UNIVERSITY OF TARTU
FACULTY OF PHYSICS AND CHEMISTRY
INSTITUTE OF CHEMICAL PHYSICS
PH.D. AND M.SC. CURRICULUM
THEORETICAL AND COMPUTATIONAL CHEMISTRY
Tartu, 1998
I Specification of the curriculum.
Speciality: theoretical and computational chemistry
Faculty: Faculty of Physics and Chemistry
Institute: Institute of Chemical Physics, University of Tartu, Department (Chair) of Theoretical Chemistry
II The Goals of the Curriculum and its place in science
II 1. Theoretical chemistry represents the core of all chemical disciplines. The computational chemistry is a relatively young but very fast developing area of research, with the applications ranging from chemical engineering to chemical physics. In addition to fundamental and applied chemistry, many interdisciplinary and high technological subjects (such as molecular biology and gene engineering, ecology and environmental studies) rely on the basic knowledge from theoretical chemistry.
II 2. The present curriculum serves as the basis for reaching the following scientific, educational and practical goals:
II 3. The present curriculum is based on teaching and research activities of the teaching and research staff of the Chair of Theoretical Chemistry, which includes 1 ordinary professor and 3 scientists (1 Ph.D., 1 Candidate of Chemistry and 1 M.Sc.).
II 4. The scientific results of the research group of the Chair of Theoretical Chemistry of the Institute of Chemical Physics, University of Tartu.
During the last 5 years the following most important scientific papers were published in CC-refereed journals:
1. H. Kuura and M. Karelson,
Differential-Conductometric Study of the Urea Addition Effects on the Structure of Aqueous and Non-Aqueous Electrolyte Solutions,
Org. React., 31, 29-34 (1993).
2. T. Sepp and M. Karelson,
Primary Salt Effect on Acid-Base Equilibria in Aqueous Strong Acid Solutions,
Org. React., 31, 35-42 (1993).
3. A.R. Katritzky, K. Yannakopoulou, P. Barczynski, M. Szafran, M.M. Karelson,
Ionization and Conductivity of N-(Aminoalkyl)benzotriazoles in Nitromethane,
Org. React., 31, 101-104 (1993).
4. M. Karelson, T. Tamm, and M.C. Zerner,
Multicavity Reaction Field Method for the Solvent Effect Description in Flexible Molecular Systems,
J. Phys. Chem., 97, 11901-11907 (1993).
5. M. Szafran, M.M. Karelson, A.R. Katritzky, J. Koput, and M.C. Zerner,
Reconsideration of Solvent Effects Calculated by Semiempirical Quantum Chemical Methods
J. Comput. Chem., 14, 371-377 (1993).
6. P. Oksman, G. Fajer, K. Pihlaja, and M. Karelson,
Electron Impact Ionization Mass Spectrometry and Intramolecular Cyclization in 2-Substituted Pyrimid(3H)ones,
J. Am. Soc. Mass Spectrom., 5, 113-119 (1994).
7. A.R. Katritzky, E.S. Ignatchenko, R.A. Barcock, V.S. Lobanov, and M. Karelson
Prediction of Gas Chromatographic Retention Times and Response Factors using a General QSPR Treatment,
Anal. Chem. 11, 1799-1807 (1994).
8. R. Murugan, M.P. Grendze, J.E. Toomey, Jr., A.R. Katritzky, V.S. Lobanov, P. Rachwal, and M. Karelson,
Predicting physical properties from molecular structure,
CHEMTECH, 24, 17-23 (1994).
9. M. Karelson and M.C. Zerner,
A Comparative Semiempirical Study of Pyrrole and Phosphole Oligomers,
Chem. Phys. Lett., 224, 213-218 (1994).
10. M. Karelson and A.R. Katritzky,
AM1 and MNDO Self-Consistent Reaction Field Calculations of Substituent Effects in Different Dielectric Media,
ACH Models in Chemistry, 131, (3-4) 415-433 (1994).
11. G.H.F. Diercksen, M. Karelson, T.Tamm and M.C. Zerner
Multicavity SCRF Calculation of the Ionic Hydration,
Int. J. Quant. Chem., 28S, 339-3(1994).
12. U. Maran, T.A. Pakkanen and M. Karelson,
A Semiempirical Study of the Solvent Effect on the Menshutkin Reaction,
J. Chem. Soc. Perkin Trans. 2, 741-748 (1994).
13. M. Karelson, K Pihlaja, T.Tamm, A. Uri, and M.C. Zerner
UV-visible spectra of some nitro-substituted porphyrins
J. Photochem. and Photobiol. A: Chemistry, 85, 119-126 (1995).
14. T.Jürimäe, M. Strandberg, M. Karelson, and J-L. Calais
A Semiempirical Study of Heterocycle Oligomers and Polymers in Different Dielectric Media
Int. J. Quant. Chem. 54, 369-379 (1995).
15. A.R. Katritzky, V. Lobanov, and M. Karelson,
QSPR: The Correlation and Quantitative Prediction of Chemical and Physical Properties from Structure,
Chem. Soc. Revs., 24, 279-287 (1995).
16. A.R. Katritzky, M. Karelson and A.P. Wells
Aromaticity as a Quantitative Concept. 6. Aromaticity Variation with Molecular Environment
J. Org. Chem., 61, 1619-1623 (1996).
17. M. Karelson, V.S. Lobanov, and A.R. Katritzky
Quantum-Chemical Descriptors in QSAR/QSPR Studies
Chem. Rev., 96, 1027-1043 (1996).
18. M. Karelson, U. Maran, and A.R. Katritzky
Theoretical Study of the Keto-Enol Tautomerism in Aqueous Solutions
Tetrahedron, 52, 11325-11328 (1996).
19. A.R. Katritzky, P. Rachwal, K.W. Law, M. Karelson, and V.S. Lobanov
Prediction of Polymer Glass Transition Temperatures Using a General Quantitative Structure-Property Relationship Treatment
J. Chem. Inf. Comput. Sci., 36, 879-884 (1996).
20. P. Huibers, V.S. Lobanov, D.O. Shah, and M. Karelson
Prediction of Critical Micelle Concentration Using a General Quantitative Structure-Property Relationship Approach. I. Nonionic Surfactants.
Langmuir, 12, 1462-1470 (1996).
21. A.R. Katritzky, Lan Mu, V.S. Lobanov and M. Karelson
Correlation of Boiling Points with Molecular Structure. I A Training Set of 298 Diverse Organics and a Test Set of 9 Simple Inorganics,
J. Phys. Chem., 100, 10400-10407 (1996).
22. J. Leis, K. Pihlaja, and M. Karelson
Synthesis of 1-Phenyl-2,4-Dimethylphosphole, the Dimer of 1-Phenyl-3,4-Dimethylphosphole-1-Oxide and 1-Phenyl-3,4-Dimethyl-2,5-Dihydrophosphole-1-Oxide
Zh. Org. Khim., 32, 446-448 (1996).
23. A.R. Katritzky, V.S. Lobanov, M. Karelson, R. Murugan, M.P. Grendze, and J.E. Toomey,
Comprehensive Descriptors for Structural and Statistical Analysis, 1. Correlations Between Structure and Physical Properties of Pyridines,
Rev. Roum. Chim., 41, 851-867 (1996)
24. U. Maran, M. Karelson, and A.R. Katritzky
A Comparative AM1 and Ab Initio Study of the Intramolecular Proton Transfer in Tautomeric Organic Compounds,
Int. J. Quant. Chem., 23S, 41-49 (1996).
25. A.R. Katritzky, P.A. Shipkova, M. Qi, D. Nichols, R.D. Burton, C.H. Watson, J.R. Eyler, T.Tamm, M.C. Zerner and M.Karelson
Study of Radical Merostabilization by Electrospray FTICR/MS
J. Am. Chem. Soc. 118, 11905-11911 (1996
26. M. Karelson
Use of Semiempirical Quantum-Chemical Molecular Descriptors in QSAR/QSPR
Abstr. Pap. Am. Chem. Soc., 211, 154-COMP (1996).
27. P.D.T. Huibers, V.S. Lobanov, D.O. Shah, A.R. Katritzky, M. Karelson
Predicting Surfactant Critical Micelle Concentration from Structure
Abstr. Pap. Am. Chem. Soc., 212, 42-COLL (1996).
28. A.R. Katritzky, L. Mu, M. Karelson
A QSPR Study of the Solubility of Gases and Vapors in Water
J. Chem. Inf. Comput. Sci., 36, 1162-1168 (1996).
29. P. Huibers, A.R. Katritzky, V.S. Lobanov, D.O. Shah, and M. Karelson
Prediction of Critical Micelle Concentration Using a General Quantitative
Structure-Property Relationship Approach. I. Anionic Surfactants.
J.Colloid Interf. Sci., 187, 113-120 (1997).
30. A.R. Katritzky, M. Karelson and V.S. Lobanov
QSPR as a means of predicting and understanding chemical and physical
properties in terms of structure
Pure & Appl. Chem., 69 , 246-248 (1997).
31. U. Maran, T.A. Pakkanen, and M. Karelson
An ab initio Study of the Menshutkin Reaction
J. Mol. Struct. (THEOCHEM), 397 , 263-272 (1997).
32. A.R. Katritzky, Lan Mu, and M. Karelson
QSPR Treatment of Unified Solvent Polarity Scale
J. Chem. Inf. Comput. Sci., 37 , 756-762 (1997).
33. A.R. Katritzky, U. Maran, M. Karelson,V.S. Lobanov
Prediction of Melting Points for the Substituted Benzenes
J. Chem. Inf. Comput. Sci., 37 , 913-919 (1997).
34. M. Karelson
Quantum Chemical Treatment of Molecules in Condensed Disordered Media,
Adv. Quant. Chem., 28 , 142-159 (1997).
35. J. Karwowski and M. Karelson (Eds.)
Recent Advances in Computational Quantum Chemistry,
Adv. Quant. Chem., vol. 28, Academic Press, New York, 1997.
36. M.Karelson and G.H.F. Diercksen
Models for Simulating Molecular Properties in Condensed Systems,
in: "Problem Solving in Computational Molecular Science: Molecules in Different Environments", S. Wilson and G.H.F. Diercksen (Eds.), Kluwer Academic Publ., Dordrecht, 1997, 215-248.
37. M.Karelson
Molecular Properties and Spectra in Solution
in: "Problem Solving in Computational Molecular Science: Molecules in Different Environments", S. Wilson and G.H.F. Diercksen (Eds.), Kluwer Academic Publ., Dordrecht, 1997, 353-387.
38. A.R. Katritzky, V.S. Lobanov, and M. Karelson
Normal Boiling Points for Organic Compounds: Correlation and Prediction by a Quantitative Structure-Property Relationship
J. Chem. Inf. Comput. Sci., 38, 28-41 (1998).
39. K. Sak, M. Karelson, and J. Järv
Quantum Chemical Modelling of the Effect of Proline Residues on Peptide Conformation
Int J. Quant. Chem., 66, 391-396 (1998).
39. A.R. Katritzky, Lan Mu, and M. Karelson
Relationships of Critical Temperatures to Calculated Molecular Properties
J. Chem. Inf. Comput. Sci., 38, 293-299 (1998).
40. A.R. Katritzky, S. Sild, V. Lobanov, and M. Karelson
Quantitative Structure-Property Relationship (QSPR) Correlation of Glass Transition Temperatures of High Molecular Weight Polymers
J. Chem. Inf. Comput. Sci., 38, 300-304 (1998).
41. A.R. Katritzky, R.D. Burton, Ming Qi, P.A. Shipkova, C.H. Watson, Z. Dega-Szafran, J.R. Eyler, M. Karelson, U. Maran, and M.C. Zerner
Fourier transform ion cyclotron resonance mass spectrometry and theoretical studies of gas phase SN2 nucleophilic substitution reactions at sp3-carbon atoms
J. Chem. Soc. Perkin Trans. 2, 825-834 (1998).
42. U. Maran, A.R. Katritzky, and M. Karelson
Theoretical study of aminoalkylation in the Mannich reaction of furan with methyleneimminium salt
Int. J. Quant. Chem. 67, 359-366 (1998).
43. J. Leis, K. D. Klika, and M. Karelson
Solvent Polarity Effects on the E/Z Conformational Equilibrium of N-1-Naphthylamides
Tetrahedron, 54, 7497-7504 (1998).
44. J. Leis, G.P. Schiemenz, and M. Karelson
Stereochemistry of Arylamides. 1. NMR Spectra of Some N-(1-Naphthyl)amides
ACH Models in Chemistry, 135, 157-171 (1998).
45. J. Leis, U. Maran, G.P. Schiemenz, and M. Karelson
Stereochemistry of Arylamides. 2. AM1 SCF and SCRF Quantum-Chemical Modelling of Some N-(1-Naphthyl)amides
ACH Models in Chemistry, 135, 173-181 (1998).
46. M.C. Menziani, P.G. De Benedetti, and M. Karelson
Theoretical Descriptors in Quantitative Structure-Affinity and Selectivity Relationship Study of Potent N4-Substituted Arylpiperazine 5-HT1A Receptor Antagonists
Bioorg. & Med. Chem., 6, 535-550 (1998).
47. A.R. Katritzky, P.A. Shipkova, M. Qi, R.D. Burton, C.H. Watson, J.R. Eyler, and M.Karelson
Cation tagging for monitoring gas phase reactions. Electrospray FTICR/MS study of ester pyrolysis
Int. J. Mass Spectr. Ion Proc., 175, 149-157 (1998)
II 5. The scientific qualifications of the Chair of Theoretical Chemistry, Institute of Chemical Physics, University of Tartu on the field of theoretical and computational chemistry:
III The Content (essence) and Organisation of Studies
III 1. The total volume of M.Sc. program is 80 credit points (CP) from which the academic education gives 40 CP and the immediate research project another 40 CP. During the studies, the student receives the education in mandatory subjects (cf. the list below), has to take at least 2 optional subjects and carry out the research on his/her Master Thesis. The results of the research have to be published in the required (minimum) amount of scientific papers in internationally refereed journals.
The total volume of Ph.D. studies is 160 CP from which 40 CP is listed as the academic education and 120 CP comes from the research work and writing up the Ph.D. dissertation.
The organisation and regulations of the master and doctoral studies are established by the orders of the Rector of University of Tartu and by the decision (06/30/1995) of the Council (Senate) of the University of Tartu.
III 2. The mandatory subjects in M.Sc. studies are: specialty, physical chemistry, and the physical methods of investigation in chemistry. The optional subjects may be chosen from all available subjects in chemistry. The time allocated for mandatory subjects in M.Sc. studies consists 50 per cent of the time of all academic studies whereas the optional courses and independent work take another 50 per cent of time. The studies include lectures and seminars or practical work in laboratory or with computers and work with literature. So far, practically all M.Sc. and Ph.D. students of the Institute of Chemical Physies, have had opportunity to continue their studies abroad in the several leading universities (Uppsala, Nice, Barcelona, Madrid (CSIC), Freiburg, Erlangen, etc.) in the framework of EC TEMPUS/PHARE JEP student mobility activities (JEP 06125 (1993-1996), JEP 11212 (1997-1998), TEMPUS IMG activities, NATO programs, in the framework of Estonian-German (BMFT) cooperation, bilateral agreements (University of Florida). The average stays in the framework of TEMPUS JEP programs have been ca 5 months, stays in the framework of TEMPUS IMG programs - 2-4 months.
III 3. The share of subjects on humanities, languages, economics, history, etc. (foreign languages, philosophy, history of arts, theology, economics, etc.) is up to 10 per cent from the total time of the academic studies.
III 4. Teaching materials (textbooks, manuals, reference books, CA, videos, CD-ROM materials, etc.) and all major scientific journals are available in the Library of the Chemistry Department, and libraries of University of Tartu and of the Estonian Academy of Sciences. Starting from the year 1993, the support of TEMPUS JEP 06125 and 11280 programmes (at least 60 000 ECU) has been extensively used to order seientifie journals and to purchase teachning materials, textbooks, etc.)
III 5. The student’s work is evaluated by their academic advisors and by the Councils of the Institute and the Department of Chemistry.
The Studies are considered to be successfully finished after completing the program of academic studies and defending the Ph.D. or M.Sc. dissertation.
III 6. At least once in a semester M.Sc. and Ph.D. students are supposed to present the results of their current studies in the seminars of the institute or chair. On grounds of these presentations the current status of the student’s work is evaluated.
IV The Infrastructure for Research Work.
IV 1. The Institute of Chemical Physics has relatively well developed experimental facilities and one of the most powerful computer network in Estonia.
The computer network of the Institute includes several powerful workstations (WS) (3 SGI Origin 200 WS with 6 R10000 processors, SGI Power Indigo2, IBM RISC 16000 WS 25T and 3AT, SGI IRIS Indigo2, SGI 02, SUN Sparc 5 and 7, SUN20). The network includes also ca 20 P2, PC 486, PC 586 for individual users. Through Internet several other computational facilities (University of Florida, UCI, Max-Planck-Institute of Astrophysics, etc.) are available.
The Institute has Bruker AC 200P FT NMR spectrometer, FT IR spectrometer, Kamda 25 and 3 other UV/VIS spectrometers, 2 ion chromatographs, 3 HPLC complexes, Nordion GC, GC-Mass-spectrometer (Varian, Magnum), the complex of measurement of a , b , g , h - radiation (Cole Parmer), complex of titration in non - aqueous solution, AES and AAS instruments, etc. It is possible to perform most experiments and practically all necessary high-level calculations using the Institute’s own facilities.
High-power, state-of-the-art FT NMR instruments (500 MHz, solid state facilities, etc.) of ICPB (Tallinn) are also available within the framework of tight cooperation between Institute of Chemical Physics (Tartu University) and ICPB (Tallinn).
IV 2. The intensive and extensive long-time worldwide scientific cooperation with a wide selection of leading universities and scientific institutions (see VI 1.) guarantees the systematic and reasonable planning of working visits and longer stays to those institutions and thereby improve also the quality of M.Sc. and Ph.D. education at home, It is important to underline that several institutions with which there is a continuous intensive cooperation (University of Florida, Princeton University, Oxford University, Uppsala University, Max-Planck-Institute of Astrophysics, University of Kiel, etc.) are leading scientific centers in the world.
Currently (1997-1998) the chair of theoretical chemistry of the Institute of Chemical Physics is involved in another EC TEMPUS JEP 11280 together with 12 other institutions from Finland, Sweden, Germany, Netherlands, Spain, UK, etc.
During 1993-1998 the total volume of different student mobility was ca 90 man-months.
IV 3. Throught the Internet all major chemical knowledge is available. All major chemical journals and CA are available (see C.4.).
IV 4. During the year 1993-1998 the following support was received from sources outside University of Tartu:
A major part of those finances has supported and will support the M.Sc. and Ph.D. studies research
IV 5. The chair has the concrete development plan of upgrading the instrumentation (both the teaching and research equipment) which is the integral part of the development plans of University of Tartu and Faculty of Physics and Chemistry of Tartu University.
V Supervision of scientific research
V 1. The principal (responsible) supervisor of the research work and M.Sc. and Ph.D. studies is the ordinary professor, head of the chair. The other faculty members and researchers may take part in the supervision of the studies and research of the Ph.D. or M.Sc. students.
V 2. The supervisor chooses the research topic on the basis of the research trends and directions at the chair and Institute and proceeding from the needs of the national educational system and economy. The supervisor is accountable before the Council of the Department of Chemistry.
V 3. The resources necessary for the research work are handled, as a rule, by the supervisor. The distribution of available resources and the ways and aims of their use is planned according to the needs of current projects and running Ph.D. or M.Sc. studies.
V 4. The supervision of the research work and degree studies is the direct responsibility of the ordinary professor. As a rule he participates in establishing and solving the problems, in the interpretation of results and in determination of further directions of students studies. As a rule, supervisor is a co-author of Ph.D. or M.Sc. students publications. However, in each specific case, the authorship or co-authorship is determined by the personal contribution of every participant.
V 5. The successfulness of the supervision is determined by the successful and timely defence of the dissertations. The efficiency of supervision of the supervisors is analysed by the Council of the Department of Chemistry.
VI Scientific Cooperation
VI 1. The Chair of Theoretical Chemistry of Institute of Chemical Physics has intensive, extensive and long-time scientific cooperation with the world leading centers on theoretical and computational chemistry, chemical physics, and physical organic chemistry in the USA, Germany, Great Britain, Sweden, Finland, Spain, Italy, etc. Some cooperation partners are listed below:
The formal criterion of the cooperation: joint research publications in internationally refereed journals or joint international grant-applications.
VI 2. The forms of the interuniversity cooperation are:
VI 3. During the last 5 years, about 40 publications have been published in internationally refereed (CC) journals in the framework of international cooperation. The international cooperation has been one of the major factors to increase the quality of teaching and research work, and helps to upgrade the research and teaching facilities according to the European standards and dimensions.
VI 4. The main criterion for the mutual evaluation of the research is its quality (the number and quality of publications, success-rate of grant applications, the defence of scientific degrees).
VI 5. The suggested referees for the evaluation of the research and Ph.D and M.Sc studies at the Chair of Theoretical Chemistry, Institute of Chemical Physics, University of Tartu:
VII The output of M.Sc. and Ph.D. studies
VII 1. At the Chair of Theoretical Chemistry, the Ph.Dr. and M.Sc. degree education started in fall 1992. Until now, 3 doctoral dissertations have been defended and 1 is presented for the defence (J. Leis). Also, 6 master theses have been defended in 1993-1998. Currently, there are 4 Ph.D. students (T. Jürimäe, A. Perkson, S. Sild, T. Tamm) and 1 M.Sc. student (A. Lomaka) at the Chair of Theoretical Chemistry. All doctoral dissertations and master theses were supervised by Prof. M. Karelson.
The list of persons who have defended Ph.D. or M.Sc. degrees at the Chair of Theoretical Chemistry of Institute of Chemical Physics on theoretical and computational chemistry is as follows:
VII 2. 1. The official rating of the evaluation commission of the Swedish Royal Academy of Sciences (1992) of the work of working group of Prof. M. Karelson was very high. The ISI Science Citation Index for publications of Prof. M. Karelson (first author) over the last decade has been 70-100 citations per year.
VII 3. The average annual publication rate for the Ph.D. students and M.Sc. students has been 1-2 per person. For the period of last 5 years, the average publication rate (CC level) for the teachers of the Chair of Theoretical Chemistry has been ca 10.
VII 4. The Chair of Theoretical Chemistry of University of Tartu has participated in organizing 4 international conferences (I and II CODESSA Meeting, Florida, 1994 ja 1995; Recent Advances in Computational Quantum Chemistry, München, 30-31 March 1996; NATO Advanced Study Institute in Physics, Bad Windsheim, 11-22 August 1996).
VII 5. During the last 2 years M.Sc. and Ph. D. students of the chair have participated in ca 10 conferences (Sanibel Symposia 1996, 1997, Bad Windsheim 1996, Helsinki 1997, Uppsala 1996, Linz 1996, Tallinn 1997, Tartu 1996, 1998, etc.).
Professor M. Karelson
Institute of Chemical Physics, Ordinary Professor of Theoretical Chemistry
17.09.1998