Dependence of Positive Binding Energies on Side ChainsA Theoretical Prediction on the Origin of Regular Ordering for the Amino Acid Residues in the Selectivity Filter

Abstract

The side-chain effects of metalated and protonated dipeptides, including GGH(+)M(+), GAH(+)M(+), AGH(+)M(+), AAH(+)M(+), GWH(+)M(+), GSH(+)M(+), GTH(+)M(+), GFH(+)M(+), GYH(+)M(+), and GVH(+)M(+) (G = glycine, A = alanine, W = tryptophan, S = serine, T = threonine, F = phenylalanine, and V = valine; M = Li, Na, and K), are theoretically explored in this paper on their positive binding energies (PBEs), which are derived from interactions of M+ with the carboxyl oxygen(s). The B3LYP/6-311++G(**)// B3LYP/6-31G(*) calculations suggest that the PBEs of dipeptides with side chain(s) are much smaller than those with no side chain (GGH(+)M(+)). Generally, larger side chains and smaller M(+) radii would lead to fewer PBEs for the M(+) involved systems. On the basis of the direct dependence of PBE on the electrostatic repulsion between two kinds of cations (H(+) and M(+)) in these dipeptide models, it could be reasonably expected that the side-chain effect on the electrostatic repulsion and consequently on the PBEs could offer one good insight, on a chemical-physical basis, into the origin of regular ordering of the amino acids when they form a filter in the K(+) channel protein (MacKinnon, et al. Science 1998, 280, 106).

CO2 capture and gas separation on boron carbon nanotubes

“…Based on the optimized structures at DFT-D level, the author calculate the wavefunctions at the B3LYP/6-311+G(d) level of theory, then AIM theory which has been used to successfully determine intermolecular interactions of different systems is used in these systems. [30][31][32][33][34][35][36][37][38][39] In the AIM analyses, The transition state between chemisorption and physisorption of CO 2 have been investigated using the complete LST (linear synchronous transit)/QST (quadratic synchronous transit) method 41 implemented in DMOL3 code. The electron distribution and transfer mechanism are determined using the Mulliken method.…”