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.

A novel tubular hydrogen-bond pattern in a new diazaphosphole oxide: a combination of X-ray crystallography and theoretical study of hydrogen bonds

2017 ◽  
Vol 73 (7) ◽  
pp. 508-516 ◽  
Author(s):  
Fahimeh Sabbaghi ◽  
Mehrdad Pourayoubi ◽  
Abolghasem Farhadipour ◽  
Nazila Ghorbanian ◽  
Pavel V. Andreev
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Coupling Constant ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Hydrogen Bond Pattern ◽  
Orbital Analysis ◽  
Tubular Array ◽  
Hydrogen Bonded

In the structure of 2-(4-chloroanilino)-1,3,2λ4-diazaphosphol-2-one, C12H11ClN3OP, each molecule is connected with four neighbouring molecules through (N—H)2...O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R 3 3(12) and R 4 3(14) hydrogen-bond ring motifs, combined with a C(4) chain motif. The hole constructed in the tubular architecture includes a 12-atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co-operating in classical hydrogen bonding, takes part in an N—H...π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen-bond pattern. The energies of the N—H...O and N—H...π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen-bonded cluster of molecules as the input file for the chemical calculations. In the 1H NMR experiment, the nitrogen-bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the 2 J H–P coupling constant.

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 structure determination of 1,2-anhydro-3,4:5,6-di-O-isopropylidene-1-C-nitro-D-mannitol

1988 ◽  
Vol 66 (7) ◽  
pp. 1600-1604 ◽  
Author(s):  
Walter A. Szarek ◽  
George W. Hay ◽  
Ramesh K. Sood ◽  
Konia Trouton ◽  
Suzanne Fortier
Keyword(s):  
Crystal Structure ◽  
Hydrogen Peroxide ◽  
Direct Methods ◽  
Major Product ◽  
Calculated Density ◽  
Aqueous Sodium ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cell Dimensions

The structure of the major product of the reaction of 1,2-dideoxy-3,4:5,6-di-O-isopropylidene-1-C-nitro-D-arabino-hex-1-enitol with 30% hydrogen peroxide and aqueous sodium hydrogencarbonate has been confirmed by X-ray crystallography to be that of 1,2-anhydro-3,4:5,6-di-O-isopropylidene-1-C-nitro-D-mannitol (2). The crystal structure of 2, C12H19NO7, is orthorhombic, P212121, with cell dimensions a = 10.269(3), b = 15.115(7), c = 9.295(8) Å, and Z = 4. The calculated density is Dx = 1.336 gcm−3. The structure was solved by direct methods and refined to a residual R = 0.052. The molecule has a 2G− conformation having bond lengths and angles in agreement with those observed in related structures, except for the C(1)—C(2), C(2)—C(3), and O(2N)—N bond distances which were found to be unusually small.

Low-spin organoiron(III) N-confused pyriporphyrin

2007 ◽  
Vol 11 (03) ◽  
pp. 172-180 ◽  
Author(s):  
Radomir Myśliborski ◽  
Krystyna Rachlewicz ◽  
Lechosław Latos-Grażyński
Keyword(s):  
Hydrogen Bond ◽  
Structural Data ◽  
Cationic Complex ◽  
Conformational Rearrangement ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Pyridine Ligands ◽  
Rearrangement Process ◽  
Equatorial Ligand

Oxidation of ( PyP H) Fe II Br , an iron(II) complex of 6,11,16,21-tetraaryl-3-aza-m-benziporphyrin ( N -confused pyriporphyrin, ( PyP H) H ) has been followed, in the presence of pyridine, by 1 H and 2 H NMR spectroscopy. One-electron oxidation with dioxygen, accompanied by deprotonation of a C (22) H fragment and formation of a Fe - C (22) bond, produced a low-spin, six-coordinate iron(III) complex [( PyP ) Fe III( py )2]+ as confirmed by combination of 1 H NMR, EPR and structural data. The characteristic patterns of 1 H NMR pyrrole and meso-aryl resonances resemble features assigned to the less common, low-spin ground electronic state (( d xz d yz )4( d xy )1) of iron(III) regular porphyrins. A conformational rearrangement process has been detected which involves two structures differentiated by macrocyclic ruffling. The structure of { H [( PyP ) Fe III( py )2]2}( Fe III Br 4)3· CH 2 Cl 2 has been determined by X-ray crystallography. The cationic complex involves a six-coordinate iron atom bound to the N -confused pyriporphyrin through its three nitrogens ( Fe - N (23) = 1.924(7), Fe - N (24) = 1.979(7), Fe - N (25) = 1.9343(7) Å) and the pirydyl trigonal C (22) atom ( Fe (1)- C (22) = 1.972(10) Å). The porphyrin is strongly ruffled, defining two deep grooves along C meso - C meso axes at right angles to each other. Two axial pyridine ligands are located in the prearranged equatorial ligand grooves. The iron lies in the N 3 C plane of the macrocycle defined by coordinating nitrogen and carbon atoms. In the solid, pairs of molecules are positioned along the line defined by Fe (1)- C (22) and Fe (2)- C (91) bonds. The structure demonstrates the head-to-head arrangement of two [( PyP ) Fe III( py )2]+ subunits revealing the adjacency of the two perimeter nitrogen atoms (the N (3)⋯ N (72) distance = 2.587(10) Å) linked by the N ⋯ H ⋯ N hydrogen bond.

Positional isomeric effect on the crystallization of chlorine-substitutedN-phenyl-2-phthalimidoethanesulfonamide derivatives

2015 ◽  
Vol 71 (9) ◽  
pp. 839-843 ◽  
Author(s):  
Serap Köktaş Koca ◽  
Resul Sevinçek ◽  
Özlem Akgül ◽  
Muhittin Aygün
Keyword(s):  
Hydrogen Bond ◽  
Biological Activities ◽  
Intermolecular Hydrogen Bond ◽  
Stacking Interactions ◽  
X Ray ◽  
Space Groups ◽  
X Ray Crystallography ◽  
Hydrogen Bond Interactions ◽  
Benzene Rings ◽  
Isomeric Effect

Theortho-,para- andmeta-chloro-substitutedN-chlorophenyl-2-phthalimidoethanesulfonamide derivatives, C16H13ClN2O4S, have been structurally characterized by single-crystal X-ray crystallography.N-(2-Chlorophenyl)-2-phthalimidoethanesulfonamide, (I), has orthorhombic (P212121) symmetry,N-(4-chlorophenyl)-2-phthalimidoethanesulfonamide, (II), has triclinic (P\overline{1}) symmetry andN-(3-chlorophenyl)-2-phthalimidoethanesulfonamide, (III), has monoclinic (P21/c) symmetry. The molecules of (I)–(III) are regioisomers which have crystallized in different space groups as a result of the differing intra- and intermolecular hydrogen-bond interactions which are present in each structure. Compounds (I) and (II) are stabilized by N—H...O and C—H...O hydrogen bonds, while (III) is stabilized by N—H...O, C—H...O and C—H...Cl hydrogen-bond interactions. The structure of (II) also displays π–π stacking interactions between the isoindole and benzene rings. All three structures are of interest with respect to their biological activities and have been studied as part of a programme to develop anticonvulsant drugs for the treatment of epilepsy.

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.

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.

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.

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