Professional Education

  • Doctor of Philosophy, Tata Institute of Fundamental Research, Mumbai, India, Chemistry (2014)
  • Master of Science, Indian Institute of Technology, Roorkee, India, Chemistry (2008)
  • Bachelor of Science, University of Calcutta, Kolkata, India, Chemistry Honours (2006)

Stanford Advisors

Current Research and Scholarly Interests

Research Area 1:
Diagnosis of Cancer by Metabolic Signatures Using Desorption Electrospray Ionization Mass Spectrometric Imaging

The important hallmark feature of tumorigenesis is the global shift in metabolism imparted by the malfunctioning of oncogenes. Oncogenes are known to regulate the key genes involved in the lipid metabolism. This phenomenon suggests that in situ analyses of cancerous cell/tissue metabolites (lipids) could reveal potential biomarkers or molecular targets to detect, diagnose and prognosticate cancer. Thus, the ability to easily record the metabolic signature of biopsy specimens (within minutes of biopsy) would eventually develop a rapid, quantitative and accurate pathology method for early detection and diagnosis of clinically relevant diseases including cancer.
Recently, an innovative form of an ambient mass spectrometry (highly sensitive analytical approach) called desorption electrospray ionization mass spectrometry (DESI-MS) has been developed to provide the microscopic examination of cancer metabolism in tissues. DESI-MS has been demonstrated to construct ion images for the visualization (distribution) of molecules/metabolites on the histological section. It appears from the our preliminary studies that imaging the spatial distribution of different phospholipids and cholesterol sulfates in different organs (lipid profiles in tissues) have significance in disease diagnosis including provision of information on tumor margins to guide doctors during surgical removal of the corresponding tumor.

Research Area 2:
Microdroplet Chemistry: From Conducting Chemical Transformation to Probing the Reaction Mechanism

The charged microdroplets, generated by the electrospray (ES) process, have been shown to ionize intact chemical species followed by their transfer to the gas phase. This ionization technique is now being routinely used as a standard soft-ionization process for different molecules including proteins, lipids, carbohydrates, and other small organic or organometallic compounds for their mass spectrometric analysis. In last two decades, several groups have extensively worked to understand the nature of the ES droplet and the mechanism that leads to the production of gas-phase ions on the millisecond timescale. Taking the advantage of special charged environments of ES droplets, and the short timescale (ms) of their evolution, we are transcending the traditional applications of electrospray process from mass spectrometry to synthetic and mechanistic organic chemistry. There are several reactions, which are hard to achieve in conventional bulk-phase, and those too take long time (e.g., from hours to days) to yield significant amount of products. Our preliminary studies on such model reactions in microdroplets show the potential application of the ES process to induce acid/base catalyzed organic transformation on the millisecond timescale in limited and confined spaces (microdroplets) under charged environments. We found marked acceleration of those reaction rates even by a factor of a million when carried out in microdroplets. The mechanism is not presently established but droplet evaporation and droplet confinement of reagents appear to be two important factors among others. We suggest that this ‘microdroplet chemistry’ could be a remarkable alternative to accelerate slow and difficult reactions, and in conjunction with mass spectrometry, it may provide a new arena to study chemical and biochemical reactions in a confined environment. This ‘microdroplet chemistry’ is still in its infancy and heightens our interests to apply this method to organic syntheses on the preparative scale.
Our studies also underscored the impressive capabilities of the ‘microdroplet chemistry’ to capture transient intermediates in solution-phase catalytic cycles of complex reactions to investigate the reaction mechanism.

All Publications

  • Potassium tert-Butoxide-Catalyzed Dehydrogenative C-H Silylation of Heteroaromatics: A Combined Experimental and Computational Mechanistic Study. Journal of the American Chemical Society Liu, W., Schuman, D. P., Yang, Y., Toutov, A. A., Liang, Y., Klare, H. F., Nesnas, N., Oestreich, M., Blackmond, D. G., Virgil, S. C., Banerjee, S., Zare, R. N., Grubbs, R. H., Houk, K. N., Stoltz, B. M. 2017; 139 (20): 6867-6879


    We recently reported a new method for the direct dehydrogenative C-H silylation of heteroaromatics utilizing Earth-abundant potassium tert-butoxide. Herein we report a systematic experimental and computational mechanistic investigation of this transformation. Our experimental results are consistent with a radical chain mechanism. A trialkylsilyl radical may be initially generated by homolytic cleavage of a weakened Si-H bond of a hypercoordinated silicon species as detected by IR, or by traces of oxygen which can generate a reactive peroxide by reaction with [KOt-Bu]4 as indicated by density functional theory (DFT) calculations. Radical clock and kinetic isotope experiments support a mechanism in which the C-Si bond is formed through silyl radical addition to the heterocycle followed by subsequent β-hydrogen scission. DFT calculations reveal a reasonable energy profile for a radical mechanism and support the experimentally observed regioselectivity. The silylation reaction is shown to be reversible, with an equilibrium favoring products due to the generation of H2 gas. In situ NMR experiments with deuterated substrates show that H2 is formed by a cross-dehydrogenative mechanism. The stereochemical course at the silicon center was investigated utilizing a (2)H-labeled silolane probe; complete scrambling at the silicon center was observed, consistent with a number of possible radical intermediates or hypercoordinate silicates.

    View details for DOI 10.1021/jacs.6b13031

    View details for PubMedID 28403611

  • Ionic and Neutral Mechanisms for C-H Bond Silylation of Aromatic Heterocycles Catalyzed by Potassium tert-Butoxide. Journal of the American Chemical Society Banerjee, S., Yang, Y., Jenkins, I. D., Liang, Y., Toutov, A. A., Liu, W., Schuman, D. P., Grubbs, R. H., Stoltz, B. M., Krenske, E. H., Houk, K. N., Zare, R. N. 2017; 139 (20): 6880-6887


    Exploiting C-H bond activation is difficult, although some success has been achieved using precious metal catalysts. Recently, it was reported that C-H bonds in aromatic heterocycles were converted to C-Si bonds by reaction with hydrosilanes under the catalytic action of potassium tert-butoxide alone. The use of Earth-abundant potassium cation as a catalyst for C-H bond functionalization seems to be without precedent, and no mechanism for the process was established. Using ambient ionization mass spectrometry, we are able to identify crucial ionic intermediates present during the C-H silylation reaction. We propose a plausible catalytic cycle, which involves a pentacoordinate silicon intermediate consisting of silane reagent, substrate, and the tert-butoxide catalyst. Heterolysis of the Si-H bond, deprotonation of the heteroarene, addition of the heteroarene carbanion to the silyl ether, and dissociation of tert-butoxide from silicon lead to the silylated heteroarene product. The steps of the silylation mechanism may follow either an ionic route involving K(+) and (t)BuO(-) ions or a neutral heterolytic route involving the [KO(t)Bu]4 tetramer. Both mechanisms are consistent with the ionic intermediates detected experimentally. We also present reasons why KO(t)Bu is an active catalyst whereas sodium tert-butoxide and lithium tert-butoxide are not, and we explain the relative reactivities of different (hetero)arenes in the silylation reaction. The unique role of KO(t)Bu is traced, in part, to the stabilization of crucial intermediates through cation-π interactions.

    View details for DOI 10.1021/jacs.6b13032

    View details for PubMedID 28462580

  • Can all bulk-phase reactions be accelerated in microdroplets? ANALYST Banerjee, S., Gnanamani, E., Yan, X., Zare, R. N. 2017; 142 (9): 1399-1402


    Recent studies have shown that microdroplet reactions are markedly accelerated compared to the corresponding bulk-phase reactions. This raises the question whether all reactions can be sped up by this means. We present a counter example, and we show that the reaction mechanism in microdroplets can differ sharply from that in bulk, especially because of the distinct microdroplet surface environment. This analysis helps to guide us how to choose and control reactions in microdroplets and provides a possible perspective on utilizing microdroplet chemistry to scale up synthesis.

    View details for DOI 10.1039/c6an02225a

    View details for Web of Science ID 000400688500001

    View details for PubMedID 28332662

  • Diagnosis of prostate cancer by desorption electrospray ionization mass spectrometric imaging of small metabolites and lipids Proceedings of the National Academy of Sciences Banerjee, S., Zare, R. N., Tibshirani, R. J., Kunder, C. A., Nolley, R., Fan, R., Brooks, J. D., Sonn, G. A. 2017; 114 (13): 3334-3339

    View details for DOI 10.1073/pnas.1700677114

  • A Study of Heterogeneous Catalysis by Nanoparticle-Embedded Paper-Spray Ionization Mass Spectrometry. Angewandte Chemie (International ed. in English) Banerjee, S., Basheer, C., Zare, R. N. 2016; 55 (41): 12807-12811


    We have developed nanoparticle-embedded paper-spray mass spectrometry for studying three types of heterogeneously catalyzed reactions: 1) Palladium-nanoparticle-catalyzed Suzuki cross-coupling reactions, 2) palladium- or silver-nanoparticle-catalyzed 4-nitrophenol reduction, and 3) gold-nanoparticle-catalyzed glucose oxidation. These reactions were almost instantaneous on the nanocatalyst-embedded paper, which subsequently transferred the transient intermediates and products to a mass spectrometer for their detection. This in situ method of capturing transient intermediates and products from heterogeneous catalysis is highly promising for investigating the mechanism of catalysis and rapidly screening catalytic activity under ambient conditions.

    View details for DOI 10.1002/anie.201607204

    View details for PubMedID 27633445

  • Acceleration of reaction in charged microdroplets QUARTERLY REVIEWS OF BIOPHYSICS Lee, J. K., Banerjee, S., Nam, H. G., Zare, R. N. 2015; 48 (4): 437-444


    Using high-resolution mass spectrometry, we have studied the synthesis of isoquinoline in a charged electrospray droplet and the complexation between cytochrome c and maltose in a fused droplet to investigate the feasibility of droplets to drive reactions (both covalent and noncovalent interactions) at a faster rate than that observed in conventional bulk solution. In both the cases we found marked acceleration of reaction, by a factor of a million or more in the former and a factor of a thousand or more in the latter. We believe that carrying out reactions in microdroplets (about 1-15 μm in diameter corresponding to 0·5 pl - 2 nl) is a general method for increasing reaction rates. The mechanism is not presently established but droplet evaporation and droplet confinement of reagents appear to be two important factors among others. In the case of fused water droplets, evaporation has been shown to be almost negligible during the flight time from where droplet fusion occurs and the droplets enter the heated capillary inlet of the mass spectrometer. This suggests that (1) evaporation is not responsible for the acceleration process in aqueous droplet fusion and (2) the droplet-air interface may play a significant role in accelerating the reaction. We argue that this 'microdroplet chemistry' could be a remarkable alternative to accelerate slow and difficult reactions, and in conjunction with mass spectrometry, it may provide a new arena to study chemical and biochemical reactions in a confined environment.

    View details for DOI 10.1017/S0033583515000086

    View details for Web of Science ID 000364764300008

    View details for PubMedID 26537403

  • Role of substituents on the reactivity and product selectivity in reactions of naphthalene derivatives catalyzed by the orphan thermostable cytochrome P450, CYP175A1 BIOORGANIC CHEMISTRY Banerjee, S., Goyal, S., Mazumdar, S. 2015; 62: 94-105


    The thermostable nature of CYP175A1 enzyme is of potential interest for the biocatalysis at ambient temperature or at elevated temperature under environmentally benign conditions. Although little is known about the substrate selectivity of this enzyme, the biocatalytic activities of CYP175A1 on different substituted naphthalenes have been studied in oxidative pathway, and the effect of the substituent on the reaction has been determined. The enzyme first acts as a peroxygenase to convert these substituted naphthalenes to the corresponding naphthols, which subsequently undergo in-situ oxidative dimerization to form dyes of different colors possibly by the peroxidase-type activity of CYP175A1. The product analyses and kinetic measurements suggested that the presence of electron releasing substituent (ERS) in the substrate enhanced the substrate conversion, whereas the presence of electron withdrawing substituent (EWS) in the substrate drastically reduced the substrate conversion. The position of the ERS in the substrate was also found to play an important role in the transformation of the substrate. The results further demonstrate that mutation of the Leu80 residue to Phe enhances the reactivity of the enzyme by favoring the substrate association in the active site. The observed rates of the enzymatic oxygenation reaction of the substituted naphthalenes followed the Hammett correlation of substituent effect, supporting aromatic electrophilic substitution mechanism catalyzed by the cytochrome P450 enzyme.

    View details for DOI 10.1016/j.bioorg.2015.08.003

    View details for Web of Science ID 000361012600010

    View details for PubMedID 26312734

  • Regioselective Oxygenation of Polyunsaturated Fatty Acids by the Thermostable P450 from Thermus thermophilus HB27 Current Biotechnology Banerjee, S., Datta Gupta, D., Mazumdar, S. 2015; 4 (3): 345-356
  • Syntheses of Isoquinoline and Substituted Quinolines in Charged Microdroplets Angew. Chem. Int. Ed. Banerjee, S., Zare, R. N. 2015; 54

    View details for DOI 10.1002/anie.201507805

  • Diagnosis of Cancer by Metabolic Signatures Using Mass Spectrometric Imaging Cutting Edge Banerjee, S. 2014
  • Induction of protein conformational change inside the charged electrospray droplet JOURNAL OF MASS SPECTROMETRY Banerjee, S. 2013; 48 (2): 193-204


    The behavior of the analyte molecules inside the neutral core of the charged electrospray (ES) droplet is not unambiguously known to date. The possibility of protein conformational change inside the charged ES droplet has been investigated. The ES droplets encapsulating the protein molecules were exposed to the acetic acid vapor in the ionization chamber to absorb the acetic acid vapor. Because of the faster evaporation of water than that of acetic acid, the droplets became enriched with acetic acid and thus altered the solvent environment (e.g. pH and polarity) of the final charged droplets from where the naked charged analytes (proteins) are formed. Thus, the perturbation of the ES droplet solvent environment resulted in the protein conformational change (unfolding) during the short lifespan of the ES droplet and that is reflected by the multimodal charge state distribution in the corresponding mass spectra. Further, the extent of this conformational change inside the ES droplet was found to be related to the structural flexibility of the protein. Although the protein conformational change inside the ES droplet has been driven by using acetic acid vapor in the present study, the results would help in the near future to understand the spontaneity of the conformational change of the analyte on the millisecond timescale of phase transition in the natural way of ES process.

    View details for DOI 10.1002/jms.3148

    View details for Web of Science ID 000314478300009

    View details for PubMedID 23378092

  • Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY Banerjee, S., Mazumdar, S. 2012; 23 (11): 1967-1980


    The gas-phase peptide ion fragmentation chemistry is always the center of attraction in proteomics to analyze the amino acid sequence of peptides and proteins. In this work, we describe the formation of an anomalous fragment ion, which corresponds to the selective deletion of the internal lysine residue from a series of lysine containing peptides upon collisional activation in the ion trap. We detected several water-loss fragment ions and the maximum number of water molecules lost from a particular fragment ion was equal to the number of lysine residues in that fragment. As a consequence of this water-loss phenomenon, internal lysine residues were found to be deleted from the peptide ion. The N,N-dimethylation of all the amine functional groups of the peptide stopped the internal lysine deletion reaction, but selective N-terminal α-amino acetylation had no effect on this process indicating involvement of the side chains of the lysine residues. The detailed mechanism of the lysine deletion was investigated by multistage CID of the modified and unmodified peptides, by isotope labeling and by energy resolved CID studies. The results suggest that the lysine deletion might occur through a unimolecular multistep mechanism involving a seven-membered cyclic imine intermediate formed by the loss of water from a lysine residue in the protonated peptide. This intermediate subsequently undergoes degradation reaction to deplete the interior imine ring from the peptide backbone leading to the deletion of an internal lysine residue.

    View details for DOI 10.1007/s13361-012-0456-1

    View details for Web of Science ID 000309941700015

    View details for PubMedID 22923014

  • Oxygenation of Monoenoic Fatty Acids by CYP175A1, an Orphan Cytochrome P450 from Thermus thermophilus HB27 BIOCHEMISTRY Goyal, S., Banerjee, S., Mazumdar, S. 2012; 51 (40): 7880-7890


    The catalytic activity of CYP175A1 toward monooxygenation of saturated and monounsaturated fatty acids of various chain lengths (C16-C24) has been investigated to assess the enzymatic properties of this orphan thermostable cytochrome P450 enzyme. The results showed that the enzyme could catalyze the reaction of monounsaturated fatty acids but not of saturated fatty acids. The product analyses using ESI-MS and GC-MS revealed an important regioselectivity in the CYP175A1 catalyzed monooxygenation of the monoenoic fatty acids depending on the ethylenic double bond (C═C) configuration. When the double bond was in cis-configuration, an epoxy fatty acid was found to be the major product and two allyl-hydroxy fatty acids were found to be the minor products. But when the double bond was in trans-configuration the product distribution was reversed. The oxygenation efficiency was found to be the highest for palmitoleic acid (chain length C16), but there was no direct correlation of the activity with the chain length or the position of unsaturation of the fatty acid. Molecular docking calculations showed that the "U"-type conformations of the monoenoic fatty acids are particularly responsible for their binding in the enzyme pocket, and that is also consistent with the observed regioselectivity in the oxygenation reaction. The present results provide evidence that CYP175A1 can catalyze the regioselective oxygenation reaction of several monoenoic fatty acids though it cannot catalyze the oxygenation of the corresponding saturated analogues. These studies may provide critical information on the nature of the enzyme pocket and of the possible natural substrate of this orphan enzyme.

    View details for DOI 10.1021/bi300514j

    View details for Web of Science ID 000309505300008

    View details for PubMedID 22938723

  • Synthesis, photophysical, electrochemical and thermal studies on carbazole-based acceptor molecules for heterojunction solar cell THIN SOLID FILMS Banerjee, S., Ali, F., Nayak, P. K., Agarwal, N. 2012; 520 (7): 2644-2650
  • Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte. International journal of analytical chemistry Banerjee, S., Mazumdar, S. 2012; 2012: 282574-?


    The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research.

    View details for DOI 10.1155/2012/282574

    View details for PubMedID 22611397

  • Evidence of Molecular Fragmentation inside the Charged Droplets Produced by Electrospray Process JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY Banerjee, S., Prakash, H., Mazumdar, S. 2011; 22 (10): 1707-1717


    The behavior of the analyte molecules inside the neutral core of the charged droplet produced by the electrospray (ES) process is not unambiguously known to date. We have identified interesting molecular transformations of two suitably chosen analytes inside the ES droplets. The highly stable Ni(II) complex of 1,8-dimethyl-1,3,6,8,10,13-hexaazacyclotetradecane (1) that consists of a positive charge at the metal center, and the allyl pendant armed tertiary amine containing macrocycle 3,4,5:12,13,14-dipyridine-2,6,11,15-tetramethyl-1,7,10,16-tetraallyl-1,4,7,10,13,16-hexaazacyclooctadeca-3,13-diene (M(4p)) have been studied by ESI mass spectrometry as the model analytes. We have shown that these two molecules are not representatively transferred from solution to gas phase by ESI; rather, they undergo fragmentation inside the charged droplets. The results indicated that a charged analyte such as 1 was possibly unstable inside the neutral core of the ES droplet and undergoes fragmentation due to the Coulombic repulsion imparted by the surface protons. Brownian motion of the neutral analyte such as M(4p) inside the droplet, on the other hand, may lead to proton attachment on interaction with the charged surface causing destabilization that leads to fragmentation of M(4p) and release of resonance stabilized allyl cations from the core of the droplet. Detailed solvent dependence and collision-induced dissociation (CID) studies provided compelling evidences that the fragmentation of the analytes indeed occurs inside the charged ES droplets. A viable model of molecular transformations inside the ES droplet was proposed based on these results to rationalize the behavior of the analyte molecules inside the charged ES droplets.

    View details for DOI 10.1007/s13361-011-0188-7

    View details for Web of Science ID 000295088400004

    View details for PubMedID 21952884

  • Non-covalent dimers of the lysine containing protonated peptide ions in gaseous state: electrospray ionization mass spectrometric study JOURNAL OF MASS SPECTROMETRY Banerjee, S., Mazumdar, S. 2010; 45 (10): 1212-1219


    Study of the non-covalent molecular complexes in gas phase by electrospray ionization mass spectrometry (ESI-MS) represents a promising strategy to probe the intrinsic nature of these complexes. ESI-MS investigation of a series of synthetic octapeptides containing six alanine and two lysine residues differing only by their positions showed the formation of non-covalent dimers, which were preserved in the gas phase. Unlike the monomers, the dimers were found to show only singly protonated state. The decrease in the solvent polarity from water to alcohol showed enhanced propensity of formation of the dimer indicating that the electrostatic interaction plays a crucial role to stabilize the dimer. Selective functionalization studies showed that ε-NH(2) of lysine and C-terminal amide (-CONH(2)) facilitate the dimerization through intermolecular hydrogen bonding network.

    View details for DOI 10.1002/jms.1817

    View details for Web of Science ID 000283610200015

    View details for PubMedID 20872902

  • Development of electrochemical sensors for nano scale Tb(III) ion determination based on pendant macrocyclic ligands ANALYTICA CHIMICA ACTA Singh, A. K., Singh, P., Banerjee, S., Mehtab, S. 2009; 633 (1): 109-118


    The two macrocyclic pendant ligands 3,4,5:12,13,14-dipyridine-2,6,11,15-tetramethyl-1,7,10,16-tetramethylacrylate-1,4,7,10,13,16-hexaazacyclooctadeca-3,13-di ene (L(1)) and 3,4,5:12,13,14-dipyridine-2,6,11,15-tetramethyl-1,7,10,16-tetra(2-cyano ethane)-1,4,7,10,13,16-hexaazacyclooctadeca-3,13-diene (L(2)) have been synthesized and explored as neutral ionophores for preparing poly(vinylchloride) (PVC) based membrane sensors selective to Tb(III) ions. Effects of various plasticizers and anion excluders were studied in detail and improved performance was observed. The best performance was obtained for the membrane sensor having a composition of L(1): PVC:1-CN:NaTPB in the ratio of 6: 32: 58: 4 (w/w; mg). The performance of the membrane based on L(1) was compared with polymeric membrane electrode (PME) as well as with coated graphite electrode (CGE). The electrodes exhibit Nernstian slope for Tb(3+) ions with limits of detection of 3.4 x 10(-8)mol L(-1) for PME and 5.7 x 10(-9)mol L(-1) for CGE. The response time for PME and CGE was found to be 10s and 8s, respectively. The potentiometric responses are independent of the pH of the test solution in the pH range 3.0-7.5 for PME and 2.0-8.5 for CGE. The CGE has found to work satisfactorily in partially non-aqueous media upto 30% (v/v) content of methanol, ethanol and 20% (v/v) content of acetonitrile and could be used for a period of 5 months. The CGE was used as indicator electrode in the potentiometric titration of Tb(3+) ions with EDTA and in determination of fluoride ions in various samples. It can also be used in direct determination of Tb(3+) ions in tap water and various binary mixtures with quantitative results.

    View details for DOI 10.1016/j.aca.2008.11.029

    View details for Web of Science ID 000262734700015

    View details for PubMedID 19110124