Embedded Files
2025
Submitted/revision
73. SiDGen: Structure-informed Diffusion for Generative modeling of Ligands for Proteins, Samyak Sangvi, Nishant Ranjan, and Tarak Karmakar*
arXiv, 2025
72. Graph-Coarsening for Machine Learning Coarse-grained Molecular Dynamics Simulations
Soumya Mondal,†, Subhanu Halder,†, Debarchan Basu, Sandeep Kumar*, and Tarak Karmakar*
arXiv, 2025 link
71. Ligand-free Au9 Nanoclusters Templated Growth of Metal-Organic Framework for Enhanced Catalysis
Ravari Kandy Aparna, Glory James, Dhananjay Gupta, Arun Karmakar, Vikas Tiwari, Sona Shaju Rose, Nonappa, Seiji Yamazo, Subrata Kundu*, Tarak Karmakar*, Sukhendu Mandal*, 2025 (under review)
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70. A Multiscale Modeling Approach to Chiral Nanocluster Self-assembly
Neha Yadav, Vikas Tiwari, Soumya Mondal, Tarak Karmakar*
J. Phys. Chem. Lett., 2025, link
69. Dynamics of gold nanocluster on MgO surface with F-center defect and its implications for CO oxidation
Vikas Tiwari, Dhananjay, and Tarak Karmakar*
J. Chem. Phys, 2025, link
68. Understanding RNA Chaperone Activity of ProQ Protein
Shilpi Singh, Nisha Kumari, Tanmay Dutta, and Tarak Karmakar*
J. Chem. Info. Mod, 2025 link
67. Insights into the Temperature-driven Competitive Pericyclic Transformations of Allyloxy Furan
Rishu Narwal, Dinesh K Gopalakrishnan, Janakiram Vaitla, and Tarak Karmakar*
Org. Biomol. Chem. 2025 link
66. Elucidating the Mechanism of Substrate Encapsulation in Supramolecular Resorcin[4]arene using Enhanced Sampling Simulations
Tanish Tyagi, Anmol, and Tarak Karmakar*
Phys. Chem. Chem. Phys. 2025, link
65. Understanding Dynamics of Nanocluster-Organic Frameworks and Gas Diffusion from Machine Learning Potential-based Simulations
Animesh Karmakar, Dhananjay Gupta, and Tarak Karmakar*
Nano Lett., 2025 link
64. Nobel Prize in Chemistry 2024 - Computational Protein Design and Structure Prediction,
Tarak Karmakar*
Resonance, 2025 link
63. Insights into the Interactions between Monolayer-Protected Metal Nanoclusters and Amyloid-beta Fibrils
Soumya Mondal and Tarak Karmakar*
Adv. Theor. Simul. (Willey), 2025 link
62. Locality Sensitive Hashing-based Dataset Reduction for Deep Potential Training
Anmol, Anuj Kumar Sirohi, Neha, Jayadeva, Sandeep Kumar, and Tarak Karmakar*
J. Chem. Theory Comput, 2025 link
61. Modelling Catalytic Reaction on Ligand-protected Metal Nanoclusters
Vikas Tiwari and Tarak Karmakar*
Chem. Sci., 2025, link
60. Atomistic Details of Nanocluster Formation from Machine-Learned Potential-based Simulations
Vikas Tiwari and Tarak Karmakar*
Nano Lett., 2025 link
59. Unveiling Interactions of Peptide-bound Monolayer Protected Metal Nanocluster with Lipid Bilayer
Soumya Mondal and Tarak Karmakar*
J. Phys. Chem. Lett., 2025 link
58. Ylide-Induced Ring Contraction of Coumarins to Benzofurans: Applications to the Synthesis of Bis-Heterocycles
Sandeep Kumar, Dinesh K Gopalakrishnan, Shashank Shrotriya, Tarak Karmakar, and Janakiram Vaitla*
Org. Lett. 2025 link
57. Ligand-mediated hexagonal close-packed self-assembly of Ag44(MNBA)30 nanocluster
Soumyadip Roy, Vikas Tiwari, Tarak Karmakar* and Indranath Chakraborty*
Small, 2025 link
56. Computational Exploration of Vinyl Sulfoxonium Ylide Chemistry
Dinesh Kumar Gopalakrishnan, Janakiram Vaitla*, and Tarak Karmakar*
Org. Biomol. Chem. 2025 link
55. Enhanced Sampling Simulations of RNA-peptide Binding using Deep Learning Collective Variables
Nisha Kumari, Sonam Dhull, and Tarak Karmakar*
J. Chem. Inf. Model., 2025, link
2024
54. Triplet Energy Migration in Cytoskeletal Polymers
Arnab Kakati, Tarak Karmakar, Aarat Kalra*
J. Phys. Chem. B, 2024 link
53. Nucleophilic Dearomatization of Activated Pyridines Using Vinyl Sulfoxonium Ylides: Application to the Synthesis of
Bis-Heterocycles
Srashti Bhardwaj, Dinesh K Gopalakrishnan, Tarak Karmakar, Janakiram Vaitla*
Organics Letters, 2024 link
52. Synthesis of Cyclic (Alkyl)(Amino)Carbene-Stabilized Copper-Iron Heterobimetallic Complexes and Their Application in Pyridine
Hydroboration
Ankita Sharma, Vikas Tiwari, Ritu Yadav, Bindusagar Das, Chinmoy Majumder, Ayantika Das, Tarak Karmakar* and Subrata Kundu*
ACS Organometallics, 2024, link
51. Unveiling the Role of Solvent in Solution Phase Chemical Reactions using Deep Potentials-based Enhanced Sampling Simulations, Anmol and Tarak Karmakar*,
J. Phys. Chem. Lett. 2024, 15, 39, 9932–9938, link
50. Diastereoselective cyclopropanation of α,β-unsaturated carbonyl compounds with vinyl sulfoxonium ylides,
Shalu Deshwal, Dinesh Kumar Gopalakrishnan, Tarak Karmakar* and Janakiram Vaitla*,
Org. Bimol. Chem., 2024 link
49. Solvent-dependent Crystal Shape of Theophylline using Constant Chemical Potential Molecular Dynamics Simulations
Neha and Tarak Karmakar*,
Phys. Chem. Chem. Phys. 2024 link
48. Graph Neural Networks for Predicting Solubility in Diverse Solvents using MolMerger incorporating Solute-solvent Interactions
Vansh Ramani and Tarak Karmakar*,
J. Chem. Theory Comput., 2024, link
47. Enhancing Coarse-Grained Models through Machine Learning
Tarak Karmakar*, Thereza A. Soares*, Kenneth M Merz*,
J. Chem. Inf. Model., 2024, 64, 8, 2931–2932 link
46. Molecular Dynamics Study on Ion-mediated Self-assembly of Monolayer-protected Nanoclusters
Vikas Tiwari, Anushna Bhattacharyya, and Tarak Karmakar*,
Nanoscale, 2024 link
45. Polymorph-Specific Solubility Prediction using Constant Chemical Potential Molecular Dynamics
Neha, Manya Aggarwal, Aashutosh Soni, and Tarak Karmakar*,
J. Phys. Chem. B, 2024 link
44. Carbene-Mediated Stereoselective Olefination of Vinyl Sulfoxonium Ylides with Diazo Compounds and Acetals
Dinesh K Gopalakrishnan, Srashti Bhardwaj, Sandeep Kumar, Tarak Karmakar*, and Janakiram Vaitla*
Chemical Communications, 2024 link
43. Visible Light-Promoted Regioselective Benzannulation of Vinyl Sulfoxonium Ylides with Ynoates,
Daksh Davas, Dinesh K Gopalakrishnan, Sandeep Kumar, Anmol, Tarak Karmakar*, and Janakiram Vaitla*
JACS Au, 2024 link
42. Stereoselective gem-Difunctionalization of Diazo Compounds with Vinyl Sulfoxonium Ylides and Thiols via Metalloradical Catalysis, Srashti Bhardwaj, Dinesh K Gopalakrishnan, Shalu Deshwal, Raju Sen, Vikas Tiwari, Tarak Karmakar,* and Janakiram Vaitla*
ACS Catalysis, 2024 link
41. Insights into the Mechanism of Peptide Fibril Formation on Gold Surface
Soumya Mondal and Tarak Karmakar*
Biophysical Chemistry, 2024, 310, 107237 link
40. Unique Reactivity of Cyclic (Alkyl)(Amino)Carbene Stabilized Acyclic Imino Olefin (AIO) Towards Dinitrogen Transfer Reagent, Bindusagar Das, Dhananjay Gupta, Aryan Chauhan, Ritu Yadav, Tarak Karmakar* and Subrata Kundu*
ChemRxiv, 2024 link
39. Electrostatic-driven Self-assembly of Janus-like Monolayer-protected Metal Nanoclusters,
Anushna Bhattacharya†, Vikas Tiwari†, and Tarak Karmakar*,
J. Phys. Chem. Lett., 2024 link
2023
38. Atomically Dilute Cu(II) Incorporated Phosphamide Polymer as a Co-operative Electrocatalyst for HER and CO2 Reduction,
Monika Chaudhary,† Mrinal Kanti Adak,† Dhananjay Gupta,† Nidhi Kumari, Avinava Kundu, Hirak Kumar Basak, Tarak Karmakar* and Biswarup Chakraborty*,
Inorg. Chem., 2023 link
37. Divergent Approach to Highly Substituted Arenes via [3 + 3] Annulation of Vinyl Sulfoxonium Ylides with Ynones,
Daksh Davas, Dinesh K Gopalakrishnan, Krishnendu Bar, Sandeep Kumar, Tarak Karmakar*, and Janakiram Vaitla*
Org. Lett. 2023 link
35. Synthesis and Applications of π-Conjugation Extended Alkenyl Sulfoxonium Ylides,
Sandeep Kumar, Daksh Davas, Krishnendu Bar, Dinesh Gopalakrishnan, Deepesh Kumar, Tarak Karmakar, Janakiram Vaitla*
Org. Lett. 2023 link
34. Understanding Molecular Aggregation of Ligand-protected Atomically-Precise Metal Nanoclusters,
Vikas Tiwari, and Tarak Karmakar*,
J. Phys. Chem. Lett., 2023, link
33. Cu(I)/N,N-Imine Ligand Catalyzed C(sp3)-C(sp) Sonogashira Coupling Reaction of Alkyl Bromides: the scope and mechanism
Swati Jain, Anmol, Ruchi Sharma, Tarak Karmakar* and M. Ramu Yadav*
Organic Letters, 2023 link
32. Expanded triazolophanes: A topological analysis of vesicular assembly,
Appa Rao Sapala, Govind P. Maurya, Hanuman Singh, Neha Mehta, Tarak Karmakar, and V. Haridas,
Organic & Biomolecular Chemistry, 2023, link
31. Non-Equilibrium Modelling of Concentration-Driven processes with Constant Chemical Potential Molecular Dynamics Simulations,
Tarak Karmakar*, Aron Finney, Matteo Salvalaglio*, Ozgur Yazaydin, Claudio Perego*,
Acc. Chem. Res. 2023 link
30. Cyclic(alkyl)(amino)carbene (CAAC) and Bicyclic (alkyl)(amino)carbene (BICAAC) Derived Glyoxal Radical Cations with Excellent Stability,
Bindusagar Das, Ritu Yadav, Ankita Sharma, Tarak Karmakar*, and Subrata Kundu*,
Chem. Commun. 2023 link
29. Engineered Graphene Grain Boundaries as Molecular Sieves for Water Desalination
DR Nalge, T Karmakar, S Bhattacharya, KB Balasubramanian,
IEEE Explore, 2023, link
28. Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters
Vikas Tiwari, Sonali Garg, Tarak Karmakar*,
ACS Applied Biomaterials, 2023, link
27. Cooperative Friedel-Crafts Alkylation of Electron-Deficient Arenes via Catalyst Activation with Hexafluoroisopropanol,
Sanjay Singh, Sankalan Mondal, Vikas Tiwari, Tarak Karmakar*, Chinmoy K Hazra* ,
Chem. Euro. J., 2023, link
26. Understanding Cyclic(alkyl)(amino)carbene-Copper Complex Catalysed N-H and O-H Bond Addition to Electron Deficient Olefin
Akshi Tyagi, Sunita Mondal, Anmol, Vikas Tiwari, Tarak Karmakar*, and Subrata Kundu*,
Chem. Commun. 2023, 59, 110-113 link
25. Collective Variables for Crystallization Simulations -- from Early Developments to Recent Advances,
Neha, Vikas Tiwari, Soumya Mondal, Nisha Kumari, Tarak Karmakar*
ACS Omega, 2023, 8, 1, 127-146, link
24. Ion-Mediated Protein Stabilization on Nanoscopic Surfaces,
Arti Sharma, Soumya Mondal, Tripti Ahuja, Tarak Karmakar*, Soumik Siddhanta*,
Langmuir, 2023, 39, 3, 1227-1237 link
2022
23. Solubility of organic salts in solvent-antisolvent mixtures: A combined experimental and molecular dynamics simulations approach
Zoran Bjelobrk, Ashwin Kumar Rajagopalan, Dan Mendels, Tarak Karmakar, Michele Parrinello, Marco Mazzotti,
J. Chem. Theory Comput. 2022, 18, 8, 4952–4959 link
22. A catalyst and solvent free route for the synthesis of N-substituted pyrrolidones from levulinic acid,
Pritam Dolui, Vikas Tiwari, Parul Saini, Tarak Karmakar, Koushik Makhal, Harshita Goyal, & Anil Jacob Elias*,
Chem. Eur. J. 2022, 28, e20220082 link
21. Computational Investigations on the Potential Role of Hygrophorones as Quorum Sensing Inhibitors against LasR Protein of Pseudomonas aeruginosa,
Anu Dalal, Tushar Kushwaha, Gourav Choudhir, Krishna K. Inampudi, Tarak Karmakar, Hariprasad P., Shivajirao L. Gholap,
J. Biomol. Struct. & Dyn. 2022 link
# Before joining IITD (2012-2021)
20. Liquid-Liquid Critical Point in Phosphorus,
Manyi Yang, Tarak Karmakar, Michele Parrinello
Physical Review Letters, 127, 080603, 2021 link
19. Solubility prediction of organic molecules with molecular dynamics simulations,
Zoran Bjelobrk, Dan Mendels, Tarak Karmakar, Michele Parrinello, and Marco Mazzotti
Crystal Growth & Design, 21, 9, 5198–5205 2021 link
18. Structural basis for the hyperthermostability of an archaeal glutaminase induced by post-translational succinimide formation, Aparna V Dongre, Sudip Das, Asutosh Bellur, Sanjeev Kumar, Anushua Chandrashekarmath, Tarak Karmakar, Padmanabhan Balaram, Sundaram Balasubramanian, Hemalatha Balaram, Biophysical Journal, 120, 17, 3732-3746, 2021 link
17. Collective Variables for the Study of Crystallization
Tarak Karmakar, Michele Invernizzi, Valerio Rizzi, Michele Parrinello
Molecular Physics, 119, 19–20, e1893848, 2021 link
16. Molecular Mechanism of Gas Solubility in Liquid: Constant Chemical Potential Molecular Dynamics Simulations
Narjes Ansari, Tarak Karmakar, Michele Parrinello
Journal of Chemical Theory and Computation, 16, 8, 5279–5286, 2020 link
15. Uncovering the Surfactants Role in Controlling the Crystal Growth of Pyridoxine Hydrochloride
Dandan Han, Tarak Karmakar, Fei Liu, Yan Wang, Weiwei Tang, Junbo Gong
Crystal Growth & Design, 19 (12), 7240-7248, 2019 link
14. Molecular Dynamic Simulations of Crystal Nucleation from Solution at Constant Chemical Potential
Tarak Karmakar, Pablo M Piaggi, Michele Parrinello
Journal of Chemical Theory and Computation, 15 (12), 6923-6930, 2019 link
13. Naphthalene crystal shape prediction from molecular dynamics simulations
Zoran Bjelobrk, Pablo M. Piaggi, Thelo Weber, Tarak Karmakar, Marco Mazzotti, Michele Parrinello
CrystEngComm, 21 (21), 3280-3288, 2019 link
12. Solvent-Mediated Morphology Selection of the Active Pharmaceutical Ingredient Isoniazid: Experimental and Simulation Studies
Dandan Han; Tarak Karmakar, Zoran Bjelobrk, Junbo Gong, Michele Parrinello
Chemical Engineering Science, 204, 320-328, 2019 (selected as a cover) link
11. A Cannibalistic Approach to Grand Canonical Crystal Growth
Tarak Karmakar, Pablo M Piaggi, Claudio Perego, Michele Parrinello
Journal of Chemical Theory and Computation, 14(5), 2678–2683, 2018 link
10. Molecular Mechanism Behind Solvent Concentration Dependent Optimal Activity of Thermomyces Lanuginosus Lipase in Biocompatible Ionic Liquid: Interfacial Activation Through Arginine Switch
Sudip Das, Tarak Karmakar and Sundaram Balasubramanian
The Journal of Physical Chemistry B, 120 (45), 11720-11732, 2016 link
Tarak Karmakar and Sundaram Balasubramanian
The Journal of Physical Chemistry B, 120 (45), 11644-11653, 2016 link
Sourav Roy, Tarak Karmakar, Lakhmeesha K Nagappa, Sundaram Balasubramanian, Hemalatha Balaram
Proteins: Structure, Function, and Bioinformatics, 84, 1658-1669, 2016 link
(equal contribution)
Tarak Karmakar, Sourav Roy, Hemalatha Balaram, Sundaram Balasubramanian
Journal of Biomolecular Structure and Dynamics 34, 1590-1605, 2016 link
6. Product Release Pathways in Human and Plasmodium falciparum Phosphoribosyltransferase
Tarak Karmakar, Sourav Roy, H Balaram, MK Prakash, Sundaram Balasubramanian
Journal of Chemical Information and Modeling, 56 (8), 1528-1538, 2016 link
Sourav Roy, Tarak Karmakar, VSP Rao, LK Nagappa, Sundaram Balasubramanian, Hemalatha Balaram
Molecular BioSystems, 11, 1410-1424, 2015 link
(equal contribution)
4. Elucidating the interaction of H2O2 with polar amino acids–Quantum chemical calculations
Tarak Karmakar, Sundaram Balasubramanian
Chemical Physics Letters 613, 5-9, 2014 link
3. CO2 migration pathways in oxalate decarboxylase and clues about its active site
Tarak Karmakar, Ganga Periyasamy, Sundaram Balasubramanian
The Journal of Physical Chemistry B 117 (41), 12451-12460, 2013 link
TG Abi, Tarak Karmakar, Srabani Taraphder
Computational and Theoretical Chemistry 1010, 53-66, 2013 link
1. Understanding proton affinity of tyrosine sidechain in hydrophobic confinement
TG Abi, Tarak Karmakar, Srabani Taraphder
Journal of Chemical Sciences 124 (1), 59-63, 2012 link
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