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 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.

Thyroid Hormone Stereochemistry. II. Molecular Structure of Thyronine HCl Ethyl Ester Monohydrate

1974 ◽  
Vol 52 (17) ◽  
pp. 3042-3047 ◽  
Author(s):  
Arthur Camerman ◽  
Norman Camerman
Keyword(s):  
Ethyl Ester ◽  
Three Dimensional ◽  
Chloride Ion ◽  
Dimensional Structure ◽  
Side Chain ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Ether Linkage ◽  
Cell Dimensions ◽  
Phenyl Rings

The three-dimensional structure of L-thyronine, the non-iodinated physiologically inactive analog of thyroxine, has been determined by single crystal X-ray diffraction and compared to the active thyroid hormones. The compound crystallized as the monohydrate of thyronine hydrochloride ethyl ester in the monoclinic space group P21 with cell dimensions a = 10.502, b = 5.165, c = 17.940 Å, β = 109.74°. The structure was solved by Patterson methods to find the chloride ion and iterative Fourier maps to locate the rest of the atoms. Refinement was by anisotropic full-matrix least squares to convergence at R = 0.048.The two phenyl rings adopt a twisted orientation with respect to each other with angles of −37° and −67° between the plane of the inter-ring ether linkage and the planes of the α- and β-rings, respectively. This orientation differs considerably from that found in the iodinated thyronines. The conformation of the alanine side chain is remarkably similar to that of the alanine in the iodinated thyronines.

The crystal and molecular structure of thiamine iodide hydroiodide

1976 ◽  
Vol 54 (19) ◽  
pp. 3001-3006 ◽  
Author(s):  
William Edward Lee ◽  
Mary Frances Richardson
Keyword(s):  
Heavy Atom ◽  
Pyrimidine Ring ◽  
Side Chain ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Iodide Ions ◽  
Cell Parameters ◽  
Weak Hydrogen Bonds ◽  
Ring Nitrogen ◽  
Heavy Atom Method

The X-ray crystal structure of thiamine iodide hydroiodide, C12H18N4OSI2, has been determined. The unit cell parameters are: a = 13.835(7), b = 7.442(4), c = 20.243(9) Å, β = 120.52(7)°, monoclinic space group P21/c, Z = 4. A total of 1445 reflections having F2 > 2σ(F2), 2θ < 40° were collected on a Picker 4-circle diffractometer with MoKα radiation by the 2θ scan technique. The structure was solved by the heavy-atom method. The iodide and sulphur atoms were refined anisotropically; only positional parameters were refined for the hydrogen atoms. Successive full-matrix least-squares refinements yielded an unweighted R-factor of 0.054. The pyrimidine ring is protonated on the ring nitrogen opposite the amino group. The relative disposition of the pyrimidine and thiazolium rings is similar to that observed in most other thiamine structures. The β-hydroxyethyl side chain of the thiazolium ring is folded in such a way that there is a short S … O contact, 2.97 Å in length. The iodide ions are involved in a number of weak hydrogen bonds.

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.

Determination of the structure of p-methylbenzamidinium formate monohydrate

1988 ◽  
Vol 53 (12) ◽  
pp. 3131-3137
Author(s):  
Bohumil Kratochvíl ◽  
Jan Ondráček ◽  
Jindřich Hašek ◽  
László Csordás
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Intermolecular Hydrogen Bonds ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The molecular and crystal structure of p-methylbenzamidinium formate monohydrate, C9H14N2O3, was solved by direct methods. The positions of all the atoms were localized and the structure was refined anisotropically. The final value of the R factor equalled 0·043 for 1 150 observed reflections (I > 1·96σ(I)). The substance crystallizes in the P21/c monoclinic space group with lattice parameters a = 1 038·9(4), b = 1 146·1(5), c = 912·4(3) pm, β = 94·77(3)0, Z = 4. The molecule contains an amidinium-carboxylate bond, formed by two intramolecular hydrogen bridges of the N-H···O type. Intermolecular hydrogen bonds are formed by the side hydrogen atoms of the amidine and the hydrogen atoms of the water molecule and are of the N-H···O and O-H···O types; they form a three-dimensional network in the crystal structure. In this, the structure of p-methylbenzamidinium formate monohydrate differs from the related structures of benzamidinium pyruvate and benzamidinium bromoacetate, characterized by infinite intermolecular chains formed through hydrogen bonding.

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 3′-azido-3′-deoxythymidine (AZT), an inhibitor of the HIV (AIDS) virus

1987 ◽  
Vol 65 (9) ◽  
pp. 2135-2139 ◽  
Author(s):  
George I. Birnbaum ◽  
Jerzy Giziewicz ◽  
Eric J. Gabe ◽  
Tai-Shun Lin ◽  
William H. Prusoff
Keyword(s):  
Active Form ◽  
Three Dimensional ◽  
Direct Methods ◽  
High Energy ◽  
Biologically Active ◽  
Dimensional Structure ◽  
Human Immunodeficiency Virus Replication ◽  
Monoclinic Space Group ◽  
Sugar Ring ◽  
Immunodeficiency Syndrome

3′-Azido-3′-deoxythymidine (AZT), an inhibitor of HIV (human immunodeficiency virus) replication, was recently found to improve the condition of patients suffering from AIDS (acquired immunodeficiency syndrome) or ARC (AIDS-related complex). An X-ray analysis of AZT was undertaken in order to determine the three-dimensional structure of this thymidine analogue. The crystals belong to the monoclinic space group P21 and the cell dimensions are a = 5.6282(4), b = 12.0130(7), c = 17.5072(10) Å, β = 95.946(5)°. The structure was determined by direct methods and refined to R = 0.028 for 2029 observed reflections. Two crystallographically independent molecules were found in the asymmetric unit. One of them, molecule A, adopts a conformation which is fairly common in nucleosides, viz. a C2′ endo/C3′ exo pucker of the furanose ring and a glycosidic torsion angle χCN = 53.4°. However, the conformation of molecule B is highly unusual. The sugar ring pucker is C3′ exo/C4′ endo and χCN = 2.3°. This high-energy conformation may represent the biologically active form of AZT. Its determination may therefore assist in the design of other inhibitors of HIV.

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.

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.

Thyroid Hormone Stereochemistry. III. Molecular Structure of Triiodothyropropionic Acid Ethyl Ester

1974 ◽  
Vol 52 (17) ◽  
pp. 3048-3053 ◽  
Author(s):  
Norman Camerman ◽  
Arthur Camerman
Keyword(s):  
Ethyl Ester ◽  
Iodine Atom ◽  
Molecular Conformation ◽  
Three Dimensional ◽  
Acid Ethyl Ester ◽  
Dimensional Structure ◽  
Monoclinic Space Group ◽  
Ether Linkage ◽  
Cell Dimensions ◽  
Phenyl Rings

The three-dimensional structure of triiodothyropropionic acid ethyl ester has been determined as part of an investigation of the stereochemistry of the thyroid hormones. The compound crystallizes in the monoclinic space group P21/c, with cell dimensions a = 14.60, b = 8.843, c = 16.70 Å, β = 111°27′; Z = four molecules per cell. The structure was determined by direct centrosymmetric phasing procedures to locate the iodine atoms and phasing on the iodines to find the light atoms. Refinement was by anisotropic full-matrix least squares to a final discrepancy value R = 0.038.The two phenyl rings in the molecule are skewed with respect to each other and are not far from being mutually perpendicular, with angles of 88 and 10° between the plane of the inter-ring ether linkage and the planes of the diiodo-ring and the monoiodo-ring, respectively. The conformation is such that the 3′-iodine atom is proximal to the diiodo-ring, similar to the molecular conformation found in the crystal structure of triiodo-L-thyronine hydrochloride.

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