Direct evaluation of individual hydrogen bond energy in situ in intra‐ and intermolecular multiple hydrogen bonds system

Abstract

The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.

Reaction mechanism of NO with hydrolysates of NAMI‐A: an MD simulation by combining the QM/MM(ABEEM) with the MD‐FEP method

“…Wilson and Ichikawa and Torrent‐Sucarrat and coworkers pointed out that the charge transfer between atoms in a molecule is overestimated by using the polarization basis sets. Huzinaka et al, Jakalian et al, Watanabe et al, and our group have shown that the use of higher levels of basis sets overestimates the overlap between their respective basis functions belonging to two atoms in a molecule. Bayly and his coworkers pointed out that when the 6‐31G* basis set is used, the polarity of a molecule calculated by the partial charges is overestimated by 10%–15% .…”

Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field

“…Wilson and Ichikawa and Torrent‐Sucarrat et al pointed out that the charge transfer between atoms in a molecule is overestimated when the polarization basis sets are used. Huzinaka et al, Jakalian et al, and Watanabe et al as well as our group , had experienced that the use of higher level of basis sets overestimates the overlap between their respective basis functions belonging to two atoms in a molecule. Bayly and coworkers pointed out that the 6–31G* basis set is used, the polarity of a molecule calculated by the partial charges is overestimated by 10–15% used .…”

ABEEM/MM OH– Models for OH–(H2O)n Clusters and Aqueous OH–: Structures, Charge Distributions, and Binding Energies

“…, and q O(OH − ) * are the valence-state energy, valence-state electronegativity, valence-state hardness, and initial charge 117 particle N, volume V, and temperature T) conditions at 298 and 278 K; temperature was kept constant by Berendsen algorithm. 130 Periodic boundary condition was applied in all three dimensions.…”

“…A QM calculation with a higher level of basis set can give more accurate predictions of energy and geometry, but it cannot give more suitable partial charges than the lower level of basis set for practical use. Because a diffuse basis function located on an atom may to some extent cover the regions of the other adjacent atoms, it will lead to a somewhat overestimating population of this atom in the Mulliken population analysis . Derouane and his co-workers suggested that STO-3G charges are more reliable.…”