Conformation of exocyclic amino groups in purines and pyrimidines: crystal structure and conformation of 1-methyl-N4-hydroxycytosine hydrochloride

1979 ◽  
Vol 57 (4) ◽  
pp. 308-313 ◽  
Author(s):  
George I. Birnbaum ◽  
Tadeusz Kulikowski ◽  
David Shugar
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Amino Groups ◽  
Neutral Form ◽  
Triclinic Space Group ◽  
Hydrochloride Salt ◽  
Cell Dimensions ◽  
Hydroxylamine Mutagenesis ◽  
Intramolecular Hydrogen ◽  
Purines And Pyrimidines

The hydrochloride salt of 1-methyl-N4-hydroxycytosine crystallizes in the triclinic space group [Formula: see text] with cell dimensions: a = 8.232(1), b = 9.293(1), c = 5.416(1) Å (1 Å = 0.1 nm); α = 91.95(1), β = 91.72(2), γ = 71.56(1)° (SE in parentheses). The structure was solved by direct methods and refined to R = 3.7% for 1514 reflections. Despite the absence of an intramolecular hydrogen bond in the solid state, the N4-hydroxy substituent is syn to the ring N(3). This conformation, which probably prevails also in the neutral form, is of relevance to the mechanism of attack of cytosine by hydroxylamine, known to involve predominantly the cytosine cation, as well as to the mechanism of hydroxylamine mutagenesis. Such conformational aspects are also relevant to other phenomena, including translation and restriction.

The structure of bilirubin

1978 ◽  
Vol 202 (1147) ◽  
pp. 249-268 ◽  
Keyword(s):  
Crystal Structure ◽  
Molecular Conformation ◽  
Direct Methods ◽  
Data Sets ◽  
Triclinic Space Group ◽  
Interplanar Angle ◽  
Cell Dimensions ◽  
Independent Molecules ◽  
Packing Arrangement ◽  
Intramolecular Hydrogen

Crystals of bilirubin are triclinic, space group P1̄ with cell dimensions a = 19.439, b = 11.707, c = 15.500 Å, †, α = 97.19, β =100.22, γ = 118.20°, Z = 4. The structure was solved by direct methods incorporating information derived from reflexion quartets and by using a set of diffractometer data containing 1408 reflexions with F obs ≥ 3σ( F obs ). The structure was refined with bond-length constraints to a final R of 0.125 by using a set of microdensitometer-measured photographic data containing 1323 unique observed reflexions. Both data sets were collected from a matured crystal whose diffraction pattern had improved considerably during a period of several weeks. Bilirubin is shown to have the Z configuration at both the C5 and C15 bridges. The two independent molecules of bilirubin in the crystal structure have very similar ‘ridge tile’ conformations: rings (A + B) and rings (C + D) form two good planes with an interplanar angle of approximately 97° and the molecule is stabilized by six intramolecular hydrogen bonds. There is no evidence for any intermolecular hydrogen bonding. Observed bond lengths suggest that bilirubin can be regarded as a 2,2' - dipyrrolylmethane with conjugating substituents at the α positions. When freshly prepared, most crystals of bilirubin have reflexions hkl ( h odd) diffuse: this observation is discussed in terms of the molecular conformation of bilirubin and the particular packing arrangement which these molecules adopt in the crystal structure.

3,3′-N,N′-Bis(amino)-2,2′-bipyridine — An unusually methylation-resistant amine

2011 ◽  
Vol 89 (8) ◽  
pp. 971-977
Author(s):  
Danielle M. Chisholm ◽  
Robert McDonald ◽  
J. Scott McIndoe
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Complex Mixtures ◽  
Amino Groups ◽  
Intramolecular Hydrogen Bonds ◽  
X Ray ◽  
Intramolecular Hydrogen

Methylation of aromatic amino groups is usually straightforward, but the formation of two intramolecular hydrogen bonds in 3,3′-N,N′-bis(amino)-2,2′-bipyridine and (or) the potential for ring methylation prevents the clean tetramethylation of this molecule. Numerous attempts to make 3,3′-N,N′-bis(dimethylamino)-2,2′-bipyridine produced only complex mixtures of variously methylated products, and the only isolated molecule was 3,3′-N,N′-bis(methylamino)-2,2′-bipyridine, for which an X-ray crystal structure was obtained.

Platin in seiner ungewöhnlichen Oxidationsstufe + III: Diplatin(III)-Komplexe der Modellnukleobase 1-Methyluracil / Platinum in its Unusual Oxidation State + III: Diplatinum(III) Complexes with the Model Nucleobase 1-Methyluracil

1983 ◽  
Vol 38 (11) ◽  
pp. 1441-1445 ◽  
Author(s):  
Bernhard Lippert ◽  
Helmut Schöllhorn ◽  
Ulf Thewalt
Keyword(s):  
Crystal Structure ◽  
Nitric Acid ◽  
Ir Spectra ◽  
Oxidation State ◽  
Structural Similarity ◽  
Single Bond ◽  
Triclinic Space Group ◽  
H Nmr ◽  
Axial Ligands ◽  
Cell Dimensions

Oxidation of the head-tail dimer cis-[(NH3)2Pt(1-MeU)]2(NO3)2 (1-MeU = 1-methyl - uracilato anion, C5H5N2O2) with a mixture of nitrous and nitric acid yields three crystalline species, [(NO2)(NH3)2Pt(C5H5N2O2)2Pt(]SrH3)2(NO2)](NO3)2 · 3 H2O (1), [(H2O)(NH3)2Pt(C5H5N2O2)2Pt(]SrH3)2(NO2)](NO3)2 · 5 H2O (2) and [(NO3)(NH3)2Pt(C5H5N2O2)2Pt(]SrH3)2(NO3)](NO3)2 · 4.5 H2O (3). The crystal structure of 2 has been determined. 2 crystallizes in the triclinic space group P1̄ with cell dimensions a= 11.959(4), b= 11.560(3), c= 11.261(2) Å, α = 89.16(2), β= 104.36(2), γ = 99.61(2)° and Z = 2. The structure was refined to R = 0.056, Rw = 0.061 on 4311 reflections. The Pt-Pt distance within the dinuclear cation of 2 is 2.574(1) Å and cor­responds to a Pt-Pt single bond. The axial ligands are N̲O2 (Ptl) and O̲H2 (Pt2), the equatorial ligands two NH3 groups, N 3 and O4 of 1-MeU for both Pt atoms. The oxidation state of Pt in 2 is +III. 1H NMR and IR spectra of 1, 2, and 3 reveal a close structural similarity of the three compounds.

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.

Crystal structure of N,N '-Ethylenebis(1,1,1-Trifluoro-4-iminopentan-2-one)

1984 ◽  
Vol 37 (4) ◽  
pp. 879 ◽  
Author(s):  
R Cea-Olivares ◽  
I Rodriguez ◽  
MJ Rosales ◽  
A Toscano
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
Enamino Ketone ◽  
Space Group ◽  
R Value ◽  
Intramolecular Hydrogen

The crystal structure of N,N'-ethylenebis(1,1,1-trifluoro-4-iminopentan-2-one) (tfaen) was determined: C12H14F6N2O2, M 342.04, monoclinic, space group P21/n, a 6.939(2), b 20.529(5), c 10.662(2) �, V 1507.84 �3 β 96.87(2)�, p(calc.) 1.506 g cm-3 (Z = 4), F(000)680, �(Cu Kα) 13.15 cm-1. The structure was solved by direct methods and refined to a final R value of 0.073 for 1198 unique reflections. Discrete molecules in the crystal are characterized by a conjugated enamino ketone structure with intramolecular hydrogen bridges.

Oxofluoro-oxalato-vanadate des vierwertigen Vanadins: Schwingungsspektrum und Struktur von Na3[VOF(C2O4)2] • 6 H2O.

1976 ◽  
Vol 31 (5) ◽  
pp. 537-540 ◽  
Author(s):  
Helmut Rieskamp ◽  
Rainer Mattes
Keyword(s):  
Crystal Structure ◽  
Oxygen Atom ◽  
Fluorine Atom ◽  
Direct Methods ◽  
Terminal Oxygen Atom ◽  
Triclinic Space Group ◽  
Trans Effect ◽  
Space Group ◽  
X Ray ◽  
In Cis

The Na and NH4 salts of the [VOF(C2O4)2]3--ion have been prepared. The crystal structure of the former has been determined from X-ray diffractometer data. The crystals are triclinic, space group P with Z = 2. The structure was solved by `direct methods' and refined to R 0.050 for 1749 reflections. In the anion, vanadium(IV) is octahedrally coordinated by a terminal oxygen atom, a fluorine atom in cis-position to the former, and two bidentate oxalate ligands. The terminal V—O-bond exhibits a strong ‘trans’ effect.

scholarly journals The reaction of 3,5-diphenyl-1,2-dithiolium-4-olate with aniline: the crystal structure of 1-phenylimino-2-phenylamino-3-phenylindene

1987 ◽  
Vol 65 (12) ◽  
pp. 2830-2833 ◽  
Author(s):  
David M. McKinnon ◽  
Peter D. Clark ◽  
Robert O. Martin ◽  
Louis T. J. Delbaere ◽  
J. Wilson Quail
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Single Crystal ◽  
Least Squares ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

3,5-Diphenyl-1,2-dithiolium-4-olate (1) reacts with aniline to form 1-phenylimino-2-phenylamino-3-phenylindene (3a). Under suitable conditions, 6-phenylbenzo[b]indeno[1,2-e]-1,2-thiazine is also formed. These structures are confirmed by alternative syntheses. The molecular structure of 3a has been determined by single crystal X-ray diffraction. Compound 3a crystallizes in the monoclinic space group C2/c with unit cell dimensions a = 20.777(3) Å, b = 6.130(3) Å, c = 31.327(3) Å, 3 = 99.59(1)°, and Z = 8. The structure was solved by direct methods and refined by least squares to a final R = 0.055. The molecular structure of 3a shows the three phenyl containing substituents to have the planes of their ring systems tilted between 40° and 60° from the plane of the indene system due to steric repulsions.

The Crystal and Molecular Structure of Butorphanol Hydrogen Tartrate

1994 ◽  
Vol 59 (6) ◽  
pp. 1361-1367 ◽  
Author(s):  
Alexandr Jegorov ◽  
Roman Sobotík ◽  
Svetlana Pakhomova ◽  
Jan Ondráček ◽  
Jiří Novotný ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystal And Molecular Structure ◽  
Direct Methods ◽  
Chair Conformation ◽  
Triclinic Space Group ◽  
Space Group

The structure of butorphanol hydrogen tartrate {(9R,13S,14S)-(-)-17-(cyclobutylmethyl)morphinan-3,14-diol (2S,3S)-(-)-hydrogen tartrate} (C21H29NO2 .C4H6O6) was solved by direct methods and refined anisotropically to the R value of 0.029 for 2 069 observed reflections. The title morphine analogue crystallizes in the triclinic space group P1 with lattice parameters a = 7.620(1), b = 9.140(1), c = 9.591(1) Å, α = 105.48(1), β = 112.91(1), γ = 84.29(1)°, Z = 1. The butorphanol B ring possesses the 3E envelope conformation with small 3H2 distortion, C and D rings have a regular chair conformation. The intramolecular N17-H17...O2 hydrogen bond is observed in crystal structure of the title compound. The butorphanol and hydrogen tartrate molecules are joined together by means of O2-H(O2)...O7, O1-H(O1)...O7' and O3-H(O3)...O8" hydrogen bonds to form networks.

Cluster Chemistry. XLVII. X-Ray Crystal Structure of OsPt2(μ-CO)3(CO)2(PPh3)3

1986 ◽  
Vol 39 (12) ◽  
pp. 2145 ◽  
Author(s):  
MI Bruce ◽  
MR Snow ◽  
ERT Tiekink
Keyword(s):  
Crystal Structure ◽  
X Ray Diffraction ◽  
Cluster Chemistry ◽  
Triclinic Space Group ◽  
X Ray ◽  
Metal Atoms ◽  
Metal Metal ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Triphenylphosphine Ligand

The crystal structure of OsPt2(μ-CO)3(CO)2(PPh3)3 has been determined by single-crystal X-ray diffraction techniques. Crystals are triclinic, space group Pī with unit cell dimensions a 13.593(4), b 15.839(4), c 12.633(8) Ǻ, α 102.97(3), β 108.18(2), γ 84.86(3)° with Z2. The structure was refined by a full-matrix least-squares procedure on 5896 reflections [I ≥ 2.5σ(I)] to final R 0.028 and Rw 0.034. A triphenylphosphine ligand binds each of the metal atoms disposed at the corners of a triangle. Each metal-metal bond is spanned by a bridging carbonyl group. The coordination about the osmium atom is completed by two terminal carbonyl groups.

Structure of [μ-S2{Ru(PCy3)('S4')}2] · 2.5 THF ·0.5 Et2O Containing Homochiral Metal Complex Fragments ['S4'2- = 1,2-Bis(mercaptophenylthio)-ethane (2-)]

1999 ◽  
Vol 54 (9) ◽  
pp. 1122-1124 ◽  
Author(s):  
Dieter Sellmann ◽  
Frank W. Heinemann ◽  
Torsten Gottschalk-Gaudig
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Double Bond ◽  
Metal Complex ◽  
Title Compound ◽  
Direct Methods ◽  
Uv Spectrum ◽  
Triclinic Space Group ◽  
X Ray ◽  
Bond Character

A crystal of the title compound [μ-S2{Ru(PCy3)(′S4′)}2] · 2.5 THF · 0.5 Et2O (1 · 2.5 THF · 0.5 Et2O), grown from a THF/Et2O solution, was investigated by single-crystal X-ray analysis. 1 · 2.5 THF · 0.5 Et2O crystallizes in the triclinic space group P1̄ with a = 14.209(4), b = 15.390(4), c = 19.526(6) Å, α = 111.29(2), ß = 100.43(2), γ = 95.65(2)°, and Z = 2. The crystal structure was solved by direct methods (wR2= 0.1520 for 12565 reflections; R1 = 0.0507 for 9205 observed reflections). The molecular structure of 1 · 2.5 THF · 0.5 Et2O is characterized by a trans η1 -η1-S2 bridge connecting two homochiral [Ru(PCy3)(′S4′)] fragments. The S-S bond length of 1.982(2) Å and a mean Ru-S(bridge) distance of 2.234(2) Å indicate partial double bond character of these bonds. The RuSSRu unit in 1 · 2.5 THF · 0.5 Et2O is a chromophore as indicated by its UV spectrum and can be described by a delocalized 4c-6e 7π system.

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