zlatko mihalić molekularno modeliranje 2 1 0 · zlatko mihalić molekularno modeliranje ......
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Zlatko Mihalić MOLEKULARNO MODELIRANJE (2+1, 0+0)
Literatura A. R. Leach, Molecular Modelling, Principles and Applications, 2. izdanje, Longman, 2001. F. Jensen, Introduction to Computational Chemistry, 2. izdanje, Wiley 2007.
C. J. Cramer, Essentials of Computational Chemistry: Theories and Models, 3. izdanje, Wiley 2017.
Asistenti doc. dr. sc. Ivan Kodrin dr. sc. Igor Rončević
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
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LITERATURA
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“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, 1838.
“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, 1929.
“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, 1808.
POVIJESNI OSVRT
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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, 1985.
“Computational chemistry is quantitative modeling of chemical phenomena by computer-
implemented techniques. (...) Computational chemistry consists of those aspects of chemical
research that are expedited or rendered practical by computers.”
K. B. Lipkowitz, D. B. Boyd, 1988.
“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, 1990. (Reviews in Computational Chemistry)
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“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.
ŠTO JE TO RAČUNALNA KEMIJA?
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GRANE TEORIJSKE KEMIJE
KVANTNA KEMIJA
RAČUNALNA KEMIJA / MOLEKULARNO MODELIRANJE
MATEMATIČKA KEMIJA (KEMIJSKA TEORIJA GRAFOVA)
TEORIJSKA KEMIJSKA KINETIKA
KEM(O)INFORMATIKA
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jednostavnija aproksimacija općenitije teorije s naglaskom na primjenljivosti, često uključuje konstante dobivene eksperimentom
nagli razvoj računala omogućuje numeričko rješavanja složenih ili analitički nerješivih jednadžbi
tumačenje prirodnih pojava pomoću skupa općenitih pravila, većinom kvantitativne prirode (matematičke jednadžbe) posjeduje sposobnost predviđanja, podložna eksperimentalnoj provjeri
MODEL
RAČUNALNI EKSPERIMENT
teorijski (kvantni) kemičari
računalni kemičari
ZNANSTVENA TEORIJA
modeliranje kemijskih sustava na računalu - treći način pristupa prirodnim znanostima
TEORIJA–MODEL–RAČUNALNI EKSPERIMENT
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POJEDINAČNE MOLEKULE (STRUKTURA, SVOJSTVA, SPEKTRI, ...)
INTERAKCIJA NEKOLIKO MOLEKULA (MEĐUMOLEKULSKI KOMPLEKSI, ...)
KEMIJSKE REAKCIJE U KONDENZIRANOJ FAZI (U OTOPINI, U KRISTALIMA, ...)
KEMIJSKE REAKCIJE (BRZINE, RAVNOTEŽA, MEHANIZMI, ...)
MNOŠTVO MOLEKULA (KLASTERI, KONDENZIRANA FAZA, ...)
OBJEKTI MODELIRANJA
ORGANIZIRANI SUSTAVI (STRUKTURA I FUNKCIJA BIOLOŠKIH SUSTAVA)
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0. Uvod
SADRŽAJ KOLEGIJA
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
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11. Analiza valne funkcije
SADRŽAJ KOLEGIJA
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