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

Abstract

To promote accuracy of the atom-bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc-Zn, Y-Cd, and Lu-Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO-3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy.

Metal Ion Modeling Using Classical Mechanics

“…Further extending their work on TMs, Yang et al fit the reference charge, electronegativity, and chemical hardness parameters for 3d, 4d, and 5d TMs in the ABEEMσπ force field. 852 More than 700 structures were contained in the training set. The target values were the Mulliken charges obtained at the HF/STO-3G (for 3d and 4d TM complexes) or HF/CEP-4G (for 5d TM complexes) level of theory, and the dipole moments calculated using larger basis sets.…”

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% .…”

“…The detailed description of the QM/MM(ABEEM) method and free energy perturbation theory can be found in our previous articles, and some ABEEMσπ parameters of ruthenium complexes were determined by our previous work, while others were calibrated and determined through a regression and least‐squares optimization procedure. The details were described in our previous articles . All ABEEMσπ parameters are listed in Supporting Information Table S1.…”

QM/MM(ABEEM) Study on the Ligand Substitution Processes of Ruthenium(III) Complex NAMI‐A

“…They are obtained by fitting the QM Mulliken charge distribution through a regression and least-squares optimization procedure. [39,40] When H 2 O molecule bonds with Ru atom, the O atom is named 108144 and the H atom is named 101144 in order to distinguish from other water molecules. [31,32,35].…”