Stanislav Šimko

PhD Candidate
Employed since: September 2015
Room: 4th floor open area



Molecular simulations of aqueous reactions

Diversification of resources is of increasing importance for all of Europe. One possible way to improve self­sufficiency is to increase utilization of renewable resources for the production of fuels and valuable chemicals.
Lignins are abundant organic polymers, which are one of the main structural components of biomass. With an annual production of 50 million tonnes, of less than 2.5% is used for production of value added chemicals and rest is burnt, lignin conversion offers promising potential as a source for the sustainable production of fuels and high value chemicals. However, neither the tertiary structure nor the sequence and monomeric composition of lignins are well defined. On the other hand, structures of the monomers that build lignins and the connections between the monomers have been documented to a large extent [1].
In my work I will build an IR and Raman spectra library of lignin fragments to aid experimentalists follow the lignin conversion pathways. I will employ Density Functional Theory and vibrational self­consistent field [2] method to compute spectra with the anharmonic contributions. At the beginning, I will calculate spectra of monomers and small oligomeric model compounds. To account for the solvent effects we will extend our work by employing combined QM/MM methods, such as the novel adaptive QM/MM approach developed in the group (Fig. 1) [3].
In parallel, my work involves the development of the above mentioned adaptive QM/MM approach that allows for a diffusion of particles into and out of the QM region while conserving energy of a system. QM and MM regions in this method are connected by a transition region where each molecule possesses a fractional QM and a fractional MM character according to its position. The new development will allow the computation of IR spectra and other dynamic properties with adaptive QM/MM. As such, this work will significantly broaden the applicability and impoct of adaptive QM/MM in the field of molecular simulations.

Illustration 1: Figure 1 Representation of lignin model compound dimer in adaptive QM/MM conditions – thick molecules are fully QM, ball-stick are partially QM and partially MM and stick are fully MM.

[1] J. Zakzeski et al., Chem. Rev.110, 3552-3599 (2010).
[2] J. M. Bowman, J. Chem. Phys. 68, 608-610 (1978).
[3] R. E. Bulo et al., J. Chem. Theory Comput. 5, 2212-2221 (2009).




PhD research at department of inorganic Chemistry and Catalysis, University of Utrecht, under the supervision of Dr. R.E. Bulo and Prof. Dr. Ir. B.M Weckhuysen.
Project title: Molecular simulations of aqueous reactions

Master’s degree in Biophysics and Chemical Physics, Faculty of mathematics physics and informatics, Comenius University, Bratislava (Slovakia)
Thesis: “Study of the Interaction of Ochratoxin A With Divalent Cations and Nucleic Acids Bases by Methods of Quantum Chemistry”

September 2014 – March 2015:
rasmus+ exchange program at Ruhr-Universität Bochum, Germany,

Bachelor’s degree in Physics, Faculty of mathematics physics and informatics, Comenius University, Bratislava (Slovakia)

Born in Slovakia


Louwen, J N; Simko, S; Stanciakova, K; Bulo, R E; Weckhuysen, B M; Vogt, E T C

Role of Rare Earth Ions in the Prevention of Dealumination of Zeolite y for Fluid Cracking Catalysts Journal Article

Journal of Physical Chemistry C, 124 (8), pp. 4626-4636, 2020, (cited By 0).

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Jiang, T; Simko, S; Bulo, R E

Accurate Quantum Mechanics/Molecular Mechanics Simulation of Aqueous Solutions with Tailored Molecular Mechanics Models Journal Article

Journal of Chemical Theory and Computation, 14 (8), pp. 3943-3954, 2018, (cited By 1).

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