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Int. J. Mol. Sci. 2011, 12, 1389-1409; doi:10.3390/ijm OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 /journal/ijms Article Comparison of Free Energy Surfaces Calculations from Ab Initio Molecular Dynamic Simulations at the Example of Two Transition Metal Catalyzed Reactions ¨ ˜ Marc Brussel , Philipp J. di Dio , Kilian Muniz and Barbara Kirchner ´ Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, University Leipzig, Linnestr. 2, D-04103 Leipzig, Germany; E-Mails: gurkete@gmx.de (M.B.); naphthalen@ (P.J.D.) ¨ Institute of Chemical Research of Catalonia (ICIQ), Av. Paısos Catalans, 16, E-43007 Tarragona, Spain; E-Mail: kmuniz@iciq.es ´ Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluıs Companys 23, E-08010 Barcelona, Spain Author to whom correspondence should be addressed; E-Mail: bkirchner@uni-leipzig.de; Tel.: +49(0)341-9736401. Received: 1 December 2010; in revised form: 4 February 2011 / Accepted: 22 February 2011 / Published: 23 February 2011 Abstract: We carried out ab initio molecular dynamic simulations in order to determine the free energy surfaces of two selected reactions including solvents, namely a rearrangement