Computational Study of Substituent Effects on the Interaction Energies of Hydrogen-Bonded Watson−Crick Cytosine:Guanine Base Pairs

Why does substitution of thymine by 6-ethynylpyridone increase the thermostability of DNA double helices?

Efficiency of 6-ethynylpyridone (E), a potential thymine (T) analogue, which forms high-fidelity base pairs with adenine (A) and gives rise to stabler DNA duplexes, with stability comparable to those containing canonical cytosine(C):guanine(G) base pairs, has been reported recently. Estimates of the interaction energies, involving geometry optimization at the DFT level (including middle range dispersion interactions) followed by single point energy calculation at MP2 level, in excellent correlation with the experimentally observed trends, show that E binds more strongly and more discriminately with A than T does. Detailed analysis reveals that the increase in base-base interaction arises out of conjugation of acetylenic π electrons with the ring π system of E, which results in not only an extra stabilizing C-H···π interaction in the EA pair, but also a strengthening of the conventional hydrogen bonds. However, the computed base-base interaction energy for the EA pair was found to be much less than that of the canonical CG pair, implying that the difference in the TA versus EA base pairing interaction alone cannot explain the large experimentally observed increase in the thermostability of DNA duplexes, where a TA pair is replaced with an EA pair. Our computations show that the conjugation of acetylenic π electrons with the ring π system also possibly plays a role in increasing the stacking potential of the EA pair, which in turn can explain its marked influence in the enhancement of duplex stability.

Cooperativity in beryllium bonds

Positive cooperativity is found in beryllium bonded complexes similar to that described for hydrogen bonded systems.

Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases

N6-methyladenine (m(6)A) is a rare base naturally occurring in DNA. It is different from the base adenine due to its N-CH(3). Therefore, the base not only pairs with thymine, but also with other DNA bases (cytosine, adenine and guanine). In this work, Møller-Plesset second-order (MP2) method has been used to investigate the binding mechanism between m(6)A and natural DNA bases in gas phase and in aqueous solution. The results show that N-CH(3) changed the way of N6-methyladenine binding to natural DNA bases. The binding style significantly influences the stability of base pairs. The trans-m(6)A:G and trans-m(6)A:C conformers are the most stable among all the base pairs. The existence of solvent can remarkably reduce the stability of the base pairs, and the DNA bases prefer pairing with trans-m(6)A to cis-m(6)A. Besides, the properties of these hydrogen bonds have been analyzed by atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and Wiberg bond indexes (WBI). In addition, pairing with m(6)A decreases the binding energies compared to the normal Watson-Crick base pairs, it may explain the instability of the N6 site methylated DNA in theory.

Modulating the Strength of Hydrogen Bonds through Beryllium Bonds

The mutual influence between beryllium bonds and inter- or intramolecular hydrogen bonds (HBs) has been investigated at the B3LYP/6-311++G(3df,2p) level of theory, using the complexes between imidazole dimer and malonaldehyde with BeH2 and BeF2 as suitable model systems. Imidazole and its dimer form very strong beryllium bonds with both BeH2 and BeF2, accompanied by a significant geometry distortion of the Lewis acid. More importantly, we have found a clear cooperativity between these two noncovalent interactions, since the intermolecular HB between the two imidazole molecules in the dimer-BeX2 complex becomes much stronger than in the isolated dimer, whereas the beryllium bond becomes also stronger in the dimer-BeX2 complex, with respect to that found in the imidazole-BeX2 complex. The effects of beryllium bonds are also dramatic on the strength of intramolecular HBs. Depending on to which center the BeX2 is attached, the intramolecular HB becomes much stronger or much weaker. The first situation is found when the beryllium derivative is attached to the HB donor, whereas the second occurs if it is attached to the HB acceptor. The first effect can be so strong as to produce a spontaneous proton transfer, as it is actually the case of the malonaldehyde-BeF2 complex.

A COMPARATIVE STUDY OF META/PARA SUBSTITUTION EFFECTS ON THE HYDROGEN-BONDED COMPLEX OF ANILINE-H2O: OBSERVATIONS FROM COMPUTATION

Compared with para-substitution, substituent effects ( R = NH 2, OH , CH 3, F , Cl , H , SiH 3, CHO , CN , NO 2) of meta-position effects on hydrogen-bonded complex of aniline with one water molecule are studied at B3LYP/6-311++G(d,p) level of theory. The differences in hydrogen bonding and some properties associated with the H -bond (such as bond length, vibrational frequency, binding energies, p K a values of aniline derivatives) are discussed between meta and para substitutions. Natural bond orbital (NBO) and atoms in molecules (AIM) analysis are applied to investigate the physical origin of the differences. The results show that the differences are mainly attributed to the variations in electron delocalization from amino group to phenyl ring (reflected by [Formula: see text] interaction) induced by substituents.

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs

The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X-adenine-thymine (X-A-T), X-thymine-adenine (X-T-A), X-guanine-cytosine (X-G-C), and X-cytosine-guanine (X-C-G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6-311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO(2)) increase the total binding energy (DeltaE) of X-G-C derivatives and the electron donating (ED) substituent (CH(3)) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH(3) in the 1 position and F in the 5 position, which in both cases the DeltaE value decreases negligibly small. With minor exceptions (X=8-CH(3), 8-F, and 9-NO(2)), both ED and EW substituents increase slightly the DeltaE values of X-A-T derivatives. The individual HB energies (E (HB)s) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO(2) substituted derivative in each case.

Prediction of interaction energies of substituted hydrogen-bonded Watson-Crick cytosine:guanine(8X) base pairs

We investigated the variation in the interaction energy between the Watson-Crick hydrogen-bonded DNA base pairs guanine and cytosine (G(8X):C), where guanine is substituted in the C8 position by 37 different functional groups. Base pairs were optimized at the B3LYP/6-311+G(2d,p) level. A base pair complex containing a more strongly electron-withdrawing group remarkably forms a more stable base pair with C. Multivariate linear regression provided a quantitative relationship between the interaction energies and descriptors generated by the quantum chemical topology (QCT) approach. The descriptors were sampled from the monomers only, not the supermolecular base pair complexes. A model with r2 = 0.96 and a root-mean-square (rms) value of 0.6 kJ/mol was obtained for a training set of 28 base pair complexes. The model was tested by an external test set of 9 complexes, yielding r2 = 0.99 and an rms value of 0.2 kJ/mol. The results indicated that the bonds C6=O6 and N2-H2 at the hydrogen-bonded frontier of the guanine derivatives play an important role in transmitting the substituent effects. A linear correlation between substitution energies and Hammett constants (sigma(m)) was also obtained for all 37 substituents, yielding r2 = 0.82 and an rms value of 1.2 kJ/mol. The model based on QCT descriptors can therefore be used for the prediction of the interaction energy of the base pair G(8x):C, strictly based on data for the G(8x) monomers only.