Computational studies intramolecular 1,5-hydrogen

Klein, R. A. Ab initio conformational studies on diols and binary diol-water systems using DPT methods. Intramolecular hydrogen bonding and 1 1 complex formation with water, J. Comput. Chem. 2002, 23, 585-599. 

Thus, the present results show that PCM is a very powerfiil tool for describing the behavior in solution of compounds able to form intramolecular hydrogen bonds. Direct computation of vicinal NMR coupling constants including vibrational averaging effects confirms this conclusion further and paves the route for more reliable quantum mechanical studies of bioactive systems. 

Positive ion fast atom bombardment mass spectrometry has been used to develop a procedure for the identification of cyclic nucleotides. Computational studies have shovm that cGMP is expected to prefer the syn-conformation, whilst cAMP prefers the anti-conformation.An intramolecular hydrogen bond between the C-2 amine fvmction of guanine and the axial oxygen atom of the cyclic phosphate is implicated in increasing the relative stability of the syn-conformation of cOlP. These conformational profiles may help to explain selectivity of binding and activation of proteins by cyclic nucleotides. 

Rios, M.A., and Rodriguez, J., Semiempirical study of compounds with OH-O intramolecular hydrogen bond, J. Comput. Chem., 13, 860-866 (1992). 

Shchavlev, A.E., Pankratov, A.N., and Shalabay, A.V., DFT computational studies on rotation barriers, tautomerism, intramolecular hydrogen bond and solvent effects in 8-hydroxyquinoline, Int. J. Quantum Chem., 106, 876-886 (2006). 

Kovacs, A., Kolossvary, I., Csonka, G.I., and Hargittai, I., Theoretical study of intramolecular hydrogen bonding and molecmar geometry of 2-trifluoromethylphenol, J. Comput. Chem., 17, 1804-1819(1996). 

In this volume mainly the theoretical studies are presented, however also examples of experimental results are included and all the computational results are strongly related to experimental techniques. The most important topics considered in the recent studies on hydrogen bond are discussed in this volume, such problems as how to estimate the energy of intramolecular H-bonds, covalency of these interactions, the distant consequences of H-bond since in earlier studies usually only the X-H- Y H-bridge was analyzed (X-H is the proton-donating bond and Y is an acceptor), the differences between H-bond and van der Waals interactions from one side and covalent bonds from the other side, the use of the Bader theory to analyze different kinds of H-bonds, the influence of weak H-bonds upon structure and function of biological molecules, etc. There are also topics related to the experimental results crystal structures, infrared and NMR techniques and many others. 

A subsequent study explicitly addressed the conformation of dimeric P-O-4 structures [84], again using MM3 and HF/6-31G in conjunction. Preliminary work on monomeric methoxylated compounds indicated the presence of an intramolecular hydrogen bond between primary alcoholic groups and the methoxyl group, stabilizing the structure. From these smaller structures, true P-O-4 dimers were constructed, in an effort to minimize computer time requirements. The most stable conformers for both threo and erythro configurations were found to be extended, rather than folded structures. 

Since this domain is conserved in several enterotoxins, one expects this 13 residue domain to be the primary reason for the toxicity of the 19-residue long protein. lETN has a simple secondary structure it has got 3 beta (/ ) turns. The /9i spans from Cys to Cys , (32 from Asn to Cys, and 02 from Cys to Cys . In addition, the crystal structure contains 5 intramolecular (i.e., within the protein) hydrogen bonds that also add to the stability of the conformation. The lETN structure is reasonably rigid (because of 3 disulfide bridges, and 5 intramolecular hydrogen bonds), making it an ideal candidate for studies by computer simulations using empirical intermolecular potentials. 

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