Research @ Renjith Thomas Lab

Research Collaborators

  • Prof Dr Yohannan Panickar, Kerala
  • Dr Ralph Puchta, University of Erlangen, Germany
  • Dr Stevan Armakovic, University of Novi Sad, Serbia
  • Prof Dr Elham Shafik Aazam, King Abdulaziz University, Saudi Arabia
  • Prof Dr Abdullah Y Alzahani, King Khalid University, Saudi Arabia
  • Prof Dr Mohammad Abdul Hakim Badawi, Tishreen University, SAR
  • Slavko Radenkovich, University of Kragujevic, Serbia
  • Dr Penny Govender, University of Johannesburg, South Africa

Modelling Non-covalent interaction

Current:

  • Manjesh Mathew

Past:

  • Aristote Matando (currently Professor, University of Congo)
  • Mebin Varghese (currently PhD student, VIT)
  • Alen Binu Mathew (currently at Autonomous University of Madrid)

Non-covalent interactions, despite their relative weakness compared to covalent bonds, are pivotal in molecular and materials science. Computational modeling, through molecular simulations and quantum chemistry calculations, enables precise description and prediction of these interactions. This computational approach aids in drug design, materials optimization, and molecular-level biological understanding. Additionally, it contributes to accurate force field development and molecular dynamics simulations, unraveling reaction mechanisms and complex system behaviors. In sum, non-covalent interactions and computational modeling are essential tools with broad interdisciplinary implications, from chemistry to biology and materials science.

In one of our recent research, we explored how caffeine interacts with ascorbic acid, which is commonly found in vitamin C supplements. These interactions can affect how drugs work and how they’re delivered in the body. We found that caffeine and ascorbic acid form specific types of hydrogen bonds when they’re in both gas and water. Understanding these interactions can help us better understand how drugs function and how they can be delivered more effectively.

A.B. Abraham, A.Y. Alzahrani, R. Thomas, Exploring non-covalent interactions between caffeine and ascorbic acid: their significance in the physical chemistry of drug efficacy, Zeitschrift Für Phys. Chemie. (2023).
A. Matondo, R. Thomas, P.V. Tsalu, C.T. Mukeba, V. Mudogo, α-methylation and α-fluorination electronic effects on the regioselectivity of carbonyl groups of uracil by H and triel bonds in the interaction of U, T and 5FU with HCl and TrH 3 (Tr = B, Al), J. Mol. Graph. Model. 88 (2019) 237–246. https://doi.org/10.1016/j.jmgm.2019.02.00

Solvation Dynamics

Current:

  • Dr Jisha Mary Joseph
  • Sneha Anna Sunny
  • Francis Thomas

Past:

  • Dr T. Pooventhiran (post doc, currently at IISER)
Theoretical studies of solvent interactions represent a crucial aspect of chemistry research, shedding light on how solvents interact with molecules and influence chemical processes. These investigations delve into the intricate details of solvation phenomena, elucidating the nature of solvent-solute interactions, solvent effects on reaction mechanisms, and the thermodynamics of solvation. By employing sophisticated theoretical models and computational simulations, scientists can predict how different solvents impact the stability, reactivity, and selectivity of chemical reactions, ultimately aiding in the design of more efficient and environmentally friendly chemical processes. Such studies are invaluable for fields ranging from drug discovery to materials science, as they provide a deeper understanding of the molecular world and guide the development of innovative solutions in various scientific endeavors. Some of the recent papers are available in the links. 
    J.M. Thomas, R. Thomas, Study of Non-Covalent Interactions Present in the Tapinarof–Ethanol System with Special Emphasis on Hydrogen-Bonding Interactions, J. Phys. Chem. B. 0 (2023) null. https://doi.org/10.1021/acs.jpcb.3c03152
    R. Thomas, T. Pooventhiran, Study of the dynamics of the interaction of glycine and GABA with water and ethanol using theoretical tools, J. Mol. Liq. 368 (2022). https://doi.org/10.1016/j.molliq.2022.120721.
    R. Thomas, T. Pooventhiran, M.A. Bakht, A.Y. Alzahrani, M.A. Salem, Study of interaction between different solvents and neurotransmitters dopamine, l-adrenaline, and l-noradrenaline using LED, QTAIM and AIMD, J. Mol. Liq. 368 (2022).
    Prathiksha, T. Pooventhiran, M. Afroz Bakht, R. Thomas, Understanding the solvation dynamics of metformin in water using theoretical tools, J. Mol. Liq. 362 (2022). https://doi.org/10.1016/j.molliq.2022.119678.
    R. Thomas, T. Pooventhiran, S.M. El-Bahy, I.H. El Azab, G. A. M. Mersal, M.M. Ibrahim, Z.M. El-Bahy, Evidence of significant non-covalent interactions in the solution of Levetiracetam in water and methanol, J. Mol. Liq. 359 (2022).

Sulphur Centered Hydrogen Bond

  • Arnav Paul (NIISER, now at University of Illinois at Urbana-Champaign)

In our research, we’ve found strong evidence for sulfur-centered hydrogen bonds involving sulfur atoms as donors in aromatic and aliphatic thiols in water. This discovery helps us understand how molecules interact in these systems, and it has broad implications, from chemistry to biology. Our work contributes to our knowledge of how sulfur atoms play a unique role in these interactions.

    A. Paul, R. Thomas, Evidences for sulfur centered hydrogen bond with sulfur atoms as a donor in aromatic thiols and aliphatic thiols in aqueous solution, J. Mol. Liq. 348 (2022). https://doi.org/10.1016/j.molliq.2021.118078.

Synthesis of bioactive compounds

Current:
  • Rajimon KJ
Past:
  • Dr N Elangovan (post-doc)

My group also works on the the synthesis and investigation of the biological activities of Schiff bases and chalcones, recognizing their pivotal roles in both synthetic chemistry and pharmacology. Schiff bases, formed through the condensation of primary amines and carbonyl compounds, are versatile intermediates known for their role in organic synthesis, particularly in drug development, owing to their diverse biological activities, including anticancer and antimicrobial properties. Chalcones, α,β-unsaturated ketones, serve as essential precursors in the synthesis of various biologically active compounds, such as flavonoids, and possess pharmacological significance, with antioxidant, anti-inflammatory, and anticancer attributes. Our group is committed to designing, synthesizing, and evaluating novel Schiff bases and chalcones, with a focus on understanding their interactions with biological systems, including enzymes and receptors

    K.J. Rajimon, N. Elangovan, A. Amir Khairbek, R. Thomas, Schiff bases from chlorine substituted anilines and salicylaldehyde: Synthesis, characterization, fluorescence, thermal features, biological studies and electronic structure investigations, J. Mol. Liq. 370 (2023). https://doi.org/10.1016/j.molliq.2022.121055.
    P. Surendar, T. Pooventhiran, N. Al-Zaqri, S. Rajam, D. Jagadeeswara Rao, R. Thomas, Synthesis of three quasi liquid Schiff bases between hexanal and adenine, cytosine, and l-leucine, structural interpretation, quantum mechanical studies and biological activity prediction, J. Mol. Liq. (2021) 117305. https://doi.org/10.1016/j.molliq.2021.117305.
    N. Elangovan, B. Gangadharappa, R. Thomas, A. Irfan, Synthesis of a versatile Schiff base 4-((2-hydroxy-3,5-diiodobenzylidene)amino) benzenesulfonamide from 3,5-diiodosalicylaldehyde and sulfanilamide, structure, electronic properties, biological activity prediction and experimental antimicrobial properties, J. Mol. Struct. 1250 (2022). https://doi.org/10.1016/j.molstruc.2021.131700.

Study of Molecular Structure

Current:
  • Rajimon KJ
Past:
  • Dr N Elangovan (post-doc)

Our research focuses on the critical investigation of organic molecules, cocrystals using spectral techniques, electronic structure studies, and the prediction of biological activity and toxicity through in-silico tools. Organic molecules are the building blocks of life, influencing chemistry and biology profoundly. Our exploration of cocrystals, utilizing advanced spectral techniques, aims to engineer novel materials with customized properties, particularly in the realm of pharmaceuticals and advanced materials. Through in-depth electronic structure studies, we unravel the quantum mechanical behavior of molecules, leading to innovations in green energy and electronic devices. Additionally, our work in predictive modeling for biological activity and toxicity empowers drug discovery and safety assessments, expediting research processes and ensuring safer products for society and the environment. Our collective efforts in these areas drive scientific innovation and contribute to a safer, more efficient, and healthier future. 

    Y.S. Mary, Y. Sheena Mary, R. Thomas, B. Narayana, Detailed Study of Three Halogenated Benzylpyrazole Acetamide Compounds with Potential Anticancer Properties, Polycycl. Aromat. Compd. 42 (2022) 6705–6719. https://doi.org/10.1080/10406638.2021.1988997.
    K. Haruna, V.S. Kumar, S.J. Armaković, S. Armaković, Y.S. Mary, R. Thomas, S.A. Popoola, A.R. Almohammedi, M.S. Roxy, A.A. Al-Saadi, Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron, Spectrochim. Acta - Part A Mol. Biomol. Spectrosc. 228 (2020). https://doi.org/10.1016/j.saa.2019.117580.
    J.S. Al-Otaibi, Y.S. Mary, S. Armaković, R. Thomas, Hybrid and bioactive cocrystals of pyrazinamide with hydroxybenzoic acids: Detailed study of structure, spectroscopic characteristics, other potential applications and noncovalent interactions using SAPT, J. Mol. Struct. 1202 (2020) 127316. https://doi.org/10.1016/j.molstruc.2019.127316.
    R. Thomas, Y.S. Mary, K.S. Resmi, B. Narayana, S.B.K. Sarojini, S. Armaković, S.J. Armaković, G. Vijayakumar, C. Van Alsenoy, B.J. Mohan, Synthesis and spectroscopic study of two new pyrazole derivatives with detailed computational evaluation of their reactivity and pharmaceutical potential, J. Mol. Struct. 1181 (2019) 599–612. https://doi.org/10.1016/j.molstruc.2019.01.014.
    R. Thomas, Y.S. Mary, K.S. Resmi, B. Narayana, B.K. Sarojini, G. Vijayakumar, C. Van Alsenoy, Two neoteric pyrazole compounds as potential anti-cancer agents: Synthesis, electronic structure, physico-chemical properties and docking analysis, J. Mol. Struct. 1181 (2019), 455–466. https://doi.org/10.1016/j.molstruc.2019.01.003.

Computational catalysis and reaction mechanism

Current:

  • Dr Ali Kairbek (Tishreen University)
  • Meera Kattoor

Past:

  • Dr Zakir Ullah, ICMAB-CSIC, Barcelona Spain

Our research is dedicated to the exciting field of computational catalysis and reaction mechanism exploration. We delve deep into the molecular intricacies of catalytic processes, employing advanced computational techniques to elucidate the fundamental mechanisms behind chemical reactions. By simulating the behavior of molecules and catalysts at the atomic and molecular levels, we uncover critical insights into how reactions occur, catalysts function, and pathways for optimizing reaction outcomes. This research not only enhances our understanding of catalysis but also has broad implications, from sustainable energy solutions to the development of novel catalysts for industrial and environmental applications.

    M.A.A.-H. Badawi, A.A. Khairbek, R. Thomas, Computational studies of the CuAAC reaction mechanism with diimine and phosphorus ligands for the synthesis of 1, 4-disubstituted 1, 2, 3-triazoles, New J. Chem. 47 (2023) 3683–3691.
    M.A. Al-Hakim Badawi, M.I. Al-Zaben, R. Thomas, DFT Studies on Mechanism of Organocatalytic Metal-Free Click 32CA Reaction for Synthesis of NH-1,2,3-triazoles, Catal. Letters. (2023). https://doi.org/10.1007/s10562-023-04374-3.
    Z. Ullah, R. Thomas, Markovnikov versus anti-Markovnikov addition and C–H activation: Pd–Cu synergistic catalysis, Appl. Organomet. Chem. 35 (2021). https://doi.org/10.1002/aoc.6077.
    Z. Ullah, R. Thomas, Mechanistic insights can resolve the low reactivity and selectivity issues in intermolecular Rauhut–Currier (RC) reaction of γ-hydroxyenone, New J. Chem. 44 (2020) 12857–12865. https://doi.org/10.1039/D0NJ02732D.