Estimation of Transition-Metal Empirical Parameters for Molecular Mechanical Force Fields

Abstract

Force-field parameters of the first row transition metals together with a few additional common elements such as those from the second (Rh, Ru) and third (Hg, Pt) rows of elements in ligated forms were determined based on the density functional theory calculations. Bonding characteristics were determined by averaging metal-ligand force constants in optimal geometries from several chosen complexes of each metal in the most common oxidation numbers and structural arrangements. Parameters of Lennard-Jones potential were determined based on a supermolecular model. Our determined molecular mechanical parameters are compared with presently available parameters published by other groups. We performed two different kinds of testing in order to demonstrate the reliability of these parameters in the case of ligated metallo complexes. First, the nonbonding potential was constructed for an additional set of 19 larger systems containing common complexes with organic molecules. The second test compares the Pt-O and Pt-H radial distribution functions for cisplatin in a box of TIP3P water with lately published studies.

Metal Ion Modeling Using Classical Mechanics

“… 654 In another approach, the VDW parameters can be fit to QM-derived PES. For example, in the work of Šebesta et al, 775 they parametrized the LJ potentials of TMs based on QM calculated PESs between the TM complexes and small molecules. They found that there is a flat minimum on the surface of their “least-square” fits (see Figure 56 ).…”

“… Surface of the least-squares fits (∑Δ 2 ) of atomic LJ parameters ε and r 0 (which is σ in eq 33 ) for Pt(II) complexes interacting with the testing molecules. Reprinted with permission from ref ( 775 ). Copyright 2016 American Chemical Society.…”

Short oligopeptides with three cysteine residues as models of sulphur-rich Cu(i)- and Hg(ii)-binding sites in proteins

“…Charges were obtained from RESP calculations following DFT/B3LYP optimization. Calculated charges are: Hg: +0.968, S: À0.798, all C(bonded to 2 hydrogens): 0.173, all C(bonded to 3 hydrogens): 0.069. van der Waals parameters were taken from the work of Šebesta et al65 for Hg: e = 1.955 kcal mol À1 ; R = 2.8 Å.…”

The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study

“…Also, the enthalpy and entropy of the formation process were measured by the isothermal titration calorimetry . In our previous computational study, we explored the aforementioned process confirming the thermodynamic characteristics of the reaction suggesting the detailed mechanism . We recognized also the importance of proton transfer (PT) as a key step for both primary metal‐adduct formation as well as for the consequent completing of the cross‐link structure.…”

“…[12] In our previous computational study, we explored the aforementioned process confirming the thermodynamic characteristics of the reaction suggesting the detailed mechanism. [13,14] We recognized also the importance of proton transfer (PT) as a key step for both primary metal-adduct formation as well as for the consequent completing of the cross-link structure. Therefore, we decided to examine the PT process as a separate reaction under the influence of hydrated metal cations and compare the reaction characteristics.…”