Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA‐LF

Abstract

To account for the distortion of the coordination sphere that takes place in complexes containing open-shell metal cations such as Cu(II), we implemented, in sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics, an additional contribution to take into account the ligand field splitting of the metal d orbitals. This term, based on the angular overlap model, has been parameterized for Cu(II) coordinated to oxygen and nitrogen ligands. The comparison of the results obtained from density functional theory computations on the one hand and SIBFA or SIBFA-LF on the other shows that SIBFA-LF gives geometric arrangements similar to those obtained from quantum mechanical computations. Moreover, the geometric improvement takes place without downgrading the energetic agreement obtained from SIBFA. The systems considered are Cu(II) interacting with six water molecules, four ammonia or four imidazoles, and four water plus two formate anions.

Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)2] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N3)2(OH)2(pyridine)2]

“…[31][32][33] Polarizable 34 and solid state 35 versions of LFMM have been implemented and we have estimated that LFMM is up to four orders of magnitude faster than the density functional theory methods which often form the QM part of QM/M simulations.…”

A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials

“…Overcoming this problem requires extending MM force fields with an explicit description of polarization, an open problem that has been the subject of intense research over the past decade. [67][68][69][70] Significant effort has been focused on the development of both polarizable protein force fields [6][7][8][9][10][11][12][13][14][15][67][68][69][70] and polariz-able models for small molecules. [15][16][17][18][19][20][21][22][23][24][25] While these methods are expected to become routine practice, no polarizable force field has so far been widely implemented for protein modeling.…”

Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics

“…As reviewed above, SIBFA has been adapted to a diversity of metal cations. These encompass the following: alkali Li(I)-Cs(I) [45], alkaline-earth Mg (II) and Ca(II) [47b], transition metals Cu(I) [62], Cu(II) [44], Zn(II) and Cd(II) [47b, 48, 61], heavy metals Pb(II) [55] and Hg(II) [70], and lanthanides and actinides [122]. Table I.…”

“…There are also other energy-decomposition analyses, such as the Constrained Space Orbital Variation (CSOV) [42] and the Symmetry-Adapted Perturbation Theory (SAPT) [43], which can both be done at the correlated level. We have resorted to the former upon dealing with open-shell cations [44] and for correlated computations [45] and are presently resorting to the latter in analyses of the interactions involving nucleic acid bases [Gresh et al, submitted].…”