Conformational features of acyclonucleosides: structure of acyclovir, an antiherpes agent

1984 ◽  
Vol 62 (12) ◽  
pp. 2646-2652 ◽  
Author(s):  
George I. Birnbaum ◽  
Miroslaw Cygler ◽  
David Shugar
Keyword(s):  
Direct Methods ◽  
Side Chain ◽  
Asymmetric Unit ◽  
Hydrogen Atoms ◽  
Torsion Angles ◽  
The Third ◽  
Cell Dimensions ◽  
Enzymatic Systems ◽  
Antiviral Activities ◽  
Independent Molecules

Crystals of acyclovir belong to the space group P21/n, and the cell dimensions are a = 25.459(1), b = 11.282 (1), c = 10.768(1) Å, β = 95.16(1)°. Intensity data were measured on a diffractometer and the structure was determined by direct methods. The asymmetric unit was found to contain three independent molecules of acyclovir and two molecules of water. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.053 for 3970 observed reflections. In two of the molecules the side chain is partially folded, while in the third one it is fully extended. The glycosidic torsion angles are in the range 91.4–104.3°. The conformational features are compared with those in other known acyclonucleosides. They are also examined in relation to the behavior of acyclonucleosides and acyclonucleotides in various enzymatic systems, including those related to antiviral activities.

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.

scholarly journals Crystal structure of 3-(3-oxo-2,3,4,4a,5,6-hexahydrobenzo[h]cinnolin-2-yl)propionic acid

2014 ◽  
Vol 70 (10) ◽  
pp. o1088-o1089
Author(s):  
Fiorella Meneghetti ◽  
Daniela Masciocchi ◽  
Arianna Gelain ◽  
Stefania Villa
Keyword(s):  
Chair Conformation ◽  
Membered Ring ◽  
Side Chain ◽  
Boat Conformation ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Compound C ◽  
Centroid Distance ◽  
Independent Molecules ◽  
Twisted Boat

The asymmetric unit of the title compound, C15H16N2O3, contains two independent molecules, which present a different conformation of the carboxylic acid side chain [C—C—C—OH torsion angles = 65.3 (7) and −170.1 (5)°]. In both molecules, the dihydropyridazinone ring adopts a geometry intermediate between a twisted-boat and a half-chair conformation, while the central six-membered ring is almost in a half-boat conformation. In the crystal, molecules are linked by O—H...Ok(k = ketone) hydrogen bonds, generating [01-1] chains. Aromatic π–π stacking contacts between the benzene and the dihydropyridazinone rings [centroid–centroid distance [3.879 (9) Å] are also observed.

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.

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.

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.

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.

scholarly journals 4-Chloro-3-ethylphenol

2014 ◽  
Vol 70 (7) ◽  
pp. o801-o801
Author(s):  
Sean H. Majer ◽  
Joseph M. Tanski
Keyword(s):  
Solid State ◽  
Title Compound ◽  
Side Chain ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Face To Face ◽  
Compound C ◽  
Centroid Distance ◽  
Π Stacking Interaction ◽  
Independent Molecules

The title compound, C8H9ClO, packs with two independent molecules in the asymmetric unit, without significant differences in corresponding bond lengths and angles, with the ethyl group in each oriented nearly perpendicular to the aromatic ring having ring-to-side chain torsion angles of 81.14 (18) and −81.06 (19)°. In the crystal, molecules form an O—H...O hydrogen-bonded chain extending along theb-axis direction, through the phenol groups in which the H atoms are disordered. These chains pack together in the solid state, giving a sheet lying parallel to (001),viaan offset face-to-face π-stacking interaction characterized by a centroid–centroid distance of 3.580 (1) Å, together with a short intermolecular Cl...Cl contact [3.412 (1) Å].

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.

scholarly journals Methyl 1-allyl-4-hydroxy-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylate

2013 ◽  
Vol 69 (11) ◽  
pp. o1698-o1698 ◽  
Author(s):  
Svitlana V. Shishkina ◽  
Igor V. Ukrainets ◽  
Lidiya A. Petrushova
Keyword(s):  
Hydrogen Bond ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Compound C ◽  
Two Component ◽  
Independent Molecules ◽  
Population Ratio ◽  
Intramolecular Hydrogen ◽  
Vinyl Group ◽  
Planar Fragment

There are two independent molecules in the asymmetric unit of the title compound, C13H13NO5S, in both of which the ester substituent is nearly coplanar [C—C—C—O torsion angles = 2.7 (7) and −0.8 (7)°] with the planar fragment of the bicycle due to the formation of a strong O—H...O intramolecular hydrogen bond. The vinyl group at the ring N atom is approximately orthogonal to the heterocyclic mean plane [C—N—C—C torsion angles = 103.1 (6) and 98.2 (5)°]. The refinement was performed on a two-component, non-merohedrally twinned crystal [population ratio = 0.483 (3):0.517 (3).

scholarly journals (S)-2-[(4-Fluorophenyl)formamido]-3-phenylpropanoic acid

IUCrData ◽  
2020 ◽  
Vol 5 (7) ◽  
Author(s):  
Kathleen S. Lee ◽  
Luke Turner ◽  
Cynthia B. Powell ◽  
Eric W. Reinheimer
Keyword(s):  
Hydrogen Bonding ◽  
Title Compound ◽  
Phenyl Ring ◽  
Room Temperature ◽  
Solid Phase ◽  
Independent Molecule ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Compound C ◽  
Independent Molecules

The title compound, C16H14FNO3, was synthesized via solid phase methods; it exhibits monoclinic (P21) symmetry at room temperature. The two independent molecules that comprise the asymmetric unit display distinct torsion angles of 173.2 (2) and 72.6 (2)° along the central sp 3 C—N bond. In the crystal, hydrogen bonding through N—H...O contacts couples the asymmetric unit molecules into pairs that align in layers extending parallel to (100) via additional O—H...O interactions. The phenyl ring of one independent molecule was found to be disordered over two sets of sites in a 0.55 (3):0.45 (3) ratio.

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