Lecture 1 - Introduction
Lecture 1 - Introduction
Lecture 1 - Introduction
Lecture 1. Introduction
◆ Text Book
0. Atkins “Physical Chemistry”
1. D. Frenkel and B. Schmit, "Understanding Molecular Simulation",
Academic Press, San Diego (1996)
2. M. P. Allen, D. J. Tildesley, "Computer Simulation of Liquids",
Clarendon, Oxford (1987)
◆ References
1. C. J. Cramer, "Essentials of Computational Chemistry",John Wiley &
Sons, New York (2002)
2. T. L. Hill, "An Introduction to Statistical Thermodynamics", Addison-
Wesley, London (1960)
Syllabus
◆ Computer Software
– Material Studio
◆ Programming Language
– C / C++ or FORTRAN, Python, Mathlab
◆ Exam
– End of the semester
◆ Small Project
– MD simulation of 2D/3D sphere
◆ Grade
– Exam (60 %), Project (20 %), QUIZ and Attendances (20%)
Overview of the Course
Lecture 1. Introduction
Lecture 2. Basic Statistics
Lecture 3. Introduction to Statistical Mechanics
Lecture 4. Model System – Force Field
Lecture 5. Molecular Monte Carlo Simulation
Lecture 6. Molecular Dynamics Simulations
Project: MD Simulation of 2D Sphere, 3D Sphere
Lecture 7,8 – Software Exercises
Lecture 9. Quantum Mechanics
Lecture 10. Molecular Modeling -1
Lecture 11. Molecular Modeling -2
Final Exam
Difficulties in Learning Molecular Modeling and Simulation
Reaction
Biology
Engineering
◆ Molecular Simulation
– Properties calculation based on many-body simulation
– Interested in bulk properties (Average of may molecules)
– Two methods are well-known
• Molecular Monte-Carlo Simulation (MC)
• Molecular Dynamics Simulation (MD)
– Two methods require force field as input
– The force field can be estimated using Molecular Modeling Technique
Molecular Modeling and Simulation
O 28
O 26
O 24
Pressure
22
20
18
N 16
14
0 200 400 600 800 1000 1200
Time
Molecular Modeling
(Computational Molecular Simulation
Quantum Chemistry) Monte Carlo
Ab-initio Molecular Dynamics
HF, DFT
Structure and Thermodynamic Properties
Energy of individual molecules Transport Properties
Molecular Modeling and Simulation
◆ Computer Modeling/Simulation become a general research tools
– Many major journals in science and engineering fields
– No. of papers are increasing
◆ Understanding the “Black Box” greatly increases the efficiency using it
◆ The technique can be applied to various field of science and engineering
– Chemistry and Physics
– Chemical Engineering
• Thermodynamics
• Transport Phenomena
• Reaction Kinetics
– Bimolecular Engineering
• Protein Structure Prediction
• Protein Binding – Pharmaceuticals design
• Enzyme Kinetics
– Material Science
• Functional Material Design
Motivation of electronic computers
◆ World War II
– US battleships can fire shells weighing as much as small car over distance up to 25 miles (~38 km)
– Physicists could write the equations that describes how atmospheric drag, wind, gravity, … would
determine the trajectory of the shell.
– US military was looking for females (with math majors) to hire the job of computing “firing tables”
– Not enough humans could be found to keep up with the need for new table
– The early success was the Harvard Mark I computer (Harvard and IBM, 1944)
– However, Mark I was not pure electronic computer (mechanical switches, relays, rotating shafts, …)
Origin of “Computer”
Human Computers
History of Using Computer
◆ MANIAC, 1952
– After World War II, scientists seek to use of computer
– N. C. Metropolis was interested in solving broad spectrum of problems on
this machine
– At Los Alamos, in the 1950, a group of researches led by Metropolis,
including John von Neumann and Stanislaw Ulam, developed Monte Carlo
Method.
Metropolis Monte-Carlo
Simulation Method
Molecular simulation B.C. (Before Computer)
◆ Approximate Theories
– Van der Waals equation for non-polar fluids
– Debye-Huckel for electrolytes
◆ Mechanical Simulation
– Plastic foam balls
– Metal bearings
• Tedious, laborious
• Quite realistic ▪ J.D.Bernal’s model of a simple liquid
Test of Test of
Model Theories
Procedure for Molecular Simulation
Statistical
Computer Simulation
Model Averaging
Implementation Result
Method
• Sir John Pople first developed G1 method (Novel Prize Winner in 1998)
• Gaussian-4 theory is now available.
Heat of Formation Tool in Accerlys Software
Properties of alternative molecules
◆ Properties Prediction for alternative refrigerant (HCFCs)
◆ Fermeglia et al. FPE, 2003
– Accurate force field (FF) calculation is most important factor
– FF is important due to complex nature of molecular associations in H-F
bonds
Properties
Molecular Structure Force Field
Phase Equilibria
100
(-) Form
(+) Form
80
Conversion
Conversion Yield (%)
60
yield (%)
40
(-)Form; 66.7%
20
(+)Form; 35.4%
0
0 20 40 60 80
100 ml
beaker
Experimental
Slow evaporation at room
temperature without acetone+ t-HBP ethanol+ t-HBP methanol+ t-HBP
mechanical vibration
❖ t-HBP
Eatt,hkl E'att,hkl E'att,hkl E'att,hkl
face
in vacuum in acetone in ethanol in methanol
{1 0 1} -21.29 -33.72 -34.09 -31.41
{1 1 1} -19.16 -71.79 -53.49 -59.73
{1 1 0} -18.93 -26.56 -32.52 -19.94
{1 0 0} -20.83 -25.36 -17.29 -21.66
{0 1 0} -9.36 -12.35 -12.40 -10.64
Molecular Modeling {0 0 1} -9.41 -16.02 -14.49 -7.39
▪ BPTI structure
• X-ray structure
▪ The lowest-energy conformation
• (b) MC simulation annealing in gas phase
• (c) In aqueous solution, by the distance-distance dielectric function
• (d) In aqueous solution, by the solvent-accessible surface area
Molecular Design/ QSAR / QSPR
◆ USA
– NSF(National Science Foundation), DOE (Department of Energy), NIST (National Institute for
Science and Technology) , DARPA (Defense Advanced Research Projects Agency) , AFOSR(Air
Force Office of Scientific Research), NIH (National Institute for Health), …
◆ UK
– CCP Project (Collaborative Computational Project)
– CCP1 - The electronic structure of molecules
CCP2 - Continuum states of atoms and molecules
CCP3 - Simulation of physical and electronic properties of surfaces and interfaces
CCP4 - Protein crystallography
CCP5 - Computer simulation of condensed phases
CCP6 - Quantum molecular dynamics
CCP9 - Computational studies of the electronic structure of solids
CCP11 - Biosequence and structure analysis
CCP12 - High Performance Computing in Engineering
CCP13 - Fibre and polymer diffraction
CCP14 - Powder and small molecule single crystal diffraction
Answer to Q3
Is it really possible to do modeling for a very complex
molecules ? Is it economical ?
◆ Moore’s Law
– Computing speed doubles every 18 months
– Order of magnitude in every 5 years
◆ Parallel computing
– Add 2-3 order of magnitude for computing
Answer to Q4