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.     

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.     

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.     

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.     

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     

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     

New flavanones from Scutellaria phyllostachya roots

The new natural flavanones (+)-5,2′-dihydroxy-6,6′,7-trimethoxyflavanone and (+)-5,2′-dihydroxy-6,6′,7,8-tetramethoxyflavanone in addition to the known flavones chrysin, norwogonin, and wogonin were isolated from Scutellaria phyllostachya roots. The structures of the isolated compounds were established using IR, UV and PMR spectra. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 24–25, January–February, 2008.     

Taxonomy of Structures Selected from the IR Spectroscopy Database

This paper reports on taxonomy of the structural formulas of organic compounds selected from an IR spectroscopy database (DB) based on the similarity between the query spectrum and DB spectra. Two molecular graph models are compared: connectivity matrix and vector representation (exhaustive set of nonisomorphic connected k-vertex fragments). In both cases, taxonomy according to the shortest distance framework of the distance graph gives a classification of structural analogs into groups (taxons). An analysis of IR spectra and common subgraphs in the respective groups of graphs reveals large structural fragments of the compounds.     

Spectroscopic study of the most important combinations of atomic groups in complex molecules of organic compounds

The IR spectra of several compounds containing the nitro group were studied. Based on these and previous data, the state of the nitro group depending on the structure of the fragments bound to the nitrophenyl group was discussed. The redistribution of the electron density at vibrations of the nitro group and the substituent atoms was considered. The effects of the π-bond system, bridging atoms separating the nitrophenyl group from the substituents, and heavy atoms adjacent to the bridging atom were characterized. The data obtained facilitates the orientation in the selection of molecular structures satisfying the specified requirements of practical applications. For Part 2, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 304–309, February, 1998.     

Effect of the Structure of Benzo- and Dibenzocrown Ethers on Their Reaction with the Aerosil Surface

The adsorption of 4-substituted benzo- and 5,5′-disubstituted dibenzocrown ethers from benzene by aerosil A-300 was studied. The ethers included a total of 45 compounds with diphenyl oxide, diphenyl, and diphenyl sulfide fragments. Analysis of the Henry coefficients (K_H) and the extent of desorption, the IR spectra of the adsorbed compounds, and the relationship between their structure and adsorption capacity indicated that all structural fragments of the crown ethers studied interact to some extent with aerosil surface fragments. The number of oxygen atoms in the polyether fragment and the size of the macrocycle are the predominant factors. A large, nonadditive increase in K_H is observed in going from pentadentate to hexadentate crown ethers. __________ Translated from Teoreticheskaya i Eksperimental'naya Khimiya, Vol. 41, No. 4, pp. 247–251, July–August, 2005.     

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     

Vibrational spectra and stereochemistry of mono- and polysaccharides. III. β-methyl-d-glucoside, α-methyl-d-glucoside,and β-methyl-d-xyloside

The IR and Raman spectra of β- and α-methyl-D-glucosides and β-methyl-D-xyloside are compared. Experimental data are correlated with theoretical calculations of the frequencies of normal vibrations. Predominant contributions (20% and more) of particular CiOi and CiC(i+1) bonds to the potential energy distribution of normal vibrations (i.e., localization of vibrations on these bonds, which form skeletons of monosaccharide molecules) are estimated. This approach is used to interpret the main distinctions between the IR and Raman spectra of the test compounds. The use of vibrational spectra in selective analysis of certain functional groups is discussed. It is shown that replacing the hydroxyl group at C1 has a specific effect on the predominant localization of vibrational modes in particular skeletal bonds (mainly in C1O1) of the monosaccharide molecules. B. I. Stepanov Institute of Physics, Belarus Academy of Sciences. V. Tshebyatovski Institute of Low Temperatures and Structural Studies, Polish Academy of Sciences. Translated fromZhurmal Strukturnoi Khimii, Vol. 36, No. 3, pp. 443–455. May–June, 1995. Translated by I. Izvekova.     

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.     

Spectral and luminescent properties of hydroxyazomethines of indoline spiropyrans

Spectral and luminescent properties of novel bifunctional compounds 1–3 based on indole spiropyrans and hydroxyazomethines have been studied in comparison with the properties of the model compounds 5’-substituted spiropyrans and azomethines in organic solvents and PMMA films at 293 and 77 K. Luminescence of compounds 1–3 is due to the presence of the azomethine fragment conjugated with the indoline ring of the spiropyran moiety and determining the long-wavelength absorption band of 1–3. Depending on the solvent, temperature, and the substituent, various combinations of the structures of the chromophore fragments are observed in 1–3: the imine or amine form of the azomethine fragment and the spirocyclic or merocyanine form of the spiropyran fragment.     

Fragment methods for IR spectrum calculations of organophosphorus compounds

For highly toxic organophosphorus compounds on the limiting lists of the International Chemical Weapons Ban Treaty, fragment methods may be used for calculating their IR vibrational spectra; this is shown for O-alkyl alkylfluorophosphonates used as examples. The geometrical parameters and the parameters of the potential and electrooptic functions are found for the major fragments of these compounds. Due to this, fast predictive computation of IR spectra of O-alkyl alkylfluorophosphonates is possible, the accuracy of calculation being sufficient for spectral identification of these compounds; a database of the calculated IR spectra may be created.     

Synthesis, characterization and photosensitivity of tetrakis-α-(2-methyl-8-quinolinoxy) metallophthalocyanines

Four amphipathic cobalt(II), nickel(II), copper (II), and zinc(II) coordination compounds of tetrakis-α-(2-methyl-8-quinolinoxy)phthalocyanine are synthesized using “DBU catalytic method”. The titled complexes are characterized by elemental analysis, mass spectra, UV-Vis, and IR spectra. In addition, the rates of photo-generated singlet oxygen and the rate constants of photo-dynamic oxidation of amino-acid substrate by the complexes are measured under the optical excitation at 670 nm, and the relations between their structures and their photosensitivities are discussed. __________ Translated from Acta Chimica Sinica, 2007, 65(16): 1605–1611 [译自: 化学学报]     

Reactions affecting the γ-lactone ring of α-santonin

The selective dehydrogenation of the eudesmanolide α-santonin and its alkylation with the introduction of an allyl fragment into its γ-lactone ring are described. It has been established that these reactions are regio- and stereo-selective. The structures of the compounds obtained were determined from their IR, UV, PMR, and mass spectra. Institute of Organic Synthesis and Coal Chemistry, Kazakhstan Academy of Sciences, Karaganda. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 518–522, September–October, 1992.     

Vibrational spectra of 1,1,3,3-tetramethyl-2-nitroguanidine and their interpretation with the use of scaling of quantum-chemical force field

The IR (4000–50 cm⁻¹) and Raman (3500–170 cm⁻¹) spectra of solid 1,1,3,3-tetramethyl-2-nitroguanidine (TMNG) were obtained. The spectra were interpreted using the scaling of the TMNG quantum-chemical force field in the B3LYP/6-311G(d,p) approximation. Transferable scale factors necessary for the interpretation of spectra of more complex related compounds were determined. The scaled harmonic force field is supposed to be used in the analysis of the available gas-phase electron diffraction data for TMNG. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 495–498, March, 2008.     

Structure of mucroflavone A

A new flavonoid, mucroflavone A, is isolated from the terrestrial part ofTanacetopsis mucronata (Regel. et Schmalh.) S. Kovalevsk. IR, mass, UV, and PMR spectra are compared with those of related compounds to provide a basis for proposing the structure 5,6,4′-trihydroxy-8,3′-dimethoxyflavone for mucroflavone A. Deceased. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 725–729, November–December, 1999.