Effective fragment method

Day, P.N., Jensen J.H., Gordon M.S., Webb S.P., Stevens W. J., Krauss M., Garmer D., Bash H. and Cohen D., An effective fragment method for modeling solvent effects in quantum mechanical calculations. J. Chem.Phys. (1996) 105 1968-1986. 

Webb SP, Gordon MS. Solvation of the Menshutkin reaction a rigorous test of the effective fragment method. J Phys Chem A 1999 103 1265-1273. 

Webb, S. R, Gordon, M. S. (1999). Solvation ofthe Menshutkin Reaction A Rigorous Test ofthe Effective Fragment Method,/ Phys. Chem. A, 103, 1265-1273. 

D. Cohen, /. Chem. Phys., 105, 1968 (1996). An Effective Fragment Method for Modeling Solvent Effects in Quantum Mechanical Calculations. 

Day PN et al (1996) An effective fragment method for modeling solvoit effects in quantum... 

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... 

This chapter reviewed some of our group s contributions to the development and application of QM/MM methods specifically as applied to enzymatic reactions, including the use of sequential MD/QM methods, the use of effective fragment potentials for reaction mechanisms, the development of the new QM/MM interface in Amber, as well as the implementation and optimization of the SCC-DFTB method in the Amber program. This last implementation allows the application of advanced MD and sampling techniques available in Amber to QM/MM problems, as exemplified by the potential and free energy surface surfaces for the reaction catalyzed by the Tripanosoma cruzi enzyme /ram-sialidasc shown here. 

Keywords Coarse-graining, Force-matching, Effective fragment potential method, Molecular... 

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... 

The first part of this book is dedicated to a discussion of mass spectrometry (MS) instrumentation. We start with a list of basic definitions and explanations (Chapter 1). Chapter 2 is devoted to the mass spectrometer and its building blocks. In this chapter we describe in relative detail the most common ion sources, mass analyzers, and detectors. Some of the techniques are not extensively used today, but they are often cited in the MS literature, and are important contributions to the history of MS instrumentation. In Chapter 3 we describe both different fragmentation methods and several typical tandem MS analyzer configurations. Chapter 4 is somewhat of an outsider. Separation methods is certainly too vast a topic to do full justice in less than twenty pages. However, some separation methods are used in such close alliance with MS that the two techniques are always referred to as one combined analytical tool, for example, GC-MS and LC-MS. In effect, it is almost impossible to study the MS literature without coming across at least one separation method. Our main goal with Chapter 4 is, therefore, to facilitate an introduction to the MS literature for the reader by providing a short summary of the basic principles of some of the most common separation methods that have been used in conjunction with mass spectrometry. 

Favretto et al. [33] proposed a procedure for the analysis of BUP and nor BUP based on RP-HPLC conpled with ion trap MS nsing an ESI ion source. The use of the ion trap allowed to obtain intense prodnct ions nnder MS-MS conditions, thus achieving better selectivity of detection with respect to LC-ESI-MS-MS methods with triple qnadrupoles where effective fragmentation in the collision cell was fonnd difficnlt to obtain. However, this method does not inclnde phase II metabolites of BUP, which can be only indirectly determined after enzymatic hydrolysis. 

Varnek, A.A. Wipff, G. Solov ev, V.P. Solotnov, A.F. Assessment of the macrocyclic effect for the complexation of crown-ethers with alkali cations using the substructural molecular fragments method. J. Chem. Inf. Comput. Sci. 2002, 42 (4), 812-829. 

Although a combinatorial fragment-based approach provides some great advantages, implementation of effective screening methods has presented a new set of challenges. One... 

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