Publications

Google Scholar

2024

Submitted/under review

50. Stereoselective Synthesis of Cyclopropanes from Vinyl Sulfoxonium Ylides and Arylidenes,

Shalu Deshwal, Dinesh Kumar Gopalakrishnan, Tarak Karmakar* and Janakiram Vaitla*, 2024 (Under review)

49. Solvent-dependent Crystal Shape of Theophylline using Constant Chemical Potential Molecular Dynamics Simulations

Neha and Tarak Karmakar*, 2024 (submitted)

48. 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

47. Effect of Cations on Monolayer-protected Nanoclusters Aggregation

Vikas Tiwari, Anushna Bhattacharyya, and Tarak Karmakar*, ChemRxiv, 2024 link

46. Polymorph-Specific Solubility Prediction using Constant Chemical Potential Molecular Dynamics

Neha, Manya Aggarwal, Aashutosh Soni, and Tarak Karmakar*, ChemRxiv, 2024 link

45. 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

44. Graph Neural Networks for Predicting Solubility in Diverse Solvents using MolMerger incorporating Solute-solvent Interactions

Vansh Ramani and Tarak Karmakar*

arXiv preprint 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

9. Molecular Dynamics and Free Energy Simulations of Phenylacetate and CO2 Release from AMDase and its G74C/C188S Mutant: A Possible Rationale for the Reduced Activity of the Latter

Tarak Karmakar and Sundaram Balasubramanian

The Journal of Physical Chemistry B, 120 (45), 11644-11653, 2016 link

8. Role of W181 in Modulating Kinetic Properties of Plasmodium falciparum Hypoxanthine Guanine Xanthine Phosphoribosyltransferase

Sourav Roy, Tarak Karmakar, Lakhmeesha K Nagappa, Sundaram Balasubramanian, Hemalatha Balaram

Proteins: Structure, Function, and Bioinformatics, 84, 1658-1669, 2016 link

(equal contribution)

7. Structural and dynamical correlations in PfHGXPRT oligomers: A molecular dynamics simulation study

Tarak Karmakar, Sourav Roy, Hemalatha Balaram, Sundaram Balasubramanian

Journal of Biomolecular Structure and Dynamics 34, 1590-1605, 2016 link