Calculation of the structure and IR spectrum of hydrogen-bonded methyl-β-D-glucopyranoside by the density-functional method

The IR spectrum and structure of methyl-β-D-glucopyranoside have been studied theoretically taking into account the influence on them of the hydrogen bond formed in the sample. Density-functional theory with the B3LYP functional in basis 6-31G(d) was used to minimize the energies and calculate the structures, electro-optical parameters, force constants, frequencies of normal harmonic vibrations, and intensities in IR spectra of the simplest H-bonded dimeric complexes of methyl-β-D-glucopyranoside. The calculated spectra of H-bonded complexes were compared with those of the free molecule and the experimental spectrum in the range 400–3700 cm^–1. Conclusions about the structure of methyl-β-D-glucopyranoside were made. The interpretation of its IR spectrum was refined.     

Calculation of the structure and IR spectrum of methyl-β-D-glucopyranoside by density functional theory

Structural-dynamic models of methyl-β-D-glucopyranoside have been constructed by a density functional method using a B3LYP functional in bases 6-31G(d) and 6-31+G(d,p). Energies have been minimized. Structures, dipole moments, polarizabilities, frequencies of normal modes in the harmonic approximation, and the intensity distribution in the molecular IR spectrum have been calculated. The calculation results have been compared with both the experimental spectra of methyl-β-D-glucopyranoside in the region 400–3700 cm^–1 and data obtained within the framework of an approach that uses the classical valence-force method to calculate normal mode frequencies and the quantum-chemical CNDO/2 technique to calculate the electronic structure.     

Conformational analysis of 2,3-dihydro-3-O-(1,4-naphthoquinon-2-yl)-2-oxo-1,4-naphthoquinone derivatives by the density functional method and IR spectroscopy

We have used the PBE/3z, B3LYP/6-31G, B3LYP/6-31G(d), and B3LYP/6-311G(d) methods to study the conformational mobility of 2,3-dihydro-3-O-(1,4-naphthoquinon-2-yl)-2-oxo-1,4-naphthoquinones (1–4). We have shown that more than 99% of these compounds exist as the major tautomeric form, while differences in the structure of the Q_2H (2,3-dihydro-2-oxo-1,4-naphthoquinones) and Q_1,4 (1,4-naphthoquinon-2-yl) moieties lead to qualitative differences in the internal rotation potentials of the ethyl substituents V(θ_Et−1) and V(θ_Et−2), and consequently each of compounds 1−4 exists as six different rotameric forms. For diquinone 3, we have calculated the dependences of the frequencies (ν) and intensities (A) of the normal vibrations on the torsional angles θ_Et−1 and θ_Et−2, and also on the changes in the geometry of the ether bond. We have found that the values of ν and A for the bands in the carbonyl region of the IR spectrum change little on going from one rotameric form to another, and also for the in-plane bends of the ether bond, and change considerably for the out-of-plane bends of the ether bond. However, for T ≤ 300 K, there is no qualitative change in the overall contour, and it can be interpreted based on a simple additive model. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 73, No. 5, pp. 573–581, September–October, 2006.     

Theoretical analysis of the effect of intermolecular interaction on ir spectra of skatole

The molecular structure and IR vibrational spectra of skatole in the isolated state, in aqueous solution, and in hexane have been calculated in the B3LYP/6-311++G(d,p) approximation. Characteristic spectral differences associated with the influence of both polar and nonpolar solvents and a hydrogen bond have been defined for the vibrational spectrum of skatole. Calculation of the isolated skatole molecule in the anharmonic approximation enabled the interpretation of the vibrational spectrum to be refined.     

Pair association and complexation with water of matrix-isolated pyridine N-oxide: A theoretical study of their manifestations in the IR spectrum

The structure and the IR spectra of three types of pair associates of pyridine N-oxide, as well as of three different complexes of this compound with one or two water molecules, are calculated in terms of the supramolecular approach by the B3LYP/6-311+G(d, p) hybrid density functional method. The experimentally observed IR spectrum of pyridine N-oxide in a low-temperature Ar matrix is theoretically interpreted in detail. The agreement in sign and magnitude between all the calculated and observed frequency shifts of fundamental vibrations shows that the hydrogen-bonded complexes make the main contribution to the formation of complex bands of self-associates.     

Calculation of the IR spectrum of (22S,23S)-24-epicastasterone

Normal vibrational frequencies and absolute IR band intensities for the biologically active steroidal phytohormone (22S,23S)-24-epicastasterone have been calculated within the framework of an original combined approach that uses classical normal coordinate analysis by means of the molecular mechanics method coupled with the quantum-chemical estimation of absolute intensities. Absorption bands in the IR spectrum of this molecule in the region 1500-900 cm⁻¹ were first interpreted based on a comparison of the experimental IR spectrum with the calculated optical-density spectral curve. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 75, No. 6, pp. 768–775, November–December, 2008.     

Computational studies of vibrational spectra and molecular properties of 6-methyluracil using HF, DFT and MP2 methods

Theoretical investigations of atomic charges, conformers, frontier molecular orbitals, molecular geometries, thermodynamic properties, hyperpolarizabilities and harmonic vibrational frequencies of 6-methyluracil (6MU) have been carried out using ab initio Hartree-Fock (HF), density functional theory (DFT) and second order M?ller-Plesset (MP2) methods. All calculations were performed using the GAMESS-US program package with the basis sets 6-31G(d,p) and 6-311G(d,p). FT-IR and Raman spectra of 6MU were recorded in the regions 50–4000 cm⁻¹ and 60–4000 cm⁻¹ respectively. Optimized geometries were obtained using the global optimization procedure. The calculated structural parameters for two conformers of 6MU have been compared with experimentally observed values. The energy barrier (ΔE=ELUMO-EHOMO) between the HOMO and LUMO is predicted on the basis of theoretical calculations. The simulated TD-DFT spectrum has been compared with experimental electronic spectrum for 6MU. The calculated potential energy distribution (PED) values have been utilized to perform vibrational assignment of the infrared and Raman spectra.     

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

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. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 73, No. 6, pp. 721–727, November–December, 2006.     

Calculation of the IR Spectrum of Ethyl Chlorophyllide a by the Method of Density Functional

The structure, frequencies of normal vibrations, and the absolute IR intensities of ethyl chlorophyllide a have been calculated by the DFT/B3LYP/6-31G(d) density functional method. The force constants have been scaled by the Pulay method. The force field of ethyl chlorophyllide a has been obtained in independent and dependent natural coordinates. The vibrational IR spectrum of ethyl chlorophyllide a has been modeled. The experimental IR spectrum of chlorophyll a has been interpreted on the basis of the calculation performed.     

Comparative study of the structural and spectral properties of tetraaza- and tetraoxaannelated tetracirculenes

The IR spectrum of a recently synthesized tetraaza[8]circulene (4N) molecule has been investigated and completely interpreted based on the calculation of the molecular structure and force field within the density functional theory (DFT) using the B3LYP/6-311G(d,p) method. The calculation has also successfully explained the X-ray diffraction data. The same method has been used to calculate the tetraoxa[8]circulene (4О) molecule and perform a comparative analysis of the IR spectra of both molecules. In contrast to 4О, the 4N molecule exhibits strong fluorescence, which hinders measurement of its Raman spectrum; hence, it is only predicted based on the DFT calculation in this study. A comparison of the IR and Raman spectra of the 4N molecule with the experimental and theoretical analogs for the 4О molecule has made it possible to assign all the observed vibrational transitions and explain the nature of normal vibrations in these complex molecules.     

Experimental and theoretical study of the IR spectrum and barriers to internal rotation of 4-hydroxypropyl-4′-cyanobiphenyl

The IR absorption spectrum of polycrystalline 4-hydroxypropyl-4′-cyanobiphenyl is measured in a KBr pellet over the range 400–4000 cm^?1. The structure of the molecule and the frequencies and the intensities of the bands in the spectrum are calculated in the approximation of the B3LYP hybrid density functional with the 6-31 G(d) and 6-31+G(d) basis sets. The normal vibrations are reliably assigned by the method of linear scaling of frequencies, which made it possible to reproduce the experimental IR spectrum with high accuracy. The barriers to internal rotation of phenyl rings and three barriers for the hydroxypropyl radical are calculated.     

Theoretical analysis of the IR and Raman spectra of acridone taking into account intermolecular hydrogen bonds

The geometric parameters, the force field, and the absolute intensities of the IR and Raman spectra of acridone, the hydrogen-bonded dimer of acridone, and its N-deuterated analogue are calculated quantum mechanically in terms of the density functional theory by the B3LYP/6-31G(d) method. The vibrational bands in the IR and Raman spectra of acridone are assigned and interpreted using the calculational data on acridone dimers and the data on the isotopic shifts of vibrational frequencies upon deuteration. The vibrations of acridone and anthraquinone are comparatively analyzed. Original Russian Text ￠ K.V. Berezin, T.V. Krivokhizhina, V.V. Nechaev, 2006, published in Optika i Spektroskopiya, 2006, Vol. 100, No. 1, pp. 20–27.     

Calculation of conformations and vibrational spectra of a fragment of the 2,6-hydroxyethyl cellulose molecule

We have used the molecular mechanics method for conformational analysis of a fragment of the molecule of a water-soluble cellulose ether: 2,6-hydroxyethyl cellulose (2,6-HEC). As a result of rotation about the C-C and C-O bonds within the bulky side substituents on the C5 and C2 backbone atoms in the fragment of the 2,6-HEC molecule, we have obtained 12 of the most stable conformers for this fragment with strain energies differing within the range 0–2.3 kcal/mol. We have shown that the most stable conformers have the following conformations for the groups of atoms on the bonds C5-C6, C6-O6, C13-O6, C10-C13: gt, g⁻, g⁺, g⁺ and gg, t, g⁺, g⁺ respectively; and on the bonds C2-O2, C11-O2, C7-C11: g⁺g⁻, g⁻, g⁺ respectively. For the conformers obtained, using the same method we calculated the frequencies and the potential energy distribution (PED) for their normal vibrations (NV). Comparative analysis showed high sensitivity of both the frequency and the PED of the normal vibrations to conformational changes within the indicated bulky substituents over the entire analyzed spectral region (800–1500 cm⁻¹ for the methylene groups). We introduce the concept of “conformational characteristicity” of both the frequency and the mode of vibration. We show that it is possible to analyze the conformations of the bulky substituents of the fragment of the 2,6-HEC molecule using its vibrational spectrum. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 73, No. 1, pp. 42–53, January–February, 2006.     

Effect of the Pyranose Ring Conformation on the Vibrational Spectra of Sugar Epoxides

Normal vibrations of two sugar epoxides — methyl 2,3-anhydro-4-deoxy--D-ribohexopyranoside and methyl 3,4-anhydro--D-talohexopyranoside — have been carried out by the molecular mechanics method. Parametrization of the force field used has been performed and the parameters of the oxirane ring for sugar epoxides have been determined. A good agreement between the experimentally observed and calculated frequencies has been obtained. The IR spectral absorption bands of the molecules under investigation in the 1500–400-cm^–1 range have been assigned on the basis of the potential energy distribution function of normal vibrations. The investigation of the potential energy surface of these molecules has shown that their pyranose ring can take conformations close to half-chair, boat, skew boat, and twist forms. Comparative analysis of the normal vibrations of various conformers has revealed that the form of the pyranose ring influences the vibrational spectra of sugar epoxides.     

Experimental and theoretical study of the IR spectrum of 4-amyloxy-4′-cyanobiphenyl

The IR absorption spectrum of polycrystalline 4-amyloxy-4′-cyanobiphenyl (5OCB) is measured in a KBr pellet over the range 400–4000 cm^?1. The structure of the molecule and the frequencies and intensities of the bands in the spectrum are calculated in the approximation of the B3LYP hybrid density functional with the 6-31G(d) and 6-31+G(d) basis sets. With the method of linear scaling of frequencies, 39 bands of the experimental IR spectrum are assigned. On the basis of calculations for related compounds, the vibrations belonging to the substituents and the biphenyl fragment are ascertained. It is shown that the IR absorption spectra of polycrystalline 4-hydroxypropyl-4′-cyanobiphenyl and 5OCB are almost identical and differ by the occurrence of three bands associated with vibrations localized on the oxyamyl radical.     

Calculation of the IR spectrum of ethylbacteriochlorophyllide (A) by the density functional method

The structure, the frequencies of the normal vibrations, and the absolute IR intensities of ethylbacteriochlorophyllide (A) are calculated in the approximation of the hybrid density functional B3LYP with the 6–31 G(d) basis set. The scaling of the quantum-mechanical force constants is performed by the Pulay method. The effective force field of ethylbacteriochlorophyllide (A) in the redundant and nonredundant coordinates is obtained. The vibrational IR spectrum is modeled. On the basis of the calculations performed, the experimentally determined IR spectrum of bacteriochlorophyll (A) is interpreted.     

Theoretical analysis of the IR spectrum of methyl-3,4-anhydro-α-D-talohexopyranoside

A detailed interpretation of the IR spectrum of methyl-3,4-anhydro-α-D-talohexopyranoside that is based on complete calculation of normal vibration frequencies and absolute IR absorption band intensities of the molecule and a comparison of the results obtained with the corresponding experimental data is given for the first time. The influence of the epoxy group on the absorption bands characteristic of the pyranose ring has been analyzed. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 75, No. 5, pp. 597–605, September–October, 2008.     

Calculation of frequencies of normal vibrations and interpretation of IR spectra for 2,3-dihydro-3-O-(1,4-naphthoquinon-2-yl)-2-oxo-1,4-naphthoquinone derivatives

We have used B3LYP/6-31(d) density functional theory to calculate the frequencies and modes of the normal vibrations of 2-oxo-2,3-dihydro-and 2-methoxy-1,4-naphthoquinones. Based on these calculations within an additive model, we have assigned the carbonyl bands in the IR spectra of 2,3-dihydro-3-O-(1,4-naphthoquinon-2-yl)-2-oxo-1,4-naphthoquinones (diquinones 1–4). We have carried out a direct calculation of the vibrational spectra for diquinones 1–4 using PBE and B3LYP correlation functionals. We have shown that the calculation of the vibrational spectra of the diquinones based on an additive model on the whole is quite consistent with the results of direct calculations and the experimental spectra. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 73, No. 6, pp. 713–720, November–December, 2006.     

Calculation of conformations and vibrational spectra of a monomeric fragment of the 2,6-carboxymethyl cellulose molecule

A theoretical conformational analysis has been carried out for the side substituents of a fragment of the molecule for 2,6-carboxymethyl cellulose (a water-soluble cellulose ether), and the frequencies and the potential energy distribution of the normal vibrations have been calculated for the most stable conformers of the ether groups of this fragment in the approximation of the molecular mechanics method. It has been shown that the most stable conformers are those that have the conformations gg, t, g⁻, g⁻, g⁻-for the groups of atoms on the bonds C5-C6, C6-O6, C13-O6, C10-C13, C10-O9 and the conformations g⁺g⁻, g⁺, g⁻, g⁻; g⁺g⁻, g⁻, g⁻, g⁻; g⁺g⁻, g⁻, g⁺, t for the groups of atoms on the bonds C2-O2, C11-O2, C7-C11, C7-O8. Comparative analysis of the calculated frequencies and the potential energy distribution of the normal vibrations for 13 of the most stable conformers showed, as in the case of the 2,6-hydroxyethyl cellulose molecule, that the frequencies and modes of the normal vibrations are highly sensitive to conformational transitions in the analyzed spectral region (800–1500 cm⁻¹). The characteristic patterns for the change in the frequencies and modes of the normal vibrations have been established in connection with conformational transitions within both side substituents. The observed conformational lability of the bulky substituents in the cellulose ether molecules and its manifestations in the vibrational spectrum provide a basis for hypothesizing that one of the major mechanisms for the process of their thermal gelation in aqueous solutions is conformational transitions within these substituents. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 1, pp. 5–15, January–February, 2007.