SEM, EDX and vibrational spectroscopic study of the phosphate mineral ushkovite MgFe3+2(PO4)2(OH)2·8H2O: Implications of the molecular structure

The mineral ushkovite has been analyzed using a combination of electron microscopy with EDX and vibrational spectroscopy. Chemical analysis shows the mineral contains P, Mg with very minor Fe. Thus, the formula of the studied ushkovite is Mg32+(PO4)2·8H2O. The Raman spectrum shows an intense band at 953 cm−1 assigned to the ν1 symmetric stretching mode. In the infrared spectra complexity exists with multiple antisymmetric stretching vibrations observed, due to the reduced tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong infrared bands around 827 cm−1 are attributed to water librational modes. The Raman spectra of the hydroxyl-stretching region are complex with overlapping broad bands. Hydroxyl stretching vibrations are identified at 2881, 2998, 3107, 3203, 3284 and 3457 cm−1. The wavenumber band at 3457 cm−1 is attributed to the presence of FeOH groups. This complexity is reflected in the water HOH bending modes where a strong infrared band centered around 1653 cm−1 is found. Such a band reflects the strong hydrogen bonding of the water molecules to the phosphate anions in adjacent layers. Spectra show three distinct OH bending bands from strongly hydrogen-bonded, weakly hydrogen bonded water and non-hydrogen bonded water. Vibrational spectroscopy enhances our knowledge of the molecular structure of ushkovite.

New insights into the molecular structure of kaolinite–methanol intercalation complexes

A series of kaolinite–methanol complexes with different basal spacings were synthesized using guest displacement reactions of the intercalation precursors kaolinite–N-methyformamide (Kaol–NMF), kaolinite–urea (Kaol–U), or kaolinite–dimethylsulfoxide (Kaol–DMSO), with methanol (Me). The interaction of methanol with kaolinite was examined using X-ray diffraction (XRD), infrared spectroscopy (IR), and nuclear magnetic resonance (NMR). Kaolinite (Kaol) initially intercalated with N-methyformamide (NMF), urea (U), or dimethylsulfoxide (DMSO) before subsequent reaction with Me formed final kaolinite–methanol (Kaol–Me) complexes characterized by basal spacing ranging between 8.6 Å and 9.6 Å, depending on the pre-intercalated reagent. Based on a comparative analysis of the three Kaol–Me displacement intercalation complexes, three types of Me intercalation products were suggested to have been present in the interlayer space of Kaol: (1) molecules grafted onto a kaolinite octahedral sheet in the form of a methoxy group (Al-O-C bond); (2) mobile Me and/or water molecules kept in the interlayer space via hydrogen bonds that could be partially removed during drying; and (3) a mixture of types 1 and 2, with the methoxy group (Al-O-C bond) grafted onto the Kaol sheet and mobile Me and/or water molecules coexisted in the system after the displacement reaction by Me. Various structural models that reflected four possible complexes of Kaol–Me were constructed for use in a complimentary computational study. Results from the calculation of the methanol kaolinite interaction indicate that the hydroxyl oxygen atom of methanol plays the dominant role in the stabilization and localization of the molecule intercalated in the interlayer space, and that water existing in the intercalated Kaol layer is inevitable.

Crystal structures and hydrogen bonding in the morpholinium salts of four phenoxyacetic acid analogues

The anhydrous salts morpholinium (tetrahydro-2-H-1,4-oxazine) phenxyacetate, C4H10NO+ C8H7O3- (I), (4-fluorophenoxy)acetate, C4H10NO+ C8H6FO3- (II) and isomeric morpholinium (3,5-dichlorophenoxy)acetate (3,5-D) (III) and morpholinium (2,4-dichlorophenoxy)acetate (2,4-D), C4H10NO+ C8H5Cl2O3- (IV), have been determined and their hydrogen-bonded structures are described. In the crystals of (I), (III) and (IV), one of the the aminium H atoms is involved in a three-centre asymmetric cation-anion N-H...O,O' R2/1(4) hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. With the structure of (II), the primary N---H...O interaction is linear. In the structures of (I), (II) and (III), the second N-H...O(carboxyl) hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV), the ion pairs are linked though inversion-related N-H...O hydrogen bonds [graph set R2/4(8)], giving a cyclic heterotetrameric structure.

Crystal engineering in two dimensions: An approach to molecular nanopatterning

We describe a surprising cooperative adsorption process observed by scanning tunneling microscopy (STM) at the liquid−solid interface. The process involves the association of a threefold hydrogen-bonding unit, trimesic acid (TMA), with straight-chain aliphatic alcohols of varying length (from C7 to C30), which coadsorb on highly oriented pyrolytic graphite (HOPG) to form linear patterns. In certain cases, the known TMA “flower pattern” can coexist temporarily with the linear TMA−alcohol patterns, but it eventually disappears. Time-lapsed STM imaging shows that the evolution of the flower pattern is a classical ripening phenomenon. The periodicity of the linear TMA−alcohol patterns can be modulated by choosing alcohols with appropriate chain lengths, and the precise structure of the patterns depends on the parity of the carbon count in the alkyl chain. Interactions that lead to this odd−even effect are analyzed in detail. The molecular components of the patterns are achiral, yet their association by hydrogen bonding leads to the formation of enantiomeric domains on the surface. The interrelation of these domains and the observation of superperiodic structures (moiré patterns) are rationalized by considering interactions with the underlying graphite surface and within the two-dimensional crystal of the adsorbed molecules. Comparison of the observed two-dimensional structures with the three-dimensional crystal structures of TMA−alcohol complexes determined by X-ray crystallography helps reveal the mechanism of molecular association in these two-component systems.

Substrate, molecular structure, and solvent effects in 2D self-assembly via hydrogen and halogen bonding

Recently, halogen···halogen interactions have been demonstrated to stabilize two-dimensional supramolecular assemblies at the liquid–solid interface. Here we study the effect of changing the halogen, and report on the 2D supramolecular structures obtained by the adsorption of 2,4,6-tris(4-bromophenyl)-1,3,5-triazine (TBPT) and 2,4,6-tris(4-iodophenyl)-1,3,5-triazine (TIPT) on both highly oriented pyrolytic graphite and the (111) facet of a gold single crystal. These molecular systems were investigated by combining room-temperature scanning tunneling microscopy in ambient conditions with density functional theory, and are compared to results reported in the literature for the similar molecules 1,3,5-tri(4-bromophenyl)benzene (TBPB) and 1,3,5-tri(4-iodophenyl)benzene (TIPB). We find that the substrate exerts a much stronger effect than the nature of the halogen atoms in the molecular building blocks. Our results indicate that the triazine core, which renders TBPT and TIPT stiff and planar, leads to stronger adsorption energies and hence structures that are different from those found for TBPB and TIPB. On the reconstructed Au(111) surface we find that the TBPT network is sensitive to the fcc- and hcp-stacked regions, indicating a significant substrate effect. This makes TBPT the first molecule reported to form a continuous monolayer at room temperature in which molecular packing is altered on the differently reconstructed regions of the Au(111) surface. Solvent-dependent polymorphs with solvent coadsorption were observed for TBPT on HOPG. This is the first example of a multicomponent self-assembled molecular networks involving the rare cyclic, hydrogen-bonded hexamer of carboxylic groups, R66(24) synthon.

A high-density association screen of 155 ion transport genes for involvement with common migraine

The clinical overlap between monogenic Familial Hemiplegic Migraine (FHM) and common migraine subtypes, and the fact that all three FHM genes are involved in the transport of ions, suggest that ion transport genes may underlie susceptibility to common forms of migraine. To test this leading hypothesis, we examined common variation in 155 ion transport genes using 5257 single nucleotide polymorphisms (SNPs) in a Finnish sample of 841 unrelated migraine with aura cases and 884 unrelated non-migraine controls. The top signals were then tested for replication in four independent migraine case-control samples from the Netherlands, Germany and Australia, totalling 2835 unrelated migraine cases and 2740 unrelated controls. SNPs within 12 genes (KCNB2, KCNQ3, CLIC5, ATP2C2, CACNA1E, CACNB2, KCNE2, KCNK12, KCNK2, KCNS3, SCN5A and SCN9A) with promising nominal association (0.00041 < P < 0.005) in the Finnish sample were selected for replication. Although no variant remained significant after adjusting for multiple testing nor produced consistent evidence for association across all cohorts, a significant epistatic interaction between KCNB2 SNP rs1431656 (chromosome 8q13.3) and CACNB2 SNP rs7076100 (chromosome 10p12.33) (pointwise P = 0.00002; global P = 0.02) was observed in the Finnish case-control sample. We conclude that common variants of moderate effect size in ion transport genes do not play a major role in susceptibility to common migraine within these European populations, although there is some evidence for epistatic interaction between potassium and calcium channel genes, KCNB2 and CACNB2. Multiple rare variants or trans-regulatory elements of these genes are not ruled out.