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.

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.

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.

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.

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.

Molecular conformation of 2′-deoxy-3′,5′-di-O-acetyl guanosine. Crystal structure and high resolution proton nuclear magnetic resonance investigations

1988 ◽  
Vol 66 (10) ◽  
pp. 2634-2639 ◽  
Author(s):  
Leo H. Koole ◽  
Henk M. Buck ◽  
Jan A. Kanters ◽  
Arie Schouten
Keyword(s):  
Molecular Conformation ◽  
Proton Nuclear Magnetic Resonance ◽  
Solution Conformation ◽  
Planar System ◽  
Equal Distribution ◽  
Triclinic Space Group ◽  
X Ray ◽  
H Nmr ◽  
Conformational Preferences ◽  
Cell Dimensions

2′-Deoxy-3′,5′-di-O-acetyl guanosine crystallizes in the triclinic space group [Formula: see text], and the cell dimensions are a = 8.643(1) Å, b = 10.122(1) Å, c = 10.391(1) Å, α = 87.04(1)°, β = 73.58(1)°, γ = 72.37(1)°, V = 830.4(2) Å3; Z = 2 molecules per cell. Least-squares refinement converged at R = 0.031 for 3450 observed reflections. The asymmetric unit consists of two independent molecules. The guanine bases are linked via N(1)—H … N(7) and N(2)—H … O(6) hydrogen bonds to form a virtually planar system. Moreover, the conformational preferences of the title compound in DMSO-d6 solution have been determined with 300 MHz 1H NMR. It is found that the X-ray structure and the solution conformation are essentially similar. The C(4′)—C(5′) linkage resides in the gauche+ (g+) or trans (t) rotamers in the solid state, while an approximately equal distribution over g+, t, and gauche− is found in solution.

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.

Synthesis and structural study of aminals derived from 8-aminoquinoline and 1-aminonaphtalene

1987 ◽  
Vol 65 (4) ◽  
pp. 687-692 ◽  
Author(s):  
Enrique Galvez ◽  
Isabel Iriepa ◽  
Antonio Lorente ◽  
Jose Miguel Mohedano ◽  
Feliciana Florencio ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Carbon Atom ◽  
Mass Spectra ◽  
The Other ◽  
Reaction Conditions ◽  
Schiff’S Base ◽  
Triclinic Space Group ◽  
X Ray ◽  
H Nmr ◽  
Cell Dimensions

Reaction of 8-aminoquinoline with pyridine-2-carboxaldehyde (2), pyridine-3-carboxaldehyde (3), pyridine-4-carboxaldehyde (4), and benzaldehyde (5) yields the corresponding aminals or Schiff's bases according to reaction conditions; analogous results are obtained from the reaction of 1-amino-naphtalene with pyridine-2-carboxaldehyde (6). On the other hand, reaction of 8-aminoquinoline with thiophene-2-carboxaldehyde or pyrrole-2-carboxaldehyde yields neither the aminal nor the Schiff's base. Crystals of 4 (C24H19N5) belong to the triclinic space group [Formula: see text]. Cell dimensions are a = 11.547(3), b = 11.759(2), c = 15.687(5) Å, α = 98.50(2)°, β = 101.61(2)°, γ = 107.28(2)°, V = 1942.6(9) Å3. Final R = 0.077 and Rw = 0.064; 3160 reflections were observed. The ir, 1H nmr of 2–6, the mass spectra of 4 and 5 and the X-ray analysis of 4 are described and discussed. Preparative features, ir, 1H nmr, analyses and crystal structure indicate that the formation of 2–6 are governed mainly by the nucleophilicity at the aldehyde carbon atom and the existence of the hydrogen bonds in the aminal.

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.

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

1988 ◽  
Vol 66 (5) ◽  
pp. 1203-1208 ◽  
Author(s):  
George I. Birnbaum ◽  
Miloš Buděšínský ◽  
Jiří Beránek
Keyword(s):  
Direct Methods ◽  
Acid Synthesis ◽  
Side Chain ◽  
Hydrogen Atoms ◽  
Orthorhombic Space Group ◽  
1H And 13C Nmr ◽  
X Ray ◽  
Anti Conformation ◽  
Cell Dimensions ◽  
Equal Population

Crystals of 5′-chloroarabinosylcytosine, an inhibitor of nucleic acid synthesis, belong to the orthorhombic space group P212121, and the cell dimensions are a = 6.801(1), b = 9.698(2) and c = 16.497(3) Å. X-ray intensity data were measured on a diffractometer and the structure was determined by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.032 for 1251 observed reflections. The conformation about the glycosyl bond is anti, the furanose ring adopts a C3′ endo/C4′ exo pucker and the conformation of the side chain is gauche+, stabilized by an intramolecular [Formula: see text] hydrogen bond. 1H and 13C nmr spectra confirm the anti conformation about the glycosyl bond. In D2O solution there is an approximately equal population of N- and S-type conformers of the furanose ring and a trans > gauche+ > gauche− distribution of the 5′-CH2Cl side chain rotamers.

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