Polarizable molecular mechanics

SIBFA [2, 13] is a polarizable molecular mechanics procedure, formulated as a sum of five energy contributions, each of which is destinated to reproduce its counterpart from reference EDA ab initio computations. The intermolecular interaction energy is formulated as ... 

As we have seen, Anisotropic Polarizable Molecular Mechanics (APMM) procedures such as SIBFA or GEM are more complex than usual classical approaches. 

Gresh N, Cisneros GA, Darden TA, Piquemal J-P (2007) Anisotropic, polarizable molecular mechanics studies of inter-, intra-molecular interactions, and ligand-macromolecule complexes. A bottom-up strategy. J Chem Theory Comput 3 1960... 

Piquemal J-P, Chevreau H, Gresh N (2007) Towards a separate reproduction of the contributions to the Hartree-Fock and DFT intermolecular interaction energies by polarizable molecular mechanics with the SIBFA potential.J Chem Theory Comput 3 824... 

Gresh N, Piquemal J-P, Krauss M (2005) Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contribution of the intermolecular interaction energy. Comparisons with parallel ab initio computations. J Comput Chem 26 1113... 

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... 

Kaminski GA, HA Stern, BJ Berne, RA Friesner (2004) Development of an accurate and robust polarizable molecular mechanics force field from ab initio quantum chemistry. J. Phys. Chem. A 108 (4) 621-627... 

Intramolecular interaction energies in model alanine and glycine tetrapep-tides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study113... 

Many-Body Effects in Systems of Peptide Hydrogen- Bonded Networks and Their Contributions to Ligand Binding A Comparison of DFT and Polarizable Molecular Mechanics. 

Gresh, N., Cisneros, G. A., Darden, T. A., and Piquemal, J.-P. Anisotropic, Polarizable Molecular mechanics studies of inter- and intramolecular interactions and ligand-macromolecule complexes. A bottom-up strategy. /. Chem. Theory Comput, 3, 1960-1986, doi 10.1021/ct700134r (2007). 

Piquemal, J.-R, Chevreau, H., Gresh, N. (2007). Toward a Separate Reproduction of the Contributions to the Hartree—Fock and DFT In-termolecular Interaction Energies by Polarizable Molecular Mechanics with the Sibfa Potential,/ Chem. Theory Comp., 3,824-837. 

Gresh N, Audiffren N, Piquemal JP, de Ruyck J, Ledecq M, Wouters J (2010) Analysis of the interactions taking place in the recognition site of a bimetallic Mg(II)-Zn(II) enzyme, isopentenyl diphosphate isomerase. A parallel quantum-chemical and polarizable molecular mechanics study. J Phys Chem B 114 4884... 

Many-body effects in systems of peptide hydrogen-bonded networks and their contributions to ligand binding A comparison of the performances of DFT and polarizable molecular mechanics ... 

Complexes of pentahydrated Zrf with guanine, adenine, and the guanine-cytosine and adenine-thymine base pairs. Structures and energies characterized by polarizable molecular mechanics and ab initio calculations "... 

Gresh N (2006) Development, validation, and applicatimis of anisotropic polarizable molecular mechanics to study ligand and drag-receptOT interactimis. Curr Pharm Design 12 2121... 

Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from Ab Initio Quantum Chemistry. 

A comprehensive study dealing with a coordination of hydrated cations Zn(ll) and Mg(ll) to guanosine 5 monophosphate was performed by Gresh (Gresh et al. 2003) in order to obtain parameters for polarizable molecular mechanics for metal - DNA and RNA simulations. 

Gresh, N., Sponer, J. E., Spakova, N., Leszczynski J., 8c Sponer, J.(2003). Theoretical study of binding of hydrated cations Zn(II) and Mg(II) to guano-sine 5 monophosphate. Towards polarizable molecular mechanics for DNA and RNA. The Journal of Physical Chemistry B, 107, 8669. 

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

Abstract We review two essential features of the intermolecular interaction energies (AE) computed in the context of quantum chemistry (QC) non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate AE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last... 

AMOEBA Atomic multipoles optimized energetics for biological applications APMM Anisotropic polarizable molecular mechanics... 

J. P. Piquemal, B. Williams-Hubbard, N.Eey, R.J. Deeth, N. Gresh, and C. Giessner-Prettre, J. Comput. Chem., 24(16), 1963-1970 (2003). Inclusion of the Ligand Field Contribution in a Polarizable Molecular Mechanics SIBFA-LF. 

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