Theoretical insight into the hybridization effect of donor and acceptor atoms on the cooperativity of C-H···N hydrogen bonds.

In the present work, the influence of hybridization on cooperativity between C-H···N hydrogen bonds is theoretically investigated. Here, C2H6, C2H4, and C2H2 are considered as hydrogen bonding donor while NH3, N2H4, N2H2, and N2 act as the hydrogen bonding acceptor. The calculations are performed at MP2/aug-cc-pVTZ level. It is observed that the stability of systems is amplified as C(sp) > C(sp2) > C(sp3) and also N(sp3) > N(sp2) > N(sp). The role of interaction and deformation energies on the stability of the systems is examined. The results indicate the contribution of interaction energy is dominant in all complexes. The strength of C-H···N hydrogen bond is estimated using interaction energy. In agreement with cooperative energies, the C-H···N hydrogen bond is respectively weakened/strengthened in the triads containing C(sp) and C(sp2)/C(sp3) where two hydrogen bonds coexist. On the other hand, the C-H···N hydrogen bond is strengthened in the ternary systems including N(sp3) and N(sp2) while an opposite behavior is obtained in the triad having N(sp).

The effect of metal alkali cations on the properties of hydrogen bonds in tautomeric forms of adenine - Guanine mismatch.

The effect of interactions of Li+, Na+ and K+ cations with two preferred configuration of the A-G mispairs, AantiGanti and AsynGanti, on the geometries and hydrogen bond energies have been studied at the MP2/6-311++G(d,p) level of theory. For each ion type, the most stable complex in AantiGanti and AsynGanti configurations are related to binding cation to N3 atom of guanine and N1 atom of adenine, respectively. The AantiGanti configuration is higher in the absolute values of binding energy than the AsynGanti configuration, indicating that AantiGanti configuration is more stable than AsynGanti ones. The results indicate that the strength of hydrogen bonds depends on the type and position of cations in considered systems. The values of hydrogen bonding energies estimated by the EML formula in AantiGanti mismatch are higher than AsynGanti case. The influences of cations binding in hydrogen bond strength are confirmed by the results of natural bond orbital (NBO) and atoms in molecules (AIM) analyses.

The influence of Cu+ binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study.

In the present work, the influence of Cu+ binding to N3- and N7-positions of hypoxanthine on energetic, geometrical and topological properties of hypoxanthine-guanine, hypoxanthine-adenine, hypoxanthine-cytosine, hypoxanthine-thymine and hypoxanthine-hypoxanthine mismatches is theoretically investigated. The calculations, in gas phase, are performed at B3LYP/6-311++G(3df,3pd) level of theory. Unlike the other mispairs, Cu+ binding to N3-position of hypoxanthine causes the proton transfer process from enol form of hypoxanthine to imino forms of adenine and cytosine. This process also occurs in all mismatches having enol form of hypoxanthine when Cu+ binds to N7-position of hypoxanthine. The mismatches are stabilized by hydrogen bonds. The influence of Cu+ on hydrogen bonds is also examined by atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Communicated by Ramaswamy H. Sarma.

A theoretical survey of substituent effects on the properties of pnicogen and hydrogen bonds in cationic complexes of PH4+ with substituted benzonitrile.

In this paper, we analyze the substituent effects on the nature and characteristics of P⋯N and H⋯N interactions in X-PhCN:PH4+ complexes (X=H, F, Cl, Br, CN, NH2, NO2, CH3 and N(CH3)2) as a working model at MP2(FC)/6-311++G(d,p) level of theory. The natural bond orbital (NBO) method as well as the quantum theory of atoms in molecules (AIM) is applied to characterize interactions in the studied complexes. In general, the pnicogen bonded systems are more stable than the corresponding hydrogen bonded cases. The strength of the interactions generally correlates well with the magnitudes of the negative electrostatic potentials of the nitrogen atom of isolated substituted benzonitrile (Vs,min(N)). The results indicate that increase in the electron withdrawing power of substituents is accompanied by decrease in the absolute value of Vs,min(N). Also, there are meaningful relationships between Vs,min(N) values and the results of AIM and NBO analyses in studied systems. Moreover, it is found that substituent effects on characteristics of P⋯N pnicogen and H⋯N hydrogen bonds can be expressed by Hammett constants.

The effects of tautomerization and protonation on the adenine-cytosine mismatches: a density functional theory study.

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.