Hydrogen bonding and vibrational spectra in kaolinite-dimethylsulfoxide and -dimethylselenoxide intercalates - A solid-state computational study

The aims of this study were to obtain accurate structural information on the dimethyl sulfoxide (DMSO) and dimethylselenoxide (DMSeO) kaolinite intercalates, paying close attention to the hydrogen-bond geometries, and to provide a detailed interpretation of the individual vibrational modes of intercalates under study and relate their energies to the formation of the hydrogen bonds. Accurate positions of all the atoms in the structures of kaolinite:dimethylsulfoxide (K:DMSO) and kaolinite:dimethylselenoxide (K:DMSeO) intercalates have been obtained by the total energy minimization in solid state at density functional theory (DFT) level of the theory. The bond distances and angles in the kaolinite 1:1 layer are in good agreement with those reported in the most recent single-crystal refinement of kaolinite. Computed geometries of DMSO and DMSeO agree well with the high-quality diffraction data and independent theoretical ab initio calculations. The organic molecules are fixed in the interlayer space mainly by three moderately strong O - H...O hydrogen bonds, of different strengths, with the O...O contact distances being within 2.739-2.932 Å (K:DMSO) and 2.681-2.849 Å (K:DMSeO). Substantially weaker C - H...O and O - H...S(Se) contacts play only a supporting role. The optimized atomic coordinates were used to calculate the individual vibrational modes between 0 and 4000 cm. The maximum red shifts of the OH-stretching modes caused by the formation of the O - H...O hydrogen bonds were 407 cm (KaDMSO) and 537 cm (K-DMeSO), respectively. The Al - O - H bending modes are spread over the large interval of 100-1200 cm, but the dominant contributions are concentrated between 800 and 1200 cm. Theoretically calculated energies of the OH- and CH-stretching modes show good agreement with the previously published figures obtained from the infrared and Raman spectra of these intercalates

Influence of synthesis conditions on the formation of a Kaolinitemethanol complex and simulation of its vibrational spectra

Kaolinite is often used as a base for the synthesis of new organo-mineral nanomaterials designed for applications in industry and in environmental protection. To make the mineral structure more likely to interact with organic molecules, a kaolinite-methanol complex (KM) can be used. In the present study, different experimental procedures were tested to investigate the formation of the KM. The kaolinitedimethyl sulfoxide intercalation compound (KDS), either wet or dried, was used as a pre-intercalate. The samples obtained were characterized using X-ray diffraction, Fourier-transform infrared spectroscopy, CHNS elemental analysis, C CP-magic angle spinning nuclear magnetic resonance (MAS NMR), and Al and Si MAS NMR techniques. The method of density functional theory with dispersion corrections (DFT-D2) was used to explain the structure and to simulate the vibrational spectra of KM. Theoretical results were compared with experimental data. The most effective formation of the KM (d = 11.1 Å wet; d = 8.7 Å dried) was observed when the dried KDS precursor was used. In such conditions the degree of intercalation reached ~98% after 24 h of reaction time. As indicated by the CHNS elemental analysis, ~1/6 of the inner-surface OH groups were grafted by OCH groups. The esterification reaction was less efficient at higher temperatures or when wet KDS was used. In the latter case, the excess of very polar dimethyl sulfoxide molecules prevented intercalation of methanol and further grafting. Detailed analysis of the results of theoretical simulations revealed that the reaction of the KDS with methanol led to the formation of kaolinite with both grafted methoxy groups and intercalated methanol, and water molecules in the interlayer space. The spectra calculated revealed the contribution of individual vibrational modes into the complex bands, i.e. the energy of C-H vibrations was in the order:vCH> vCH> vCH> vCH

Crystal Structure, Infrared Spectra and DFT Study of Benzyl 2,3-Anhydro-β-D-Ribopyranoside

The crystal structure of benzyl 2,3-anhydro-β-D-ribopyranoside is orthorhombic, P2₁2₁2₁, Z = 4. The pyranose ring adopts the E_O conformation distorted considerably to the ⁵H_O direction. The molecules of the title compound are linked into infinite chains running along the a-axis by bifurcated O–H···O hydrogen bonds. Interaction energies of these hydrogen bonds are significantly different, ~−5.4 for the bond with the smaller and ~−1.1 kcal/mol for the bond with the larger O···O separation. The hydrogen-bond pattern is completed by the two weaker C–H···O intermolecular hydrogen bonds, aiming at the epoxy oxygen atom. IR vibrational spectrum was interpreted by means of comparison with the full list of vibrational modes predicted using DFT method in the solid state. While till 1495 cm⁻¹ the individual bands can be reconciled with single calculated modes, the region below this limit is populated by heavily overlapped HCH, HCO, HOC, COC and HCC bending modes merged with few ν(CC) and ν(CO) modes. The respective “red” shifts of the positions of the ν(OH) bands correlate well with the size of the O···O separation