Dr Ganapati Natarajan, M. Sci.  , Ph. D (Cantab) - Indian Institute of Technology, Chennai - Post-Doctoral Research Associate (Project Officer)

Dr Ganapati Natarajan

M. Sci. , Ph. D (Cantab)

Indian Institute of Technology, Chennai

Post-Doctoral Research Associate (Project Officer)

Chennai, Tamil Nadu | India

Main Specialties: Chemistry

Additional Specialties: Theoretical and computational nanoscience, materials science, condensed matter physics, theoretical chemistry

ORCID logohttps://orcid.org/0000-0002-3820-6034

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Dr Ganapati Natarajan, M. Sci.  , Ph. D (Cantab) - Indian Institute of Technology, Chennai - Post-Doctoral Research Associate (Project Officer)

Dr Ganapati Natarajan

M. Sci. , Ph. D (Cantab)


I am a computational materials scientist with diverse and wide-ranging interests in computer simulations, theoretical physics and chemistry, and the applications of mathematics and computer science in materials science. I mainly use computational methods such as DFT and molecular dynamics, to study the ground and excited states of in many different materials, include molecules, polymers, clusters, glasses and compare the results with experiment.


1999 BA (Hons) Experimental and theoretical Physics, Trinity College University of Cambridge, UK.
2000 M. Sci (Hons) Experimental and theoretical Physics at Trinity College Cambridge, UK.

2011 Ph. D (hons) in Chemistry in the amorphous materials group (Ab initio molecular dynamics simulations of amorphous arsenic sulphide).
Postdoc: Collaborating with an experimental nanomaterials group at IIT Madras.

I have 25+ international peer-reviewed journal publications including several contributions in world-reputed chemistry and nanoscience journals such as Science Advances, Nature communications, JACS, ACS Nano, Angewandte Chemie International, etc.

Research outcomes (with co-workers/collaborators)

Topological structure and properties of metal nanoclusters,

I identified the Borromean Rings topology in the metal nanocluster Au25(SR)18, which is the most stable of its kind.

Developed various structural representation schemes for monolayer protected clusters including systematic positional identification scheme for ligand protected metal nanoclusters.

Thermodynamics of intercluster Reactions of monolayer protected noble metal clusters.

Computed the DFT energies of gold and silver subsituents in different positional isomers of Ag44(SR)30 and Au25(SR)18 nanomolecules.

Structure of supramolecular cluster heterodimer (Ag25-Au25) was found by global minimum obtained from a combination of molecular docking (Force field and Density functional theory methods. The energetics of the exchange reaction were computed.

Structure of supramolecular adducts of monolayers (gold nanoclusters-cyclodextrin, fullerene-silver nanoclusters), cluster assemblies. The structures of isomers of CFn (cluster fullerene adducts) were computed using DFT and Collision cross section calculations using the Projection approximation method.

Structure of curcumin keto tautomer identified by a combination of conformer search, DFT and Trajectory CCS calculations including estimating for the bending angle of the keto tautomer, which has not yet been crystallized.

Photoinduced effects in chalocogenide glasses - Created realistic models of amorphous arsenic sulfide as evidenced by the number and type of coordination defects and homopolar bonds, molecular fragments present in the models and studied their structural, electronic and vibrational properties.

Atomic vibrations in disordered materials- Found a model for the origin of the boson peak in atomic vibrations.

Primary Affiliation: Indian Institute of Technology, Chennai - Chennai, Tamil Nadu , India


Additional Specialties:

Research Interests:

View Dr Ganapati Natarajan’s Resume / CV


Mar 2003 - Feb 2011
Deparment of Chemistry, University of Cambridge
Ph. D Chemistry
Amorphous materials group, Thesis title: Computational studies of amorphous arsenic sulphide
Oct 1997 - Jul 2000
University of Cambridge Trinity College
M. Sci. Natural Sciences (Physics)
Theoretical physic/condensed matter physics options
Oct 1997 - Jun 1999
Trinity College
B. A (Hons) Natural Sciences (Experimental and Theoretical Physics)


Apr 2012 - Mar 2012
DST Unit on Nanoscience, Deparment of Chemistry, Indian Institute of Technology Madras
Project Officer (Post-Doctoral Research Associate)
Noble metal Nanoclusters, Supramolecular molecular cluster adducts, intercluster reactions, curcumin, ice
Jan 2012 - Feb 2012
Jawaharlal Nehru Centre for Advanced Scientific Research
Research Associate
Theoretical Sciences Unit
Jul 2011 - Nov 2011
SN Bose National Centre for Basic Sciences
Research Associate
Atomic Materials Research Unit
Jun 1999 - Sep 1999
University of Cambridge Department of Chemistry
Summer Research Associate
Apr 2012
Indian Institute of Technology Madras
Project Officer (Post-Doctoral Research Associate)
Chemistry, DST Unit on Nanoscience




431Profile Views

381PubMed Central Citations

Thirty-Fold Photoluminescence Enhancement Induced by Secondary Ligands in Monolayer Protected Silver Clusters




In this paper, we demonstrate that systematic replacement of secondary ligand, PPh3 leads to enhancement in the nearinfrared (NIR) photoluminescence (PL) of [Ag29(BDT)12(PPh3)4]3-. While replacement of PPh3 with other monophosphines enhances luminescence slightly, replacement with diphosphines of increasing chain length leads to drastic PL enhancement, as high as 30 times than the parent cluster, [Ag29(BDT)12(PPh3)4]3-. Computational modelling suggests that the emission is a ligand to metal charge transfer (LMCT) which is affected by the nature of the secondary ligand. Control experiments with systematic replacement of secondary ligand confirm the influence of it in the emission. The excited state dynamics shows this emission to be phosphorescence in nature which arises from the triplet excited state. This enhanced luminescence has been used to develop a prototypical O2 sensor. Moreover, a similar enhancement is also found for [Ag51(BDT)19(PPh3)3]3-. The work presents an easy approach to the PL enhancement of Ag clusters for various applications.

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February 2019

Rapid isotopic exchange in nanoparticles.

Sci Adv 2019 Jan 4;5(1):eaau7555. Epub 2019 Jan 4.

DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India.

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http://dx.doi.org/10.1126/sciadv.aau7555DOI Listing
January 2019
6 Reads

Isomerism in Supramolecular Adducts of Atomically Precise Nanoparticles

J. Am. Chem. Soc. 2018, 140 (42), 13590–13593

J. Am. Chem. Soc.

to be added.

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November 2018

Atomically Precise Nanocluster Assemblies Encapsulating Plasmonic Gold Nanorods.

Angewandte Chemie International Edition 2018, 57 (22), 6522–6526.

Angewandte Chemie International Edition

To be added. 

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June 2018

Interparticle reactions: An emerging direction in nanomaterials chemistry

Acc. Chem. Res. 2017, 50 (8), 1988–1996

Accounts of chemical research


Nanoparticles exhibit a rich variety in terms of structure, composition, and properties. However, reactions between them remain largely unexplored. In this Account, we discuss an emerging aspect of nanomaterials chemistry, namely, interparticle reactions in solution phase, similar to reactions between molecules, involving atomically precise noble metal clusters. A brief historical account of the developments, starting from the bare, gas phase clusters, which led to the synthesis of atomically precise monolayer protected clusters in solution, is presented first. Then a reaction between two thiolate-protected, atomically precise noble metal clusters, [Au25(PET)18] and [Ag44(FTP)30]4– (PET = 2-phenylethanethiol, FTP = 4-fluorothiophenol), is presented wherein these clusters spontaneously exchange metal atoms, ligands, and metal–ligand fragments between them under ambient conditions. The number of exchanged species could be controlled by varying the initial compositions of the reactant clusters. Next, a reaction of [Au25(PET)18] with its structural analogue [Ag25(DMBT)18] (DMBT = 2,4-dimethylbenzenethiol) is presented, which shows that atom-exchange reactions happen with structures conserved. We detected a transient dianionic adduct, [Ag25Au25(DMBT)18(PET)18]2–, formed between the two clusters indicating that this adduct could be a possible intermediate of the reaction. A reaction involving a dithiolate-protected cluster, [Ag29(BDT)12]3– (BDT = 1,3-benzenedithiol), is also presented wherein metal atom exchange alone occurs, but with no ligand and fragment exchanges. These examples demonstrate that the nature of the metal–thiolate interface, that is, its bonding network and dynamics, play crucial roles in dictating the type of exchange processes and overall rates. We also discuss a recently proposed structural model of these clusters, namely, the Borromean ring model, to understand the dynamics of the metal–ligand interfaces and to address the site specificity and selectivity in these reactions.

In the subsequent sections, reactions involving atomically precise noble metal clusters and one- and two-dimensional nanosystems are presented. We show that highly protected, stable clusters such as [Au25(PET)18] undergo chemical transformation on graphenic surfaces to form a bigger cluster, Au135(PET)57. Finally, we present the transformation of tellurium nanowires (Te NWs) to Ag–Te–Ag dumbbell nanostructures through a reaction with an atomically precise silver cluster, Ag32(SG)19 (SG = glutathione thiolate).

The starting materials and the products were characterized using high resolution electrospray ionization mass spectrometry, matrix assisted laser desorption ionization mass spectrometry, UV/vis absorption, luminescence spectroscopies, etc. We have analyzed principally mass spectrometric data to understand these reactions.

In summary, we present the emergence of a new branch of chemistry involving the reactions of atomically precise cluster systems, which are prototypical nanoparticles. We demonstrate that such interparticle chemistry is not limited to metal clusters; it occurs across zero-, one-, and two-dimensional nanosystems leading to specific transformations. We conclude this Account with a discussion of the limitations in understanding of these reactions and future directions in this area of nanomaterials chemistry.

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July 2017

17 Citations

Impact Factor 20.955

2 Reads

Au 22 Ir 3 (PET) 18 : An Unusual Alloy Cluster through Intercluster Reaction

J. Phys. Chem. C., 8 (13), 2787–2793.

The Journal of Physical Chemistry Letters 2017

To be added

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June 2017
1 Read

Structure–Reactivity Correlations in Metal Atom Substitutions of Monolayer-Protected Noble Metal Alloy Clusters.

J. Phys. Chem. C 2017, 121 (41), 23224–23232.

The Journal of Physical Chemistry C

To be added. 

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June 2017

Structure-conserving spontaneous transformations between nanoparticles

Nat. Commun. 2016, 7, 13447

al Nature communications

Ambient, structure- and topology-preserving chemical reactions between two archetypal nanoparticles, Ag25(SR)18 and Au25(SR)18, are presented. Despite their geometric robustness and electronic stability, reactions between them in solution produce alloys, AgmAun(SR)18 (m+n=25), keeping their M25(SR)18 composition, structure and topology intact. We demonstrate that a mixture of Ag25(SR)18 and Au25(SR)18 can be transformed to any arbitrary alloy composition, AgmAun(SR)18 (n=1–24), merely by controlling the reactant compositions. We capture one of the earliest events of the process, namely the formation of the dianionic adduct, (Ag25Au25(SR)36)2−, by electrospray ionization mass spectrometry. Molecular docking simulations and density functional theory (DFT) calculations also suggest that metal atom exchanges occur through the formation of an adduct between the two clusters. DFT calculations further confirm that metal atom exchanges are thermodynamically feasible. Such isomorphous transformations between nanoparticles imply that microscopic pieces of matter can be transformed completely to chemically different entities, preserving their structures, at least in the nanometric regime.

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November 2016

27 Citations

Impact Factor 13.691

[Au 25 (SR) 18 ] 2 2− : A Noble Metal Cluster Dimer in the Gas Phase.

Chemical Communications 2016, 52 (54), 8397–8400.

Chemical Communications

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August 2016

Intercluster Reactions between Au25(SR)18 and Ag44(SR)30

J. Am. Chem. Soc., 2016, 138 (1), 140–148

Journal of the American Chemical Society

We present the first example of intercluster reactions between atomically precise, monolayer protected noble metal clusters using Au25(SR)18 and Ag44(SR)30 (RS– = alkyl/aryl thiolate) as model compounds. These clusters undergo spontaneous reaction in solution at ambient conditions. Mass spectrometric measurements both by electrospray ionization and matrix assisted laser desorption ionization show that the reaction occurs through the exchange of metal atoms and protecting ligands of the clusters. Intercluster alloying is demonstrated to be a much more facile method for heteroatom doping into Au25(SR)18, as observed by doping up to 20 Ag atoms. We investigated the thermodynamic feasibility of the reaction using DFT calculations and a tentative mechanism has been presented. Metal core-thiolate interfaces in these clusters play a crucial role in inducing these reactions and also affect rates of these reactions. We hope that our work will help accelerate activities in this area to establish chemistry of monolayer protected clusters.

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December 2015

49 Citations

Impact Factor 14.357

1 Read

A unified framework for understanding the structure and modifications of atomically precise monolayer protected gold clusters

J. Phys. Chem. C 2015, 119 (49), 27768–27785

The Journal of Physical Chemistry C

Atomically precise monolayer protected clusters are molecules comprising a few-atom cluster core of a noble metal, typically Au or Ag, surrounded by a protective layer of ligands, exhibiting many special optical, electrical, catalytic, and magnetic properties, and are emerging as important materials in biology, medicine, catalysis, energy conversion and storage, and sensing. The structural diversity of these clusters or aspicules, as we definitively term them, meaning shielded molecules, combining the Greek word aspis (shield) with molecule, is rapidly increasing due to new compositions and modification routes such as ligand-exchange, alloying, or supramolecular functionalization. We present a structural analysis of the most stable cluster of this kind, Au25(SR)18, and propose a Borromean rings diagram for the cluster, showing its topological configuration of three interlocked (Au8S6)-rings. This simplified two-dimensional diagram is used to represent its structure and modifications via ligand or metal atom substitution uniquely. We enumerate and name its isomers with two-ligand or metal atom substituents. Among the several structural insights obtained, the identification of the Borromean rings-interlocked configuration in Au25(SR)18 may explain its high geometric stability and indicate a possible general unified structural viewpoint for these clusters without the division between core and staple motifs. On the basis of our structural analysis, we developed a structure-based nomenclature system that can be applied to both describe and understand the structure and modifications of gold thiolate clusters, AuM(SR)N, and is adaptable to the general case of MM(X)N (M, metal and X, ligand). The application of structural analysis and diagrams to Au38(SR)24 and Au102(SR)44, revealing the possible formation of the cluster core by stacking or growth of rings of metal atoms, is also presented.

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November 2015

28 Citations

Impact Factor 4.484

Probing Molecular Solids with Low-Energy Ions

Annual Review of Analytical Chemistry

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June 2013

5 Citations

1 Read

New Type of Charged Defect in Amorphous Chalcogenides.

Physical Review Letters 2005, 94 (8)

Physical Review Letters

To be added here. 

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June 2005

Origin of the Boson Peak in Systems with Lattice Disorder

Phys. Rev. Lett. 2001, 86 (7), 1255–1258

Physical Review Letters

The origin of the boson peak in models with force-constant disorder has been established by calculations using the coherent potential approximation. The analytical results obtained are supported by precise numerical solutions. The boson peak in the disordered system is associated with the lowest van Hove singularity in the spectrum of the reference crystalline system, pushed down in frequency by disorder-induced level-repelling and hybridization effects.

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February 2001

238 Citations

Impact Factor 8.839

Camouflaging Structural Diversity: Co-crystallization of Two Different Nanoparticles Having Different Cores But the Same Shell

Angewandte Chemie International Edition

Two ligand-protected nanoscale silver moieties, [Ag46(SPhMe2)24(PPh3)8](NO3)2 and [Ag40(SPhMe2)24(PPh3)8](NO3)2 (abbreviated as Ag46 and Ag40, respectively) with almost the same shell but different cores were synthesized simultaneously. As their external structures are identical, the clusters were not distinguishable and become co-crystallized. The occupancy of each cluster was 50 %. The outer shell of both is composed of Ag32S24P8, which is reminiscent of fullerenes, and it encapsulates a well-studied core, Ag14 and a completely new core, Ag8, which correspond to a facecentered cube and a simple cube, respectively, resulting in the Ag46 and Ag40 clusters. The presence of two entities (Ag40 and Ag46 clusters) in a single crystal and their molecular formulae were confirmed by detailed electrospray ionization mass spectrometry. The optical spectrum of the mixture showed unique features which were in good agreement with the results from time-dependent density functional theory (TD-DFT).


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November -0001

Top co-authors

Thalappil Pradeep
Thalappil Pradeep

Indian Institute of Technology - Madras

Manoj Kumar Panwar
Manoj Kumar Panwar

Indian Institute of Technology Madras

Ganesan Paramasivam
Ganesan Paramasivam

Indian Institute of Technology Madras

Abhijit Nag
Abhijit Nag

University of Glasgow

Papri Chakraborty
Papri Chakraborty

Indian Institute of Technology Madras