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Progress in Chemistry 2012, No.06 Previous issue Next issue
Special Issue of Quantum Chemistry
Theoretical Study of the Mechanism of Methanol Steam Reforming over Pd/ZnO
Chen Zhaoxu, Huang Yucheng, He Xiang
2012, 24 (06): 873-878 |
Published: 24 June 2012
Abstract
With the ever-increasing attention to clean energy and environmental protection, developing new energy sources becomes a heated issue all over the world. Hydrogen energy is a clean and efficient energy source, and methanol steam reforming (MSR) is an important means to produce hydrogen. In this paper we review the theoretical studies of the MSR on Pd/ZnO during the past decade. We first review the investigations on the structures and compositions of Pd/ZnO catalysts modeled by Pd-Zn alloy. Then we summarize the work of adsorption and dissociation of water on the flat and stepped surfaces of Pd-Zn alloy. Surface chemistry of methanol, methoxy and formaldehyde on Pd-Zn alloy and other pertinent surfaces is described, followed by the discussion of the MSR reaction mechanism. Finally the conclusions and outlook are presented. Contents
1 Introduction
2 Investigations on Pd/ZnO catalysts
3 Water adsorption and dissociation on alloy surfaces
3.1 Water on mono-and multi-layer Pd-Zn(111) surfaces
3.2 Water on mono-and multi-layer Pd-Zn(221) surfaces
4 The chemistry of methanol and related species
4.1 Adsorption and dissociation of methanol
4.2 Adsorption and dissociation of methoxy
4.3 Adsorption and dissociation of formaldehyde
5 Reaction mechanism of methanol steam reforming
6 Conclusions and Outlook
Theoretical Studies on the Mechanisms of [2+2] Cycloaddition Reactions
Fang Decai
2012, 24 (06): 879-885 |
Published: 24 June 2012
Abstract
[2+2] cycloaddition reaction is one type of the most important reactions in the field of organic chemistry, and the mechanisms of [2+2] cycloaddition reactions are always hot topic both for experimental and theoretical researchers. In this paper, three types of [2+2] cycloaddition reactions, including simple olefins or alkynes, cumulenes, Th compounds, have been classified and reviewed. The obtained results indicated that the cycloaddition reactions involving simple olefins or alkynes are proceeding in diradical mechanism generally, and the others are proceeding in either concerted or zwitterion mechanism, all of which have been elucidated with frontier molecular orbital interactions. Contents
1 Introduction
2 [2+2] cycloaddition reactions of olefins or alkynes
3 [2+2] cycloaddition reactions of cumulenes X=Y=Z
3.1 [2+2] cycloaddition reactions of ketene
3.2 [2+2] cycloaddition reactions of keteniminium and 2-aza-allene cations
4 [2+2] cycloaddition reactions of Th-containing compounds
5 Conclusions and Outlooks
Elongation Method for Delocalized Nano-wires
Yuriko Aoki, Feng Long Gu
2012, 24 (06): 886-909 |
Published: 24 June 2012
Abstract
The elongation method, originally proposed for theoretical synthesis of aperiodic polymers, has been reviewed. The reliability and efficiency of the elongation method have been proven by various systems. By means of orbital shift, the elongation method has been successfully applied to delocalized p-conjugated systems. During the elongation process, some strongly delocalized orbitals are assigned to active orbitals and joined with the interaction of the attacking monomer. The elongation method is also applied to determine the NLO properties of delocalized porphyrin wires.
Abstract
Electronic band structure is one of the most fundamental properties of a material that plays a crucial role in many important applications, and its accurate description has been a long-standing challenge for the first-principles electronic structure theory. Kohn-Sham Density-functional theory (KS-DFT) within local density or generalized-gradient approximations (LDA/GGA), currently the “standard model” for first-principles computational materials science, suffers from the well-known band gap problem. A lot of efforts have been invested to improve the description of band gaps within the framework of Kohn-Sham DFT or its generalized formalisms. On the other hand, many-body perturbation theory (MBPT) based on Green's function G (GF) provides a different and conceptually more rigorous framework for electronic band structure. The central ingredient of the GF-based MBPT is the exchange-correlation self-energy xc, which can be formally obtained by solving a set of complicated integro-differential equations, named Hedin's equations. The GW approximation, in which xc is simply a product of G and the screened Coulomb interaction (W), is currently the most accurate first-principles approach to describe electronic band properties of extended systems. Compared to LDA/GGA, the computational efforts required for GW calculations are much heavier, so that its applications have been limited to relatively small systems. In this work, we review the basic principles, latest developments, and remaining challenges of first-principles electronic band structure theory from both DFT and GF-based MBPT perspectives. It is hoped that new ideas on further developments can be obtained by setting up the connection between the two different theoretical frameworks. Contents
1 Introduction:Electronic band structures and the band gap problem
1.1 Experimental measurements of electronic band structures
1.2 Theoretical treatments of electronic band structures and the band gap problem
2 Electronic band structures frommean-field approaches
2.1 Hartree theory
2.2 Hartree-Fock theory
3 Electronic band structures from density functional theory
3.1 Density functional theory and Kohn-Sham equations
3.2 The band gap problem and its origin
3.3 The optimized effective potential and related methods
3.4 Generalized Kohn-Sham methods
4 Electronic band structures from Green's function based many-body perturbation theory
4.1 Green's function
4.2 Self-energy and quasi-particle equations
4.3 Hedin's equations and GW approximation
4.4 The G0W0 approach and self-consistency
5 Concluding remarks
Recent Developments in Radiationless Transitions
Niu Yingli, Lin Chinkai, Yang Ling, Yu Jianguo, He Rongxing, Pang Ran, Zhu Chaoyuan, Hayashi Michitoshi, Lin Sheng Hsien
2012, 24 (06): 928-949 |
Published: 24 June 2012
Abstract
In this paper, we will introduce recent works on the mathematical treatments and the first-principle calculations concerning the internal conversion rates for the cases with anharmonic potentials, and conical intersecting potentials. The simulations of absorption and emission spectra with anharmonic effects are also presented to check the validity of the potential energy surfaces obtained from the quantum chemical calculations. The effect of conical intersection on internal conversion has attracted considerable attention. In this paper a different approach will be proposed and applied to pyrazine. Another important non-radiative process, molecular vibrational relaxation, is also treated by applying the adiabatic approximation to the ab initio anharmonic potential energy surfaces in this paper. The vibrational relaxation rates in water dimer and aniline are chosen to demonstrate the calculation.
Computational Photochemistry
Liu Yajun
2012, 24 (06): 950-956 |
Published: 24 June 2012
Abstract
This review starts with the most basic concepts in photochemistry, followed by the introduction of developing process of theoretical methods and the related typical applications, as well as our comments. We pursue a goal that the readers can integrally understand the discipline of computational photochemistry by this review. We also indicated the effect of hardware development and the current difficulties and problems in the computational photochemistry for peer discussion. Contents
1 Introduction
2 Basic concepts in photochemistry
2.1 Potential energy surface
2.2 Vertical and adiabatic excitation energy
2.3 Conical intersection
3 Development of computational methods and typical applications in photochemistry
3.1 Semi-empirical methods
3.2 Single-reference ab initio methods
3.3 Multi-reference ab initio methods
3.4 TDDFT methods
3.5 Some combined or improved methods
3.6 Brief comments on all kinds of methods
4 Effect of the development of hardware on the computational photochemsitry
5 Conclusions and outlook
Recent Theoretical Progress on Photochemical reactions at the Solid/Solution Interface
Li Yefei, Liu Zhipan
2012, 24 (06): 957-963 |
Published: 24 June 2012
Abstract
TiO2 nanoparticles have been widely utilized in photocatalysis, but the atomic level understanding on their working mechanism falls much short of expectations. In this short review, we briefly introduce the recent theoretical progress in photocatalysis carried out in our research group. Extensive density functional theory (DFT) calculations combined with the periodic continuum solvation model have been utilized to compute the electronic structure of extended surfaces, nanoparticles in aqueous solution and provide the reaction energetics for the key elementary reaction. It is demonstrated that the equilibrium shape of nanoparticle is sensitive to its size from 1 to 30 nm, and the sharp crystals possess much higher activity than the flat crystals in oxygen evolution of water splitting, which in combination lead to the morphology dependence of photocatalytic activity. Contents
1 Introduction
2 Methods
3 Electronic structure of TiO2 in aqueous surrounding
4 OER mechanism on extended surfaces
5 Electronic structure of anatase nanoparticle in aqueous surrounding
6 The thermodynamics relationship between particle size and shape
7 Photoactivity of nanoparticles
8 Outlook
First-Principle Simulation of Soft X-Ray Spectroscopy
Hua Weijie, Gao Bin, Luo Yi
2012, 24 (06): 964-980 |
Published: 24 June 2012
Abstract
Soft x-ray photon spectroscopy represents a category of instrumental techniques to effectively probe the electronic and chemical structure of molecules, surfaces, and a variety of complexes by core excitations or de-excitations. The basic computational methods, based on the density functional theory, for different absorption and emission processes are reviewed in this paper. Special attention has been paid to the practical implementations and applications of different methods. Details on the simulations of commonly used K-edge x-ray photoelectron, absorption, and emission spectra for a wide range of illustrative examples including molecules, fullerenes, carbon nanotubes, graphenes and DNA, are provided.
Many-Body Green's Function Theory for the Study of Excited States
Ma Yuchen, Liu Chengbu
2012, 24 (06): 981-1000 |
Published: 24 June 2012
Abstract
Many-body Green's function theory is a first-principle method used to investigate excited states, which is based on a set of Green's function equations. This theory includes GW method, which is used to calculate the properties of quasiparticles, and Bethe-Salpeter equation, which describes the motion of the electron-hole pair. GW method predicts orbital energies, band structures and quasiparticle lifetimes with high accuracy, while Bethe-Salpeter equation is a promising approach to study excitation energy, optical absorption spectrum and excited-state dynamics. Many-body Green's function theory uses self-energy operator to describe the exchange and correlation interactions among electrons and those between electron and hole. Here we give an overview of the fundamental concepts and principles of many-body Green's function theory, and a discussion on its applications in various materials. Contents
1 Introduction
2 GW method
2.1 One-particle Greens function
2.2 Hedins equations
2.3 GW approximation
2.4 Dielectric function
2.5 Quasiparticle correction
2.6 Applications
3 Bethe-Salpeter equation
3.1 Two-particle Greens function
3.2 Bethe-Salpeter equation
3.3 Tamm-Dancoff approximation and Random-phase approximation
3.4 Dynamical screening effect
3.5 Applications
4 Excited-state dynamics
4.1 BSE force
4.2 Combination of constrained densityfunctional theory and many-body Greensfunction theory
5 Conclusions and Outlook
Ab Initio Computational Method for Classical Valence Bond Theory
Su Peifeng, Wu Wei
2012, 24 (06): 1001-1007 |
Published: 24 June 2012
Abstract
In modern quantum chemistry, valence bond (VB) theory and molecular orbital (MO) theory are the two general theoretical approaches for chemical bonding. VB theory provides clear interpretation and chemical insights by employing covalent and ionic VB structures explicitly. This review focuses on the methodology development of the current modern classical VB methods in the improvement of computational accuracy and the extension of application areas. Moreover, the further development of modern classical VB methods is briefly prospected. Contents
1 Introduction
2 Ab initio VB methods
2.1 VBSCF
2.2 BOVB
2.3 VBCI
2.4 VBPT2
3 Ab initio VB methods for complicated systems
3.1 VBSCF
3.2 VBSM
3.3 VB/MM
4 Conclusion and perspective
Stability Rule of Ⅲ-ⅤPolyhedral Clusters
Jia Jianfeng, Wu Haishun
2012, 24 (06): 1008-1022 |
Published: 24 June 2012
Abstract
The recent investigation about the stability rules of Ⅲ-Ⅴ clusters is summarized. The Cn clusters, CnXn (X=H, F) clusters, BnNn clusters, (HBNH)n clusters, Nn clusters and carbonyl boron (BCO)n clusters are included in the present review. The most famous rules to determine the stable fullerene are isolated pentagon rule and pentagon adjacency penalty rule, which both state that pentagon in Cn cluster should be separated as far as possible. However, CnXn (X=H, F) clusters have tube-like structure, in which pentagons cluster together. The most stable BnNn clusters comprise four-, six-membered rings, in which, four-membered rings are separated as far as possible. The most stable (HBNH)n clusters, however, have needle-like structure. Although N atom is isoelectronic species of CH unit, the structure of most stable Nn clusters is remarkably different from that of CnHn. The most stable Nn clusters comprise three-, five- and six-membered rings, and have tube-like structure. The most stable (BCO)n clusters comprise three- and six-membered rings. The further investigations about the stability rule of Ⅲ-Ⅴ clusters will focus on the partially hydrogenated or fluorinated fullerenes. Contents
1 Introduction
2 Stabilityrules of fullerene Cn clusters
2.1 Discover of C60 fullerene
2.2 Isolated pentagon rule
2.3 Pentagon adjacency penalty rule
3 Tool to generate the model of polyhedral cluster
3.1 Program of Ring Spiral
3.2 Programs of Plantri, Fullgen and CaGe
4 Stabilityrules of XnHn and XnFn
4.1 Stability rule of XnHn (X=C, Si, Ge, Sn; n=4—24)
4.2 Stability rule of CnHn and CnFn (n=26—60)
4.3 Endo structure of C60H60 and C60F60
5 Stabilityrules of other fullerene-like polyhedral cluters
5.1 Stability rule of BnNn clusters
5.2 Stability rule of (HBNH)n clusters
5.3 Stability rule of Nn clusters
5.4 Stability rule of (BCO)n clusters
6 Conclusions and outlook
A New Generation Density Functional XYG3
Zhang Igor, Ying Xuxin
2012, 24 (06): 1023-1037 |
Published: 24 June 2012
Abstract
There is growing evidence, showing that the widely-used approximate functionals, such as B3LYP, degrade as the system becomes large, underestimate reaction barrier heights and fail to bind van der Waals systems, etc. The success of the Kohn-Sham implementation of density functional theory (DFT) depends on the quality of the exchange-correlation functional. This paper provides an overview of the recent progress on the construction of a new generation of doubly hybrid density functionals (DHDFs). We pointed out that the theoretical basis of DHDFs lies in Görling-Levy (GL) coupling-constant perturbation theory and adiabatic connection method, and we proposed that the current available DHDFs can be classified into three groups by their different references used to construct the second order perturbation energy. We systematically examined the performance of various DHDFs. Finally, possible directions for future development of DHDFs are forecasted. Contents
1 Overview of modern density functional theory
1.1 Hohenberg-Kohn theory and Kohn-Sham scheme
1.2 Jacob's ladder of approximate DFT methods
2 New generation of doubly hybrid density functionals
2.1 Adiabatic connection method and Becke's hybrid functionals
2.2 Görling-Levy coupling-constant perturbation theory
2.3 Derivation of the doubly hybrid density functional XYG3
2.4 Three types of current doubly hybrid density functional
3 Systematic evaluation of XYG3
3.1 Heats of formation
3.2 Bond dissociation enthalpy
3.3 Reaction barrier height
3.4 Non-bonding interaction
4 Conclusion and outlook
Electronegativity Equalization
Yang Zhongzhi
2012, 24 (06): 1038-1049 |
Published: 24 June 2012
Abstract
Electronegativity is the power of an atom attracting electron to itself in a molecule. It is a basic concept in chemistry. Pauling proposed the first electronegativity scale and after then many electronegativity scales were proposed. It is only on the basis of density functional theory that the concept and electronegativity principle were precisely proved theoretically. In recent decades, there have been some important developments of the electronegativity theory. Applying the electronegativity equalization model or method, one can rapidly calculate the charge distribution of a large molecule and then calculate the related properties, even molecular structure and reactivity indexes. The usual electronegativity equalization method divides a molecule only to atomic regions its accuracy and application are limited although it is simple and intuitive. Atom-bond electronegativity equalization method divides a molecule into not only atomic regions but also bond and lone-pair regions so that it can rapidly and accurately calculate molecular charge distribution and other properties, and recently it is also applied to develop a new generation of polarizable force field. Contents
1 Introduction
2 Electronegativity
2.1 Classical electronegativity scales
2.2 Modern electronegativity ideas
3 Electronegativity in density functional theory and related physical quantities
3.1 The first-order derivatives: chemical potential μ and electron density ρ
3.2 The second-order derivatives: global hardness, local hardness and local softness, fukui function
3.3 Electronegativity equalization principle
4 Modern electronegativity equalization method (EEM)
4.1 Mortier electronegativity equalization method (EEM)
4.2 Atom-bond electronegativity equalization method (ABEEM)
5 Conclusion
Ab Initio Computation Based Design of Three-Dimensional Structures of Carbon Allotropes
Wu Menghao, Dai Jun, Zeng Xiaocheng
2012, 24 (06): 1050-1057 |
Published: 24 June 2012
Abstract
Carbon can exist in many different forms at different temperatures and pressures. Some allotropes of carbon have been predicted in theory but still have not been found in nature. In this article, we mainly overview a number of three-dimensional (3D) crystalline carbon allotropes, predicted by ab initio calculations. Particular attention will be placed on the carbon foams, which possess porous structures with a large surface area. Carbon foams are mostly composed of graphite segments connected by different types of carbon bonds. We will also review 3D carbon superstructures of low-dimensional allotropes, typically built from carbon fullerenes, nanobuds, nanotubes and graphene nanoribbons, as well as various other 3D crystalline carbon structures. Some of these carbon superstructures are composed of mixed sp-sp2 carbon or pure sp2 carbon (e.g., H-6, bct-4, C-20, K4), and some have larger mass density than diamond (C8, hP3, tl12, tp12), and some can be transformed from graphite at room temperature and high pressure (e.g., M carbon, bct-4 carbon, W carbon, Z carbon). Some of these theoretically predicted carbon allotropes may be synthesized in the laboratory in future.
A Fragmentation Approach to Quantum Calculation of Large Molecular Systems
Mei Ye, He Xiao, Ji Changge, Zhang Dawei, John Z.H. Zhang
2012, 24 (06): 1058-1064 |
Published: 24 June 2012
Abstract
Fragmentation method has opened a new door for the development of quantum mechanical methods and their applications to large molecules. In the past decade, we have evidenced much progress in this field, and this development is believed to be continued in the future. This article provides a brief overview on the recent development of fragmentation-based methods for electron structure calculation of large molecular systems, with highlight on contribution by researchers from China in this field.
Coherent Two Dimensional Infrared Spectroscopy of Proteins: Concepts and Simulations
Song Jian, Zhuang Wei
2012, 24 (06): 1065-1081 |
Published: 24 June 2012
Abstract
The nonlinear optical response of peptide molecules to femtosecond infrared pulse sequences contains rich information on their structure, fluctuations and motions. we reviewed in this article the basic concepts as well as the simulation protocol for 2DIR signals associated with the amide backbone vibrational transitions of proteins. Starting with a general introduction of the perturbative picture of nonlinear optical response of excitonic systems, an introduction is given for constructing an effective fluctuating vibrational Hamiltonian based on classical MD simulation and a DFT electrostatic map. Several techniques for simulating the nonlinear response using the fluctuating Hamiltonian are then surveyed, these include the stochastic Liouville equations (SLE),numerical propagation (NP) and cumulant expansion of Gaussian fluctuation (CGF). Applications are presented to two dimensional infrared signal of peptides and peptide complexes.
Highly Accurate Ab Initio Potential Energy Surface for Chemical Reactions
Zhang Chunfang, Ma Haitao, Bian Wensheng
2012, 24 (06): 1082-1093 |
Published: 24 June 2012
Abstract
Potential energy surface (PES) is the cornerstone of all theoretical studies of chemical reaction dynamics. With the development in theoretical and computational methods, not only the accuracy of the PESs for the ground state of triatomic or tetra-atomic reaction systems has been improved greatly, but also substantial progress has been made in the construction of coupled PESs for multiple states of some typical reactions and high-dimensional PESs for polyatomic systems with more than six atoms. The PESs of some prototype reactions have been discussed in this review, including highly accurate PESs of the ground electronic state, coupled PESs involving non-adiabatic effects, such as the Renner-Teller effect and spin-orbit coupling, and high-dimensional PESs for polyatomic systems. Contents
1 Introduction
2 Overview of the development of the potential energy surface
3 Construction methods of the ab initio potential energy surface
3.1 Highly accurate ab initio methods
3.2 Construction methods
4 Several prototypes
4.1 Ground-state surfaces for triatomic or tetraatomic systems
4.2 Coupled PESs
4.3 High-dimensional PESs
5 Conclusions and Outlook
Structures and Time-Evolution Dynamics of Solvated Electron in Ionic Liquids
Bu Yuxiang
2012, 24 (06): 1094-1104 |
Published: 24 June 2012
Abstract
Structures, states and time-evolution dynamics of excess electron in ionic liquid medium are surveyed. On the basis of the ab initio calculations and molecular dynamics simulations, we discussed the solvation energetics, structural characters, possible existing states and state-to-state conversion mechanisms associated with solvation of excess electron in the imidazolium-type, the pyridinium-type, and the quaternary ammonium-type chloride room temperature ionic liquids, and a representative alkali-metal halide molten salt, and analyzed the nature of efficient conduction of electrons in such media and the important role of constituent ions of the ionic liquids. The conduction band structure consisted of the lowest unoccupied molecular orbital of the cations is a decisive factor in determining the solvated states and stability of the excess electron in ionic liquids, and any factors which affect or change the conduction band structure do considerably affect solvation of excess electron in ionic liquids. However, the rapid state-to-state conversion dynamics and electron migration do not sensitively depend on the diffusion dynamics of the constituent ions, but are controlled by ionic liquid fluctuation. This kind of solvated-electron-based electron migration mechanism provides a new electron transfer pathway in such ionic media or other liquid media. Contents
1 Introduction
2 Computation and molecular dynamics simulation methods
3 Electronic structure of ionic liquids
4 Presolvation state of excess electron
5 Time-evolution dynamics of solvated electron
6 Structures and properties of solvated electron
7 Conclusions and outlook
Approximate Theoretical Methods for Nonadiabatic Dynamics of Polyatomic Molecules
Lan Zhenggang, Jiushu Shao
2012, 24 (06): 1105-1119 |
Published: 24 June 2012
Abstract
Nonadiabatic dynamics is ubiquitous in photo-physical and photo-chemical processes. The description of nonadiabatic transitions requires the treatment of coupled electron-nuclei motions. Exact quantum dynamical calculations, due to the insurmountable computational scaling with the size of the system, are only applicable to small molecular systems. In recent years, several approximat methods based on the quantum-classical dynamics were proposed to describe the nonadiabatic dynamics of polyatomic molecular systems. This article provides a concise review of different versions of quantum-classical dynamics approaches including the classical Ehrenfest method, the surface-hopping technique, and the mixed-quantum-classical dynamics in terms of the Winger representation. The pros and cons of the on-the-fly numerical implementation of these schemes combining the ab initio electronic structure calculations are discussed and perspectives on further development of quantum-classical treatment of nonadiabatic dynamics are given. Contents
1 Introduction
2 Hamiltonian and nonadiabatic dynamics
3 Classical Ehrenfest dynamics and surface-hopping dynamics
3.1 Mean-field (or classical Ehrenfest) dynamics
3.2 Surface-hopping dynamics
4 Mixed-quantum-classical dynamics based on wigner representation
5 Conclusions and outlook
Theoretical Studies for Photodissociation Dynamics of Small Molecules
Bin Jiang, Daiqian Xie
2012, 24 (06): 1120-1128 |
Published: 24 June 2012
Abstract
Photodissociation is one of the key issues in chemistry. Quantum state resolved photodissociation dynamics provides us the remarkable understanding for the photodissociation reaction mechanism at the atomic and molecular level. Our knowledge about the nature of the photodissociation process is largely enriched with the combination of experimental and theoretical studies and great advances have been achieved for the state-to-state photodissociation dynamics in the last 40 years. This article reviews the progress in theoretical studies for state-to-state photodissociation dynamics of small molecules and summarizes the photodissociation dynamics for H2O and CH3I. Finally, the open questions and challenges in this field are also addressed. Contents
1 Introduction
2 General theory of state-to-state photodissociation dynamics
3 Photodissociation dynamics for H2O: adiabatic versus nonadiabatic pathway
4 Photodissociation dynamics for CH3I: spin-orbit Coupling and multiple pathway dissociation
5 Conclusions and outlook
Hierarchical Equations of Motion for Quantum Dissipation and Quantum Transport
Zheng Xiao, Xu Ruixue, Xu Jian, Jin Jinshuang, Hu Jie, Yan Yijing
2012, 24 (06): 1129-1152 |
Published: 24 June 2012
Abstract
In this review we give a comprehensive account of a hierarchical equations of motion (HEOM) approach to the characterization ofstationary and dynamic properties of open quantum systems.This approach is rooted at the Feynman-Vernon influence functional path integral formalism, but much more implementable numerically and operationally for the study of various complex molecular dynamics and quantum transport in strongly correlated electronic systems.By construction, HEOM resolves nonperturbatively the combined effects of many-particle interaction, system-bath coupling,and non-Markovian memory.Finally the practicality of HEOM to address physical and chemical problems is exemplified with a model simulation of coherent two-dimensional spectroscopy signals of a biological light-harvesting system and a time-dependent quantum transport system involving dynamic Kondo transition.
State-to-State Reactive Scattering by Quantum Wavepacket Method
Sun Zhigang, Zhang Donghui
2012, 24 (06): 1153-1165 |
Published: 24 June 2012
Abstract
The studies of gaseous reactive scattering dynamics by quantum wave packet method, especially at product-states resolved level, are reviewed. The current numerical methods for extracting product-states resolved attributives using quantum wave packet method are discussed. This theory now can present detailed and accurate predictions on the dynamics and kinetics of reactions containing three or four atoms. Several typical reactive scattering systems which have been studied using quantum wave packet method at product-states resolved level are briefed. Contents
1 Introduction
2 Brief review of historical development of quantum wave packet method applications in reactive scattering field
3 Theoretical methods of quantum wave packet
3.1 Discrete variable representation
3.2 Construction of initial wave packet and S-matrix extraction
3.3 Popular propagators
4 Theoretical methods for extraction product-states resolved information using quantum wave packet method
4.1 Product Jacobi coordinate based method
4.2 Reactant Jacobi coordinate based method
4.3 Reactant product-decoupling method
5 Typical reactive scattering systems studied by quantum wave packet method at product-states resolved level
5.1 Typical triatomic molecules reactive scattering
5.2 Typical tetraatomic molecules reactive scattering
6 Conclusions and outlook
Non-Condon Effect and Time-Dependent Wave-Packet Method on Electron Transfer
Zhang Weiwei, Zhong Xinxin, Si Yubing, Zhao Yi
2012, 24 (06): 1166-1174 |
Published: 24 June 2012
Abstract
Due to the importance of electron transfer in chemistry, material, biology and etc., a variety of theoretical models has been proposed to investigate electron transfer. In the present paper, we summarize the approaches for electron transfer proposed by us, which include the non-Condon electron transfer rate theory based on the Fermi's golden rule and time-dependent wave-packet method for the consideration of the coherence motion of electron. Their potential applications, combining with quantum chemical calculations for the reorganization energy and electronic coupling, have been demonstrated with use of two examples. One is the mobility of the organic semiconductor dithiophene-tetrathiafulvalene (DT-TTF), and the other is the triplet-triplet energy transfer (TTET) in the fluorene dimer. Contents
1 Introduction
2 Methodologies
2.1 Non-Condon electron transfer rate theory
2.2 Time-dependent wave-packet approach
2.3 Computational approaches for reorganization energy and electronic coupling
3 Numerical tests and applications
3.1 Numerical tests of non-Condon electron transfer rate theory and time-dependent wave-packet approach
3.2 Mobility of the organic semiconductor dithiophene-tetrathiafulvalene (DT-TTF)
3.3 Triplet-triplet energy transfer (TTET) in fluorene dimer
4 Conclusion
Computational Simulations of Zinc Enzyme: Challenges and Recent Advances
Wu Ruibo, Cao Zexing, Zhang Yingkai
2012, 24 (06): 1175-1184 |
Published: 24 June 2012
Abstract
Zinc enzymes play a variety of essential biological roles, and their functions and/or structural organizations are critically dependent on the zinc binding site. However, the zinc coordination shell is so complicated that an accurate and powerful theoretical simulation protocol is highly required in calculation. Herein, we review the recent studies of the selected zinc enzymes by the state-of-the-art combined quantum mechanism/molecular mechanism molecular dynamics (QM/MM MD) simulations in probing the reaction mechanism and revealing the relationship of structure and function. Meanwhile, the accuracy of all the current available pairwise force fields to describe zinc coordination structure is very poor, so the recent development of force fields for zinc enzyme is also presented. By the end of this review, some prospects and suggestions are given for further exploration of zinc enzyme. 1 Significance and challenges of zinc enzymes
1.1 Zinc enzyme
1.2 Challenges of experimental research in zinc enzyme
1.3 Challenges of computational research in zinc enzym
2 Recent advance of computational research in zinc enzyme
2.1 QM/MM study of zinc enzyme
2.2 Force field development for zinc enzyme
3 Outlook
Structural Predications and Photophysical Simulations for Materials
Lin Chensheng, Cheng Wendan, Zhang Weilong, Zhang Hao, He Zhangzhen
2012, 24 (06): 1185-1198 |
Published: 24 June 2012
Abstract
The key question of the successful designs for the nonlinear optical materials with a good performance lies in the credible and effective predictions of material's crystal structure and molecular structure. Then, the computational simulations of the photophysical properties will be made based on structural information of materials. In this article, we will describe the applications of a global search evolutionary algorithm coded in USPEX software, which successfully predicted the crystal structures of Ba2BiInS5/Se5 with second-order nonlinear optics in far infrared region. At the same time, we will also introduce the optimized structures of embedded fullerenes C2@Sc4@C80-Ih and Sc4C2@C80-Ih based on the DFT method. Based on the predicted and optimized structures of materials, we use the sum-over-states method, coded by ourselves in BGP software, combined with the calculation method of excitation-state properties to simulate the state-related and frequency-dependent nonlinear optical properties of molecular crystals, nano-structured molecules, biological proteins and the other systems. Here, the nonlinear optical properties involve the different optical processes of second-order, third-order polarizabilities and two-photon and three-photon absorption cross-sections. In addition, the calculations of second-order and third-order susceptibilities will be also described for some ionic crystals based on the solid energy band theory combined with anti-harmonic oscillator model. Contents
1 Introduction
2 Structural predications
2.1 Predications of crystal structures
2.2 Optimizations of molecular structures
3 Simulations of nonlinear optical properties
3.1 Computational nonlinear optical properties of molecular crystals and carbon nano-molecules
3.2 Simulations of nonlinear optics of ionoic crystals
4 Conclusions and outlook
Enhanced Sampling Method in Molecular Simulations
Yang Lijiang, Shao Qiang, Gao Yiqin
2012, 24 (06): 1199-1213 |
Published: 24 June 2012
Abstract
Molecular simulations play more and more important roles in the studies of chemistry, physics, biology and material sciences, etc. However, due to the limitations of the current computing power, there is still a huge gap between the timescale which can be reached in molecular simulations and that observed in the experiments. Applications of the enhanced sampling method can effectively extend the timescale being approached, so that it improves greatly the thermodynamics and kinetics calculation ability of the molecular simulations. In this paper, the developments and comparisons of the different enhanced sampling methods are introduced briefly, and then the integrated tempering enhanced sampling method (ITS) and its applications to the protein folding simulations are presented in details. At last, the new challenges and prospects in the field of the enhanced sampling methods' development and application are summarized. Contents
1 Introduction
2 Enhanced sampling in the energy and configuration space based on the integrated tempering method
3 Applications: thermodynamics studies of protein folding
4 Future developments
5 Summaries
Abstract
N-H···OC、C-H···OC、N-H···N and C-H···N hydrogen bonds are the main factors for the formation of protein a-helices and b-sheets and for the formation of the double helices of the deoxyribonucleic acid. These hydrogen bonds also play important roles in the processes of the protein-nucleic acid recognition, in the processes of the protein replication, and in the processes of transcription and expression of genetic information from DNA to protein. Accurate and rapid determination of the strengths of the hydrogen bonds and their dynamic properties in DNA and protein systems is very important for correctly simulating and therefore deeply understanding the mechanism of protein folding processes and the formation mechanism of the double helices of the deoxyribonucleic acid and for designing new biomolecular materials possessing special function. In this review, a dipole-dipole hydrogen bonding model and its applications to the hydrogen-bonded complexes containing peptide amides and/or nucleic acid bases are introduced. Contents
1 Introduction
2 Hydrogen bond model and parameterization
2.1 The dipole-dipole hydrogen bonding model
2.2 Parameterization
3 Applications
3.1 Calculation of the hydrogen bond strengths and hydrogen bonding potential energy curves for amide-amide and amide-water hydrogen-bonded dimers
3.2 Calculation of the total binding energies and potential energy curves for hydrogen-bonded complexes made of peptide amides and nucleic acid bases
3.3 Calculation of the total binding energies and potential energy curves for protein β-sheets
4 Conclusion and outlook