The Si-O bond breaking event in the a-quartz at the first triplet （T1） excitation state is studied by using ab initio molecular dynamics （AIMD） and nudged elastic band calculations. A meta-stable non-bridging oxyg...The Si-O bond breaking event in the a-quartz at the first triplet （T1） excitation state is studied by using ab initio molecular dynamics （AIMD） and nudged elastic band calculations. A meta-stable non-bridging oxygen hole center and E1 center （NBOHC-E） is observed in the AIMD which consists of a broken Si-O bond with a Si-O distance of 2.54A. By disallowing the re-bonding of the Si and 0 atoms, another defect configuration （lll- Si/V-Si） is obtained and validated to be stable at both ground and excitation states. The NBOHC-E is found to present on the minimal energy pathway of the initial to IlI-Si/V-Si transition, showing that the generating of the NBOHC-E is an important step of the excitation induced structure defect. The energy barriers to produce the NBQHC-E＇ and Ⅲ-Si/V-Si defects are calculated to be 1.19 and 1.28eV, respectively. The electronic structures of the two defects are calculated by the self-consistent GW calculations and the results show a clear electron transition from the bonding orbital to the non-bonding orbital.展开更多
The formation and breaking of intramolecular hydrogen bonds of bilirubin in CDCl_3-DMSO-d_6 binary solvent have been investigated by means of NMR spectroscopy.The chemical shifts of protons at dipyrrinone lactam C=O a...The formation and breaking of intramolecular hydrogen bonds of bilirubin in CDCl_3-DMSO-d_6 binary solvent have been investigated by means of NMR spectroscopy.The chemical shifts of protons at dipyrrinone lactam C=O and N-H,Pyrrole N-H,C-5,C-15 and methylene groups of 8,12-propionic acid side-chains changed markedly as a function of composition of the binary solvent.The hydrogen bond formation is dependent on the conformation of propionic acid side-chains.展开更多
DFT/6-311 + g** level calculations are performed tp study the electron transfer bond-breaking reaction of CH3-X. The calculated values are in good agreement with the experimental results or the empirical model. Throug...DFT/6-311 + g** level calculations are performed tp study the electron transfer bond-breaking reaction of CH3-X. The calculated values are in good agreement with the experimental results or the empirical model. Through analyzing the change of the energy and the charge densilty along hte reaction path, the bond-breaking in ET reaction for CH3X is investigated.展开更多
Shear deformation mechanisms of diamond-like carbon(DLC)are commonly unclear since its thickness of several micrometers limits the detailed analysis of its microstructural evolution and mechanical performance,which fu...Shear deformation mechanisms of diamond-like carbon(DLC)are commonly unclear since its thickness of several micrometers limits the detailed analysis of its microstructural evolution and mechanical performance,which further influences the improvement of the friction and wear performance of DLC.This study aims to investigate this issue utilizing molecular dynamics simulation and machine learning(ML)techniques.It is indicated that the changes in the mechanical properties of DLC are mainly due to the expansion and reduction of sp3 networks,causing the stick-slip patterns in shear force.In addition,cluster analysis showed that the sp2-sp3 transitions arise in the stick stage,while the sp3-sp2 transitions occur in the slip stage.In order to analyze the mechanisms governing the bond breaking/re-formation in these transitions,the Random Forest(RF)model in ML identifies that the kinetic energies of sp3 atoms and their velocities along the loading direction have the highest influence.This is because high kinetic energies of atoms can exacerbate the instability of the bonding state and increase the probability of bond breaking/re-formation.Finally,the RF model finds that the shear force of DLC is highly correlated to its potential energy,with less correlation to its content of sp3 atoms.Since the changes in potential energy are caused by the variances in the content of sp3 atoms and localized strains,potential energy is an ideal parameter to evaluate the shear deformation of DLC.The results can enhance the understanding of the shear deformation of DLC and support the improvement of its frictional and wear performance.展开更多
Monitoring subtle changes in ionic current flow through a nanopore could be applied to observe single molecule reaction. Here,we introduced cysteine to substitute for lysine at position 238 constructing a mutant aerol...Monitoring subtle changes in ionic current flow through a nanopore could be applied to observe single molecule reaction. Here,we introduced cysteine to substitute for lysine at position 238 constructing a mutant aerolysin K238 C. It could be regarded as a nanoreactor to efficiently visualize chemical bonds making and breaking. The compound 5,5′-dithiobis-(2-nitrobenzoic acid)(DTNB) was selected as a reactant coming into collisions on the interface of the pore to occur a reversible reaction. Our results showed that the mutant aerolysin could respond to three molecules of DTNB simultaneously and reflect corresponding levels with distinguishable current signals. Therefore, this method constitutes a simple, generic tool for monitoring single molecule reaction, which evokes a guidance for the mutant aerolysin towards the application of tracking other more reactions at single molecule level.展开更多
To test the theory of dissociative electron transfer, a simple model describing the kinetics of electron transfer bond breaking reactions was used. The Hamiltonian of the system was given. The homogeneous and heterog...To test the theory of dissociative electron transfer, a simple model describing the kinetics of electron transfer bond breaking reactions was used. The Hamiltonian of the system was given. The homogeneous and heterogeneous kinetic data fit reasonably well with an activation driving force relationship derived from the Marcus quadratic theory. In the heterogeneous case, there is a good agreement between the theoretical calculation and the experimental result, while in the homogeneous case, a good agreement is only observed for the tertiary halides. This is due to the stability of tertiary radical resulting from the sterical effect.展开更多
基金Supported by the National Natural Science Foundation of China under Grant Nos 10744048 and 11202032the Defense Industrial Technology Development Program of China under Grant No B1520132013
文摘The Si-O bond breaking event in the a-quartz at the first triplet （T1） excitation state is studied by using ab initio molecular dynamics （AIMD） and nudged elastic band calculations. A meta-stable non-bridging oxygen hole center and E1 center （NBOHC-E） is observed in the AIMD which consists of a broken Si-O bond with a Si-O distance of 2.54A. By disallowing the re-bonding of the Si and 0 atoms, another defect configuration （lll- Si/V-Si） is obtained and validated to be stable at both ground and excitation states. The NBOHC-E is found to present on the minimal energy pathway of the initial to IlI-Si/V-Si transition, showing that the generating of the NBOHC-E is an important step of the excitation induced structure defect. The energy barriers to produce the NBQHC-E＇ and Ⅲ-Si/V-Si defects are calculated to be 1.19 and 1.28eV, respectively. The electronic structures of the two defects are calculated by the self-consistent GW calculations and the results show a clear electron transition from the bonding orbital to the non-bonding orbital.
文摘The formation and breaking of intramolecular hydrogen bonds of bilirubin in CDCl_3-DMSO-d_6 binary solvent have been investigated by means of NMR spectroscopy.The chemical shifts of protons at dipyrrinone lactam C=O and N-H,Pyrrole N-H,C-5,C-15 and methylene groups of 8,12-propionic acid side-chains changed markedly as a function of composition of the binary solvent.The hydrogen bond formation is dependent on the conformation of propionic acid side-chains.
文摘DFT/6-311 + g** level calculations are performed tp study the electron transfer bond-breaking reaction of CH3-X. The calculated values are in good agreement with the experimental results or the empirical model. Through analyzing the change of the energy and the charge densilty along hte reaction path, the bond-breaking in ET reaction for CH3X is investigated.
基金The simulations in this work are supported by the High-Performance Computing Center of Central South University.
文摘Shear deformation mechanisms of diamond-like carbon(DLC)are commonly unclear since its thickness of several micrometers limits the detailed analysis of its microstructural evolution and mechanical performance,which further influences the improvement of the friction and wear performance of DLC.This study aims to investigate this issue utilizing molecular dynamics simulation and machine learning(ML)techniques.It is indicated that the changes in the mechanical properties of DLC are mainly due to the expansion and reduction of sp3 networks,causing the stick-slip patterns in shear force.In addition,cluster analysis showed that the sp2-sp3 transitions arise in the stick stage,while the sp3-sp2 transitions occur in the slip stage.In order to analyze the mechanisms governing the bond breaking/re-formation in these transitions,the Random Forest(RF)model in ML identifies that the kinetic energies of sp3 atoms and their velocities along the loading direction have the highest influence.This is because high kinetic energies of atoms can exacerbate the instability of the bonding state and increase the probability of bond breaking/re-formation.Finally,the RF model finds that the shear force of DLC is highly correlated to its potential energy,with less correlation to its content of sp3 atoms.Since the changes in potential energy are caused by the variances in the content of sp3 atoms and localized strains,potential energy is an ideal parameter to evaluate the shear deformation of DLC.The results can enhance the understanding of the shear deformation of DLC and support the improvement of its frictional and wear performance.
基金supported by the National Natural Science Foundation of China (21421004, 21777041, 21327807)the Program of Introducing Talents of Discipline to Universities (B16017)+1 种基金Innovation Program of Shanghai Municipal Education Commission (2017-0107-00-02-E00023)the Fundamental Research Funds for the Central Universities (222201718001, 222201717003)
文摘Monitoring subtle changes in ionic current flow through a nanopore could be applied to observe single molecule reaction. Here,we introduced cysteine to substitute for lysine at position 238 constructing a mutant aerolysin K238 C. It could be regarded as a nanoreactor to efficiently visualize chemical bonds making and breaking. The compound 5,5′-dithiobis-(2-nitrobenzoic acid)(DTNB) was selected as a reactant coming into collisions on the interface of the pore to occur a reversible reaction. Our results showed that the mutant aerolysin could respond to three molecules of DTNB simultaneously and reflect corresponding levels with distinguishable current signals. Therefore, this method constitutes a simple, generic tool for monitoring single molecule reaction, which evokes a guidance for the mutant aerolysin towards the application of tracking other more reactions at single molecule level.
基金theNaturalScienceFoundationofShandongProvince (No .Y99B0 1) theNationalKeyLaboratoryFoundationofCrystalMaterialtheNationalNaturalScienceFoundationofChina (No.2 96 730 5 )
文摘To test the theory of dissociative electron transfer, a simple model describing the kinetics of electron transfer bond breaking reactions was used. The Hamiltonian of the system was given. The homogeneous and heterogeneous kinetic data fit reasonably well with an activation driving force relationship derived from the Marcus quadratic theory. In the heterogeneous case, there is a good agreement between the theoretical calculation and the experimental result, while in the homogeneous case, a good agreement is only observed for the tertiary halides. This is due to the stability of tertiary radical resulting from the sterical effect.
