Solid state and solution conformations of 1 -(β-D-2′,3′-secoribofuranosyl)-5,6-dichlorobenzimidazole, an acyclonucleoside analogue

1985 ◽  
Vol 63 (6) ◽  
pp. 1215-1221 ◽  
Author(s):  
George I. Birnbaum ◽  
Ryszard Stolarski ◽  
Zygmunt Kazimierczuk ◽  
David Shugar
Keyword(s):  
Direct Methods ◽  
Monoclinic Space Group ◽  
Intensity Data ◽  
Asymmetric Unit ◽  
X Ray ◽  
H Nmr ◽  
Cell Dimensions ◽  
Independent Molecules ◽  
Unit Cell Dimensions ◽  
Glycosidic Torsion Angle

The title compound crystallizes in the monoclinic space group P21, with two independent molecules in the asymmetric unit (Z = 4). The unit cell dimensions are a = 11.861(2), b = 7.897(1), c = 14.527(3) Å, β = 91.28(1)°. X-ray intensity data were measured on a diffractometer, and the crystal structure was determined by direct methods. Least-squares refinement converged at R = 0.036 for 2980 reflections. The glycosidic torsion angle [C(2)—N(1)—C(1′)—O(1′)] is 53.9° in molecule A and 129.8° in molecule B. In both molecules, the orientation of C(1′)—O(1′) to C(2′)—O(2′) is trans. The conformations about C(3′)—C(4′) and C(4′)—C(5′) are different in each of the two molecules. These features are compared with those of acyclonucleoside analogues with antiviral activity. The conformation in aqueous medium was examined with the aid of high-resolution 1H nmr spectroscopy, and the results are compared with those obtained from the X-ray analysis.

The crystal structure of 4,7-oxido-7-methyl-7-hydroxymethyl-2,2,6,6-tetramethylpiperidin-1-oxyl

1982 ◽  
Vol 60 (18) ◽  
pp. 2392-2397 ◽  
Author(s):  
M. Cygler
Keyword(s):  
Direct Methods ◽  
Chair Conformation ◽  
Hydroxyl Group ◽  
Piperidine Ring ◽  
Monoclinic Space Group ◽  
Intensity Data ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

4,7-Oxido-7-methyl-7-hydroxymethyl-2,2,6,6-tetramethylpiperidin-1-oxyl, C12H22NO3, crystallizes in the monoclinic space group P21/m with unit cell dimensions a = 8.041(1), b = 13.348(1), c = 5.945(1) Å, β = 95.90(1)°, Z = 2. Intensity data were measured on a diffractometer and the structure solved by direct methods. The least-squares refinement converged at R = 0.039 for 1304 reflections. Two enantiomeric molecules, differing in the position of the OH group, occupy the same site in the asymmetric unit (each with a probability of 0.5) giving rise to a disorder of the hydroxyl group. The piperidine ring adopts the usual chair conformation, with C—C—C—C torsion angles being intermediate between those observed for C(4) mono- and for bisubstituted nitroxypiperidine derivatives. The N—O bond is 1.282(2) Å long, and it makes an angle of 18.5(2)° with the CNC plane. Molecules are connected by O—H … O hydrogen bonds. The influence of the degree of substitution at C(4) on ring geometry is discussed.

scholarly journals The reaction of 3,5-diphenyl-1,2-dithiolium-4-olate with aniline: the crystal structure of 1-phenylimino-2-phenylamino-3-phenylindene

1987 ◽  
Vol 65 (12) ◽  
pp. 2830-2833 ◽  
Author(s):  
David M. McKinnon ◽  
Peter D. Clark ◽  
Robert O. Martin ◽  
Louis T. J. Delbaere ◽  
J. Wilson Quail
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Single Crystal ◽  
Least Squares ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

3,5-Diphenyl-1,2-dithiolium-4-olate (1) reacts with aniline to form 1-phenylimino-2-phenylamino-3-phenylindene (3a). Under suitable conditions, 6-phenylbenzo[b]indeno[1,2-e]-1,2-thiazine is also formed. These structures are confirmed by alternative syntheses. The molecular structure of 3a has been determined by single crystal X-ray diffraction. Compound 3a crystallizes in the monoclinic space group C2/c with unit cell dimensions a = 20.777(3) Å, b = 6.130(3) Å, c = 31.327(3) Å, 3 = 99.59(1)°, and Z = 8. The structure was solved by direct methods and refined by least squares to a final R = 0.055. The molecular structure of 3a shows the three phenyl containing substituents to have the planes of their ring systems tilted between 40° and 60° from the plane of the indene system due to steric repulsions.

Solid State and Solution Structures of an Adenine Analogue of the Antiviral Acyclonucleoside 9-(1,3-Dihydroxy-2-propoxymethyl)guanine

1990 ◽  
Vol 45 (7-8) ◽  
pp. 915-921 ◽  
Author(s):  
Joachim Granzin ◽  
Wolfram Saenger
Keyword(s):  
Solid State ◽  
Biological Activities ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Extended Form ◽  
Solution Structures ◽  
Cell Dimensions ◽  
Independent Molecules ◽  
Unit Cell Dimensions ◽  
C Nmr

Abstract The title compound. 9-(1,3-dihydroxy-2-propoxymethyl)adenine (DHP-Ade). an analogue of the antiviral acyclonucleoside 9-(1,3-dihydroxy-2-propoxymethyl)guanine (DHPG), crystallizes in the monoclinic space group P21. with unit cell dimensions of a = 10.848(4), b = 8.765(3), c = 11.432(4) Å. β = 102.14(3)° . with two independent molecules in the asymmetric unit. The crystal structure of DHP-Ade was determined and compared with that for DHPG. The solution conformations of both acyclonucleosides were also determined with the aid of 1H and ,13C NMR spectroscopy. In the solid state the acyclic chain may adopt a “folded” form, i.e. gauche about the C(1′)-O(1′) bond (as in DHP-Ade), or an “extended” form (as in DHPG), results which corre- spond to the rotations about this bond in solution. A general discussion is presented of the conformations of the acyclic chains of various acyclonucleosides, from the antiviral 9-(2-hydroxyethoxymethyl)guanine (Acyclovir, ACV) through to 2′,3′-seco-nucleosides, both in the solid state and in solution, and the relevance of these to biological activities.

Ab initiostructure determination of sulfathiazole polymorph V from synchrotron X-ray powder diffraction data

1999 ◽  
Vol 32 (3) ◽  
pp. 436-441 ◽  
Author(s):  
Fung Choy Chan ◽  
Jamshed Anwar ◽  
Robert Cernik ◽  
Paul Barnes ◽  
Rory McHardy Wilson
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Computational Modelling ◽  
Direct Methods ◽  
Polymorphic Form ◽  
Monoclinic Space Group ◽  
Powder Diffraction Data ◽  
Asymmetric Unit ◽  
X Ray ◽  
Unit Cell Dimensions

The crystal structure of sulfathiazole [4-amino-N-(2,3-dihydro-2-thiazolylidene)benzenesulfonamide, C9H9N3O2S] polymorphic form V has been determined from high-resolution synchrotron X-ray powder diffraction data. The structure is monoclinic, space groupP21/n,Z= 8, with two molecules in the asymmetric unit. The unit-cell dimensions area= 14.3296 (3),b= 15.2733 (2),c= 10.4428 (2) Å and β = 91.052 (1)° with cell volumeV= 2285.13 (8) Å3. The structure has been solved by direct methods without recourse to any computational modelling techniques for generating possible structures. The unrefined structure obtained from direct methods gave anRwpvalue of 36.5%. Refinement of atomic and displacement parameters yielded a finalRwpof 12.54% (Rp= 9.37%). The conformations of the two molecules in the asymmetric unit are nearly identical and very similar to that found in other forms of sulfathiazole. The molecular packing is characterized by molecular sheets lying perpendicular to theaaxis. Each sheet is two molecules thick, being integrated by hydrogen bonding. With 16 non-H atoms in the molecule and two molecules in the asymmetric unit, this structure represents a further advance in terms of the complexity of an organic structure solved from X-ray powder diffraction data.

Carcinogenic alkylation of nucleic acid bases. Solid state and solution studies of O2-isopropyl-2′-deoxythymidine

1988 ◽  
Vol 66 (7) ◽  
pp. 1628-1634 ◽  
Author(s):  
George I. Birnbaum ◽  
Krishan L. Sadana ◽  
M. Tahir Razi ◽  
Terry Lee ◽  
Rudy Sebastian ◽  
...  
Keyword(s):  
Direct Methods ◽  
Pyrimidine Ring ◽  
Intensity Data ◽  
Nucleic Acid Bases ◽  
Hydrogen Atoms ◽  
X Ray ◽  
H Nmr ◽  
Nmr Data ◽  
Solution Studies ◽  
Cell Dimensions

O2-Isopropyl-2′-deoxythymidine (i2dT) crystallizes in the tetragonal space group P43212, and the cell dimensions are a = b = 8.7667(2), c = 37.1943(12) Å. X-ray 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 = 0.036 for 1780 observed reflections. In analogy with other O-alkylated bases, the exocyclic O2—C8 bond is syn-periplanar to the C2—N3 bond in the pyrimidine ring. Angular distortions in the base can be correlated with those observed in O4-alkylated pyrimidines and O6-alkylated guanines. The conformation of the glycosyl bond is anti with χCN = 27.1°. The furanose ring adopts a C2′ endo pucker and the conformation about C4′—C5′ is gauche+. 1H nmr data show that these conformations are also preferred in solution.

X-ray and 1H nmr analyses of 5-(m-benzyloxybenzyl)-1-[(1,3-dihydroxy-2-propoxy)methyl]uracil, an acyclonucleoside inhibitor of uridine phosphorylase

1986 ◽  
Vol 64 (12) ◽  
pp. 2376-2381 ◽  
Author(s):  
George I. Birnbaum ◽  
Jean-Robert Brisson ◽  
Shi Hsi Chu ◽  
Zhi Hao Chen ◽  
Elizabeth C. Rowe
Keyword(s):  
Direct Methods ◽  
Uridine Phosphorylase ◽  
Hydrogen Atoms ◽  
Gauche Conformation ◽  
Triclinic Space Group ◽  
X Ray ◽  
H Nmr ◽  
Cell Dimensions ◽  
Nuclear Overhauser ◽  
Glycosidic Torsion Angle

The title compound crystallizes in the triclinic space group [Formula: see text] and the cell dimensions are a = 16.890(3), b = 9.586(2), c = 6.316(1) Å, α = 91.09(1), β = 93.50(1), γ = 93.04(1)°. X-ray intensity data were measured on a diffractometer, and the crystal structure was determined by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.056 for 3454 observed reflections. Adjacent six-membered rings are approximately perpendicular to one another. The glycosidic torsion angle [C(6)—N(1)—C(1′)—O(4′)] is 96.2(2)°. In the acyclic moiety, both C—OH bonds are gauche with respect to C(4′)—O(4′). The gauche conformation is also dominant in solution, as determined by high-resolution 1H nmr spectroscopy. Results of nuclear Overhauser experiments lead to conclusions about the flexibility of the molecule.

The External Shape of Human γ GI Immunoglobulin from Crystal Sections

1971 ◽  
Vol 29 ◽  
pp. 428-429
Author(s):  
L. W. Labaw
Keyword(s):  
Molecular Weight ◽  
Sodium Phosphate ◽  
Osmium Tetroxide ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Large Molecular Weight ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Crystallographic Axes

Crystals of a human γGl immunoglobulin have the external morphology of diamond shaped prisms. X-ray studies have shown them to be monoclinic, space group C2, with 2 molecules per unit cell. The unit cell dimensions are a = 194.1, b = 91.7, c = 51.6Å, 8 = 102°. The relatively large molecular weight of 151,000 and these unit cell dimensions made this a promising crystal to study in the EM.Crystals similar to those used in the x-ray studies were fixed at 5°C for three weeks in a solution of mother liquor containing 5 x 10-5M sodium phosphate, pH 7.0, and 0.03% glutaraldehyde. They were postfixed with 1% osmium tetroxide for 15 min. and embedded in Maraglas the usual way. Sections were cut perpendicular to the three crystallographic axes. Such a section cut with its plane perpendicular to the z direction is shown in Fig. 1.This projection of the crystal in the z direction shows periodicities in at least four different directions but these are only seen clearly by sighting obliquely along the micrograph.

Configurational and conformational studies on condensation products of biogenic amines with 2,5-anhydro-D-mannose

1985 ◽  
Vol 63 (11) ◽  
pp. 2915-2921 ◽  
Author(s):  
Ian M. Piper ◽  
David B. MacLean ◽  
Romolo Faggiani ◽  
Colin J. L. Lock ◽  
Walter A. Szarek
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Direct Methods ◽  
Conformational Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Twist Conformation ◽  
Cell Dimensions ◽  
Internal Hydrogen Bond

The products of a Pictet–Spengler condensation of tryptamine and of histamine with 2,5-anhydro-D-mannose have been studied by X-ray crystallography to establish their absolute configuration. 1(S)-(α-D-Arabinofuranosyl)-1,2,3,4-tetrahydro-β-carboline (1), C16H20N20O4, is monoclinic, P21 (No. 4), with cell dimensions a = 13.091(4), b = 5.365(1), c = 11.323(3) Å, β = 115.78(2)°, and Z = 2. 4-(α-D-Arabinofuranosyl)imidazo[4,5-c]-4,5,6,7-tetrahydropyridine (3), C11H17N3O4, is orthorhombic, P212121 (No. 19), with cell dimensions a = 8.118(2), b = 13.715(4), c = 10.963(3) Å, and Z = 4. The structures were determined by direct methods and refined to R1 = 0.0514, R2 = 0.0642 for 3210 reflections in the case of 1, and to R1 = 0.0312, R2 = 0.0335 for 1569 reflections in the case of 3. Bond lengths and angles within both molecules are normal and agree well with those observed in related structures. In 3 the base and sugar adopt a syn arrangement, which is maintained by an internal hydrogen bond between O(2′) and N(3). The sugar adopts a normal 2T3 twist conformation. The sugar has the opposite anti arrangement in the β-carboline 1 and the conformation of the sugar is unusual; it is close to an envelope conformation with O(4′) being the atom out of the plane. This conformation is caused by a strong intermolecular hydrogen bond from O(5′) in a symmetry-related molecule to O(4′). Both compounds are held together in the crystal by extensive hydrogen-bonding networks. The conformations of the compounds in solution have been investigated by 1H nmr spectroscopy, and the results obtained were compared with those obtained by X-ray crystallography for 1 and 3.

Preliminary crystallographic studies on glutamine synthetase from Mycobacterium tuberculosis

1999 ◽  
Vol 55 (4) ◽  
pp. 865-868 ◽  
Author(s):  
Harindarpal S. Gill ◽  
Gaston M.U. Pfluegl ◽  
David Eisenberg
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Glutamine Synthetase ◽  
Etiologic Agent ◽  
Asymmetric Unit ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Dimensions ◽  
The One ◽  
Unit Cell Dimensions ◽  
Axes Of Symmetry

The etiologic agent of tuberculosis, Mycobacterium tuberculosis, has been shown to secrete the enzyme glutamine synthetase (TB-GS) which is apparently essential for infection. Four crystal forms of a recombinant TB-GS were grown. The one chosen for synchrotron X-ray data collection belongs to space group P212121 with unit-cell dimensions 208 × 258 × 274 Å, yielding 2.4 Å resolution data. A Matthews number of 2.89 Å3 Da−1 is found, corresponding to 24 subunits of molecular mass 1300 kDa in the asymmetric unit. From earlier work, the structure of Salmonella typhimurium GS, which is 51% identical in sequence to TB-GS, is known to be dodecameric with 622 symmetry. Self-rotation calculations on the TB-GS X-ray data reveal only one set of sixfold and twofold axes of symmetry. A Patterson map calculated from the native X-ray data confirms that there are two dodecamers in the asymmetric unit, having both their sixfold and twofold axes parallel to one another.

Synthesis and Structure of cis-Dioxobis(pyrimidine-2-thiolato-N,S)molybdenum(VI)

1992 ◽  
Vol 45 (11) ◽  
pp. 1933 ◽  
Author(s):  
PR Traill ◽  
AG Wedd ◽  
ERT Tiekink
Keyword(s):  
Least Squares ◽  
Octahedral Geometry ◽  
Distorted Octahedral Geometry ◽  
Monoclinic Space Group ◽  
Full Matrix ◽  
X Ray ◽  
Distorted Octahedral ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The characterization of two MoVI complexes, cis -[MoO2(2-pymS)2] and cis -[MoO2(2-pyS)2] (where 2-pymSH is pyrimidine-2-thiol and 2-pySH is pyridine-2-thiol), and their reaction with Ph3P are reported. The X-ray structure of cis -[MoO2(2-pymS)2] shows the molybdenum atom to exist in a distorted octahedral geometry defined by two mutually cis oxygen atoms and two chelating 2-pymS ligands so that the two sulfur atoms occupy approximate trans positions. Crystals of cis -[MoO2(2-pymS)2] are monoclinic, space group P 21/n, with unit cell dimensions: a 9.301(3), b 12.121(2), c 11.303(3) �, β 112.62(3)�, V 1176.3 �3, Z 4. The structure was refined by a full-matrix least-squares procedure to R 0.067 for 1858 reflections with I ≥ 2.5 (I).

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