A new method to analyze the distribution of water molecules around the bases in DNA is presented. This method relies on the notion of a "hydrated building block," which represents the joint observed hydration around all bases of a particular type, in structures of a particular conformation type. The hydrated building blocks were constructed using atomic coordinates from 40 structures contained in the Nucleic Acid Database. Pseudoelectron densities were calculated for water molecules in each hydrated building block using standard crystallographic procedures. The electron densities were fitted to obtain "average building blocks," which represent bases with waters only at average or probable positions. Both types of building blocks were used to construct models of hydrated DNA oligomers. The essential features of the solvent structure around d(CGCGAATTCGCG)2 in the B form and d(CGCGCG)2 in the Z form were reproduced.
A study of systems containing the title moiety is described, with special reference to the anomeric effect. We have calciilated ab initio, using Gaussian-80 with the 3-21G basis set, all basic conformations of methylene-diamine (H2N-CH2-NH,) and its N-methyl derivative with full geometry optimization of energy minima and barriers. The structural data thus obtained, were then employed to parameterize Allinger's M"2-80 force field in a procedure similar to that described for oxygen derivatives, including hydrogen-bonding effects and C -N bond shortening in tertiary amines. This modification, termed MM2-AE was then used to calculate larger molecules, including N,N'-di-and N, N, N', "-tetramethylmethylenediamine, various 1,3-diazane systems, and 1,4,5,8-tetraazadecalin derivatives of established (x-ray) structures. The results are discussed in light of their verificative and predictive power and appear to valida.te MM2-AE as a useful computational procedure.
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