57. Unraveling the impact of binary vs. ternary alcohol solutions on the conformation and solvation of the SARS-CoV-2 receptor-binding domain
R. Gazi, and M. Jana* Phys. Chem. Chem. Phys. 2025, 27, 7028. DOI 10.1039/D4CP04402A
56. Proline concentration driven thermostability and hydration properties of ubiquitin
R. Gazi, Sonu Kumar, and M. Jana* J. Mol. Liq. 2025, 424, 127108 . DOI https://doi.org/10.1016/j.molliq.2025.127108
55. Comparative Bindings of Glycosaminoglycans with CXCL8 Monomer and Dimer: Insights from Conformational Dynamics and Kinetics of Hydrogen Bonds.
S. Dhurua, S. Maity, B. Maity, and M. Jana* J. Phys. Chem. B 2024, 128, 42, 10348–10362 . DOI: https://doi.org/10.1021/acs.jpcb.4c03670
54. Conformational preferences of heparan sulfate to recognize the CXCL8 dimer in aqueous medium: degree of sulfation and hydrogen bonds.
S. Dhurua, and M. Jana* Phys. Chem. Chem. Phys. 2024, 26, 9317. DOI https://doi.org/10.1039/D3CP04706G
53. Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations.
S. Maity, S. Pahari, S. Santra and M. Jana* J. Chem. Inf. Model. 2024, 64, 3841 - 3854 DOI:https://doi.org/10.1021/acs.jcim.3c01991
52. Isoflavones and lysozyme interplay: Molecular insights into binding mechanisms and inhibitory efficacies of isoflavones against protein modification.
S. Das, S. Nudrat, S. Maity, M. Jana*, V. K. Belwal, and A. S. Roy* Chemical Physics Impact, 8, 2024, 100643. DOI: https://doi.org/10.1016/j.chphi.2024.100643
51. Boron-containing fullerene-based salts with cyclic carbonate solvents as electrolytes for Li-ion batteries and beyond
P. Giri, S. Barath, S. Dhurua, S. Maity, R. Gazi, and M. Jana* Phys. Chem. Chem. Phys. 2024, 26, 9317. DOI https://doi.org/10.1039/ D3CP04706G
50. Binding Interaction of Coumarin Derivative Daphnetin with Ovalbumin: Molecular Insights into the Complexation Process and Effects of Metal Ions and pH in the Binding and Antifibrillation Studies.
S. Nudrat, B. Maity, S. Quraishi, I. Karankumar, K. Kumari, M Jana*, and A. S. Roy* Mol. Pharmaceutics 2024, 21, 9, 4708–4725.
DOI: https://doi.org/10.1021/acs.molpharmaceut.4c00675
49. Construing the Interactions of Coumarin Derivatives with the Main Protease of Stomach Pepsin Using Spectroscopic and Computational Analyses: Insights into the Binding Thermodynamics, Antifibrillation Studies, and Enzymatic Assay.
S. Nudrat, S. Maity, S. Khare, K. Kumari, M. Jana*, and A. S. Roy* ACS Food Sci. Technol. 2024, 4, 1, 245–262 DOI: https://doi.org/10.1021/acsfoodscitech.3c00495
48. Inhibition of amyloid formation of bovine hemoglobin by bioactive phenolic acids: an elaborate investigation into their binding properties with the protein using multi-spectroscopic and computational techniques.
S. Lyndem, P. Giri, Aneesha S. L. , A. Bhatta, K. Kumari, M. Jana*, and A. S. Roy* New J. Chem, 2024, 48, 12362-12386. DOI: 10.1039/D4NJ01106F
47. Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation
S. Dhurua, and M. Jana* J. Chem. Inf. Model. 2023, 63, 5660 - 5675 DOI: https://doi.org/10.1021/acs.jcim.3c00668
S. Nudrat, P. Giri, D. L. Nongbri, K. Kumari, S. Quraishi, M. Jana*, K. Aguan, A. S. Roy* , ACS Food Sci. Technol. 2023, 3, 866, DOI: https://doi.org/10.1021/acsfoodscitech.3c00055
45. Conformational Features and Hydration Dynamics of Proteins in Cosolvents: A Perspective from Computational Approaches
R. Gazi, S. Maity, and M. Jana* ACS Omega (Invited mini review). 2023, 8, 2832–2843 DOI: https://doi.org/10.1021/acsomega.2c08009
44. Solid state synthesis of bispyridyl-ferrocene conjugates with unusual site selective 1,4-Michael addition, as potential inhibitor and electrochemical probe for fibrillation in amyloidogenic protein
B. Halder, A. Mitra, S. Dewangan, R. Gazi, N. Sarkar, M. Jana, S. Chatterjee* J. Mol. Struct. 2023, 1273, 134362 DOI: https://doi.org/10.1016/j.molstruc.2022.134362
43. Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation
S. Dhurua, and M. Jana* ChemPhysChem. 2023, 24, e202200440 DOI: https://doi.org/10.1002/cphc.202200440
42. Influence of Aqueous Arginine Solution on Regulating Conformational Stability and Hydration Properties of the Secondary Structural Segments of a Protein at Elevated Temperatures: A Molecular Dynamics Study
S. Santra, and M. Jana* J. Phys. Chem. B 2022, 126, 1462. DOI: https://doi.org/10.1021/acs.jpcb.1c09583
41. Binding of bioactive esculin and esculetin with hen egg white lysozyme: Spectroscopic and computational methods to comprehensively elucidate the binding affinities, interacting forces, and conformational alterations at molecular level.
S. Lyndem, R. Gazi, V. K. Belwal, A. Bhatta, M. Jana*, A. Roy* J. Mol. Liq. 2022, 360, 119423. DOI: https://doi.org/10.1016/j.molliq.2022.119423
40. Predicting the evolution of number of native contacts of a small protein by using deep learning approach.
S. Santra, and M. Jana* Comput. Biol. Chem. 2022, 97, 107625. DOI: https://doi.org/10.1016/j.compbiolchem.2022.107625
39. Potency of New Boron-Based Heterocyclic Anion Receptor Additives to Regulate the Solvation and Transport Properties of Li-ions in Ethylene Carbonate Electrolyte of Li-Ion Battery: An Atomistic Molecular Dynamics Study.
R. Parida, S. Pahari, M. Jana* J. Power Sources, 2022, 521, 230962. DOI: https://doi.org/10.1016/j.jpowsour.2021.230962
38. Combined spectroscopic and computational approaches for the recognition of bioactive flavonoid 6-hydroxyflavone by human serum albumin: Effects of non-enzymatic glycation in the binding.
S. Sarmah, S. Dhurua, V. K. Belwal, S. Lyndem, M. Jana*, A. S. Roy* J. Mol. Liq. 2022, 346, 118288. DOI: https://doi.org/10.1016/j.molliq.2021.118288
37. Molecular recognition of two bioactive coumarin derivatives 7-hydroxycoumarin and 4-methyl-7-hydroxycoumarin by hen egg white lysozyme: Exploring the binding mechanism, thermodynamic parameters and structural changes using multispectroscopic and computational approaches.
S. Lyndem, R. Gazi, M. Jana*,V. K. Belwal, A. S. Roy* J. Biomol. Struct. Dynam., 2022, 40, 13872. DOI: https:doi.org/10.1080/07391102.2021.1995499
S. Santra, and M. Jana* J. Comput. Biophys. Chem., 2022, 21, 391-404. DOI:https://doi.org/10.1142/S2737416521420011
35. Analyzing the driving forces of insulin stability in the basic amino acid solutions: A perspective from hydration dynamics.
S. Santra, S. Dhurua, M. Jana* J. Chem. Phys., 2021, 154, 084901 DOI: https://doi.org/10.1063/5.0038305 This article is the part of Special Collection in Honor of Women in Chemical Physics and Physical Chemistry
34. Unraveling the Origin of Interactions of Hydroxychloroquine with the Receptor-Binding Domain of SARS-CoV-2 in Aqueous Medium.
S. Santra, S. Giri, M. Jana* Chem. Phys. Lett., 2021, 764, 138280. DOI: https://doi.org/10.1016/j.cplett.2020.138280
33. Conformational changes of GDNF-derived peptide induced by heparin, heparan sulfate, and sulfated hyaluronic acid – Analysis by circular dichroism spectroscopy and molecular dynamics simulation.
L. Satish, S. Santra, M. V. Tsurkan, C. Werner, M. Jana, H. Sahoo* Int. J.Biol. Macromol 2021, 182, 2144 DOI: https://doi.org/10.1016/j.ijbiomac.2021.05.194
32. Metal-Free One-Pot Synthesis of 2-(2-Hydrazinyl) Thiazole Derivatives Using Graphene Oxide in a Green Solvent and Molecular Docking Studies.
A. Das, S. Dey, S, Chakraborty, A. Barman, R. N. Yadav, R. Gazi, M. Jana, Md. F. Hossain* ChemistrySelect 2021, 6, 9552 DOI: https://doi.org/10.1002/slct.202102642
31. Non-enzymatic glycation of human serum albumin modulates its binding efficacy towards bioactive flavonoid chrysin: A detailed study using multi-spectroscopic and computational methods
S. Sarmah, S. Pahari, S. Das, V. K. Belwal, M. Jana*, A. Roy*, J. Biomol. Struct. Dynam., 2021, 39, 476-492 . DOI: https://doi.org/10.1080/07391102.2019.1711196
30. In-Silico Investigation of the Conformational Properties of the Disaccharide Units of Chondroitin, Dermatan and Heparan Sulphate in Aqueous Medium.
S. Dhurua, R. Parida, M. Jana* J. Indian. Chem. Soc. 2021, 98, 100064 DOI: https://doi.org/10.1016/j.jics.2021.100064 This article is the part of Special Issue:SI: Professor D C Mukherjee Festschrift
29. Insights into the Sensitivity of Arginine Concentration to Preserve the Folded Form of Insulin Monomer Under Thermal Stress.
S. Santra and M. Jana*, J. Chem. Inf. Model., 2020, 60, 6, 3105–3119. DOI: https://doi.org/10.1021/acs.jcim.0c00006
28. Doped deltahedral organo-Zintl superalkali cations
G. N. Reddy, R. Parida, A. Munoz-Castro, M. Jana, S. Giri*, Chem. Phys. Lett. 2020, 759, 137952. DOI: https://doi.org/10.1016/j.cplett.2020.137952
27. Elucidation of molecular interaction of bioactive flavonoid luteolin with human serum albumin and its glycated analogue using multi-spectroscopic and computational studies.
S. Sarmah, S. Pahari, V. Belwal, M. Jana*, A. Roy*, J. Mol. Liq. 2020, 318, 114147. DOI: 10.1016/j.molliq.2020.114147
26. Superhalogens as Building Blocks of Super Lewis Acids.
G. N. Reddy, R. Parida, P. Jena, M. Jana, S. Giri*, ChemPhysChem. 2019, 20, 1607. DOI: doi.org/10.1002/cphc.201900267
25. Interactions Between CD44 and HA16: An Investigation on Multiple Binding Modes of the Complex by Using Molecular Dynamics Simulation Studies.
D. Paul, S. Santra, M. Jana* , J. Indian Chem. Soc. Special Issue on " Theoretical and Computational Chemistry ", 2019, 96, 851-861. DOI: https://indianchemicalsociety.com/journal/abstract_details.php?journal=Nzc=
24. Lysozyme-luteolin binding: Molecular insights into the complexation process and the inhibitory effects of luteolin towards protein modification.
S. Das, S. Pahari, S. Sarmah, M. Rohman, D. Paul, M. Jana*, A. Roy*, Phys. Chem. Chem. Phys. 2019, 21, 12649-12666. DOI: https://doi.org/10.1039/C9CP01128E
23. A New Class of Superhalogen Based Anion Receptor in Li-ion Battery Electrolytes.
R. Parida, G. N. Reddy, A. Chakraborty, S. Giri, M. Jana* J. Chem. Inf. Model., 2019, 59, 2159-2164. DOI: https://doi.org/10.1021/acs.jcim.9b00035 This article is part of the Women in Computational Chemistry special issue.
22. [8] Cyclo-1, 4-Naphthylene: A Possible New Member in Hole Transport Family
A. Chakraborty, G.N Reddy, M. Jana*, S. Giri* Chem. Phys. Lett. 2019, 715, 153. DOI: https://doi.org/10.1016/j.cplett.2018.11.008
21. Microscopic investigation on empirical force-field model dependent structure and dynamical properties of amino acids in aqueous medium.
S. Santra, T. Kundu, M. Jana* J. Indian Chem. Soc. (Invited Lecture Article), 2018, 95, 1617-1630.
20. An Insight into the Binding of 6-Hydroxyflavone with Hen Egg White Lysozyme: A Combined Approach of Multi-Spectroscopic and Computational Studies
S. Das, S. Santra, M. A. Rohman, M. Ray, M. Jana*, A. S. Roy* J. Biomol. Struct. Dynam., 2018, 37, 4019-4034. DOI: 10.1080/07391102.2018.1535451
19. Effects of ethanol on the secondary structure specific hydration properties of Chymotrypsin Inhibitor 2 in its folded and unfolded forms.
D. Mohanta and M. Jana* Mol. Simul. 2018, 44, 1278. DOI: https://doi.org/10.1080/08927022.2018.1496246
18. Can 2,2,2-trifluoroethanol be an efficient protein denaturant than methanol and ethanol under thermal stress ?
D. Mohanta and M. Jana* Phys. Chem. Chem. Phys. 2018, 20, 9886. DOI:https://doi.org/10.1039/C8CP01222A
17. Picosecond Solvation Dynamics in Nanoconfinement : Role of Water and Host-Guest Complexation
S. Biswas, S. Santra, S. Yesylevskyy, J. Maiti, M. Jana*, R. Das* J. Phys. Chem. B. 2018, 122, 3996. DOI: https://doi.org/10.1021/acs.jpcb.7b10376
16. Conformational disorder and solvation properties of the key-residues of a protein in water-ethanol mixed solutions.
D. Mohanta, S. Santra, M. Jana* Phys. Chem. Chem. Phys. 2017, 19, 32636. DOI: https://doi.org/10.1039/C7CP06022J
15. Insights into the Mechanism of Ground and Excited State Double Proton Transfer Reaction in Formic Acid Dimer.
S. Giri, R. Parida, M. Jana, S. Gutiérrez-Oliva, A. ToroLabbe* J. Phys. Chem. A. 2017, 121, 9531. DOI: https://doi.org/10.1021/acs.jpca.7b09819
14. Residue Specific Interaction of an Unfolded Protein with Solvents in Mixed Water-Ethanol Solutions: A Combined Molecular Dynamics and ONIOM Study.
D. Mohanta, S. Santra, G. N. Reddy, S. Giri, M. Jana* J. Phys. Chem. A. 2017, 121, 6172. DOI: https://doi.org/10.1021/acs.jpca.7b05955
13. The Beckmann rearrangement in the framework of reaction electronic flux.
S. Giri, R. Inostroza-Rivera, M. Jana* Theor. Chem. Acc. 2017, 136, 9. DOI:https://doi.org/10.1007/s00214-016-2025-3
12. Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.
M. Yang, T. A. d’Ortoli, E. Säwén, M. Jana, G. Widmalm, A.D. MacKerell Jr. Phys. Chem. Chem. Phys. 2016, 18, 18776. DOI: https://doi.org/10.1039/C6CP02970A
11. Effect of ethanol concentrations on temperature driven structural changes of Chymotrypsin Inhibitor 2.
D. Mohanta and M. Jana* J. Chem. Phys. 2016, 144, 165101. DOI: https://doi.org/10.1063/1.4947239
10. CHARMM Drude polarizable force field for aldopentofuranoses and methyl-aldopentofuranosides
M. Jana and A. D. MacKerell Jr.* J. Phys. Chem. B 2015, 119, 7846. DOI: https://doi.org/10.1021/acs.jpcb.5b01767
9. In silico studies of properties of water hydrating a small protein
S. K. Sinha, M. Jana, K. Chakraborty and S. Bandyopadhyay* J. Chem. Phys. 2014, 14, 22D502. DOI: https://doi.org/10.1063/1.4895533
8. Molecular dynamics study of β-cyclodextrin-phenylalanine (1:1) inclusion complex in aqueous medium.
M. Jana* and S. Bandyopadhyay* J. Phys. Chem. B 2013, 117, 9280. DOI: https://doi.org/10.1021/jp404348u
Publications from IIT Kharagpur
7. Restricted dynamics of water around a protein-carbohydrate complex: Computer simulation studies
M. Jana and S. Bandyopadhyay* J. Chem. Phys. 2012, 137, 055102. DOI: 10.1063/1.4739421
6. Conformational flexibility of a protein–carbohydrate complex and the structure and ordering of surrounding water
M. Jana and S. Bandyopadhyay* Phys. Chem. Chem. Phys. 2012, 14,6621-6631. DOI: https://doi.org/10.1039/C2CP24104H
5. Vibrational spectrum of water confined in and around cyclodextrins.
M. Jana and S. Bandyopadhyay* Chem. Phys. Lett. 2011, 509, 181-185. DOI: https://doi.org/10.1016/j.cplett.2011.04.103
4. Hydration properties of .alpha-, beta-, and gamma-cyclodextrin from molecular dynamics simulations.
M. Jana and S. Bandyopadhyay* J. Phys. Chem. B 2011, 115, 6347-6357. DOI: https://doi.org/10.1021/jp2013946
3. Kinetics of hydrogen bonds in aqueous solutions of cyclodextrin and its methyl-substituted forms
M. Jana and S. Bandyopadhyay*, J. Chem. Phys. 2011, 134, 025103. DOI: https://doi.org/10.1063/1.3530781
This article is selected for publication in JCP: BioChemical Physics 5 (January, 2011).
This article is selected for publication in Virtual Journal of Biological Physics Research 21 (January 15, 2011).
2. Low-frequency vibrational spectrum of water around cyclodextrin and its methyl-substituted derivatives
M. Jana and S. Bandyopadhyay*, Langmuir 2010, 26, 14097-14102. DOI: https://doi.org/10.1021/la101927g
Microscopic investigation of the hydration properties of cyclodextrin and its substituted forms
M. Jana and S. Bandyopadhyay*, Langmuir 2009, 25, 13084-13091. DOI: https://doi.org/10.1021/la902003y