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−1. The maximum red shifts of the OH-stretching modes caused by the formation of the O-H⋯O hydrogen bonds were 407 cm−1 (K-DMSO) and 537 cm−1 (K-DMeSO), respectively. The Al-O-H bending modes are spread over the large interval of 100–1200 cm−1, but the dominant contributions are concentrated between 800 and 1200 cm−1. 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.

Vibrational spectra of two kaolinite-dimethylsulfoxide intercalates, obtained using inelastic neutron scattering (INS), were analyzed with a view to understanding the dynamics of the hydrogen atoms in the structure. The main focus was on the spectral region 0–1700 cm−1, which is difficult to analyze using optical spectroscopy. The experimental vibrational spectra of kaolinite:dimethylsulfoxide and kaolinite:d6-dimethylsulfoxide collected using two different spectrometers were interpreted by means of the solid-state DFT calculations. Calculated spectra were obtained by both normal-mode analysis and molecular dynamics going beyond the harmonic approximation. The Al-O-H bending modes were found to be spread over the large interval 100−1200 cm−1, with the dominant contributions located between 800 and 1200 cm−1. The shape of the individual hydrogen spectrum depends on whether or not the respective hydrogen atom is involved in an O-H⋯O hydrogen bond and on its strength. The modes corresponding to the in-plane movements of the inner-surface hydrogen atoms are well defined and always appear at the top of the intervals of energy transfer. In contrast, the modes generated by the out-of-plane movements of the hydrogen atoms are spread over large energy intervals extending down to the region of external (lattice) modes. The C-H modes are concentrated mainly in the three regions 1200–1450 cm−1, 800–1100 cm−1, and 0–400 cm−1. While the first two regions are typical of the various deformational modes of methyl groups, the low-energy region is populated by the modes corresponding to the movements of the whole dimethylsulfoxide molecule.

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, 13C CP-magic angle spinning nuclear magnetic resonance (MAS NMR), and 27Al and 29Si 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 (d001 = 11.1 Å — wet; d001 = 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 OCH3 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: νasCHmet > νasCHmtx > νsCHmet > νsCHmtx.

The crystal chemistry characteristics of a hydroxyl-fluor apatite from a recently discovered kalsilite-bearing leucitite from Abruzzi, Italy, were investigated by electron microprobe, single crystal X-ray diffraction, IR, Raman and micro-Raman spectroscopy. The apatite has exceptionally high S and relatively high Si, Sr and LREE, whereas the HREE content is negligible. The IR spectra confirm the presence of OH calculated from formula difference. A high positive correlation between Ca-site Substitution Index (CSI = 100(10-Ca)/Ca) and Tetrahedral Substitution Index (TSI = 100 (Si+C+S)/P atom/a.p.f.u.) and a systematic parallel increase in REE, S and Si indicate two substitution mechanisms, i.e. REE3+ + Si4+ = Ca2+ + P5+ and Si4+ + S6+ = 2 P5+. Site occupancy data and bond lengths, determined from structural refinements on selected samples, demonstrate that LREE and Sr show a marked preference for the Ca2 site, even though in the LREE-rich samples a partial substitution of LREE for Ca in the Cal site was observed.

Tetrahedral distances (from 1.535 to 1.541 Å.) reflect the substitution of Si4+ and S6+ for P5+, which is also confirmed by vibrational spectra. As (SiO4)4− and (SO4)2− substitute for (PO4)3−, the relative intensity of v1 Raman bands of (SO4)2− (at 1007 cm−1) and (SiO4)4− (at 865 cm−1) increase systematically, while that of phosphate decreases and the five components of phosphate v3 modes disappear. Moreover, the (PO4)3− Raman peak broadening is linearly correlated with the Si and S concentrations.

Apatite crystals are sometimes zoned with compositions varying from SiO2 = 1.15–2.07 wt.%, Σ(LREE2O3) = 0.56–1.08 wt.% and SrO = 0.58–1.02 wt.% in the core to 3.98–5.03, 4.14–6.73 and 1.97–2.17, respectively, in the rim. A sharp, strong enrichment in Sr and LREE in the rim indicate that the apatite suddenly became an acceptor of these elements in the late stages of crystallization.

A CO-bearing member of the hydroxylapatite–hydroxylellestadite series occurs as a Si-rich part of a hydroxylapatite–hydroxylellestadite series mineral (hydroxylapatitess) in a skarn xenolith from Tadano, Fukushima Prefecture, Japan. Hydroxylapatitess is composed of Si-poor and Si-rich parts. The Si-poor part is F-rich hydroxylapatite. The infrared spectrum of the Si-rich part demonstrates the presence of B-type CO3. A representative analysis of the Si-rich part yielded the empirical formula Ca4.989[(PO4)1.315 (SiO4)0.848 (SO4)0.368(CO2.943)0.480]∑3.011(OH0.629 Cl0.264 F0.107)∑1.000 on the basis of 8 cations, assuming Si = S + C. There is a very strong inverse correlation between Si and P in both the Si-poor and Si-rich parts. These data indicate that the substitution mechanism (SO4,CO3)2– + (SiO4)4– = 2(PO4)3– probably occurs in hydroxylapatite ss. Therefore, it was concluded that the Si-rich part corresponds to a CO3-bearing hydroxylapatite–hydroxylellestadite series mineral with CO3 partially replacing SO4. Most of the Si-rich part shows CO3 > SO4 and its composition approaches Ca5(SiO4)1.5(CO3,SO4)1.5(OH,Cl,F).