Novel H-bonded base pairs as potential repeat units for information-bearing macromolecular duplexes: A B3LYP/6-31G∗ search

Novel H‐bonded base dimers as repeat units for information‐bearing self‐associative duplexes: A B3LYP/6‐31G* search

“…The range of values for the interaction energies obtained here for these novel base pairs have been compared above with values obtained using the HF/6‐31G**, MP2 and DFT regimes for the whole set of 30 DNA base pairs, and the ranges are very comparable indeed. Our B3LYP/6‐31G* results may also be compared with the results of a previous similar study on hetero‐associative pairs,19 as well as with earlier PM3 SCF‐MO work done on analogous systems 17, 18. We note that while the hetero‐associative pairs have their would‐be N ‐glycoside bonds either pointing in the same direction or else away from each other, all the viable self‐associative pairs of this study have their N ‐glycoside bonds pointing only in the same direction.…”

“…Use of the MP2/6‐311++G(d,p) single point calculations on the B3LYP/6‐31G* geometries leads to values of the BSSE‐uncorrected pairing energy E p (MP2) which compare favorably with the BSSE‐uncorrected B3LYP/6‐31G* optimized values, being −20.48 for the A1 : A1 dimer, −23.15 kcal/mol for the A2 : A2 dimer, and −21.47 kcal/mol for the A1 : A2 pair. These large values of the pairing energy may be linked to ( a ) the presence in each pair of two H‐bonds of the CO…HN type, rated as strong in our earlier studies,17–19 ( b ) relatively small values for the H‐bond lengths R hb and R xy (Table 2), being respectively 1.785 and 2.813 Å for the A1 : A1 pair, about 2.758 and about 2.759 Å for the A2 : A2 pair, and 1.759 or 1.765 and 2.793 or 2.796 Å for the A1 : A2 pair, and ( c ) the near‐linearity of the H‐bonds, where values of the H‐bond angle θ hb given in Table 2 are 172.3° for the A1 : A1 pair, 172.9° or 173.1° for the A2 : A2 pair, and 172.4° or 172.7° for the A1 : A2 pair.…”

“…so as to build up a variety of duplex structures. This study aims to explore the potential of wholly synthetic bases and base pairs to serve as repeat units for information‐bearing macromolecular duplexes, as was the focus of our earlier studies 17–19…”

“…Buam and Lyngdoh17, 18 used the PM3 SCF‐MO method to study H‐bonded pairing among various nitrogenous bases to determine the suitability of such pairs to serve as repeat units for information‐bearing macromolecules, dealing with self‐associative dimers of nitrogenous heterocycles as well as hetero‐associative pairs. We also used the B3LYP/6‐31G* approach to design hetero‐associative base pairs along similar lines 19…”

“…Unlike in our former study,19 we now focus on self‐association as a basis for designing the repeat units of the macromolecular duplex. For a base monomer to be able to H‐bond with itself, the basic requirement is that the base should contain both a proton donor and a proton acceptor within itself.…”