Research Topics

Optical spectroscopy relies on the interaction of light with matter to analyze, interpret and predict various materials. The phenomenon of light scattering (be it absorption, emission etc.) relates to the changes in the molecular/atomistic properties of the material in question. Vibrational spectroscopy, as the name suggests, measures the vibrational motions of molecular bonds in question and is thus chemically sensitive. Prabuddha has implemented various forms of infrared spectroscopy: linear FTIR to Raman to highly complicated multidimensional IR, Sum Frequency Generation (SFG) spectroscopy to a wide range of problems. Some of those areas are briefly presented below.

Diagnostic IR and Raman imaging of cancer cells/tissue and tracking drug delivery


Prabuddha’s current research goal is to understand molecular origins for changes in the micro-environment in the nanoscale using optical spectroscopy. For the growth and manifestation of chronic diseases like cancer these micro-environmental changes contribute immensely and if not detected early often leads to fatality. A precise knowledge of the molecular processes behind cancer and a thorough understanding of its dynamics of proliferation in the tumor environment can help us diagnose faster and engineer better and sustainable applications to prevent their growth.

Nanomaterials, a controlled self-assembly of various building blocks, show enormous promise for diverse medical fields such as diagnostic imaging, therapy and image guided therapies. One of the most attractive properties that has been prominent in preclinical studies, shows the benefits of carbon nanoparticles in reducing drug toxicity and increasing its efficacy.

Tunable luminescent Carbon nanoparticles

Picture2Carbon materials were derived from natural macromolecules with well defined compositions, structures that can be tuned into nanostructures with controlled functional properties. Natively, most carbon nanoparticles (CNPs) emit in the blue green spectral range, but are limited to in-vivo biological use by limited light penetration at these wavelengths and overlap with tissue autofluorescence. Next generation CNPs were engineered in collaboration with the Pan group at UIUC Bioengineering to emit in the near infrared (NIR) region to avoid this interference. This was achieved through a multi-arm polyethylene glycol (MA-PEG) passivating ligand.

Carbon nanoparticles for controlled drug delivery

Controlled and triggered release of therapeutics was realized by loading the drug (Pentoxifylline) on the CNPs within a thermoresponsive polymer ligand PNIPAM. The acidic environment at the tumor sites incite a phase transition in the capped polymers that result with a controlled and sustained release of drugs.

1. Carbon Nanospheres: Tunable Luminescent Carbon Nanospheres with Well-Defined Nanoscale Chemistry for Synchronized Imaging and Therapy,  Small,  05/2015; 11(36). DOI:10.1002/smll.201500728. (Back Cover Feature Article)
Prabuddha Mukherjee · Santosh K. Misra · Mark C. Gryka · Huei‐Huei Chang · Saumya Tiwari · William L. Wilson · John W. Scott ·Rohit Bhargava · Dipanjan Pan

Passivating ligands in CNPs as a Raman probe, cellular internalization and Cancer preventive agents

Picture3Recently Prabuddha and coworkers reported passivating strategies for b-carotene on CNPs to produce colloidal carotene nanoparticles to study their anti-proliferative effect on cancer cells, track their cellular internalization with IR and Raman imaging techniques. This single functional molecule b-carotene serves multiple purposes such as targeting, measuring and regressing cancer cells.

1. Vibrational Spectroscopy and Imaging for Concurrent Cellular Trafficking of Co-localized Doxorubicin and Deuterated Niosomes, Nanoscale,  8(5) January 2016 DOI: 10.1039/C5NR07975F
Santosh K. Misra · Prabuddha Mukherjee · Ayako Ohoka · Aaron Star Schwartz-Duval · Saumya Tiwari · Rohit Bhargava · Dipanjan Pan

2. Regulating Biocompatibility of Carbon Spheres via Defined Nanoscale Chemistry and a Careful Selection of Surface Functionalities, Scientific Reports,  10/2015; 5. DOI:10.1038/srep14986
Santosh K Misra · Huei-Huei Chang · Prabuddha Mukherjee · Saumya Tiwari · Ayako Ohoka · Dipanjan Pan

3. Colloidal Carotene Carbon Nanoparticles for Synchronized Chemical Imaging, Enriched Cellular Uptake and Therapy. (Submitted)
Santosh K Misra · Prabuddha Mukherjee · Huei-Huei Chang · Saumya Tiwari · Mark Gryka · Rohit Bhargava · Dipanjan Pan

4. Defined Host-guest Chemistry on NanoCarbon for Sustained Inhibition of Cancer. (Submitted)
Fatemeh Ostadhossein · Santosh Kumar Misra · Prabuddha Mukherjee · Alireza Ostadhossein · Enrique Daza · Saumya Tiwari · Shachi Mittal · Mark C. Gryka · Rohit Bhargava · Dipanjan Pan

Raman spectroscopy to elucidate internal structure of semiconductor nanoparticles  


proposal1

Heterostructured nanocrystals (H-NCs) are a diverse class of materials in which multiple chemical components are mixed together as alloys, fused composites, or complexly interfaced core/shell particles. The diversity of materials, reaction conditions and temporal evolution in their synthesis is vast, providing the capability to invent novel and continuously tunable optical, electronic, and mechanical properties, as well as multi-functionality in a single nanoparticle. The study, ability to precisely engineer H-NCs for specific properties, and eventual use rests on knowledge of their internal structures. Whereas H-NC size, morphology, and composition are readily determined through standard analytical measurements such as electron microscopy (EM) and energy dispersive X-ray, their internal structures cannot be distinguished with high accuracy.

Brightness of these spherical HNCs is governed by their internal structure, the extent of quantum confinement, band edge absorption energies etc. Band edge absorption properties can be tuned by tweaking the size of these NCs while the nature and extent of quantum confinement can be modified by growing a shell. Here we synthesized a unique series of 42 different quantum dots, composed of two chemical domains (CdS:CdSe), arranged into 8 comprehensive architectures. Chemometric analyses of Raman spectra were used to correlate their vibrational signatures with their internal structures.

1. Spectroscopic Determination of the Internal Structure of Nanocrystals. (Submitted)
Prabuddha Mukherjee · Sung Jun Lim · Tomasz P. Wrobel · Rohit Bhargava · Andrew Smith

Broad Band Sum Frequency Generation (BBSFG) spectroscopy of electrified surfaces


In-situ characterization of solid electrolyte interfaces (SEI)

Solid electrolyte interphases (SEI) play a crucial role for the functioning of rechargeable Lithium ion batteries. It selectively allows Li to intercalate into and diffuse out of the anode during the charging and the discharging process. This improves the battery capacity and facilitates more efficient charge-discharge cycles. SEI is composed of products formed by the reduction of electrolyte (organic carbonates) that adheres to the electrode surface. However, the dynamics of the formation of the SEI is not totally understood. The figure below depicts a simple hypothetical cartoon of the SEI formation on the anode surface where the electrolyte reduction products dimerize and form the passivating layer on the surface.

At the initial stages of SEI formation two interfaces start growing simultaneously as shown in the figure above. The first one is between the electrode and the SEI (Interface 1), the latter amid the electrolyte and the SEI (Interface 2). Existing spectroscopic techniques are inadequate to monitor the formation of these two interfaces simultaneously. Using a polycrystal Au as a model anode a we have reported the first SFG spectra of a SEI. Fundamental understanding of the SEI formation on  more realistic electrodes such as carbon that is used in commercial lithium ion batteries is desired.

1. In Situ Probing of Solid-Electrolyte Interfaces with Nonlinear Coherent Vibrational SpectroscopyJournal of The Electrochemical Society 12/2011; 159(3):A244-A252. DOI:10.1149/2.022203jes,
Prabuddha Mukherjee · Alexei Lagutchev · Dana D Dlott

2. Solid Electrolyte Interfaces and Interphases in Lithium Batteries: In Situ Studies Using Nonlinear Optical Probes, MRS Online Proceeding Library, 01/2012; 1388. DOI:10.1557/opl.2012.7,
Prabuddha Mukherjee · Alexei Lagutchev · Dana D Dlott

Reduction of Carbon dioxide with room temperature ionic liquid (RTIL) catalysts at low overpotentials

CO2projectRoom temperature ionic liquid [EMIM] BF4 is ideally suited for CO2 electroreduction since the necessary CO2 intermediate can be stabilized at the interface of the electrode by complexing with the [EMIM] cation. We have investigated the potentiodynamic behavior of of an interfacial CO2 complex with EMIM cations on polycrystalline catalysts. COstarts to get reduced at around -0.25 V vs SHE which is unprecedented low overpotential for the reaction. We have cycled the potential on Pt electrode between 0.5 V to -1.0 V for 15 times. The figure above shows a series of SFG  spectra at the 1st and the last cycle. CO2 complexes with EMIM at the Pt surface at negative potentials and we observe it at ~2350 cm-1 in both Fig. a and b. At the 15th cycle the CO (band at 2080 cm-1 in fig. b) formed from CO2 reduction almost saturates the electrode.

1. In Situ Spectroscopic Examination of a Low Overpotential Pathway for Carbon Dioxide Conversion to Carbon Monoxide,  The Journal of Physical Chemistry C,  06/2012; 116(26):15307-15312. DOI: 10.1021/jp210542v·
Brian A. Rosen · John L. Haan · Prabuddha Mukherjee · Björn Braunschweig · Weih Zhu · Amin Salehi-Khojin · Dana D. Dlott ·Richard I. Masel

Reaction pathways of Ethanol oxidation on Pt electrode under acidic conditions

Ethanol is cheaply available and can be used as a fuel. A molecule of Ethanol, if copletely oxidised, generates 14 electrons. But seldom do we achieve it. Hence there is an enormous interest in understanding the reaction mechanism of ethanol oxidation. We have used an isotopically labelled ethanol molecule to understand the reaction mechanism. The mechanism below shows that in order to achieve total oxidation of ethanol one needs to break the 12C-13C bond efficiently.

This would produce equal proportion of 12C and 13C fragments. Upon complete oxidation we expect similar coverage of 12CO and 13CO respectively. So we expect that both the 12CO and 13CO have similar intensities. But in the SFG spectra we observe that the intensity of the 12CO to be less than 13CO. This implies either those two species are not present in the same amounts or there might be an energy tranfer between these two vibrational modes. However, ab-inito calculations predict energy transfer from 13CO to 12CO and not the other way around. Thus we find that efficient oxidation of the 12C- species is the limiting step for the ethanol oxidation reaction.

1. Study of Ethanol Electrooxidation in Alkaline Electrolytes with Isotope Labels and Sum-Frequency Generation,  Journal of Physical Chemistry Letters,  09/2011; 2(17-17):2236-2240. DOI: 10.1021/jz200957e
Robert B. Kutz · Bjoern Braunschweig · Prabuddha Mukherjee ·Dana D. Dlott · Andrzej Wieckowski

2. Reaction pathways of ethanol electrooxidation on polycrystalline platinum catalysts in acidic electrolytes, Journal of Catalysis 01/2011; 278(2):181-188. DOI:10.1016/j.jcat.2010.11.018
Robert B. Kutz · Björn Braunschweig · Prabuddha Mukherjee ·Rachel L. Behrens · Dana D. Dlott · Andrzej Wieckowski

3. Sum-frequency generation of acetate adsorption on Au and Pt surfaces: Molecular structure effectsThe Journal of Chemical Physics, 12/2010; 133(23):234702. DOI:10.1063/1.3507257
Björn Braunschweig · Prabuddha Mukherjee · Robert B Kutz ·Andrzej Wieckowski · Dana D Dlott

4. Real-Time Investigations of Pt(111) Surface Transformations in Sulfuric Acid Solutions, Journal of the American Chemical Society 10/2010 ; 132(40):14036-8. DOI:10.1021/ja106618z
Björn Braunschweig · Prabuddha Mukherjee · Dana D Dlott ·Andrzej Wieckowski

5. Spectroscopy of Electrified Interfaces with Broadband Sum Frequency Generation: From Electrocatalysis to Protein Foams, Book Chapter: Vibrational Spectroscopy at Electrified Interfaces, 07/2013: pages 120-150; , ISBN: 9781118157176
Björn Braunschweig · Prabuddha Mukherjee · Robert B. Kutz ·Armin Rumpel · Kathrin Engelhardt · Wolfgang Peukert · Dana D. Dlott · Andrzej Wieckowski

2DIR spectroscopy of isotopically labeled  membrane proteins.


Picture4Characterizing membrane proteins is very challenging. In his dissertation, Prabuddha explored the extent to which 2DIR spectroscopy can be used to characterize these membrane proteins. Being an ultrafast technique, 2DIR is sensitive to the frequency modulations from the environment such as solvent induced hydrogen bonding interactions. Transmembrane proteins with its interfacial water molecules and membrane headgroups can also engage in ultrafast bonding and attractive interactions that modulates the amide I vibrational frequencies. The two transmembrane proteins that Prabuddha investigated with infrared spectroscopy here are CD3ζ and M2 ion channel. Both these proteins are more than 100 residues long, with 19-21 residues spanning the transmembrane portion. Although CD3ζ protein helps in the T-cell reception, the transmembrane part does not have any such biological function where as M2 is a pH regulated ion channel. The ion channel helps the influenza virus protrude into the cell and destroy it.

In order to characterize the transmembrane domain it was imperative to measure structural fluctuations at a different depth inside the membrane. This would be possible only if we characterized individual residues and uncoupled the dynamics of the rest from it. To obtain residue specific data, we set out to identify and characterize one residue of the protein separated from the rest. So the method we adopt to achieve this is isotope labeling. Isotope labeling a carbonyl from 12C=16O to 13C=18O increases the reduced mass of the oscillator by 1.1 times. This increase in the reduced mass shifts the absorption frequency of the amide I band roughly by 60 cm-1 from 1650 cm-1 to 1590 cm-1. Being separated out from the rest of the backbone carbonyls, the isotope labeled carbonyl stretch behaves like a local vibrational mode. The frequency shifts, caused by the coupling with the rest of the carbonyls, scales inversely to this 60 cm-1 frequency difference. This being a small value, the effect of the coupling is very negligible for isotope labels. Coupling contributions ruled out, we focused on the analyzing IR lineshapes to get the trend.Picture6

Analysis of the 2DIR lineshapes of a lone oscillator one can predict the environmental fluctuations around a bond. A line narrowed 2D spectrum suggests an inhomogeneous surrounding, whereas a circular spectrum tells us about an isotropic environment that all the vibrators are exposed to. The inhomogeneous broadening of the spectrum implies a wide distribution of frequencies suggesting a diverse environment that affect the vibration of the bond. These environments include local hydrogen bonding (in case of water), strong electrostatic interactions due to ions (glassy material), charged groups (membrane headgroups), and also non interactive hydrophobic interactions. A homogeneous lineshape, in the case of N-methyl Acetamide in D2O, suggest that the surrounding environment of the peptide bond fluctuates very fast and averages out sooner than the experimental timescales.

Mathematically, the dynamical information reflected in the lineshapes can be modelled through a frequency fluctuation correlation function, which can be a combination of fast decays and slow decays. The fast decay corresponds to a fast dephasing time and slower decay with the larger time constants reflect how inhomogeneous or static the surroundings are. The value of the fitting parameters is representative of the type of environment in quantitative terms. A part of the research focus in the Zanni group has been to extract and fit the 2D lineshapes using these parameters across the transmembrane and understand/interpret their trend, if there exists one.

Picture5Although the fitting parameters to the experimental data give us an idea about the dynamical timescales of the specific site, it is imperative that we visualize the motion of the system (the protein, lipid and water molecules) as a whole. To achieve this we run computer generated molecular dynamics simulations of the system much smaller to the actual size studied with experiments. This can be thought as conducting the same experiment, except now through computers. If the dynamical parameters extracted from this computer experiment are similar to the experimental data, it would mean that a realistic modeling of the system has been achieved. A proper model would be able to give insights about how the individual site dynamics contribute to the entire motion and this would be instrumental in characterizing systems and the surroundings in which they reside. The correlation functions were converted to lineshape functions using the cumulant expansion. The exponent of these lineshape functions decayed to 0 by 4-5 ps that matched to the experimentally obtained results.

1. Gating Mechanism of the Influenza A M2 Channel Revealed by 1D and 2DIR Spectroscopies, Structure, 03/2009; 17(2):247-54. DOI:10.1016/j.str.2008.12.015
Joshua Manor · Prabuddha Mukherjee · Yu-Shan Lin · Hadas Leonov · James L Skinner · Martin T Zanni · Isaiah T Arkin

2. Picosecond dynamics of a membrane protein revealed by 2DIR, Proceedings of the National Academy of Sciences, 04/2006 103(10):3528-33. DOI:10.1073/pnas.0508833103
Prabuddha Mukherjee · Itamar Kass · Isaiah T Arkin · Martin T Zanni