Nacrite crystals from a vug within a matrix of dickite at Red Mountain near Silverton, Colorado, have a = 8.906(2), b = 5.146(1), c = 15.664(3) Å, β = 113.58(3)°, V = 657.9(3) Å3, and space group Cc. The structure was solved by direct methods to determine phase angles, followed by electron density maps to locate all atoms. Refinement by least-squares ceased at R = 4.5%. Each 7 Å layer has structural detail very similar to those of dickite and kaolinite, although nacrite stacking is based on — a/3 interlayer shifts along the 8.9 Å axis (with octahedral cations alternating between the I and II sites in successive layers), whereas dickite and kaolinite are based on shifts of — a/3 along the 5.1 Å axis (with octahedral cations in the same set of sites in each layer). The angle of tetrahedral rotation is 7.8°, and the octahedral counterrotations are 7.6° and 8.1°. The H+ protons were located on DED maps. The inner 0..H1 vector points exactly toward the vacant octahedron and is depressed — 18.6° away from the level of the octahedral cations. All three surface OH groups have 0...H vectors at 50° to 66° to (001), although OH2 may not participate in interlayer hydrogen bonding. All three interlayer OH-H-O contacts are bent to angles between 132° and 141° and form contacts between 2.94 and 3.12 Å. The interlayer separation of 2.915 Å is slightly larger than in dickite, interpreted as due to a less favorable meshing of the oxygen and hydroxyl surfaces in nacrite—a direct consequence of layer shifts along the 8.9 Å axis.

A detailed structural characterization of organo-clays is a key in understanding their properties. In this work, mono-, di-, tri-, and tetra-butylammonium (nBA; n = 1–4) cations intercalated in the layered clay mineral montmorillonite (Mnt) have been studied for the first time by combining a theoretical approach based on density functional theory (DFT) and infrared spectroscopy. The DFT calculations revealed the detailed structure and position of nBA cations in the interlayer space. A relation between the basal spacing (d001 parameter) and the cation size and structure was found, and explained with respect to the structure, composition, and size of the organic cations. Hydrogen bonds between -NHx/-CH3/-CH2 groups of the nBA cations and oxygen atoms of the basal planes of the Mnt layers were found to be an important factor for the arrangement and energetic stabilization of cations in the interlayer space. The N-H-O hydrogen bonds are stronger than C-H-O hydrogen bonds and the stabilization decreases with decreased number of bands. Analysis of DFT-calculated vibrational modes helped in understanding a problematic region of the experimental infrared spectra (4000–3000 cm-1), in which assignment of all vibrational modes unambiguously was not possible because of a significant overlap of broad bands.

A hybrid of montmorillonite (Mnt) and rifampicin (RIF) was synthesized and the structure and stability of the drug carrier system clarified. Density functional theory calculations involving dispersion corrections (DFT-D3) were performed to characterize interactions acting in the interlayer space of montmorillonite intercalated with rifampicin. The structure and stability of the RIF-Mnt intercalated complex were determined. Calculations revealed the deformation of the molecular structure of rifampicin after intercalation into the Mnt interlayer space due to the clay environment. The ansa chain of RIF was bent in the interlayer space compared with the structure of the RIF molecule in the monocrystal. RIF was keyed into the Mnt surface by means of numerous hydrogen bonds of weak to moderate strength. The calculated vibrational spectrum from ab initio molecular dynamics (AIMD) was in good agreement with the FTIR measured spectra and helped to analyze the overlapped vibrational bands. Based on analysis of structural stability, theoretical calculations revealed that Mnt is a suitable drug carrier for delayed release of the RIF drug. Batch adsorption experiments showed the large adsorption capacity of montmorillonite for RIF.

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.

A new occurrence of kintoreite, ideally PbFe3(PO4)(PO3OH)(OH)6, is described from the Tripi mine, Alì, Peloritani Mountains, northeastern Sicily, Italy. Kintoreite occurs as yellow equant crystals, up to 0.05 mm in size, on quartz, associated with another alunite-supergroup mineral currently under study. The studied grains of kintoreite are chemically zoned, showing the occurrence of two distinct domains. Electron microprobe analyses gave (in wt.%): SO3 5.47(27), P2O5 17.55(14), Al2O3 7.81(35), Fe2O3 23.81(44), PbO 35.11(41), H2Ocalc 9.93, total 99.68 (darker domains) and SO3 6.03(5), P2O5 16.66(23), Al2O3 4.22(2), Fe2O3 27.31(6), PbO 33.78(22), H2Ocalc 10.25, total 98.25 (brighter domains). On the basis of 14 O atoms per formula unit (apfu) and (P+S) = 2 apfu, the darker and brighter domains have chemical formula Pb1.00(Fe3+1.89Al0.97)Σ2.86[P1.57S0.43O7.43(OH)0.57][(OH)5.58(H2O)0.42]Σ6.00 and Pb0.98(Fe3+2.21Al0.53)Σ2.74[P1.51S0.49O7.49(OH)0.51][(OH)5.18(H2O)0.82]Σ6.00, respectively. Single-crystal X-ray diffraction was performed on a grain extracted from the same sample. Unit-cell parameters are a = 7.2191(10), c = 16.834(3) Å, V = 759.8(3) Å3 and Z = 3; space group R$\bar{3}$m. The crystal structure was refined on the basis of 226 unique reflections with Fo > 4σ(Fo) and 31 least-square parameters to R1 = 0.0415. Kintoreite is isotypic with other alunite-supergroup minerals. Micro-Raman spectroscopy suggests the possible occurrence of H2O groups, supporting the possible protonation of (OH) groups as a charge-balance mechanism in this mineral. Kintoreite may play an environmental role in the Alì area, where previous authors detected high concentrations of potentially toxic elements in soils.

Khademite, ideally Al(SO4)F(H2O)5, from the Monte Arsiccio mine, Apuan Alps, Tuscany, Italy, has been characterised through quantitative electron microprobe analysis, micro-Raman spectroscopy and single-crystal X-ray diffraction. Khademite occurs as colourless to whitish tabular crystals, up to 5 mm. Electron microprobe analysis (in wt.%, average of 20 spot analyses) gave: SO3 35.43, Al2O3 21.27, F 6.92, H2Ocalc 39.73, sum 103.35, –O = F 2.92, total 100.43. On the basis of 10 anions per formula unit, assuming the occurrence of 5 H2O groups and 1 (F+OH) atom per formula unit, its chemical formula can be written as Al0.96S1.02O4[F0.84(OH)0.16]Σ1.00⋅5H2O. The Raman spectrum of khademite is characterised by the occurrence of vibrational modes of SO4 groups and by broad and strong bands due to the O–H stretching modes. Khademite is orthorhombic, space group Pcab, with unit-cell parameters a = 11.1713(2), b = 13.0432(3), c = 10.8815(2) Å, V = 1585.54(5) Å3 and Z = 8. The crystal structure refinement converged to R1 = 0.0293 on the basis of 2359 unique reflections with Fo > 4σ(Fo) and 152 refined parameters. The crystal structure of khademite is characterised by the alternation, along b, of two distinct kinds of {010} layers, one formed by [001] rows of isolated Al-centred octahedra, connected to each other through H bonds, and the other showing isolated SO4 groups. Along b, oxygen atoms belonging to SO4 groups act as acceptor of H bonds from H2O groups coordinating Al atoms. The new data improved the description of the H bonds in khademite and led us to discuss about the possible existence of its (OH)-analogue, rostite. In addition, Raman spectroscopic data were collected on the same crystal used for the crystal-chemical characterisation, allowing a comparison with previous results.

The crystal structure of the fibrous mineral arangasite, Al2F(PO4)(SO4)·9H2O from the Alyaskitovoje deposit, Eastern Yakutiya, Russia, was solved using low-temperature single-crystal data from synchrotron radiation and refined against F 2 to R = 9.8%. Arangasite crystallizes in the monoclinic space group P2/a, with unit-cell parameters a = 7.073(1), b = 9.634(2), c = 10.827(2) Å, β = 100.40(1)°, V = 725.7(7) Å3 and Z = 2. The positions of all the independent H atoms were obtained by difference- Fourier techniques and refined in an isotropic approximation. The arangasite crystal structure is built from one-dimensional chains of Al octahedra and PO4 tetrahedra sharing vertices, quasi-isolated SO4 tetrahedra and H2O molecules. All O atoms are involved in the system of H bonding, acting as donors and/or acceptors. Hydrogen bonding serves as the only mechanism providing linkage between the main structural fragments, thus maintaining the framework. Chains of corner-sharing Al octahedra and P tetrahedra in the arangasite structure are topologically identical to the chains built from (Fe, Al) octahedra and P tetrahedra in the crystal structure of destinezite, Fe2(OH)(PO4)(SO4)·6H2O. It has been shown that in spite of very similar chemical formulae, arangasite and sanjuanite, Al2(OH)(PO4)(SO4)·9H2O, are not isotypic.

Hydrothermal synthesis produced the new compound SrCo2(AsO4)(AsO3OH)(OH)(H2O). The compound belongs to the tsumcorite group (natural and synthetic compounds with the general formula M(1)M(2)2(XO4)2(H2O,OH)2; M(1)1+,2+,3+ = Na, K, Rb, Ag, NH4, Ca, Pb, Bi, Tl; M(2)2+,3+ = Al, Mn3+, Fe3+, Co, Ni, Cu, Zn; and X5+,6+ = P, As, V, S, Se, Mo). It represents (1) the first Sr member, (2) the until now unknown [7]-coordination for the M(1) position, (3) the first proof of (partially) protonated arsenate groups in this group of compounds, and (4) a new structure variant.

The crystal structure of the title compound was determined using single-crystal X-ray diffraction data. The compound is monoclinic, space group P21/a, with a = 9.139(2), b = 12.829(3), c = 7.522(2) Å, β = 114.33(3)°, V = 803.6(3) Å3, Z = 4 [wR2 = 0.065 for 3530 unique reflections]. The hydrogen atoms were located experimentally.

Marécottite, ideally Mg3[(UO2)4O3(OH)(SO4)2]2(H2O)28, a triclinic, Mg-dominant member of the zippeite group, was described originally from a small uranium deposit at La Creusaz in Wallis (Switzerland). It has recently been found at Jáchymov (Czech Republic), where it forms exceptional crystals, up to 0.3 mm across. According to an electron microprobe study of these crystals, marécottite from Jáchymov is chemically similar to the material from the La Creusaz deposit. However, the Jáchymov crystals exhibit more cation substitution (Zn2+ and Mn2+ for Mg2+). The chemical composition of marécottite from Jáchymov corresponds to the empirical formula [(Na0.05K0.07)Σ0.12(Mg1.83Zn0.41Mn0.41Cu0.15Ni0.08)Σ2.88Al0.07]Σ3.07(UO2)8[(SO4)3.77(SiO4)0.21]Σ3.98O6(OH)1.84·28H2O (the mean of four representative spots; calculated on the basis of eight U atoms and 28 H2O per formula unit and 1.84 OH for charge balance). According to single-crystal X-ray diffraction, marécottite from Jáchymov is triclinic, P1, a = 10.8084(2), b = 11.2519(3), c = 13.8465(3) Å, α = 66.222(2), β = 72.424(2), γ = 70.014(2)o, V = 1421.57(6) Å3 and Z = 1. The crystal structure was refined from a highly redundant dataset (30,491 collected reflections) to R1 = 0.0367 for all 7042 unique reflections. The refined structure confirms the previously determined structure for the crystal from the La Creusaz deposit. An extensive network of hydrogen bonds is an important feature that keeps the whole structure together, but the positions of H atoms had not been determined previously. The H-bond scheme proposed based on a detailed bond-valence analysis and the role of different types of molecular H2O in the structure is discussed.

This is a tour of a physical chemist through 65 years of protein chemistry from the time when emphasis was placed on the determination of the size and shape of the protein molecule as a colloidal particle, with an early breakthrough by James Sumner, followed by Linus Pauling and Fred Sanger, that a protein was a real molecule, albeit a macromolecule. It deals with the recognition of the nature and importance of hydrogen bonds and hydrophobic interactions in determining the structure, properties, and biological function of proteins until the present acquisition of an understanding of the structure, thermodynamics, and folding pathways from a linear array of amino acids to a biological entity. Along the way, with a combination of experiment and theoretical interpretation, a mechanism was elucidated for the thrombin-induced conversion of fibrinogen to a fibrin blood clot and for the oxidative-folding pathways of ribonuclease A. Before the atomic structure of a protein molecule was determined by x-ray diffraction or nuclear magnetic resonance spectroscopy, experimental studies of the fundamental interactions underlying protein structure led to several distance constraints which motivated the theoretical approach to determine protein structure, and culminated in the Empirical Conformational Energy Program for Peptides (ECEPP), an all-atom force field, with which the structures of fibrous collagen-like proteins and the 46-residue globular staphylococcal protein A were determined. To undertake the study of larger globular proteins, a physics-based coarse-grained UNited-RESidue (UNRES) force field was developed, and applied to the protein-folding problem in terms of structure, thermodynamics, dynamics, and folding pathways. Initially, single-chain and, ultimately, multiple-chain proteins were examined, and the methodology was extended to protein–protein interactions and to nucleic acids and to protein–nucleic acid interactions. The ultimate results led to an understanding of a variety of biological processes underlying natural and disease phenomena.

The three-dimensional structure of the 56 residue polypeptide Apis mellifera chymotrypsin/cathepsin G inhibitor 1 (AMCI-1) isolated from honey bee hemolymph was calculated based on 730 experimental NMR restraints. It consists of two approximately perpendicular β-sheets, several turns, and a long exposed loop that includes the protease binding site. The lack of extensive secondary structure features or hydrophobic core is compensated by the presence of five disulfide bridges that stabilize both the protein scaffold and the binding loop segment. A detailed analysis of the protease binding loop conformation reveals that it is similar to those found in other canonical serine protease inhibitors. The AMCI-1 structure exhibits a common fold with a novel family of inhibitors from the intestinal parasitic worm Ascaris suum. The pH-induced conformational changes in the binding loop region observed in the Ascaris inhibitor ATI are absent in AMCI-1. Similar binding site sequences and structures strongly suggest that the lack of the conformational change can be attributed to a Glu → Gln substitution at the P1′ position in AMCI-1, compared to ATI. Analysis of amide proton temperature coefficients shows very good correlation with the presence of hydrogen bond donors in the calculated AMCI-1 structure.