Ligand field molecular mechanics

Deeth RJ (2001) The ligand field molecular mechanics model and the stereoelectronic effects of d and s electrons. Coord Chem Rev 212 11... 

Although the properties which can be computed are limited, LFT has provided for over half a century a reasonably useful, semi-quantitative picture of metal-ligand bonding in Werner-type coordination complexes (3,25-27). In the present context, the advantage of LFT is its computational efficiency. Therefore, we added LFT to MM to give the ligand field molecular mechanics (LFMM) method (28). 

Computer programs for empirical force-field calculations that use other concepts have been tested, and some of these will be discussed elsewhere in this book. Among these approaches are one based on a pure central force-field model, used for simple organic compounds [208], an equipotential surface force-field model, used for carbonyl cluster complexes [99,103], and a program that includes ligand field terms, developed for transition metal complexes in the LFMM model (ligand field molecular mechanics) [21, 105, 108]. 

The angular overlap approach has also been used as a component in a more mathematically sophisticated approach to metal-ligand interactions, the ligand field molecular mechanics (LFMM) method, which has applications to a variety of concepts discussed in this chapter. ... 

Ligand Field Molecular Mechanics (LFMM). Thus, LFMM is based on a combination of a conventional force field with terms explicitly capturing electronic effects, which takes the following functional form ... 

Deeth RJ, Fey N, Williams-Hubbard B (2005) DommiMOE an implemcmtatimi of ligand field molecular mechanics in the molecular operating environment. J Comput Chem 26 123... 

The second solution is used in the MOMEC program and the ligand field molecular mechanics (LFMM) method as implemented in DOMMINO. In both cases, instead of using an L-M-L angle bend term, explicit ligand-ligand 1,3-nonbonded interactions are permitted which, in the spirit of VSEPR theory or points on a sphere (POS), facilitate the treatment of any coordination number. 

One way that molecular mechanics methods have been adapted to transition metal applications is by including one orbital-based term in the force field to describe the metal center. These terms are typically based on semiempirical methods or even some variation of ligand field theory. 

More detailed aspects of protein function can be obtained also by force-field based approaches. Whereas protein function requires protein dynamics, no experimental technique can observe it directly on an atomic scale, and motions have to be simulated by molecular dynamics (MD) simulations. Also free energy differences (e.g. between binding energies of different protein ligands) can be characterised by MD simulations. Molecular mechanics or molecular dynamics based approaches are also necessary for homology modelling and for structure refinement in X-ray crystallography and NMR structure determination. 

Piquemal J-P, Williams-Hubbard B, Fey N, Deeth RJ, Gresh N, Giessner-Prettre C (2003) Inclusion of the ligand field contribution in a polarizable molecular mechanics SIBFA LF. J Comput Chem... 

The background theory that underlies the FEP method as well as the molecular mechanics force fields that relate molecular structure to energy are reviewed in section one of the book. Section two describes the use of free energy calculations for determining molecular properties of ligands, including solvation, as calculated using both implicit and explicit water... 

In an attempt to aid interpretation of the IR spectrum of MbCO we decided to model the full protein by use of a hybrid quantum mechanics/molecular mechanics approach (QM/MM), to evaluate changes in the CO stretching frequency for different protein conformations. The QM/MM method used [44] combines a first-principles description of the active center with a force-field treatment (using the CHARMM force field) of the rest of the protein. The QM-MM boundary is modeled by use of link atoms (four in the heme vinyl and propionate substituents and one on the His64 residue). Our QM region will include the CO ligand, the porphyrin, and the axial imidazole (Fig. 3.13). The vinyl and propionate porphyrin substituents were not included, because we had previously found they did not affect the properties of the Fe-ligand bonds (Section 3.3.1). It was, on the other hand, crucial to include the imidazole of the proximal His (directly bonded to the... 

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