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Novel H‐bonded base dimers as repeat units for information‐bearing self‐associative duplexes: A B3LYP/6‐31G* search
Author(s) -
Neihsial Siamkhanthang,
Lyngdoh Richard H. Duncan
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20942
Subject(s) - macromolecule , chemistry , counterpoise , base (topology) , base pair , nucleobase , set (abstract data type) , isomorphism (crystallography) , density functional theory , associative property , computational chemistry , computer science , crystallography , mathematics , basis set , dna , pure mathematics , mathematical analysis , biochemistry , crystal structure , programming language
Density functional theory at the B3LYP/6‐31G* level with counterpoise correction has been employed to study six sets of nitrogenous bases for the capacity of each to form H‐bonded dimers restricted to a chosen pairing configuration. These results are augmented by MP2/6‐311++G(d,p) single point calculations on the B3LYP/6‐31G* optimized geometries. Each set has two bases, including substituted azoles, imidazoles, pyrimidines, and fused ring systems. This study aims to determine the suitability of each set to furnish H‐bonded base pairs which may serve as repeat units for self‐associative H‐bonded macromolecular duplexes with the capacity to store and replicate information at the molecular level. Out of the various possibilities tested here, a set of two substituted pyrimidines best satisfies the prescribed criteria and may be put forward as a good candidate to yield isomorphic repeat units for designing such synthetic information‐bearing macromolecular duplexes. The optimized configurations of these chosen base pairs as calculated at the B3LYP/6‐31G* level compare well with those calculated at the B3LYP/6‐31++G(d,p) and MP2/6‐31G(d,p) levels, and indicate that isomorphism of the two base pairs is independent of method used. Assuming a one‐to‐one correspondence for encoding information in the macromolecule, such a set of two bases can allow the macromolecule to encode up to 8 types of encrypted species. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008