Showing papers in "Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry in 1972"

The Crystal Structure of Adenosine

Abstract: The crystal structure of adenosine, C10Ht3NsO4, has been determined from the intensities of 1333 reflections, each measured at least four times on an automated diffractomcter. The crystals are monoclinic, space group P21, with a=4.825 (1), b= 10"282 (2), c= 11.823 (1)/~, fl=99.30 (1) °, and two molecules per cell. Least-squares refinement of coordinates and anisotropic temperature factors for all atoms, including hydrogen, led to an R index of 0-024 and standard deviations of about 0.003 A, for bond distances between pairs of heavy atoms. The anomalous scattering by nitrogen and oxygen was used to confirm the absolute configuration of the sugar ring. The conformation of the ribose ring is C(3') endo; the torsion angle about the glycosidic bond is 9.9 °. Intermolecular interactions include a full complement of hydrogen bonds, a relatively short C(2)-H.. .O(2') contact (3.09 A,), and parallel stacking of adenine rings with an interplanar spacing of 3"57/~.

Survey of the geometry and environment of water molecules in crystalline hydrates studied by neutron diffraction

Abstract: 1972) The bond lengths and angles in water molecules, derived from over 40 neutron-diffraction studies of crystalline hydrates, are analysed statistically. A 'quasi-normal' spread of the dimensions and con- sequent deviations from an average model, affecting both water molecules and their environment, is associated with strains due to local failures of Pauling's second rule. This interpretation is consistent with linear correlations between pairs of bond lengths and/or angles. A new, more general classification of water molecules in crystalline hydrates, based on cation coordination, is proposed. The water mol- ecules are arranged in five classes, according to the number of coordinated cations and to the position of the cations with respect to the lone-pair orbitals; each class may be further subdivided on the basis of the chemical nature of the cations. Introduction The water molecule plays an important role in the packing of crystalline hydrates, both because it partici- pates in hydrogen bonds linking anions and also be- cause, through its lone-pair orbitals, it is a satisfactory ligand for many cations. The approximately tetrahedral environment usually assumed by the water molecule has often been idealized and used for tentative estimates of the hydrogen-atom coordinates; constant molecular geometry and, some- times, linearity of hydrogen bonds and/or planarity of the water-acceptor group are assumed. In fact, both the conformation of the water molecule and the geom- etry of its environment do depend, to some extent, on the specific situations in different compounds. Neutron diffraction is the only technique that allows unambiguous location of hydrogen atoms of the water molecule in solid hydrates with estimated standard deviations (e.s.d.'s) comparable with those of the other atoms; while very accurate X-ray data may allow the location of hydrogen atoms, their e.s.d.'s are generally too high for quantitative discussion. Of the fifty or so crystal structures of hydrates (April 1972)studied in three dimensions by neutron diffraction, the results for 41 are reviewed here, with the 90 water molecules involved. Compounds with disorder in water molecules (cf. Ferraris, Jones & Yerkess, 1972b) or other atoms or atomic groups (cf. some alums) have been excluded. The appropriate planes (Fig. 1) and bond lengths and angles were recomputed and are summarized in Tables 1 and 2 according to a classification reported be- low. All distances and angles are uncorrected for thermal motion since, even when reported, such corrections are merely indicative. While Tables 1 and 2 deal with * Paper presented at the 6th Hungarian Conference on X-ray, Electron, and Neutron Diffraction; 28th May-lst June 1972, Si6fok, Hungary. Research supported by the C. N. R. all types of hydrogen bonds involving water molecules, the results to be discussed concern mainly O...O hydrogen bonds, since only for these does the number of cases studied by neutron diffraction allow statistical correlations. The following symbols are used (Fig. 1): W= oxygen atom of the water molecule; HI, H2 = hydrogen atoms of the water molecule; A 1,A2 = acceptors of hydrogen bonds; C1, C2, C3 = atoms contacting W; ~0 = H- W-H angle; tpl = A 1. • • W. • • A 2 angle; cq, ~2 = W-H- • • A angles; J~,Jz=angles between W...C1 and W-H; 7r = plane of the water molecule; zq = plane of 14, C2 and C3; ?1, Yz = angles between H- • • A and n; e~, ez, e3 = angles between W. • • C and n; e = C2. • • W. • • C3 angle; ~, = angle between ~z and nl; oA, o)2 =angles between the ~z-nl intersection straight line and W-H. ;~ ~C3

The crystal structure of all-trans retinal1

Abstract: ABRAHAMS, S. C. 8~ PRINCE, E. (1962). J. Chem. Phys. 36, 50. BACON, G. E. (1969). Acta Cryst. A25, 391. BINAS, H. (1966). Z. anorg, allg. Chem. 347, 133. BUSING, W. R. & LEVY, H. A. (1964). Acta Cryst. 17, 142. CALLERI, M. t~ FERRARIS, G. (1967). Per. Mineral, 36, 1. CASSIEN, M., HERPIN, P. & PERMINGEAT, F. (1966). Bull. Soc. franc. Min~r. Crist. 89, 18. CHIDAMBARAM, P., SEQUEIRA, A. • SIKKA, S. K. (1964). J. Chem. Phys. 41, 3616. COOPER, M. J. (1969). Acta Cryst. A25, 488. COPPENS, P. (1970). Chap. 6 in Thermal Neutron Diffraction. Edited by B. T. M. WILLIS. Oxford Univ. Press. COULSON, C. A. (1970). Chap. 5 in Thermal Neutron Diffraction. Edited by B. T. M. Wn.Lm. Oxford Univ. Press. CURRY, N. A., DENNE, W. A. & JONES, D. W. (1968). Bull. Soc. Chim. France, p. 1748. DENNE, W. A. & JONES, D. W. (1969). Aeta Cryst. A25, S 125. FERRARIS, G., JONES, D. W. & YERKESS, J. (1971a). Acta Cryst. B27, 349. FERRARIS, G., JONES, D. W. 8¢. YERKESS, J. (1971b). Acta Cryst. B27, 354. FISCHER, E. (1960). Chem. der Erde, 20, 162. GUI~RIN, H. (1941). Ann. Chim. 16, 101. MARTIN, C., DURIF, A. & AVERBUCH-POUCHOT, M.-T. (1970). Bull. Soc. fi'anf. MinOr. Crist. 93, 397.

A comprehensive X-ray study of the ferroelectric–ferroelastic and paraelectric–paraelastic phases of Gd2(MoO4)3

Abstract: The crystal structure of Gdz(MoO4)a has been investigated both at room temperature and at elevated temperatures below and above the ferroelectric-ferroelastic transition temperature (~ 160°C). Space group, unit-cell dimensions, and formula units per unit cell are" Pba2 (C8v), a= 10"3881 +0"0003, b= 10"4194+0.0004, c= 10"7007+0.0006/~,, Z = 4 at 25°C and PS421m (D~), a=7.393 +0.002, c= 10.670 + 0.004/~, Z= 2 at 183 °C. Full-matrix least-squares refinements have been carried out with anisotropic thermal parameters with two single-crystal diffractometer data sets measured at 25 and 183 °C, yielding conventional R values of 0.032 (3000 reflections) and 0-028 (880). The high-temperature structure comes close to the average structure of the two ferroelectric-ferroelastic orientations. The differences in interatomic distances between the two modifications are all less than 0.05 .~. Ferroelectric-ferroelastic switching can be accomplished through two macroscopically equivalent switching mechanisms. Changes in interatomic distances of nearest neighbors upon switching are all less than 0.05 ,~,. The main difference between the two ferroelectric-ferroelastic orientations results through movements of several oxygen atoms by as much as 0.7.~. The spontaneous polarization was calculated assuming point charges Gd 3+ and [MOO4]'from positional parameters: Ps = 0.175/tC.cm -2, in good agreement with experiment. Since most of the dipole moments cancel out within the unit cell, Gd2(MoO4)3 can be described as a canted antiferroelectric. The temperature dependence of intensities and peak widths of superstructure reflections has been monitored through the transition temperature. Below the transition temperature, temperature-dependent physical properties can be accounted for by gradual changes in positional parameters towards the high-temperature structure. The mechanism of the phase transition is discussed in terms of the 'positional order-disorder' and the 'soft mode' model. The results obtained in the refinement of the room-temperature structure are compared with results of an independent study of this structure by Keve, Abrahams & Bernstein.

The crystal structure of the orthorhombic form of l-(+)-histidine

Abstract: L-(+)-Histidine (C6NaO2H9) crystallizes in the orthorhombic space group P212121, with a = 5-177, b = 7.322, c= 18.87 A, and Z=4. Data were collected with Mo Kct radiation, using balanced filters. The structure was solved by direct phasing methods and refined to a final agreement index of 0.034 for all reflections. The conformation of the molecule is that of the open, extended form, and is stabilized principally by an imramolecular hydrogen bond between the amino nitrogen atom and the adjacent imidazole nitrogen atom. Where this conformation is found in proteins, it is likely to reduce the chemical reactivity of tha+ ;midazole group, because one of the imidazole nitrogen atoms is sterically hindered by the peptide ba,.~, one.

The crystal and molecular structure of trehalose dihydrate

Abstract: The crystal structure of trehalose dihydrate has been solved by direct methods and refined to an R index of 0-057 using anisotropic refinement. The space group is P212121 and four formula units of C12HzzOz~.2HzO are contained in the unit cell of dimensions a= 17.90, b= 12.21 and c= 7.586 A. The two glucopyranose residues in the trehalose molecule have the chair 4C1 form, and are bonded by the a 1 --+ 1 glycosidic link in approximate twofold symmetry. Departures from symmetry are found in torsion angles about the e 1 -+ 1 link and in conformations of the primary alcohol groups O(6)H and O(6')H. The C-O bond lengths show systematic trends similar to those in other e-pyranose sugars and at the same time show some characteristic features related to the e 1 -~1 link of the two glucose residues. There are two indirect intramolecular hydrogen bonds incorporating water molecules. Neither the ring oxygens nor the glycosidic linkage oxygen accept hydrogen bonds. The molecular packing in the crystal is mainly determined by the hydrogen bonds.