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.

Conformation of methyl 3,6-dideoxy-α-D-arabino-hexopyranoside, the immunodominant sugar of Salmonella serogroup D1: crystal structure, 1H nmr analysis, and semi-empirical calculations

1985 ◽  
Vol 63 (3) ◽  
pp. 739-744 ◽  
Author(s):  
George I. Birnbaum ◽  
David R. Bundle
Keyword(s):  
Minimum Energy ◽  
Direct Methods ◽  
Anomeric Effect ◽  
Pyranose Ring ◽  
Hydrogen Atoms ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
H Nmr ◽  
Cell Dimensions ◽  
Semi Empirical

Methyl 3,6-dideoxy-α-D-arabino-hexopyranoside (methyl tyveloside) crystallizes in the orthorhombic space group P212121 and the cell dimensions are a = 7.478(1), b = 7.933(1), c = 14.064(1) 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 = 0.038. The pyranose ring exists as an almost perfect 4C1 chair and the conformation adopted by the glycosidic methyl group is in agreement with the requirements of the exo-anomeric effect. Both acetal oxygen atoms act as hydrogen-bond acceptors, and the [Formula: see text] bond distances are in agreement with this feature. The 1H nmr spectrum shows that the conformation of the pyranose ring in aqueous solution is indistinguishable from that in the crystal. The minimum energy conformation of a pentasaccharide fragment of a Salmonella O-antigen, calculated with tyvelose coordinates obtained by bond modification, is in good agreement with the conformation which was calculated with tyvelose coordinates obtained from the X-ray analysis.

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.

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.

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.

scholarly journals Dynamics of Water in Crystal Hydrates

1967 ◽  
Vol 22 (9) ◽  
pp. 1440-1451 ◽  
Author(s):  
Ingo Berthold ◽  
Alarich Weiss
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Dynamical Behaviour ◽  
Water Molecules ◽  
Intensity Data ◽  
Two Dimensional ◽  
Fourier Synthesis ◽  
Hydrogen Atoms ◽  
X Ray ◽  
H Nmr

The crystal structure of Na2S2O6·2 H2O has been refined by means of single crystal X-ray intensity data. The structure of the isotypic Li2S2O6·2 H20 was also determined by single crystal studies. Two dimensional differential FOURIER synthesis revealed the approximate positions of the hydrogen atoms. From 1H-NMR investigations, the crystal structure, and information gained by IR spectroscopy the complete atomic arrangement in these two substances was obtained. The influence of the dynamical behaviour of the water molecules is taken into account in determining the hydrogen positions.

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.

Reaktion von 1.4-Dienen mit Metallkomplexen, I Darstellung und Röntgenstrukturanalyse eines π-enyl-Komplexes der Zusammensetzung (C8H13PdCl)2/ Reaction of 1,4-Dienes with Metal Complexes, I Synthesis and X-ray Structure Determination of a π-enyl Complex of Composition (C8H18PdCl)2

1976 ◽  
Vol 31 (4) ◽  
pp. 455-462 ◽  
Author(s):  
Peter Feldhaus ◽  
Richard Ratka ◽  
Hermann Schmid ◽  
Manfred L. Ziegler
Keyword(s):  
Metal Complexes ◽  
Structure Determination ◽  
Three Dimensional ◽  
Fourier Methods ◽  
X Ray ◽  
H Nmr ◽  
Nmr Data ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Reaction of (C6H5CN)2PdCl2 and 1,3-dimethylenecyclohexane led to an exocyclic π-enyl complex of formula (C8H13PdCl)2-bis(η3-2-methylene-6-methylcyclohexyl)(di-µ-chloro)-dipalladium. IR and 1H NMR data are in agreement with this formulation.The compound is monoclinic, with unit cell dimensions α = 499.97 ± 0.08, b =1342.26 ± 0.19, c =1379.60 ± 0.20 pm, β = 99.43 ± 0.02°, space group C5h2-P21/C, Ζ = 2, dX-ray = 1.83 g/cm3.The structure was determined from three-dimensional X-ray data by Patterson and Fourier methods. Least squares refinement by use of 1045 independent reflections has reached R1 = 5.6%.

An X-Ray Study of the Synthetic Intermediate 9-Cyano-1,10-Dimethyl-6-Ethylenedioxy-1-Octalin

1975 ◽  
Vol 53 (2) ◽  
pp. 192-194 ◽  
Author(s):  
Harry Lynton ◽  
Pik-Yuen Siew
Keyword(s):  
Crystal Structure ◽  
Total Synthesis ◽  
Direct Methods ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
X Ray ◽  
Ring Junction ◽  
Cell Dimensions ◽  
R Value ◽  
Synthetic Intermediate

The crystal structure of the synthetic intermediate, 9-cyano-1,10-dimethyl-6-ethy]enedioxy-1-octalin, C15H21O2N, was solved by direct methods. The compound crystallizes in the space group p21/c with cell dimensions a = 12.282(4), b = 7.144(3), c = 15.619(5) Å, β = 104.04(1)°. Refinement was carried out isotropically for hydrogen and anisotropically for non-hydrogen atoms using full matrix least squares to an R-value of 0.043 for 1669 observed reflections.This compound, which has a cis configuration at the octalin ring junction, is a precursor to a moiety of the alkaloid thelepogine. The cis conformation is essential for total synthesis of thelopogine by this route.

Structure and conformation of 2′,5′-anhydroarabinosylcytosine: X-ray, 1H nmr and 13C nmr analyses

1987 ◽  
Vol 65 (2) ◽  
pp. 271-276 ◽  
Author(s):  
George I. Birnbaum ◽  
Miloš Buděšínský ◽  
Jiří Berànek
Keyword(s):  
Direct Methods ◽  
Coupling Constants ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Solution Conformation ◽  
Torsion Angles ◽  
X Ray ◽  
Bicyclic System ◽  
Anti Conformation ◽  
Cell Dimensions

Crystals of 2′,5′-anhydroarabinosylcytosine hemihydrate belong to the monoclinic space group P21. The cell dimensions are a = 9.643(2), b = 10.328(1), c = 10.544(2) Å, β = 94.55(1)°. X-ray intensity data were measured on a diffractometer and the structure was determined by direct methods. Least-squares refinement, which included all nucleoside hydrogen atoms, converged at R = 0.041 for 2298 observed reflections. The asymmetric unit contains two molecules of the nucleoside and one molecule of water. In both nucleoside molecules, the conformation about the glycosyl bond is and, with XCN values of 15.5(3) and 26.3(3)°, respectively. In the bicyclic sugar moiety, the arabinofuranose rings adopt a C(3′)exo/C(2′)endo conformation and are highly puckered (τm = 57°). The solution conformation was studied by 1H and 13C nmr spectroscopy. A difference nOe proton nmr spectrum and 3J(C,H) coupling constants reveal an anti conformation in solution, with torsion angles very similar to those obtained from X-ray analysis. A comparison of observed 3J(H,H) coupling constants with those calculated on the basis of a modified Karplus equation shows significant differences, probably due to the presence of the bicyclic system.

Characterization of a γ-radiation-induced decomposition product of thymidine. Crystal and molecular structure of the (−)cis(5R,6S) thymidine glycol

1987 ◽  
Vol 65 (11) ◽  
pp. 2618-2623 ◽  
Author(s):  
Frank E. Hruska ◽  
Rudy Sebastian ◽  
André Grand ◽  
Lucienne Voituriez ◽  
Jean Cadet
Keyword(s):  
Pyrimidine Ring ◽  
Orthorhombic Space Group ◽  
Γ Radiation ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Cell Dimensions ◽  
Radiation Induced ◽  
Induced Decomposition

X-ray crystallography was used to determine the structure of (−)cis(5R,6S)-5,6-dihydroxy-5,6-dihydrothymidine, a γ-radiation induced product of thymidine. The crystals belong to the orthorhombic space group P212121 and have cell dimensions a = 8.420(1) Å, b = 10.422(1) Å, and 13.552(1) Å. The half-chair pucker of the 5,6-saturated pyrimidine ring is similar to that observed for the isolated base with the cis configuration, and is described by the Cremer–Pople parameters Q = 0.48 Å, θ = 62°, and [Formula: see text]. The conformation about the N-glycosyl bond is anti; the χ angle (−111.6(5)°) lies at one extreme of the range previously seen for nucleosides (−180 to −115°). The pucker 2T1 of the sugar (P = 151.2°; τm = 36.5°) contrasts with the O4′-endo type of pucker seen in 5,6-dihydrothymidine (0T4) and (5S)-5-hydroxy-5,6-dihydrothymidine (0T1). The conformation about the C4′—C5′ bond is gauche+. The solid state structure is similar to that determined in aqueous solution by 1H nmr.

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