MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Jo˛ef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10


Course Description

Biomolecular Simulations


Nanosciences and Nanotechnologies, third-level study programme


doc. dr. Janez Mavri


Students will gain insight into the problems of intermolecular simulations: quantum-mechanical methods, molecular mechanics-based methods enabling thermal averaging, the modelling of chemical reactions in solutions, enzymatic reactions and the planning of inhibitors. Practical work involving the use of computers constitutes an integral part of this course.


· Time-dependent and time-independent Schrödinger equation
· Force field
· Chemical reactions in the gas phase
· Molecular dynamics and the Monte Carlo simulation
· Refinement: Incorporation of experimental data
· How to calculate free energy differences
· Chemical reaction in an enzymatic environment
· Simulation of tunnelling: the Born-Oppenheimer approximation
· Design of inhibitors on the basis of the transition-state structure
· Model study i) proton dynamics in the apoenzyme of HIV-1 protease
· Model study ii) Irreversible inhibition of HIV-1 protease
· Model study iii) Carcinogenesis caused by aromatic substances
· Future of biomolecular simulations

Course literature:

Warshel, A. (1991): Computer modeling of chemical reactions in enzymes and slutions. J. Wiley

Field, M.J. (2002): Simulating enzyme reactions: Challenges and Perpectives. J. Comp. Chem. 23, str: 48 – 58.

Mavri, J. (1998): Irreversible inhibition of the HIV-1 protease. Int. J. Quant. Chem. 69, str: 753 – 759.

Lensink, M.F., Mavri, J. in Berendsen, H.J.C. (1999): Simulation of a slow reaction with quantum character: Neutral hydrolysis of a carboxylic ester. J. Comp. Chem. 20, str: 886 – 895.

Significant publications and references:

MAVRI, Janez, KOLLER, Jože, HADŽI, Dušan. Calculations by the semi-ab initio method SAM1 on some hydrogen-bonded systems. J. mol. struct.[Print ed.], 1997, vol. 416, str. 261-268

MAVRI, Janez, HADŽI, Dušan. Influence of solvation on the hydrogen bond in hydrogene malonate: an ab initio and semiempirical study. J. mol. struct., Theochem

MAVRI, Janez, HADŽI, Dušan. Modelling of ligand-receptor interactions: ab-initio and DFT calculations of solvent reaction field effects on methylated ammonium-[pi] and -acetate complexes. J. mol. struct., Theochem


• seminar and oral exam

Students obligations:

• seminar and oral exam