Shao Xueguang**,Jiang Haiyan,Cai Wensheng. Advances in Biomolecular Computing[J]. Progress in Chemistry, 2002, 14(01): 37-.
Hou Tingjun,Xu Xiaojie*. Applications of Genetic Algorithms to Computer-Aided Drug Design[J]. Progress in Chemistry, 2004, 16(01): 35-.
Hou Tingjun,Xu Xiaojie**. Calculations of Free Energies Based on the Combination of Molecular Dynamics Simulations and Continuum Solvation Model[J]. Progress in Chemistry, 2004, 16(02): 153-.
Li Wei**,Han Yongcai,Zhang Jinli. Advances in Computer Simulation of Macromolecule Self-assembly[J]. Progress in Chemistry, 2004, 16(03): 431-.
Haihua Song*,Jing Song. The Application of Computer-Aided Molecular Design in Selecting Solvents for Extractive Distillation[J]. Progress in Chemistry, 2006, 18(09): 1188-1193.
Guizhao Liang1,Hu Mei1,Yuan Zhou1,Zhiliang Li 1,2*. Modeling Techniques of Multidimensional Quantitative Structure-Activity Relationship in Computer-Aided Drug Design[J]. Progress in Chemistry, 2006, 18(01): 120-130.
Yi Xu1**,Junjiang lv1,Feng Ren1, Rong Chen1,Jiali Lu1, Zhiyu Wen2 . Progress on Computer Assisted Electrophoresis Microchip Design[J]. Progress in Chemistry, 2006, 18(04): 488-493.
Lei Yonglin**,Huo Jichuan,Duan Xiaohui,Ye Xu,Sun Chengcai. The Relations Between Carbocyanine Structures and Properties and Its Quantum Chemical Theoretic Calculation[J]. Progress in Chemistry, 2007, 19(06): 878-883.
Ye Deju1, Luo Xiaomin1, Shen Jianhua1, Zhu Weiliang1, Shen Xu1,2 , Jiang Hualiang1,2, Liu Hong1**
Liu Yuanhai1 Wang Yongjian2 Yu Ao1** Zhang Xinrui1 Li Jiuhong1. Quantum Chemistry Computation on pKa Values of Organic Compounds in Solution[J]. Progress in Chemistry, 2008, 20(09): 1241-1250.
Li Cailin Chen Yungui Wu Chaoling Zhou Jingjing PangLijuan. Theoretical and Experimental Studies on Metal-Carbon-Based Materials for Hydrogen Storage[J]. Progress in Chemistry, 2009, 21(6): 1101-1106.
Hydrogen is the most promising energy carrier in future and hydrogen storage technology is the key problem for hydrogen application. With the development of computational materials science, density functional theory(DFT) and first principles quantum mechanical calculations have been effectively utilized to study the performance of existing hydrogen storage materials and explore new light hydrogen storage materials. The theoretical and experimental studies on metal-carbon-based hydrogen storage materials in recent years are reviewed in this paper, including metal-decorated carbon nanotubes,C60 and transition-metal-ethylene complexes, and so on. The future of metal-carbon-based hydrogen storage materials is also anticipated.
Contents 1 Introduction 2 Metal decorated carbon-nanotubes and C60 hydrogen storage materials 2.1 Progress on experimental research 2.2 Progress on theoretical research 3 Transition-metal-ethylene complexes hydrogen storage 3.1 Progress on experimental research 3.2 Progress on theoretical research 4 Outlook
. Computational Chemistry of Protein Kinase A and Its Inhibitor Balanol[J]. Progress in Chemistry, 2010, 22(05): 993-1001.
Protein kinases regulate signal transduction pathways in cell by phosphorylating the protein kinase substrate, and they are important targets in drug design. Protein kinase A (PKA) is the first kinase that was obtained X-ray structure of its catalytic domain, and is regarded as prototype for protein kinase superfamily. The progress in computational chemistry study of protein kinase A has been reviewed, including the molecular dynamics simulation study of PKA holoenzyme and its C subunit and R subunit in aqueous solution, phosphoryl transfer mechanism, the binding free energy predicting and flexible docking of C subunit with its inhibitor balanol. Various computational approaches are applied to this system, including molecular dynamics simulation, dock, homology modeling, QM/MM.
Contents 1 Introduction 2 Molecular dynamics simulation study on PKA 2.1 Molecular dynamics simulation study on C subunit 2.2 Modeling of the complex of C subunit and R subunit 2.3 Molecular dynamics simulation study on R subunit 3 Phosphoryl transfer mechanism 4 Balanol 4.1 Prediction of binding free energy 4.2 Flexible protein-flexible ligand docking 4.3 Mechanism of high selectivity of balanol analogue BD2 4.4 Functional role of structure water molecules in the recognition of C subunit and BD2 5 Conclusion and outlook
. Theoretical Calculation of Cyclodextrins[J]. Progress in Chemistry, 2010, 22(05): 803-811.
Cyclodextrins have played an important role in the development of supramolecular chemistry. They have been extensively studied both experimentally and theoretically due to their special physical and chemical properties. In this paper, the progress in the theoretical calculations of the cyclodextrin chemistry over the past decade is reviewed. In particular, some recent applications of molecular dynamics simulations and free-energy calculations in the investigation of the recognition and assembly behavior of cyclodextrins are emphasized. In addition, the theoretical research trends of cyclodextrins are discussed.
Contents 1 Introduction 2 Computational methods 2.1 Quantum mechanics (QM) 2.2 Molecular mechanics/molecular dynamics (MM/MD) 2.3 Docking 2.4 Quantitative structure–activity relationship (QSAR) 3 Applications of molecular modeling to the study of cyclodextrins 3.1 Structural features of cyclodextrins 3.2 Hydration of cyclodextrins 3.3 Molecular recognition by cyclodextrins 3.4 Molecular self-assembly of cyclodextrins 4 Conclusion and outlook
Dongqi Wang, Wilfred F. van Gunsteren. Recent Advances in Computational Actinide Chemistry[J]. Progress in Chemistry, 2011, 23(7): 1566-1581.
We briefly reviewed the recent advances in computational actinide chemistry during the past ten years. They cover two issues: the geometrical and electronic structures, and reactions. The former addresses the An—O and M—An (M is another metal atom including An) bonds in the actinide molecular systems, and the latter the hydration and ligand exchange, the disproportionation, the oxidation, the reduction of uranyl, hydroamination, and the photolysis of uranium azide.
Contents 1 Introduction 2 Treatment of relativistic effects 3 Computational Models 3.1 Density functional theory 3.2 Wavefunction based ab initio methods 4 Applications in actinide chemistry 4.1 The role of 5f orbitals 4.2 Geometry and electronic structure 4.3 Reactions 5 Conclusion and outlook 6 Acknowledgement
Enrico Clementi, Giorgina Corongiu(author);Shuai Zhigang;Ma Zhongyun;Zhang Tian;Shang Yuan(translator). With Computers from Atoms to Macromolecular Systems[J]. Progress in Chemistry, 2011, 23(9): 1795-1830.
Zheng Yansheng, Zhuo Zhihao, Mo Qian, Li Junsheng. Molecular Simulation and Quantum Chemistry Calculation of Ionic Liquids[J]. Progress in Chemistry, 2011, 23(9): 1862-1870.
Molecular simulation is an effective method to study microstructure, thermodynamics and dynamic properties of ionic liquids from the molecule interaction.While quantum chemistry calculations can be used to study structure, properties and catalysis mechanism of ionic liquids theoretically at the molecular and electronic level.In this paper, the recent progress of molecular simulation applied in ionic liquids was reviewed; the studiees of different ionic liquids using molecular dynamic simulation and quantum chemistry calculations to obtain the structural properties, spectral properties (infrared spectrum,Raman spectrum) and reaction mechanisms of ionic liquids are mainly introduced.It aims to provide some theoretical advises for the research of structure-property relationship,interaction of ion pair,catalytic acivity sity,reaction pathway,activation energy, vibrational frequencies and design of ionic liquids.
Contents 1 Introduction 2 Molecular simulation of ionic liquids 3 Quantum chemical calculation of ionic liquids 3.1 Structural properties 3.2 Spectral properties 3.3 Reaction mechanism 4 Perspective
Shen Juan, Jin Bo, Jiang Qiying, Zhong Guoqing, Huo Jichuan. Computer Simulation Studies on Apatite Crystal and Its Interaction with Biologic Molecules[J]. Progress in Chemistry, 2012, 24(05): 737-746.
Contents 1 Introduction 2 Applications of computer simulation to the apatite crystal 3 Applications of computer simulation to the apatite substitution 4 The interaction of apaptite and other molecules or ions 4.1 The interaction of apaptite and water molecules 4.2 The interaction of apaptite and haloid ions 4.3 The interaction of apaptite and citric acid molecules 4.4 The interaction of apaptite and biologic molecules 5 Conclusions and Outlook
Lin Yingwu. Computer-Aided Rational Protein Design: From Myoglobin to Nitric Oxide Reductases[J]. Progress in Chemistry, 2012, 24(05): 784-789.
Contents 1 Introduction 2 Myoglobin: an ideal scaffold for protein molecular design 3 Nitric oxide reductase: both a chance and a challenge for protein molecular design 4 Exploring unknown areas: ongoing of protein molecular design 5 Conclusion and outlook
Su Peifeng, Wu Wei. Ab Initio Computational Method for Classical Valence Bond Theory[J]. Progress in Chemistry, 2012, 24(06): 1001-1007.
Wu Ruibo, Cao Zexing, Zhang Yingkai. Computational Simulations of Zinc Enzyme: Challenges and Recent Advances[J]. Progress in Chemistry, 2012, 24(06): 1175-1184.
Liu Yajun. Computational Photochemistry[J]. Progress in Chemistry, 2012, 24(06): 950-956.
Wu Menghao, Dai Jun, Zeng Xiaocheng. Ab Initio Computation Based Design of Three-Dimensional Structures of Carbon Allotropes[J]. Progress in Chemistry, 2012, 24(06): 1050-1057.
Sun Zhigang, Zhang Donghui. State-to-State Reactive Scattering by Quantum Wavepacket Method[J]. Progress in Chemistry, 2012, 24(06): 1153-1165.
Huang Cuiying, Li Yang, Wang Changsheng. Accurate and Rapid Calculation of the Hydrogen Bond Strengths and Hydrogen Bonding Potential Energy Curves for the Hydrogen-Bonded Complexes Containing Peptide Amides and/or Nucleic Acid Bases[J]. Progress in Chemistry, 2012, 24(06): 1214-1226.
Ren Yanrong, Tian Feifei, Zhou Peng. Computational Peptidology[J]. Progress in Chemistry, 2012, (9): 1674-1682.
Sheng Yuping, Yan Nan, Zhu Yutian, An Jian. Computer Simulation of Self-Assembly of Block Copolymers in Selective Solvent[J]. Progress in Chemistry, 2014, 26(0203): 358-365.
Due to the difference in the property of each block, block copolymers can self-assemble into various nanoscale morphologies spontaneously, including sphere, rod, ring, lamella, vesicle and compound micelle etc. These micelles have potential applications in nanotechnology such as drug delivery, catalysts, electronic information and so on. Recently, the computer simulations are widely used to monitor the process of self-assembly, reveal the mechanism of self-assembly, and illuminate the influence of various control factors on micellar structures, which can provide mentality and theoretical support for the experimental research. This review mainly summarizes the latest progresses in computer simulation of self-assembly of block copolymers in selective solvent, and discussed various effects on the micellar morphologies and the process of self-assembly. Moreover, the future development in this filed is also discussed in this review.
Contents 1 Introduction 2 Self-assembly of AB diblock copolymers in selective solvents 3 Self-assembly of ABA triblock copolymers in selective solvents 3.1 Self-assembly of ABA triblock copolymers in A-selective solvents 3.2 Self-assembly of ABA triblock copolymers in B-selective solvents 4 Self-assembly of ABC triblock copolymers in selective solvents 4.1 Self-assembly of ABC triblock copolymers in A-and C-selective solvents 4.2 Self-assembly of ABC triblock copolymers in C-selective solvents 4.3 Self-assembly of ABC miktoarm star terpolymers in selective solvents 5 Self-assembly of mixtures of copolymers in selective solvents 6 Conclusion and outlook
Li Yanchun, Li Yang. Computer Simulation Study on the Molecular Design and the Self-Assembly Process of Au-Nanoparticle and Polymer Composite System[J]. Progress in Chemistry, 2015, 27(7): 848-852.
Contents 1 Introduction 1.1 Au-nanoparticles 1.2 Polymers 2 Computer simulation methods 2.1 Quantum chemistry,QC 2.2 Molecular dynamics,MD 2.3 Brownian dynamics,BD 2.4 Dissipative particle dynamics,DPD 3 Assembly of Au-nanoparticles and polymer composites 3.1 Au-nanoparticles and homopolymer 3.2 Au-nanoparticles and copolymer 4 Conclusion
Xiaoyao Yin, Fei Li, Xiaochen Bo, Zhigang Luo, Xiaolei Zuo. Computation in Chemistry:A Summary of the Development and Models of DNA Computing[J]. Progress in Chemistry, 2017, 29(11): 1297-1315.
Haochuan Chen, Haohao Fu, Xueguang Shao, Wensheng Cai. Importance Sampling Methods and Free Energy Calculations[J]. Progress in Chemistry, 2018, 30(7): 921-931.
Jinghao Liu, Xueqian Wu, Yufeng Wu, Jiamei Yu. Computational Study on Adsorption and Separation of C2 and C3 Hydrocarbons by Metal-Organic Frameworks[J]. Progress in Chemistry, 2020, 32(1): 133-144.
Hydrocarbons play an important role in industrial productionses. The separation and purification of hydrocarbons is one of the most important industrial processes. The separation of low carbon hydrocarbon gases is extremely difficult since their physicochemical properties are similar. The minor differences are their molecular size and valence state. The traditional separation methods suffer from the high energy consumption and low efficiency. Metal-organic frameworks show superiority in separations due to their unique properties including high specific surface area, high porosity and controllable structure size. Computational simulation has been widely used in the investigations of adsorption and separation of MOFs since it can describe the adsorption and separation process at the microscopic level. This paper reviews the recent advances in computational simulations for the adsorption and separation of low-carbon hydrocarbons by metal-organic frameworks. The difficulties and future developments in the study of adsorption and separation of low carbon hydrocarbons by metal-organic frameworks have also been discussed.