A simple model, i.e. sodium di(2-ethylhexyl) sulfosuccinate (AOT) represented by one-head and two-tail beads tied together by a harmonic spring and water or isooctane by one bead, was put forward via Dissipative Parti...A simple model, i.e. sodium di(2-ethylhexyl) sulfosuccinate (AOT) represented by one-head and two-tail beads tied together by a harmonic spring and water or isooctane by one bead, was put forward via Dissipative Particles Dynamics (DPD) simulation method. Using the changes of interfacial tension between water and oil phase, a ternary phase diagram of AOT/water/isooctane system was drawn. From the simulation, one conclusion is shown that DPD simulation can be considered as an adjunct to experiments.展开更多
Density Functional Theory (DFT) method was used in this paper to study one-carbon transfer from 1,10-tetrahydroquinoxaline, an analogue of tetrahydrofolic acid, to methylamine. This reaction can be completed via two ...Density Functional Theory (DFT) method was used in this paper to study one-carbon transfer from 1,10-tetrahydroquinoxaline, an analogue of tetrahydrofolic acid, to methylamine. This reaction can be completed via two paths. From the computation result we can conclude that a general-acid catalysis exists in this reaction. By computation we find DFT has its limitation in describing a newly incorporated structure with a unit charge.展开更多
The selected-state probabilities of collinear ion-pair formation process Na+I2→Na++I2-on Aten-Laming-Los two-State potential energy surface have been calculated by using LCAC-SW method. The results show that reaction...The selected-state probabilities of collinear ion-pair formation process Na+I2→Na++I2-on Aten-Laming-Los two-State potential energy surface have been calculated by using LCAC-SW method. The results show that reaction probabilities are oscillatory with collision energy; the threshold energy of this ioniZation reaction is 2.8 ev, which is in modest agreement with experimental result.展开更多
To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our resul...To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.展开更多
The structure of eight-carbon monolayers on the H-terminated Si(III) surface was investigated by molecular simulation method. The best substitution percent 50% for octene or octyne-derived monolayer can be obtained u...The structure of eight-carbon monolayers on the H-terminated Si(III) surface was investigated by molecular simulation method. The best substitution percent 50% for octene or octyne-derived monolayer can be obtained using molecular mechanics calculation. And the densely packed, well-ordered monolayer on Si(III) surface can be shown through energy minimization in the suitable-size simulation cell.展开更多
文摘A simple model, i.e. sodium di(2-ethylhexyl) sulfosuccinate (AOT) represented by one-head and two-tail beads tied together by a harmonic spring and water or isooctane by one bead, was put forward via Dissipative Particles Dynamics (DPD) simulation method. Using the changes of interfacial tension between water and oil phase, a ternary phase diagram of AOT/water/isooctane system was drawn. From the simulation, one conclusion is shown that DPD simulation can be considered as an adjunct to experiments.
基金This work was supported by the grant from the National Natural Science Foundation of China (No. 29973021)
文摘Density Functional Theory (DFT) method was used in this paper to study one-carbon transfer from 1,10-tetrahydroquinoxaline, an analogue of tetrahydrofolic acid, to methylamine. This reaction can be completed via two paths. From the computation result we can conclude that a general-acid catalysis exists in this reaction. By computation we find DFT has its limitation in describing a newly incorporated structure with a unit charge.
文摘The selected-state probabilities of collinear ion-pair formation process Na+I2→Na++I2-on Aten-Laming-Los two-State potential energy surface have been calculated by using LCAC-SW method. The results show that reaction probabilities are oscillatory with collision energy; the threshold energy of this ioniZation reaction is 2.8 ev, which is in modest agreement with experimental result.
基金supports of the National Key Basic Research Priorities Program(No.2003CCA027)the National Natural Science Foundation of China(No.20573064).
文摘To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.
基金supported by the National Natural Science Foundation of China (No.20173032).
文摘The structure of eight-carbon monolayers on the H-terminated Si(III) surface was investigated by molecular simulation method. The best substitution percent 50% for octene or octyne-derived monolayer can be obtained using molecular mechanics calculation. And the densely packed, well-ordered monolayer on Si(III) surface can be shown through energy minimization in the suitable-size simulation cell.
