Syllabus I. General information about the course and practical works Course title: Calculation methods for biomolecular systems



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Babeş-Bolyai University

Faculty of Physics

Department of Biomedical Physics

Academic Year: 2008-2009

Semester I

Syllabus


I. General information about the course and practical works

Course title: Calculation methods for biomolecular systems


Level

Master

Code




No. of credits




Weekly hours

2 course + 2 laboratory works

Place:

Computer network in the Faculty of Physics, room no. 214

Time schedule

Monday, 16p.m.-18p.m.


II. Lecturer

Name

Vasile CHIŞ

Academic title

Professor

Scientific title

PhD

E-mail

vchis@phys.ubbcluj.ro

Phone

0264405300 ext. 5153

Ore de audienţă

Joi, 9-11


III. Course description

This course aims to present the physical theories behind the methods used in molecular modeling and simulations, with emphasis put on molecules and complex molecular systems of biological and biochemical relevance. Particularly, this course is focused on the unified presentations of the methods of molecular electronic structure calculations used for studying the structure, properties and intra or intermolecular interactions the final goal being to provide students with a solid background of physical and mathematical apparatus. Theoretical informations will be presented together with practical examples so that the students will be able to understand how the computational techniques work and how accurate can be the computational techniques used for molecular electronic structure investigations.



The necessity of this course lies in the fact that more and more researchers are using computer simulations in order to better understand the properties of different molecular systems, the experiments "on the computer" becoming in the last time a very useful research tool. The course aims to persuade students, the future researchers, that a deeper understanding of how the programs used for molecular simulation can lead to a substantial improvement in the effectiveness of their use. Presentation of the theoretical methods of molecular modeling will be accompanied by the presentation of the algorithms of these methods, case studies and many examples.
Course objectives: understanding of theories used in the calculation of the electronic structure of molecules and the approximations on which they are based; understanding how the basis sets are constructed and the correct use of them from the perspective of a compromise between the accuracy of the theoretical results and computational resources nedded, understanding and explaining the phenomenon of electron correlation; understanding the principles of DFT methods; approximations made in understanding the empirical and semiempirical methods and their correct use for the calculation of various molecular properties such as structure, energy, molecular orbital energies, normal mode analysis, hyperfine coupling tensors, shielding tensors and chemical shifts, analysis of potential energy surfaces, the calculation and correct use of the molecular conceptors related to the molecular reactivity, analyzing the relationship between molecular structure and activity, the correct use of solvation models and the analysis of the solvent influence on the molecular properties, modeling the intra and intermolecular hydrogen bonding; conformational analysis, the use of the studied methods and techniques in the molecular design, etc.
Competencies:

  1. The students should:

  • have theoretical insights and sufficient skills to independently apply the achieved knowledge to define and formulate research problems in the computational chemistry and physics, use information retrieval, data collection, experiment and/or computer methods to solve such problems

  • have advanced skills in modeling molecular systems using the computers

  • be able to solve physico-chemical by applying knowledge and skills from adjacent fields such as mathematics, informatics and biochemistrys

  • be able to critically analyse and evaluate scientific models

  • be able to work in projects, and also to plan and lead projects.


IV. References

  1. A.Szabo, N.S.Ostlund, Modern Quantum Chemistry; Introduction to Advanced Electronic Structure Theory, McGraw-Hill Publishing Company, New York, 1989

2. Wolfram Koch, Max C. Holthausen, A Chemist’s Guide to Density Functional Theory, Wiley, 2001

  1. A. Hinchliffe, Modelling Molecular Structures in Wiley Series in Theoretical Chemistry, (D. Clary et al. Eds.), John Wiley and Sons, Chichester, 2000

  2. D. C. Young, Computational Chemistry, John Wiley and Sons, 2001

  3. J. B. Foresman, A. Frisch, Exploring Chemistry with Electronics Structure Methods, Gaussian Inc., 1996

6. Koh96 W. Kohn, A. D. Becke, and R. G. Parr, Density Functional Theory of Electronic Structure, J. Phys. Chem.100, 12974-12980 (1996)

7. J. N. Israelachvili, Intermolecular and Surface Forces, Academic Press, 1998



  1. O.M. Becker, A.D. MacKerell Jr., B. Roux, M. Watanabe (Eds.), Computational Biochemistry and Biophysics, Marcel Dekker Inc., New York, 2001

9. A. Volkov, P. Coppens, Calculation of Electrostatic Interaction Energies in Molecular Dimers from Atomic Multipole Moments Obtained by Different Methods of Electron Density Partitioning, Journal of Computational Chemistry, 25, 921-934 (2004)

10. M. L. Senent, S. Wolson, Intramolecular Basis Set Superposition Errors, International Journal of Quantum Chemistry, Vol. 82, 282–292 (2001)

11. Christopher J. Cramer and Donald G. Truhlar, Implicit Solvation Models: Equilibria, Structure, Spectra and Dynamics, Chem. Rev. 99, 2161-2200(1999)

12. Jay William Ponder, TINKER - Software Tools for Molecular Design, 2003

13. G.R. Desiraju, Crystal Design: Structure and Function, John Wiley and Sons, 2003

14. Martin Schutz, Steve Brdarski, Per-Olof Widmark, Roland Lindh, and Gunnar Karlstrom, The water dimer interaction energy: Convergence to the basis set limit at the correlated level, J. Chem. Phys. 107 4597-4605 (1997)

15. M. de Cuyper, J.W.M. Bulte (Eds.), Physics and Chemistry Basis of Biotechnology, Kluwer, 2001

16. R. Freitag, Synthetic Polymers for Biotechnology and Medicine, Eurekah.com, 2003



Optional references

  1. P.W.Atkins, Molecular Quantum Mechanics, Oxford University Press, 1983

  2. P.W.Atkins, Solutions Manual for Molecular Quantum Mechanics, Oxford University Press, 1983

  3. R.G.Parr, W.Yang, Density Functional Theory of Atoms and Molecules, Oxford University Press, New York, 1989

  4. J.A.Pople, D.L.Beveridge, Aproximate Molecular Orbitals Theory, McGraw-Hill, New York, 1970

  5. W.J.Hehre, L.Radom, P.v.R.Schleyer, J.A.Pople, Ab Initio Molecular Orbital Theory, John Willey & Sons, New York, 1986

  6. F.Jensen, Introduction to Computational Chemistry, John Wiley and Sons, New York, 2001

  7. Kwang-Hwi Cho, Jaebum Choo, Sang-Woo Joo, J. Mol. Struct., 738 (2005) 9–14

  8. Jorge M. Seminario, Angelica G. Zacarias, and James M. Tour, J. Am. Chem. Soc. 2000, 122, 3015-3020


V. Used materials:

a) for course: computer, videoprojector, whiteboard, dedicated software (Gaussian 03W)

b) for laboratory works: computer, videoprojector, whiteboard, dedicated software (Gaussian 03W)
VI. Tentative schedule

VI.a COURSE

Course no.

Topic

No. of hours

References

1

Hartree-Fock-Roothan theory

Atomic units, molecular Hamiltonian; Born-Oppenheimer approximation; Hartree-Fock and Hartree-Fock-Roothaan approximation



2

[1] pag.22-33

[2] 3-14


[3] 109-121

[4] 19-21

[5] 253-259


2

Basis sets

Slater type orbitals; Gaussian type orbitals; Contractions; Contraction schemes;

Mulliken population analysis


2

[5] 97-103

[4] 78-89; 99-103

[3] 154-171


3

Electron correlation

Spin correlation; Static correlation; Dynamic correlation; Post Hartree-Fock methods



2

[4] 21-25

[5] 114-117; 265-267

[3] 186-208


4

Principles of DFT methods

Hohenberg-Kohn theoremes; Kohn-Sham formalism; Local density approximation; Exchange-correlation functionals



2

[2] 29-88

[3] 218-227

[4] 42-46

[5] 118-124

[6] 96


5

Excited molecular states

Time dependent density functional theory



2

[4] 216-220


6

TDDFT calculations

HOMO-LUMO gaps; UV-Vis spectra calculation



2

[5] 213-218

7

Semiempirical calculations

Huckel and extended Huckel method; INDO, ZINDO, AM1, PM3 and SAM1 methods



2

[4] 32-39

[5] 111-113




8

Modeling weak interactions

Intra and intermolecular interactions; Van der Waals interactions



2

[2] 217-236

[7] 83-105; 122-133



9

Intermolecular interactions

Conformers and tautomers; Conformational analysis; Molecular clusters; Calculation of interaction energies; Basis set superposition error



2

[8] 69-90

[9]


[10]

[7] 31-133



10

Potential energy surfaces

Stationary points; transition states



2

[2] 239-255

[4] 173-177

[3] 230-279


11

Calculation of molecular spectra

Magnetic properties – ESR and NMR spectra; normal modes of vibration; IR intensities and Raman activities; Polarizability and hyperpolarizability



2

[3] 265-300

12

Molecular conceptors related to molecular reactivity

Energies of the frontier molecular orbitals;Ionization potentials, Electron affinity, Protonation energies, Fukui functions, Molecular electrostatic potential



2

[2] 163-168


13

Modeling the interaction between molecules and metalic or non-metalic surfaces

Molecular self-assembly; SERS spectra



2

[23]

14

Solvent effects

Continuum solvation methods; Onsager, CPM and IPCM methods; Discrete solvation methods; Oniom method;



2

[4] 206-212

[3] 250-260

[8] 133-152

[5] 237-242

[11]



VI.b Laboratory

Lab.

Topic

No. of hours

References

1

Molecula geometry specification; Cartezian coordinates; Z-matrix formalism

2

[3] pag. 241-245

[4] 73-75




2

Fractional and cartezian coordinates; Tinkre program

2

[12]

3

Geometry optimizations

2

[5] 39-59

4

Hydrogen bonds in the molecular design

2

[13] 1-76

[14]


5

Conformers and tautomers

2

[4] 179-191

[8] 69-90



6

Normal modes of vibration; Calculation of vibrational spectra

2

[8] 153-168

[4] 92-96

[2] 130-136

[5] 61-69



7

Calculation of NMR spectra

2

[2] 197-209

[4] 252-254

[8] 253-274


8

Calculation of ESR spectra of paramagnetic systems

2

[3] 304-316

[2] 211-214

[4] 110-111


9

Solvent effects: Solvent modeling; continuum and discrete models of solvation ONIOM

2

[11]

[3] 250-260

[8] 133-152


10

Molecular recognition


2

[13] 77-152

11

Free radicals; Calculation of hyperfine coupling tensors;

2

[15] 249-272

12

Imprinted molecular polymers


2

[16] 134-154

13

Molecules with potential application in molecular electronics


2

[24]

14

Computer aided drug design


2

[8] 351-370


VII. Grading

The final grade will be based on a weighted average of the total possible points available in the following categories:

2 Midterm examinations 50 %

Final Examination 20 %

Homework assignments 20 %

Summaries of research papers 10%

EXAMS: Midterm examinations will be write-on tests covering concepts discussed in class, including general descriptions, derivations, and application problems. They will be spaced about equally through the semester. The final examination will be similar in construction to the midterm exams, but will be comprehensive.

ASSIGNMENTS: Homework assignments will come from the textbook problems, and will be turned in every 3 weeks. Completing and understanding the homework assignments is essential to performing well on the exams and mastering a challenging subject such as this one.

During the semester you will be expected to locate, study, and summarize two physico-chemical research papers from the scientific literature written in the past 5 years. The subject will be decided based on your own research interests.

Prof.dr. Vasile Chiş






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