The introduction of artificial ±b/3 stacking faults into well-crystallized kaolinite by intercalating and removing hydrazine had no observable effect on the solid-state 29Si nuclear magnetic resonance spectrum of kaolinite. Also, the introduction of such stacking faults did not alter the hydroxyl-stretching region of the infrared spectrum, implying no change in the hydrogen bonding between the displaced layers. Calculations of Si...H distances and Si-O...H angles from reported structures for kaolinite indicated that the resolution of the two Si chemical environments was due to differences in hydrogen-bonding at the surface of the silicate sheet.

The possible physical and chemical forces controlling the volume change behavior of kaolinite were ascertained from the sediment volume of kaolinite in various solvents under no external load condition and from conventional oedometer measurements of kaolinite in several pore fluids. The minimum sediment volume of 14.5 cm3/10 g clay occupied by kaolinite in water where repulsive (R) forces were dominant indicated that the R contribution was insignificant for kaolinite. The maximum sediment volume of 25.0 cm3/10 g clay in benzene where coulombic attraction forces were significant suggested that electrostatic attraction between silicate sheets and midplane cations and van der Waals forces were not appreciable for kaolinite. The positive edge-negative face bonding of kaolinite particles in benzene was unlikely because the protons required to impart a positive charge to the edges were not available in the nonpolar solvent. The 3688 cm−1 band in the infrared spectrum of a kaolinite-dimethylamine sample decreased by 10 cm−1 on H-bond formation of the solvent molecule with the exposed structural hydroxyls of the octahedral sheet. The adsorbed solvent molecules likely H-bonded with an adjacent clay particle. That such interparticle H-bonds controlled the sediment volume and interparticle attraction in kaolinite was indicated by the decrease in sediment volume with increase in dipole moment of the solvent molecule, i.e., 25.0 cm3/10 g clay in n-heptane (dipole moment, μ = 0), 23.5 cm3/10 g clay in toluene (μ = 0.36), 17.0 cm3/10 g clay in ethanol (μ = 1.67), and 14.5 cm3/10 g clay in water (μ = 1.84).

In the oedometer tests with various pore fluids, a high void ratio (i.e., volume of voids/volume of solids) of ≈ 1.3 was obtained for kaolinite in n-heptane, and hexane (μ ≅ 0) at an external pressure of 1 kg/cm2 probably because the weakly bonded kaolinite particles were randomly oriented. At the corresponding applied pressure a lower void ratio of 0.88 resulted in water (μ = 1.84) where the stronger hydrogen bond between flat layer surfaces of adjacent particles favored a parallel orientation of clay particles.

The variations in void ratio-external pressure relationship indicated that kaolinite underwent lower compressibility in a solvent with low dipole moment and vice versa. Thus, the interparticle H-bond did not play a significant role in controlling the shear resistance and volume change behavior. The volume change behavior was essentially controlled by frictional forces and clay fabric. In nonpolar solvents the random arrangement of kaolinite particles and the frictional forces mobilized a high shear resistance on the application of a consolidation pressure, resulting in a lower compressibility. In a solvent with high dipole moment the parallel array of clay particles mobilized less shear resistance and produced a greater compression.

2H NMR spectra of synthetic deuterated kaolinite have been collected in the temperature range from 150 K to 350 K. Hydroxyl groups show a Pake doublet pattern with an asymmetry factor of 0. They are almost fixed spatially, and undergo a wobbling motion with increasing temperature. The quadrupole coupling constant is 273 ± 3 kHz at 150 K, which indicates that interlayer hydrogen bonding is relatively weak.

Some aspects of the crystal structure of illite are not understood properly yet, in spite of its abundance and significance as a component of soils, sediments, and low-grade metamorphic rocks. The present study aimed to explore the role of hydronium cations in the interlayer space of illite in a theoreticalexperimental approach in order to clarify previous controversial reports. The infrared spectroscopy of this mineral has been studied experimentally and by means of atomistic calculations at the quantum mechanical level. The tetrahedral charge is critical for the stability of the hydronium cations, the presence of which has probably been underestimated in previous studies. In the present study, computational studies have shown that the hydronium cations in aqueous solutions are likely to be intercalated in the interlayer space of illite, exchanging for K cations. During the drying process these cations are stabilized by hydrogen bonds in the interlayer space of illite.

Divalent sulfur (S) forms a chalcogen bond (Ch-bond) via its σ-holes and a hydrogen bond (H-bond) via its lone pairs. The relevance of these interactions and their interplay for protein structure and function is unclear. Based on the analyses of the crystal structures of small organic/organometallic molecules and proteins and their molecular electrostatic surface potential, we show that the reciprocity of the substituent-dependent strength of the σ-holes and lone pairs correlates with the formation of either Ch-bond or H-bond. In proteins, cystines preferentially form Ch-bonds, metal-chelated cysteines form H-bonds, while methionines form either of them with comparable frequencies. This has implications for the positioning of these residues and their role in protein structure and function. Computational analyses reveal that the S-mediated interactions stabilise protein secondary structures by mechanisms such as helix capping and protecting free β-sheet edges by negative design. The study highlights the importance of S-mediated Ch-bond and H-bond for understanding protein folding and function, the development of improved strategies for protein/peptide structure prediction and design and structure-based drug discovery.

Graphene (G) has attracted great interest because of its excellent chemical and electrical properties. However, the aggregation of graphene restricts its application. Herein, linoleic acid sodium salt (LASS), a low-cost and environmentally friendly material, was used to improve the dispersion of graphene through covalent interaction. Then, the mixture (G@LASS) was integrated with acrylic resin matrix via hydrogen bond between the carboxyl and ester groups. The excellent interfacial compatibility between G@LASS and acrylic matrix, as well as good dispersibility of G@LASS, was demonstrated by Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, Raman, and scanning electron microscopy tests. Compared with acrylic matrix, the surface hydrophobicity of G@LASS@Acrylic increased considerably because of its compact structure. G@LASS@Acrylic composites meet the requirement of antistatic materials when the content of G was only about 0.5 wt%. The results showed that conductive pathways were established successfully through this method.

Rectorite (REC) was modified with dodecyl benzyl dimethyl ammonium chloride (1227) to form an organic-modified rectorite, termed OREC. The OREC was used as a filler additive to modify gel polymer electrolytes (GPEs) which consisted of polymethyl methacrylate (PMMA), propylene carbonate (PC) and LiClO4. Studies of ionic conductivity and viscosity of liquid electrolytes and pure PC, respectively, clearly showed that these properties are greatly influenced by temperature and the amount of OREC added; a consequence of the interactions between the components of CPEs. The Fourier transform infrared (FTIR) spectroscopy results indicated that there were two kinds of interaction: namely (1) a strong hydrogen bond between Si–OH and C=O of PC and (2) a weak interaction between Li+ and C=O. Inverse gas chromatography (IGC) research supported the FTIR interpretation, indicating that the two interactions exist and that the H bond is the stronger of the two. In CPEs, the polymer matrix of PMMA merely supports the active components and does not influence the interactions between them. The OREC greatly increased the crucial plasticizer maintenance property when the amount of clay added was optimum.

The crystal structure, including hydrogen positions, of borcarite, Ca4Mg[B4O6(OH)6](CO3)2, monoclinic, a = 17.840(4), b = 8.380(2), c = 4.445(1) Å, β = 102.04(3)°, V = 649.9(3) Å3, space group C2/m, has been refined by full-matrix least-squares methods to R = 2.5% and wR = 3.0% for 1020 unique observed [|F| ≥ 5σ(F)] reflections collected using Mo-Kα X-radiation. The H positions were located on difference-Fourier maps and were refined using the ‘soft’ constraint that O-H distances are ∼ 0.96 Å. The 4:4T FBB (fundamental building block) of the borcarite structure contains four Bϕ4 tetrahedra (ϕ = unspecified ligand) which share corners to form a four-membered polyhedral ring. Borcarite is the only mineral known to contain this FBB. The FBBs do not polymerize, but each shares three anions with an Mgϕ6 octahedron on either side, forming rods of composition [MgB4O6(OH)6]4- along the c-axis. The rigidity of these rods is enhanced by hydrogen bonding, and individual rods are connected through Caϕ8 polyhedra, Cϕ3 triangles and hydrogen bonds.

Ab initio total energy calculations based on the local density approximation (LDA) and using a conjugate-gradient solver for the Kohn-Sham equations have been performed for cordierite, brucite, (Mg(OH)2) and diaspore (AlOOH). The calculated fractional coordinates of all structures are in good agreement with experimental diffraction data. The angle of the non-linear hydrogen bond in diaspore is reproduced well. The Raman active OH stretching frequency in brucite has been calculated using the frozen phonon approach and the calculated stretching frequency is in very good agreement with the observed value. The energetically most favourable calculated orientation of the proton-proton vector of an H2O molecule incorporated in the structural channels of cordierite agrees with findings deduced from spectroscopic data, and the calculated energy of hydration is in reasonable agreement with calorimetric data. It is therefore concluded that ab initio total energy calculations can confidently be used to predict properties of hydrogen bonded structures, which is difficult with conventional parameterized static lattice energy minimization calculations. An extension to the model is necessary to improve the agreement of the predicted to the observed lattice parameters for small structures.

Marshallsussmanite (IMA2013-067) is a new pyroxenoid mineral from the Wessels mine, Kalahari Manganese Field, Northern Cape Province, South Africa. Marshallsussmanite has ideal formula NaCaMnSi3O8(OH) and triclinic P$\bar{1}$ symmetry. Marshallsussmanite forms vitreous pink bladed crystals to 2.1 cm. The mineral shows perfect cleavage on both {100} and {001}. The chemical composition from electron microprobe (average of 20 analyses) and inductively coupled plasma mass spectrometer analysis (average of three analyses) is Li2O 0.43, Na2O 8.06, MgO 0.08, CaO 15.33, MnO 21.79, SiO2 51.71; totalling 97.40 wt.%. The empirical formula, normalized to 3 Si and assuming 1 H apfu is Li0.100Na0.906Ca0.953Mg0.007Mn1.071Si3O8(OH). Unit-cell parameters from single crystal X-ray diffraction are a = 7.7854(4), b = 6.9374(4), c = 6.8516(3) Å, α = 90.683(3)°, β = 94.330(3)°, γ = 102.856(3)°, V = 359.59(3) Å3; Z = 2. The crystal structure refinement converged with Robs = 0.0248 and site occupancy refinement gives crystal chemistry [Na0.948Li0.052][Ca0.793Mn0.207] [Mn0.937Ca0.063]Si3O8(OH). Marshallsussmanite is a single chain silicate with a repeat interval of three tetrahedra (i.e. dreier chain). Marshallsussmanite is a member of the pectolite group of pyroxenoids, which also includes barrydawsonite-(Y), cascandite, pectolite, serandite and tanohataite. Parallel silicate chains form layers, intercalated with well-ordered cation layers. Calcium and Mn both exhibit octahedral coordination, while Na has four bonded interactions in a coordination sphere (radius 3 Å) of seven separate O atoms. Procrystal electron density and bond valence modelling results are compared. The mineral has an unusually strong hydrogen bond with O4⋅⋅⋅O3 separation of 2.458(2) Å. Unlike pectolite and serandite, O4 in marshallsussmanite acts as an H-bond donor and O3 is an H-bond acceptor. Cation ordering in pyroxenoids has a substantial impact on the H position and corresponding H-bonding schemata.

X-ray and neutron fiber diffraction has been used to study cellulose as it is converted from its naturally occurring crystal phase, cellulose I, to an activated crystal phase, cellulose IIII, by ammonia treatment. The detailed crystal structures determined for cellulose Iβ, an intermediate ammonia-cellulose I complex, and cellulose IIII, reveal a structural transition pathway: hydrogen bonded sheets of chains in cellulose Iβ slip with respect to each other to accommodate the penetrating ammonia guest molecules in the intermediate complex. On evaporation of ammonia from the intermediate complex, there is a relative small change in chain packing as an inter-sheet ammonia bridge is replaced by an inter-sheet hydrogen bond in cellulose IIII. When cellulose IIII is heated it converts back to cellulose Iβ. Both ammonia-cellulose I and cellulose IIII have extended chains of cooperative hydrogen bonds in relatively open crystal structures that may add to their susceptibility to rapid change.

Anticodon hairpins are structural motifs with contradictory functions. The recognition by aminoacyl synthetases implies extended interactions with the anticodon base triplet and thus, usually, an unfolding of the anticodon loop. The recognition by the ribosome and cognate interaction with a mRNA codon implies, on the other hand, the formation of a mini-helix with a canonical anticodon hairpin structure as observed by crystallography and NMR. To be able to understand the various properties of this motif, a precise description of its structural conservation is required. Here, on the basis of phylogenetic, structural, and molecular dynamics data, we discuss a conserved interaction established between the ribose of the U33 and the base at position 35, either a purine or a pyrimidine. This interaction involves the hydrogen bonding donor or acceptor potential of the hydroxyl group of U33 and has to be integrated in an extended definition of the anticodon hairpin. The extended structural signature provides also an explanation for the role played by pseudouridines at position 35.

The contribution of the Ser45 hydrogen bond to biotin binding activation and equilibrium thermodynamics was investigated by biophysical and X-ray crystallographic studies. The S45A mutant exhibits a 1,700-fold greater dissociation rate and 907-fold lower equilibrium affinity for biotin relative to wild-type streptavidin at 37 °C, indicating a crucial role in binding energetics. The crystal structure of the biotin-bound mutant reveals only small changes from the wild-type bound structure, and the remaining hydrogen bonds to biotin retain approximately the same lengths. No additional water molecules are observed to replace the missing hydroxyl, in contrast to the previously studied D128A mutant. The equilibrium ΔG°, ΔH°, ΔS°, ΔC°P, and activation ΔG[Dagger] of S45A at 37 °C are −13.7 ± 0.1 kcal/mol, −21.1 ± 0.5 kcal/mol, −23.7 ± 1.8 cal/mol K, −223 ± 12 cal/mol K, and 20.0 ± 2.5 kcal/mol, respectively. Eyring analysis of the large temperature dependence of the S45A off-rate resolves the ΔH[Dagger] and ΔS[Dagger] of dissociation, 25.8 ± 1.2 kcal/mol and 18.7 ± 4.3 cal/mol K. The large increases of ΔH[Dagger] and ΔS[Dagger] in the mutant, relative to wild-type, indicate that Ser45 could form a hydrogen bond with biotin in the wild-type dissociation transition state, enthalpically stabilizing it, and constraining the transition state entropically. The postulated existence of a Ser45-mediated hydrogen bond in the wild-type streptavidin transition state is consistent with potential of mean force simulations of the dissociation pathway and with molecular dynamics simulations of biotin pullout, where Ser45 is seen to form a hydrogen bond with the ureido oxygen as biotin slips past this residue after breaking the native hydrogen bonds.

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 ± 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0–1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 Å/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in φ, ψ angles. For β-sheet residues, a decrease in ψ angles by 1–2°/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 ± 0.343 and 0.519 ± 0.261 ppm/2 kbar, respectively) than for β-sheet (0.295 ± 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in β-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in β-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place.