Zlatko Mihalić MOLEKULARNO MODELIRANJE (2+1, 0+0)
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1 Zlatko Mihalić MOLEKULARNO MODELIRANJE (2+1, 0+0) Asistenti doc. dr. sc. Ivan Kodrin dr. sc. Igor Rončević Literatura A. R. Leach, Molecular Modelling, Principles and Applications, 2. izdanje, Longman, F. Jensen, Introduction to Computational Chemistry, 2. izdanje, Wiley C. J. Cramer, Essentials of Computational Chemistry: Theories and Models, 3. izdanje, Wiley Uvjet za potpis prisutvovanje testovima na kojima se rješavanjem zadatka na računalu provjerava praktično znanje iz modeliranja Ispit usmeni, uz prethodnu eventualnu provjeru praktičnog znanja na računala u slučaju neprolazne ocjene iz testova MM LITERATURA MM
2 POVIJESNI OSVRT We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation. J. L. Gay-Lussac, All of chemistry, and with it crystallography, would become a branch of mathematical analysis which, like astronomy, taking its constants from observation, would enable us to predict the character of any new compound and possibly the source from which its formation might be anticipated. Ch. Babbage, The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the application of these laws leads to equations much too complicated to be soluble. P. A. Dirac, MM ŠTO JE TO RAČUNALNA KEMIJA? Computational chemistry attempts to model all aspects of real chemistry as closely as possible by using calculations rather than experiment. P. v. R. Schleyer, Computational chemistry is quantitative modeling of chemical phenomena by computerimplemented techniques. (...) Computational chemistry consists of those aspects of chemical research that are expedited or rendered practical by computers. K. B. Lipkowitz, D. B. Boyd, Computational chemistry sometimes involves application of computerized algorithms from quantum theory, but computational chemistry is certainly more than quantum chemistry. (...) Molecular mechanics, molecular dynamics, computer graphics, molecular modeling, and computer-assisted molecular design are other important aspects of computational chemistry. K. B. Lipkowitz, D. B. Boyd, (Reviews in Computational Chemistry) MM
3 ŠTO JE TO RAČUNALNA KEMIJA? Computational chemistry is a branch of theoretical chemistry that uses a digital computer to model systems of chemical interest. In this discipline, the computer itself is the primary instrument of research. Computational chemistry permits calculation of quantities which can be measured experimentally, such as molecular geometries of ground and excited states, heats of formation, and ionization potentials. Alternatively, quantities not readily accessible by existing experimental techniques, such as geometries of transition states and detailed structure of liquids, may be evaluated. Because of the increasing power and availability of computers, and the simultaneous development of well-tested and reliable theoretical methods, the use of computational chemistry as an adjunct to experimental research has increased rapidly. McGraw-Hill Science & Technology Encyclopedia. MM GRANE TEORIJSKE KEMIJE KVANTNA KEMIJA RAČUNALNA KEMIJA / MOLEKULARNO MODELIRANJE MATEMATIČKA KEMIJA (KEMIJSKA TEORIJA GRAFOVA) TEORIJSKA KEMIJSKA KINETIKA KEM(O)INFORMATIKA MM
4 TEORIJA MODEL RAČUNALNI EKSPERIMENT ZNANSTVENA TEORIJA tumačenje prirodnih pojava pomoću skupa općenitih pravila, većinom kvantitativne prirode (matematičke jednadžbe) posjeduje sposobnost predviđanja, podložna eksperimentalnoj provjeri teorijski (kvantni) kemičari MODEL jednostavnija aproksimacija općenitije teorije s naglaskom na primjenljivosti, često uključuje konstante dobivene eksperimentom nagli razvoj računala omogućuje numeričko rješavanja složenih ili analitički nerješivih jednadžbi RAČUNALNI EKSPERIMENT modeliranje kemijskih sustava na računalu - treći način pristupa prirodnim znanostima računalni kemičari MM OBJEKTI MODELIRANJA POJEDINAČNE MOLEKULE (STRUKTURA, SVOJSTVA, SPEKTRI,...) INTERAKCIJA NEKOLIKO MOLEKULA (MEĐUMOLEKULSKI KOMPLEKSI,...) KEMIJSKE REAKCIJE (BRZINE, RAVNOTEŽA, MEHANIZMI,...) MNOŠTVO MOLEKULA (KLASTERI, KONDENZIRANA FAZA,...) KEMIJSKE REAKCIJE U KONDENZIRANOJ FAZI (U OTOPINI, U KRISTALIMA,...) ORGANIZIRANI SUSTAVI (STRUKTURA I FUNKCIJA BIOLOŠKIH SUSTAVA) MM
5 SADRŽAJ KOLEGIJA 0. Uvod 1. Ploha potencijalne energije (PES) 2. Molekularna mehanika 3. Traženje stacionarnih točaka na PES (optimizacija) 4. Kvantna mehanika, Hartree-Fockov model 5. Konformacijska analiza 6. Orbitale 7. Kvalitativna molekularno-orbitalna teorija (QMOT) 8. Lokalizacija molekularnih orbitala 9. Post-HF metode: CI, MPn, CC 10. Sustavno pretraživanje plohe potencijalne energije MM SADRŽAJ KOLEGIJA 11. Analiza valne funkcije 12. Teorija funkcionala elektronske gustoće (DFT) 13. Utjecaj otapala na brzinu ravnotežu kemijskih reakcija 14. Računanje kinetičkih i termodinamičkih parametara 15. Izodezmičke reakcije 16. Prijelazna struktura i reakcijske staze 17. Spektroskopija i fotokemija 18. Molekularna dinamika 19. Višeslojni modeli (QM/MM prisup) 20. Molekularno uklapanje (docking) 21. Prikazi i programi MM
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