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.

Synthesis, Spectroscopic Studies, Crystal Structure and Conformation Analysis of N-(2-Fluoro-3-methoxy)-salicylaldimine

2002 ◽  
Vol 57 (6) ◽  
pp. 685-690 ◽  
Author(s):  
H. Ünver ◽  
E. Kendi ◽  
K. Güven ◽  
T. Nuri Durlu
Keyword(s):  
Crystal Structure ◽  
Minimum Energy ◽  
Spectroscopic Studies ◽  
Hydrogen Atoms ◽  
Orthorhombic Space Group ◽  
Stable Conformation ◽  
H Nmr ◽  
Mechanical Methods ◽  
Intramolecular Hydrogen ◽  
Semi Empirical

Abstract The new Schiff base ligand N-(2-fluoro-3-methoxy)-salicylaldimine (C14H12NO2F) (1) has been synthesised and studied by using, IR, 1H NMR, 13C NMR, UV-visible, GC-MS techniques, X-ray structure analysis and AM1 semi-empirical quantum mechanical methods. Compound 1 crystallises in the orthorhombic space group P212121 with a =12.5461(1), b =18.0495(1), c =5.2615(1) Å . An intramolecular hydrogen bond connects O1 and N1 [2.575(2)Å], the hydrogen atom being bonded essentially to the oxygen atom. Minimum energy conformations were calculated as a function of two torsion angles θ1 (C6-C7-C8-N1) and θ2 (C7-C8-N1-C9), varied every 10 degrees. The optimized geometry of the crystal structure corresponding to the non-planar conformation is the most stable conformation in all calculations. The results strongly indicate that the minimum energy conformation is primarily determined by hydrogen-hydrogen repulsions between the ortho-hydrogen atoms on the aldehyde rings. Complementary IR, 1H NMR and UV measurements in solution and in the solid state were carried out.

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.

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.

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.

The reaction of chloro(triphenylphosphine)gold(I) with 1-methylthymine

1987 ◽  
Vol 65 (7) ◽  
pp. 1568-1575 ◽  
Author(s):  
R. Faggiani ◽  
H. E. Howard-Lock ◽  
C. J. L. Lock ◽  
M. A. Turner
Keyword(s):  
Aqueous Methanol ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Cell Dimensions ◽  
Cell Data ◽  
Unit Cell Data ◽  
Related Compounds ◽  
C Nmr

1-Methylthyminato-N3-triphenylphosphinegold(I) was prepared by reacting chloro(triphenylphosphine)gold(I) with 1-methylthymine in aqueous methanol at pH 11. The product was examined by X-ray crystallography and was found to have the orthorhombic space group C2221 (no. 20) with cell dimensions a = 12.760(7) Å, b = 11.530(2) Å, c = 31.893(5) Å, and eight formula units in the unit cell. Data were collected with use of MoKα radiation and a Syntex P21, diffractometer. The crystal structure was determined by standard methods and refined to R = 0.112 and Rw = 0.076 on the basis of 4760 unique reflections. Bond lengths and bond angles are normal. Packing in the crystal lattice is dominated by the triphenylphosphine rings which arrange roughly as blades of a propellor and are the source of the crystal's chirality. The title and related compounds were also examined by 1H nmr, 13C nmr, and vibrational spectroscopy.

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

1987 ◽  
Vol 65 (2) ◽  
pp. 326-331 ◽  
Author(s):  
Leo H. Koole ◽  
Henk M. Buck ◽  
Jan A. Kanters ◽  
Arie Schouten
Keyword(s):  
Crystal Structure ◽  
Molecular Conformation ◽  
Proton Nuclear Magnetic Resonance ◽  
Solution Conformation ◽  
Orthorhombic Space Group ◽  
One Dimensional ◽  
X Ray ◽  
H Nmr ◽  
Conformational Preferences ◽  
Cell Dimensions

2′-Deoxy-3′,5′-di-O-acetyl adenosine crystallizes in the orthorhombic space group P212121, and the cell dimensions are a = 7.768(1) Å, b = 12.890(1) Å, c = 15.495(1) Å; Z = 4 molecules per cell. Least-squares refinement converged at R = 0.054 for 1752 observed reflections. The adenine bases are linked via N6—H … N1 and N6—H … N7 hydrogen bonds, in such a way that infinite one-dimensional chains are formed. Comments are made on the fact that this structure is entirely different from the parallel dimer that was found for 3′,5′-di-O-acetyl thymidine. Furthermore, the conformational preferences of the title compound in aqueous solution have been determined with 300- and 500-MHz 1H nmr. It is found that the X-ray structure and the solution conformation are essentially similar, except for the C4′—C5′ conformation, that is γ− in the solid state, and predominantly γ+ in solution.

Crystal Structure and Conformation of N-(5-Chlorosalicylidene)- 2-hydroxy-5-chloroaniline

2002 ◽  
Vol 57 (6) ◽  
pp. 651-656 ◽  
Author(s):  
Yalçün Elerman ◽  
Mehmet Kabak ◽  
Ayhan Elmali
Keyword(s):  
Crystal Structure ◽  
Minimum Energy ◽  
Am1 Calculations ◽  
Hydrogen Atoms ◽  
Orthorhombic Space Group ◽  
Stable Conformation ◽  
Planar Conformation ◽  
Planar Molecules ◽  
Intramolecular Hydrogen ◽  
Semi Empirical

Abstract N-(5-Chlorosalicylidene)-2-hydroxy-5-chloroaniline was synthesized and its crystal structure determined. It crystallizes in the orthorhombic space group Pna21 with a = 14.668(4), b = 6.084(3), c = 27.980(4) Å , R = 0.051 for 4788 independent reflections). There are two independent nearly planar molecules in the asymmetric unit. The intramolecular hydrogen bonds occur between the pairs of atoms N1 and O1 [2.553(6) Å], N1 and O2 [2.585(5) Å], N2 and O3 [2.567(6) Å], N2 and O4 [2.620(5) Å], the hydrogen atoms essentially being bonded to the nitrogen atoms. The neighboring molecules are linked via an intermolecular O-H···O hydrogen bond [2.557(5) Å ]. Conformations of the title compound were investigated by semi-empirical quantum mechanical AM1 calculations. The optimized geometry of the molecular structure corresponding to the nearly planar conformation is the most stable conformation in the calculations. The results strongly indicate that the minimum energy conformation is primarily determined by non-bonded steric interactions.

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.

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