The crystal and molecular structure of 5-(propyn-1-yl)-1-(β-D-arabinofuranosyl)uracil. A very short C≡C triple bond

1984 ◽  
Vol 62 (1) ◽  
pp. 147-152 ◽  
Author(s):  
Mlroslaw Cygler ◽  
Wayne F. Anderson ◽  
Jerzy Giziewicz ◽  
Morris J. Robins
Keyword(s):  
Triple Bond ◽  
Crystal And Molecular Structure ◽  
Direct Methods ◽  
Pyrimidine Ring ◽  
Side Chain ◽  
X Ray Diffraction ◽  
X Ray ◽  
Anti Conformation ◽  
Sugar Ring ◽  
Glycosidic Torsion Angle

The crystal structure of 5-(propyn-1-yl)-1-(β-D-arabinofuranosyl)uracil, an analog of the active antiherpes nucleoside 1-(β-D-arabinofuranosyl)thymine, was determined by X-ray diffraction. The compound crystallizes in the space group P212121 with a = 4.925(1), b = 14.326(2), c = 17.454 Å. Reflections were measured on a diffractometer and the structure was solved by direct methods. Least-squares refinement converged at R = 0.032 for 1159 observed reflections. The sugar ring exhibits an 3E or a C(3′)endo conformation with a pseudorotation angle P = 28.3° and puckering amplitude τm = 31.7°. The orientation of the —CH2OH side chain is g+. The base is in an anti conformation with respect to the sugar ring, with a glycosidic torsion angle χ = 33.7°. Changes in the C(5)—C(6) and C(6)—N(1) bond lengths suggest some interaction of the propynyl group with the pyrimidine ring. The C≡C bond length of 1.121 Å is very short. Its shortening could result from intermolecular interactions with the neighboring pyrimidine ring and nearby oxygen atoms.

The crystal and molecular structure of 1,4-diphenyl-2,2′,3,3′,5,5′,6,6′-octamethylcyclo-1,4-diphospha-2,3,5,6-tetrasilahexane, a phosphorus–silicon heterocycle

1979 ◽  
Vol 57 (2) ◽  
pp. 174-179 ◽  
Author(s):  
A. Wallace Cordes ◽  
Paul F. Schubert ◽  
Richard T. Oakley
Keyword(s):  
Molecular Structure ◽  
Crystal And Molecular Structure ◽  
Direct Methods ◽  
Chair Conformation ◽  
Monoclinic Space Group ◽  
Single Bond ◽  
X Ray Diffraction ◽  
Full Matrix ◽  
X Ray ◽  
Bond Lengths

The crystal structure of 1,4-diphenyl-2,2′,3,3′,5,5′,6,6′-octamethylcyclo-1,4-diphospha-2,3,5,6-tetrasilahexane, (PhPSi2Me4)2, has been determined by single crystal X-ray diffraction. The crystals are monoclinic, space group P21/c, with a = 9.866(1), b = 11.921(1), and c = 11.324(2) Å, β = 104.31(1)°, Z = 2, and ρcalcd = 1.15 g/cm3. The structure was solved by direct methods and was refined by full-matrix least-squares procedures to a final R of 0.060 and Rw of 0.078, for 1173 reflections with intensities greater than 3σ. The (PhPSi2Me4)2 molecule lies on a crystallographic centre of symmetry, and the six-membered P2Si4 ring has a chair conformation with equatorial phenyl groups. The endocyclic angles at P (104.4(1)°) and Si (104.9(2)°) are intermediate between those found in cyclic hexaphosphine and hexasilane molecules, and the Si—Si and P—Si distances of 2.345(3) and 2.252(4) Å, respectively, correspond to single bond lengths, with no appreciable evidence for secondary pπ → dπ bonding between phosphorus and silicon. The Si—C (1.867(8) Å) and P—C (1.828(7) Å) bond lengths are also normal. The variations in the Si—P—C (101.6(2)°, 108.6(2)°), P—Si—C (range 106.2(3)–120.0(3)°), and Si—Si—C (range 105.8(3)–113.7(3)°) angles indicate that the positions of the exocyclic methyl and phenyl groups are influenced by both intra- and intermolecular steric forces.

The Two-step Synthesis and Crystal and Molecular Structure of Tetracyclo[6.4.0.02,11.04,9]dodec-6-ene-3,10-dione

1975 ◽  
Vol 53 (14) ◽  
pp. 2068-2075 ◽  
Author(s):  
Yuen-Mui Ngan ◽  
Steven J. Rettig ◽  
John R. Scheffer ◽  
James Trotter
Keyword(s):  
Crystal And Molecular Structure ◽  
Direct Methods ◽  
Membered Ring ◽  
Diels Alder ◽  
High Yield ◽  
Side Chain ◽  
X Ray ◽  
Long Wavelength ◽  
Vinyl Group ◽  
Alder Adduct

The photochemistry of the trans-1,3,5-hexatriene-p-benzoquinone Diels–Alder adduct has been investigated. Irradiation of this material in its long wavelength n → π* absorption band leads to a single photoproduct in high yield. A single crystal X-ray structure determination shows this product to be tetracyclo[6.4.0.02,11.04,9]dodec-6-ene-3,10-dione, the result of a novel regiospecific intramolecular 2 + 2 photoaddition between the side chain vinyl group and the enedione double bond. Crystals of tetracyclo[6.4.0.02,11.04,9]dodec-6-ene-3,10-dione are monoclinic, a = 7.5290(7), b = 19.072(1), c = 6.7237(4) Å, β = 107.918(6) °, Z = 4, space group P21/n. The structure was solved by direct methods and was refined by full-matrix least-squares procedures to a final R of 0.041 for 1603 reflections with I ≥ 3σ(I). The structure consists of well-separated molecular units. Bond distances are: C=O, 1.216 and 1.219(2), C=C, 1.318(2), mean C(sp3)—C(sp2), 1.508, mean C(sp3)—C(sp3), 1.560 in the four-membered ring and 1.544 elsewhere, mean C(sp3)—H, 0.99, and mean C(sp2)—H, 0.95 Å. Bond distances between nonhy drogen atoms have been corrected for thermal motion. A possible rationalization for the observed photoprocess is discussed in terms of conformational and radical stability effects.

The preparation and the crystal and molecular structure of S3N2NH2+BF4−; a molecular orbital study of the protonation of the trisulphur trinitride anion

1984 ◽  
Vol 62 (9) ◽  
pp. 1822-1827 ◽  
Author(s):  
Clifford G. Marcellus ◽  
Richard T. Oakley ◽  
A. Wallace Cordes ◽  
William T. Pennington
Keyword(s):  
Molecular Structure ◽  
Molecular Orbital ◽  
Crystal And Molecular Structure ◽  
Direct Methods ◽  
Membered Ring ◽  
Molecular Orbital Calculations ◽  
X Ray Diffraction ◽  
Triclinic Space Group ◽  
X Ray ◽  
Molecular Orbital Study

Protonation of the trisulphur trinitride ion, S3N3−, with tetrafluoroboric acid yields the ring-contracted S-amino thiodithiazyl salt, S3N2NH2+BF4−. The crystal and molecular structure of this salt has been determined by X-ray diffraction. The crystals are triclinic, space group P1, with a = 5.445(2), b = 7.346(3), c = 9.473(5) Å, α = 85.89(4), β = 83.92(3), γ = 82.13(3)°, V = 372.6(4) Å3, Dc = 2.02 g cm−3, and Z = 2. The structure was solved by direct methods and refined by full-matrix least-squares procedures to give a final R = 0.060. The structure of the five-membered ring with a single exocyclic NH2 group bonded to sulphur is discussed in relation to other S3N2NR derivatives. The reasons for the instability of six-membered rings of the type S3N3R are discussed in the light of MNDO molecular orbital calculations on an S3N3H model.

Structure and conformation of 5-methoxymethyl-2′-deoxycytidine

1990 ◽  
Vol 68 (6) ◽  
pp. 836-841 ◽  
Author(s):  
Zongchao Jia ◽  
Guy Tourigny ◽  
Louis T. J. Delbaere ◽  
Allan L. Stuart ◽  
Sagar V. Gupta
Keyword(s):  
Three Dimensional ◽  
Antiviral Agent ◽  
Crystallographic Analysis ◽  
Dimensional Structure ◽  
Side Chain ◽  
X Ray ◽  
Envelope Conformation ◽  
Anti Conformation ◽  
Sugar Ring ◽  
Antiherpes Activity

The three-dimensional structure of the antiviral agent 5-methoxymethyl-2′-deoxycytidine (MMdCyd) was deduced by X-ray crystallographic analysis. MMdCyd crystallized in space group P21 with a = 7.9255(6) Å; b = 16.1505(15) Å, c = 10.1861(5) Å, β = 103.801(5)°, and Z = 4 (2 molecules per asymmetric unit); R = 0.044 (Rw = 0.046) for 2560 observed reflections with net I > 3σ(I). The furanose ring adopts the C(3′)-exo envelope conformation (3E) in molecule A and the C(2′)-endo envelope conformation (2E) in molecule B. In the sugar ring of both crystallographically independent molecules A and B, the side chain at C(5′) has the g+ conformation. This appears to be a preferred geometry required for antiherpes activity in 2′-deoxyribonucleosides. The glycosyl linkage is anti with χ = 213.7° for the A molecule and 222.2° for the B molecule. With respect to this anti conformation, the methoxy group at C(5) in molecules A and B exhibits different conformations; it is on the same side of the pyrimidine plane as the deoxyribofuranose ring oxygen (O4′) in molecule B and on the opposite side in molecule A. Keywords: antiherpes agent, conformation, 5-methoxymethyl-2′-deoxycytidine, crystal structure.

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.

Crystal structure of (±)-2-[4-(4-chlorophenoxymethyl)phenoxy]propionic acid

1982 ◽  
Vol 35 (10) ◽  
pp. 2151 ◽  
Author(s):  
G Smith ◽  
CHL Kennard ◽  
WL Duax ◽  
DC Swenson
Keyword(s):  
Crystal Structure ◽  
Propionic Acid ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Side Chain ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrogen Bonded

The crystal structure of (�)-2-[4-(4-chlorophenoxymethyl)phenoxy]propionic acid has been determined by direct methods using three-dimensional X-ray diffraction data. The crystals are triclinic, P1, Z 2, a 9.345(2), b 12,602(2), c 6.741(1) �, α 101.37(1), β 97.42(1), γ 101.75(1)�. The structure refined to give a final R 0.084 for 2172 observed reflections. The acid molecules form centrosymmetric hydrogen bonded cyclic dimers [O. . .O,2.619(4) �] about a centre of symmetry in the cell. The oxopropionic acid side chain has a synplanar-synplanar (carbonyl) conformation while the planar p-chlorophenoxymethyl substituent in the p-position has a synclinal orientation relative to the primary phenoxy residue.

Crystal and Molecular Structure of Methylpropylglyoxal Bis(amidinohydrazone) Sulphate Monohydrate

1997 ◽  
Vol 52 (9) ◽  
pp. 1114-1118 ◽  
Author(s):  
Mikko Koskinen ◽  
Ilpo Mutikainen ◽  
Jere T. Koskinen ◽  
Hannu Elo
Keyword(s):  
Crystal And Molecular Structure ◽  
Side Chain ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Related Factors ◽  
Triclinic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Analogous Compound ◽  
Packing Effects

Abstract A single-crystal X-ray diffraction study was performed on methylpropylglyoxal bis(amidinohydrazone) (M PGBG) sulphate monohydrate. The bis(amidinohydrazone) dication was found to exist exclusively in the form of the anti-anti isomer, with an all-trans configuration of the glyoxal bis(amidinohydrazone) chain, just as do the free base, the monocation and the dication of glyoxal bis(amidinohydrazone) and the dications of all mono-and dialkylglyoxal bis(amidinohydrazones) so far studied. MPGBG sulphate monohydrate crystallizes in the triclinic space group Pl̅ with unit cell parameters a = 8.860(2), b = 9.195(2), c = 10.788(2) Å, α = 73.71(3), β = 77.59(3), γ = 65.28(3)° and with Z = 2. When the structure is compared with that of propylglyoxal bis(amidinohydrazone) (PGBG) sulphate, an analogous compound that is devoid of the methyl group of MPGBG, a distinct difference can be observed regard­ing the conformation of the propyl side chain. In the MPGBG dication, the propyl group is directed away from the glyoxal bis(amidinohydrazone) chain, whilst in the case of the PGBG dication it is tangled around the glyoxal bis(amidinohydrazone) moiety. Whether this difference results from packing effects and related factors, or whether it is a result of a more fundamental difference between MPGBG and PGBG, remains to be studied. The observed difference may contribute to the biochemical differences between the two compounds.

Crystal structure determination of the conformation of two bicyclo[3.3.1]nonan-ones

1985 ◽  
Vol 63 (6) ◽  
pp. 1166-1169 ◽  
Author(s):  
John F. Richardson ◽  
Ted S. Sorensen
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Chair Conformation ◽  
Molecular Structures ◽  
Boat Conformation ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Final Agreement

The molecular structures of exo-7-methylbicyclo[3.3.1]nonan-3-one, 3, and the endo-7-methyl isomer, 4, have been determined using X-ray-diffraction techniques. Compound 3 crystallizes in the space group [Formula: see text] with a = 15.115(1), c = 7.677(2) Å, and Z = 8 while 4 crystallizes in the space group P21 with a = 6.446(1), b = 7.831(1), c = 8.414(2) Å, β = 94.42(2)°, and Z = 2. The structures were solved by direct methods and refined to final agreement factors of R = 0.041 and R = 0.034 for 3 and 4 respectively. Compound 3 exists in a chair–chair conformation and there is no significant flattening of the chair rings. However, in 4, the non-ketone ring is forced into a boat conformation. These results are significant in interpreting what conformations may be present in the related sp2-hybridized carbocations.

Crystal and molecular structure of diorganoammonium oxalatotrimethylstannate, [R2NH2][Me3Sn(C2O4)] (R=i-Bu, cyclohexyl)

2011 ◽  
Vol 34 (5-6) ◽  
pp. 127-130 ◽  
Author(s):  
Yaya Sow ◽  
Libasse Diop ◽  
Kieran C. Molloy ◽  
Gabrielle Kociok-Köhn
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Diffraction Study ◽  
Crystal And Molecular Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Trigonal Bipyramidal ◽  
Trans Complex ◽  
A Chain ◽  
Distorted Trigonal Bipyramidal

Abstract The title compounds [R2NH2][C2O4SnMe3](R=i-Bu, Cy), in which tin atoms adopt a distorted trigonal bipyramidal configuration, have been prepared and submitted to an X-ray diffraction study. These compounds have been obtained from the reaction of (Cy2NH2)2C2O4·H2O or (i-Bu2NH2)2C2O4 with SnMe3Cl. In both [R2NH2][C2O4SnMe3] compounds, the trans complex has an almost regular trigonal bipyramidal geometry around the tin atom. The SnMe3 residues are connected as a chain with bridging oxalate anions in a trans-SnC3O2 framework, the oxygen atoms being in axial positions. The cations connect linear adjacent chains through NH…O hydrogen bonds giving layered structures.

Reminiscences and discoveries: Dorothy Hodgkin and the Indian connection

1996 ◽  
Vol 50 (1) ◽  
pp. 115-127 ◽  
Keyword(s):  
Large Angle ◽  
Direct Methods ◽  
Statistical Fluctuation ◽  
Organic Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Angle Scattering ◽  
Molecular Sizes ◽  
Indian Institute Of Science

Dorothy Hodgkin - as crystallographer, scientist and human being - far surpasses most, and so it is not easy to write about her many-splendoured personality. Instead, my aim here will he to discuss her influence on the growth of X-ray crystallography in India, directly through those who worked with her and indirectly by her travelling all over this country. In such an account, one must be pardoned for some personal element creeping in. In the twenties, India had developed a fairly strong tradition in X-ray physics. The six-week visit of C.V. Raman to Europe in 1921 greatly changed his research interests. On seeing the blue of the Mediterranean he started his researches on the scattering of light in liquids which finally culminated in the discovery of what is now called the Raman Effect. His encounter with Sir William Bragg and his work on naphthalene structure started three lines of research in India. First, Raman fabricated an X-ray tube and was amongst the earliest to use X-ray diffraction as a structural tool to study liquids. He showed that while in large-angle scattering the haloes reflected specific molecular sizes and packing shapes, small-angle scattering was directly related to the statistical fluctuation of density in a liquid. Second, Raman knew that Bragg’s first structure of naphthalene was not consistent with its birefringence, while the second one was. With this as cue he and his school launched extensive studies on the optical and magnetic anisotropy of organic crystals to get vital information on the arrangements of molecules in the crystalline state. Third, one of his students, Kedareshwar Bannerjee, was amongst the earliest to probe into the problem of phase determination by direct methods and for this he used Bragg’s data on naphthalene. Unfortunately, in spite of this early lead, it was not until 1951 that the first crystal structure was solved in India using Fourier methods by Gopinath Kartha. The Indian Institute of Science (IISc) had great hopes of starting a powerful school of X-ray crystallography when G.N. Ramachandran came back from Cambridge. But he went over to Madras, and there he established one of the most renowned Schools of Biophysics. With Gopinath Kartha he solved the structure of collagen.

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