The crystal and molecular structure of thiamine iodide hydroiodide

1976 ◽  
Vol 54 (19) ◽  
pp. 3001-3006 ◽  
Author(s):  
William Edward Lee ◽  
Mary Frances Richardson
Keyword(s):  
Heavy Atom ◽  
Pyrimidine Ring ◽  
Side Chain ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Iodide Ions ◽  
Cell Parameters ◽  
Weak Hydrogen Bonds ◽  
Ring Nitrogen ◽  
Heavy Atom Method

The X-ray crystal structure of thiamine iodide hydroiodide, C12H18N4OSI2, has been determined. The unit cell parameters are: a = 13.835(7), b = 7.442(4), c = 20.243(9) Å, β = 120.52(7)°, monoclinic space group P21/c, Z = 4. A total of 1445 reflections having F2 > 2σ(F2), 2θ < 40° were collected on a Picker 4-circle diffractometer with MoKα radiation by the 2θ scan technique. The structure was solved by the heavy-atom method. The iodide and sulphur atoms were refined anisotropically; only positional parameters were refined for the hydrogen atoms. Successive full-matrix least-squares refinements yielded an unweighted R-factor of 0.054. The pyrimidine ring is protonated on the ring nitrogen opposite the amino group. The relative disposition of the pyrimidine and thiazolium rings is similar to that observed in most other thiamine structures. The β-hydroxyethyl side chain of the thiazolium ring is folded in such a way that there is a short S … O contact, 2.97 Å in length. The iodide ions are involved in a number of weak hydrogen bonds.

Structure and conformation of the anticodon nucleoside 5-methoxyuridine in the solid state and in solution

1983 ◽  
Vol 61 (10) ◽  
pp. 2299-2304 ◽  
Author(s):  
George I. Birnbaum ◽  
Wayne J. P. Blonski ◽  
Frank E. Hruska
Keyword(s):  
Solid State ◽  
Three Dimensional ◽  
Direct Methods ◽  
Pyrimidine Ring ◽  
Dimensional Structure ◽  
Side Chain ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Cell Dimensions ◽  
Enol Tautomer

The three-dimensional structure of 5-methoxyuridine (mo5U) was determined with much higher precision than in a previous study (Hillen etal. J. Carbohydr. Nucleosides Nucleotides, 5, 23 (1978)). The crystals belong to the monoclinic space group P21 and the cell dimensions are a = 8.916(2), b = 14.372(2), c = 4.714(1) Å, β = 97.44(2)°. Intensity data were measured with a diffractometer and the structure was solved by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.031. The conformation about the glycosyl bond is anti (χCN = 23.1°), the pucker of the ribose ring is C(3′)endo, and the conformation of the —CH2OH side chain is gauche+. A comparison of the bond lengths N(3)—C(4) and C(4)—O(4) with those in uridine does not support the conclusion of Hillen etal. about a shift to the enol tautomer in mo5U. However, there are other changes in the geometry of the pyrimidine ring due to substitution at C(5). A conformational analysis, based on 1H and 13C nmr data, shows that the preferred conformation in solution is that observed in the solid state.

Studies on tellurium-carbon bonded compounds. II. The crystal structure of [Heptane-3,5-dionato(2 - )]tellurium(II) ('1,1′-Dimethylacetylacetone tellurium(II)')

1977 ◽  
Vol 30 (3) ◽  
pp. 487 ◽  
Author(s):  
JC Dewan ◽  
J Silver
Keyword(s):  
Crystal Structure ◽  
Least Squares ◽  
Title Compound ◽  
Heavy Atom ◽  
Chair Conformation ◽  
Heterocyclic Ring ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
Heavy Atom Method

The structure of the title compound has been determined by the heavy- atom method from 973 reflections, measured with a diffractometer, and refined by full-matrix least-squares methods to R 0.030. Crystals are monoclinic, space group P21, a = 8.69(1), b = 4.86(1), c = 10.14(2) Ǻ, β = 98.7(1)�, Z = 2. In the discrete molecules of the complex a tellurium(II) atom is bonded to one bivalent heptane-3,5-dione ligand through the α-carbon atoms [Te-C 2.184(6), 2.206(7) Ǻ; C-Te-C 89.7(3)�], forming a heterocyclic ring of chair conformation with the methyl substituents both in equatorial positions. The molecules are arranged in a zig-zag polymeric manner about the 21 axes at x = 0 and z = 0. All hydrogen atoms have been located.

Crystal and Molecular Structure of the Synthetic Intermediate, 2-Bromo-3-methoxy-5-hydroxy-5,6,7,8,9,10,13,14-octahydro-8-methyl-10,13-N-acetylaminomethano-phenanthrene, C19H24O3NBr

1973 ◽  
Vol 51 (16) ◽  
pp. 2637-2638 ◽  
Author(s):  
H. Lynton ◽  
P. Y. Siew
Keyword(s):  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Full Matrix ◽  
Cell Dimensions ◽  
Ring Nitrogen ◽  
Unit Cell Dimensions ◽  
Synthetic Intermediate ◽  
Heavy Atom Method

Crystals of the synthetic intermediate, 2-bromo-3-methoxy-5-hydroxy-5,6,7,8,9,10,13,14-octahydro-8-methyl-10,13-N-acetyl aminomethano-phenanthrene, C19H24O3NBr, are monoclinic, space group P21/n, unit cell dimensions a = 10.62(1), b = 14.47(2), c = 23.88(2) Å, β = 99.4(2)°, z = 8 with two molecules in the asymmetric unit. The structure was solved by the heavy atom method and refined by full matrix least squares to R = 0.096 for 2120 observed reflections. The conformation was found to be cis at the junction between rings A and B making further cyclization to obtain an A ring nitrogen bridge not possible.

Crystal structure of methyl,2-mercaptopyrimidinatomercury(II)

1978 ◽  
Vol 56 (4) ◽  
pp. 560-563 ◽  
Author(s):  
Chung Chieh
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Nmr Spectra ◽  
Heavy Atom ◽  
Pyrimidine Ring ◽  
Optically Active ◽  
Hydrogen Atoms ◽  
H Nmr ◽  
R Factor ◽  
Heavy Atom Method

Methyl,2-mercaptopyrimidinatomercury(II) was synthesized from methylmercuric hydroxide and 2-mercaptopyrimidine in aqueous solution. The crystal is orthorhombic with a = 4.063(2), b = 9.901(4), c = 18.808(15) Å, Dm = 2.88(1), Z = 4, Dc = 2.867 g cm−3, space group P212121. The structure was solved by the heavy atom method using 605 diffractometer measured reflections. The final R factor was 0.069. The key bond lengths and angles are: Hg—S, 2.39(2) Å, Hg—CH3, 2.13(6) Å, [Formula: see text] 174°. The CH3HgS— group bends out of the plane of the pyrimidine ring and the Hg atom interacts rather strongly with one of the ring nitrogens with an Hg—N distance of 2.83 Å. However, the Hg … N interaction is very labile in solution, since the two hydrogen atoms in the meta positions are equivalent from the 1H nmr spectra in both CDCl3 and DMSO solutions. The solution of the compound is not optically active.

scholarly journals Crystallographic studies of SarV, a global regulator fromStaphylococcus aureus

2015 ◽  
Vol 71 (8) ◽  
pp. 1038-1041
Author(s):  
Yang Song ◽  
Fan Zhang ◽  
Xu Li ◽  
Jianye Zang ◽  
Xuan Zhang
Keyword(s):  
Heavy Atom ◽  
Size Exclusion ◽  
Monoclinic Space Group ◽  
Molecular Replacement ◽  
Global Regulator ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Exclusion Chromatography ◽  
Heavy Atom Method

SarV, a member of the SarA protein family, is a global transcriptional regulator which has been reported to be involved in the regulation of autolysis inStaphylococcus aureus. In this study, SarV fromS. aureuswas successfully cloned, expressed, purified and crystallized. X-ray diffraction data were collected to 2.10 Å resolution. The crystals of SarV belonged to the monoclinic space groupP21, with unit-cell parametersa= 36.40,b= 119.64,c= 66.80 Å, α = γ = 90, β = 98.75°. The Matthews coefficient and the solvent content were estimated to be 2.57 Å3 Da−1and 52%, respectively, suggesting the presence of four molecules in the asymmetric unit. The results of size-exclusion chromatography (SEC) indicated thatS. aureusSarV exists as a homodimer in solution. Unfortunately, the structure cannot be solved by molecular replacement because of the low sequence identity ofS. aureusSarV to known structures. Further phase determination by selenomethionine single-wavelength anomalous dispersion (SAD) and the heavy-atom method is in progress.

The Crystal and Molecular Structure of sym-fac-(1,4,7-Triazaheptane)-(S)-aspartatocobalt(III) Diperchlorate Dihydrate

1994 ◽  
Vol 59 (5) ◽  
pp. 1052-1058 ◽  
Author(s):  
Jan Ondráček ◽  
Jana Ondráčková ◽  
Jaroslav Maixner ◽  
František Jursík
Keyword(s):  
Molecular Structure ◽  
Aspartic Acid ◽  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Membered Ring ◽  
Boat Conformation ◽  
Hydrogen Atoms ◽  
Orthorhombic System ◽  
Anisotropic Temperature ◽  
Heavy Atom Method

The crystal and molecular structure of s-fac-[Co((S)-Asp)(dien)]ClO4 . HClO4 .2 H2O (dien = 1,4,7-triazaheptane) was solved by the heavy atom method. The position parameters of the non-hydrogen atoms and their anisotropic temperature parameters were refined based on 1 726 observed reflections with a final value of R = 0.073. The substance crystallizes in the orthorhombic system in the space group P212121, Z = 4, a = 8.506(1), b = 17.171(2), c = 13.277(1) Å. The structure involves hydrogen bonds between the O2, O4 and HN2 atoms of aspartic acid and the two molecules of water. The five-membered dien chelate rings take the asymmetric envelope conformations. The five-membered ring of (S)-aspartic acid possesses the symmetric envelope conformation whereas the six-membered ring exhibits the skew boat conformation.

Determination of the structure of bis(propyldithiocarbamate)nickel(II)

1990 ◽  
Vol 55 (4) ◽  
pp. 1010-1014 ◽  
Author(s):  
Jiří Kameníček ◽  
Richard Pastorek ◽  
František Březina ◽  
Bohumil Kratochvíl ◽  
Zdeněk Trávníček
Keyword(s):  
Molecular Structure ◽  
Title Compound ◽  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Planar Configuration ◽  
Compound C ◽  
Heavy Atom Method

The crystal and molecular structure of the title compound (C8H16N2NiS4) was solved by the heavy atom method and the structure was refined anisotropically to a final R factor of R = 0.029 (wR = 0.037) for 715 observed reflections. The crystal is monoclinic, space group P21/c with a = 948.3(2), b = 776.9(2), c = 1 167.4(2) pm, β = 125.14(2)°, Z = 2. The molecule contains two four-membered NiSCS rings of approximately planar configuration with the Ni atom situated at a centre of symmetry. The molecules are arranged in chains along the c-axis of the unit cell.

Structure and conformation of the hydrochloride of pseudoisocytidine, an antileukemic C-nucleoside

1980 ◽  
Vol 58 (16) ◽  
pp. 1633-1638 ◽  
Author(s):  
George I. Birnabaum ◽  
Kyoichi A. Watanabe ◽  
Jack J. Fox
Keyword(s):  
Heavy Atom ◽  
Three Dimensional ◽  
Direct Methods ◽  
Dimensional Structure ◽  
Side Chain ◽  
Hydrogen Atoms ◽  
Triclinic Space Group ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Sugar Ring

The three-dimensional structure of pseudoisocytidine hydrochloride was determined by X-ray crystallography. The crystals belong to the triclinic space group P1 and the cell dimensions are a = 6.623(2), b = 8.053(2), c = 6.201(2) Å, α = 108.35(2), β = 101.36(2), γ = 93.54(2) °. Intensity data were measured with a diffractometer and the structure was solved by a combination of heavy-atom and direct methods. Least-squares refinement, which included hydrogen atoms, converged at R = 0.040. The conformation about the glycosyl bond is anti (χCC = 21.6°), the pucker of the furanose ring is C(1′)exo, and the conformation of the —CH2OH side chain is gauche–trans (t). An examination of bond lengths indicates that of the three main resonance forms of the isocytosine cation the fully conjugated one contributes more to the structure than the cross-conjugated one. Bond angles in the sugar ring reflect its rare conformation.

Crystal and Molecular Structure of Dithiocyanato(triphenylarsine)mercury(II)

1975 ◽  
Vol 53 (22) ◽  
pp. 3383-3387 ◽  
Author(s):  
Joseph Hubert ◽  
André L. Beauchamp ◽  
Roland Rivest
Keyword(s):  
Molecular Structure ◽  
Least Squares ◽  
Coordination Number ◽  
Diffraction Data ◽  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Heavy Atom Method

The crystal and molecular structure of dithiocyanato(triphenylarsine)mercury(II) has been determined from X-ray diffraction data. The crystals are monoclinic, space group P21/c, with a = 10.290(7), b = 21.199(23), c = 10.719(7) Å, β = 112.00(2)°, and Z = 4. The structure has been solved by the heavy-atom method and refined by block-diagonal least-squares calculations. The agreement factor R obtained for 2607 'observed' reflections is 0.030. The crystal consists of single molecules. The 'characteristic' coordination number of mercury is three, with two sulfur and one arsenic atoms at the apexes of a triangle. The nitrogen atoms of the thiocyanate groups are at 2.67 and 2.74 Å from the adjoining mercury atoms and therefore link the different molecules together.

Crystal Structure of Adeninium Trichloromercurate(II),

1975 ◽  
Vol 53 (15) ◽  
pp. 2345-2350 ◽  
Author(s):  
Monique Authier-Martin ◽  
André L. Beauchamp
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Least Squares ◽  
Title Compound ◽  
Heavy Atom ◽  
Chloride Ions ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Space Group ◽  
Heavy Atom Method

The title compound belongs to space group P21/c with a = 23.99(1), b = 4.245(2), c = 25.98(1) Å, β = 117.58(7)°, and Z = 8. The structure was solved by the heavy-atom method and refined by block-diagonal least squares on 2589 independent observed reflections. All non-hydrogen atoms were refined anisotropically and some of the hydrogen atoms were located but their parameters were not refined. The final values of R and Rw were 0.042 and 0.047, respectively.The two nonequivalent mercury atoms have very similar environments. Two short Hg—Cl bonds (2.34–2.38 Å) at ∼ 165° define a quasi-molecular HgCl2 unit. Overall octahedral coordination is completed with two chloride ions at 2.76–2.84 Å and two chlorine atoms at 3.19–3.26 Å on neighboring HgCl2 quasi-molecules. HgCl6 octahedra share edges to form twofold ribbons in the b direction. This pattern of octahedra is identical with the onereported for β-NH4HgCl3. The cations are pairs of N(1)-protonated adenine molecules linked by two N(10)—H(10)… N(7) hydrogen bonds and stacked in the b direction. Water molecules act as acceptors in moderately strong hydrogen bonds with acidic protons H(1) and H(9) of adeninium ions. Other generally weaker hydrogen bonds exist between the various parts of the structure.

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