Xiangyu Jia

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*Institute for Advanced Interdisciplinary Research East China Normal University, Shanghai 200062, P. R. China Center for Laser and Computational Biophysics State Key Laboratory of Precision Spectroscopy and Department of Physics Institute of Theoretical and Computational Science East China Normal University, Shanghai 200062, P. R. China NYU-ECNU Center for(More)
Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a 1000-fold reduction in biotin binding affinity. In this work, we carry out molecular dynamics simulations and apply an end-state free energy method to calculate the binding free energies of biotin(More)
In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the(More)
An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y.(More)
The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin(More)
The Fenna-Matthews-Olson (FMO) light-harvesting complex is now one of the primary model systems for the study of excitation energy transfer (EET). However, the mechanism of the EET in this system is still controversial. In this work, molecular dynamics simulations and the electrostatic-embedding quantum-mechanics/molecular-mechanics single-point(More)
A series of iminopyridine ligated Co(II) (1a–7a) and Ni(II) (1b–7b) complexes were synthesized. The structures of complexes 3a, 4a, 5a, 7a, 5b, and 6b were determined by X-ray crystallographic analyses. Complex 3a formed a chloro-bridged dimer, whereas 4a, 5a, and 7a, having a substituent (4a, 5a: CH3; 7a: Br) at the 6-position of pyridine, producing the(More)
The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast,(More)
The alcohol-based cosolvent 2,2,2-trifluoroethanol (TFE) has been used widely in protein science and engineering. Many experimental and computational studies of its impact on protein structure have been carried out, but consensus on the mechanism has not been reached. In the past decade, several molecular mechanical models have been proposed to model the(More)
A new family of bis(N-arylcarboximidoylchloride)pyridine cobalt(II) complexes with the general formula [2,6-(ArN=CCl)2C5H3N]CoCl2 (Ar = 2,4,6-Me3C6H2, 4a; 2,6-(i)Pr2C6H3, 4b; 2,6-Me2C6H3, 4c; C6H5, 4d; 4-Cl-2,6-Me2C6H2, 4e) and a typical Brookhart-Gibson-type reference complex [2,6-(2,4,6-Me3C6H2N=CMe)2C5H3N]CoCl2 (5a) were synthesized and characterized.(More)
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