The C–H bond activation in alkane dehydrogenation reactions is a key step in determining the reaction rate.To understand the impact of entropy,we performed ab initio static and molecular dynamics free energy simulati...The C–H bond activation in alkane dehydrogenation reactions is a key step in determining the reaction rate.To understand the impact of entropy,we performed ab initio static and molecular dynamics free energy simulations of ethane dehydrogenation over Co@BEA zeolite at different temperatures.AIMD simulations showed that a sharp decrease in free energy barrier as temperature increased.Our analysis of the temperature dependence of activation free energies uncovered an unusual entropic effect accompanying the reaction.The unique spatial structures around the Co active site at different temperatures influenced both the extent of charge transfer in the transition state and the arrangement of 3d orbital energy levels.We provided explanations consistent with the principles of thermodynamics and statistical physics.The insights gained at the atomic level have offered a fresh interpretation of the intricate long-range interplay between local chemical reactions and extensive chemical environments.展开更多
Quantum mechanics and molecular dynamics are used to simulate guanidinium ionic liquids. Results show that the stronger interaction exists between guanidine cation and chlorine anion with interaction energy about 109....Quantum mechanics and molecular dynamics are used to simulate guanidinium ionic liquids. Results show that the stronger interaction exists between guanidine cation and chlorine anion with interaction energy about 109.216 kcal/mol. There are two types of spatial distribution for the title system： middle and top. Middle mode is a more stable conformation according to energy and geometric distribution. It is also verified by radial distribution function. The continuous increase of carbon dioxide （CO2） does not affect the structure of ionic liquids, but CO2 molecules are always captured by the cavity of ionic liquids.展开更多
The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re- sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to lo...The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re- sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to low-sulfur diesel fuel. It was attempted to correlate the molecular structures of fatty acids, such as carbon chain length, degree of saturation and hy- droxylation, to their lubricity enhancement, which was evaluated by the High-Frequency Reciprocating Rig （HFRR） meth- od. The efficiency order was supported by the density functional theory （DFT） calculations and the molecular dynamics （MD） simulations. The lubricity enhancing properties of fatty acids are mainly determined by the cohesive energy of adsorbed films furmed on iron surface. The greater the cohesive energy, the more efficiently the fatty acid would enhance the lubricity of low-sulfur diesel fuel.展开更多
H‐ZSM‐5 zeolite is a typical catalyst for methanol‐to‐olefins(MTO)conversion.Although the performance of zeolite catalysts for MTO conversion is related to the actual location of acid sites in the zeolite framewor...H‐ZSM‐5 zeolite is a typical catalyst for methanol‐to‐olefins(MTO)conversion.Although the performance of zeolite catalysts for MTO conversion is related to the actual location of acid sites in the zeolite framework,the catalytic roles of the acid sites in different pore channels of the H‐ZSM‐5 zeolite are not well understood.In this study,the MTO reaction network,involving the aromatic cycle,alkene cycle,and aromatization process,and also the diffusion behavior of methanol feedstock and olefin and aromatic products at different acid sites in the straight channel,sinusoidal channel,and intersection cavity of H‐ZSM‐5 zeolite was comparatively investigated using density functional theory calculations and molecular dynamic simulations.The results indicated that the aromatic cycle and aromatization process occurred preferentially at the acid sites in the intersection cavities with a much lower energy barrier than that at the acid sites in the straight and sinusoidal channels.In contrast,the formation of polymethylbenzenes was significantly suppressed at the acid sites in the sinusoidal and straight channels,whereas the alkene cycle can occur at all three types of acid sites with similar energy barriers and probabilities.Consequently,the catalytic performance of H‐ZSM‐5 zeolite for MTO conversion,including activity and product selectivity,can be regulated properly through the purposive alteration of the acid site distribution,viz.,the location of Al in the zeolite framework.This study helps to elucidate the relation between the catalytic performance of different acid sites in the H‐ZSM‐5 zeolite framework for MTO conversion,which should greatly benefit the design of efficient catalyst for methanol conversion.展开更多
We study the binding of molecular oxygen to a （5, 0） single walled SiC nanotube, by means of density functional calculations. The center of a hexagon of silicon and carbon atoms in sites on SiCNT surfaces is the mos...We study the binding of molecular oxygen to a （5, 0） single walled SiC nanotube, by means of density functional calculations. The center of a hexagon of silicon and carbon atoms in sites on SiCNT surfaces is the most stable adsorption site for 02 molecule, with a binding energy of -38.22 eV and an average Si-O binding distance of 1.698 A. We have also tested the stability of the 02-adsorbed SiCNT/CNT with ab initio molecular dynamics simulation which have been carried out at room temperature. Furthermore, the adsorption of 02 on the single walled carbon nanotubes has been investigated. Our first-principles calculations predict that the 02 adsorptive capability of silicon carbide nanotubes is much better than that of carbon nanotubes. This might have potential for gas detection and energy storage.展开更多
The Grand Canonical Monte Carlo(GCMC) simulation method was used to investigate the adsorption properties of quinoline homologues(quinoline, 2-methyl quinoline, and 2,4-dimethyl quinoline) on the FAU zeolite. The adso...The Grand Canonical Monte Carlo(GCMC) simulation method was used to investigate the adsorption properties of quinoline homologues(quinoline, 2-methyl quinoline, and 2,4-dimethyl quinoline) on the FAU zeolite. The adsorption heat, adsorption isotherms, and adsorption sites of them were obtained. At the temperature ranging from 673.15 to 873.15 K, the Henry constant of quinoline homologues calculated on the FAU zeolite was applied to simulate their adsorption heat. And its value was more in accordance with the related data reported in the literature. The results showed that their isosteric heat decreased in the following order: 2,4-dimethyl quinoline(118.63 kJ/mol) > 2-methyl quinoline(110.45 kJ/mol) > quinoline(98 kJ/mol), and complied with the order of their adsorbate basicity. The competitive adsorption of three components of quinoline homologues on the FAU zeolite was calculated numerically at a temperature of 773.15 K and a pressure range of 0.1—100 MPa under the Universal force field. Their adsorption capacity decreased in the following order: quinoline > 2-methyl quinoline > 2,4-dimethyl quinoline. The smaller the molecule size of the adsorbate, the greater the saturated adsorption capacity would be. It was found that the quinoline homologues could be adsorbed in the main channels of 12- membered-ring framework of the zeolite. Simultaneously, the influence of silica/alumina ratio on the adsorption property of quinoline homologues in FAU zeolite was studied. The smaller the silica/alumina ratio, the greater the isosteric heat and adsorption capacity would be.展开更多
The DFT-based （density fimctional theory） ab initio quantum mechanical methods have been applied to study the basicity of the nitrogen-containing compounds in petroleum. The results have indicated that there is a di...The DFT-based （density fimctional theory） ab initio quantum mechanical methods have been applied to study the basicity of the nitrogen-containing compounds in petroleum. The results have indicated that there is a distinct relationship between the protonation energy of nitrogen-containing compounds and their basicity. The more negative the protonation energy, the stronger the basicity is. It has been also found that aliphatic amines are more basic than pyridines or aromatic amines, and all these compounds are more basic than pyrroles. The addition of the aromatic rings can influence the basicity of anilines, while the 5- and 6-membered heterocyclic compounds function differently. The solvent properties may affect the basicity of these nitrogen-containing compounds.展开更多
Objective Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the causative agent for coronavirus disease 2019(COVID-19),is responsible for the recent global pandemic.As there are no effective drugs or vaccine...Objective Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the causative agent for coronavirus disease 2019(COVID-19),is responsible for the recent global pandemic.As there are no effective drugs or vaccines available for SARS-CoV-2,we investigated the potential of flavonoids against SARS-CoV-2 main protease 6YNQ.Methods In silico molecular simulation study against SARS-CoV-2 main protease 6YNQ.Results Among the 21 selected flavonoids,rutin demonstrated the highest binding energy(−8.7 kcal/mol)and displayed perfect binding with the catalytic sites.Conclusions Our study demonstrates the inhibitory potential of flavonoids against SARS-CoV-2 main protease 6YNQ.These computational simulation studies support the hypothesis that flavonoids might be helpful for the treatment of COVID-19.展开更多
Objective Rheumatoid arthritis(RA)is an autoimmune disease involving the synovial lining of the major joints.Current therapies have noteworthy side effects.Our study involved in silico evaluation of Ehretia laevis(E.l...Objective Rheumatoid arthritis(RA)is an autoimmune disease involving the synovial lining of the major joints.Current therapies have noteworthy side effects.Our study involved in silico evaluation of Ehretia laevis(E.laevis)phytoconstituents targeting tumor necrosis factor-α(TNF-α).Methods Molecular docking studies performed to investigate the binding pattern of the plant E.laevis phytoconstituents along with the crystal structure of TNF-α(PDB ID:2 AZ5)using AutoDock Vina followed by a study of interacting amino acid residues and their influence on the inhibitory potentials of the active constituents.Further the pharmacokinetic profile and toxicity screening carried out using Swiss ADME and pk CSM.Results The docked results suggest that lupeol(-9.4 kcal/mol)andα-amyrin(-9.4 kcal/mol)has best affinity towards TNF-αcompared to standard drug thalidomide(-7.4 kcal/mol).The active chemical constituents represents better interaction with the conserved catalytic residues,leading to the inhibition/blockade of the TNF-α-associated signaling pathway in RA.Furthermore,pharmacokinetics and toxicity parameters of these phytochemicals were within acceptable limits according to ADMET studies.Conclusion The binding potential of phytoconstituents targeting TNF-αshowed promising results.Nonetheless,it encourages the traditional use of E.laevis and provides vital information on drug development and clinical treatment.展开更多
In cells, the interactions of distinct signaling transduction pathways originating from cross-talkings between signaling molecules give rise to the formation of signaling transduction networks, which contributes to th...In cells, the interactions of distinct signaling transduction pathways originating from cross-talkings between signaling molecules give rise to the formation of signaling transduction networks, which contributes to the changes (emergency) of kinetic behaviors of signaling system compared with single molecule or pathway. Depending on the known experimental data, we have constructed a model for complex cellular signaling transduction system, which is derived from signaling transduction of epidermal growth factor receptor in neuron. By the computational simulating methods, the self-adaptive controls of this system have been investigated. We find that this model exhibits a relatively stable selfadaptive system, especially to over-stimulation of agonist, and the amplitude and duration of signaling intermediates in it could be controlled by multiple self-adaptive effects, such as 'signal scattering', 'positive feedback', 'negative feedback' and 'B-Raf shunt'. Our results provide an approach to understanding the dynamic behaviors of complex biological systems.展开更多
Surface eigenstress and eigendisplacement models were used to investigate the surface stress, surface relaxation and surface elasticity of thin films with different surface orientations. Molecular dynamics simulations...Surface eigenstress and eigendisplacement models were used to investigate the surface stress, surface relaxation and surface elasticity of thin films with different surface orientations. Molecular dynamics simulations and first-principles calculations were conducted on face-centered cubic Au films with the focus on relaxation induced nonlinear initial deformation. The simu- lation results verify the theoretical predictions of the size dependency of surface energy density and surface stress, and the non- linear scaling law of the size-dependent Young＇s modulus of thin films. The mechanism of the size-dependent behaviors was further explored at the atomic bonding level with the charge density field. The Au atomic bonding at surfaces is enhanced compared to its interior counterpart and therefore the nominal Young＇s modulus of the Au thin films is larger when the film thickness is smaller.surface elasticity,展开更多
The non-Condon effect plays an important role in the process of electron transfer (ET). Several theoretical models have been proposed to investigate its effect on ET rates. In this paper,we overview a theoretical meth...The non-Condon effect plays an important role in the process of electron transfer (ET). Several theoretical models have been proposed to investigate its effect on ET rates. In this paper,we overview a theoretical method for the calculations of the non-Condon ET rate constants proposed by us,and its applications to organic semiconductors. First,full quantum expressions of the non-Condon ET rates are presented with the electronic couplings having exponential,Gaussian and linear dependences in terms of the nuclear coordinates,respectively. The proposed formulas have closed forms in time domain and they thus can be easily applied in multi-mode systems. Then,the driving force dependences of the ET rates involving the non-Condon effect are calculated with the use of full quantum mechanical formulas. It is found that these dependences show very different prop-erties from the Marcus one. As an example of applications,the approaches are used to investigate the non-Condon effect on the mobility of the organic semiconductor dithiophene-tetrathiafulvalene (DT-TTF). The results manifest that the non-Condon ef-fect enhances ET rates compared with the Condon approximation,and static fluctuations of electronic coupling dominate the ET rate in the DT-TTF,which has been confirmed by the molecular dynamics simulation.展开更多
文摘The C–H bond activation in alkane dehydrogenation reactions is a key step in determining the reaction rate.To understand the impact of entropy,we performed ab initio static and molecular dynamics free energy simulations of ethane dehydrogenation over Co@BEA zeolite at different temperatures.AIMD simulations showed that a sharp decrease in free energy barrier as temperature increased.Our analysis of the temperature dependence of activation free energies uncovered an unusual entropic effect accompanying the reaction.The unique spatial structures around the Co active site at different temperatures influenced both the extent of charge transfer in the transition state and the arrangement of 3d orbital energy levels.We provided explanations consistent with the principles of thermodynamics and statistical physics.The insights gained at the atomic level have offered a fresh interpretation of the intricate long-range interplay between local chemical reactions and extensive chemical environments.
基金ACKNOWLEDGMENTS This work was supported by the Open Project Program of Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education, Hunan University of Science and Technology, China （No.E21104）, the National Natural Science Foundation of China （No.21201062 and No.21172066）, and the International Cooperation Project （No.2013DFG60060）.
文摘Quantum mechanics and molecular dynamics are used to simulate guanidinium ionic liquids. Results show that the stronger interaction exists between guanidine cation and chlorine anion with interaction energy about 109.216 kcal/mol. There are two types of spatial distribution for the title system： middle and top. Middle mode is a more stable conformation according to energy and geometric distribution. It is also verified by radial distribution function. The continuous increase of carbon dioxide （CO2） does not affect the structure of ionic liquids, but CO2 molecules are always captured by the cavity of ionic liquids.
基金supported by the Fundamental Research Funds for the Central Universities of China(11CX06036A)
文摘The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re- sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to low-sulfur diesel fuel. It was attempted to correlate the molecular structures of fatty acids, such as carbon chain length, degree of saturation and hy- droxylation, to their lubricity enhancement, which was evaluated by the High-Frequency Reciprocating Rig （HFRR） meth- od. The efficiency order was supported by the density functional theory （DFT） calculations and the molecular dynamics （MD） simulations. The lubricity enhancing properties of fatty acids are mainly determined by the cohesive energy of adsorbed films furmed on iron surface. The greater the cohesive energy, the more efficiently the fatty acid would enhance the lubricity of low-sulfur diesel fuel.
文摘H‐ZSM‐5 zeolite is a typical catalyst for methanol‐to‐olefins(MTO)conversion.Although the performance of zeolite catalysts for MTO conversion is related to the actual location of acid sites in the zeolite framework,the catalytic roles of the acid sites in different pore channels of the H‐ZSM‐5 zeolite are not well understood.In this study,the MTO reaction network,involving the aromatic cycle,alkene cycle,and aromatization process,and also the diffusion behavior of methanol feedstock and olefin and aromatic products at different acid sites in the straight channel,sinusoidal channel,and intersection cavity of H‐ZSM‐5 zeolite was comparatively investigated using density functional theory calculations and molecular dynamic simulations.The results indicated that the aromatic cycle and aromatization process occurred preferentially at the acid sites in the intersection cavities with a much lower energy barrier than that at the acid sites in the straight and sinusoidal channels.In contrast,the formation of polymethylbenzenes was significantly suppressed at the acid sites in the sinusoidal and straight channels,whereas the alkene cycle can occur at all three types of acid sites with similar energy barriers and probabilities.Consequently,the catalytic performance of H‐ZSM‐5 zeolite for MTO conversion,including activity and product selectivity,can be regulated properly through the purposive alteration of the acid site distribution,viz.,the location of Al in the zeolite framework.This study helps to elucidate the relation between the catalytic performance of different acid sites in the H‐ZSM‐5 zeolite framework for MTO conversion,which should greatly benefit the design of efficient catalyst for methanol conversion.
文摘We study the binding of molecular oxygen to a （5, 0） single walled SiC nanotube, by means of density functional calculations. The center of a hexagon of silicon and carbon atoms in sites on SiCNT surfaces is the most stable adsorption site for 02 molecule, with a binding energy of -38.22 eV and an average Si-O binding distance of 1.698 A. We have also tested the stability of the 02-adsorbed SiCNT/CNT with ab initio molecular dynamics simulation which have been carried out at room temperature. Furthermore, the adsorption of 02 on the single walled carbon nanotubes has been investigated. Our first-principles calculations predict that the 02 adsorptive capability of silicon carbide nanotubes is much better than that of carbon nanotubes. This might have potential for gas detection and energy storage.
文摘The Grand Canonical Monte Carlo(GCMC) simulation method was used to investigate the adsorption properties of quinoline homologues(quinoline, 2-methyl quinoline, and 2,4-dimethyl quinoline) on the FAU zeolite. The adsorption heat, adsorption isotherms, and adsorption sites of them were obtained. At the temperature ranging from 673.15 to 873.15 K, the Henry constant of quinoline homologues calculated on the FAU zeolite was applied to simulate their adsorption heat. And its value was more in accordance with the related data reported in the literature. The results showed that their isosteric heat decreased in the following order: 2,4-dimethyl quinoline(118.63 kJ/mol) > 2-methyl quinoline(110.45 kJ/mol) > quinoline(98 kJ/mol), and complied with the order of their adsorbate basicity. The competitive adsorption of three components of quinoline homologues on the FAU zeolite was calculated numerically at a temperature of 773.15 K and a pressure range of 0.1—100 MPa under the Universal force field. Their adsorption capacity decreased in the following order: quinoline > 2-methyl quinoline > 2,4-dimethyl quinoline. The smaller the molecule size of the adsorbate, the greater the saturated adsorption capacity would be. It was found that the quinoline homologues could be adsorbed in the main channels of 12- membered-ring framework of the zeolite. Simultaneously, the influence of silica/alumina ratio on the adsorption property of quinoline homologues in FAU zeolite was studied. The smaller the silica/alumina ratio, the greater the isosteric heat and adsorption capacity would be.
基金supported by the"973"project envisaged in the State Key Basic R&D Program(2006CB202505).
文摘The DFT-based （density fimctional theory） ab initio quantum mechanical methods have been applied to study the basicity of the nitrogen-containing compounds in petroleum. The results have indicated that there is a distinct relationship between the protonation energy of nitrogen-containing compounds and their basicity. The more negative the protonation energy, the stronger the basicity is. It has been also found that aliphatic amines are more basic than pyridines or aromatic amines, and all these compounds are more basic than pyrroles. The addition of the aromatic rings can influence the basicity of anilines, while the 5- and 6-membered heterocyclic compounds function differently. The solvent properties may affect the basicity of these nitrogen-containing compounds.
文摘Objective Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the causative agent for coronavirus disease 2019(COVID-19),is responsible for the recent global pandemic.As there are no effective drugs or vaccines available for SARS-CoV-2,we investigated the potential of flavonoids against SARS-CoV-2 main protease 6YNQ.Methods In silico molecular simulation study against SARS-CoV-2 main protease 6YNQ.Results Among the 21 selected flavonoids,rutin demonstrated the highest binding energy(−8.7 kcal/mol)and displayed perfect binding with the catalytic sites.Conclusions Our study demonstrates the inhibitory potential of flavonoids against SARS-CoV-2 main protease 6YNQ.These computational simulation studies support the hypothesis that flavonoids might be helpful for the treatment of COVID-19.
文摘Objective Rheumatoid arthritis(RA)is an autoimmune disease involving the synovial lining of the major joints.Current therapies have noteworthy side effects.Our study involved in silico evaluation of Ehretia laevis(E.laevis)phytoconstituents targeting tumor necrosis factor-α(TNF-α).Methods Molecular docking studies performed to investigate the binding pattern of the plant E.laevis phytoconstituents along with the crystal structure of TNF-α(PDB ID:2 AZ5)using AutoDock Vina followed by a study of interacting amino acid residues and their influence on the inhibitory potentials of the active constituents.Further the pharmacokinetic profile and toxicity screening carried out using Swiss ADME and pk CSM.Results The docked results suggest that lupeol(-9.4 kcal/mol)andα-amyrin(-9.4 kcal/mol)has best affinity towards TNF-αcompared to standard drug thalidomide(-7.4 kcal/mol).The active chemical constituents represents better interaction with the conserved catalytic residues,leading to the inhibition/blockade of the TNF-α-associated signaling pathway in RA.Furthermore,pharmacokinetics and toxicity parameters of these phytochemicals were within acceptable limits according to ADMET studies.Conclusion The binding potential of phytoconstituents targeting TNF-αshowed promising results.Nonetheless,it encourages the traditional use of E.laevis and provides vital information on drug development and clinical treatment.
基金This research is supported by the National Natural Science Foundation of China (No. 70071040).
文摘In cells, the interactions of distinct signaling transduction pathways originating from cross-talkings between signaling molecules give rise to the formation of signaling transduction networks, which contributes to the changes (emergency) of kinetic behaviors of signaling system compared with single molecule or pathway. Depending on the known experimental data, we have constructed a model for complex cellular signaling transduction system, which is derived from signaling transduction of epidermal growth factor receptor in neuron. By the computational simulating methods, the self-adaptive controls of this system have been investigated. We find that this model exhibits a relatively stable selfadaptive system, especially to over-stimulation of agonist, and the amplitude and duration of signaling intermediates in it could be controlled by multiple self-adaptive effects, such as 'signal scattering', 'positive feedback', 'negative feedback' and 'B-Raf shunt'. Our results provide an approach to understanding the dynamic behaviors of complex biological systems.
基金supported by the Hong Kong Research Grants Council(Grant No.622312)
文摘Surface eigenstress and eigendisplacement models were used to investigate the surface stress, surface relaxation and surface elasticity of thin films with different surface orientations. Molecular dynamics simulations and first-principles calculations were conducted on face-centered cubic Au films with the focus on relaxation induced nonlinear initial deformation. The simu- lation results verify the theoretical predictions of the size dependency of surface energy density and surface stress, and the non- linear scaling law of the size-dependent Young＇s modulus of thin films. The mechanism of the size-dependent behaviors was further explored at the atomic bonding level with the charge density field. The Au atomic bonding at surfaces is enhanced compared to its interior counterpart and therefore the nominal Young＇s modulus of the Au thin films is larger when the film thickness is smaller.surface elasticity,
基金supported by the National Natural Science Foundation of China (20833004 and 21073146)Research Fund for the Doctoral Program of Higher Education of China (200803840009)
文摘The non-Condon effect plays an important role in the process of electron transfer (ET). Several theoretical models have been proposed to investigate its effect on ET rates. In this paper,we overview a theoretical method for the calculations of the non-Condon ET rate constants proposed by us,and its applications to organic semiconductors. First,full quantum expressions of the non-Condon ET rates are presented with the electronic couplings having exponential,Gaussian and linear dependences in terms of the nuclear coordinates,respectively. The proposed formulas have closed forms in time domain and they thus can be easily applied in multi-mode systems. Then,the driving force dependences of the ET rates involving the non-Condon effect are calculated with the use of full quantum mechanical formulas. It is found that these dependences show very different prop-erties from the Marcus one. As an example of applications,the approaches are used to investigate the non-Condon effect on the mobility of the organic semiconductor dithiophene-tetrathiafulvalene (DT-TTF). The results manifest that the non-Condon ef-fect enhances ET rates compared with the Condon approximation,and static fluctuations of electronic coupling dominate the ET rate in the DT-TTF,which has been confirmed by the molecular dynamics simulation.
