Publications

Selected publications: Prof. Nilashis Nandi & Co workers

Monograph

Nilashis Nandi

Chirality in Biological Nanospaces: Reactions in Active Sites (Monograph)

CRC Press.

Print ISBN: 978-1-4398-4002-3

eBook ISBN: 978-1-4398-4003-0.

DOI: 10.1201/b11010-1

Invited Book Chapters in Edited Books

1. A. Saha, S. Kundu, S. Dutta and N. Nandi

Molecular Studies of the Inhibition of Aminoacyl tRNA Synthetases in Bacterial

Pathogens

(Eds. Zaheer-ul-Haq, Angela K. Wilson), ebook on ‘Frontiers in Computational Chemistry’, Volume 4, eISBN: 978-168108-441-1, eISSN: 2352-9458, ISBN: 978-1-68108-442-8, ISSN: 2352-944X, Pages: 91-143, Bentham Science Publishers.

Doi: 10.2174/9781681084411118040005

2. S. Kundu and N. Nandi

Structure and Dynamics of Biological Nanospace: Active Site of Aminoacyl tRNA

Synthetase

(Invited chapter)

Encyclopedia of Nanoscience and Nanotechnology (Ed. Hari Singh Nalwa), American Scientific Publishers

ISBN: 1-58883-217-1

2019, 30, 141-197.

3. N. Nandi, S. Dutta,

Molecular Interactions in Biomimetics and Biosystems: Chirality and Confinement at Nanodimension”

Encyclopedia of Biocolloid and Biointerface Science (Ed. Hiroyuki Ohshima), Wiley.

Invited chapter, p. 195, 2015, ISBN: 978-1-118-54276-7

4. S. Dutta Banik, N. Nandi,

Chirality and Protein Biosynthesis,

(Invited Chapter), Chapter 5, special volume on “Biochirality: Origin, Evolution and Molecular Recognition”, Springer series Topics in Current Chemistry, 333, Editor, Prof. Dr. Pedro Cintas, 2013

(print) ISBN: 978-3-642-37625-2.

5. S. Dutta Banik, N. Nandi

Architectonics of active sites: Life processes at nanodimension; (Book chapter in book

entitled Manipulation of Nanoscale Material: An Introduction to Nanoarchitectonics), Ed: K. Ariga,

Royal Society of Chemistry.

2012, 213-241.

ISBN: 978-1-84973-415-8

ISSN: 1757-7136

6. N.Nandi, K. Thirumoorthy, D. Vollhardt

Chirality and Dipolar interaction in Membrane Mimetic Amphiphilic Molecules".

In book entitled “Structure and Dynamics in Membranous Interfaces”, Edited by K. Nag, John Wiley, N.J. USA 2008, 191-225.

7. N. Nandi, D. Vollhardt

Chirality and molecular recognition in biomimetic organized films

Book chapter in book entitled “Bottoms up nanofabrication: Supramolecules, self-assemblies and organized films”, editor K. Ariga, H.S.Nalwa, American Scientific Publishers (invited chapter) 2006, Chapter 5, 1-29.

8. S. Kundu and N. Nandi,

Structure and Dynamics of Biological Nanospace: Active Site of Aminoacyl tRNA Synthetase,

Journal of Encyclopedia of Nanoscience and Nanotechnology, 2016, xx, 1-57

Refereed Journal Publications

71. S. Chowdhury and N. Nandi,

Dynamics of the Catalytic Active Site of Isoleucyl tRNA Synthetase from Staphylococcus aureus bound with Adenylate and Mupirocin,

(Invited article for festschrift issue of Prof. Kankan Bhattacharyya)

J. Phys. Chem. B, 2022, 126 (3), 620-633

DOI: 10.1021/acs.jpcb.1c08555

70. S. Laskar, R. Das, S. Kundu, A. Saha, N. Nandi, Y. Chowdhury and S. Ghosh,

Whole exome sequencing identifies the potential role of genes involved in p53 pathway in Nasopharyngeal Carcinoma from Northeast

India,

Gene,2022, 812, 146099

DOI: 10.1016/j.gene.2021.146099

69. A. Saha and N. Nandi

Role of the Transfer Ribonucleic Acid (tRNA) Bound Magnesium Ions in the Charging Step of Aminoacylation Reaction in the Glutamyl tRNA Synthetase and the Seryl tRNA Synthetase Bound with Cognate tRNA,

Journal of Biomolecular Structure and Dynamics, 2021, 1-60

DOI: 10.1080/07391102.2021.1914732

68. A. Saha, S. Dutta and N. Nandi,

Inhibition of seryl tRNA synthetase by seryl nucleoside moiety (SB-217452) of

albomycin antibiotic,

Journal of Biomolecular Structure and Dynamics, 2020, 38 (8), 2440-2454.

DOI: 10.1080/07391102.2019.1635912

67. S. Dutta and N. Nandi,

Classical Molecular Dynamics Simulation of Seryl tRNA Synthetase and Threonyl tRNA Synthetase bound with tRNA and Aminoacyl Adenylate,

Journal of Biomolecular Structure and Dynamics, 2018, 37, 336-358.

DOI: 10.1080/07391102.2018.1426498

66. S. Dutta, S. Kundu, A. Saha and N. Nandi,

Dynamics of the Active Site Loops in Catalyzing Aminoacylation Reaction in Seryl and Histidyl tRNA Synthetases,

Journal of Biomolecular Structure and Dynamics, 2017, 36, 878-892.

DOI: 10.1080/07391102.2017.1301272.

65. A. Biswas, R. Prasad Mandal, S. Dutta, N. Nandi and S. De,

Catalytic and photocatalytic behavior of TiO2 based nanoparticles—their use in the synthesis of a novel TICT probe,

Mater. Res. Express 2, 2015, 065011, 1-16

DOI:10.1088/2053-1591/2/6/065011

64. S. Dutta and N. Nandi,

Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri,

J. Phys. Chem. B, 2015, 119, 10832−10848.

DOI: 10.1021/jp511585w

63. N. Nandi and D. Vollhardt

Advances in Colloid and Interface Science (Prof. Wolfgang Helfrich Festschrift)

Helfrich's Concept of Intrinsic Force and its Molecular Origin in Bilayers and Monolayers

Journal of Adv Colloid Interface Sci, 2014, 208, 110-120

DOI: 10.1016/j.cis.2014.03.001

62. S. Dutta, S. Kundu and N. Nandi

Analysis of Debye Waller Factor and Molecular Dynamics Simulation of Seryl tRNA Synthetase

J. Ind. Chem. Soc. 2014, 91, 1125-1144.

61. S. Dutta, K. Choudhury, S. Dutta Banik and N. Nandi

Active Site Nanospace of Aminoacyl tRNA Synthetase: Difference between the Class I and Class II Synthetases

Journal of Nanoscience and Nanotechnology (Special issue on Nanospace), 2014, 14, 2280-2298.

DOI: 10.1166/jnn.2014.8534

60. D. Ghosh, N. Nandi and N. Chattopadhyay

Differential Föster Resonance Energy Transfer from the Excimers of Poly (N-vinylcarbazole) to Coumarin 153

J. Phys. Chem. B. 2012, 116, 4693-4701.

DOI: 10.1021/jp300727e

59. S. Dutta Banik, S. Debnath and N. Nandi

A significant difference in the reaction mechanism of the first step of the aminoacylation reaction in class I and class II synthetases

J. Ind. Chem. Soc. 2012, 89, 1-8.

58. S. Dutta Banik and N. Nandi,

Mechanism of the activation step of the aminoacylation reaction: A significant difference between class I and class II synthetases.

J. Biomol. Struct. & Dyn. 2012, 30, 701-715.

DOI: 10.1080/07391102.2012.689701

57. S. Dutta Banik and N. Nandi,

Computational analysis of the structure and stability of the tetrahedral intermediate in the peptide bond formation reaction in peptidyl transferase center.

J. Ind. Chem. Soc. 2011, 88, 1687-1695.

56. S. Dutta Banik and N. Nandi,

Influence of the conserved active site residues of histidyl tRNA synthetase on

the mechanism of aminoacylation reaction,

Biophys. Chem. 2011, 158, 61-72.

DOI: 10.1016/j.bpc.2011.05.006

55. D. Vollhardt, N. Nandi and S. Dutta Banik,

Nanoaggregate Shapes at the Air/Water Interface,

Physical Chemistry Chemical Physics (Perspective article), 2011, 13, 4812.

DOI: 10.1039/C0CP02196B

54. G. Brezesinskii, C. Stefaniu, D. Nandy, S. Dutta Banik, N. Nandi and D. Vollhardt,

Cross sectional area increase at phase transition on compression: an unexpected phenomenon observed in an amide monolayer,

J. Phys. Chem. C. 2010, 114, 15695-15702.

DOI: 10.1021/jp104358z

53. S. Dutta Banik and N. Nandi

Aminoacylation Reaction in the Histidyl-tRNA Synthetase: Fidelity Mechanism of the Activation Step

J. Phys. Chem. B , 2010, 114, 2301–2311

DOI: 10.1021/jp910730s

52. S. Dutta Banik and N. Nandi (Invited article for honorary issue of Prof. H. Kuhn)

Orientation and Distance Dependent Chiral Discrimination in the First Step of the Aminoacylation Reaction: Integrated Molecular Orbital and Semi-empirical method (ONIOM) Based Calculation

Colloids and Surfaces B: Biointerfaces 2009, 74, 468-476.

DOI: 10.1016/j.colsurfb.2009.07.019

51. N.Nandi and S. Dutta Banik

Molecular Understanding of the Influence of Chirality and Interaction in Soft Systems: From Biomimetics to Biosystems, A Retrospection

J. Surface Sci. Technol., 2009, 25, 1-18.

50. N. Nandi

Chiral Discrimination in the Confined Environment of Biological Nanospace: Reactions and Interactions involving Amino Acids and Peptides

International Reviews in Physical Chemistry, 2009, 28, 111-167.

DOI: 10.1080/01442350902999682

49. N.Nandi, K. Thirumoorthy, D. Vollhardt

Chiral discrimination in Stearoyl Amine Glycerol Monolayers.

Langmuir, 2008, 24, 9489-9494.

DOI: 10.1021/la801247t

48. K. Thirumoorthy and N.Nandi

The role of chirality of the sugar ring in the ribosomal peptide synthesis

J. Phys. Chem. B. 2008, 112, 9187-9195.

DOI: 10.1021/jp8032066

47. K. Thirumoorthy, K. Soni, N.Nandi,

The molecular recognition of dipeptide by oligoglycyl head group of amphiphile: A quantum chemical study

J. NanoScience and Nanotechnology with special focus on Advanced material for nanoscience and nanotechnology (invited article), 2008, 8, 1-13.

DOI: 10.1166/jnn.2009.j077

46. N.Nandi and D. Vollhardt

Chirality and Recognition in Amphiphilic assemblies

Curr. Opinion Coll. Surf. (invited article) 2008, 13, 40-46.

45. K. Thirumoorthy, K. Soni, T. Arun, N. Nandi,

Chiral Discrimination in biomimetic systems: Phenyl Alanine

J. Chem. Sci. 2007, 119, 517-523.

44. K. Thirumoorthy and N.Nandi

Homochiral Preference in Peptide Synthesis in Ribosome: The Role of U2620, Amino and Peptidyl Terminals

J. Phys. Chem. B. 2007, 111, 9999-10004.

DOI: 10.1021/jp073959i

43. K. Thirumoorthy, N.Nandi and D. Vollhardt

The Role of Dipolar Interaction in the Mesoscopic Domains of Phospholipid Monolayers: Dipalmitoyl phosphatidyl choline and Dipalmitoyl phosphatidyl ethanolamine

Langmuir. 2007, 23, 6991-6996.

DOI: 10.1021/la070168z

42. K. Thirumoorthy and N. Nandi

Water Catalyzed Peptide Bond Formation in L-Alanine Dipeptide: The Role of Weak Hydrogen Bonding

J. Mol. Struc. (Theo Chem), 2007, 818, 107-118.

DOI: 10.1016/j.theochem.2007.05.017

41. N. Nandi and D. Vollhardt

Molecular Interactions in Amphiphilic Assemblies: Theoretical Perspective (Invited review)

Acc. Chem. Res. 2007, 40, 351-360.

DOI: 10.1021/ar600057b

40. K. Thirumoorthy and N. Nandi

Ab-Initio Study of the Chiral Discrimination in Alanine

Current Science, 2007, 92, 75-80.

39. K. Thirumoorthy, N. Nandi, D. Vollhardt, O. N. Oliveira, Jr.

Semiempirical Quantum Mechanical Calculations of Dipolar Interaction between Dipyridamole and Dipalmitoyl Phosphatidyl Choline in Langmuir Monolayers

Langmuir, 2006, 22, 5398-5402

DOI: 10.1021/la0602416

38. K. Thirumoorthy, N.Nandi, D. Vollhardt

Prediction of the Handedness of the Domains of Monolayers of D-N-Palmitoyl Aspartic Acid: Integrated Molecular Orbital and Molecular Mechanics Based Calculation

Invited article; special issue

Coll. Surf. A, 2006, 282-283, 222-226.

DOI: 10.1016/j.colsurfa.2005.10.086

37. K. Thirumoorthy and N. Nandi

Comparison of the Intermolecular Energy Surfaces of Amino Acids: Orientation-Dependent Chiral Discrimination

J. Phys. Chem. B., 2006, 110, 8840 – 8849.

DOI: 10.1021/jp055295n

36. K. Thirumoorthy and N.Nandi

Correlation between the molecular chirality of the sugar ring on the mesoscopic aggregate morphology in RNA and DNA mimetic systems

Chem. Phys. Lett. 2005, 414, 336-340.

DOI:10.1016/j.cplett.2005.08.121

35. N. Nandi

Study of chiral recognition of model peptides and odorants: Carvone and camphor

Article highlighted in the issue

Current Science, 2005, 88, 1929-1937.

34. K. Thirumoorthy, N.Nandi, D. Vollhardt

Role of Electrostatic Interactions for the Domain Shapes of Langmuir Monolayers of Monoglycerol Amphiphiles

J. Phys. Chem. B. 2005, 109, 10820-10829

DOI: 10.1021/jp0510948

33. N. Nandi

Role of Secondary Level Chiral Structure in the Process of Molecular Recognition of Ligand: Study of Model Helical Peptide,

J. Phys. Chem. B. 2004, 108, 789-797.

DOI: 10.1021/jp035296k

32. N. Nandi, D. Vollhardt and G. Brezesinski

Chiral Discrimination Effects in Langmuir Monolayers of 1-O-Hexadecyl Glycerol

J. Phys. Chem. B. 2004, 108, 327-335.

DOI: 10.1021/jp0308559

31. N. Nandi

Molecular Study of Heterochiral Preference in Biomimetic Monolayers

Research communication

Current Science, 2004, 87, 1581-1584.

30. N Nandi and D. Vollhardt, R. Rudert

Atomistic Calculation of the Pair Potential of Chiral Amino Acid Amphiphile in Langmuir Monolayer

Coll. Surf. A, 2004, 250, 279-287.

DOI: https://doi.org/10.1016/j.colsurfa.2004.07.033

29. N. Nandi and D. Vollhardt

Anomalous temperature dependence of domain shapes in Langmuir Monolayer: Role of dipolar repulsion

Letter to the editor

J. Phys. Chem. B, 2004, 108, 18793-18795.

DOI: 10.1021/jp0461697

28. N. Nandi and D. Vollhardt

The effect of molecular chirality on the morphology of biomimetic monolayer

Review Article

Chem. Rev. 2003, 103, 4033-4076.

DOI: 10.1021/cr0006674

27. N. Nandi and D. Vollhardt

Correlation between the microscopic and mesoscopic chirality in Langmuir monolayers

Review Article

Thin Solid Films. 2003, 433, 12-21.

DOI: 10.1016/S0040-6090(03)00298-0

26. N. Nandi

Molecular origin of the recognition of chiral odorant by chiral lipid: Interaction of dipalmitoyl phosphatidyl choline and carvone,

Letter to the editor

J. Phys. Chem. A. 2003 107, 4588-4591.

DOI: 10.1021/jp030076s

25. N. Nandi and D. Vollhardt

Chiral discrimination effects in Langmuir Monolayers: Monolayers of Palmitoyl Acid, N-Stearoyl Serine Methyl Ester and N-Tetradecyl –γ,δ-dihydroxypentanoic Acid Amide

J. Phys. Chem. B. 2003, 107, 3464-3475.

DOI: 10.1021/jp0218591

24. N. Nandi and D.Vollhardt

Molecular origin of chiral interaction in chiral biomimetic systems: dipalmitoyl phosphatidyl choline Langmuir monolayer,

J. Phys. Chem. B. 2002, 106, 10144-10149.

DOI: 10.1021/jp020578q

48. N. Nandi and D.Vollhardt

Molecular origin of chiral interaction in chiral biomimetic systems: dipalmitoyl phosphatidyl choline Langmuir monolayer (Addition and correction)

J. Phys. Chem. B. 2003, 107, 1932.

DOI: 10.1021/jp022539k

22. N. Nandi, R.K.Roy, Anupriya, S. Upadhaya, D.Vollhardt

Chiral interaction in enantiomeric and racemic dipalmitoyl phosphatidyl choline Langmuir monolayer,

J. Surf. Sci.Tech. 2002, 18, 51.

DOI: 10.18311/jsst/2002/2033

21. N. Nandi and D.Vollhardt

Prediction of the handedness of the chiral domains of amphiphilic monolayers: monolayer of amino acid amphiphiles.

Coll. Surf. A, 2002, 198-200, 207-221.

20. N. Nandi and B. Bagchi

Reply to the comment by S.Boresh and O. Steinhauser on the letter by N.Nandi and B.Bagchi entitled “anomalous dielectric relaxation in aqueous protein solution”

J. Phys. Chem. 2001, 105, 5509 - 5510.

DOI: 10.1021/jp983327j

19. D. Vollhardt and N. Nandi

Effect of chirality on the morphology of biomimetic systems

Ann. Rep. Max Planck Inst. Coll. Interface Sci. Interface division, Max Planck Gesellschaft, 2001,16.

18. N. Nandi and D.Vollhardt

Microscopic study of chiral interactions in Langmuir Monolayer: Monolayers of N-Palmitoyl Aspartic Acid and N-Stearoyl Serine Methyl Ester

Coll. Surf. A. 2000, 183-185, 67-83.

DOI: 10.1016/s0927-7757(01)00540-4

17. N. Nandi and K. Bhattacharya, B. Bagchi

Dielectric relaxation and solvation dynamics of complex chemical and biological systems. (Review)

Chem. Rev. 2000, 100, 2013-2045.

DOI: 10.1021/cr980127v

50. N.Nandi and B. Bagchi

Anomalous Dielectric Relaxation of Aqueous Protein Solutions (Letter to the Editor),

J. Phys. Chem. A, 1998, 102, 8217 - 8221.

DOI: 10.1021/jp983327j

15. N. Nandi

Solubilization of n-alkane solubilizates - Part II: solubilization in ionic surfactants

Ind. J. Chem. A, 1998, 37, 114-117.

14. N.Nandi and B. Bagchi

Dielectric relaxation of biological water.

J. Phys. Chem. B. 1997,101, 10954 - 10961.

DOI: 10.1021/jp971879g

13. N.Nandi and B. Bagchi

Prediction of the senses of helical amphiphilic assemblies from effective intermolecular potential; studies on chiral monolayers and bilayers.

J. Phys. Chem. B. 1997, 101, 1343 - 1351.

DOI: 10.1021/jp9605111

12. R.Biswas and N.Nandi, B. Bagchi

Solvation dynamics in monohydroxy alcohols; Agreement between theory and different experiments.

J. Phys. Chem. B. 1997,101, 2968 - 2979.

DOI: 10.1021/jp962705m

11. N. Nandi

Solubilization of n-decane into n-decyl polyoxyethylene surfactants: a cavity forming free energy based model.

Ind. J. Chem. A, 1996, 35, 625 - 628.

10. N. Nandi and B. Bagchi

Ultrafast solvation dynamics of an ion in the gamma cyclodextrin cavity; the role of restricted environment.

J. Phys. Chem. 1996, 100, 13914 - 13919.

DOI: 10.1021/jp960134s

9. N. Nandi and B. Bagchi

Molecular origin of the intrinsic bending force for the helical morphology observed in chiral amphiphilic assemblies: concentration and size dependence

J. Am. Chem. Soc. 1996, 118, 11208 - 11216.

DOI: 10.1021/ja9533757

8. N. Nandi and B. Bagchi

Microscopic origin of the chirality driven morphologies of the amphiphilic monolayers and bilayers.

Ind. J. Chem. A. 1996, 35, 536 - 545.

7. N. Nandi

Application of Scaled Particle Theory to Alkyl Aryl surfactants.

J. Mol. Struc. (THEO CHEM) 1995, 332, 301 - 311.

DOI: 10.1016/0166-1280(94)03897-T

6. N. Nandi and B. Bagchi

Ultrafast solvation dynamics of an ion in a restricted environment.

Ind. J. Chem. A, 1995, 34, 845 - 849.

5. N. Nandi, S. Roy and B. Bagchi

Ultarfast solvation dynamics in water: Isotope effects and comparison with experimental results.

J. Chem. Phys. 1995, 102, 1390 - 1397.

DOI: 10.1063/1.468925

4. N. Nandi, S. Roy and B. Bagchi

Ionic and dipolar solvation dynamics in water.

Proc. Ind. Acad. Sci. 1994, 106, 1297 - 1306.

3. N. Nandi and I.N. Basumalick

Application of Scaled Particle Theory to the problem of micellization II. Cationic and nononic surfactants

J. Phys. Chem. 1993, 97, 3900 - 3903.

DOI:10.1021/j100117a041

2 N. Nandi and I.N. Basumalick

Prediction of partition coefficient by Scaled Particle Theory,

Z. Phys. Chem. (neue folge), 1991, 173, 179 - 189.

DOI: 10.1524/zpch.1991.173.Part_2.179

1. N. Nandi and I.N. Basumalick

Application of Scaled Particle Theory to the problem of micellization.

J. Phys. Chem., 1990, 94, 2537 - 2540.

DOI: 10.1021/j100369a058