proceeds in four oneelectron stages to form paramagnetic mono- and trianions as intermediates. Quinopyrocatechols, which are intermediates in the synthesis of di-o-quinones, were isolated and characterized. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 804–809, April, 1997.