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MOLECULAR MODELING Research group at the Faculty of Sciences, University of Novi Sad

We are focused to the application and improvement of advanced oxidation processes and to the application of the most popular and efficient software packages for the purpose of molecular modeling. In that sense it is our goal to acquire as much as possible computational and software resources, to gain necessary experience in their application and to become widely known research group when it comes to the research employing tools of molecular modeling approach.

So far, we are mainly interested in organic molecules. There are several reasons for that. Firstly, middle sized organic molecules can be investigated using relatively modest computational and software resources. However, thanks to the cooperation with our friends and colleagues we are also able to investigate periodic structures as well. Currently, our most important goals include development of collaboration with researchers all over the world and establishment of the laboratory for molecular modeling within the University of Novi Sad. Bellow you can find out to which areas we are focused in our research.

Theoretical investigations of curved carbon systems - buckybowls

Although we firstly started with theoretical investigation of drug molecules such as metoprolol, acebutolol and atenolol soon we changed our focus to buckybowls (also known as π-bowls, molecular bowls, etc). The reason for that was that sumanene (one of the typical representatives of buckybowls) has significant symmetry which reduced the computational time that we had available. Actually, we started with an old lap top (MSI VR610X) and we had to perform anything in order to reduce the computational time :).

So far we have published several papers dealing with sumanene, among which the two of them have been published in Physical Chemistry Chemical Physics and International Journal of Hydrogen Energy journals. Currently we are focused to the investigation of optoelectronic properties of buckybowls.

Software tools that we use:

Schrödinger Materials Science Suite

QuantumWise ATK

GAMESS 2013 R1





Sumanene and corannulene can be thought of as fullerene fragments

Nanotubes, graphene and fullerenes

Carbon nanotubes, boron nitride nanotubes, graphene nanosheets and related structures are very popular, especially when it comes to the theoretical research. Works where the influence of both covalent and non-covalent modifications are investigated are numerous and each month you can find several published papers dealing with this topic. The main reason for this is the fact that these structures are again relatively easy for theoretical investigation with very limited computational and software resources. Of course this doesn’t stop researchers from all over the world to be creative and find theoretical aspects related to these structures that haven’t been commented. Of course, the popularity of these structures affected us significantly. So far we have published several papers dealing with aforementioned structures and many more will come.

In one of our papers we have investigated optoelectronic properties of BN nanotubes

Ionic liquids

Thanks to our dear friend and colleague Milan Vraneš a year ago we were introduced into the magnificent world of ionic liquids. In the last year we were focused on theoretical and experimental investigation of the new BMIM based ionic liquid that was synthesized by Milan’s group. In general, ionic liquids are seen as alternatives for volatile organic solvents, they are non-flammable, recyclable and therefore they are also called green solvents.

Third generation of ionic liquids is particularly interesting because it contains active pharmaceutical ingredients. This leads to the possibilities to synthesize ionic liquids with biological activities. Since properties of ionic liquids can be finely tuned by appropriate selection of constituting ions and their modifications, it is only a question when this class of materials is going to be widely applied in the industry and pharmaceutics.

For the investigation of ionic liquids we use combination of DFT and MD simulations and it seems that we are the first who used Desmond for MD simulations of ionic liquids.  

MEP and ALIE surfaces of new ionic liquid

Interaction of IL with water

Theory and Experiment

Although scientists very frequently focus to either theory or experiment, we tend to focus to both aspects of science. Therefore, our research papers frequently contain both experimental and theoretical results. Nevertheless, in our house :) Sanja is more inspired by experiment, while Stevan favors theory. We have to be honest, it is really interesting when you have experimental chemist and theoretical physicist working together (in marriage).

Theoretical investigation of reactive and degradation properties of drug molecules

Understanding reactive properties of molecules that serve as active components of pharmaceutical care products is of great importance for at least two important scientific areas - pharmacy and environmental protection.

Thanks to the results obtained by DFT calculations and MD simulations development of new drugs can be rationalized and optimized. In the same time aforementioned results can serve as valuable resources for the development of procedures for the removal of organic pollutants from water resources.

Thanks to our collaboration with C. Yohannan Panicker and his team we have the opportunity to theoretically investigate various newly synthesized molecules with potentially important biological activities. In this area we are particularly interested in possibilities to predict degradation properties by using information collected by combination of DFT calculations and MD simulations.

Optimized structures of a) acebutolol, b) metoprolol and c) atenolol

Experimental studies of advanced oxidation processes

Sanja is mainly interested in photocatalytic degradation of organic molecules with application of transition metal oxides such as TiO2 and ZnO. This very interesting scientific area is of great importance for the practical applications when it comes to the alternative procedures for water purification. Namely, organic molecules that serve as active components of pharmaceutical care products are synthesized to be stable in water surrounding and therefore to be able to exhibit their biological activity in human and animal organisms. Their stability hardens removal from the water and the conventional water purification methods are not efficient. In this case forced degradation based on advanced oxidation processes is seen as alternative.

In the same time forced degradation studies are demanding from the aspects of necessary time and resources. Chalenges regarding forced degradation are greatly rationalized and optimized thanks to the combination of DFT calculations and MD simulations, since these theoretical procedures can significantly help when it comes to the prediction of molecule sites prone to autoxidation and hydrolysis.

Suggested degradation path of metoprolol under UVA in presence of TiO2

(Abramovic et al. J. Hazard. Mater. 198, 2011, 123)


Gaussian 03 with GaussView 5

Studies of charge transport properties at molecular level enables rationalization and optimization of experiments in the area of sensors and photovoltaic devices. In this area calculations and simulations can be done with isolated molecules and periodic structures. In the case without periodicity we perform calculations of reorganization energies and charge coupling, thanks to which it is possible to calculate charge transfer rates within Marcus semi-empirical approach. We also apply MD simulations in order to simulate the amorphous phase from which we extract possible pairs of molecules for which we calculate transfer rates at DFT level. In the case of non-periodic structures we are interested in thermally activated delayed fluorescence (TADF), which can be studied by calculations of energy differences between S1 and T1 states. TADF mechanism is important because it allows production of precious-metal-free OLED devices.

In the case of periodic structures we are interested for calculations of charge transport properties employing the combination of DFT and Non-equilibrium Greens functions (NEGF) methods. This approach allows not only investigation of transport properties of periodic structures, but it also allows investigation of transport properties of molecules at interfaces. Nowadays, studies related to single molecule transport are very important.

Molecular transport and organic photovoltaics

Illustration of TADF mechanism

Modeled system for investigation of transport properties