The diolefin of [2-2]paracyclophane (C16H12) forms monoclinic crystals with a 0 =6.866, b 0 = 11.636, c o =7.640/~, fl = 116.9 °, and two molecules in the unit cell in space group P21/c. The structure has been refined by full matrix three-dimensional least-squares methods, and the final parameters include small corrections for molecular libration. The aromatic rings are bent into a boat form about 14 ° at each end, and the bonds to the a-carbons are bent an additional 15 ° from the plane of the edge of each aromatic ring. The ring deformation may also be described as a folding of 16 ° about a line between the p-substituted atoms. The exocyclic single bond distance is 1.51/~, at least 0.02/~ longer than normal. The lengthening is attributed in part to the orthogonality of the u-systems in the molecule and in part to intramolecular strain. Other distances are normal. The distribution of strain in the molecule is discussed.
Pyrimidine 2',3'-cyclic phosphates are substrates for the enzyme ribonuclease, and are formed in the enzymatic hydrolysis of ribonucleic acid. The hydrated sodium salt of p-cytidineo2',3 '-cyclic phosphate forms monoclinic crystals of space group P21 with a = 6.737, b = 11.007, and c = 19.54 A, , f ? = 95.0°, and two nucleotides in the asymmetric unit. X-Ray diffraction data to 28 = 125' were collected with a diffractome:er using Cu K a radiation. The structure was solved by Patterson and Fourier synthesis methods in conjunction with the tangent formula, and was refined using block-diagonal least-squares methods. The final R value was 4.7 for the 1964 reflections used in the refinement and 5.2% for all 2442 data. Both of the cytosine bases are in the syn conformation about the P-glycosidic bond, and seem to be locked in this unusual conformation. The bicyclic ribosephosphodiester ring system holds the sugar with the ribose ring carbons nearly in one plane and the oxygens puckered. The H atoms on C(2') and C(3') are thus eclipsed, with dihedral angles of 1 and 4'. The conformations about the exocyclic CHzOH bond are gauche-gauche and gauche-trans for the two anions. The nucleotides pack into base-stacked antiparallel-stranded ribbons, held together with intra-and inter-ribbon hydrogen bonds and coordination and hydrogen bonding through the hydrophilic sodium ion-water molecule region. yclic 2',3'-phosphate esters of cytidine and uridine C are intermediates in the ribonuclease-catalyzed hydrolysis of ribonucleic acid, and are themselves substrates for ribonuclease. The molecular structures of these esters are thus relevant to the proposal and evaluations of precise mechanisms for ribonuclease catalysis. Saenger and Eckstein2 have reported the structure of cyclic uridine 2',3'-O,O-phosphorothioate, but this is the first detailed study of a cytidine cyclic ester. As was noted in the preliminary report on this work3 the structure found for the cytidine 2',3'-cyclic phosphate, prepared using dicyclohexylcarbodiimide, is unusual and quite different from that of the cyclic uridine phosphorothioate prepared by a different means.j The cytosine bases are in the syn conformation about the glycosidic bond and they seem to be locked in this conformation. The bicyclic ribose-phosphodiester ring system imparts unusual rigidity to the ribose, with O(1') the only atom which easily puckers. On? of the two nucleotides in the crystal has O(1') 0.48 A out of the sugar plane, and the other ribose is virtually planar. These conformations are very unusual and leave I-I(2') and H(3') eclipsed. Saenger and Eckstein2 observed a similar rigidity in the ribose ring of the uridine compound, with O(1') 0.29 A out of the sugar ring. The rates of hydrolysis of uridine and cytidine 2',3 '-cyclic phosphates differ, the cytidine ester being hydrolyzed to cytidine 3'-phosphate at twice the rate of the uridine ester in the presence of ribonuclease.6 The rate difference must be explained in terms of structure and the chemical nature of the bases in the...
A 100-MHz pmr study of tetraethylammonium salts of 2',3'-CMP, 2',3'-UMP, and 3'-CMP in CD3OD, D20, and ethylene glycol over a temperature range of -50 to 150°has been done to investigate the solution conformations of these nucleotides.values for the Karplus equation were derived from the solution coupling constants and the crystal-structure geometry of 2',3'-CMP. We suggest J0 = 7.16 Hz for a dihedral angle between vicinal protons of 0 to t/2 and = 10.1 Hz for tt/2 to as suitable values for nucleoide protons. Populations of conformations of the exocyclic CH-.OH group were derived for several nucleotides and nucleosides. The barrier to rotation is small. The near constancy of the H(6) chemical shift for 2',3'-CMP and the marked change in this shift for 3'-CMP with temperature can be accounted for by assuming a fixed conformation for the base in 2',3'-CMP and a syn-anti equilibrium for 3'-CMP. The barrier to rotation for 3'-CMP in methanol lies between 3 and 7 kcal/mol. 2',3'-CMP appears to be locked in the syn conformation. Consideration of published data suggests that 5'-pyrimidine nucleotides are also syn-anti mixtures at room temperature. Solutionproperties and conformations of nucleotides and nucleosides have been extensively studied in recent years.2-8 The conformations of these compounds are of particular interest because they are well defined in the crystalline state9 and relevant to nucleic acid structure and to the mechanism of action of ribonuclease and deoxyribonuclease. Nucleotides and nucleosides have been studied in a sufficiently wide range of crystal environments to permit generalization to solution conformation in some cases. An example is the previous paper in this series10 on the crystal structure of 0-cytidine 2',3'-cyclic phosphate, an intermediate in the ribonuclease-catalyzed hydrolysis of ribonucleic acid. This structure was both unusual and especially rigidly defined because of the bicyclic ribose-phosphodiester ring system.We report here a pmr11 investigation of the solution conformations of 2',3'-CMP and related nucleotides. We have found that the bases in 2',3'-CMP and 2',3'-UMP are in the syn conformation about the 0-glycosidic bond over a wide temperatute range; 3'-CMP in methanol or water is a mixture of syn and anti conformers with the anti conformer the lower energy form. The barrier to base rotation in methanol was estimated to be between 3 and 7 kcal/mol. In addition, estimates of the populations of conformers about(1) Postdoctoral trainee under National Institutes of Health Grant GM-94.(2) .
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.