The Kosenkov Group

Physical Chemistry at Monmouth University


Physical Chemistry

Chemical Education

Designing next generation of solar cells based on artificial photosynthesis

Molecular Orbital of Bactereochlorophyll A.
Figure.1: Molecular Orbital of Bactereochlorophyll A.

Our goal is to reveal the relations between structure of photosynthetic proteins and their ability to efficiently transfer energy in naturally occurring light harvesting processes. These findings help us to propose a design for solar cells that mimic natural photosynthesis.

In recent years, there has been much advancement in improving solar cell technology, and one of the areas being explored is the development of technology based on photosynthetic systems found in nature. One of the most promising models in this field uses the peridinin-chlorophyll light harvesting complexes. These molecular complexes have a very well-studied structure and high efficiency for collecting energy. Peridinin molecules belong to the well-known carotenoid pigment family. The energy of light is absorbed by peridinin molecules leading to the formation of electronic excited states and then transferred to the chlorophyll (Figure 1) molecule of the complex.

Peridinins also play a pivotal role in quenching chlorophyll triplet excited states preventing formation of harmful oxygen radicals; protecting the entire complex from photodamage. Currently, we are investegating the electronic excited states of the chlorophylls and carotenoids (peridinins) suing using ab-initio computational methods. The rates of the excitation energy transfer between chlorophyll and peridinin molecules are estimated using Förster dipole-dipole model and advanced quantum mechanical thechniques. Go to top

Modeling DNA binding of Naphthalene Diimide Derived Potential Anti-Cancer Drugs

Figure.2: Model of a drug molecule docked to DNA
Figure.2: Model of a drug molecule docked to DNA

In order to inhibit cancer cell growth, small organic molecules (ligands) can be bonded to DNA G-quadruplex structures to halt telomere maintenance. These molecules regulate telomerase activity and thermally stabilize the G-quadruplex, providing a non-destructive treatment for cancer.

Our research is focused on the investigation of di- and tetra-substituted naphthalene diimide ligands, functionalized by N-methyl-piperazine side-chains of varying length. The density functional theory (DFT) and docking simulation techniques (Figure 2) are used to simulate the possible interactions the ligands may exhibit with the telomere DNA G-quadruplex and to model the low energy conformations the ligand may take in the gas phase or in solution. By combining the information we obtained from these simulations we can gain a better understanding about how the molecule will interact with cancer cells and in other medical applications. Go to top

The Solvent Effects on the Electronic Transitions in Viologens

Figure.3: Electrostatic potential of viologen
Figure.3: Electrostatic potential of viologen

The study of bipyridinium derivatives — viologens has been ongoing for the last decade. Currently, the interest has evolved into creating new electrochemical displays to supplant LCD and LED displays. This issue that arises is that solvatochromism still remains a largely unknown phenomenon due to the exceedingly complex coupling of many different interactions.

At this time additional research is performed on this distinct class of compounds for a comprehensive understanding on what occurs during the solvatochromic shift (Figure 3). The information obtained will aid in the construction of a better class of electrochemical displays for years to come. The purpose of this research project is to study the interactions between viologens and common organic solvents (water, dimethyl sulfoxide, etc.) in order to understand the mechanisms of solvent effect of the electronic transitions in the molecules. Go to top

The Thermochemistry of Isomerization of Eight-Coordinate Rhenium Complexes

Eight-Coordinate Rhenium hydrate complex
Figure.4: Eight-Coordinate Rhenium hydrate complex

The controlled movement of chemical groups during the isomerization of metal complexes has potential applications in building nano-motors and even assembling robots at nanoscale. Currently, we are investigating the isomerization process of the eight-coordinate metal complex: pentahydrido-3-methylpyridinebis (triphenylphosphine) rhenium(V) [ReH5(PPh3)2(CH3)C5N (Figure 4) using quantum chemical techniques. The thermochemistry and kinetcs of the isomerization process is investigated using high level quantum mechanical methods. Go to top

Modeling light sensitive proteins for non-invasive control of neurons

Neuronal cells can be made directly sensitive to light by the covalent or non-covalent attachment of small photoisomerizable molecules - photoswitches. Investigating mechanisms of interactions between photoswitch molecule and ion channels of neurons and exploring effects of protein structure on light-induced conformation changes we contribute to the development of new tools for precise control of ion channel blockage that leads to development of new types of anesthetics. Go to top

Speeding-up computational chemistry using graphics processing units (GPUs)

Modern quantum chemical methods require enormous computer resources for handling molecular systems containing just a few hundred atoms. In addition to utilization of computer clusters and supercomputer systems we want to take advantage of using graphics processing units (GPUs) - devices that have hundreds of computational cores running in parallel (unlike conventional desktop computers that have only a few cores) to speed up computations. Go to top

Chemical Education

Integrating Chemistry Laboratory Instrumentation into the Industrial Internet

This project is designed to improve physical chemistry and instrumental analysis laboratory courses for undergraduate students by employing as teaching tools novel technologies in electronics and data integration using the industrial Internet. In the project students build, calibrate, and program an automatic titrator using an open-source microcontroller platform and standard pH probes, and integrate the instrument into the Internet. The proposed approach is flexible and can be used to enable integration of various laboratory instruments (e.g. temperature, pressure, salinity probes etc.) into the industrial Internet. The hardware and software are open-source which makes possible further modification and development by the academic community.

For more details see:

Nicole Famularo, Yana Kholod, and Dmytro Kosenkov, "Integrating Chemistry Laboratory Instrumentation into the Industrial Internet: Building, Programming, and Experimenting with an Automatic Titrator", J. Chem. Educ., 2016, 93(1), 175-181. DOI: 10.1021/acs.jchemed.5b00494

Software Download

Circuit schematics
11/15/2016 updated_scheme.pdf  
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Transient Absorption Spectroscopy with 3D-Printed Temperature Controlled Sample Holder

The laboratory unit demonstrates a project-based approach to teaching physical chemistry laboratory where upper-division undergraduates carry out a transient-absorption experiment investigating kinetics of cis-trans isomerization of N, N-dimethyl-4, 4-azodianiline. Students participate in modification of a standard flash-photolysis spectrometer adding a temperature controlled sample holder. The sample holder is open-source and can be reproduced with 3D-printing technology. Students build and use the experimental setup. Based on observer kinetics of cis-trans isomerization students carry out data analysis estimating energy, enthalpy, entropy, and Gibbs free energy of activation.

For more details see:

Dmytro Kosenkov, James Shaw, Jennifer Zuczek, and Yana Kholod, "Transient Absorption Spectroscopy of Cis-Trans Isomerization of N, N-Dimethyl-4, 4-Azodianiline with 3D-Printed Temperature Controlled Sample Holder", J. Chem. Educ., 2016, (ASAP) DOI: 10.1021/acs.jchemed.5b00494

3D-Printable Design Download
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