We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures,...We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.展开更多
We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, a...We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide foldinz landscapes.展开更多
By introducing the concept of spring energy of permanent dipole and taking the conforma-tions of solvent molecules into account,the formulas of electrostatic solvation energy in equilibrium and nonequilibrium are deri...By introducing the concept of spring energy of permanent dipole and taking the conforma-tions of solvent molecules into account,the formulas of electrostatic solvation energy in equilibrium and nonequilibrium are derived from the explicit solvent scheme,with the spatial distribution of the discrete permanent charges and induced dipoles of the sol-vent molecules involved. The energy change of sol-ute due to the variation of wave function from the case of vacuum to that in solution is estimated by treating the solvent effect as external field in the it-eration cycles of the self-consistent field. The ex-pression for spectral shift is deduced and applied to the processes of light absorption and emission in solution. According to the new formulations,the av-eraged solvent electrostatic potential/molecular dy-namics program is modified and adopted to investi-gate the equilibrium solvation energy of water mole-cule and spectral shift of acrolein.展开更多
Modeling the kinetics of the preparing process is necessary to produce a product with the appropriate particle properties and minimum production cost.Owing to the lackness of crystal size distributor （CSD） informati...Modeling the kinetics of the preparing process is necessary to produce a product with the appropriate particle properties and minimum production cost.Owing to the lackness of crystal size distributor （CSD） information,however,solvent-mediated phase transformation encounters difficulty in modeling the kinetics as compared to solution crystallization.Consequently,a model was established by making the product CSD to move along by horizontal translation to obtain the CSDs of the stable phase in the process of transformation.Then the moment method was used to solve the popular balance equation,and the least square nonlinear regression method was applied to estimate the kinetics parameters.The model has been successfully used to simulate the transformation of CaSO4？2H2O to α-CaSO4？1/2H2O in an isothermal seeded batch crystallizer with different stirring speeds,and it is beneficial to producing high performance α-CaSO4？1/2H2O crystals which have the right particle characteristics.展开更多
The extraction equilibrium mathematic models for gadolinium,terbium and dysprosium in HCl-1.5 mol/L HEH(EHP)system covering a relatively wide range of lanthanide concentration and acidity,have been developed.There are...The extraction equilibrium mathematic models for gadolinium,terbium and dysprosium in HCl-1.5 mol/L HEH(EHP)system covering a relatively wide range of lanthanide concentration and acidity,have been developed.There are four independent variables and nine parameters.The average relative error is 4.56%.A computer program for the simulation of the counter current solvent extraetion process has also been written.Thus,the Gd,Tb and Dy concentrations in both aqueous and organic phase in eaeh stage as well as the aqueous acidity may be calculated.Product purities,distribution ratio and extraction factors may also be obtained thereby.The simulation results so obtained may serve as the referenee data for designing solvent ex- traction processes including those processes providing apart from the conventional outgoing organic stream, outgoing raffinate and an extra outgoing third exit stream either organic or aqueous.展开更多
目的通过一组单线性梯度洗脱实验获取线性溶剂强度模型的参数值,为色谱图的预测提供所必须的参数值。方法首先,在实验中固定流动相组成的起始和结束值,通过改变梯度洗脱的时间,从而改变梯度的斜率(B)。测定溶质在这些梯度条件下的保留时...目的通过一组单线性梯度洗脱实验获取线性溶剂强度模型的参数值,为色谱图的预测提供所必须的参数值。方法首先,在实验中固定流动相组成的起始和结束值,通过改变梯度洗脱的时间,从而改变梯度的斜率(B)。测定溶质在这些梯度条件下的保留时间,计算其流出色谱柱时所对应的流动相组成(φR)。然后,将描述φR与B之间关系的数学公式对实验数据进行非线性拟合,从而获取线性溶剂强度模型的参数值。拟合基于Levenberg-Marquardt算法,通过Excel中的Visual Basic for Applications(VBA)语言编程实现。结果计算机程序的可靠性通过实验进行验证。以12种芳环化合物为分离的对象,以C18柱为固定相,含1%乙酸的甲醇-水溶液为流动相,应用所编写的程序对单线性梯度洗脱实验数据进行处理,获取溶剂强度模型的参数值。然后,根据所得到的参数值预测多线性梯度洗脱条件下的色谱图,得到的理论色谱图与实验色谱图吻合。结论所建立的方法可快速准确地获取线性溶剂强度模型的参数值,具有良好的实用价值。展开更多
In order to clarify the extraction process with saponified extractant, the solvent extraction experiments of rare earth elements(REEs), lanthanum and cerium, by using partly saponified 2-ethylhexyl phosphoric acid mon...In order to clarify the extraction process with saponified extractant, the solvent extraction experiments of rare earth elements(REEs), lanthanum and cerium, by using partly saponified 2-ethylhexyl phosphoric acid mono-2-ethylhexyl ester(EHEHPA, HL) from hydrochloric acidic solutions have been performed. The concentration of initial aqueous rare earth ion was in a range of 0.0010–0.1000 mol·L^(-1); EHEHPA in a range of 0.2877–0.8631 mol·L^(-1) with saponification rate of 0.3(mole fraction), and the initial aqueous p H in a range of 1.00–4.00. Firstly, the extracted species were determined by the saturation extraction capacity method. Secondly, according to the equilibrium aqueous pH values, the extraction processes were divided into three different categories: extraction with saponified EHEHPA, extraction with un-saponified EHEHPA, and hydrolysis process. Finally, for the first two processes, in order to predict the distribution ratio, two semi-empirical calculation models were developed with.The calculation results are in good agreement well with the experimental data.展开更多
Aqueous phase layer around bubble and water droplet are two additional processes in solvent sublation. In the dynamic process of mass transfer, they are always neglected, but they are very important in the investigati...Aqueous phase layer around bubble and water droplet are two additional processes in solvent sublation. In the dynamic process of mass transfer, they are always neglected, but they are very important in the investigation of thermodynamic equilibrium. In this paper, the effect of water droplet in solvent sublation was discussed in detail, and the previous mathematical model of solvent subaltion was improved. Matlab 6.5 was used to simulate the process of water droplets, and the comparison between the previous hypothesis and the improvement in this paper showed the superiority, especially in the investigation of thermodynamic equilibrium. Moreover, the separation and concentration of the complex compound dithizone-Co（Ⅱ） from aqueous phase to n-octanol by solvent sublation also proved the improved mathematical model was reasonable.展开更多
Solvent effects on 2,4-dinitrotoluene（2,4-DNT） molecule in different solvents（toluene, ethanol, and water） were studied via DFT PCM method at B3LYP/6-311＋G（d,p） level. The influences of these solvents on the mo...Solvent effects on 2,4-dinitrotoluene（2,4-DNT） molecule in different solvents（toluene, ethanol, and water） were studied via DFT PCM method at B3LYP/6-311＋G（d,p） level. The influences of these solvents on the molecular structure, vibrational spectra, charge distribution, and dipole moment were studied as well. The results show that PCM computations are successful in describing the vibrational spectra of 2,4-DNT molecules in these solutions and the solvent effects on the low frequency vibrational spectra are weak.展开更多
基金Supported by the National Natural Science Foundation of China under Grant Nos 31200545,11274206 and 11574184
文摘We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.
基金supported by the National Natural Science Foundation of China(Grant No.21203178)the National Natural Science Foundation of China(Grant No.21373201)+2 种基金the National Natural Science Foundation of China(Grant No.21433014)the Science and Technological Ministry of China(Grant No.2011YQ09000505)“Strategic Priority Research Program”of the Chinese Academy of Sciences(Grant Nos.XDB10040304 and XDB100202002)
文摘We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide foldinz landscapes.
基金Acknowledgements This work was supported by the National Natural Science Foundation of China （Grant No. 20533070）, and the Specialized Research Fund for the Doctoral Program of Higher Education （Grant No. 20050610039）.
文摘By introducing the concept of spring energy of permanent dipole and taking the conforma-tions of solvent molecules into account,the formulas of electrostatic solvation energy in equilibrium and nonequilibrium are derived from the explicit solvent scheme,with the spatial distribution of the discrete permanent charges and induced dipoles of the sol-vent molecules involved. The energy change of sol-ute due to the variation of wave function from the case of vacuum to that in solution is estimated by treating the solvent effect as external field in the it-eration cycles of the self-consistent field. The ex-pression for spectral shift is deduced and applied to the processes of light absorption and emission in solution. According to the new formulations,the av-eraged solvent electrostatic potential/molecular dy-namics program is modified and adopted to investi-gate the equilibrium solvation energy of water mole-cule and spectral shift of acrolein.
文摘Modeling the kinetics of the preparing process is necessary to produce a product with the appropriate particle properties and minimum production cost.Owing to the lackness of crystal size distributor （CSD） information,however,solvent-mediated phase transformation encounters difficulty in modeling the kinetics as compared to solution crystallization.Consequently,a model was established by making the product CSD to move along by horizontal translation to obtain the CSDs of the stable phase in the process of transformation.Then the moment method was used to solve the popular balance equation,and the least square nonlinear regression method was applied to estimate the kinetics parameters.The model has been successfully used to simulate the transformation of CaSO4？2H2O to α-CaSO4？1/2H2O in an isothermal seeded batch crystallizer with different stirring speeds,and it is beneficial to producing high performance α-CaSO4？1/2H2O crystals which have the right particle characteristics.
文摘The extraction equilibrium mathematic models for gadolinium,terbium and dysprosium in HCl-1.5 mol/L HEH(EHP)system covering a relatively wide range of lanthanide concentration and acidity,have been developed.There are four independent variables and nine parameters.The average relative error is 4.56%.A computer program for the simulation of the counter current solvent extraetion process has also been written.Thus,the Gd,Tb and Dy concentrations in both aqueous and organic phase in eaeh stage as well as the aqueous acidity may be calculated.Product purities,distribution ratio and extraction factors may also be obtained thereby.The simulation results so obtained may serve as the referenee data for designing solvent ex- traction processes including those processes providing apart from the conventional outgoing organic stream, outgoing raffinate and an extra outgoing third exit stream either organic or aqueous.
文摘目的通过一组单线性梯度洗脱实验获取线性溶剂强度模型的参数值,为色谱图的预测提供所必须的参数值。方法首先,在实验中固定流动相组成的起始和结束值,通过改变梯度洗脱的时间,从而改变梯度的斜率(B)。测定溶质在这些梯度条件下的保留时间,计算其流出色谱柱时所对应的流动相组成(φR)。然后,将描述φR与B之间关系的数学公式对实验数据进行非线性拟合,从而获取线性溶剂强度模型的参数值。拟合基于Levenberg-Marquardt算法,通过Excel中的Visual Basic for Applications(VBA)语言编程实现。结果计算机程序的可靠性通过实验进行验证。以12种芳环化合物为分离的对象,以C18柱为固定相,含1%乙酸的甲醇-水溶液为流动相,应用所编写的程序对单线性梯度洗脱实验数据进行处理,获取溶剂强度模型的参数值。然后,根据所得到的参数值预测多线性梯度洗脱条件下的色谱图,得到的理论色谱图与实验色谱图吻合。结论所建立的方法可快速准确地获取线性溶剂强度模型的参数值,具有良好的实用价值。
基金Supported by the National Basic Research Program of China(2012CBA01203)the National Natural Science Foundation of China(9021003420221603)
文摘In order to clarify the extraction process with saponified extractant, the solvent extraction experiments of rare earth elements(REEs), lanthanum and cerium, by using partly saponified 2-ethylhexyl phosphoric acid mono-2-ethylhexyl ester(EHEHPA, HL) from hydrochloric acidic solutions have been performed. The concentration of initial aqueous rare earth ion was in a range of 0.0010–0.1000 mol·L^(-1); EHEHPA in a range of 0.2877–0.8631 mol·L^(-1) with saponification rate of 0.3(mole fraction), and the initial aqueous p H in a range of 1.00–4.00. Firstly, the extracted species were determined by the saturation extraction capacity method. Secondly, according to the equilibrium aqueous pH values, the extraction processes were divided into three different categories: extraction with saponified EHEHPA, extraction with un-saponified EHEHPA, and hydrolysis process. Finally, for the first two processes, in order to predict the distribution ratio, two semi-empirical calculation models were developed with.The calculation results are in good agreement well with the experimental data.
文摘Aqueous phase layer around bubble and water droplet are two additional processes in solvent sublation. In the dynamic process of mass transfer, they are always neglected, but they are very important in the investigation of thermodynamic equilibrium. In this paper, the effect of water droplet in solvent sublation was discussed in detail, and the previous mathematical model of solvent subaltion was improved. Matlab 6.5 was used to simulate the process of water droplets, and the comparison between the previous hypothesis and the improvement in this paper showed the superiority, especially in the investigation of thermodynamic equilibrium. Moreover, the separation and concentration of the complex compound dithizone-Co（Ⅱ） from aqueous phase to n-octanol by solvent sublation also proved the improved mathematical model was reasonable.
基金Supported by the National Natural Science Foundation of China(No.10534010)
文摘Solvent effects on 2,4-dinitrotoluene（2,4-DNT） molecule in different solvents（toluene, ethanol, and water） were studied via DFT PCM method at B3LYP/6-311＋G（d,p） level. The influences of these solvents on the molecular structure, vibrational spectra, charge distribution, and dipole moment were studied as well. The results show that PCM computations are successful in describing the vibrational spectra of 2,4-DNT molecules in these solutions and the solvent effects on the low frequency vibrational spectra are weak.
