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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