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.     

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.     

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     

Crystallographic analysis of atomic structures and the phenomenological mechanism of crystallization

A theoretical study of the structure and vibrational spectrum of methyl-β-D-glucopyranoside is performed with allowance for the hydrogen bond effect on them. At the density functional theory level with the use of the B3LYP functional in the 6–31G(d) basis set the structural dynamic models of a free molecule of methyl-β-D-glucopyranoside and its simplest complexes with hydrogen bonding in the form of dimers with different structures are constructed. Energies are minimized; structures, electro optical parameters, force constants, and normal vibrational frequencies in the harmonic approximation and their intensities in IR spectra are calculated; the hydrogen bond energy is estimated. Based on the calculation, the conclusions are drawn about the structure of the methyl-β-D-glucopyranoside sample, the formation and interpretation of its IR spectrum, and the possibilities of the used density functional theory method.     

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.     

Synthesis,characterization, spectroscopy and thermal analysis of rare earth picrate complexes with <Emphasis Type="Italic">L</Emphasis>-leucine

Rare earth picrate complexes with L-leucine (Leu) were synthesized and characterized. Elemental analysis (CHN), EDTA titrations and thermogravimetric data suggest a general formula RE(pic)₃2Leu⋅5H₂O (RE=La–Lu, Y and pic=picrate). IR spectra indicate the presence of water and suggest that L-leucine is coordinated to the central ion through the nitrogen of the aminogroup. The absorption spectrum of the solid Nd compound indicates that the metal-ligand bonds show a weak covalent character. Emission spectra and biexponential behavior of the luminescence decay of the Eu compound suggest the existence of polymeric species. Thermal analysis results indicate that all the compounds present a similar behavior, with five major thermal decomposition steps. The final products are rare earth oxides. A slow heating rate is necessary to observe all decomposition steps.     

Computer-Assisted Verification of Agreement Between IR Spectrum and Hypothetical Chemical Structure

A method is suggested for estimating the agreement between the IR spectrum and the hypothetical structure of an organic compound. The technique is based on coverage of the molecular graph by the structural fragments revealed for the compounds selected from the database using the maximal similarity criterion between the spectra of the compounds and the query spectrum. The efficiency of this approach is demonstrated by reference to some examples and by analyzing two data samples with correct and wrong structure assignments to spectra.     

Organotins as a Locking Agent in the Formation of Dinuclear Complexes

In this paper the synthesis and characterization of new heterobimetallic compounds with a ligand derived from diacetylpyridine, hydrazine and salicylaldehyde has been reported. The open end of the ligand was locked with R₂SnCl₂ followed by the insertion of a transition metal ion in the cavity thus formed by locking the ligand. These compounds are characterized by TGA/DSC, IR, ¹H and ¹³CNMR, electronic spectra, magnetic moment and conductivity measurements. The disappearance of ν(O–H) and appearance of ν(Sn–O) in the IR spectrum of the Sn(saldp)R₂ {where saldp = bis(salicylaldehydehydrazone)diacetylpyridine and R = –CH₃, –C₄H₉} suggests the complex formation with R₂SnCl₂. The IR spectra of the complexes exhibited a blue shift in ν(C=N) indicating coordination of the azomethine nitrogen. The complexes are non-electrolytes in DMSO. The ¹HNMR and ¹³CNMR spectra of the complexes are not much different from that of the free ligand except for the disappearance of the signal at 9 ppm due to phenolic protons. The methyl or butyl protons attached to the tin appear at their usual places. The TGA profile of the ligand and its mononuclear complexes exhibit a three-step pyrolysis, although the binuclear complexes decompose in two steps leaving behind tin oxide as the final product.     

Balanoinvolin,a new steroid derivative from <Emphasis Type="Italic">Balanophora involucrate</Emphasis>

A new compound, β-sitosterylglucoside-3′-O-linoleate, named balanoinvolin, and three known compounds coniferin, methylconiferin, and 4-O-β-D-glucopyranosylconiferyl aldehyde, were isolated from Balanophora involucrate Hook. f. and their structures were determined by MS and 1D/2D NMR spectra. Published in Khimiya Prirodnykh Soedinenii, No. 3, pp. 315–317, May–June, 2009.     

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.     

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.     

Synthesis of (1<Emphasis Type="Italic">R</Emphasis>,2<Emphasis Type="Italic">R</Emphasis>)-1,2-bis-(5-(4-hydroxynaphthalen-1-ylazo)-[1,3,4]thiadiazol-2-yl)-ethane-1,2-diol

In this study, (1R,2R)-1,2-bis-(5-amino-1,3,4-thiadiazol-2-yl)ethane-1,2-diol (2), was synthesized by using (2R,3R)-(+)-Tartaric acid (1) as starting compound. Then the diazo component 3 was obtained from 2 and 1-naphthol. In addition, the structures of the synthesized compounds 2 and 3 were confirmed by elemental analyses, IR, ¹H-NMR, and ¹³C-NMR spectra. __________ Published in Kimiya Prirodnikh Soedinenii, No. 5, pp. 465–466, September–October, 2005.     

Synthesis and structures of 3-hydroxy-6-(R-phenylazo)-7,8-benzo-1,2,3,4-tetrahydroquinolines as products of analytical test reactions for nitrite and nitrate anions

An improved procedure was proposed for the synthesis of 3-hydroxy-7,8-benzo-1,2,3,4-tetrahydroquinoline, which is used as a reagent for the analytical test reaction for nitrate and nitrite anions based on azo coupling with diazo compounds. 3-Hydroxy-6-(R-phenylazo)-7,8-benzo-1,2,3,4-tetrahydroquinolines (R = 2-COOH, 4-COOH, or 4-SO₃H) were synthesized by azo coupling reactions in 65–70% yields. The structures of these compounds were confirmed by elemental analysis, ¹H NMR and IR spectroscopy, and X-ray diffraction. Based on the X-ray data, the bathochromic shift in the UV spectrum of the o-carboxy isomer compared to the p-carboxy isomer (Δλ_max = 50 nm) is attributed to a strong intramolecular hydrogen bond. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1027–1031, June, 2006     

New glycosidic and other constituents from hulls of <Emphasis Type="Italic">Oryza sativa</Emphasis>

Three new compounds, 4-hydroxymethylene-7-(9,9,13-trimethylcyclohexyl)-heptanyl-3′,7′,7′-trimethylcyclohexa-2′,4′-dien-1′-oate (1), 1-(n-hexadec-7-enoxy)-6-(n-octadecanoxy)-β-D-glucopyranoside (2), and (Z)-12-hydroxy-9-octadecenoic acid-12-β-D-glucopyranoside (3), along with the known compound hexacosanoic acid (4), were isolated and identified from the rice hulls of Oryza sativa. Their structures were elucidated by 1D and 2D NMR spectroscopic techniques (¹H-¹H COSY, ¹H-¹³C HETCOR, DEPT) aided by EIMS, FABMS, HRFABMS, and IR spectra. Published in Khimiya Prirodnykh Soedinenii, No. 4, pp. 344–347, July–August, 2007.     

Structure and spectroscopy of NaNd(SP)<Subscript>4</Subscript> chelate: a new type of lanthanide luminophore

Lanthanide β-diketones and their derivatives are extensively studied coordination compounds, due to their luminescent properties and many possible applications. The tetrakisNd(III) complex with phosphorylated sulfonylamides derivatives of β-diketones was synthesized. The X-ray diffraction showed that the compound of formula {[Na[Ln(SP)₄]} _n (SP = C₆H₅S(O)2NP(O)(OCH₃)₂; Ln = Nd(III) crystallize in the monoclinic P2₁/c space group with the following unit-cell parameters: a = 22.006(4)A, b = 11.075(2)A, c = 22.334(5)A, and β = 118.71(3)°. The molecular structure of the investigated compound is polymeric. The lanthanide ions as well as the sodium ions are coordinated by sulfonyl and phosphoryl groups of the ligand, and because of the bridging behavior, link different units of the polymer. High-resolution absorption, emission, and excitation spectra of neodymium crystals were measured at 298, 77, and 4K temperatures. The sensitized emission of [Na[Nd(III)(L)₄]} _n chelate in the IR range of the spectrum was recorded. This kind of the compounds can be used in organic light emitting diodes in compact display technology. The spectral characteristic of the compound is controlled by donor–acceptor properties and electron-hole transporting chemical groups. Those factors affect the energy level location, energy transfer (ET), electron–phonon coupling, and finally the luminescence quantum yield. The optical behavior of the title compound was characterised by crystal field (CF), correlation crystal field (CCF), and electron transition probability calculations. X-ray structural data and the nephelauxetic effect check the role of the character of the bonding. The IR spectra were used to analyze the vibronic components in electronic transitions. The role of ligands, singlet and triplet states in energy transfer, are discussed. The ET mechanism and emission quenching pathways are proposed. Some spectroscopic parameters will be compared with earlier reported NaNdWo₄ × H₂O (Wo = CCl₃ CONPO(OCH₃)₂).     

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     

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]     

Inorganic crystal structure database. Design and operational experience

The Inorganic Crystal Structure Database is a section of the Databank on the Properties of Materials for Electronics that was created at the Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. The database, which is supplied with constantly updated software, includes quantitative structural data and is designed for solving materials-technology problems. The database contains information on crystal structures of complex and ordinary oxides (including compounds with HTSC properties), chalcogenides, intermetallic compounds, inorganic complexes, etc. More than 20 scientific works on different topics were performed using the database. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 3, pp. 559–563, May–June, 1995. Translated by L. Smolina     

Synthesis and IR spectra of 5-phenyl-2-(1-phenyl-2-trichloroacetylethenyl)pyrrole

5-Phenyl-2-(1-phenyl-2-trichloroacetylethenyl)pyrrole was synthesized by the reaction of 2-phenylpyrrole with 1-phenyl-2-trichloroacetylacetylene on silicon oxide. The structure of an intramolecular proton-transfer H-complex was assigned to the title compound based on analysis of its IR spectra in solutions in the temperature range of 165–298 K. Published inIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 11, pp. 1945–1947, November, 2000.