computational chemistryweiwu.xmvb.org/ppt_cc/cc0.pdf · 计 算 化 学 computational chemistry ....
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Chemistry
Analytical Biochemistry Inorganic Organic Physical
Chemistry
Analytical Biochemistry Inorganic Organic Physical
化学是实验科学？
Chemistry
Analytical Biochemistry Inorganic Organic Physical
化学是实验科学？
没有计算就没有科学？
如果没有计算机？
Chemistry
Analytical Biochemistry Inorganic Organic Physical
Computational & Theoretical Chemistry?
Chemistry
Analytical Biochemistry Inorganic Organic Physical
Computational & Theoretical Chemistry?
A merging point of Chemistry, Physics, Biology, Mathematics and Computer Science
前 言
• 化学：研究分子的构造，变换，和性质的科学 • 理论(计算）化学：结合数学方法和物理定律研究
化学相关过程 • 分子：带电荷的粒子（原子核和电子） • 分子的区别：原子核，电子数，原子核位置
计算化学的研究内容 • Electronic structure determinations • Geometry optimizations • Frequency calculations, IR spectra, NMR spectra, Raman
spectra… • Transition structures • Protein modeling, e.g. folding and docking of inhibitors • Electron and charge distributions, dipole moment • Potential energy surfaces (PES) • Rate constants for chemical reactions (kinetics) • Thermodynamic calculations- heat of reactions, energy of
activation • And more and more
理论（物理学） 牛顿力学（分子力学） 量子力学 热力学 统计力学 严格的数学解仅限于含2个粒子的体系 在许多情况下，可以获得数值解 (Numerical solution)
理论(Theory), 模型(Model)， 计算(Computation)
理论(Theory)
• A theory is one or more rules that are postulated to govern the behavior of physical systems.
Comfortable • Such rules are expressed in the form of a mathematical
equation. E=mc2 • Applicable range of a theory. Classical mechanics Quantum mechanics
Model Approximations! Valence-Shell-Electron-Pair Repulsion Model
Constants! Theory: Generality
Computation: To use digital technology to solve the
mathematical equations defining a particular theory or model.
计算化学已经迅速成为化学学科的一个重要分 学科。
计算化学：通过计算的手段研究解决化学问题
计算化学 实验手段
计算化学 理论化学
理论与计算化学
Cost and Efficiency
Experiments vs Computations
Chemical waste disposal Computational technology
More and more expensive or less and less?
Hardware & Software
How to maximize the accuracy while minimizing investment?
Speed
Memory
Storage
Hardware Software
Code (Fortran, C++) Compiler
Assemblers
Method & Algorithm
The general objectives of computational chemistry:
• Confirm and predict experimental results;
What Can Modern Computational Chemistry Do?
• Elucidate the nature of molecular structure and understand the relationship between structrues and properties.
Advantages of being a computational chemist:
• Flexbility; • Tidy; • Broad interests; • No chemical hazard.
A Brief History of Theoretical Chemistry
1803 – Dalton's atomic theory: all matter is composed of atoms.
1906 – Gilbert Lewis: valence theory (Lewis structure)
1927 – Heitler and London: solved the electronic structure of H2+
1950’s – The first ab initio Hartree-Fock calculations on diatomic molecules; Slater and Gaussian orbitals
1960’s – Hückel method and semi-empirical ab initio methods
1970’s – Ab initio methods
1980’s – Electron-correlated methods
1990’s – Density functional theory
2000’s – Combined QM/MM molecular dynamics simulations; protein and drug design
1926 – Quantum mechanics: Schrödinger equation
国际研究现状 理论与计算化学已成为独立的学科 主要杂志 Journal of Chemical Theory and Computation (JCTC)
Journal of Computational Chemistry (JCC)
Journal of Theoretical and Computational Chemistry (JTCC)
International Journal of Quantum Chemistry (IJQC)
Theoretical Chemical Account (TCA)
主要学会组织 World Association of Theoretical and Computational Chemists (WATOC)
International Academy of Quantum Molecular Science
主要会议
国内研究现状
厦大理论化学现状
理论与计算化学研究所 固体表面物理化学国家重点实验室 福建省理论与计算化学重点实验室
教授6人，副教授3人； 院士（1人） 长江特聘教授（1人） 闽江特聘（2人） 厦大特聘（2人）
理论，方法，程序，计算 量子化学，化学反应动力学，分子力学，统计力学 理论方法发展与计算程序研发 生命相关体系计算 纳米相关体系计算
牛顿力学
maF =
2
2
dtdm
ddV r
r=−
r(t)r =
量子力学 (Quantum mechanics)
Schrödinger方程 tΨiHΨ∂∂
=
)()()()(),()(),(
/
rErrHertr
rHtrHiEt
Ψ=ΨΨ=Ψ
=−
定态的
∑
∑∑
>
=
=
∂∂
+∂∂
+∂∂
=∇
∇−==
+=
ijij
iiii
ii ii
i
VVzyx
mTT
VTH
)(
2
2
2
2
2
2
22
22
1
由于核的质量远大于电子，运动速度远低于电子
的速度，引进近似： 在固定核构型下的电子运动 核在电子作用势的运动
)()())((),()(),(),(
),()(),(
),(),(),(
RERRETrRRErRrRH
rRRrRTHH
VVVTHVVVTTH
rRErRrRH
nTnen
eeee
enT
neT
eennneee
eennneneT
TTTT
Ψ=Ψ+Ψ=Ψ
ΨΨ=Ψ+=
+++=++++=Ψ=Ψ
Born Oppenheiner近似
电子结构理论
反应动力学
Atomic Units (a.u.)
本课程的教学目的
介绍计算化学的基本理论与方法
介绍量子化学的基本概念和基础知识
介绍计算机语言与量子化学程序
本课程的特点：
理论，科学问题，科学计算
参考书
F. Jensen, Introduction Computational Chemistry, John & Wiley, New York, 1999
C. J. Cramer, Essentials of Computational Chemistry Theories and Models, Wiley, West Sussex, 2004
I. N. Levine, Quantum Chemistry, third, forth, fifth Ed. Prentice Hall, New Jersey, 200x
课程要求： 考勤 20% 作业上课 30% 期末考试 50%