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.     

Plant Coumarins. 3. (+)-PTeryxin from <Emphasis Type="Italic">Peucedanum terebinthaceum</Emphasis>

The potentially medically valuable pyranocoumarin (+)-pteryxin was isolated for the first time from Peucedanum terebinthaceum Fischer et Turcz. The structure of (+)-pteryxin was rigorously proved using mass spectrometry, NMR, IR, and UV spectroscopy and comparison of the spectral characteristics of this compound and its basic hydrolysis products (+)-cis- and (−)-trans-khellactone and angelic and acetic acids. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 468–470, September-October, 2008.     

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     

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.     

Structure of mucroflavone B

A new flavonoid, mucroflavone B, is isolated from the terrestrial part ofTanacetopsis mucronata (Regel. et Schmalh.) S. Kovalevsk. IR, mass, UV, and PMR spectra and a comparison with those of similar compounds provide a basis for proposing the structure 5,6,4′-trihydroxy-7,8,3′-trimethoxyflavone for mucroflavone B. Deceased. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 730–733, November–December, 1999.     

Polysaccharides ofUngernia. XV. A study of the pectin substances of the leaves ofUngernia tadschicorum

Pectin substances have been isolated from the leaves ofUngernia tadschicorum and characterized. A galacturonan has been obtained by partial hydrolysis. On the basis of the results of IR spectroscopy and periodiate — nitric acid oxidation, its structure has been established as an α-1→4-bound polymer-homolog. Institute of the Chemistry of Plant Substances, Academy of Sciences of the Republic of Uzbekistan, Tashkent, FAX (3712) 62 73 48. Translated from Khimiya Prirodnykh Soedinenii, No. 3, 320–322, May–June, 1994.     

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.     

Influence of aluminium precursor on physico-chemical properties of aluminium hydroxides and oxides

The process of hydrolysis of aqueous aluminium sulfate was carried on in ammonia medium at 100°C and for different time intervals (0, 20, 39 or 59 h). The products thus obtained were calcined at 550, 900 or 1200°C for 2 h with the aim to obtain aluminium oxides. The materials were studied with the following methods: thermal analysis, IR spectroscopy, X-ray diffraction, low-temperature nitrogen adsorption, adsorption–desorption of benzene vapours and scanning electron microscopy. Freshly precipitated material was an amorphous basic aluminium sulfate which after prolonged refluxing at elevated temperature in a mother liquor underwent a phase transformation into highly crystalline NH₄Al₁₃(SO₄)₂(OH)₆ containing tridecameric unit Al₁₃. It was accompanied by a decrease of specific surface area and the formation of a porous structure less accessible for benzene molecules. Regardless of the duration of the hydrolysis process, all products were characterised with poorly developed porous structure and hydrophilic character. Their calcination at the temperature up to 1200°C resulted in the formation of α-Al₂O₃ via transition forms of γ/η- and δ-Al₂O₃. The samples of aluminium oxides obtained after calcination at 550 and 900°C had higher values of specific surface area than starting materials due to processes of dehydroxylation and desulfurization. The process of calcination up to 900°C was reflected in developing of not only porous structure but also hydrophobic character of prepared materials. The S _BET values calculated for the oxide samples obtained from aged products of hydrolysis at 1200°C were lower than for the analogous sample prepared without the ageing step. It was concluded that prolonged refluxing at elevated temperature of the products of hydrolysis of aluminium sulfate decreased thermal stability of final aluminium oxides.     

Rearrangement Pathways of the <Emphasis Type="BoldItalic">a</Emphasis><Subscript><Emphasis Type="BoldItalic">4</Emphasis></Subscript> Ion of Protonated YGGFL Characterized by IR Spectroscopy and Modeling

The structure of the a ₄ ion from protonated YGGFL was studied in a quadrupole ion trap mass spectrometer by ‘action’ infrared spectroscopy in the 1000–2000 cm^–1 (‘fingerprint’) range using the CLIO Free Electron Laser. The potential energy surface (PES) of this ion was characterized by detailed molecular dynamics scans and density functional theory calculations exploring a large number of isomers and protonation sites. IR and theory indicate the a ₄ ion population is primarily populated by the rearranged, linear structure proposed recently (Bythell et al., J. Am. Chem. Soc. 2010, 132, 14766). This structure contains an imine group at the N- terminus and an amide group –CO–NH₂ at the C-terminus. Our data also indicate that the originally proposed N-terminally protonated linear structure and macrocyclic structures (Polfer et al., J. Am. Chem. Soc. 2007, 129, 5887) are also present as minor populations. The clear differences between the present and previous IR spectra are discussed in detail. This mixture of gas-phase structures is also in agreement with the ion mobility spectrum published by Clemmer and co-workers recently (J. Phys. Chem. A 2008, 112, 1286). Additionally, the calculated cross-sections for the rearranged structures indicate these correspond to the most abundant (and previously unassigned) feature in Clemmer’s work.     

Isolation of secoisolariciresinol diglucoside from lignan-containing extract of <Emphasis Type="Italic">Linum usitatissimum</Emphasis> seeds

An effective method for obtaining secoisolariciresinol diglucoside (SDG) purified of lignan from extract of Linum usitatissimum seeds was proposed. The lignan-containing concentrate obtained by aqueous ethanol extraction with microwave irradiation was purified using column chromatography. The structure of the compound was confirmed using IR, mass, and NMR spectra. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 21-23, January–February, 2009.     

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.     

Reaction of 1-chloro-2-phenylethane-2,2-dithiol with divalent metal (Cu, Hg, Pb, Fe, Co, and Ni) salts

Reactions of 1-chloro-2-phenylethane-2,2-dithiol with lead(II) acetate and mercury(II) chloride lead to 1-chloro-2-phenylethane-2,2-dithiolates of lead and mercury. The reactions with copper(II) chloride, iron(II) sulfate hydrate, cobalt (II) chloride hydrate, and nickel(II) acetate give metal-containing compounds C₁₆H₁₈S₄M. The¹H NMR, IR, and ESR spectra of the obtained compounds were recorded; their specific dark electroconductivities and activation energies of dark conductivity were determined, and their film-forming ability was studied. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1224–1226, June, 1997.     

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.     

X-ray photoelectron study of relaxation processes in Ni72Mo14B14 and Ni72Nb14B14 melts

The time dependence of the chemical structure of the surface layers of nickel melts is investigated for the first time by X-ray photoelectron spectroscopy. Changes in the chemical structure of amorphous alloys obtained from the same melts are investigated according to depth. Translated fromZhumal Struktumoi Khimii, Vol. 39, No. 6, pp. 1103–1106, November–December, 1998.     

Formation of triphenylmethyl radicals upon alkaline hydrolysis of diphenyl sulfophthalide

Triphenylmethyl radicals (TPMR) with ano-positioned sulfonate group are generated by alkaline hydrolysis of diphenyl sulfophthalide in DMSO. Electronic and ESR spectra of these radicals are characterized. It is suggested that the radicals result from one-electron transfer reactions. Triarylmethyl radicals are also formed in alkaline hydrolysis of polyarylenesulfophthalides. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2015–2017, October, 1999.     

Vibrational Spectroscopy and Analytical Electron Microscopy Studies of Fe–V–O and In–V–O Thin Films

Summary.  Orthovanadate (M ³⁺VO₄; M = Fe, In) and vanadate (Fe₂V₄O₁₃) thin films were prepared using sol-gel synthesis and dip coating deposition. Using analytical electron microscopy (AEM), the chemical composition and the degree of crystallization of the phases present in the thin Fe–V–O films were investigated. TEM samples were prepared in both orientations: parallel (plan view) and perpendicular (cross section) to the substrate. In the first stages of crystallization, when the particle sizes were in the nanometer range, the classical identification of phases using electron diffraction was not possible. Instead of measuring d values, experimentally selected area electron diffraction (SAED) patterns were compared to calculated (simulated) patterns in order to determine the phase composition. The problems of evaluating the ratio of amorphous and crystalline phases in thin films are reported. Results of TEM and XRD as well as IR and Raman spectroscopy showed that the films made at lower temperatures (300°C) consisted of nanograins embedded in the dominating amorphous phase. Characteristic vibrational spectra allowed to distinguish between the different crystalline phases, since the IR and Raman bands showed broadening due to the decreasing particle size of the films thermally treated at lower temperatures. Vibrational analysis also showed that the electrochemical cycling of crystalline films led to spectra that were in close agreement with the spectra of the nanocrystalline films prepared at lower temperatures. The formation of a nanocrystalline structure is therefore a prerequisite for obtaining a higher charging/discharging stability of Fe–V–O and In–V–O films. Received October 4, 2001. Accepted (revised) November 23, 2001     

Synthesis and investigation of the electronic structure of molybdenum tetrasulfide and its lithium intercalates

An X-ray amorphous phase of molybdenum tetrasulfide with the analytical formula MoS₄ has been sythesized. Quantum chemical modeling of the suggested local structure of MoS₄ and EHT calculation of the electronic structure of the basic (Mo₂S₄)⁴⁺ fragment are reported. The electronic structure of molybdenum tetrasulfide and its lithium intercalates was investigated by X-ray emission and X-ray photoelectron spectroscopy. It is shown that the change in the electronic structure of the starting molybdenum tetrasulfide to four lithium atoms per formula unit in the intercalate may be considered in the rigid band model. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 4, pp. 727–734, July–August, 1996. Translated by L. Smolina     

Model for the description of the dynamic and electrooptic properties of hydrogen bonds

A semiempirical one-parameter model is proposed to describe the dynamic and electrooptic properties of hydrogen bonds. The model allows one to determine all parameters that are necessary for calculating the vibrational spectra of complexes using the strength of intermolecular binding. The experimental IR spectra of some hydrogen-bonded systems are compared to the corresponding spectra calculated by this model. It is shown that the model is applicable to calculating the first-to-third order vibrations of any hydrogen-bonded complex. N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 255–268, March–April, 1995.     

Flavonoid glycosides from Astragalus galegiformis leaves

New flavonoid oligosides, the structures of which were established by chemical transformations and UV, IR, PMR, and ¹³C NMR spectra, were isolated from Astragalus galegiformis leaves. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 555–558, November–December, 2006.     

Configuration and conformation of taibaihenryiin T isolated from <Emphasis Type="Italic">Phlomis umbrosa</Emphasis>

Taibaihenryiin T was isolated for the first time from Phlomis umbrosa Turcz, and its structure was elucidated on the basis of IR and NMR spectra analysis. Its molecular configuration, conformation, and crystal structure were also characterized by X-ray structure analysis. The infrequency of the C–O–O–C group is manifested in this molecular configuration, and hydrogen bonding assembles the molecules into a three-dimensional networking structure in the crystal.