- 作 者: ( "zexing cao" OR "ze-xing cao" )
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Water-Regulated Mechanisms for Degradation of Pesticides Paraoxon and Parathion by Phosphotriesterase: Insight from QM/MM and MD SimulationsChemistry - An Asian Journal (IF 4.568) Pub Date : 2022-05-19 ,DOI:10.1002/asia.202200439Yuzhuang Fu, Fangfang Fan, Binju Wang, Zexing CaoThe enzymatic degradation of pesticides paraoxon (PON) and parathion (PIN) by phosphotriesterase (PTE) has been investigated by QM/MM calculations and MD simulations. In the PTE-PON complex, Zn α and Zn β in the active site are five- and six-coordinated, respectively, while both zinc ions are six coordinated with the Zn α -bound water molecule (WT1) for the PTE-PIN system. The hydrolytic reactions ...
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QM/MM and MM MD simulations on decontamination of the V-type nerve agent VX by phosphotriesterase: toward a comprehensive understanding of steroselectivity and activityPhysical Chemistry Chemical Physics (IF 3.676) Pub Date : 2022-04-18 ,DOI:10.1039/d2cp00773hFangfang Fan, Yongchao Zheng, Yuzhuang Fu, Yuwei Zhang, He Zheng, Changjiang Lyu, Linyu Chen, Jun Huang, Zexing CaoDue to deadly toxicity and high environmental stability of the nerve agent VX, an efficient decontamination approach is desperately needed in tackling its severe threat to human security. The enzymatic destruction of nerve agents has been generally considered as one of the most effective ways, and here the hydrolysis of VX by phosphotriesterase (PTE) was investigated by extensive QM/MM and MM MD simulations ...
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Hydroboration of CO2 to Methyl Boronate Catalyzed by a Manganese Pincer Complex: Insights into the Reaction Mechanism and Ligand EffectInorganic Chemistry (IF 5.165) Pub Date : 2022-03-31 ,DOI:10.1021/acs.inorgchem.2c00285Lin Zhang, Yaqi Zhao, Chong Liu, Min Pu, Ming Lei, Zexing CaoThe conversion of carbon dioxide to fuels, polymers, and chemicals is an attractive strategy for the synthesis of high-value-added products and energy-storage materials. Herein, the density functional theory method was employed to investigate the reaction mechanism of CO2 hydroboration catalyzed by manganese pincer complex, [Mn(Ph2PCH2SiMe2)2NH(CO)2Br]. The carbonyl association and carbonyl dissociation ...
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Electron Regulation of Single Indium Atoms at the Active Oxygen Vacancy of In2O3(110) for Production of Acetic Acid and Acetone through Direct Coupling of CH4 with CO2Chemistry - An Asian Journal (IF 4.568) Pub Date : 2022-01-27 ,DOI:10.1002/asia.202101383Denghui Ma, Zexing CaoState Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 360015 P. R. ChinaThe replacement of single indium atoms by Ga and Al at the active oxygen vacancy (Ov) site of In2O3(110) surface can significantly facilitate the direct coupling of CO2 and CH4 to C2 and C3 products. ...
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Dynamic Locking of Interfacial Side Reaction Sites Promotes Aluminum-Air Batteries Close to Theoretical CapacityAdvanced Sustainable Systems (IF 6.271) Pub Date : 2021-12-29 ,DOI:10.1002/adsu.202100420Yuanlin Huang, Lei Fang, Yu Gu, Pingshi Wang, Hao Yan, Yanjie Wang, Zexing Cao, Zhaowu Tian, Bingwei Mao, Li ZhangState Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemistry College of Chemistry and Chemical Engineering Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM) Tan Kah Kee Innovation Laboratory Xiamen University Xiamen Fujian 361005 ChinaAluminum metal has been regarded as a promising anode material for aqueous metal-air batteries. However, the stable cycling of Al anodes is challenging due to the severe parasitic corrosion of Al metal in alkaline electrolytes. Here, a novel additive, n-octylphosphonic acid (OPA), is introduced into the typical NaOH electrolyte system to improve the interfacial stability of Al anodes and thus promote ...
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Rational Design of Main Group Metal-Embedded Nitrogen-Doped Carbon Materials as Frustrated Lewis Pair Catalysts for CO2 Hydrogenation to Formic AcidACS Applied Materials & Interfaces (IF 9.229) Pub Date : 2021-12-22 ,DOI:10.1021/acsami.1c20230Yue Zhang, Yirong Mo, Zexing CaoDeveloping efficient and inexpensive main group catalysts for CO2 conversion and utilization has attracted increasing attention, as the conversion process would be both economical and environmentally benign. Here, based on the main group element Al, we designed several heterogeneous frustrated Lewis acid/base pair (FLP) catalysts and performed extensive first-principles calculations for the hydrogenation ...
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Degradation of pesticides diazinon and diazoxon by phosphotriesterase: insight into divergent mechanisms from QM/MM and MD simulationsPhysical Chemistry Chemical Physics (IF 3.676) Pub Date : 2021-12-06 ,DOI:10.1039/d1cp05034fYuzhuang Fu, Yuwei Zhang, Fangfang Fan, Binju Wang, Zexing CaoEnzymatic hydrolysis by phosphotriesterase (PTE) is one of the most effective ways of degrading organophosphorus pesticides, but the catalytic efficiency depends on the structural features of substrates. Here the enzymatic degradation of diazinon (DIN) and diazoxon (DON), characterized by PS and PO, respectively, have been investigated by QM/MM calculations and MM MD simulations. Our calculations demonstrate ...
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Aggregation-induced emission spectra of triphenylamine salicylaldehyde derivatives via excited-state intramolecular proton transfer revealed by molecular spectral and dynamics simulationsRSC Advances (IF 3.361) Pub Date : 2021-11-18 ,DOI:10.1039/d1ra07388eQing Zhang, Yuanyuan Li, Zexing Cao, Chaoyuan Zhu
Aggregation-induced emission (AIE) spectra accompanied by excited state intramolecular proton transfer (ESIPT) for two triphenylamine salicylaldehyde derivatives (namely, TS and TS-OMe) are investigated by performing molecular spectral and dynamics simulations associated with the hybrid quantum mechanics/molecular mechanics (QM/MM) at the quantum level of the time-dependent density functional theory
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Adsorption and Decomposition of Sarin on Dry and Wet Cu2O(111) and CuO(111) Surfaces: Insight from First-Principles CalculationsThe Journal of Physical Chemistry C (IF 4.126) Pub Date : 2021-10-27 ,DOI:10.1021/acs.jpcc.1c07072Denghui Ma, Zexing CaoState Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of ChinaAdsorption and destruction of the nerve agent sarin (GB) on the pristine and hydroxylated/water surfaces of copper oxides have been investigated by extensive first-principles calculations, and the unsaturated Cu site in both CuO(111) and Cu2O(111) surfaces was predicted to have strong GB-adsorption ability through its bonding interaction with the phosphoryl oxygen of sarin. Decomposition of GB on the ...
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Anti-Electrostatic Main Group Metal–Metal Bonds That Activate CO2The Journal of Physical Chemistry Letters (IF 6.475) Pub Date : 2021-08-04 ,DOI:10.1021/acs.jpclett.1c02134Chuan-Kai Tang, Ya-Zhou Li, Fang Ma, Zexing Cao, Yirong MoThere has been growing interest in the CO2 capture and reduction by transition-metal-free catalysts. Here we performed a proof-of-concept study using an ab initio valence bond method called the block-localized wave function (BLW) method. The integrated BLW and density function theory (DFT) computations demonstrated that heterobimetallic Ae+/Al(I) (Ae represents alkaline earth metals Mg and Ca) Lewis ...
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Conformational change of His64 and substrate transportation: Insight into a full picture of enzymatic hydration of CO2 by carbonic anhydraseFrontiers in Chemistry (IF 5.221) Pub Date : 2021-06-28 ,DOI:10.3389/fchem.2021.706959Yuzhuang Fu, FangFang Fan, Yuwei Zhang, Binju Wang, Zexing Cao
The enzymatic hydration of CO2 into HCO3- by carbonic anhydrase (CA) is highly efficient and environment-friendly measure for CO2 sequestration. Here extensive MM MD and QM/MM MD simulations were used to explore the whole enzymatic process, and a full picture of the enzymatic hydration of CO2 by CA was achieved. Prior to CO2 hydration, the proton transfer from the water molecule (WT1) to His64 is the
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Tuning the Activity of Molybdenum Carbide MXenes for CO2 Electroreduction by Embedding the Single Transition-Metal AtomThe Journal of Physical Chemistry C (IF 4.126) Pub Date : 2021-06-15 ,DOI:10.1021/acs.jpcc.1c03713Yue Zhang, Zexing CaoState Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, ChinaMo2C electrocatalysts may reduce CO2 to CH4 with the low overpotentials, but also accelerate the hydrogen evolution reaction (HER). Here a series of the transition-metal-embedded Mo2C (M@Mo2C) MXenes are screened by first-principles calculations, and Cr@Mo2C, Mn@Mo2C, Fe@Mo2C, and Co@Mo2C are predicted to have higher activity and selectivity toward CO2ER than HER, compared to the pristine Mo2C. In ...
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Explore the interaction mechanism between zein and EGCG using multi-spectroscopy and molecular dynamics simulation methodsFood Hydrocolloids (IF 9.147) Pub Date : 2021-06-01 ,DOI:10.1016/j.foodhyd.2021.106906Chengzhi Liu, Nan Lv, Gerui Ren, Ruibo Wu, Binju Wang, Zexing Cao, Hujun XieZein as a kind of carrier material has attracted extensive interest, while the interaction mechanism between zein and nutrients is still elusive. In this work, the binding mechanism of zein with epigallocatechin-3-gallate (EGCG) was investigated via multi-spectroscopy and molecular dynamics (MD) simulation. The quenching of zein by EGCG is mainly static quenching, and the secondary structure of zein ...
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Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOXACS Catalysis (IF 13.084) Pub Date : 2021-05-06 ,DOI:10.1021/acscatal.1c00898Jia Liu, Peng Wu, Shengheng Yan, Yuanyuan Li, Zexing Cao, Binju WangThe combined molecular dynamics (MD) simulations and quantum mechanical/molecular mechanics (QM/MM) calculations have been performed to address the longstanding issue of the “dioxygen activation” by the nonheme diiron monooxygenase myo-inositol oxygenase (MIOX). MIOX utilizes a mixed-valence Fe2(III)Fe1(II) cluster for catalysis. It is well recognized that the Fe2(III) site is responsible for the substrate ...
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Packing Effect on Light Emission of Naphthyridine-Based Luminophor: Insights from Quantum Mechanics and Quantum Mechanics/Molecular Mechanics CalculationsThe Journal of Physical Chemistry B (IF 2.991) Pub Date : 2021-03-15 ,DOI:10.1021/acs.jpcb.1c01557Qing Zhang, Zexing CaoState Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of ChinaLuminescent properties of the naphthyridine-based luminophor, 2,7-di(9,9-dimethylacridin-10(9H)-yl)-1,8-naphthyridine (DMAC-ND), have been explored by using quantum mechanics and quantum mechanics/molecular mechanics calculations. Based on different packing models for DMAC-ND monomer in tetrahydrofuran (THF) solution and its crystal and amorphous aggregated states, the morphology dependence of light ...
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CO2 Activation and Capture on a Si-Doped h-BN Sheet: Insight into the Local Bonding Effect of Single Si SitesThe Journal of Physical Chemistry C (IF 4.126) Pub Date : 2021-03-01 ,DOI:10.1021/acs.jpcc.0c10080Lei Fang, Zexing CaoState Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, ChinaInert CO2 is only physically adsorbed on the surface of h-BN and graphene two-dimensional (2D) materials. However, a Si-doped h-BN sheet is able to capture CO2 directly through chemisorption under mild conditions. Herein, first-principles calculations and ab initio molecular dynamics (AIMD) simulations have been performed to explore the interaction between CO2 and the Si-doped h-BN sheet, and CO2 activation ...
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Catalytic Coupling of CH4 with CO2 and CO by a Modified Human Carbonic Anhydrase Combined with Oriented External Electric Fields: Mechanistic Insights from DFT CalculationsOrganometallics (IF 3.876) Pub Date : 2020-12-09 ,DOI:10.1021/acs.organomet.0c00676Denghui Ma, Hujun Xie, Zexing CaoThe leading edge of biocatalysis is human intervention to expand the specificity of the reactions, so that enzymes can catalyze an impressive range of challenging chemical reactions. Here density functional theory (DFT) calculations were used to explore the catalytic coupling of CH4 with CO2 and CO into value-added chemicals by a rhodium(I)-substituted human carbonic anhydrase [Rh(hCAII)] under the ...
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Atomically dispersed Cu and Fe on N-doped carbon materials for CO2 electroreduction: insight into the curvature effect on activity and selectivityRSC Advances (IF 3.361) Pub Date : 2020-11-26 ,DOI:10.1039/d0ra08857aYue Zhang, Lei Fang, Zexing Cao
CO2 electroreduction reaction (CO2ER) by single metal sites embedded in N-doped graphene (M@N-Gr, M = Cu and Fe) and carbon nanotubes (M@N-CNT, M = Cu and Fe) has been explored by extensive first-principles calculations in combination with the computational hydrogen electrode model. Both atomically dispersed Cu and Fe nanostructures, as the single atom catalysts (SACs), have higher selectivity towards
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Planar Tetracoordinate Silicon in Organic Molecules As Carbenoid‐Type Amphoteric Centers: A Computational StudyChemistry - A European Journal (IF 5.236) Pub Date : 2020-10-25 ,DOI:10.1002/chem.202004298Yuwei Zhang, Caiyun Zhang, Yirong Mo, Zexing CaoDesigning and synthesizing a stable compound with a planar tetracoordinate silicon (ptSi) center is a challenging goal for chemists. Here, a series of potential aromatic ptSi compounds composed of four conjugated rings shared by a centrally embedded Si atom are theoretically designed and computationally verified. Both Born–Oppenheimer molecular dynamics (BOMD) simulations and potential energy surface ...
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Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions.Journal of Chemical Theory and Computation (IF 6.006) Pub Date : 2020-09-14 ,DOI:10.1021/acs.jctc.0c00551Yuwei Zhang,Zexing Cao,John Zenghui Zhang,Fei XiaThe double-well model is usually used to describe the conformational transition between two states of a protein. Since conformational changes usually occur within a relatively large time scale, coarse-grained models are often used to accelerate the dynamic process due to their inexpensive computational cost. In this work, we develop a double-well ultra-coarse-grained (DW-UCG) model to describe the ...
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QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase.Physical Chemistry Chemical Physics (IF 3.676) Pub Date : 2020-08-22 ,DOI:10.1039/d0cp03053hRonny Cheng,Chun Wu,Zexing Cao,Binju WangNitrite reductases are enzymes that aid in the denitrification process by catalyzing the reduction of nitrite to nitric oxide gas. Since this reaction is the first committed step that involves gas formation, it is regarded to be a vital step for denitrification. However, the mechanism of copper-containing nitrite reductase is still under debate due to the discrepancy between the theoretical and experimental ...
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Oxygen migration and optical properties of coronene oxides and their persulfurated derivatives: insight into the electric field effect and the oxygen-site dependence.Physical Chemistry Chemical Physics (IF 3.676) Pub Date : 2020-08-11 ,DOI:10.1039/d0cp03381bQing Zhang,Yuanyuan Li,Zexing CaoOxygen migration and spectroscopic properties of coronene (C24) epoxides and persulfurated coronene (PSC) oxides have been investigated by using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The rim-oxide is predicted to be more energetically favorable than the oxygen-centered configuration, and the application of an external electric field can accelerate the ...
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Tackling the Inertness of CO2: Facile Activation and Electroreduction on the Metal-Free SiN4C4 Monolayer SheetThe Journal of Physical Chemistry C (IF 4.126) Pub Date : 2020-08-03 ,DOI:10.1021/acs.jpcc.0c06076Lei Fang, Caiyun Zhang, Xinrui Cao, Zexing CaoCapture and activation of CO2 play a crucial role in its catalytic transformation into fuels and chemicals. Here a two-dimensional SiN4C4 monolayer material with dispersed SiN4 sites was predicted to have high stability and unusual capability to tackle the inertia of CO2 by extensive first-principles calculations and ab initio molecular dynamics simulations. The chemical adsorption of CO2 on the SiN4C4 ...
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pH-Dependent transfer hydrogenation or dihydrogen release catalyzed by a [(η6-arene)RuCl(κ2-N,N-dmobpy)]+ complex: a DFT mechanistic understandingRSC Advances (IF 3.361) Pub Date : 2020-3-11 ,DOI:10.1039/c9ra10651kChenguang Luo, Longfei Li, Xin Yue, Pengjie Li, Lin Zhang, Zuoyin Yang, Min Pu, Zexing Cao, Ming Lei
The reaction mechanism of the pH-dependent transfer hydrogenation of a ketone or the dehydrogenation of formic acid catalyzed by a [(η6-arene)RuCl(κ2-N,N-dmobpy)]+ complex in aqueous media has been investigated using the density functional theory (DFT) method. The TM-catalyzed TH of ketones with formic acid as the hydrogen source proceeds via two steps: the formation of a metal hydride and the transfer
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Mechanisms and kinetics of the low-temperature oxidation of 2-methylfuran: insight from DFT calculations and kinetic simulations.Physical Chemistry Chemical Physics (IF 3.676) Pub Date : 2020-01-23 ,DOI:10.1039/c9cp05937gYuanyuan Li,Zexing CaoThe low-temperature oxidation (LTO) mechanisms of the 2-methylfuran (2-MF) biofuel and the corresponding thermodynamic and kinetic properties have been explored by density functional theory (DFT) and composite G4 methodologies as well as kinetic simulations. The O2 addition to the main furylCH2 radical from the methyl dehydrogenation in 2-MF forms three peroxide radicals PO1, PO2, and PO3 with the ...
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Isoelectronic Doping and External Electric Field Regulate the Gas-Separation Performance of GraphdiyneThe Journal of Physical Chemistry C (IF 4.126) Pub Date : 2020-01-17 ,DOI:10.1021/acs.jpcc.9b11062Lei Fang, Zexing CaoState Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, ChinaThe first-principles calculations and molecular dynamics (MD) simulations have been used to explore the effects of boron nitride (BN) doping and an external electric field on the diffusion of gases (N2, CO, H2, CO2, and CH4) through a graphdiyne (GDY) membrane. BN-doped graphdiyne-like monolayers (GDY-BN and GDY-fBN) were predicted to have better permeability than the GDY membrane for the diffusion ...
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Theory Demonstrated a “Coupled” Mechanism for O2 Activation and Substrate Hydroxylation by Binuclear Copper MonooxygenasesJournal of the American Chemical Society (IF 15.419) Pub Date : 2019-11-20 ,DOI:10.1021/jacs.9b09172Peng Wu, Fangfang Fan, Jinshuai Song, Wei Peng, Jia Liu, Chunsen Li, Zexing Cao, Binju WangMultiscale simulations have been performed to address the longstanding issue of the "dioxygen activation" by the binucle-ar copper monooxygenases (PHM and DβM), which were traditionally classified as the "noncoupled" binuclear copper enzymes. Our QM/MM calculations rule out that CuM(II)-O2• is an active species for H-abstraction from the substrate. By contrast, CuM(II)-O2• would abstract an H atom ...
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Persulfurated Coronene and Its Chalcogenide Analogues: Insight into Effects of Peripheral SubstitutionThe Journal of Physical Chemistry A (IF 2.781) Pub Date : 2019-11-18 ,DOI:10.1021/acs.jpca.9b08401Qing Zhang,Zexing CaoState Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 360015, ChinaThe density functional theory (DFT) and time-dependent DFT methods have been used to investigate the persulfurated coronene (PSC) and its chalcogenide analogues (POC and PSeC), derived from the substitution of sulfur, oxygen, and selenium for all hydrogen atoms in coronene, respectively. The presence of peripheral S–S in PSC results in a σ-type lowest unoccupied molecular orbital and the dark low-lying ...
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Mechanistic Features in Al(I)-Mediated Oxidative Addition of Aryl C-F Bonds: Insights From Density Functional Theory Calculations.Frontiers in Chemistry (IF 5.221) Pub Date : 2019-09-26 ,DOI:10.3389/fchem.2019.00596Xiangfei Zhang,Ping Li,Binju Wang,Zexing Cao
The oxidative addition of a range of robust aryl C-F bonds to a single Al(I) center supported by a (NacNac)- bidentate ligand ((NacNac)- = [ArNC(Me)CHC(Me)NAr]- and Ar = 2,6- Pr 2 i C6H3) have been explored by density functional theory calculations. Our calculations demonstrate that the Al(I) center-mediated C-F insertion generally proceeds via the concerted mechanism that involve both the donation
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A Comprehensive Understanding of Enzymatic Degradation of the G-Type Nerve Agent by Phosphotriesterase: Revised Role of Water Molecules and Rate-Limiting Product ReleaseACS Catalysis (IF 13.084) Pub Date : 2019-07-01 ,DOI:10.1021/acscatal.9b01877Fangfang Fan,Yongchao Zheng,Yuwei Zhang,He Zheng,Jinyi Zhong,Zexing CaoNerve agents are highly toxic organophosphorus compounds, and the wild-type phosphotriesterase (PTE) enzyme is capable of hydrolyzing these organophosphates but with a low catalytic efficiency. Here the whole enzymatic detoxification process of the G-type nerve agent sarin by the PTE enzyme, including the substrate delivery, the chemical reaction, and the product release, has been explored by extensive ...
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