Nucleotides crystal structure

Table 7.12. Relative proportion in hydrogen bonds in a sample of 120 nucleoside and nucleotide crystal structure [62]...

In the nucleoside and nucleotide crystal structures, the OH O hydrogen bonds are the most common. In general, these molecules do not crystallize as readily as do the carbohydrates, and in consequence, all the data, with only one exception, are from X-ray analyses. In addition, only about a quarter of the crystal structures reported are of sufficient quality to permit either direct or indirect location of all the functional hydrogen atoms. As is often the case the larger the molecule, the less accurate are the crystal structure analyses, hence most of the data refer to compounds with less than 12 carbon atoms. 

The data in Thble 7.17 are the same type of analysis as in Thble 7.16, using only the nucleoside and nucleotide crystal structures [62]. 

This type of hydrogen bond has the same acceptor groups as the N-H bond. It is found more commonly in the nucleoside and nucleotide crystal structures, where it accounts for nearly one tenth of all the hydrogen bonds. There are no P-OH + -N hydrogen bonds, since the acceptors are invariably protonated, P=0 -HN. This is in contrast to the P-OH- -0=C bond, where the 0=C group is rarely protonated in crystal structures. 

Table 8.9. Three-centered/bifurcated hydrogen-bond configurations in purine and pyrimidine (P P) and nucleoside and nucleotide crystal structures (N N)...

In the nucleoside and nucleotide crystal structures, intramolecular hydrogen bonding is not uncommon between ribose 0(2r)H -0(3 ) and 0(3 )H 0(2 ) hydroxyls and 0(5 )H 0(4 furanose). With very few exceptions, these are the minor components of three-center hydrogen bonds with H 0 distances between 2.1 and 2.9 A and O - H O angles in the range 90 0 to 116 °. They occur because other inter- or intramolecular forces in the crystal confer a favorable conformation to which these weak interactions add a small energetic advantage. 

Table 9.1. Some important intramolecular hydrogen bonds between bases and riboside observed in nucleoside and nucleotide crystal structures...

Table 11.2. Summary of the two-center and three-center hydrogen-bond lengths to Cl ions in the purine, pyrimidine, nucleoside and nucleotide crystal structures, normalized from X-ray data...

Table 17.1. Proportion of hydrogen bonds in a selection of nucleoside and nucleotide crystal structures versus the purines and pyrimidines [61, 62] see also Tables 7.12 and 7.14...

In the survey of nucleoside and nucleotide crystal structures [62], there are five clear examples of C(6)H 0(50 hydrogen bonds of which three are three-centered (Thble 10.2). All are in pyrimidine nucleosides. For the purine nucleosides and nucleotides, there are insufficient structure determinations with hydrogen atoms located from X-ray data to draw any conclusions. However, in many nucleoside and nucleotide crystal structures, the nonhydrogen atom C- 0(50 distances are... 

A Selection of Cyclic Hydrogen-Bonding Patterns Formed in Nucleoside and Nucleotide Crystal Structures... 

Selected crystal structures of cytidlne and its derivatives. The cytidine-related nucleoside and nucleotide crystal structures for which reliable hydrogen-bond patterns can be reported include five nucleotides. Amongst the nucleotides there is more variety than with the uridine compounds. There are three hydrates, four hydrochlorides, and a nitrate. The conjugated NH2 group is always involved as a donor, but never as an acceptor. Several different configurations are observed ... 

---