Ab initio molecular dynamics for open-shell transition metals
从头计算分子动力学方法及其应用
收稿日期:2004-12-21基金项目:山东省自然科学基金资助项目(Y2003A01)和石油科技中青年创新基金(04E7038)作者简介:蓝建慧(1979-),女(汉族),山东即墨人,硕士研究生,专业方向为计算物理。
文章编号:100025870(2005)0420143204综述从头计算分子动力学方法及其应用蓝建慧,卢贵武,黄乔松,李英峰,朱 阁(中国石油大学物理科学与技术学院,山东东营257061)摘要:从头计算分子动力学方法把密度泛函理论和分子动力学方法有机地结合起来,使电子的极化效应及化学键的本质均可用计算机分子模拟方法进行研究,是目前计算机模拟实验中最先进、最重要的方法之一。
文章简述了从头计算分子动力学方法的基本原理,介绍了该方法在水、水溶液及其他氢键液体的结构与动力学研究中的应用。
关键词:从头计算;密度泛函理论;分子动力学;计算机分子模拟中图分类号:O 35 文献标识码:AMethod of ab initio molecular dynamics and its applicationsLAN Jian 2hui ,L U Gui 2wu ,HUAN G Qiao 2song ,L I Y ing 2feng ,ZHU G e(College of Physics Science and Technology in China U niversity of Pet roleum ,Dongying 257061,China )Abstract :The ab initio molecular dynamics method ,which combines the density functional theory with the molecular dy 2namics methodology ,made it convenient to study the electronic polarization effects and the nature of the chemical bonds in term of the computer molecular simulation.The method is one of the most im portant and advanced com puter simulation ex 2periment methods.The basic principle of the ab initio molecular dynamics method and its applications in structure and dy 2namics research of liquid water ,aqueous solutions and other hydrogen 2bond liquids were introduced.K ey w ords :ab initio ;density functional theory ;molecular dynamics ;computer molecular simulation 现代凝聚态理论研究应用最普遍的方法之一是分子动力学(MD )方法。
分子动力学软件选择
分子动力学软件选择There are widely used packages like AMBER, CHARMm and X-PLOR/amber/amber.html//CHARMm and X-PLOR both use the same forcefield. Amber's is different.If you're Wintel-bound, you could try Hyperchem, which has a free downloadable demo: /products/hc5_features.htmlIt has a nice structure build capability (the other packages havepowerful languages, but can be intimidating to new users).OpenSource adherents can find a wealth of free packages at SAL, anexcellent site:/Z/2/index.shtmlMy personal favourites are MMTK, EGO and VMD/NAMD.I compiled a list of free and commerical programs at/chemistry/soft_mod_en.htmlmodeling in solution is possible e.g. with these programs (to the best of my knowledge):commercial: AMSOL, GROMOS, Titanfree: GAMESOL, GROMACS, MOIL, OMNISOL, TinkerYou find links to all of these programs at/chemistry/soft_mod_en.htmlPAPA (计算粒状物料的三维并行分子动力学计算程序)【URL】http://www.ica1.uni-stuttgart.de/Research/Software_P3T/papa.html【作者】 ICA 1 Group, Institute of Computer Applications (ICA) of the University of Stuttgart【语言版本】 English【收费情况】免费【用途】 Characteristic:dissipative interaction for rotating, rough, spherical particlesgeometry elements: walls, cylinders, spheres, etc freely configurablematerial properties of walls and particles freely configurable for an arbitray number of materialsobject oriented, written in C++full checkpointing supportedseveral compilation options: support of X11 graphics, reduction to 2D, debugging aids, etc. Applications:simulation of granular media, silo filling and steady flow problems, sphere packings of mono- and polydisperse systemProtoMol (分子动力学并行计算软件)【URL】/~lcls/Protomol.html【作者】 LCLS Group at the University of Notre Dame【语言版本】 English【操作系统】 SunOS 5.8, IRIX 6.5, Linux 2.4, AIX 5.1【收费情况】免费【用途】 PROTOMOL is an object-oriented component based framework for molecular dynamics simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping has been used to improvelong-term efficiency, and the use of fast electrostatic force evaluation algorithms like plain Ewald, Particle Mesh Ewald, and Multigrid summation further improves performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators. In addition, PROTOMOL has been designed to interact with VMD, a visualization engine developed by the University of Illinois that is used for displaying large biomolecular systems in three dimensions. PROTOMOL is free distributed software, and the source code is in cluded.【相关链接】VMD (分子可视化软件)美国圣母大学：计算生命科学实验室Claessen站点的分子模型化软件【URL】/chemistry/soft_mod_en.html【简介】Molecular ModelingCommercial Software3D Viewer: converts 2D structures into 3D with simple MM2Alchemy 2000: semi empirical, QSAR, Protein, Polymer, LogPAMPAC: semiempirical quantum mechanical programAMSOL: semi empirical, solvation models for free energies of solvation in aqueous solutions and in alkane solventsPersonal CAChe: visualize molecules in 3D, search for conformations, analyze chemical reactivity and predict properties of compoundsQuantum CAChe: Personal CaChe plus molecular dynamics and semi-empirical MOPAC and ZINDO quantum mechanicsChem3D: MOPAC and Gaussian integration, ChemProp, ...Gaussian 98W: MP2, MP3, MP4, MP5, HF, CASSCF, GVB, QCISD, BD, CCSD, G1, G2, ZINDO, ONIOM calculations, DFT excited states, VCD intensities, ...GROMOS: general-purpose molecular dynamics computer simulation package for the study of biomolecular systemsHyperchem Suite: semi empirical, RMS Fit, Molecule Presentations, Sequence Editor, Crystal Builder, Sugar Builder, Conformational Search, QSAR Properties, ScriptEditor ...(Hyperchem Pro, Hyperchem Std.)Jaguar: electronic structure calculationMacroModel: allows the graphical construction of complex chemical structures mechanics and dynamics techniques in vacuo or in solutionMOPAC 2000: the latest version of MOPACSpartan: MM, semiempirical, ab initio, DFT, ...Titan: TITAN is the union of Wavefunction's versatile, easy-to-use interface with fast, computational algorithms from Schr鰀inger's JaguarWinMOPAC: based on MOPACShareware/Freeware3D Viewer for ISIS Draw: converts 2D structures into 3D with simple MM2Biomer: online java applet, model builders for polynucleotides (DNA/RNA), polysaccharides and proteins, interactive molecule editor, AMBER force-field based geometry optimization, simulated annealing with molecular dynamics, and the ability to save gif, jpeg, and ppm imagesChem3D Net: demo version of Chem3DCOLUMBUS: high-level ab initio molecular electronic structure calculationsDalton: quantum chemistry programGAMESOL: calculate free energies of solvation based on fixed, gas-phase solute geometries interfacing GAMESSGAMESS: General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry packageGaussian Basis Set: get any Gaussian basis set you can imagineGROMACS: fully automated topology builder for proteins, molecular dynamics, leap-frog integrator, position langevin dynamics, normal mode analysis, electrostatics,non-equilibrium MD, NMR refinement with NOE data, large number of powerful analysis tools, ...Hückel: constructs the Hückel matrix, the programs then calculate, displayMOIL: molecular modeling, energy minimization and molecular dynamics simulation for biomolecules like proteinsMoldy: molecular dynamics simulation program, liquids, solids, rigid surfacesMOPAC: general purpose semiempirical molecular orbital package for the study of chemical structures and reactionsMOPAC 5.08mn: modified version of MOPACNWChem: quantum package for supercomputers and Linux, SCF, RHF, UHF, DFT, CASSCF, interface to Python programming languageOMNISOL: calculating free energies of solvation for organic molecules containing H, C, N, O, F, S, Cl, Br, and I in water and organic solventsPC GAMESS: GAMESS for the Intel communityQ: molecular dynamics package designed for free energy calculations in biomolecular systemTinker: molecular modeling software is a complete and general package for molecular mechanics and dynamicsVMD (分子可视化软件)【URL】/Research/vmd/【作者】 Biophysics Group,University of Illinois at Urbana-Champaign (UIUC)【语言版本】 English【收费情况】免费【用途】 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL to provide high performance 3-D molecular graphics【相关链接】RasMol:3D分子结构显示程序PDB文件显示程序KineMage美国伊利诺依大学：理论生物物理学研究组JMV (Java分子可视化工具)ProtoMol (分子动力学并行计算软件)ORAC (用于模拟溶剂化生物分子的分子动力学计算程序, 意大利佛罗伦萨大学)【URL】http://www.chim.unifi.it/orac/【作者】 Massimo Marchi and P. Procacci【语言版本】 English【操作系统】 UNIX【收费情况】免费【用途】 ORAC is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles. The integration of the equations of motion in any ensemble can be carried out with the r-RESPA multiple time step integrator and electrostatic interactions can be handled with the Smooth Particle Mesh Ewald method.【备注】A parallel version of ORAC4.0 (MPI/T3E) is available upon request to:Massimo MarchiSection de Biophysique des Proteines et des Membranes,DBCM, DSV, CEA, Centre d'Etudes,Saclay, 91191 Gif-sur-Yvette Cedex, FRANCEVirtual Molecular Dynamics Laboratory (分子动力学软件)【URL】/vmdl/index.html【作者】 Amit Bansil, Lidia Braunstein【语言版本】 English【收费情况】免费【用途】 The Virtual Molecular Dynamics Laboratory enables the student to visualize atomic motion, manipulate atomic interactions, and quantitatively investigate the resulting macroscopic properties of biological, chemical, and physical systems.The Virtual Laboratory is a suite of research-based molecular dynamics software toolsand project-based curriculum guides. The software tools are: "Simple Molecular Dynamics (SMD)", "Universal Molecular Dynamics", and "Water".【相关链接】美国波士顿大学聚合物研究中心(可视化模拟)DL_POLY (分子动力学模拟软件)【URL】/msi/software/DL_POLY/【作者】 W. Smith and T.R. Forester【语言版本】 English【收费情况】免费DL_POLY is supplied to individuals under a licence and is free of cost to academic scientists pursuing scientific research of a non-commercial nature. A group licence is also available for academic research groups. All recipients of the code must first agree to the terms of the licence.Commercial organisations interested in acquiring the package should approach Dr. W. Smith at Daresbury Laboratory in the first instance. Daresbury Laboratory is the sole centre for distribution of the package.【用途】 DL_POLY is a general purpose serial and parallel molecular dynamics simulation package originally developed at Daresbury Laboratory by W. Smith and T.R. Forester under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Molecular Simulation Group (MSG) at Daresbury Laboratory. The package is the property of the Central Laboratory of the Research Councils.Two versions of DL_POLY are currently available. DL_POLY_2 is the original version which has been parallelised using the Replicated Data strategy and is useful for simulations of up to 30,000 atoms on 100 processors. DL_POLY_3 is a version which uses Domain Decomposition to achieve parallelism and is suitable for simulations of order 1 million atoms on 8-1024 processors.DL_POLY (分子动力学模拟软件)【URL】/msi/software/DL_POLY/【作者】 W. Smith and T.R. Forester【语言版本】 English【收费情况】免费DL_POLY is supplied to individuals under a licence and is free of cost to academicscientists pursuing scientific research of a non-commercial nature. A group licence is also available for academic research groups. All recipients of the code must first agree to the terms of the licence.Commercial organisations interested in acquiring the package should approach Dr. W. Smith at Daresbury Laboratory in the first instance. Daresbury Laboratory is the sole centre for distribution of the package.【用途】 DL_POLY is a general purpose serial and parallel molecular dynamics simulation package originally developed at Daresbury Laboratory by W. Smith and T.R. Forester under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Molecular Simulation Group (MSG) at Daresbury Laboratory. The package is the property of the Central Laboratory of the Research Councils.Two versions of DL_POLY are currently available. DL_POLY_2 is the original version which has been parallelised using the Replicated Data strategy and is useful for simulations of up to 30,000 atoms on 100 processors. DL_POLY_3 is a version which uses Domain Decomposition to achieve parallelism and is suitable for simulations of order 1 million atoms on 8-1024 processors.PMDS (并行分子动力学模板库)【URL】http://stencil.koma.jaeri.go.jp/【作者】 Japan Atomic Energy Research Institute【语言版本】 English【收费情况】免费【用途】 Parallel Molecular Dynamics Stencil (PMDS) is an assembly of subroutine programs for executing parallel short-range molecular-dynamics simulations of solids. PMDS is written in C language using MPI for parallelization, and is designed to separate and conceal parts of the programs for parallel algorithms such as inter-processor communications so that parallel programming for force calculation can be done in the same way as serial programming; it can be easily revised according to physical models.MDRANGE (分子动力学计算ion ranges)【URL】http://beam.helsinki.fi/~knordlun/mdh/mdh_program.html【作者】 Kai Nordlund【语言版本】 English【收费情况】免费【用途】 The official name of the program is MDRANGE. However, in the actual program files the shorter, more convenient name mdh (abbreviated from Molecular Dynamics High-energy) is used. Both names therefore (at least for now) mean exactly the same program. The program is a molecular dynamics (MD) simulation program tailored for effective calculation of ion ranges. The word effective used here must be understood in the context of high-energy molecular dynamics calculations.What it doesCalculates ion ranges in solidsCalculates deposited energiesCalculates the primary recoil spectrumObtaining stopping powers possible indirectlyIon and sample elements which can be used: anyEnergy range in which calculation can be done: roughly 1 eV/amu - 10 MeV/amuEnergy range in which use is justified: roughly 100 eV/amu - 100 keV/amuMDRANGE3.0: option for Puska-Echenique-Nieminen-Ritchie(PENR)-electronic stopping model [Sil00]. Needs charge density file from user.MDRANGE3.0: option for Brandt-Kitakawa(BK)-electronic stopping model. Needs charge density file from user.【备注】Kai NordlundAccelerator Laboratory, University of Helsinki, P.O. BOX 43, FIN-00014 Helsinki, Finland (email kai.nordlund@helsinki.fi)Car-Parrinello分子动力学(CPMD, ab-initio分子动力学计算软件)【URL】/【作者】 Jurg Hutter【语言版本】 English【操作系统】 Unix/Linux【下载】 /ftp.html【收费情况】免费【用途】泛函：LDA，LSD，GGA，自由能密度泛函。
分子反应动力学（势能面）基本概念
搜索的内容：各种概念介绍分子反应动力学：分为：宏观反应动力学(Macroscopic Kinetics) 微观反应动力学（Microscopic Kinetics）即为分子反应动力学（Molecular Reaction Dynamics）。
（不同定义表述）1.在原子、分子的层次上研究化学反应微观动态和机理的一门科学，它所研究的基元反应和基元化学物理过程能够使人们了解化学反应的机理。
2.应用现代物理化学的先进分析方法，在原子、分子的层次上研究不同状态下和不同分子体系中单分子的基元化学反应的动态结构，反应过程和反应机理。
（张爱丽）3.分子反应动力学是现代物理与化学之间的一门边缘学科，是化学物理学科的一个重要分支。
它深入到分子或原子层次来研究化学反应的微观动态和机理。
分子反应动力学的研究主要包括：1）构建反应体系的势能面；2）计算该体系的微观动力学参量（如截面），这些参量是反应物的初态及产物终态的函数；3)通过积分截面得到宏观动力学参量（速率常数）注：基元反应:在反应中一步直接转化为产物的反应（又称简单反应）。
基元反应本身是指没有中间产物，一步完成的反应。
目前验证基元反应最科学的方法包括量子化学的模拟计算和以飞秒激光为代表的分子动力学手段。
通过计算机模拟反应过程可以得到一个反应的模拟过程，数据时很好的预测手段。
通过飞秒激光得到反应过程中各种物质的光谱变化，可以推断反应（张爱丽）过程中到底什么物质或者是物质的什么状态发生反应，从而最终确定反应的过程。
势能面的构建势能面的意义：基于电子运动和核运动可分离假定的势能面概念是现代化学物理学最重要的思想之一。
从动力学理论计算的角度来讲，势能面是最基本也是非常重要的一个因素，势能面的准确程度对动力学计算的结果有直接影响。
势能面的形状反映出整个化学反应过程的全貌以及反应的始终态、中间体和过渡态的基本态势。
在势能面上连接这些态的一条最容易实现的途径就是整个化学反应的路径。
数值模拟方法与实验方法对比
数值模拟方法与实验方法对比摘要：科学研究与解决工程问题的基础在于物理实验与实物观测，但是采用实物模型进行物理实验的研究周期长、投入大，有时甚至无法在实物上进行，如对天体物理的研究。
而现代科学研究方法的核心则是通过观测或实验建立研究对象的数学模型，基于数学模型进行研究与分析。
在数学模型上进行的数值模拟研究具有研究周期短、安全、投入少等优点，已经成为现代科研不可或缺的工具。
关键词：科学研究；实验；数值模拟1 数值模拟方法介绍数值模拟实际上可以理解为用计算机来做实验，其可以形象地再现实验情景，与做实验并无太大区别。
数值模拟方法的应用对象分为三个层次：（1）宏观层次：常见的工程建筑、制造设备、零件等；（2）界观层次：材料的微观组织与性能，如金属材料的晶粒度影响其屈服强度；（3）微观层次：基本物理现象与机理，如金属材料凝固时的结晶与晶粒生长过程。
宏观与界观层次的数值模拟方法包括：有限差分方法(FiniteDifferenceMethod,FDM)、有限单元法(FiniteElementMethod,FEM)、边界单元方法(Boundary Element Method,BEM)、有限体积方法(Finite Volume Method,FVM)、无网格方法(Mesh less Method)。
微观层次的数值模拟方法包括：第一原理法(First Principle Simulation)、元胞自动机方法(Cellular Automata)、蒙特卡洛方法(Monte Carlo Method )、分子动力学方法(Molecular Dynamics)，分为经典方法、嵌入原子模型(Embedded Atom Model)、从头计算(Ab initio calculation)的方法。
虽然在工程技术领域内能使用的数值模拟方法有很多种，但是就其实用性和广泛性而言，有限单元法是最为突出的。
有限单元法的基本原理是将一个连续的求解域分割成有限个单元，用未知参数方程表征单元的特性，然后将各个单元的特征方程组合成大型代数方程组，通过求解方程组得到结点上的未知参数，获取结构内力等需要考察的输出结果。
杂化效应诱导压缩应变碳纳米管能带结构研究
杂化效应诱导压缩应变碳纳米管能带结构研究房慧;阮兴祥;毛春瑜;梁程;黄翠萍;白小花【摘要】采用第一性原理对压缩应变下超小口径碳纳米管的带隙和能带结构展开研究.总能曲线显示(3,0)～(8,0)单壁碳纳米管在小于10％的小应变区展现弹性行为.能带结构的计算结果显示,超小口径的(3,0)、(4,0)、(5,0)、(6,0)碳纳米管能在较大的压缩应变(＜10％)下较好地保持金属性,而管径相对较大的(7,0)、(8,0)碳纳米管实现了半导体性到金属性的转变,表明超小口径碳纳米管在压缩应变下不同常规的大口径碳管的电学行为.进一步的分析表明,超小口径碳纳米管带隙的变化行为与传统大口径碳纳米管的不同结果主要来源于严重卷曲引发的矿π杂化效应对费米能级附近带态的能量和性质产生剧烈的影响,进而说明基于传统碳纳米管的规律已不适用于超小口径碳纳米管.【期刊名称】《沈阳师范大学学报（自然科学版）》【年(卷),期】2017(035)001【总页数】5页(P34-38)【关键词】单壁碳纳米管;压缩;应变;电子结构;第一性原理【作者】房慧;阮兴祥;毛春瑜;梁程;黄翠萍;白小花【作者单位】广西民族师范学院物理与电子工程学院,广西崇左532200;北京工业大学新型功能材料教育部重点实验室,北京100124;广西民族师范学院物理与电子工程学院,广西崇左532200;广西民族师范学院物理与电子工程学院,广西崇左532200;广西民族师范学院物理与电子工程学院,广西崇左532200;广西民族师范学院物理与电子工程学院,广西崇左532200;广西民族师范学院物理与电子工程学院,广西崇左532200【正文语种】中文【中图分类】O469碳纳米管因其独特的力学[1]和电学[2]特性成为电子学、光学和应力传感纳米器件相关科学研究中的明星材料。
理想的单壁碳纳米管可以看成由石墨烯片卷曲而成的无缝中空管状结构,其电学特性与其自身的原子几何排列结构尤其是它的石墨烯片的卷曲矢量(手性参数)[3]密切相关。
量子化学主要研究方向及使用工具
我整理了一下大家的研究方向和主要工具，编成这个全家福。
如果其中有遗漏和错误请告诉我。
现在一共有22位同行加入这个大家庭了，新来的朋友和还没跟贴的朋友请跟贴说明。
这个全家福将会不定期增补。
(按跟贴顺序)1. gobin34, 主要研究方向：分子间弱相互作用. 工具： ADF, Turbomole, Gaussian, G amess. email: fan@chemie.uni-siegen.de2. O0O0O0O0，研究方向：激光光谱学。
计算主要集中在IIIA族单卤化物双原子分子激发态的相对论量化计算上。
现在主要用GAMESS，DALTON。
ADF，DIRAC，MOLFDIR偶尔用。
初学量化的时候，也用过盗版HyperChem和Gaussian。
本来还准备用MOLCAS或NOLPRO的，无奈老板是实验派。
3. spinsight, 研究方向：固体NMR及其在分子筛研究中的应用。
量化计算是一个辅助手段，主要想计算化学位移，以及研究分子筛的结构，催化反应机理等等。
现在主要是用Gaussian。
4. elizerbeth,主要研究方向纳米尺度上的电阻(conductance on the nanoscale system)主要用工具：Gaussian,V ASP,DFT++email:站内信箱 (注：该版斑竹及创版人)5. Chemis,主要研究领域催化反应机理，粒子-分子反应机理，金属簇；使用软件有gaussian,NWChem,ADF,Gamss等，尽力拓展。
email:chjwang@6. silali, 本人感兴趣的是含离子的分子体系，优化用GA（自造的东东），然后再GAUSS IAN一下，作些性质计算。
一直在WIN下作，目前正向LINUX平台过度。
7. Alwens,曾做过计算材料的东西，使用ADF，Gaussian，Gamess。
现主要集中于从事ab initio Molecular Dynamics，同时将来开展QM/MM的研究。
cp2k检查格式 -回复
cp2k检查格式-回复CP2K is a computational chemistry software package that is widely used in the field of computational chemistry and materials science. It provides a wide range of functionalities for studying molecular systems and condensed matter. In this article, we will explore the different aspects of CP2K, its usage, and how it can be beneficial in scientific research.1. Introduction to CP2KCP2K stands for "Car-Parrinello-2.0 Toolkit" and is an open-source software package specifically designed for molecular simulations. It is based on density functional theory (DFT) and utilizes pseudopotentials to describe the electronic structure of atoms and molecules. CP2K is capable of performing various simulations, including molecular dynamics, ab initio molecular dynamics, and metadynamics.2. Features and FunctionalitiesCP2K offers a wide range of features and functionalities that make it a powerful tool for computational chemistry research. Some of the notable capabilities of CP2K are as follows:- Efficient implementation of hybrid DFT methods such as the popular B3LYP functional, which allows for accurate calculations of electronic properties.- Inclusion of various dispersion correction methods like D3 and TS to accurately account for van der Waals interactions in molecular systems.- Ability to perform simulations at different levels of theory including Hartree-Fock, semi-empirical methods, and many more. - Support for periodic boundary conditions, which makes CP2K suitable for studying extended systems and surfaces.- Effective treatment of solvation effects through the inclusion of implicit solvent models like COSMO and explicit solvent models like the SPC/E water model.- Implementation of advanced sampling techniques like replica exchange molecular dynamics (REMD) and metadynamics, which allow for exploration of complex energy landscapes.3. Usage and ApplicationsCP2K is widely used by researchers in the field of computational chemistry and materials science. Some of the common applications of CP2K include:- Prediction of molecular structures, energies, and spectroscopic properties of organic and inorganic molecules.- Study of reaction mechanisms and kinetics in complex chemical systems.- Investigation of the electronic properties and energy transfer processes in materials.- Simulation of surface reactions and catalysis.- Exploration of the thermodynamics and stability of materials under different conditions.- Prediction of properties of biomolecules, such as proteins and DNA.4. Benefits and LimitationsCP2K offers several benefits for computational chemistry research. It provides an efficient and reliable framework for performing accurate molecular simulations. The open-source nature of CP2K allows researchers to customize and modify the code to suit their specific needs. Additionally, the extensive documentation and user-friendly interface make it accessible to both experts and beginners in the field.However, like any other software package, CP2K also has certainlimitations. One limitation is the high computational cost associated with some of its advanced simulation methods, which can make it time-consuming for large systems. The steep learning curve associated with the software may also pose a challenge for new users. However, these limitations can be mitigated through proper understanding, optimization, and efficient use of computational resources.5. ConclusionIn conclusion, CP2K is a powerful computational chemistry software package that provides a wide range of functionalities for researchers in the field of computational chemistry and materials science. With its extensive capabilities, it allows for accurate and efficient simulations of molecular systems and condensed matter. Despite some limitations, CP2K continues to be a valuable tool for studying the properties and behaviors of atoms, molecules, and materials. Its open-source nature and active community support make it an excellent choice for those involved in scientific research.。
太赫兹与水的相互作用:机理、应用和新趋势
太赫兹与水的相互作用：机理、应用和新趋势范姝婷;马莹玉;舒国响;钱正芳【摘要】自21世纪以来,太赫兹技术因受到世界各国的重视和扶持而取得迅猛发展.介绍液态水分子网络在太赫兹波段的振动和弛豫模式,以及太赫兹波与水分子之间相互作用的原理.评述基于此机理太赫兹在生物医学,尤其是关于癌症检测领域的发展与挑战,介绍了本课题组目前开展的工作.展望围绕太赫兹波与水相互作用产生的新研究与新技术.【期刊名称】《深圳大学学报（理工版）》【年(卷),期】2019(036)002【总页数】7页(P200-206)【关键词】电磁波物理;太赫兹;太赫兹时域光谱;太赫兹成像;生物医学应用;癌症检测;水分子网络【作者】范姝婷;马莹玉;舒国响;钱正芳【作者单位】深圳大学物理与光电工程学院,广东深圳518060;深圳大学电子与信息工程学院,广东深圳518060;深圳大学电子与信息工程学院,广东深圳518060;深圳大学物理与光电工程学院,广东深圳518060【正文语种】中文【中图分类】TN219;TN247太赫兹(1 THz=1 012 Hz)通常指频率在0.1～10.0 THz，波长介于30～3 000μm的电磁波，其位于微波与红外波之间，是电子学向光学的过渡区．曾经在很长的一段时间里，该频段的研究进展缓慢，一度被称作“THz空隙”，是电磁波谱中唯一有待全面开发的频谱资源．太赫兹的研究始于20世纪80年代，在1975年AUSTON[1]发明光电导开关之后，于21世纪初开始迅速发展，美国、欧盟、日韩以及中国都先后将太赫兹技术列为21世纪重点发展的技术之一，其中，美国于2004年将太赫兹技术列为“改变未来世界的十大技术”之一；日本国家信息与通讯技术研究院于2006年发布“太赫兹技术五年计划”，致力于建立国家层面的太赫兹技术基础结构设施，包括但不限于太赫兹半导体器件、脉冲太赫兹波测试系统，以及太赫兹材料数据库[2]．基于各国的大力扶持和有关太赫兹源、探测及调制等器件的深入研究，“THz空隙”正逐渐被填补．2017年中国科技部发布《关于发布国家重点研发计划变革性技术关键科学问题重点专项2017年度项目申报指南的通知》，计划下拨总经费约3.9亿元人民币，而其中重点项目之一就是面向生物医学应用研究的新型太赫兹辐射源．水在太赫兹的应用，尤其是在生物医学相关应用研究中是不可回避的话题，且在各个应用领域中均占有重要地位．例如，在太赫兹肿瘤检测中，目前确定的成像机理之一就是以肿瘤与健康组织中水分含量的区别为依据；在生物化学的基础研究中，利用太赫兹波对水分子网络本身，以及生物大分子[3]、糖类[4]、盐离子[5]与周围液相水分子网络的相互作用吸引了大量的研究关注．本研究围绕太赫兹与水的相互作用展开评述，介绍太赫兹波与水分子之间相互作用的机理；阐述基于此机理的太赫兹生物医学方面的相关研究，尤其是关于癌症检测领域中的发展与挑战；最后介绍太赫兹波与水相互作用产生的新研究与新技术．1 太赫兹波与水分子相互作用的机理图1 一种可能的水分子网络局部结构[7]Fig.1 A hypothesized local structure of liquid water network[7]图2 液态水在0.1 GHz～4 000 THz的吸收谱[15]Fig.2 The absorption spectrum of liquid water from 0.1 GHz to 4 000 THz[15]水与其他液体相比具有很多特殊的性质[6]，在微观层面上，造成这些特殊性质的原因尚无定论．目前，学界普遍认为这与水中广泛存在的氢键有关．1个水分子可自由地与其周围至多4个水分子形成氢键，因此有可能在局部形成一个如图1所示的四面体结构[7]．氢键组成的水分子网络在分子热运动的过程中被打乱及重排所需要的时间在皮秒或亚皮秒量级[8]，所对应的电磁波频率范围恰好位于太赫兹波段．因此，液态水对0.1～10.0 THz波具有很强的吸收特性，根据Beer Lambert法则(Ein/Eout=e-αl，其中， Ein和Eout分别表示入射和出射的电场强度； l表示电磁波在媒介中走过的路径长度)，计算其吸收系数α为104～105 m-1．图2为液态水在0.1 GHz到4 000 THz之间的吸收谱．可见，其中一个较强的吸收峰位于5.4 THz(约180 cm-1)，这个吸收峰被解释为氢键的伸展及受限平移等振动模式；另一个较弱的吸收峰在更低频的1.8 THz(约60 cm-1)左右，对此振动模式的解释目前还存在一些争议，它曾被认为是氢键的弯曲振动或平行于氢键的平移振动[9]，GUILLOT等[10]通过从头计算分子动力学(ab-initio molecular dynamics)仿真发现，这一弱红外吸收峰源自单个水分子在四面体框架结构中的快速摇摆运动．随后其他研究[11-12]也都支持了这一观点：这些较低频率(<3 THz)的振动模式来自于单个水分子本身,与水分子永久偶极矩(permanent dipole moment)而非感应偶极矩(induced dipole moment)相关，弱化了氢键在1.8 THz振动模式中的作用．当频率进一步降低，弛豫振荡过程成为主导，在毫米波太赫兹范围内，实验观测到纯弛豫模式的特征时间在8 ps左右，对应特征频率为20 GHz，这一弛豫振荡峰的尾部延伸至太赫兹波段，对太赫兹波段中水的介电、吸收特性起主导作用．随着技术的进步，RØNNE等[13]用太赫兹时域光谱(terahertz time domain spectroscopy, THz-TDS)系统测量了液态水在0.2～2.0THz的复介电常数，发现在20 GHz～1.8 THz还存在未知的作用机理，解释太赫兹波段水与电磁波相互作用的机理也成为近年来的热门研究[14-17]．可见，一旦水分子网络结构的动态平衡被打破，重新建立所需要的分子转动或位置替代的过程时间在皮秒或亚皮秒量级，因此液态水分子对太赫兹波十分敏感，太赫兹技术对于深入研究水分子网络的结构与动态过程有着十分重要的意义．2 太赫兹癌症检测2.1 起源、发展与瓶颈水跟生物体的关系密切，因此太赫兹生物医学成为太赫兹应用研究中最早的一个方向．其中，癌症检测又是太赫兹生物医学应用的开端．早在21世纪初期，剑桥大学以及英国TeraView公司的研究团队就对21个病例的皮肤基底细胞癌离体样本进行太赫兹成像[18]．在太赫兹图像中肿瘤的边界与组织病理切片染色后的显微照片中显示的肿瘤组织有较好的匹配，且肿瘤与健康组织之间的对比度足以界定肿瘤边界．肿瘤组织相对于健康组织对太赫兹波的吸收更强．目前，导致这种吸收差异的原因并不清楚．WOODWARD等[18]指出，这种差异最可能来源于皮肤组织中水分含量的不同，或者来自于水分子与皮肤中的蛋白质等生物大分子的官能团结合导致其振动模式的改变．此项工作后，国内外研究人员对多种癌症进行了广泛的太赫兹成像与光谱分析[19]，涉及乳腺[20]、宫颈[21]及脑[22]等各个部位的原发癌．但太赫兹成像技术却始终未在临床应用上获得认可．限制其发展的主要因素有：① 现阶段仍缺乏太赫兹波对肿瘤与健康组织的区分能力，以及作用机理等相关基础生物问题的深入研究．虽然以上针对各种肿瘤的研究都显示，肿瘤在太赫兹波段与周围健康组织有一定的对比度，但鲜有研究能够阐明造成这种对比度的机理．即使在太赫兹波段出现明显的区别，也不能直接证明这是由癌症组织所致．恶性肿瘤判断的黄金标准依然是病理学切片．为增强癌症检测的特异性，一些研究将目光转向肿瘤标记物的太赫兹光谱探测上，如唾液中乳腺癌的重要标志蛋白[23]、脑胶质瘤标志物[24]以及肝癌早期标志物[25]的探测；② 水分子对太赫兹波的吸收是癌症检测中不可回避的问题．太赫兹波光子能量低，不会对生物体产生电离作用，这使太赫兹成为理想的非侵入式癌症检测工具．但受限于生物体中大量水分子对太赫兹波的吸收，太赫兹波不可能穿透人体，对内部组织直接成像．因此，除皮肤癌之外，非侵入的特性显然对其他癌症的在体诊断意义不大；③ 现有太赫兹系统的硬件、软件并没有达到临床癌症检测的要求．硬件上，目前较成熟的成像方法依然是逐点扫描式成像，其成像速度慢，空间分辨率受衍射极限的限制一般在100 μm左右．针对这一挑战，科学家们近年来对压缩感知、近场成像及固体浸没显微成像等技术进行探索，并取得一定进展[26-28]．在软件方面，从太赫兹响应中提取样品特征参数的数据处理算法，其准确度和可靠性尚有待提高．如英国国家物理实验室的NAFTALY等[29]将几种标准样本分别寄给16 个不同国家和地区的太赫兹实验室进行单独测试，结果发现各个实验室反馈的测试结果存在巨大差别．以上都是太赫兹成像技术在走向临床过程中所遇到的挑战及发展瓶颈．2.2 生物组织成像对比度机制的深入研究太赫兹癌症检测的研究应着眼于成像机理的研究，而非单纯的横向扩展．2010年，PICKWELL-MACPHERSON教授课题组的SY等[30]用福尔马林浸泡过的样本进行太赫兹时域光谱测量实验，证明水分的差异并不是太赫兹成像唯一的对比机制，以肝硬化样本来讲，至少有50%～66% 的对比度来自于组织结构与成分的差异．2016 年，CHOPRA 等[31]从细胞尺度上研究纤维母细胞的密度对太赫兹信号的影响，发现纤维母细胞的密度增加会减小组织在太赫兹波段的折射率，由于肿瘤跟健康组织的重要区别之一是其细胞的增殖能力强，此项研究对肿瘤与健康组织在太赫兹波段对比度机制的研究有一定的参考意义．针对成像对比度机制的探索，本课题组对太赫兹波与生物组织中各成分相互作用的机理展开系统研究[32]．利用不同配比的明胶、去离子水及油脂制作乳腺组织仿体，仿体中加入少量甲醛促进蛋白质相互交联，并加入少量对甲基苯甲酸和正丙醇减少高浓度的明胶在水溶液中的聚积沉淀，然后对其太赫兹频段的复介电常数进行测量和分析，最后与真实乳腺癌组织中的纤维组织、肿瘤组织和脂肪的复介电常数进行对比．结果显示，在1 THz以上的高频部分，某些配比的仿体可以很好模拟真实组织的介电损耗(ε″)，而低频部分则与真实组织相差较大，如图3．其中，m(w)、m(g)及m(o)分别为仿体中水、明胶及油脂的质量分数.考虑到高频部分主要受单个分子的转动模式影响，而低频部分则由氢键集体断裂及重排的弛豫过程主导，我们推断，仿体中所用的明胶与真实组织中的蛋白质在成分和结构上的不同，可能导致水分子与蛋白质结合的氢键存在差异，进而影响仿体混合物的低频特性．图3 不同配比的仿体与真实组织中的纤维、肿瘤、脂肪的复介电常数虚部的对比[32]Fig.3 The comparison among the imaginary parts of complex permittivities of phantoms and those of fibers, tumors, and adipose tissue in breast[32]本课题组利用相对分子质量不等的明胶配制不同浓度的水溶液，对仿体中的蛋白质进行独立分析，并用有效介质理论计算出的水溶液的复介电常数，与实验值进行比较，结果如图4(虚线为对0.2 THz数据的线性拟合)[33]．可见，在低频区域，随着蛋白质含量的增加，有效介质理论计算出的有效介电损耗与实验测得的水溶液实际介电损耗差异呈近似线性增加；而在高频区域，两者几乎吻合．我们的初步结果证明，蛋白质含量的差异是影响生物组织太赫兹低频介电特性的因素之一．通过分析肿瘤组织与正常组织在太赫兹低频波段的介电常数，可得这两种组织在蛋白质含量上的差别，这将合理解释肿瘤组织与健康组织在太赫兹波段的对比度机制，有助于太赫兹癌症检测研究向纵深发展．图4 不同相对分子质量的明胶溶液利用有效介质理论计算与实验测得的介电常数虚部在0.2～1.0 THz 的差随明胶浓度的变化[33]Fig.4 The variation of thedifference between the calculated and the measured imaginary parts of permittivities of samples with different molar weights between 0.2 THz and1.0 THz for with various concentrations[33]2.3 提高参数提取准确性的数据处理算法研究针对样品介电和吸收等特性参数提取的准确性，德国的PUPEZA等[34]、法国的DUVILLARET等[35]、澳大利亚的WITHAYACHUMNANKUL等[36-37]所在的团队在早期做了较多的工作，包括对实验不确定性的探索以及对薄膜样品多重反射的处理等．近年来英国国家物理实验室的NAFTALY等[38-39]在参数提取方法的国际化标准建立上进行了调研．从太赫兹在癌症的体检测上考虑，反射式系统相对于透射式系统具有更强的实用性．本课题组在2016年对反射式太赫兹系统样品参数的提取算法进行改进．传统的计算公式假定入射在样品与参考物表面的太赫兹波具有完全相同的相位，然而在实际测试中入射波的相位不可能完全相同，据此计算会导致相位错误，造成计算结果的偏差．造成相位错误的原因既有系统端的不稳定性，也有样品端的不稳定性．其中，系统端的不稳定性包括飞秒激光脉冲在光纤中传输时由于光纤抖动而造成的相位变化，以及扫描成像时位移台的机械抖动造成的相位变化．样品端的不稳定性主要因为样品和参考物的反射平面在实际操作中很难保持完全一样，导致样品与参考物相对太赫兹发射器的距离不一样，造成入射波相位的不一致．在太赫兹波段，0.1 ps的时域漂移就会对样品吸收系数测量的准确性造成巨大影响．本课题组针对系统端的不稳定性对传统数据采集和处理算法进行改进，以成像窗下表面反射信号为基准，利用成像窗的介电特性计算参考信号，使参考信号与样品信号的采集在同一次测量中完成，从而避免两次脉冲之间入射波的相位差，如图5．其中，去离子水均匀分布于图中圆环内，成像参数为0.5 THz水的吸收系数；σ为虚线框中数据的标准差；α、 n、ε′及ε″分别为吸收系数、折射率、介电常数实部和虚部.此算法不仅将参数提取的不确定性(标准差)缩小到近七分之一，也将测试时间缩短到近二分之一[40] ．随后，CHEN等[41]进一步发展并在太赫兹时域光谱系统的数据采集软件中实现了该算法．3 最新技术进展与趋势太赫兹波与水的相互作用限制了太赫兹波在生物组织中的穿透深度，为在体成像带来很多挑战与限制．近年来一些国际团队对水加以利用，开展了很多有趣且意义重大的研究．图5 太赫兹反射成像参数提取的算法改进[40]Fig.5 Improving the algorithm of parameter extraction for terahertz reflection imaging[40]例如，美国罗彻斯特大学的ZHANG教授、北京首都师范大学张存林教授、俄罗斯圣彼得堡国立信息技术机械与光学大学组成的联合团队[42]，首次报道了利用超短激光脉冲照射液态水薄膜产生太赫兹波．这项工作的发表扩充了此前仅能利用固体、气体及等离子体产生太赫兹辐射的手段，证明物质的4种状态均可产生太赫兹波．虽然此项技术最终的应用方向尚不能确定，但能证明人体中大量存在的水有主动辐射太赫兹波的潜能，因此，此项研究是振奋人心的突破性工作．将太赫兹与其他互补性技术相结合，开展二维光谱技术的研究成为近年来的热点之一．例如，二维拉曼-太赫兹光谱技术被用于研究液态水分子网络的微观结构以及离子的水合作用对水分子网络的影响机制[43-44]．SHALIT等[45]利用此技术将盐溶液的黏度这一宏观特性与分子间氢键的集体振动模式联系起来，首次从分子层面证明溶液中的阳离子是通过改变水分子之间的振动模式，而不是通过离子与水分子之间的相互作用来改变水网络结构的．GRECHKO等[46]利用二维超宽频太赫兹-红外-可见光(2D terahertz-infrared-visible, 2D TIRV)光谱技术研究液态水中分子间作用力和分子内作用力的耦合，揭示了液态水分子内部O—H拉伸振动与低频(1.5～7.5 THz)分子间振动，包括1.8 THz的疑似氢键弯曲振动和5.4 THz的氢键拉伸模式，具有很强的耦合特性．可见，合理利用太赫兹与其他技术优势互补的多维光谱技术，可对样品特性进行更有深度、更全面的检测．结语21世纪以来，太赫兹技术在各个国家的大力扶持下发展迅猛，伴随而来的是学术界和工业界对太赫兹应用领域的探索与开拓．由于太赫兹与水密切相关，生物医学研究成为太赫兹应用研究中最主要的领域之一．太赫兹波与水分子及其网络相互作用的研究是太赫兹技术生物医学应用领域的重要课题，其不仅在生物化学等基础学科领域有着重要的意义，在揭示太赫兹癌症检测的对比度机制上，也扮演重要角色．15年来，国内外对大量肿瘤组织进行太赫兹波成像及光谱分析，但太赫兹技术距离临床应用尚有很大距离．太赫兹技术与其他光谱技术相结合的非线性及多维度检测技术是目前应用研究的趋势．如何利用多种技术优势互补并最终走向应用是一个跨学科、跨领域的问题，需要各方学者协同解决．参考文献：【相关文献】[1] AUSTON D H. 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