The crystal structure of the dipotassium salt of uridine 5'-diphosphate

C9H12N2Ot2P22-. 2K + .3H20 is orthorhombic, P2~2~2p with a = 18.977 (5), b - 22.597 (6), c = 8.995 (2) A, Z = 8. The structure was refined to R = 0.059 for 2587 observed reflexions. The two molecules of the asymmetric unit have very similar conformations with a 2'- endo sugar pucker and a folded pyrophosphate chain. They form a dimer, coordinated by the K + ions but without direct bridging between the base and the pyrophosphate within each individual molecule. One uracil base has the keto-enol and the other the diketo form. The extended structure shows alternating hydrophobic and hydrophilic regions.

Conformational studies of the triphenylphosphazenyl side chain in cyclophosphazenes. I. Crystal and molecular structure of N3P3C15(NPPh3)

The title compound, C t8H~sC15NaP4, crystallizes in the monoclinic space group P2~/n with a = 20.14 (2), b = 8.69 (1), c = 14.92 (2) A, fl = 98.8 (3) ° , Z = 4. The structure was determined from visual data and refined to R = 0-069 for 1450 reflections. The cyclophosphazene ring is non-planar. The exocyclic NPPh 3 group exhibits type I conformation [R. A. Shaw (1975). Pure Appl. Chem. 44, 317-341] in which the N-P bond is perpendicular to the adjacent P-CI bond.

Structure of a cyclic water tetramer in a nucleotide crystal host and a hypothetical model for water cluster growth

Structure of a cyclic water tetramer in channels (pores) formed by self-assembly of N6-methyl-5'-AMP center dot Na-2 molecules is described and a hypothetical model is proposed for growth of water clusters. (C) 2010 Elsevier B.V. All rights reserved.

Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

A novel metal binding mode of a pyrimidine nucleotide. Crystal structure of [Cu(5′-UMP)(im)2(H2O)]·4H2O

X-ray analysis of the ternary complex [Cu(5′-UMP)(im)2(H2O)]·4H2O, where 5′-UMP uridine-5′-monophosphate and IM = imidazole, reveals a novel metal binding mode of pyrimidine nucleotide through the ribose group.

An unusual axial co-ordination of phenolate oxygen to copper(II): crystal structure of chloro(2-[bis(2-pyridylmethyl)aminomethyl]-4-nitrophenolato)copper(II)

A tripod ligand possessing two pyridine moieties and a phenolato group as pendants forms a mononuclear complex with an axial copper(II)–phenolate co-ordination in a square-pyramidal environment.

Conformational Variability in Modified Nucleosides. Crystal and Molecular Structure of 2',3'-O-Isopropylidene Inosine

The crystal structure of 2',3'-O-isopropylidene inosine shows a number of interesting features. The four independent molecules in the asymmetric unit exhibit significant conformational variations. Ribose puckers fall in the O(4')-exo region, unfavourable in unsubstituted nucleosides. Hypoxanthine bases show base-pairing (I.I) in a manner analogous to the guanine self pairs (G.G) in 2',3'-O-isopropylidene guanosine but with a C(2)-H…O(6) hydrogen bond instead of N(2)-H…O(6).

Crystal Structure of Sodium Deoxyinosine Monophosphate

The crystal and molecular structure of sodium deoxyinosine monophosphate (5'-dIMP) has been determined by x-ray crystallographic methods. The crystals belong to orthorhombic space group P212121, with a = 21.079(5) Aring, b = 9.206(3) Aring and c = 12.770(6) Aring. This deoxynucleotide shows common nucleotide features namely anti conformation about the glycosyl bond, C2' endo pucker for the deoxyribose sugar and gauche-gauche orientation for the phosphate group. The sodium ion is directly coordinated to the O3' atom, a feature observed in many crystal structures of sodium salts of nucleotides.

Crystal and Molecular Structure of Sclerophytin F Methyl Ether from the Soft Coral Cladiella krempfi

new cembranoid diterpene was isolated from the soft coral Ckdiella h p f ifrom Minicoy Island (India), and its structure was established by X-ray crystallography to be sclerophytin F methyl ether (21 with the R absolute configuration at all six epimeric centers,assuming a configuration similar to that of sclerophytin C. Compound 2 may be an artifact of the isolation process.

Organometallic chemistry of diphosphazanes *1: VIII. Synthesis, spectroscopic studies and crystal structure of fac-[Mo(CO)3(MeCN)Ph2PN(iPr)P(Ph)(DMP)], and its reactions with tertiary phosphines

The reaction of fac-[Mo(CO)3(MeCN)3] with the unsymmetrical diphosphazane Ph2PN(iPr)P(Ph)(DMP) (L) gives the complex fac-[Mo(CO)3(MeCN)(L)] (2) in almost quantitative yield. The structure of the complex has been determined by an X-ray diffraction study. The compound reacts with PR3 (where R = Ph, OPh) to give fac-[Mo(CO)3(PR3)(L)] (3a, 4a), which undergoes an intramolecular isomerization to afford mer-[Mo(CO)3(PR3)(L)] (3b, 4b). Synthesis of cis-[Mo(CO)4(L)] (1) and fac-[MO(CO)3L] (2a) and their spectroscopic data are also reported.

Structure and conformation of the calcium complex of cyclo(Ala-Leu-Pro-Gly)2 in two crystal forms

Crystal structures of two different forms of the calcium perchlorate complex of cyclo(Ala-Leu-Pro-Gly)2 have been determined and refined using X-ray crystallographic techniques. Orthorhombic form: C32H52N8O8.Ca(ClO4)2.7H2O.2CH3OH, space group C222(1), a = 14.366, b = 18.653, c = 19.824 A, Z = 4, R = 0.068 for 2208 observed reflections. Monoclinic form: C32H52N8O8.Ca(ClO4)2.4H2O, space group C2, a = 21.096, b = 10.182, c = 11.256 A, beta = 103.33 degrees, Z = 2, R = 0.075 for 2165 observed reflections. The cyclic peptide molecule in both the structures has the form of a twofold symmetric, slightly elongated bowl. Type II' beta-turns, involving Gly and Ala at the corners, exist at the two ends of the molecule. The interior of the molecule is substantially hydrophilic, and the external surface of the bowl is largely hydrophobic. The calcium ion is located at the centre of the mouth of the bowl-like molecule. In both crystal forms, four peptide carbonyl oxygens from the cyclic peptide and two solvent oxygens coordinate to the metal ion. The mode of complexation may be described as incomplete encapsulation as, for example, in the case of metal complexes of antamanide. In the crystal structures the complex ions are held together by hydrogen bonds involving perchlorate ions and water molecules. The molecular structure observed in the crystals is entirely consistent with the results of solution studies, which also indicate the conformation of the cyclic peptide in the complex to be similar to that of the uncomplexed molecule.