Some results obtained using the CNDO/2 technique in the calculations of the IR spectra of polyatomic molecules

Korolevich, M. V.

doi:10.1016/0166-1280(94)80046-4

Cited by 14 publications

(16 citation statements)

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“…The band intensities match when comparing the theoretical and experimental spectra of methyl-β-D-glucopyranoside, analogous to the situation for unsubstituted monosaccharides [12,14,15]: extensive sections of the compared spectra are close or match in the ranges 1500-1200 cm -1 and 1200-1050 cm -1 . The theoretical spectrum in the 1050-950 cm -1 range has weaker intensity than the experimental spectrum, but the general character of the observed spectrum in this interval and the ratio of the integrated intensities of the bands making up the spectrum are reproduced by the calculation.…”

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confidence: 56%

“…The calculation results here are completely consistent with experiment. Thus the intensity of the vibration corresponding to the band at 1465 cm -1 in the spectrum of β-D-glucose [15] is three times lower than the intensity of the vibration responsible for the band at 1464 cm -1 in the spectrum of methyl-β-Dglucopyranoside. The vibration of the oxymethyl group ν 15 = 1502 cm -1 forms the high-frequency wing of the contour under consideration.…”

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confidence: 89%

“…Vibrations of the β-D-glucose molecule that are similar in shape and intensity have frequencies lower by 20 cm -1 [15]. According to experiment, with oxymethyl substitution at C (1) this leads to an ν 20 cm -1 shift of the doublet band with maxima at 1012 and 1030 cm -1 (the spectrum of β-D-glucose) toward higher frequencies.…”

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confidence: 95%

“…In constructing the force field for the methyl-β-D-glucopyranoside molecule for the molecular fragment O (5) -C (1) H-O-CH 3 , the force constants were taken from the force field for methyl-β-D-glucopyranoside tetranitrate [16]; for the rest of the molecule, all the force constants were transferred from the β-D-glucose molecule [15].…”

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confidence: 99%

“…for different organic compounds. These programs have been used to carry out a full theoretical analysis of the frequencies and intensities and a detailed interpretation of the IR spectra for a number of monosaccharides and selectively substituted monosaccharide nitrates [10][11][12][13][14][15][16][17][18][19][20].…”

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confidence: 99%

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Theoretical interpretation of spectral signs of an oxymethyl group in the IR spectrum of methyl-β-D-glucopyranoside

Korolevich

Zhbankova

2006

J Appl Spectrosc

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For the first time, we have assigned the observed absorption bands and interpreted the IR spectrum of methyl-β-D-glucopyranoside in detail in the 1500-800 cm -1 region, based on a full calculation of the frequencies and absolute intensities of the normal vibrations of the molecule and their comparison with the experimental data. We have identified two groups of spectral signs indicating an oxymethyl substituent has replaced the hydroxyl group on the C (1) atom in the glucopyranoside: absorption bands of medium intensity due to the characteristic vibrations of the substituent, and intense bands due to an unusual "interaction" between many structural moieties.Introduction. Vibrational spectroscopy is undoubtedly one of the most widespread methods for structural analysis of compounds, and it has found broad application in solving a number of problems of practical importance. We should note that the connections between the vibrational spectra and the structure of molecules are complex and distinctive. Consequently, as the molecules become more complicated, interpretation of the spectra requires drawing on as extensive a set of experimental data as possible (the results of analysis of other parameters, besides the frequencies, of the IR absorption bands and the lines in the Raman spectra; in a number of cases, study of the spectra of deuterated derivatives, etc.) and theoretical analysis of the molecular vibrations.Theoretical study of the spectra of specific classes of complicated compounds requires special procedures and approaches, and ignoring this fact may lead to significant reduction in the obtainable data, and often to insufficiently substantiated and erroneous conclusions. Such compounds include carbohydrates in particular.Properties of monosaccharides that are of practical value are mainly determined by the steric arrangement (conformation, configuration) of the individual groups of atoms determining the system of intramolecular and intermolecular interactions. But extracting information about the fine details of the structure of carbohydrates from observed vibrational spectra is an extremely difficult task, due to the complexity of the structure of these compounds, the strong dependence of their spectra on steric factors, and the diversity of the conformational forms of the molecules. A necessary condition for correct interpretation of vibrational spectra of monosaccharides and their derivatives is a full calculation of the frequencies and intensities of the molecular vibrations for these compounds. In this case, systematic study of whole classes of compounds with gradually more complicated molecular structures is especially important.Extensive experimental data on the vibrational spectra of carbohydrates has been accumulated and systematized at the Institute of Physics (National Academy of Sciences of Belarus) under the direction of R. G. Zhbankov [1][2][3][4][5]. A special procedure has been developed and an original software package has been created to calculate the frequencies, modes, potential energy d...

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confidence: 56%

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confidence: 89%

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confidence: 95%

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confidence: 99%

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confidence: 99%

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Theoretical interpretation of spectral signs of an oxymethyl group in the IR spectrum of methyl-β-D-glucopyranoside

Korolevich

Zhbankova

2006

J Appl Spectrosc

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GLYCAM06: A generalizable biomolecular force field. Carbohydrates

et al. 2007

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A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both α-and β-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.

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Theoretical study of vibrational spectra of monosaccaride nitrates

Korolevich

Zhbankov

1999

Spectroscopy of Biological Molecules: New Directions

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Some results obtained using the CNDO/2 technique in the calculations of the IR spectra of polyatomic molecules

Cited by 14 publications

References 5 publications

Theoretical interpretation of spectral signs of an oxymethyl group in the IR spectrum of methyl-β-D-glucopyranoside

Theoretical interpretation of spectral signs of an oxymethyl group in the IR spectrum of methyl-β-D-glucopyranoside

GLYCAM06: A generalizable biomolecular force field. Carbohydrates

Theoretical study of vibrational spectra of monosaccaride nitrates

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