Research Projects

The CHM396Y0 course within the Summer Abroad Program offers the possibility to conduct research in different aspects of modern chemistry. Students who register will learn how to deal with quantum chemical problems, and will work on a project under one of the following topics:

 
Model Aided Biofuel Design: Systematic Theoretical Investigation for High Energy Molecules

Dr. Milán Szőri

 

The need for more environmentally friendly energy sources and the limited fossil resources encourage current research to convert biomass into renewable products. Next-generation production of biofuels from lignocellulosic biomass is a topic of intense research and a range of oxygenated compounds is being proposed as future fuels or components for fuel blends [1-3]. Ethers and esters are such alternative biofuels or fuel additives [4]. Oxygenates derived through the selective catalytic refunctionalization of carbohydrates of lignocellulosic biomass can be tailored to exhibit desired physico-chemical fuel properties that unlock the full potential of advanced internal combustion engines [5]. Considering the molecular structure of the fuel as adjustable parameter, it is possible to find the most promising molecular entities, if computational property prediction is employed to virtually screen the generated structures with regard to key physico-chemical fuel properties.

In the current proposal, following stoichiometry are selected for such investigation providing individual project for students, namely: C4H8O, C5H10O, C5H10O2 and C6H12O. All the possible constitutional isomers of these selected molecular formula will be generated by Molgen 5.0 software [6]. Then, the relevant physical-chemical properties of these isomers, such as heat of formation and heat of combustion, will be computed by Gaussian 09 quantum chemistry program package. The students involved in this project can contribute with their findings to the deeper understanding of biofuel and combustion.

 

References

1. Huber, G. W.; Iborra, S.; Corma, A. Synthesis of transportation fuels from biomass: chemistry, catalysts, and engineering. Chem. Rev. 2006, 106, 4044–4098.

2. Janssen, A. J.; Kremer, F.W.; Baron, J. H.; Muether, M.; Pischinger, S.; Klankermayer, J. Energy Fuels 2011, 25 4734–4744.

3. Kohse-Höinghaus, K.; Oßwald, P.; Cool, T. A.; Kasper, T.; Hansen, N.; Qi, F.; Westbrook, C. K.; Westmoreland, P. R. Biofuel Combustion Chemistry: From Ethanol to Biodiesel. Angew. Chem., Int. Ed. 2010, 49, 3572-3597.

4. Bansch, C.; Kiecherer, J.; Szőri, M.; Olzmann, M. Reaction of Dimethyl Ether with Hydroxyl Radicals: Kinetic Isotope Effect and Prereactive Complex Formation J. Phys. Chem. A 2013, 117, 8343-8351.

5. Dahmen, M.; Marquardt, W. Model-Based Design of Tailor-Made Biofuels, Energy Fuels, 2016, 30, 1109–1134.

6. R. Gugisch, A. Kerber, A. Kohnert, R. Laue, M. Meringer, C. Rucker, A. Wassermann, MOLGEN 5.0 Reference Guide. 2009.

 

 
 Formation of the molecules in interstellar medium 
~ The building blocks of life ~

Dr. Anita Rágyanszki

 

„Far out in the uncharted backwaters of the unfashionable end of the Western Spiral arm of
the Galaxy lies a small unregarded yellow sun. Orbiting this at a distance of roughly ninety-eight
million miles is an utterly insignificant little bluegreen planet whose apedescended life
forms are so amazingly primitive that they still think digital watches are a pretty neat idea.”
                                                                                                            Douglas Adams, Hitchhiker’s Guide to the Galaxy
 
 

         In the universe, the presence of matter is not uniformly distributed. There are regions, where matter is concentrated, namely galaxies, which occupies only a small portion of the observable, vast space. In these formations, matter cycles between stellar systems and interstellar mediums

1–3.  The dispersion of chemical elements from stars into the interstellar medium occurs at the end of a star’s lifetime. Interstellar periods, can be diffuse or dense clouds, depending on their temperature and the molecular density. The diffuse clouds have a temperature between 50-100 K, and a molecular density of n=10-1000 cm-3.  In contrast to that, in the dense clouds the temperature is 15-20 K, and the molecular density is n=103-106 cm-3 4.

Plenty of molecules have been detected in molecular clouds, specifically in dense clouds, in interstellar mediums in the last 100 years, but the actual formation mechanisms which is exists in interstellar medium remain unclear 5. Their molecular composition reflects the balance between chemical evolution via reactions, destruction of molecules by light from stars or by cosmic rays, as well as condensation, and subsequent reaction on dust grains.

The aim of this project is to study how interstellar atoms combine to form molecules in the gas phase. In this project, a new chemical model for the mechanisms of formation of molecules have been developed to represent all the possible formation reaction pathways.

 

Proposed projects:

 

Formation, decomposition, and rearranging mechanism of

  • H2C2O+NH+N2
  • CO2+CH4
  • (NH2)2CO+H2O
  • HCONH2+H2

in interstellar medium, in dense clouds.

 

References:
1. Herbst, E. The Chemistry of Interstellar Space. Angew. Chemie Int. Ed. English 29, 595–608 (1990).
2. Herbst, E. Chemistry in the Interstellar Medium. Annu. Rev. Phys. Chem. 46, 27–54 (1995).
3. Herbst, E. & van Dishoeck, E. F. Complex Organic Interstellar Molecules. Annu. Rev. Astron. Astrophys. 47, 427–480 (2009).
4. Tielens, A. G. G. M. & Allamandola, L. J. Composition, structure, and chemistry of interstellar dust. 134, 397–469 (1987).
5. Nuth III, J. A., Charnley, S. B. & Johnson, N. M. Chemical Processes in the Interstellar Medium : Source of the Gas and Dust in the Primitive Solar Nebula. Meteorites Early Sol. Syst. II 147–167 (2006).

 

Why can we Smell the Stinky Cat?
Structure, Vibrations and Olfaction – Rational Design of Odorants

Dr. Béla Fiser

 

Olfaction is the least understood within the traditional senses with many open questions about the process of smelling [1,2]. There are two main theories regarding olfaction: shape theory or structure odor relationship (SOR) and the vibration theory of olfaction (VTO). According to the SOR, the smell character of a molecule is determined by its shape, size and functional groups. Furthermore, the binding conformation of the odorant molecule is also important (‘key and lock’). In contrast to the shape theory, the other theory says, the olfactory receptors detect specific vibrational modes of the molecules by a quantum mechanism and these vibrations define the odor of the molecules [3]. The truth probably lies somewhere in between and the reality works like the combination of both models.

In the current proposal four carefully selected odorous molecules (acetone (C3H6O), thioacetone (C3H6S), acetic acid (C2H4O2) and 2-mercaptoethanol (C2H6SO)) will be studied by computational chemical tools. All the possible constitutional isomers of the selected molecules (based on their molecular formula) will be generated by Molgen 5.0 [4]. Then, the physical-chemical properties (including the vibrational modes) of these isomers will be computed. Based on the properties of the known odorants new odorous species will be selected from the set of their isomers. The most promising molecules will be tested experimentally and the computed and measured physical-chemical properties of the structures will be correlated with the intensity of their odor. The students involved in this project can contribute with their findings to the deeper understanding of olfaction.

References
1.  L. Turin, F. Yoshii, Structure-Odor Relations: A Modern Perspective. in Handbook of olfaction and Gustation (Ed. R. L. Doty), Marcel Dekker, New York, 2002.
2.  B. Auffarth, Understanding smell - The olfactory stimulus problem, Neuroscience & Biobehavioral Reviews, 2013, 37(8), 1667-1679.
3. S. Gane, D. Georganakis, K. Maniati, M. Vamvakias, N. Ragoussis, E. M. C. Skoulakis, L. Turin, Molecular Vibration-Sensing Component in Human Olfaction, PLoS ONE, 2013,8(1), e55780.
4. R. Gugisch, A. Kerber, A. Kohnert, R. Laue, M. Meringer, C. Rucker, A. Wassermann, MOLGEN 5.0 Reference Guide. 2009.

 

A Prelude to “Modular” Protein Folding:
Building Models for Understanding Peptide Conformational Transformations

John Justine Villar 

 

“Problems are best solved not on the level where they appear to occur but on the next level above them…. Problems are best solved by transcending them and looking at them from a higher viewpoint. At the higher level, the problems automatically resolve themselves because of that shift in point of view, or one might see there was no problem at all.”

-David R. Hawkins

Proteins are the machines and building blocks of living cells. These are predominantly assembled from 20 amino acids, and are used for structural support, storage, transport of other substances, signaling from one part of the organism to another, movement, and defense against foreign substances, among others. There are huge numbers of different proteins, with each one performing its specific task.

After the successful deciphering of the genetic code that defines how the amino acid sequences of proteins are coded in the DNA, one of the major missing steps in understanding the chemical basis of life is the protein folding problem – the task of understanding and predicting how the information coded in the amino acid sequence of proteins at the time of their formation translates into the three-dimensional structure of the biologically active protein.

Knowledge of how such a protein would fold would allow one to predict its chemical and biological properties. This would help the researchers understand the mechanism of hereditary and infectious diseases, aid in designing drugs with specific therapeutic properties, and of growing biological polymers with specific material properties. Misfolded peptides are the causes of multiple neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, amyloidosis, and ALS [3]. Furthermore, there is up to 70 orders of magnitude, i.e., 1070, more drug-sized molecules that are still unexplored, that may have a potential to provide cure to the said disorders.

Different structures of the same molecule have distinct physicochemical properties. One of the most explicit a posteriori properties of the structure of a molecule is its energy. The energy of a molecule is dependent on parameters such as its environment and conformation.

 

One aspect of dissecting this problem is then to observe the energy profile of a protein of interest, as the potential energy of a foldamer allows us to determine the relative stability of each possible conformation.

In principle, finding the stable foldamers of a protein requires an efficient sampling of the entire conformational space of the protein, to which there is an associated potential energy surface (PES). A local minimum of the associated PES may correspond to the energy of native fold.

Building the conformational potential energy surface (PES) of a molecule are important because they aid us in visualizing and understanding the relationship between potential energy and molecular geometry, and in understanding how prediction methods locate and characterize structures of interest. However, the time and space complexity of electronic structure calculations, commonly used to generate PES, increases exponentially with an increasing number of atoms [1,2,5].

The goal of this study is to understand the topology and dynamics of protein folding through constructing models of conformational transformations in small peptides that precisely mimic the associated potential energy surfaces [1,2].

This will provide valuable insights on the mechanisms of protein folding, such as minima and transition states, while saving computational time and resources that is necessary with current popular methods.

 

A special focus of this project would be given to a simple dipeptide CH3-CO-NH-CH2-CO-NH-CH2-CO-NH-CH3 which could change from an extended form to a b-turn [4]. This is the most common type of nonrepetitive structure recognized in proteins and comprise, on average, 25% of the residues. Turns play an important part in proteins, as they provide a direction change for the polypeptide chain and have been implicated in molecular recognition and in protein folding.

 

References:
[1] J. J. S. Villar, A. R. L. Valdez, D. H. Setiadi, I. G. Csizmadia, B. Fiser, B. Viskolcz, A. Rágyanszki. Dimension Reduction in Protein Conformational Analysis: A Two-Rotor Mathematical Model of Amino Acid Diamide Conformational Potential Energy Surfaces., submitted.
[2] A. Rágyanszki, K. Z. Gerlei, A. Suranyi, A. Kelemen, S. J. K. Jensen, I. G. Csizmadia, B. Viskolcz. Big data reduction by fitting mathematical functions: A search for appropriate functions to fit ramachandran surfaces. Chem. Phys. Lett. 625 (2015) 91-97.
[3] Reynaud, E.  Protein Misfolding and Degenerative Diseases. Nature Education 3 (2010) 28.
[4] A. Perczel, M. A. McAllister, P. Csaszar, I. G. Csizmadia. Peptide models 6. New beta-turn conformations from ab initio calculations confirmed by x-ray data of proteins. J. Am. Chem. Soc. 115 (1993) 4849–4858.
[5] M. R. Peterson, I. G. Csizmadia. Analysis of the topological features of the conformational hypersurface of n-butane, J. Am. Chem. Soc. 100 (1978) 6911-6916