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Theoretical Study of 1,3-Dipolar Cycloaddition of Hydrazoic Acid to Substituted Ynamines

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Chinese Journal of Chemical Physics 2009年第2期22卷 143-148页

作者： Xiao-fang Chen Kun Yang ke-li han State key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China

The 1,3-dipolar cycloaddition reactions of various substituted ynamines with hydrazoic acid were theoretically investigated with the high-accuracy CBS-QB3 method. Two regioisomers, 4-amine, and 5-amine substituted adducts, were obtained, with the former as the preferred yield. This regioselectivity is rationalized by the frontier molecular orbital theory. The reactivity and synchronicity are enhanced with the increase of the electron-withdrawing character of the substitute on ynamine fragment. The calculations also show that the effect of solvent increases the activation energy, and the reaction becomes even harder in polar solvent.

关键词： 1,3-dipolar cycloaddition Hydrazoic acid Internal alkyne CBS-QB3 Solvent effect Substituent effect Frontier molecular orbital theory

Time-dependent Density Functional-based Tight-bind Method Efficiently Implemented with OpenMP Parallel and GPU Acceleration

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Chinese Journal of Chemical Physics 2013年第6期26卷 635-645,I0003页

作者： Guo-hong Fan ke-li han Guo-zhong He State key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics ChineseAcademy of Sciences Dalian 116023 China

The time-dependent density functional-based tight-bind （TD-DFTB） method is implemented on the multi-core and the graphical processing unit （GPU） system for excited state calcu-lations of large system with hundreds or thousands of atoms. Sparse matrix and OpenMP multithreaded are used for building the Hamiltonian matrix. The diagonal of the eigenvalue problem in the ground state is implemented on the GPUs with double precision. The GPU- based acceleration fully preserves all the properties, and a considerable total speedup of 8.73 can be achieved. A Krylov-space-based algorithm with the OpenMP parallel and CPU acceleration is used for finding the lowest eigenvalue and eigenvector of the large TDDFT matrix, which greatly reduces the iterations taken and the time spent on the excited states eigenvalue problem. The Krylov solver with the GPU acceleration of matrix-vector product can converge quickly to obtain the final result and a notable speed-up of 206 times can be observed for system size of 812 atoms. The calculations on serials of small and large systems show that the fast TD-DFTB code can obtain reasonable result with a much cheaper computational requirement compared with the first-principle results of CIS and full TDDFT calculation.

关键词： Density-functional theory Tight-binding method Time-dependent densityfunctional theory Excited state Graphical processing unit Krylov iterative algorithm Sparse matrix OpenMP

Rh(Ⅱ) carbene S-H insertion into H_2S via the stepwise mechanism

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Chinese Chemical Letters 2007年第1期18卷 107-110页

作者： Zhen Feng liu Xian Fang Yue Qiang Wei ke li han State key Laboratory of Molecular Reaction Dynamics~ Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China

The mechanism of Rh（Ⅱ） carbene S-H insertion into H2S in gas phase has been studied by B3LYP functional. Calculation results showed that the Rh（Ⅱ） carbene S-H insertion into H2S took only stepwise channels and n... 详细信息

关键词： Sulfonium ylides 1,2-Hydrogen shift Density functional calculations Dirhodium(Ⅱ) carbene

Semi-Quantitatively Designing Two-Photon High-Performance Fluorescent Probes for Glutathione S-Transferases

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Research 2020年第1期2020卷 1191-1201页

作者： Xue-Xiang Zhang Huan Qi Mei-Heng Lu Song-Qiu Yang Peng li Hai-long Piao ke-li han State key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China CAS key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China Institute of Molecular Sciences and Engineering Shandong UniversityQingdao 266237China

Glutathione S-transferases(GSTs),detoxification enzymes that catalyze the addition of glutathione(GSH)to diverse electrophilic molecules,are often overexpressed in various tumor *** fluorescent probes for GSTs have often adopted the 2,4-dinitrobenzenesulfonyl(DNs)group as the receptor unit,they usually suffer from considerable background reaction noise with GSH due to excessive electron ***,weakening this reactivity is generally accompanied by loss of sensitivity for GSTs,and therefore,finely turning down the reactivity while maintaining certain sensitivity is critical for developing a practical ***,we report a rational semiquantitative strategy for designing such a practical two-photon probe by introducing a parameter adopted from the conceptual density functional theory(CDFT),the local electrophilicityω_(k),to characterize this *** expected,kinetic studies establishedω_(k)as efficient to predict the reactivity with GSH,and probe NI3 showing the best performance was successfully applied to detecting GST activities in live cells and tissue sections with high sensitivity and signal-to-noise *** electron transfer of naphthalimide-based probes,captured by femtosecond transient absorption for the first time and unraveled by theoretical calculations,also contributes to the negligible background noise.

关键词： reactivity Probe negligible

Photoinducednonadiabatic Dynamics of isolated GFP chromophorewith surface-hopping method

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Photoinducednonadiabatic Dynamics of isolated GFP chromophor...

Impact of Borate on Structure of Antifreeze Glycoproteins

第十三届全国化学动力学会议

作者： li Zhao ke-li han State key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences

＜正＞The green fluorescent （GFP）has beenwidelyused in molecular biology for its special spectral *** are a great deal of experimental and theoretical investigations on the GPF chromophore （p-HBDI） for itsverydiff...

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Chinese Journal of Chemical Physics 2021年第6期34卷 659-669,I0001,I0007-I0012页

作者： Feng-qin Long Tan Jin ke-li han Wei Zhuang State key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China State key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhou 350002China University of Chinese Academy of Sciences Beijing 100049China

Antifreeze glycoproteins(AFGPs)facilitate the survival of various organisms in the polar region by preventing internal ice accumulation via an adsorption-inhibition *** of AFGP antifreeze activity by the borate buffers has been widely acknowledged as the direct experimental evidence supporting the hydroxyl,rather than methyl,binding *** the other hand,perturbation of borate binding on the AFGP configuration,which might have considerable influence on the binding efficiency of not only the hydroxyl but also the methyl groups,has rarely been quantitatively *** we studied,using molecular dynamics simulations,the perturbation on the configuration of a solvated AFGP8 protein induced by the binding of one single borate *** the freezing point,this binding not only makes the disaccharide groups adjacent to the borate-binding disaccharide close to each other but also affects the entire AFGP8 *** structural changes induced by the binding of borate on different disaccharide sidechains exhibit clear site-specificities and the effect of borate binding on the structural changes is significantly reduced at higher *** study is valuable for further understanding the relationship between the structure and antifreeze activity of these antifreeze glycoproteins.

关键词： Antifreeze glycoproteins Borate anions Molecular dynamics Clustering analysis

Transient Absorption of the Chlorophyll a in Ethanol

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Chinese Journal of Chemical Physics 2006年第1期19卷 6-10页

作者： Ying Shi Y. J. Shiu Charlene Su S.H. lin ke-li han State key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 115023 Institute of Atomic and Molecular Sciences Academia Sinica.Taipei Department of Chemistry National Taiwan University Taipei

The excited state of Chlorophyll a is *** by ferntosecond transient absorption. The transient absorption spectra of Q band and By band of Chlorophyll a in ethanol have been observed. The fast kinetics of Chlorophyll a which exhibit two ultrafast components were also ineasured. The one is assigned to transient absorption of the inhomogencously broadened ground state absorption spectrum, while the other is the response of the solvent to the change of the electron configuration in the excited state due to solvation dynamics of the polar solvent molecules. To understand the anisotropy of Chlorophyll a in ethanol, the anisotropy profile was also performed by 405 nm excitation and found that the anisotropy profile is 0.143. The possible combination of θda, θdb and η at at excitation of By band has been simulated.

关键词： Femtosecond Chlorophyll a Transient absorption

The distribution characteristics of short period geomagnetic variations in Shaanxi region

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Acta Seismologica Sinica(English Edition) 1998年第6期11卷 64-72页

作者： GUO HUA FAN TONG QI YAO ke li han ke JIA ZHU ZUO WEN GU Institute of Geophysics, China Seismological Bureau, Beijing 100081, China 1. Institute of Geophysics China Seismological Bureau 100081 Beijing China

In order to investigate the characteristics of short period geomagnetic variations in Shaanxi region, a temporary measurement profile from Shiquan in the southern part of Shaanxi to Ningxian in Gansu was set up in September of 1996 to carry out simultaneous observation of three component geomagnetic variations along the profile. The vertical transfer functions, the horizontal transfer functions and the spectral component′s relationship of each period segment at each site in the period range from 3 min to 2 h were statistically calculated. Random data theory was applied to the data processing for reference, which led to a relatively good result. Analysis of the data point out that short period geomagnetic variations are affected by the regional influence of underground anomalous inductive current concentration between Wugong and Qianling in the nearly E W direction and by the influence of local inductive current in nearby area of measurement site. The main distribution feature is that vertical transfer functions reverse between Wugong and Qianling and frequency responses of the transfer functions have maximum at period about 20 min.

关键词： geomagnetic vertical transfer function geomagnetic horizontal transfer function anomalous inductive current concentration

Ab Initio Study of the Reaction: H + SO_2→HO + SO

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Chinese Chemical Letters 1998年第2期9卷 181-185页

作者： Rong Shun ZHU Jian Hua HUANG ke li han and Guo Zhong HE(State key Laboratory of Molecular Reaction Dynamics,Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023) Chinese Acad Sci Dalian Inst Chem Phys State key Lab Mol React Dynam Dalian 116023 Peoples R China

The reaction of H+ SO2→HO + SO was theoretically investigated sing ab initio MOmethods, and HF/TZV (d, p) level of theory was employed to locate stationary points which werethen characterized by calculation of the vibrational frequencies. Energies were estimated at the optimized geometries using MP2/TZV (d, p) calculations. The results show that the caIculated geometries- frequencies. and thermochemical data were in good agreement with available experi-mental values. The IRC calculations confirmed that nonplanar HSO2 and HOSO adducts shouldbe more reasonable than those of planar conformation.

关键词： Hydrogen Sulfur dioxtde Reaction Ab initio calculation