The dioxygen activation catalyzed by 4-hydorxylphenyl pyruvate dioxygenase(HPPD)were reinvestigated by using hybrid quantum mechanics/molecular mechanics(QM/MM)approaches at the B3LYP/6-311++G(d,p):AMBER level.These s...The dioxygen activation catalyzed by 4-hydorxylphenyl pyruvate dioxygenase(HPPD)were reinvestigated by using hybrid quantum mechanics/molecular mechanics(QM/MM)approaches at the B3LYP/6-311++G(d,p):AMBER level.These studies showed that this reaction consisted of two steps including the dioxygen addition/decarboxylation and hetero O-O bond cleavage,where the first step was found to be rate-determining.The former step initially runs on a septet potential energy surface(PES),then switches to a quintet PES after crossing a septet/quintet minimum energy crossing point(MECP)5-7M2,whereas the rest step runs on the quintet PES.The reliability of our theoretical predictions is supported by the excellent agreement of the calculated free-energy barrier value of 16.9 kcal/mol with available experimental value of 16-17 kcal/mol.The present study challenges the widely accepted view which holds that the O2activation catalyzed byα-keto glutamate(α-KG)dioxygenase mainly runs on the quintet PES and provides new insight into the catalytic mechanism ofα-KG dioxygenase and/or other related Fe(Ⅱ)-dependent oxygenase.展开更多
The infrared （IR） spectra of the N-methylacetamide molecule in water are calculated by using the MD simulation with high-level QM]MM corrections. The B3LYP and MP2 levels with 6-31 I＋＋G＊＊ basis set are used for ...The infrared （IR） spectra of the N-methylacetamide molecule in water are calculated by using the MD simulation with high-level QM]MM corrections. The B3LYP and MP2 levels with 6-31 I＋＋G＊＊ basis set are used for the QM region, respectively, Our results show all IR spectra at the B3LYP level are well consistent with the corresponding MP2 results. A dynamical charge fluctuation is observed for each atom along the simulation trajectories due to the electrostatic polarization （EP） effects from surrounding solvent environment, We find that the QM/MM corrected IR spectra satisfactorily reprodnce the experimental vibrational features of amide 1-11I modes.展开更多
Metal–organic frameworks (MOFs) as photocatalysts and photocatalyst supports combine several advantages of homogeneous and heterogeneous catalyses, including stability, post-reaction separation, catalyst reusability,...Metal–organic frameworks (MOFs) as photocatalysts and photocatalyst supports combine several advantages of homogeneous and heterogeneous catalyses, including stability, post-reaction separation, catalyst reusability,and tunability, and they have been intensively studied for photocatalytic applications. There are several reviews that focus mainly or even entirely on experimental work. The present review is intended to complement those reviews by focusing on computational work that can provide a further understanding of the photocatalytic properties of MOF photocatalysts. We first present a summary of computational methods, including density functional theory, combined quantum mechanical and molecular mechanical methods, and force fields for MOFs. Then, computational investigations on MOF-based photocatalysis are briefly discussed. The discussions focus on the electronic structure, photoexcitation, charge mobility, and photoredox catalysis of MOFs, especially the widely studied Ui O-66-based MOFs.展开更多
P450 cin(CYP176 A1) isolated from Citrobacter braakii is a biodegradation enzyme that catalyzes the enantiospecific conversion of 1,8-cineole to(1 R)-6β-hydroxycineole. In many P450 family members the mechanism of pr...P450 cin(CYP176 A1) isolated from Citrobacter braakii is a biodegradation enzyme that catalyzes the enantiospecific conversion of 1,8-cineole to(1 R)-6β-hydroxycineole. In many P450 family members the mechanism of proton delivery for O2activation is proposed to require a conserved acid-alcohol dyad in the active area, while P450 cin has no such residue with alcohol but asparagine instead. In the present work, the mechanism of the first proton transfer of O2activation in P450 cin has been investigated by molecular dynamics(MD) and hybrid quantum mechanics/molecular mechanics(QM/MM) techniques. The MD simulation suggests there are two hydrogen bonding networks around the active site, one involving Asp241 and the other involving Glu356. According to our MD and QM/MM calculations, this Asp241 channel is proposed to be the energy accessible. MD results show that the hydrogen bonds around the substrate may contribute to regio-and stereo-oxidation of the substrate.展开更多
Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 （CYP2D6） is a key enzyme for d...Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 （CYP2D6） is a key enzyme for drug metabolism and responsible for the metabolism of about one third marketed drugs. Aripiprazole is an atypical an- tipsychotic and metabolized by CYP2D6 to its hydroxylated form. In this study, a series of computational methods were performed to understand how CYP2D6 accomplishes the 4-hydroxylation of aripiprazole. Molecular docking and molecular dynamics simulations were first performed to prepare the initial conformations for QM/MM calcula- tions. The results revealed two possible conformations for the drug-CYP2D6 complex. The ONIOM method for QM/MM calculations was then carried out to show detailed reaction pathways for the CYP2D6-catalyzed aripipra- zole hydroxylation reaction, which demonstrated that the dominant reactive channel was electrophilic and involved an initial attack on the n-system of the dichlorophenyl group of aripiprazole to produce cation δ-complex. Further- more, the product complex for each conformation was thermodynamically stable, which is in good agreement with previous reports.展开更多
目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys...目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys)并计算其结合分数(binding score)。然后将得出的分数与从QM/MM计算的结合能力以Z-score和辨别力(DP)作比较。从而评估Surflex-Dock和QM/MM的准确性。结果:Surflex-Dock的DPi值比QM/MM高,显示Surflex-Dock的辨别力较低。结论:因QM/MM计算速度慢,本研究认为Surflex-Dock可用作快速虚拟筛选,而较准确的QM/MM则适合用于对拥有较高结合分数的化合物进行再评分(rescoring)。展开更多
Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics（QM/MM） study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylam...Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics（QM/MM） study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylamine N-acetyltransferases（NATs） and the results strongly support a direct acetyl group transfer process rather than a stepwise one.The isoniazid was strictly restrained in proper relative position to accept the acetyl group by a Hydrogen-bond network formed by the residues at the active center.The residues,His110 and Cys70,would be functioned as ＇general base＇ rather than ＇general acid＇.If all the residues（including H2O molecules） were removed from the system,the activation energy will be increased from 145.1 to 243.3 kJ/mol.The calculations met the experimental data with good agreement.展开更多
基金supported by the National Key R&D Program(No.2021YFD1700100)National Natural Science Foundation of China(Nos.21837001,21273089)+2 种基金the Open Project Fund of the Key Laboratory of the Pesticides and Chemical Biology of Central China Normal University(No.2018-A01)the Fundamental Research Funds for the Central Universitiesthe Fundamental Research Funds for the South-Central University for Nationalities(No.CZW20020)。
文摘The dioxygen activation catalyzed by 4-hydorxylphenyl pyruvate dioxygenase(HPPD)were reinvestigated by using hybrid quantum mechanics/molecular mechanics(QM/MM)approaches at the B3LYP/6-311++G(d,p):AMBER level.These studies showed that this reaction consisted of two steps including the dioxygen addition/decarboxylation and hetero O-O bond cleavage,where the first step was found to be rate-determining.The former step initially runs on a septet potential energy surface(PES),then switches to a quintet PES after crossing a septet/quintet minimum energy crossing point(MECP)5-7M2,whereas the rest step runs on the quintet PES.The reliability of our theoretical predictions is supported by the excellent agreement of the calculated free-energy barrier value of 16.9 kcal/mol with available experimental value of 16-17 kcal/mol.The present study challenges the widely accepted view which holds that the O2activation catalyzed byα-keto glutamate(α-KG)dioxygenase mainly runs on the quintet PES and provides new insight into the catalytic mechanism ofα-KG dioxygenase and/or other related Fe(Ⅱ)-dependent oxygenase.
基金supported by the National Natural Science Foundation of China(22275097,61875090,21772095,and 91833306)the Key Giant Project of Jiangsu Educational Committee(19KJA180005)+5 种基金the Fifth 333 Project of Jiangsu Province of China(BRA2019080)the 1311 Talents Program of Nanjing University of Posts and Telecommunicationsthe Natural Science Foundation of Jiangsu Higher Education Institutions(22KJB150030)the Scientific Starting Fund from Nanjing University of Posts and Telecommunications(NUPTSF)(NY219160)the Natural Science Foundation of Nanjing University of Posts and Telecommunications(NY221092 and NY222148)the Open Research Fund of State Key Laboratory of Organic Electronics and Information Displays。
基金supported by the Natural Science Foundation of China(Nos.21306070 and 20966003)the Science&Technology Programs of Education Department of Jiangxi Province(No.GJJ12191)
文摘The infrared （IR） spectra of the N-methylacetamide molecule in water are calculated by using the MD simulation with high-level QM]MM corrections. The B3LYP and MP2 levels with 6-31 I＋＋G＊＊ basis set are used for the QM region, respectively, Our results show all IR spectra at the B3LYP level are well consistent with the corresponding MP2 results. A dynamical charge fluctuation is observed for each atom along the simulation trajectories due to the electrostatic polarization （EP） effects from surrounding solvent environment, We find that the QM/MM corrected IR spectra satisfactorily reprodnce the experimental vibrational features of amide 1-11I modes.
基金supported as part of the Nanoporous Materials Genome Center by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, under Award No. DE-FG0217ER16362
文摘Metal–organic frameworks (MOFs) as photocatalysts and photocatalyst supports combine several advantages of homogeneous and heterogeneous catalyses, including stability, post-reaction separation, catalyst reusability,and tunability, and they have been intensively studied for photocatalytic applications. There are several reviews that focus mainly or even entirely on experimental work. The present review is intended to complement those reviews by focusing on computational work that can provide a further understanding of the photocatalytic properties of MOF photocatalysts. We first present a summary of computational methods, including density functional theory, combined quantum mechanical and molecular mechanical methods, and force fields for MOFs. Then, computational investigations on MOF-based photocatalysis are briefly discussed. The discussions focus on the electronic structure, photoexcitation, charge mobility, and photoredox catalysis of MOFs, especially the widely studied Ui O-66-based MOFs.
基金supported by the National Natural Science Foundation of China(No.21573237,21603227,21403242,21703246)the Natural Science Foundation of Fujian Province(2017J05032)
文摘P450 cin(CYP176 A1) isolated from Citrobacter braakii is a biodegradation enzyme that catalyzes the enantiospecific conversion of 1,8-cineole to(1 R)-6β-hydroxycineole. In many P450 family members the mechanism of proton delivery for O2activation is proposed to require a conserved acid-alcohol dyad in the active area, while P450 cin has no such residue with alcohol but asparagine instead. In the present work, the mechanism of the first proton transfer of O2activation in P450 cin has been investigated by molecular dynamics(MD) and hybrid quantum mechanics/molecular mechanics(QM/MM) techniques. The MD simulation suggests there are two hydrogen bonding networks around the active site, one involving Asp241 and the other involving Glu356. According to our MD and QM/MM calculations, this Asp241 channel is proposed to be the energy accessible. MD results show that the hydrogen bonds around the substrate may contribute to regio-and stereo-oxidation of the substrate.
基金the China Postdoctoral Science Foundation，Shanghai Committee of Science and Technology，National Natural Science Foundation of China，Innovation Program of Shanghai Municipal Education Commission
文摘Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 （CYP2D6） is a key enzyme for drug metabolism and responsible for the metabolism of about one third marketed drugs. Aripiprazole is an atypical an- tipsychotic and metabolized by CYP2D6 to its hydroxylated form. In this study, a series of computational methods were performed to understand how CYP2D6 accomplishes the 4-hydroxylation of aripiprazole. Molecular docking and molecular dynamics simulations were first performed to prepare the initial conformations for QM/MM calcula- tions. The results revealed two possible conformations for the drug-CYP2D6 complex. The ONIOM method for QM/MM calculations was then carried out to show detailed reaction pathways for the CYP2D6-catalyzed aripipra- zole hydroxylation reaction, which demonstrated that the dominant reactive channel was electrophilic and involved an initial attack on the n-system of the dichlorophenyl group of aripiprazole to produce cation δ-complex. Further- more, the product complex for each conformation was thermodynamically stable, which is in good agreement with previous reports.
文摘目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys)并计算其结合分数(binding score)。然后将得出的分数与从QM/MM计算的结合能力以Z-score和辨别力(DP)作比较。从而评估Surflex-Dock和QM/MM的准确性。结果:Surflex-Dock的DPi值比QM/MM高,显示Surflex-Dock的辨别力较低。结论:因QM/MM计算速度慢,本研究认为Surflex-Dock可用作快速虚拟筛选,而较准确的QM/MM则适合用于对拥有较高结合分数的化合物进行再评分(rescoring)。
基金Supported by the National Natural Science Foundation of China (No. 20603030 and No. 21103080)the Natural Science Foundation of Shandong Province (No. ZR2010BL023)
文摘Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics（QM/MM） study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylamine N-acetyltransferases（NATs） and the results strongly support a direct acetyl group transfer process rather than a stepwise one.The isoniazid was strictly restrained in proper relative position to accept the acetyl group by a Hydrogen-bond network formed by the residues at the active center.The residues,His110 and Cys70,would be functioned as ＇general base＇ rather than ＇general acid＇.If all the residues（including H2O molecules） were removed from the system,the activation energy will be increased from 145.1 to 243.3 kJ/mol.The calculations met the experimental data with good agreement.
基金supported by the National Science Foundation(Grant number:0817940to HG)the DOE Office of Biological and Environmental Research-Genome to Life Program through the BioEnergy Science Center(BESC)(to FC)+2 种基金the Sun Grant Initiative(to FC)the computer resources(Newton)from University of Tennessee Knoxvillethe NSF TeraGrid resources provided by the University of Texas at Austin
