A set of force field parameters for the radical cation of diazabicycle alkane are derived by "substracting" nonbonded molecular mechanics energies (MM2 method) from corresponding molecular orbital energies (...A set of force field parameters for the radical cation of diazabicycle alkane are derived by "substracting" nonbonded molecular mechanics energies (MM2 method) from corresponding molecular orbital energies (MNDO method) using a model compound containing the chemical structure to be parameterized. A general discussion of the N, N’ two-center three electrones bond in radical cations. The results are satisfactory.展开更多
Ionic liquids (ILs) have been widely used in separation, catalysis, electrochemistry, etc., and one of the most outstanding characteristics is that ILs can be tailored and tuned for specific tasks. In order to design ...Ionic liquids (ILs) have been widely used in separation, catalysis, electrochemistry, etc., and one of the most outstanding characteristics is that ILs can be tailored and tuned for specific tasks. In order to design and make better use of ionic liquids, the structures and properties relationship is indispensable. Both molecular dynamics and Monte Carlo simulations have been proved useful to understand the behavior of molecules at the microscale and the properties of the system. However, the quality of such simulations depends on force field parameters describing the interactions between atoms. All-atom (AA) or the united-atom (UA) force fields will be chosen because of the demand for more exact results or the lower computational cost, respectively. In order to make a systematic comparison of the two force fields, molecular simulations for four kinds of acyclic guanidinium-based ionic liquids (cations: (R2N)2C=N+<, anion: nitric or perchloric acid) were performed based on the AA and the UA force fields in this work. AA force field parameters were derived from our previous work (Fluid Phase Equilib., 2008, 272: 1-7), and the UA parameters were proposed in this work. Molecular dynamics simulation results for the AA and UA force fields were compared. Simulation densities are very similar to each other. Center of mass radial distribution functions (RDFs), site to site RDFs and spatial distribution functions (SDFs) were also investigated to depict the microscopic structures of the ILs.展开更多
In this work,we developed the CHARMM all-atom force field parameters for the nonstandard biological residue chalcone,followed by the standard protocol for the CHARMM27 force field development.Target data were generate...In this work,we developed the CHARMM all-atom force field parameters for the nonstandard biological residue chalcone,followed by the standard protocol for the CHARMM27 force field development.Target data were generated via ab initio calculations at the MP2/6-31G* and HF/6-31G* levels.The reference data included interaction energies between water and the model compound F(a fragment of chalcone).Bond,angle,and torsion parameters were derived from the ab initio calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters of standard residues.The optimized CHARMM parameters perform well in reproducing the target data.We expect that the extension of the CHARMM27 force field parameters for chalcone will facilitate the molecular simulation studies of the reaction mechanism of intramolecular cyclization of chalcone catalyzed by chalcone isomerase.展开更多
文摘A set of force field parameters for the radical cation of diazabicycle alkane are derived by "substracting" nonbonded molecular mechanics energies (MM2 method) from corresponding molecular orbital energies (MNDO method) using a model compound containing the chemical structure to be parameterized. A general discussion of the N, N’ two-center three electrones bond in radical cations. The results are satisfactory.
基金supported by the General Program Youth of National Natural Science Foundation of China (20903098, 21073194, 21106146)State Key Laboratory of Multiphase Complex Systems (MPCS-2011-D-05)
文摘Ionic liquids (ILs) have been widely used in separation, catalysis, electrochemistry, etc., and one of the most outstanding characteristics is that ILs can be tailored and tuned for specific tasks. In order to design and make better use of ionic liquids, the structures and properties relationship is indispensable. Both molecular dynamics and Monte Carlo simulations have been proved useful to understand the behavior of molecules at the microscale and the properties of the system. However, the quality of such simulations depends on force field parameters describing the interactions between atoms. All-atom (AA) or the united-atom (UA) force fields will be chosen because of the demand for more exact results or the lower computational cost, respectively. In order to make a systematic comparison of the two force fields, molecular simulations for four kinds of acyclic guanidinium-based ionic liquids (cations: (R2N)2C=N+<, anion: nitric or perchloric acid) were performed based on the AA and the UA force fields in this work. AA force field parameters were derived from our previous work (Fluid Phase Equilib., 2008, 272: 1-7), and the UA parameters were proposed in this work. Molecular dynamics simulation results for the AA and UA force fields were compared. Simulation densities are very similar to each other. Center of mass radial distribution functions (RDFs), site to site RDFs and spatial distribution functions (SDFs) were also investigated to depict the microscopic structures of the ILs.
基金National Institute of Biological Science, Beijing 102206,Chinasupported by the Major State Basic Research Development Programs of China(2011CBA00701)+3 种基金the National Natural Science Foundation of China(20973077,20973049)the Doctoral Fund of Ministry of Education of China(20112303110005)the Foundation for the Department of Education of Heilongjiang Province (1152G010,11551077)the Science Foundation for Leading Experts in Academe of Harbin of China(2011RFJGS026)
文摘In this work,we developed the CHARMM all-atom force field parameters for the nonstandard biological residue chalcone,followed by the standard protocol for the CHARMM27 force field development.Target data were generated via ab initio calculations at the MP2/6-31G* and HF/6-31G* levels.The reference data included interaction energies between water and the model compound F(a fragment of chalcone).Bond,angle,and torsion parameters were derived from the ab initio calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters of standard residues.The optimized CHARMM parameters perform well in reproducing the target data.We expect that the extension of the CHARMM27 force field parameters for chalcone will facilitate the molecular simulation studies of the reaction mechanism of intramolecular cyclization of chalcone catalyzed by chalcone isomerase.
