Photosensitizers and Applications
Renjith Thomas, T Pooventhiran
Renjith Thomas, Anila Skariah
S.R. Begum, D.J. Rao, K.V.R. Rao, Y. Ramakrishna, N. Elangovan, T. Pooventhiran, R. Thomas, Spectral Characterization and Quantum Mechanical Studies of 5-Amino-2-(6-(2-Hydroxyethyl)-3-Oxononyl) Cyclohex-2-Enone Isolated from a Marine Algae, Biointerface Res. Appl. Chem. 13 (2023). https://doi.org/10.33263/BRIAC135.413.
R. Jayachitra, G. Thilagavathi, A. Kanagavalli, N. Elangovan, S. Sowrirajan, R. Thomas, Photophysical properties of (E)-4-((1-phenylethylidene)amino)-N-(pyrimidin-2-yl) benzenesulfonamide; synthesis, characterization, wavefunction and docking studies, J. Indian Chem. Soc. 100 (2023). https://doi.org/10.1016/j.jics.2023.100903.
R. Jayachitra, G. Thilagavathi, A. Kanagavalli, N. Elangovan, A. Sirajunnisa, S. Sowrirajan, R. Thomas, Synthesis, Computational, Electronic spectra, and molecular docking studies of 4-((diphenylmethylene)amino)-N-(pyrimidin-2-yl)benzenesulfonamide, J. Indian Chem. Soc. 100 (2023). https://doi.org/10.1016/j.jics.2022.100836.
J.M. Thomas, R. Thomas, Study of Non-Covalent Interactions Present in the Tapinarof − Ethanol System with Special Emphasis on Hydrogen- Bonding Interactions, (2023). https://doi.org/10.1021/acs.jpcb.3c03152.
G. Thilagavathi, R. Jayachitra, A. Kanagavalli, N. Elangovan, A. Sirajunnisa, K.J. Rajimon, S. Sowrirajan, R. Thomas, (E)-4-((4-chlorobenzylidene)amino)-N-(thiazole-2yl) benzenesulfonamide: Synthesis, characterization and electronic structure theory and docking studies, J. Indian Chem. Soc. 100 (2023). https://doi.org/10.1016/j.jics.2023.100910
A. Kanagavalli, R. Jayachitra, G. Thilagavathi, N. Elangovan, S. Sowrirajan, R. Thomas, Synthesis, characterization, computational, excited state properties, wave function, and molecular docking studies of (E)-4-((2-hydroxybenzylidene)amino)N-(thiazol-2-yl) benzenesulfonamide, J. Indian Chem. Soc. 100 (2023). https://doi.org/10.1016/j.jics.2023.100885.
T. Pooventhiran, K.R.S. Murthy, R. Kalambukattu, R.K. Joseph, R. Thomas Study of the Electronic Properties of a Fluoropyrazolecarbonitrile Derivative and Enhancement of Spectral Properties on Adsorption with Fullerene, Biointerface Res. Appl. Chem. 13 (2023) 342. https://doi.org/10.33263/BRIAC134.342
R. Jayachitra, M. Padmavathy, A. Kanagavalli, G. Thilagavathi, N. Elangovan, S.Sowrirajan, R. Thomas, Synthesis, computational, experimental antimicrobial activities and theoretical molecular docking studies of (E)-4-((4-hydroxy-3-methoxy-5-nitrobenzylidene) amino)-N-(thiazole-2-yl) benzenesulfonamide, J. Indian Chem. Soc. 100 (2023). https://doi.org/10.1016/j.jics.2022.100824.
G. Thilagavathi, R. Jayachitra, A. Kanagavalli, E. N, A. Sirajunnisa, S. S, R. Thomas, Synthesis, computational, molecular docking studies and photophysical properties of (Z)-N-(pyrimidin-2-yl)-4-(thiophen-2-ylmethylene)amino) benzenesulfonamide, J. Indian Chem. Soc. 100 (2023). https://doi.org/10.1016/j.jics.2022.100835.
A. V Ilavarasi, F. Paularokiadoss, L.M. Novena, T. Pooventhiran, S. Erkan, C.A. Celaya, R. Thomas, D.R. Ampasala, T. Christopher Jeyakumar, Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins, Chem. Phys. Impact. 7 (2023). https://doi.org/10.1016/j.chphi.2023.100289.
T. Pooventhiran, A.Y.A. Alzahrani, K.J. Rajimon, R. Thomas, Solvent interaction and dynamics of neurotransmitters L‐aspartic acid and L‐glutamic acid with water and ethanol, J. Mol. Struct. 1273 (2023). https://doi.org/10.1016/j.molstruc.2022.134347.
T. Sanakarganesan, N. Elangovan, S. Chandrasekar, E. Ganesan, V. Balachandran, S. Sowrirajan, K. Balasubramani, R. Thomas, Synthesis, Hirshfeld surface analysis, computational, wave function properties, anticancer and cytotoxicity activity of di[(p-chlorobenzyl) (dibromo)] (4,7-dimethyl-1,10-phenanthroline)tin (IV) complex, Inorganica Chim. Acta. 547 (2023). https://doi.org/10.1016/j.ica.2022.121361.
S. Tabassum, P. Thangaiyan, S. Govindaraju, N.K. Daniel, R. Thomas, Pyrazole Derivative Containing Naphthalene Moiety: Cytotoxocity (Breast and Cervical Cancer), Antibacterial and Antifungal Studies Using Experimental and Theoretical Tools, Polycycl. Aromat. Compd. 43 (2023) 8544–8561. https://doi.org/10.1080/10406638.2022.2149564
A. Kanagavalli, R. Jayachitra, G. Thilagavathi, M. Padmavathy, N. Elangovan, S. Sowrirajan, R. Thomas, Synthesis, structural, spectral, computational, docking and biological activities of Schiff base (E)-4-bromo-2-hydroxybenzylidene) amino)-N-(pyrimidin-2-yl) benzenesulfonamide from 5-bromosalicylaldehyde and sulfadiazine, J. Indian Chem. Soc. 100 (2023). https://doi.org/10.1016/j.jics.2022.100823.
P. Surendar, T. Pooventhiran, S. Rajam, D.J. Rao, N. Manigandan, A. Irfan, R. Thomas, Organic Quasi-Liquid Schiff Bases from Biomolecules: Synthesis, Structure and Quantum Mechanical Studies, Biointerface Res. Appl. Chem. 13 (2023) 1–46. https://doi.org/10.33263/BRIAC132.107
J. S.Al-Otaibi, Y.S. Mary, Y.S. Mary, R. Trivedi, B. Chakrabory, R. Thomas, Cluster formation between an oxadiazole derivative with metal nanoclusters (Ag/Au/Cu), graphene quantum dot sheets, SERS studies, and solvent effects, Struct. Chem. 34 (2023) 867–877. https://doi.org/10.1007/s11224-022-02052-5.
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. https://doi.org/10.1039/D2NJ06173B
J.S. Al-Otaibi, Y.S. Mary, Y.S. Mary, R. Thomas, R.A. Costa, DFT Investigations on the Interactions Between Pyrimidine Derivatives and Ag/Au/Cu Metal Clusters: Solvation Effects and Reactivity Analysis, J. Clust. Sci. (2023). https://doi.org/10.1007/s10876-023-02429-4.
P. Anaikutti, M. Selvaraj, J. Prabhakaran, T. Pooventhiran, T.C. Jeyakumar, R. Thomas, P. Makam, Indolyl-4H-chromenes: Multicomponent one-pot green synthesis, in vitro and in silico, anticancer and antioxidant studies, J. Mol. Struct. (2022) 133464. https://doi.org/10.1016/j.molstruc.2022.133464
J.S. Al-Otaibi, Y.S. Mary, Y.S. Mary, R. Thomas, Evidence of cluster formation of pyrrole with mixed silver metal clusters, Ag<inf>x</inf>-M<inf>y</inf> (x = 4,5, y = 2/1 and M = Au/Ni/Cu) using DFT/SERS analysis, Comput. Theor. Chem. 1208 (2022). https://doi.org/10.1016/j.comptc.2021.113569
A Systematic Computational Protocol for Deconstructing Non-Covalent Interactions: BerchNCI 1.0
Non-covalent interactions constitute the fundamental organizing principles of supramolecular assemblies; however, the accurate modeling of these subtle, dispersion-driven forces remains a formidable challenge in theoretical chemistry. In this work, we formally propose the Berchmans Protocol for Modelling Non-Covalent Interactions 1.0 (BerchNCI 1.0), a comprehensive, hierarchical computational workflow designed to decipher the electronic anatomy of NCIs with benchmark precision.
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Electron Upconversion Enables CP and CS Bond Formation Under Mild Oxidative Conditions: A Theoretical Study
Meera's first paper as the part of her PhD thesis published in Journal of Computational Chemistry. The work has been based on some of the finidngs of Prog Igor Alabugin of Florida State University, USA. Traditional methods for forming carbon–phosphorus (C–P) and carbon–sulfur (C–S) bonds often rely on strong oxidants that generate high-energy carbocation intermediates, frequently leading to unwanted side reactions. In this work, we employ DFT to investigate an alternative mechanism operating under basic conditions that utilizes three-electron bond formation and concomitant electron upconversion. Our computational results reveal a radical-anionic pathway initiated by a cyclization to form a 2-center-3-electron (2c-3e) bond, followed by the oxidation of the resulting upconverted radical-anion by mild oxidants such as molecular oxygen . This pathway is shown to be both thermodynamically and kinetically favored over conventional two-electron routes, providing a more controlled and selective strategy for C–P and C–S bond construction. These findings suggest that electron-upconversion mechanisms can significantly advance green chemistry by reducing dependence on harsh reagents and minimizing synthetic side reactions.
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Sneha & Ananya’s paper in Journal of Physical Chemistry B
PhD student Sneha Anna Sunny's paper on the Mapping the Interaction Landscape of Adenosine and Minoxidil Sulfate Using an Independent Gradient Model Based on Hirshfeld Partition and Interaction Region Indicator. Ananya Prakash is a final year MSc Physics student of our college who worked in our lab as part of the Kerala Theoretical Physics Initiative (KTPI) student project initiative,
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Manjesh Mathew: Benchmarking Computational Approaches for Proton Affinity
In this collaborative study with Dr Ralph Puchta, Manjesh Mathew, PhD student assessed the proton affinities and gas phase basicities of molecules ranging from ammonia to proton sponges like PMG using computational methods including B3LYP, BP86, PBEPBE, APFD, wB97XD, and M062X with the def2tzvp basis set. The M062X method showed the highest accuracy, closely matching experimental results for all examples, especially those containing heteroatoms, while APFD and wB97XD tended to overestimate values. Dispersion corrections were evaluated but found not to significantly affect basicity predictions. Computational and Theoretical Chemistry
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Alen Binu Abraham : Non-Covalent Interactions of Caffeine and Ascorbic Acid
In this study, we explored the non-covalent interactions between caffeine and ascorbic acid, focusing on their hydrogen bonding in both gas and solvent (water) phases, using Density Functional Theory. The binding energy calculations revealed significant interactions with values of −14.65 kcal/mol in the gas phase and −11.62 kcal/mol in water. Through Natural Bond Orbital, RDG, AIM, and LED analyses, we confirmed the stabilization energy and electron delocalization in the caffeine-ascorbic acid complex, enhancing our understanding of drug-drug interactions and their implications for drug efficacy and delivery systems. Abraham, Alen Binu, Alzahrani, Abdullah Y. and Thomas, Renjith. "Exploring non-covalent interactions between caffeine and ascorbic acid: their significance in the physical chemistry of drug efficacy" Zeitschrift für Physikalische Chemie, vol. 238, no. 2, 2024, pp. 401-420.
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Gayathri: Hydrogen Bonding and Dynamics of Prontosil in Water and Methanol
In this theoretical study, we investigated the solvation energies of prontosil, a pioneering sulfa drug, in water and methanol using DFT/M06-2X/cc-pVDZ level of theory. Our findings reveal that prontosil shows more favorable interactions with methanol than water, as evidenced by NBO, RDG, QTAIM analyses, and local energy decomposition (LED) analysis using DLPNO-CCSD(T). The prontosil-methanol complex displayed the lowest binding energy and highest stability, suggesting methanol as a more suitable solvent for prontosil in terms of molecular interactions and stability. These insights are further corroborated by ab initio molecular dynamics simulations, underscoring the importance of solvent choice in drug design and molecular interaction studies. Here is the link to "Understanding the hydrogen bonding preferences and dynamics of prontosil in water and methanol":
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Jisha’s paper in Journal of Physical Chemistry-B (ACS)
Postdoc Dr Jisha's latest paper Assessing the Noncovalent Interaction of Deucravacitinib and Ethanol with Special Reference to an Independent Gradient Model Based on Hirshfeld Partition
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Rajimon’s first bioactive chalcone paper in JMS
Rajimons Chalcone paper in collaboration with Prof Sarojini, Mangalore Univeristy
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Metalfree cycloaddition in New Journal of Chemistry
The paper investigates the metal-free [3+2] cycloaddition reaction between phenyl azide and phenyl enaminone to selectively synthesize 1,2,3-triazoles. Using computational methods, it explores the reaction pathways (1,4- and 1,5-pathway), solvent effects, and the impact of phenyl azide substituents, offering insights into the reaction mechanism and the role of water as a solvent and catalyst.
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Rajimon : Schiff base derived from 4-Chloroaniline and 2-Formylphenol
PhD student Rajimon KJ's 6th first-authored paper in Journal of Molecular Structure (Elsevier). Comprehensive assessment of schiff base derived from 4-Chloroaniline and 2-Formylphenol: Molecular architecture, experimental with computational bioactivity profiling, emphasizing anticancer efficacy against pulmonary and mammary carcinoma cell models
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Cu-Schiff base complex in Polyhedron
PhD student Rajimon KJ's 7th first-authored paper was published in Polyhedron (Elsevier). Structural, spectroscopic, and biological properties of an asymmetric Cu (II) Schiff-base complex: Synthesis, DNA/BSA interactions, and antimicrobial potential with experimental and computational insights
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Collaborative paper with Prof BK Sarojini, Mangalaore University
Supramolecular and computational analysis of Fluconazole −2−chloro−5−nitrobenzoic acid cocrystal. PhD student, Rajimon KJ was a visitor at her lab last year.
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