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Modeling transition metals in supramolecular assemblies, in general, is extremely challenging due to polarization and charge transfer. In this work, we demonstrate that the inherent shortcomings of additive force fields in modeling Cu+–ether-O and Cu+–olefin-C interactions are rooted in the Lorentz–Berthelot rules. A general method for investigating transition-metal-containing molecular assays using classical force fields is, therefore, proposed. In this strategy, QM/MM calculations have been performed to determine the potential of mean force (PMF) describing the interaction of a cation and a specific functional group. van der Waals parameters for the corresponding pairs of particles have then been optimized using the NBFIX feature of the CHARMM force field to fit the QM/MM PMF. This method has been applied to decipher the mechanism underlying the “dialing” of a molecular machine controlled by Li+ and Cu+ cations, indicating that the process is controlled by the competition between cation–ether-O and cation–olefin-C interactions. Journal of Chemical Theory and Computation, 2019.

Recent publications


Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01
Dora Pinto; Craig Fenwick; Christophe Caillat; Chiara Silacci; Serafima Guseva; Francois Dehez; Christophe Chipot; Sonia Barbieri; Andrea Minola; David Jarrossay; Georgia D. Tomaras; Xiaoying Shen; Agostino Riva; Maciej Tarkowski; Olivier Schwartz; Timothee Bruel; Jeremy Dufloo; Michael S. Seaman; David C. Montefiori; Antonio Lanzavecchia; Davide Corti; Giuseppe Pantaleo; Winfried Weissenhorn;
Microbe (2019) 26 (5): 623-637.e8
Enzyme-mimetic self-catalyzed polymerization of polypeptide helices
Ziyuan Song; Hailin Fu; Ryan Baumgartner; Lingyang Zhu; Kuo-Chih Shih; Yingchun Xia; Xuetao Zheng; Lichen Yin; Christophe Chipot; Yao Lin; Jianjun Cheng;
Nature Communications (2019) 121 (11): 3676-
Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism
Abhishek Singharoy; Christopher Maffeo; Karelia H. Delgado-Magnero; David J.K. Swainsbury; Melih Sener; Ulrich Kleinekathofer; John W. Vant; Jonathan Nguyen; Andrew Hitchcock; Barry Isralewitz; Ivan Teo; Danielle E. Chandler; John E. Stone; James C. Phillips; Taras V. Pogorelov; M. Ilaria Mallus; Christophe Chipot; Zaida Luthey-Schulten; D. Peter Tieleman; C. Neil Hunter; Emad Tajkhorshid; Aleksei Aksimentiev; Klaus Schulten;
Cell (2019) 179 (5): 1098-1111.e23

News

- Renewal of the Laboratoire International Associé CNRS-University of Illinois at Urbana-Champaign on November 2016
- An update of ParseFEP is available in the latest version of VMD.
- 新的分子动力学讲义 (Dissemination).
 

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Laboratoire International Associé
CNRS-UIUC
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