The Effective Fragment Potential

In this contribution, we describe work from our group in the development and application of alternatives that allow the explicit inclusion of environment effects while treating the most relevant part of the system with full quantum mechanics. The first methodology, dubbed MD/QM, was used for the study of the electronic spectrum of prephenate dianion in solution [18] and later coupled to the Effective Fragment Potential (EFP) [19] to the study of the Claisen rearrangement reaction from chorismate to prephenate catalyzed by the chorismate mutase (CM) enzyme [20]. 

Another method that has been applied by our group to the study of enzymatic reactions is the Effective Fragment Potential (EFP) method [19]. The EFP method (developed at Mark Gordon s group at Iowa State University) allows the explicit inclusion of environment effects in quantum chemical calculations. The solvent, which may consist of discrete solvent molecules, protein fragments or other material, is treated explicitly using a model potential that incorporates electrostatics, polarization, and exchange repulsion effects. The solute, which can include some... 

COARSE-GRAINED INTERMOLECULAR POTENTIALS DERIVED FROM THE EFFECTIVE FRAGMENT POTENTIAL APPLICATION TO WATER, BENZENE, AND CARBON TETRACHLORIDE... 

Chorismate mutase catalyzes the Claisen rearrangement of chorismate to prephenate at a rate 106 times greater than that in solution (Fig. 5.5). This enzyme reaction has attracted the attention of computational (bio)chemists, because it is a rare example of an enzyme-catalyzed pericyclic reaction. Several research groups have studied the mechanism of this enzyme by use of QM/MM methods [76-78], It has also been studied with the effective fragment potential (EFP) method [79, 80]. In this method the chemically active part of an enzyme is treated by use of the ab initio QM method and the rest of the system (protein environment) by effective fragment potentials. These potentials account... 

M.S. Gordon, M.A. Freitag, P. Bandyopadhyay, J.H. Jensen, V. Kairys, W.J. Stevens, The effective fragment potential method A QM-based MM approach to modeling environmental effects in chemistry, J. Phys. Chem. A105 (2001) 293. 

The effective fragment potential (EFP) is a more recent scheme that goes beyond interaction modeling. It incorporates electrical response and is targeted... 

Ohta K, Yoshioka Y, Morokuma K, Kitaura K (1983) The effective fragment potential method an approximate ab initio MO method for large molecules. Chem Phys Lett 101 12-17... 

Merrill GN, Gordon MS. Study of small water clusters using the effective fragment potential model. J Phys Chem A 1998 102 2650-2657. 

Jensen JH, Gordon MS. An approximate formula for the intermolecular Pauli repulsion between closed shell molecules II. Application to the effective fragment potential method. J Chem Phys 1998 108 4772-4782. 

The Effective Fragment Potential A General Method for Predicting Intermolecular Interactions... 

R. Balawender, B. Safi, P. Geerlings, Solvent Effects on the Global and Atomic DET-Based Reactivity Descriptors Using the Effective fragment Potential Model. Solvation of Ammonia,/. Phys. Chem. A, 2001, 105, 6703-6710. 

Flick, J. C., Kosenkov, D., Hohenstein, E. G Sherrill, C. D., and Slipchenko, L. V. (2012]. Accurate prediction of noncovalent interaction energies with the effective fragment potential method Comparison of energy components to symmetry-adapted perturbation theory for the S22 test set,/. Chem. Theory Comput 8, pp. 2835-2843, doi 10.1021/ct200673a. 

Slipchenko, L. V, and Gordon, M. S. Electrostatic energy in the effective fragment potential method Theory and application to benzene dimer. /. Comput Chem., 28, 276-291 (2007). 

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