Manikandan Paranjothy

Chemical Dynamics Research Group

Our research group is interested in looking into the dynamics of chemical reactions using the principles of classical and quantum mechanics. Understanding a chemical reaction from a static picture the potential energy surface is insufficient in completely describing the process. One needs to look at the dynamics i.e., the time-dependent nuclear motion at the atomic level. Classical trajectory simulations with potentials and gradients computed on-the-fly using electronic structure theory packages, a methodology known as direct dynamics, is used in most of our simulations. The group is interested in studying organic reaction mechanisms and pathways, modeling gas phase experiments and studying the associated dynamics. Research work is going on to understand mechanisms of covalent adduct formation between DNA base pairs with few select carcinogens and chemistry of negatively charged arenes.

Research Interests

Biography

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Research Interests

Biography

Manikandan Paranjothy completed M.Sc. degree in Chemistry from Bharathiar University, Coimbatore and Ph.D. in Theoretical Chemistry from Indian Institute of Technology, Kanpur, India, in October 2009. Subsequently, he worked as a post doctoral research associate with Prof. William L. Hase at Texas Tech University, USA, from November 2009 to January 2013. He joined IIT Jodhpur in February 2013.

Projects

Title: Chemical Dynamics Simulations of Complex Organic Reactions: Mechanistic Insights and Microsolvation Effects

Sponsoring Agency: Department of Science and Technology - Science and Engineering Research Board (DST - SERB)

Duration: 3 years (2014-17)

Summary: This project involves the classical chemical dynamics simulation of complex organic reactions. The simulations will be focused on fragmentation chemistry of protonated tryptophan and diacetylene reactions with various hydrocarbons. Since the early 1960's classical trajectory simulations have been used to study chemical reactions. The components of a classical trajectory simulation are (1) developing or choosing a potential energy surface for the chemical problem under investigation; (2) selecting initial conditions for the ensemble of trajectories to be calculated; (3) numerical integration of the classical equations of motion, that is, either Newton's or Hamilton's, to determine the atomic-level motion for each trajectory; and (4) transformation of the trajectories final atomic coordinates and momenta to properties that may be compared with experiment and/or a theoretical model. The potential functions required for integrating the classical trajectories can be analytical functions or can be computed quantum mechanically using an appropriately chosen level of electronic structure theory, using on-the-fly techniques. Such a method, known as direct dynamics, is possible with the advancement of high-speed computers.

Title: Modeling Organic and Biochemical phenomena via Direct Chemical Dynamics Simulations

Sponsoring Agency: Department of Science and Technology - Science and Engineering Research Board (DST - SERB)

Duration: 3 years (2020-23)

Summary: In this project, state-of-the-art direct dynamics methodology along with appropriate electronic structure theory will be used to investigate important and interesting chemical phenomena. Two different problems will be addressed: (a) mechanisms of covalent adduct formation between DNA base pairs with few select carcinogens, and (b) chemistry of negatively charged arenes. Exposure to certain toxic compounds leads to the formation of covalent DNA adducts in human cells which results in cell mutation and eventually cancer. The covalent bond formation can occur at different ring N, C, and O atoms of the DNA bases. An atomic level dynamics investigation of covalent adduct formation between DNA bases and a few select carcinogenic molecules will be undertaken. The results from these simulations are expected to provide a detailed atomic level mechanistic information about DNA adduct formation useful in drug designing. Gas phase reactions of negatively charged aromatic anions is important since more than 80% of the molecules employed in pharmaceutical applications contain aromatic or heteroaromatic rings. Also, this topic is gaining considerable attention in the astrophysics community due to the detection of negative ions in the interstellar medium. To some extent, chemistry of these molecules have been investigated by the mass spectrometry and electronic structure theory community but detailed mechanistic studies are not available. Dynamics investigation of select unimolecular and bimolecular reactions of arene anions will be performed. Such atomic level simulations are expected to provide a better understanding of experimental spectra and assistance in synthetic organic chemistry.



Publications

Group (Present)