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.     

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.     

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.     

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     

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.     

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.     

Reduction of chemical noise in electrospray ionization mass spectrometry by supplemental IR activation

Supplemental infrared (IR) activation was applied to reduce background chemical noise and increase analyte ion signal in a linear ion trap mass spectrometer. Peptides, proteins, and small molecules were all introduced by electrospray ionization, and when regions of chemical noise were isolated and subjected to IR irradiation, protonated analyte molecules were observed in the product ion mass spectra. By isolating the entire mass range (e.g., m/z 400–2000) and then irradiating all ions in the trap, supplemental IR activation increased the signal of singly protonated peptides by almost 70% and by 40%–55% for the lower charge states of cytochrome c. This increase in analyte ion signal was less dramatic for the higher charge states of peptides and proteins. The chemical noise present in the mass spectra is attributed to incomplete desolvation of the electrospray, as the abundance of the protonated peptides observed upon supplemental IR activation of the chemical noise decreased with higher inlet capillary temperatures. Collision activation was not as effective for desolvating the ions present in the chemical noise.     

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.     

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     

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.     

IR Spectra of Paracetamol and Phenacetin. 1. Theoretical and Experimental Studies

IR spectra of paracetamol and phenacetin have been measured for powder crystals of these compounds and for their solutions in chloroform and dimethylsulfoxide. Ab initio calculations of their equilibrium geometry and vibrational spectra were carried out for spectrum interpretation. Differences between the experimental IR spectra of solutions and crystalline samples have been analyzed. Variations of molecular structure from the isolated state to molecular crystal were estimated based on the difference between the optimized molecular parameters of free molecules and the experimental bond lengths and angles evaluated for the crystal forms of the title compounds. The role of hydrogen bonds in the structure of molecular crystals of paracetamol and phenacetin is investigated, and spectral ranges with maximal intermolecular interactions are determined.     

Analysis of band intensities in the IR spectra of macromolecular assemblies

Band intensities in the IR spectra of oscillator chain assemblies are calculated. It is shown that the dependences of the band intensity on temperature and on the concentration of the second conformation are nonlinear and are determined by the orientation of the vector of the oscillator dipole moment derivative with respect to the extension coordinate along the rotation axis. In the case of vibrations of the main chain, for bands with perpendicular dichroism, the contributions to the band intensity from the change in the orientation of the vector of the oscillator dipole moment derivative with respect to the extension coordinate and from the change in the vibration shape are compensated by each other. Bands with parallel dichroism, for which this compensation is absent, are more sensitive to changes in the chain conformation. This approach is illustrated by analysis of the vibrational spectra of isotactic and syndiotactic polymethyl methacrylate and polyethylene terephthalate. Institute of Construction Engineering, Kazan. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 359–365, March–April, 1995. Translated by I. Izvekova     

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.     

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.     

IR spectroelectrochemical studies of Fe2V4O13, FeVO4 and InVO4 thin films obtained via sol-gel synthesis

In this paper we generalize the IR spectroscopic properties of M³⁺VO₄ (M=Fe, In) orthovanadate and Fe₂V₄O₁₃ films. The films were prepared using the sol-gel synthesis route from M³⁺ nitrates and vanadium oxoisopropoxide. The vibrational bands in the IR absorbance spectra of the films are classified in terms of terminal V-O stretching (1050–880 cm^–1), bridging V-O^...Fe and V^...O^...Fe stretching (880–550 cm^–1), mixed V-O-V deformations and Fe-O stretching (<550 cm^–1) modes. Ex situ IR spectra of films were measured after consecutive charging/discharging to various intercalation coefficients x and correlated to the current peaks in the cyclic voltammetry curves measured in 1 M LiClO₄/propylene carbonate electrolyte. We classified the ex situ IR spectra of charged/discharged films according to their vibrational band changes. The results reveal that, for small values of the intercalation coefficient, crystalline FeVO₄, InVO₄ and Fe₂V₄O₁₃ films exhibit a simultaneous decrease in the intensity of all IR bands while the band frequencies remain unaffected. For the higher intercalation levels, IR mode frequencies are shifted, signaling the presence of reduced vanadium. Further charging leads to an amorphization of the film structure, which was established from the similarity of the IR spectra of charged films with those of amorphous films prepared at lower annealing temperatures. The results confirm that ex situ IR spectroelectrochemical measurement is an effective way to assess the structural changes in films with different levels of intercalation. Electronic Publication     

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.     

IR dichroism study of orientational ordering of liquid-crystalline acrylates

Orientational ordering of four liquid-crystalline acrylates induced by the surface of KBr plates over a wide temperature range was studied by the IR dichroism technique. IR spectra of homogeneously aligned samples were used to calculate the angles between the direction of the transition moment for a series of vibrations of the mesogenic fragment and its long axis. A method for calculation of the homeotropic orientation parameter of molecules was proposed. The orientation parameters of homogeneously and homeotropically aligned samples in the nematic, smectic (A), and chiral smectic (I andH) phases were calculated. Thein situ photopolymerization of acrylates in the smectic phases occurs with retention of the orientational ordering in the polymer films formed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 319–323, February, 1999.     

Intensity of bands of the C≡C stretching modes in the IR spectra and conjugation in silylacetylenes

A comparative study of the integrated extinction coefficients (A) of the C≡C stretching bands in the IR spectra of acetylene derivatives Me₃SiC≡CR, HC≡CR, and Me₃CC≡CR was carried out. The resonance interactions of substituents with a triple bond are the main cause of the changes in the values ofA. The total resonance effect of the Me₃Si fragment involves both acceptor (d, π-conjugation) and donor (σ, π-conjugation) components; d, π-conjugation dominates in the silylacetylenes studied. Theσ _R ⁰ resonance constant of the Me₃Si substituent in compounds Me₃SiC≡CR is 0.17±0.02. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 76–80. January 1997.     

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.