Deuterated gamma-malonic acid: its neutron crystal structure in relationship to other polymorphs of aliphatic dicarboxylic acids.

Three complete neutron diffraction datasets have been collected for deuterated malonic acid single crystals, DOOC(CD(2))COOD, above (153 K), just below (56 K) and further below (50 K) the low-temperature phase transition (T(c) = 57 K). The structural details obtained for this transition, studied previously solely by spectroscopic and calorimetric techniques, clearly establish its first-order nature. At 153 K, the space group is P\bar 1, Z = 2, Z' = 1. The molecules are packed as linear chains linked end-to-end by asymmetric hydrogen bonds so that the carboxyl groups form cyclic dimers. The deuterons in the carboxyl links are ordered. Neighboring chains are cross-linked through C-D...O hydrogen bonds. Upon cooling through the transition the cell doubles along the a axis. Molecules which are equivalent by symmetry above T(c) become independent below T(c) owing to conformational changes in alternate chains. At 50 K, the space group is P\bar 1, Z = 4, Z' = 2. Thermal motion analysis, using for all three temperatures the same segmented rigid-body model, reveals a large torsional motion around the one COOD group associated with the conformational change. Refinements were carried out on all three datasets with an anharmonic structural model, including higher-order displacement tensors (Gram-Charlier expansion up to fourth order). Only atoms involved in torsional motion exhibit a significant anharmonic component which increases with temperature.

Structure of strontium hydroxide octahydrate, Sr(OH)2.8H2O, at 20, 100 and 200 K from neutron diffraction.

The crystal structure of Sr(OH)2*8H2O has been determined at 20, 100 and 200 K from neutron diffraction data. The structure consists of double layers of H2O and OH- ions separated by Sr2+ along the c axis. The Sr2+ ions are eight-coordinated by water O atoms in a square antiprism configuration. Each H2O molecule is engaged in three hydrogen bonds. The OH- ions form chains of acceptor and donor bonds along the fourfold axis with O atoms engaged in four bonds with H2O molecules, such that both non-equivalent O atoms have square-pyramidal environments of five H atoms and the overall bonding configurations of distorted octahedra.

Structures of furanosides: geometrical analysis of low-temperature X-ray and neutron crystal structures of five crystalline methyl pentofuranosides.

Crystal structures of all five crystalline methyl D-pentofuranosides, methyl alpha-D-arabinofuranoside (1), methyl beta-D-arabinofuranoside (2), methyl alpha-D-lyxofuranoside (3), methyl beta-D-ribofuranoside (4) and methyl alpha-D-xylofuranoside (5) have been determined by means of cryogenic X-ray and neutron crystallography. The neutron diffraction experiments provide accurate, unbiased H-atom positions which are especially important because of the critical role of hydrogen bonding in these systems. This paper summarizes the geometrical and conformational parameters of the structures of all five crystalline methyl pentofuranosides, several of them reported here for the first time. The methyl pentofuranoside structures are compared with the structures of the five crystalline methyl hexopyranosides for which accurate X-ray and neutron structures have been determined. Unlike the methyl hexopyranosides, which crystallize exclusively in the C(1) chair conformation, the five crystalline methyl pentofuranosides represent a very wide range of ring conformations.

Structure and thermal vibrations of spermine phosphate hexahydrate from neutron diffraction data at 125 K.

Spermine phosphate hexahydrate crystallizes in space group P2(1)/a with unit-cell dimensions a = 7.931 (1), b = 23.158 (5), c = 6.856 (2) A, and beta = 113.44 (2) degrees at 125 K with unit-cell contents [(C10H30N4)2(4+)(HPO4)4(2-).12H2O]. The packing of spermines and monohydrogen phosphates in this crystal structure has features which may be relevant to the binding of spermine to DNA. Another important structural feature is the presence of channels containing water that is hydrogen bonded as in ice-Ih with disordered protons. The channels occur between sheets of spermine long chains and are also bordered by hydrogen-bonded monohydrogen phosphate chains. The hydrogen-bonding scheme of these water chains proposed on the basis of an earlier X-ray study is now confirmed. Nuclear positions, anisotropic mean-square (m.s.) displacements, an overall scale factor and two extinction parameters (rho and g) were refined using full-matrix least-squares giving values of R(F0(2)) = 0.09, Rw(F0(2)) = 0.11 and S = 1.02. Thermal vibrational analysis revealed that the backbone of the spermine cation can be described as a single rigid segment with a substantial libration of 27 deg2 around the spermine molecular long axis.

The electrostatic potential for the phosphodiester group determined from X-ray diffraction.

The charge density distribution in the crystal structure of ammonium dimethylphosphate at 123 K has been determined from x-ray diffraction data (MoK alpha) using 8437 reflections with sin theta/lambda less than 1.33 A-1 [NH4+.(CH3)2PO4-, M(r) = 143.08, monoclinic, P2(1)/c, a = 10.007(1), b = 6.926(1), c = 9.599(2) A, beta = 105.40(1) degrees, V = 641.4(3) A3, Z = 4, F000 = 304, Dx = 1.4815 g.cm-3, mu = 3.726 cm-1]. Least-squares structure refinement assuming Stewart's rigid pseudoatom model (variables including Slater-type radial exponents and electron populations for multipole terms extending to octapoles for C, N, O, and P, and dipoles for H) gave R(F2) = 0.039 for all reflections. The dimethylphosphate anion is in the gauche-gauche conformation and has approximate twofold symmetry. One phosphoryl O atom forms three hydrogen bonds and the other forms one. Neither of the ester O atoms is hydrogen bonded. For the dimethylphosphate anion isolated from the crystal structure, a map of the electrostatic potential obtained using the pseudoatom charge parameters shows that the phosphoryl O atoms are considerably more electronegative than the ester O atoms. The electrostatic potential distribution obtained in this way has been fitted by least squares to a system of atom-centered point charges. The potential calculated from these point charges agrees with the experimental result. It also agrees reasonably well with potentials obtained from three other systems of point charges that are widely used as part of the semiempirical force field for molecular mechanics and molecular dynamics calculations involving nucleic acids.

Electrostatic properties of 1-methyluracil from diffraction data.

1-Methyluracil (1-methyl-2,4-dioxopyrimidine), C5H6-N2O2, M(r) = 126.12, orthorhombic, Ibam, a = 13.188 (6), b = 13.175 (5), c = 6.214 (3) A, V = 1079.7 (8) A3, Z = 8, Dx = 1.552 g cm-3, lambda (Mo K alpha) = 0.7107 A, mu = 1.317 cm-1, F(000) = 528, T = 123 K, R(F2) = 0.068 for 2996 reflections with sin theta/lambda less than 1.08 A-1. The electronic charge-density distribution has been analyzed in terms of Stewart's rigid pseudoatom model, using restricted Slater radial functions and angular multipole terms extending to octapoles for C, N and O, and quadrupoles for H pseudoatoms. Three different structure refinements have been carried out based on two X-ray diffraction data sets from different crystals collected at temperatures differing by about 20 K. The molecular dipole moment is 6.4 (27) D. Maps of the electrostatic potential for a molecule isolated from the crystal show that atoms O2 and O4 confer overall electro-negativity on one side of the molecule while the CH groups and the C1 methyl group confer electropositivity on the other. For the centrosymmetric hydrogen-bonded dimer (N3-H3...O4'; H...O distances 1.77 A) the electrostatic potential shows electropositive bridges between the molecules. These features are lacking for the C-H...O interactions (distances H6...O2, 2.37; H11...O4, 2.34 A). The electron density and its Laplacian have been determined at the intramolecular bond-critical points and also for the intermolecular H...O interactions. Values for the former are characteristic of covalent bonds. Values of the electron density and Laplacian for the C-H...O interactions are very small and have little or no significance in terms of their e.s.d.'s. The electrostatic energy of interaction for the N-H...O hydrogen-bonded dimer is -10 (12) kJ mol-1. The attractive electrostatic energy increases to -67 (33) kJ mol-1 for a centrosymmetric planar tetramer in which the C-H...O interactions are also formed.

Structure of disodium methyl phosphate hexahydrate.

2Na+.CH3O4P2-.6H2O, Mr = 264.09, monoclinic, Pc, a = 7.277 (1), b = 6.298 (2), c = 11.477 (4) A, beta = 92.44 degrees, V = 525.5 A3, Z = 2, Dx = 1.669 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 35.26 cm-1, F(000) = 276, T = 298 K, R = 0.028 for 781 independent reflections. Three P-O bond lengths are the same (1.513 A) within experimental error, with the ester P-O bond length significantly longer [1.626 (3) A]. The Na ions are octahedrally coordinated by water O atoms and have no direct interaction with the phosphate O atoms. Water molecules form three hydrogen bonds with each phosphate O atom, except the ester O atom which at most forms one weak interaction.

Electrostatic potential for O-H-O in tetragonal ammonium dihydrogenphosphate.

NH4H2PO4, Mr = 115.03, tetragonal, I42d, a = 7.500 (1), c = 7.550 (2) A, V = 424.7 A3, Z = 4, D chi = 1.799 g cm-3, lambda(Cu K alpha) = 1.5418 A, mu = 49.08 cm-1, F(000) = 240, T = 298 K, R = 0.021 for 99 independent reflections. The O-H-O system with O...O distance 2.493 (3) A is described in terms of the H atom in a single site undergoing anisotropic thermal vibrations. Then the O...H distance is 1.31 (9) A, the O-H-O angle is 145 (8) degrees and the maximum mean-square amplitude of vibration for H is 1.1 (7) A2. However, the probability distribution function for the proton could well have a double peak as reported in isomorphous KH2PO4 from high-resolution neutron diffraction. The electrostatic potential well in which the H occurs has a minimum of -1.13 e A-1.

Structure and thermal vibrations of adenosine from neutron diffraction data at 123 K.

The crystal structure of adenosine, C10H13N5O4, Mr = 267.24, has been refined by full-matrix least-squares methods using single-crystal neutron diffraction data (sin theta/lambda less than 0.79 A-1) measured at 123 K. Crystal data at 123 K: monoclinic, P2l, Z = 2, a = 4.7885 (8), b = 10.240 (2), c = 11.772 (2) A, beta = 99.59 (2) degrees, V = 569.2 A3, lambda = 1.0402 (1) A, Dn = 1.559 Mg m-3, mu = 191.1 m-1, F(000) = 175.72 fm, R(F2) = 0.044, wR(F2) = 0.055, S = 1.13 for 2450 reflections with F2 greater than 0.0. Bond lengths and angles have e.s.d.'s less than 0.002 A and 0.1 degrees for non-H atoms and less than 0.004 A and 0.3 degrees for H atoms. Values are in general agreement with those previously obtained from room-temperature X-ray data and with those obtained for 9-methyladenine by neutron diffraction at 126 K. Small displacements of amino H atoms from the least-squares plane through the non-H atoms of the adenine part appear to be the result of hydrogen bonding. There is an intermolecular interaction C2--H2...O2' with an H...O distance of 2.20 A. In its thermal vibrations, the adenosine molecule behaves as two rigid segments with a torsional libration about the glycosidic bond of 14.4 deg2 at 123 K. The force constant for this libration, as determined from the diffraction data, is 73 (10) J mol-1 deg-2.