The configurations of molecular clusters have significant impacts on their growth into fine particles in atmosphere.In this paper,we explore the topology space of the structure of H2SO4·NH3 dimer with a novel sam...The configurations of molecular clusters have significant impacts on their growth into fine particles in atmosphere.In this paper,we explore the topology space of the structure of H2SO4·NH3 dimer with a novel sampling technique of meta-dynamics(MTD)method and ab initio molecular dynamics simulations.The simulations are carried out at the temperatures of both 50 K and 242 K,which represent the typical high and low latitudes of troposphere.The results show that,compared with only traditional MD simulations,the structure samplings are significantly accelerated with MTD method.Therefore,more isomers of the dimer are discovered within the same simulation time scale.In addition,the results show that MTD is more efficient for circumstances with high temperature.展开更多
In ab initio molecular dynamics(AIMD)simulations of chemical reactions,it is important but difficult to identify the chemical species in the trajectory automatically and quickly.In this paper,based on the chemical gra...In ab initio molecular dynamics(AIMD)simulations of chemical reactions,it is important but difficult to identify the chemical species in the trajectory automatically and quickly.In this paper,based on the chemical graph theory,an algorithm for molecular species identification,according to the molecular coordinates and empirical bond length database,is presented.As an example,the chemical species in condensed glycine at room temperature are investigated with our algorithm in detail.The chemical species,including canonical and zwitterionic glycine,their protonated and de-protonated states,and the free protons,are all identified,counted and recorded correctly.Potential applications and further development of the algorithm are also discussed.展开更多
It has been demonstrated that low energy electrons(LEEs)can induce serious DNA damages including bases loss and even single and double strand breaks.Experiments also showed that LEE induced DNA damages will be reduced...It has been demonstrated that low energy electrons(LEEs)can induce serious DNA damages including bases loss and even single and double strand breaks.Experiments also showed that LEE induced DNA damages will be reduced with the presence of amino acids.For understanding of the protection of amino acids to DNA,the stability of 6 kinds of thymine and glycine(T-g)dimers with planar configurations with an excess electron were studied with density functional theory(DFT)method.The results show that,when the excess electron is vertically attached,all the dimers become more active with higher energy.After re-optimization,4 kinds(66.7%)of T-g dimers become more stable than the corresponding neutral states.For the most stable anionic dimer noted as[34-A]-,the excess electron is localized on the thymine,while one proton transfers from glycine to thymine.The proton transformation decreases the activities and prevents further reactions of the excess electron.For other three dimers,there is no chemical topology change.The glycine attracts the excess electron with hydrogen-bonding to the thymine.展开更多
文摘The configurations of molecular clusters have significant impacts on their growth into fine particles in atmosphere.In this paper,we explore the topology space of the structure of H2SO4·NH3 dimer with a novel sampling technique of meta-dynamics(MTD)method and ab initio molecular dynamics simulations.The simulations are carried out at the temperatures of both 50 K and 242 K,which represent the typical high and low latitudes of troposphere.The results show that,compared with only traditional MD simulations,the structure samplings are significantly accelerated with MTD method.Therefore,more isomers of the dimer are discovered within the same simulation time scale.In addition,the results show that MTD is more efficient for circumstances with high temperature.
基金The authors thank Dr.Gareth Tribello of Queen’s University Belfast for helpful discussions on the algorithm.This work was partially supported by the program of the Key Laboratory for Aerosol-Cloud-Precipitation of CMA-NUIST(No.KDW1304)the National Natural Science Foundation of China(Grant No.11105075).
文摘In ab initio molecular dynamics(AIMD)simulations of chemical reactions,it is important but difficult to identify the chemical species in the trajectory automatically and quickly.In this paper,based on the chemical graph theory,an algorithm for molecular species identification,according to the molecular coordinates and empirical bond length database,is presented.As an example,the chemical species in condensed glycine at room temperature are investigated with our algorithm in detail.The chemical species,including canonical and zwitterionic glycine,their protonated and de-protonated states,and the free protons,are all identified,counted and recorded correctly.Potential applications and further development of the algorithm are also discussed.
基金This work is supported by Natural Science Foundation of Jiangsu Province of China(No.BK20171456).
文摘It has been demonstrated that low energy electrons(LEEs)can induce serious DNA damages including bases loss and even single and double strand breaks.Experiments also showed that LEE induced DNA damages will be reduced with the presence of amino acids.For understanding of the protection of amino acids to DNA,the stability of 6 kinds of thymine and glycine(T-g)dimers with planar configurations with an excess electron were studied with density functional theory(DFT)method.The results show that,when the excess electron is vertically attached,all the dimers become more active with higher energy.After re-optimization,4 kinds(66.7%)of T-g dimers become more stable than the corresponding neutral states.For the most stable anionic dimer noted as[34-A]-,the excess electron is localized on the thymine,while one proton transfers from glycine to thymine.The proton transformation decreases the activities and prevents further reactions of the excess electron.For other three dimers,there is no chemical topology change.The glycine attracts the excess electron with hydrogen-bonding to the thymine.
