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Introduction to computational chemistry - MC260C59
Title: Úvod do počítačového modelování
Czech title: Úvod do počítačového modelování
Guaranteed by: Department of Physical and Macromolecular Chemistry (31-260)
Faculty: Faculty of Science
Actual: from 2014
Semester: winter
E-Credits: 3
Examination process: winter s.:
Hours per week, examination: winter s.:0/2, C [HT]
Capacity: unlimited
Min. number of students: unlimited
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Note: enabled for web enrollment
Guarantor: prof. RNDr. Jiří Vondrášek, CSc.
Teacher(s): prof. RNDr. Jiří Vondrášek, CSc.
Last update: prof. RNDr. Jiří Vondrášek, CSc. (14.05.2012)

Základní literatura:

A. R. Leach. Molecular Modelling. Principles and Applications. Addison Wesley Longman, Essex, England, 1996. [Broad introduction to many aspects of molecular modeling and computational chemistry techniques, covering basic concepts, quantum and molecular mechanics models, techniques for energy minimization, molecular dynamics, Monte Carlo sampling, free energy simulations, and drug design applications]

M.P. Allen and D.J. Tildesley. Computer Simulation of Liquids. Oxford University Press, New York, 1987. [Good advanced reference book for molecular simulations]

Další doporučená literatura:

A.D. Bates and A. Maxwell. DNA Topology. In Focus series, Oxford Univeristy Press, New York, 1993. [Beautiful paperback on the highter organizational forms of DNA]

C. Branden and J. Tooze. Introduction to Protein Structure. second edition, Garland Publishing Inc., New York, 1999. [An up-to-date and nicely illustrated protein structure textbook dealing with basic structural principles as well as the relationship among structure, function, and enginnering. The latter part includes chapters on transcription regulation, signal transduction, immune regulation, membrane and fibrous prteins, and virus structures.]

P. Bratley, B. L. Fox, and L. E. Schrage. A Guide to Simulation. Springer-Verlag, New York, 1987. [Good introduction to Monte Carlo simulations]

C. L. Brooks, III, M. Karplus, and B.M. Pettitt. A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. Wiley Interscience, New York, 1988. [Nice collection on protein simulations]

U. Burkert and N.L. Allinger. Molecular Mechanics. American Chemical Society, Washington D.C., 1980. [Basic introductory monograph on molecular mechanics]

C.R. Cantor and P.R. Schimmel. Biophysical Chemistry. Vol.1,2,3. W.H. Freeman and Company, San Fransisco, 1980. [Basic introductory monograph on molecular mechanics]

N. R. Cohen, Editor. Guidebook on Molecular Modeling in Drug Design. Academic Press, San Diego, 1996. [Modern reference for molecular modeling as applied to drug design problems, containing contributed chapters by industrial and academic scientists, on problem formulation (database analysis, docking), modeling tools, and medicinal chemistry applications]

Computational Molecular Dynamics: Challenges, Methods, Ideas -- Proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, May 21-24, 1997, P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich,. R. D. Skeel, Eds., Lecture Notes in Computational Science and Engineering, Vol. 4 (Series Editors M. Griebel, D. E. Keyes, R. M. Nieminen, D. Roose, and T. Schlick), Springer-Verlag, Berlin and New York, 1999. [Collection of articles from the presentations invited to the May 1997 Berlin conference on macromolecular-simulation algorithms. The books contains sections on the following topics: conformational dynamics, thermodynamic modeling, enhanced time-stepping algorithms, quantum-classical simulations, and parallel force field evaluation]

T.E. Creighton, Editor. Protein Folding. W.H. Freeman & Company, New York, 1992. [Nice collection with general topics regarding prteins covered]

D. Eisenberg and D. Crothers. Physcial Chemistry with Applications to the Life Science. Benjamin Cummings, Menlo Park, California, 1979. [Wonderful physical chemistry textbook, with useful biomolecular information]

A. Fersht. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman and Company, New York, 1999. [A comprehensive perspective of both enzyme catalysis and protein folding by a pioneer researcher, an updated version of the author's 1995 text on Enzyme Structure and Mechanism; the text reviews protein structure, emphasizing general principles, as well as reviewing recent advances and insights from theoretical approaches]

D. Frenkel and B. Smit. Understanding Molecular Simulations. From Algorithms to Applications. Academic Press, San Diego, California, 1996. [Excellent introduction to computer simulation of molecular systems, containing a nice mix of mathematical details and more informal, decriptive text. The focus is on onte Carlo and molecular dynamics methodologies, through comparison and contrast analysis, including simple algorithmes and numerical illustrations. Some improtant recent methodological advances are also included]

L.M. Gierasch and J. King, Editors. Protein Folding, Deciphering the Second Half of the Genetic Code. AAAS, Washington D.C., 1990. [Interesting and beautifully illustrated colletion of articles; best bet: Jane Richardson's origami analogues of protein folding motifs!]

H. Gould and J. Tobochnik. An Introduction to Computer Simulation Metheods: Appkications to Physical Systems. Part 1 and 2 Addison-Wesley, Reading, MA, 1988. [A good introduction to computer simulations, with a focus on classical mechanics in Part 1 and statistical physics in Part 2. The material is made highly accessible to undergraduates by the inclusion of many simple numerical examples, useful illustrations, and programming segments.]

A.Y. Grosberg and A.R. Khokhlov. Giant Molecules. Here, There, and Everywhere... Academic Press, San Diego, California, 1997. [A lively introduction to polymer physics, with nice illustrations and enticing color plates, aptly fitting a beautiful subject. In the format of a coffee-table book, the authors cover important subjects like the wide range of polymeric subjects, ideal chain models and their properties, Brownian motion, biological polymers, and polymer dynamics. An accompnaying CD-ROM animates polymer motion, incluidng reptation and coil collapse.]

J.M. Haile. Molecular Dynamics Simulations: Elementary Methods. Wiley, New York, 1992. [Elementary text on molecular dynamics]

M. Kalos and P. A. Whitlock. Monte Carlo Methods. John Wiley & Sons, New York, 1986. [Good introduction to Monte Carlo techniques ]

K.B. Lipkowitz and D.B. Boyd, Editors. Reviews in Computational Chemistry. VCH Publishers, New York, 1990 -- [Nice series of book, with volumes appearing annually with comprehensive reviews and tutorials on many aspects of computational chemistry]

J.A. McCammon and S.C. Harvey. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, 1987. [First book on biomolecular dynamics simulations]

D.A. McQuarrie. Statistical Mechanics. Harper Collins Publishers, New York, 1976. [Good reference text]

National Research Council report. Mathematical Challenges from Theoretical / Computational Chemistry, National Academy Press, Washington D.C., 1995. [Panel report on the opportunities for collaboration, past achievments, and future possibilities between mathematical and chemical scientists]


D.C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge University Press, Cambridge, England., 1995. [Elementary ext on molecular dynamics focusing on software details]

W. Saenger. Principles of Nucleic Acid Structure. Springer Advanced Texts in Chemistry, Springer-Verlag, New York, 1984. [Wonderful guide to the richness of DNA structure, with an amazing breadth of topics]

R.R. Sinden. DNA Structure and Function. cademic Press, San Diego, California, 1994. [Nice up-to-date textbook on DNA structure]

G.E. Schulz and R.H. Schirmer. Principles of Protein Structure. Springer Advanced Texts in Chemistry, Springer-Verlag, New York, 1990. [Nice advanced text on the rapidly-changing field of protein folding]

L. Stryer. Biochemistry. W.H. Freeman, New York, latest edition (fourth in 1995). [Wonderful biochemistry textbook, up to date]

W. Van Gunsteren and P. Weiner, Editors (1989) and W. Van Gunsteren, P. Weiner, and A.T. Wilkinson, Editors (1993, 1996): Computer Simulation of Biomolecular Systems: Theoretical and Experimentational Applications. Vol. 1,2,3. ESCOM, Leiden, The Netherlands, 1989, 1993, 1996. [Good series on biomolecular simulations, covering both algorithms and applications]

Syllabus -
Last update: prof. RNDr. Jiří Vondrášek, CSc. (14.05.2012)

Brief review of the basic principles of quantum mechanics of atoms and molecules. Potential energy surfaces and intermolecular interactions : Quantum mechanical ab initio calculations within Born-Oppenheimer approximation and modelling of calculated energy by model potentials for simple atoms, ions and molecules. Concept of short range and long range interactions. Modelling of interactions involving macrobodies like planar surfaces, macrospheres etc. Molecular Mechanics calculations.

Simple applications of molecular modelling :

Study of an assembly of atoms or molecules (cluster and/or bulk phases). Approximation of the total potential energy as the sum of pair potentials. Concept of large number of microstates, averages and basic principles of Monte carlo and Molecular Dynamics simulations.

Water and small organic molecules :

Non-polarizable and polarizable rigid models. Flexible models and calculation of force constants. Structural and dielectric properties of a polar medium : Continuum models versus molecular models. Calculation of structure, energy and free energy through simulations using molecular models.

Macromolecules :

Study of self organized assemblies, bio-molecules like peptides, proteins, membranes and ion channels through simulations. Concept of hydrophobic and hydrophilic interactions. Use of molecular modelling in drug design.

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