All-atom molecular dynamics （MD） simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen...All-atom molecular dynamics （MD） simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.展开更多
All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution. Intramolecular distances, root-mean-square deviation, r...All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution. Intramolecular distances, root-mean-square deviation, radius of gyration, and solvent-accessible surface are used to characterize the properties of the carnosine. Carnosine can shift between extended and folded states, but exists mostly in extended state in water. Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance （NMR） experiment. The NMR experimental results are consistent with the molecular dynamics simulations.展开更多
An all-atom dimethyl sulfoxide （DMSO） and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. An...An all-atom dimethyl sulfoxide （DMSO） and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bonds and weak C-H- ~ ~ O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The stable aggregates of （DMSO）m＇S=O…… HW-OW-（H20）n might play a key role in this region. Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.展开更多
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
The interactions and structures of the urea-water system are studied by an all-atom molecular dynamics （MD） simulation. The hydrogen-bonding network and the radial distribution functions are adopted in MD simulation...The interactions and structures of the urea-water system are studied by an all-atom molecular dynamics （MD） simulation. The hydrogen-bonding network and the radial distribution functions are adopted in MD simulations. The structures of urea-water mixtures can be classified into different regions from the analysis of the hydrogen-bonding network. The urea molecule shows the certain tendency to the self-aggregate with the mole fraction of urea increasing. Moreover, the results of the MD simulations are also compare with the chemical shifts and viscosities of the urea aqueous solutions, and the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data such as chemical shifts of the hydrogen atom and viscosity.展开更多
N,N-dimethylacetamide （DMA） has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water syste...N,N-dimethylacetamide （DMA） has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions （RDFs） and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.展开更多
All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied i...All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.展开更多
The hybrid atomistic structure-based model has been validated to be effective in investigation of G-quadruplex folding.In this study,we performed large-scale conventional all-atom simulations to complement the folding...The hybrid atomistic structure-based model has been validated to be effective in investigation of G-quadruplex folding.In this study,we performed large-scale conventional all-atom simulations to complement the folding mechanism of human telomeric sequence Htel24 revealed by a multi-basin hybrid atomistic structure-based model.Firstly,the real time-scale of folding rate,which cannot be obtained from the structure-based simulations,was estimated directly by constructing a Markov state model.The results show that Htel24 may fold as fast as on the order of milliseconds when only considering the competition between the hybrid-1 and hybrid-2 G-quadruplex conformations.Secondly,in comparison with the results of structure-based simulations,more metastable states were identified to participate in the formation of hybrid-1 and hybrid-2 conformations.These findings suggest that coupling the hybrid atomistic structure-based model and the conventional all-atom model can provide more insights into the folding dynamics of DNA G-quadruplex.As a result,the multiscale computational framework adopted in this study may be useful to study complex processes of biomolecules involving large conformational changes.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
为了准确预测全氮材料的生成焓,基于原子化反应,采用B3PW91、B3P86、B3LYP、X3LYP、O3LYP、M052X、M062X、M06HF、B2PLYP 9种密度泛函分别对52种多氮化合物的气相生成焓进行了计算。通过与实验数据对比,双杂化泛函B2PLYP的平均绝对偏差...为了准确预测全氮材料的生成焓,基于原子化反应,采用B3PW91、B3P86、B3LYP、X3LYP、O3LYP、M052X、M062X、M06HF、B2PLYP 9种密度泛函分别对52种多氮化合物的气相生成焓进行了计算。通过与实验数据对比,双杂化泛函B2PLYP的平均绝对偏差最小,为30.1 k J·mol^(-1),且优于G4方法,选择该泛函计算了N_4(T_d)、_N6(D_(3h))、N_8(O_h)、N_(10)(D_(5h))及N_(12)(D_(6h))5种全氮分子的气相生成焓,计算结果依次为756.4,1338.2,1878.5,2144.3,2787.0 k J·mol^(-1)。展开更多
文摘All-atom molecular dynamics （MD） simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.
文摘All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution. Intramolecular distances, root-mean-square deviation, radius of gyration, and solvent-accessible surface are used to characterize the properties of the carnosine. Carnosine can shift between extended and folded states, but exists mostly in extended state in water. Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance （NMR） experiment. The NMR experimental results are consistent with the molecular dynamics simulations.
文摘An all-atom dimethyl sulfoxide （DMSO） and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bonds and weak C-H- ~ ~ O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The stable aggregates of （DMSO）m＇S=O…… HW-OW-（H20）n might play a key role in this region. Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.
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This work was supported by the National Natural Science Foundation of China （No.20903026）, the Doctoral Scientific Research Foundation of the Natural Science Foundation of Guangdong Province （No.7301567）, and the Research Foundation of Guangdong Pharmaceutical University （No.2006YKX05）.
文摘The interactions and structures of the urea-water system are studied by an all-atom molecular dynamics （MD） simulation. The hydrogen-bonding network and the radial distribution functions are adopted in MD simulations. The structures of urea-water mixtures can be classified into different regions from the analysis of the hydrogen-bonding network. The urea molecule shows the certain tendency to the self-aggregate with the mole fraction of urea increasing. Moreover, the results of the MD simulations are also compare with the chemical shifts and viscosities of the urea aqueous solutions, and the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data such as chemical shifts of the hydrogen atom and viscosity.
基金This work was supported by the Doctoral Scientific Research Foundation of the Natural Science Foundation of Guangdong Province, China （No.7301567） and the Research Foundation of Guangdong Pharmaceutical University, China （No.2006YKX05）.
文摘N,N-dimethylacetamide （DMA） has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions （RDFs） and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.
基金Supported by the National Natural Science Foundation of China(No.20903026)the Talents Introduction Foundation for Universities of Guangdong Province(2011)Scientific Research Foundation of the Natural Science Foundation of Guangdong Province(No.S2011010002483)
文摘All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.
基金the National Natural Science Foundation of China(Grant Nos.11504043,61671107,31670727,and 61771093)the Science Foundation of Shandong Province of China(Grant No.ZR2016JL027)+1 种基金the Taishan Young Scholars Program of Shandong Province of China(Grant No.tsqn20161049)the Youth Science and Technology Innovation Plan of Universities in Shandong,China(Grant No.2019KJE007)。
文摘The hybrid atomistic structure-based model has been validated to be effective in investigation of G-quadruplex folding.In this study,we performed large-scale conventional all-atom simulations to complement the folding mechanism of human telomeric sequence Htel24 revealed by a multi-basin hybrid atomistic structure-based model.Firstly,the real time-scale of folding rate,which cannot be obtained from the structure-based simulations,was estimated directly by constructing a Markov state model.The results show that Htel24 may fold as fast as on the order of milliseconds when only considering the competition between the hybrid-1 and hybrid-2 G-quadruplex conformations.Secondly,in comparison with the results of structure-based simulations,more metastable states were identified to participate in the formation of hybrid-1 and hybrid-2 conformations.These findings suggest that coupling the hybrid atomistic structure-based model and the conventional all-atom model can provide more insights into the folding dynamics of DNA G-quadruplex.As a result,the multiscale computational framework adopted in this study may be useful to study complex processes of biomolecules involving large conformational changes.
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.
文摘为了准确预测全氮材料的生成焓,基于原子化反应,采用B3PW91、B3P86、B3LYP、X3LYP、O3LYP、M052X、M062X、M06HF、B2PLYP 9种密度泛函分别对52种多氮化合物的气相生成焓进行了计算。通过与实验数据对比,双杂化泛函B2PLYP的平均绝对偏差最小,为30.1 k J·mol^(-1),且优于G4方法,选择该泛函计算了N_4(T_d)、_N6(D_(3h))、N_8(O_h)、N_(10)(D_(5h))及N_(12)(D_(6h))5种全氮分子的气相生成焓,计算结果依次为756.4,1338.2,1878.5,2144.3,2787.0 k J·mol^(-1)。
