Hydrogen bonding, IR spectrum, and the structure of methyl-β-D-glucopyranoside

Abstract

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.

Calculation of the Structure and IR Spectrum of 2,3-di-O-Nitromethyl-β-D-Glucopyranoside by the Density Functional Method

“…Figure 2 shows the experimental IR spectrum and those calculated for complexes IIa and IIIa and the free molecule. An analysis of the calculated IR spectra of H-bonded complexes IIa and IIIa and the dimeric H-bonded complexes [1][2][3] in the range 3150-3700 cm -1 led to the following conclusion. The presence of H-bonded complexes I, II, and III in the sample caused the appearance of two weak bands corresponding to q(O-H) stretching modes of the free molecule ν 87 = 3540 and ν 86 = 3538 cm -1 in addition to four bands of anomalously high intensity that were shifted to low frequency by 108-216 cm -1 ( Table 3).…”

“…The cores (vicinity of the H bridges) of H-bonded complexes II, IIa, III, and IIIa were identical. The calculated IR spectra of H-bonded complexes IIa and IIIa and dimeric H-bonded complexes of methyl-β-D-glucopyranoside [1][2][3] enabled the effect of the H-bond on the spectrum of 2,3-di-O-nitromethyl-β-D-glucopyranoside to be rather fully explained.…”

“…Basis set 6-31G(d) was chosen owing to results from calibration of several basis sets that were used in similar calculations. It turned out to be optimal for application to alcohols [14][15][16][17][18][19][20], ketones (benzophenone and its bromo-substituted derivatives [21][22][23]), cyanobiphenyls [22], and glucose derivatives [1-3, 12, 13]. Therefore, we considered it to be universal and applicable to the studied species.…”

“…The current state of these methods and the algorithms and computing programs gave hope that using them would be successful. Explicit consideration of the H-bond in the modeling reproduced the IR spectrum, which was closer to the experimental one [1][2][3]. This problem as applied to 2,3-di-O-nitromethyl-β-D-glucopyranoside was solved before [13].…”

“…The frequencies of molecular normal modes should be split into two components after forming the dimer. Frequencies assigned to a mode of any molecular fragment could be split differently (from 0 to 100 cm -1 ) [2,3] depending on its distance from the H bridge. The calculated spectra of H-bonded complexes IIa and IIIa contained frequencies of 2,3-di-O-nitromethyl-β-D-glucopyranoside and EtOH.…”