Atomic Thermal Parameters Research Articles

Trans-Reduction of 5-phenyl-1,2,3,4,5,6-hexahydroazepino[4,5-b]indole. X-Ray crystallographic study of the geometry of an intermolecular N–H ⋯ phenyl hydrogen bond

The stereochemistries of the two isomeric products (5) and (6) obtained in equal amounts from trans-reduction of 3-benzyl-5-phenyl-1,2,3,4,5,6-hexahydroazepino[4,5-b]indole (3) have been determined by spectral and single-crystal X-ray analyses. Monoclinic crystals of (5) belong to space group P21/c, with a= 22.005(10), b= 10.270(5), c= 13.577(7)A, β= 106.42(1)°, Z= 8. The crystal structure was solved by direct methods, and atomic positional and thermal parameters refined by least-squares calculations to R 0.051 over 3 293 reflections measured by diffractometer. The two molecules defining the asymmetric crystal unit have identical conformations and are associated in a like manner in the solid state by N–H ⋯ N (mean N ⋯ N 3.26 A) and N–H ⋯ phenyl (mean calculated H ⋯ phenyl 2.32 A) hydrogen bonds.

A cis–syn photodimer of thymine: Thy[1(CH2–CHOH–CH2)1']Thy

CI3HI6N40 5, monoclinic, P21/n, a = 6.227(1), b = 16.222(4), c = 13.085 (2)A, fl = 93.80 (2) ° , Z = 4, D c = 1.55 Mg m -3, g(Cu Ka) = 1.04 mm -l. The final R value is 0.045 for 1446 reflexions and 199 parameters. The molecule (isomer Z) has the cis-syn configuration. Both pyrimidine rings adopt non-planar conformations: ring A is a distorted sofa and ring B a flattened chair. The cyclobutane ring is puckered. The seven-membered diazacycloheptane ring has a slightly twisted chair conformation. Introduction. The investigation of base-base interactions in nucleic acid strands is strongly complicated by the hydrogen bonds or phosphodiester linkages. Knowledge of these interactions is important to elucidate the secondary or tertiary structures of nucleic acids. For elimination of some of the hydrogen bonds between bases, Browne, Eisinger & Leonard (1968) suggested the investigation of base-base interactions in the dinucleotide analogs in which the bases are connected by the polymethylene chain B ( C H 2 ) n B ' (where B and B' are residues of uracil, thymine or cytosine). Some of the connexions of B(CHE)n-B ' type undergoing the photoreaction yield photodimers c(6) whose stereochemistry can be used as a model for N(1) c(2) natural photoproducts (Leonard, Golankiewicz, 0(2) McCredie, Johnson & Paul, 1969). N(3) The investigation of photodimers [bis(5-alkylc(4) uracils)] connected by the trimethylene bridge in the 0(4) c(5) 1,1'-position was carried out as a continuation of c(9) studies on dinucleotide analogs (Rajchel & Golanc(5') kiewicz, 1976). T h y l l ( C H 2 C H O H C H 2) l ' ]Thy, C(9') containing the hydroxyl group in the trimethylene c(4') bridge, is a derivative of the above-mentioned o(4') N(Y) compounds (Rajchel & Golankiewicz, 1981). 0(29 Crystals were obtained by the slow cooling of an c(2') aqueous solution. A crystal of dimensions 0.15 x 0.20 N(I') C(6') C(7') c(8) c(7) 0(8) * The abbreviation is that proposed by Cohn, Leonard & Wang (1974). 0567-7408/82/030999-03501.00 x 0.40 mm, sealed in a glass capillary, was used for data collection. Cell parameters and intensities of reflexions were measured on a Syntex P21 diffractometer with monochromated Cu Ka radiation. The 0--20 scan mode, with variable scan rate, was applied and the integrated intensities were determined by peak-profile analysis by the method of Lehmann & Larsen (1974) (program PRAN; Jask61ski, 1979). The structure was solved with M U L T A N (Germain, Main & Woolfson, 1971). All H atoms were found on a difference Fourier map. The H-atom parameters were not refined. Full-matrix least-squares refinement with 1446 reflexions [I _> 1.96o(1)] gave R = 0.045 and R w = 0.050. The weighting scheme was w = Fo/F t if F o < F t, w = 1 if F t Table 1. Atomic coordinates (X10 4) and thermal parameters for non-hydrogen atoms

Bonding in a binuclear metal carbonyl: experimental charge density in Mn2(CO)10

X-ray diffraction data (Ag Ka and Mo Net radiation) have been collected at 74 K on dimanganese decacarbonyl Mn2(CO)I 0, and the crystal structure was refined. The atomic positional and thermal parameters were determined from high-angle AgKa data to avoid systematic errors due to bonding effects. The molecular geometry is discussed. The distortions are larger than at room temperature: for example, the torsion angle of the two Mn(CO) 5 fragments is 50.2 °, compared to 47.4 ° at room temperature, and 45 ° for an ideal D4a symmetry. 'X-X' deformation-density maps were computed and averaged over chemically equivalent sites. No significant charge-density accumulation is observed on the Mn-Mn bond. The configuration around the Mn atoms is essentially octahedral, with about 75% of the 3d electrons in the diagonal orbitals (dxy,d~z,dy ~) and the remaining 25% in d: and dx2_/. Atomic charges were determined both by direct integration and by least-squares refinement. Directly integrated charges are very small. Mn seems slightly negative. Both methods of charge integration show a clear difference between axial and equatorial carbonyls, which is confirmed by comparing their electron density with that of free carbon monoxide: the differences are characteristic of a a-bonding n-backbonding mechanism, and are larger for the axial carbonyls than for the equatorial carbonyls. This confirms the stronger bonding of the axial carbonyls, also responsible for the longer C-O bond and the shorter Mn-C bond.

Nuclear magnetic resonance and X-ray stereochemical studies on 1-benzyltetrahydroisoquinolinium salts

The relative stereochemistry at positions 1 and 2 of N,N-dialkyl-1-benzyl-1,2,3,4-tetrahydroisoquinolinium salts has been assigned via a combination of 1H and 13C n.m.r. studies and confirmed by single-crystal X-ray analysis of trans-N-3-hydroxypropyl-5′-methoxylaudanosinium perchlorate [trans-2j)] and cis-N-3-hydroxypropyl-5′-methoxylaudanosinium iodide [cis-(2h)] monohydrate. Quaternization of either laudanosine or 5′-methoxylaudanosine with an alkyl iodide leads to major isomers which possess a trans-relationship between the entering N-alkyl group and the 1-benzyl substituent; these isomers characteristically have the less shielded 1-H and N-methyl protons in deuteriochloroform. Crystals of trans-(2j) and cis-(2h) monohydrate both belong to the monoclinic system, Space group P21/c, with a= 8.123(4), b= 20.380(8), c= 16.710(6)Å, β= 102.14(5)°, Z= 4 for the former, and a= 11.475(5), b= 17.749(6), c= 14.278(5)Å, β= 113.51(5)°, Z= 4, for the latter compounds. Full-matrix least-squares refinement of atomic positional and thermal parameters converged at R= 0.082 [2 215 reflections] for (trans-(2j) and 0.077 [2 987 reflections] for (cis-(2h) monohydrate. The stereochemistry of the protonation products arising from these tetrahydroisoquinoline bases is also discussed.

Structures of Langbeinite-Type K2Mn2(SO4)3 in Cubic and Orthorhombic Phases

Structures of cubic and orthorhombic phases of langbeinite-type K 2 Mn 2 (SO 4 ) 3 have been determined at 20°C and -90°C by X-ray diffraction. Thermal parameters of oxygen atoms in the cubic phase are remarkably anisotropic and show unusually high values, whereas those in the orthorhombic phase are rather normal. The change in bond lengths and angles at the transition clarifies a rigid body motion of SO 4 group. It is concluded that the principal structural change at the cubic-orthorhombic transition is characterized by ordering of sulfate groups.

Manganese 3d and 4s electron-density distribution in phthalocyaninatomanganese(II)

A new analysis of the 116 K single-crystal X-ray diffraction data set of good accuracy on β-phthalocyaninatomanganese(II) has yielded individual 3d and 4s orbital populations on the manganese atom of significant accuracy and qualitative estimates of bonding electron density in the macrocycle ring. The manganese orbital populations (x and y along Mn–N vactors, z perpendicular to the square plane of co-ordinated nitrogen atoms) have been determined by a least-squares refinement procedure as dxy1.5(2), dxz0.6(2), dyz0.7(2), dz20.9(2), dx2–y20.1(2), and 4s2.0(3). Difference-Fourier syntheses indicate the aspherical nature of the valence charge density on the manganese atom, and the presence of bonding charge density in the ligand. In the later stages of the structural and orbital population analyses, allowance was made in the scattering model for overlap charge density by placing small spherical charges of variable population and radial extent between C–C and C–N atom pairs and in the Mn–N vectors. The present treatment of the data differs from the previous analysis in that refinement of atomic positional and thermal parameters has been based upon intensities (I), and all 2 265 observations with (sinθ)/λ⩽ 0.662 A–1, rather than on structure factor amplitudes (|F|) and only the 1 608 reflections with I > 3σ(I). Full-matrix least-squares refinement on the basis of a spherical atom model yielded R 0.045, and bond lengths and angles of improved accuracy are reported. The atomic positional and thermal parameters thus obtained have been used to generate a set of ‘difference structure factors,’Fd, containing, principally, information about the valence charge density on the manganese atom. These Fd values have been analysed by least-squares refinement in terms of aspherical density arising from 3d and 4s orbital populations on the manganese atom. The present analysis has established that worthwhile information on chemical bonding in a molecule as large as a transition-metal macro-cycle can be obtained from a low-temperature X-ray data set of good quality, and acts a guide for a program to involve the collection of low-temperature data sets of excellent quality for this purpose.

L3-Edge anomalous scattering of x-rays by praseodymium and samarium

Measurements are reported for the anomalous scattering of x-rays by atoms of praseodymium and samarium at wavelengths through their L/sub 3/ absorption edges. Values of both f' and f'', the real and imaginary components of the anomalous scattering, were derived from diffraction experiments using synchrotron radiation. Both components exhibit exceptionally large changes in a narrow interval of wavelength, changes which offer a useful tool for solving the phase problem in crystal structure analysis. Crystals of sodium praseodymium ethylenediaminetetraacetate octahydrate and the isomorphorphous samarium, crystallize in the noncentric space group Fdd2. The atomic coordinates and thermal parameters were determined using Mo K..cap alpha.. radiation. The values found for the anomalous scattering terms are plotted, and listed, with the respective R values for each data set. For each data set, f' exhibits the striking resonance line which is observed in the absorption curves. 1 figure, 2 tables.

Structure of aristone, a unique indole alkaloid from Aristotelia chilensis(mol.) stuntz, by X-ray crystallographic analysis

Aristone, aristoteline, aristotelinine, and aristotelone were isolated from Aristotelia chilensis and belong to a unique class of alkaloids found only in the genus Aristotelia. The structure of aristone was determined by X-ray diffraction techniques. Crystals are orthorhombic, space group P212121, with cell dimensions a= 11.075(3), b= 18.004(4), and c= 7.973(1)A and Z= 4. The crystal structure was determined by direct methods and atomic positional and thermal parameters were refined by full-matrix least-squares techniques to a R value of 3.8% utilizing 1 717 reflexions. The molecule contains a planar indole moiety with the remainder of the molecule forming a basket-like cavity. There are a number of carbon valence angles less than 105° which indicate internal strain; however, there are no significant intramolecular interactions.

A structure-factor least-squares refinement procedure for macromolecular structures using constrainedandrestrained parameters

A method of structure-factor least-squares refinement of constrained groups linked by distance restraints has been developed for the refinement of macromolecular structures. Each constrained group can have any number of variable dihedral rotation parameters within the group in addition to the rigid-body translational, rotational and thermal parameters. The matrix of normal equations may be either full or sparse and provision is made for solution by matrix inversion or the conjugate-gradient iterative method. This procedure has been successfully used for 3 Å data and should be applicable even for lower-resolution data and especially for cases with a poorer data-per-atom ratio. The structure of yeast phenylalanine tRNA has been refined with this procedure from a starting crystallographic R value of 42% to a final R value of 25% with isotropic 'group" thermal parameters and 22% with isotropic atomic thermal parameters for 8207 independent reflections at 2.7 Å resolution. The proper stereochemistry of bond distances, angles and van der Waals contacts for the restrained atoms was maintained within reasonable limits throughout the refinement. Although originally developed for nucleic acids, this procedure is directly applicable to the refinement of protein structures. In addition, a combination of applying distance restraints between groups and least-squares fitting of these groups to target coordinates has been used purely as an idealization process for imposing proper stereochemistry on an approximate model.

A refinement analysis of the crystallography of the phospholipid, 1,2-dilauroyl-DL-phosphatidylethanolamine, and some remarks on lipid—lipid and lipid-protein interactions

A least-squares refinement analysis of atomic positional and thermal parameters in a single crystal of 1,2-dilauroyl-DL-phosphatidylethanolamine: acetic acid has been based on the X-ray diffraction intensities of 1132 independent reflexions, assessed by automatic microdensitometry. The final unweighted discrepancy index is 0.16 with e.s.ds of the bond lengths ranging from 0.02 to 0.12 A. The general features of our earlier, lessprecise analysis are confirmed. The close-packed arrangement of the phospholipid molecules is discussed in relation to electron microscopy and diffraction studies of the structures of membranes from Acholeplasma laidlawii and Halobacterium halobium.

Yttrium carbonate hydroxide

YOHCO3, or thorhombic, P212~2~; a = 4.809 (1), b=6 .957 (l), c=8 .466 (1) A; Z = 4 , de= 3.89 g c m -a. The final R for 737 reflections was 0.0518. The carbonate-group distances and angles are C-O(1) 1.288 (9), C-O(2) 1.279 (9), C-O(3) 1-287 (8) A, O(1)-C-O(2) 122.8 (7), O(1)-C-O(3) 118-7 (6), and O(2)-C-O(3) 1183 (7) °. The carbonate ion is bidentate to two different Y atoms. The distortion in the angles of the carbonate is at tr ibuted to this bonding scheme. The Y atoms' coordinat ion is a monocapped square ant ipr ism with two hydroxyls and seven carbonate oxygens surrounding the Y. Introduction. Commercia l ly available yt t r ium carbonate powder was placed in a 9 % solution of NH4CI saturated with CO2. The solution was then heated in a hydrothermal reactor for 7 d at 360°C and 750 atm. Intensity data were collected on a Syntex P21 automated diffractometer with Mo K~ X-radiat ion and a graphite monochromator (2=0.71069 A). A set of 737 unique reflections with I > 3owas obtained with 20_< Fig. 1. Drawing of the coordination polyhedron of Y in YOHCOa. One of the bidentate carbonates projecting towards the reader has been omitted for clarity. 70 ° . An absorpt ion correction was applied, the crystal being approximated as a non-reentrant polyhedron with p = 208.5 cm -1. Transmission factors varied from 0.35 to 0.71. The structure was solved with the Patterson function and refined anisotropically with full-matrix least squares to a conventional R=0.0518. Atom coordinates and thermal parameters are listed in Table 1. Interatomic distances less than 3.0 A and angles in the carbonate ion are listed in Table 2.* * A list of structure factors has been deposited with the British Library Lending Division as Supplementary Publication No. SUP 31920 (8 pp.). Copies may be obtained through The Executive Secretary, International Union of Crystallography, 13 White Friars, Chester CH1 1NZ, England. Table 2. Bond distances (t~) and angles (0) Symmetry code (a) x, y, z (b) k x , y , k+z Y-O(1) (a) 2-430 (7) (c) 2.430 (7) (d) 2943 (8) Y-O(2) (d) 2470 (6) (d) 2463 (6) Y-O(3) (a) 2.478 (6) (d) 2616 (7) (e) 2.615 (6) Y-O(4) (d) 2.236 (6) (a) 2.252 (5) (c) k+x, k y , z (d) x , k+y, k z O(1)-O(4) (d) 2.895 (9) (c) 2-976 (9)

The di-π-methane rearrangements of 1,4-dihydro-1,4-methano- and -ethanonaphthalene-5,8-diols

Direct photolysis of 1,4-dihydro-1,4-methanonaphthalene-5,8-diol (1a) gave tetracyclo[5.4.0.02,4.03,6]undeca-1(7),8,10-triene-8,11-diol (2a), the structure of which was established by spectral data and conversion into the known diacetate (2b). Photolysis of the 1,4-ethano-derivative (1g) gave tetracyclo[6.4.0.02,4.03,7]dodeca-1(8),9,11-triene-9,12-diol (2d), identified from spectral data. An X-ray crystallographic study of its diacetate (2e) showed that the crystals are orthorhombic, space group Pnma, a= 8.37(2), b= 18.60(3), c= 9.49(2)Å, Z= 4, with 50% occupation of equivalent positions by enantiomer pairs to produce a disordered structure. The structure was solved by direct methods and atomic positions and thermal parameters were refined by full-matrix least-squares calculations and Fourier methods. Studies with the 2,3,6,7-tetradeuterio-derivatives of (1a) and (1g) showed that the rearrangements are of the di-π-methane–vinylcyclopropane type.

Crystal and molecular structure of carolenalone, a cycloheptenone sesquiterpene lactone from North Carolina Helenium autumnale L.

X-Ray single crystal analysis has established the structure and relative stereochemistry of the title compound (I). Crystals are orthorhombic, space group P212121, a= 7.31 (1), b= 21.20(1), c= 9.210 A, Z= 4. The structure was solved by direct methods and atomic positional and thermal parameters were refined by full-matrix leastsquares calculations to R 0.078 over 476 reflections from diffractometer measurements. The cycloheptenone ring adopts a flattened twist-chair conformation in which the C:C·C:O system with a torsion angle of –157° is distinctly non-planar. The cyclopentane and γ-lactone rings are both in envelope conformations; the C(11) methyl group is β-oriented.

The crystal structures of a series of salts of phthalic acid. Diammonium phthalate (NH4)2(OOC.C6H4.COO)

The crystal structures of a series of salts of phthalic acid. Diammonium phthalate (NH4)2(OOC.C6H4.COO)

The crystal and molecular structure of sym- trans-DI-μ-acetatobis[ o-(t)-butyl- o-tolylphosphino)benzyl]dipalladium-(II) a complex formed by an internal metallation reaction

The structure of [Pd(OAc){CH 2C 6H 4P-t-Bu( o-tolyl)}] 2 has been determined from three dimensional X-ray diffractometer data. The compound crystallizes in the space group P 1 , Z = 2, with a reduced triclinic unit cell a = 12.989, b = 15.643, c = 20.325 Å, α = 130.85, β = 117.91, γ = 94.08°. A least squares refinement of atomic positional and thermal parameters, based on 5436 observed reflections has converged to discrepancy indices, R 1 and R 2, of 0.044 and 0.058. The structure consists of independent dimeric molecules packed with cyclohexane molecules of crystallization. [ o-(t-butyl- o-tolylphosphino)benzyl]palladium(II) fragments are bridged by the two acetate groups so that each palladium has a slightly distorted planar coordination; the molecule has approximate C 2 symmetry with a Pd…Pd non-bonding distance of 3.413(1) Å. The mean Pd-P and Pd-C bond lengths are 2.204(2) and 2.033(5) Å respectively, other mean distances being Pd-O 2.13(1), C-C(methyl) 1.497(4), O-C(acetate) 1.247(6). C-C(benzyl) 1.497(7) Å. The solvated cyclohexane molecules are disordered.

Tricarbonylbis(dimethylphenylphosphine)iridium(I) perchlorate

Ir(CO)3(PMezPh)2)C104, IrP2C1OvCI9H22 , monoclinic, P21/c, a=10.45 (1), b=15.38 (2), c= 14.71 (2) A., fl=99.6 (2) °, Z=4, Dx= 1.86, Dr,= 1.84 g cm -3, V=2331 A 3. The coordination of iridium is trig- onal bipyramidal with the phosphine ligands in the axial positions. The orientation of the phenyl rings gives the cation approximate Cz symmetry. isotropic temperature factors for the other atoms. The weighting scheme used in the final cycles was w= 1/(5+Fo+O.O2F 2) and the final R value was 10.4%. The atomic coordinates and thermal parameters are given in Table 1.*

A neutron diffraction determination of the crystal structure of α-phase potassium nitrate at 25 degrees C and 100 degrees C

The structure of alpha -phase potassium nitrate (KNO3) has been determined at room temperature (25 degrees C) and closer to the alpha to beta transition temperature at 100 degrees C, from three-dimensional neutron diffraction data. The present results indicate that the potassium atoms experience small but significant displacements, predominantly along the (001) direction, as the temperature is increased. They also suggest that the NO3 groups are nonplanar, with the plane of the oxygen atoms making a small angle to the a-b face of the unit cell. Analysis of the atomic anisotropic thermal parameters, obtained from the least-squares refinements, suggests that the RMS vibrational amplitudes of the potassium atoms increase along the (001) direction as the temperature increases.

Solid hexafluorobenzene

X-ray analysis of hexafluorobenzene at 120 K has shown that the space group is P21/n(C 2h 5), with six molecules per unit cell, and a = 16·82, b = 9·17, c = 5·76A, β = 95·8°. Four of the molecules in the unit cell are in general positions (Wyckoff position e) and two are in special positions at centres of symmetry (Wyckoff position c). At both types of site, the molecules are planar to within 0·01 A; in them C-C = 1·36 ± 0·02 A and C-F = 1·32 ± 0·017 A. The thermal libration tensors, calculated from the atom thermal parameters, show that molecular oscillations are less constrained at type e than at type c sites.

Crystal structure of the basic erbium tetramethyl-heptanedionate, Er8O(thd)10(OH)12

The crystal structure of the basic erbium diketonate, Er8O(thd)10(OH)12, which occurs as a minor by-product in the synthesis of tris(2,2,6,6-tetramethylheptane-2, 5-dionato)erbium(III), Er(thd)3, has been studied at room temperature by X-ray diffraction. The space group isPbcn and the crystal data area = 18·376(19),b = 31·625(35),c = 27·914(28) A,Z = 4,D c = 1·38 gcm−3,D m = 1·37 gcm−3. Full-matrix least-squares refinement of atomic and isotropic thermal parameters, using 3103 non-zero intensities obtained by counter methods, terminated with a conventionalR of 0·116. The Er atoms were found to be chelated by one thd group each and to cluster around a central oxygen atom. An inner sphere of four erbium atoms which surround the oxygen in a distorted tetrahedral fashion are bonded to five hydroxyl groups each and are eight-coordinate. An outer sphere of four erbiums which formally complete a dodecahedron around the central oxygen are bonded to four hydroxyl groups each and are seven-coordinate. The seventh ligand atom belongs to a non-chelating thd group which is bonded through oxygen to two different erbium atoms. Each hydroxyl group is bonded to three erbium atoms, two of which belong to either the inner or the outer sphere. The coordination geometries of the erbium ions are all related to capped trigonal prisms and thet-butyl groups are directed outwards. As a consequence the material behaves as a typical non-polar substance and sublimes together with Er(thd)3, apparently without decomposition.

Crystal and molecular structure of bis(2,2,6,6-tetramethylheptane-5-thiolo-3-onato)nickel(II)

The crystal structure of the nickel(II) chelate of the monothio derivative of 2,2,6,6-tetramethyl-heptane-3, 5-dione has been studied at room temperature by X-ray diffraction methods. The space group isP21/c and the crystal data area = 19·96(2),b = 10·25(1),c = 12·45(1) A, β = 102·17(5) °Z = 4,D m = 1·22,D c = 1·23 g cm−3. Full-matrix least-squares refinement of atomic and anisotropic thermal parameters, using 2109 non-zero intensities obtained by counter methods, terminated with a conventionalR of 0·105. The nickel was found to be surrounded by acis arrangement of two oxygen and two sulphur atoms which is almost planar, but slightly distorted towards a tetrahedron. All the evidence obtained supports extensive delocalization in the chelate rings, and the entire molecule has pseudomm symmetry. Thecis, rather thantrans relationship of the ligand atoms may indicate weak S-S interaction.