The structure of the zwitterion inosine cyclic 3',5'-monophosphate (cIMP) monohydrate. Analysis of torsional flexibility in the furano–phosphate moiety

Sundaralingam, M.; Haromy, T. P.; Prusiner, P.

doi:10.1107/s0567740882006293

Cited by 13 publications

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“…An extremely short N−H···O (P) hydrogen bond is revealed in the structure of 3 [Figure , Table ]. The N···O distance is much shorter than that in Emsley's compound [C 6 H 11 N 3 H 2 ] + [H 2 PO 4 ] - [N···O 2.611, 2.661 Å]. 4a,− An examination of the structures available in the Cambridge database showed that the N(−H)···O (P) distance in 3 is at the lower end for such hydrogen bonds (cf. Figure ).…”

Section: Resultsmentioning

confidence: 99%

Very Strong C−H···O, N−H···O, and O−H···O Hydrogen Bonds Involving a Cyclic Phosphate

2001

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Very short C-H...O, N-H...O, and O-H...O hydrogen bonds have been generated utilizing the cyclic phosphate [CH2(6-t-Bu-4-Me-C6H2O)2]P(O)OH (1). X-ray structures of (i) 1 (unsolvated, two polymorphs), 1...EtOH, and 1...MeOH, (ii) [imidazolium](+)[CH2(6-t-Bu-4-Me-C6H2O)2PO2](-)...MeOH [2], (iii) [HNC5H4-N=N-C5H4NH](2+)[(CH2(6-t-Bu-4-Me-C6H2O)2PO2)2](2-)...4CH3CN...H2O [3], (v) [K, 18-crown-6](+)[(CH2(6-t-Bu-4-Me-C6H2O)2P(O)OH)(CH2(6-t-Bu-4-Me-C6H2O)2PO2)](-)...2THF [4], (vi) 1...cytosine...MeOH [5], (vii) 1...adenine...1/2MeOH [6], and (viii) 1...S-(-)-proline [7] have been determined. The phosphate 1 in both its forms is a hydrogen-bonded dimer with a short O-H...O distance of 2.481(2) [triclinic form] or 2.507(3) A [monoclinic form]. Compound 2 has a helical structure with a very short C-H...O hydrogen bond involving an imidazolyl C-H and methanol in addition to N-H...O hydrogen bonds. A helical motif is also seen in 5. In 3, an extremely short N-H...O hydrogen bond [N...O 2.558(4) A] is observed. Compounds 6 and 7 also exhibit short N-H...O hydrogen bonds. In 1...EtOH, a 12-membered hydrogen-bonded ring motif, with one of the shortest known O-H...O hydrogen bonds [O...O 2.368(4) A], is present. 1...MeOH is a similar dimer with a very short O(-H)...O bond [2.429(3) A]. In 4, the deprotonated phosphate (anion) and the parent acid are held together by a hydrogen bond on one side and a coordinate/covalent bond to potassium on the other; the O-H...O bond is symmetrical and very strong [O...O 2.397(3) A].

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Section: Resultsmentioning

confidence: 99%

Very Strong C−H···O, N−H···O, and O−H···O Hydrogen Bonds Involving a Cyclic Phosphate

2001

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“…For derivatives [15][16][17][18][19] with substituent Y trans (3, Z = 0, Y = substituent), 1,3-syn axial repulsions resulting from the axial P=0 should be very similar to those in the diesters themselves. Here, stereoelectronic interactions must account for the measured differences in geometries ( , ', bond angles) and bond lengths compared to the diesters.…”

Section: Introductionmentioning

confidence: 99%

“…Since the interest of this paper is in the conformations of the phosphate and ribose rings of nucleoside cyclic 3',5'-monophosphates and derivatives thereof, we have not complied available information on the conformations of the nucleobases with regard to C(l')-N rotation, i.e., the glycosyl torsion angle. Comparisons of glycosyl torsion angles for the diesters (1,2, 5-9) of Table I can be found in refs 15 and 17. Glycosyl torsion angles for [10][11][12][13][14][15][16][17][18][19] show no evident systematic correlation with phosphorus configuration. The related question of the nature of intramolecular interactions in the solid state, which can involve H bonding between nucleobases and also nucleobase-phosphate oxyanion interactions, has not been addressed.…”

Section: Introductionmentioning

confidence: 99%

Solid-state conformations of nucleoside cyclic 3',5'-monophosphate derivatives. Effects of substituents on phosphorus on ring geometries and n/.sigma.* orbital interactions

Setzer¹,

Bentrude²

1991

J. Org. Chem.

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X-ray crystal structure data for seven nucleotide cyclic 3',5'-monophosphates, nine neutral cyclic nucleotide-based phosphate triesters, phosphonates, and phosphoramidates, and X-ray results for one new neutral, cyclic nucleotide-based phosphate triester were compared. Clearly evident is the pronounced flattening of the phosphate ring about phosphorus. This effect is greater for the neutral derivatives and assigned in part to an increased degree of stabilization arising from overlap of the p-like lone pair orbitals on 0(30 and 0(50 with the a* orbital of the axial substituent on phosphorus. Support for this interpretation is seen in shorter P-0(30 and P-0 (50 bonds noted for the neutral derivatives. The degree of flattening also is enhanced by steric repulsions involving axial substituents on phosphorus. Most of the structural features of these phosphate ring-based systems were successfully modeled by MNDO calculation on monocyclic analogues. Comparisons of these findings were made to those summarized earlier for the X-ray structures of the analogous monocyclic rings, for which ab initio calculations on systems that modeled those rings had been carried out. Similarities and differences between the cyclic nucleotide-based derivatives and the monocyclic systems were noted.

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Why is DNA polymorphic while RNA is not?

Sundaralingam

Rao

2009

Int. J. Quantum Chem.

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In DNA, the base-sugar hydrophobic interactions between the 2'-methylene group of the 2'-deoxyribose sugar and the base (H6 in pyrimidines and H8 in purines) on the 3'-side appear to act as a ball joint and facilitate the A-DNA c, B-DNA conformational interconversion by lowering the pseudorotational barrier. These and other sugar-base interactions coupled with the inherently more flexible 2'-deoxyribofuranose ring allow DNA to occur in a variety of polymorphic helical states. In contrast, the 2'-hydroxyl group in RNA not only sterically disfavors the B-type structure, but the inherently less flexible ribofuranose ring is further stabilized in the A-type structure by intramolecular hydrogen-bonded water bridge between the 2'-OH group and the base (02 in pyrimidines and N3 in purines).. This lack of flexibility of RNA dictates that DNA-RNA hybrid structures assume the A-type helix.DNA is found to occur in a number of polymorphic structural forms [l]. Besides the familiar right-handed A-and B-type double helical structures [2-51, the possibility of left-handed Z-type structures [6] has recently emerged. The capacity of DNA to adopt these and possibly other conformational structures in local regions has provided an attractive mechanism for understanding the way genes are turned on and off. On the other hand, RNA is less flexible than its cousin DNA and has been found so far to display only the A-type structure. It appears that nature has designed these differences in DNA and RNA for their separate biological roles.Chemically, RNA differs from DNA in that its main chain consists of ribofuranose sugars rather than 2'-deoxyribofuranose sugars. In addition, the base thymine in DNA occurs in the demethylated form, uridine, in RNA. In this article, we investigate the effect of these two chemical differences, one in the main chain and the other in a side chain base, on the overall structural and conformational properties of DNA and RNA. Some Structural Features of A-, B-, and Z-DNAIn both A-DNA and B-DNA, a 2'-methylene hydrogen atom of the sugar is in van der Walls contact with the base on the 3'-side ( hydrophobic interactions can be visualized as a mechanical ball joint which aids the "smooth" C3'-endo (A-DNA) ff C2'-endo (B-DNA) interconversion.* Thus, the flexibility of the sugar (or pseudorotational mobility) is related not only to the glycosyl torsion angle of the attached base (C3'-endo, low x; and C2'-endo, high x) [8] but also is transmitted to the base on the 3'-side. When the 3'-base is a thymine, this base-sugar "stacking" interaction is augmented by the involvement of the 5-methyl group (Fig. 2). It would then appear that the methylene-base(H61H8) and also the methylene-methyl (of T) interactions would tend to reduce the sugar-pucker interconversion barrier and contribute to the flexibility of DNA, particularly in AT-rich regions [lo].*The pseudoration barriers €or the interconversion have been variously estimated for the ribose and deoxyribose systems. While there is still no single value for these ba...

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The structure of the zwitterion inosine cyclic 3',5'-monophosphate (cIMP) monohydrate. Analysis of torsional flexibility in the furano–phosphate moiety

Cited by 13 publications

References 19 publications

Very Strong C−H···O, N−H···O, and O−H···O Hydrogen Bonds Involving a Cyclic Phosphate

Very Strong C−H···O, N−H···O, and O−H···O Hydrogen Bonds Involving a Cyclic Phosphate

Solid-state conformations of nucleoside cyclic 3',5'-monophosphate derivatives. Effects of substituents on phosphorus on ring geometries and n/.sigma.* orbital interactions

Why is DNA polymorphic while RNA is not?

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