Chemistry driven by delocalized molecular motions
Chemical reactions are often conceptualized by making and breaking one bond at a time. The idea of localized bond alterations inhibits intuitive thinking about the structure as a whole. Our research group (Dasgupta research group link to website) is focusing on creating a thematic to use collective motions existing in the molecular structure to drive selective and efficient chemistry. Efforts are being directed to precisely measure and model these motions along with developing synthetic strategies to harness it appropriately for efficient photoinduced chemistry.
Vibrations driving ultrafast ET: Ultrafast photoinduced charge transfer reaction is usually the first step towards solar energy conversion. Currently supramolecular structures incorporate donor-acceptor pairs based on distance and orientation constraints. This static picture limits the performance of such structures as we often overlook the dynamic nature of these reactions due to poor mechanistic understanding of the driving reaction coordinate(s). Using steady state and time-resolved electronic and vibrational spectroscopies, we try to derive mechanistic information of photoinduced reactions occurring in homogenous solutions and also at solid-molecule interfaces. The experimental data is modeled by MD simulations which would enhance the insight into these processes. Our work aims to use the thermally accessible collective motions to drive efficient photochemistry in molecular assemblies.
ET driven enzymatic reactions: Enzymes are nature’s molecular devices for carrying out selective chemistry with high turnover rates. However, little is known about how collective modes in these proteins all coherently work together to make the reaction so efficient. As a first step towards understanding these pathways, we are working towards elucidating reaction mechanism of an electron-triggered isomerization reaction of prolycopene, a large conjugated carotenoid, to lycopene which is an important step in biosynthesis of photoactive trans carotenoids.
Controlling ET rates via conformational flexibility: In order to develop new photocatalysts for multi-electron oxidations or reductions, we have to control electron transfer reaction by priming them for the product release step. To achieve this, a systematic approach is needed to optimize reorganization penalty in ET steps. We are using a flexible ligand design to carry out the multi-electron redox chemistry, and addressing the question of optimized reorganization energies.
More information about our methods and activities in this area can be found here
Spin Dynamics: Electron Spin Polarization and Relaxation
Boltzmann distribution is the distribution of particles among various energy levels at thermal equilibrium, to which all systems attempts to reach when left to evolve. For example, when a molecule transitions to an electronic excited state by absorbing light, it can relax back to the ground state apparently without any agent causing the de-excitation. However, as each state is generally a stationary state, transition from an excited state to the ground state requires a suitable perturbation that is as important as the perturbation causing the excitation process. Any non-Boltzmann distribution while evolving towards Boltzmann distribution experiences perturbations that drive the evolution. Our research on Spin Dynamics attempts to understand mechanistic details that govern the generation electron spin systems in non-Boltzmann distribution and their evolution to Boltzmann distribution governed by the perturbing electron spin-lattice relaxation processes.
Very often, the primary photochemical event results in the formation of paramagnetic species, such as triplet states or free radicals with their spin distribution deviating from Boltzmann distribution. Their spins are said to be polarised. There are very small but important magnetic interactions that play crucial roles in controlling the dynamics of such species.
An example in photochemistry (spectra on left in figure): When acetone is photolyzed in 2-propanol by a steady-state UV light, the EPR spectrum of the photogenerated radical (CH3)2C•OH shows the usual absorptive (A) signal with characteristic hyperfine lines, whose relative intensities are governed by the degeneracy of the nuclear spin arrangements. But if a pulsed laser is used as the photolyzing source, and the EPR spectrum of the radical is recorded immediately after the laser pulse in a time-resolved mode, the EPR spectrum of the radical shows anomalous intensities in the hyperfine lines. Some lines appear in emission (E), some in enhanced absorption.
An example in photophysics (spectra on right in figure): Excited states are often quenched by free radicals through energy transfer mechanism without involvement of any chemical reaction. When the stable radical TEMPO quenches an excited naphthalene triplet state, the EPR spectrum of the TEMPO radical, which normally gives the usual absorptive (A) steady-state EPR signal, gives emissive (E) EPR signal post quenching due to spin selective interactions.
Such remarkable observation of anomalous EPR signals indicates that there are very specific interactions, coming into play in the presence of light, that drive the spins from the usual Boltzmann distribution to a non-Boltzmann one, and can even cause an inversion of spin population. Occurrence of such non-Boltzmann distributions carries rich information on the ultra-fast photophysical and photochemical processes. Magnetic resonance spectroscopy, such as EPR and NMR, is an aptly suitable technique to study spin dynamics in photochemical systems, and gain important insights into the unique intra- and intermolecular interactions which are not observable by any other spectroscopic techniques.
Within the Chemical Physics and Dynamics group we use time-resolved EPR spectroscopy, nano- and pico-second laser flash photolysis techniques and time-resolved fluorescence to study primary events of a photochemical reaction and the associated spin dynamics, in homogeneous solutions and in confined systems, where molecular motions are restricted. We aim to understand the interactions giving rise to spin-selective pathways, and how spatial restrictions govern the evolution. More information about our methods and activities in this area can be found here.
The tryptic Peptides from a cytochrome P450 enzyme show sequence specific association of with multiwalled carbon nanotubes by localization of hydrophobic residues around the nanotube. In the Biochemistry and Systems Biology and the Chemical Biology and Bioinorganic Chemistry groups, a model-free approach has been used to study the association of peptides onto multiwalled carbon nanotubes (MWCNT) in aqueous solution at ambient pH to understand the molecular basis of interaction of the peptides with MWCNT. The peptides obtained by tryptic digestion of cytochrome P450cam from P. putida were allowed to interact with MWCNT and several peptides were found to bind to the nanotube leading to formation of stable homogeneous dispersion of the bio-nano conjugates of MWCNT. The peptides bound to the MWCNT were separated from the unbound peptides and sequence analyses by tandem MS/MS technique identified the strongly bound peptides as well as the unbound and the weakly bound peptides. The peptide-MWCNT conjugate was further characterized by TEM as well as Raman and other spectroscopy.
The screening of the peptides bound onto MWCNT from a mixture of tryptic peptides of cytochrome P450cam provided a simple route for obtaining 12 peptide sequences that were strongly associated to the nanotubes. Cytochrome P450cam is chosen in the present study as it consists of a significant fraction of hydrophobic residues distributed all over the protein. However, one could apply similar approach to screen peptides from any large protein for binding to carbon nanotubes. A model based on the hydrophobicity of residues in the peptides suggested that the amphiphilic peptides with localised hydrophobic residues at the center or at one end of the sequence form stable dispersions of the peptide-MWCNT conjugates.
The present studies on MWCNT further supported that the surfactant like property of the peptide for association of the hydrophobic surface of the nanotube is essential to form stable dispersions of the MWCNT in solution. The Raman spectroscopic results establish the non-covalent interaction between MWCNT and the peptides. The experimental results suggest that MWCNT-peptide conjugate had predominant β-sheet structure and have excellent hydrophobic-hydrophilic balance that is suitable for the non-covalent functionalization, good dispersion stability of the MWCNT-peptide conjugate. The design criteria employed herein can also be applied to the coating of other nanomaterials and more functionalities can be engineered into the peptide by inserting other peptide domains, which can further used in synthesis of nanoconjugates and heterostructures for a variety of applications. For further information, visit our lab website
Proteins and the Computational Microscope
The structure and associated thermal motions of proteins are both intimately connected to their function. Experimental studies and theoretical models have been able to establish some ground rules to connect protein structure and function. For instance, the shape of a protein and electric charge of amino acids on the protein surface can reveal the types of molecules the protein can bind (The human hand shaped polymerase enzyme shown in Fig 1a utilizes a helix-turn-helix structural motif to clutch DNA fragments). Physico-chemical reactions often occur at special active sites inside the protein which contain prosthetic groups (light induced isomerization of a retinal chromophore in rhodopsin, a transmembrane protein shown in Fig 1b, triggers a cellular response in the eye leading to vision). On the other hand, connecting the thermal motions of proteins to their associated function has proven to be a formidable challenge. Why? First, no single experimental or computational method can probe the entire temporal range of thermal motions in biomolecules ranging from femotoseconds to seconds (Fig 1c). Second, it is an open challenge to separate out thermal motions and assign the contributions on different timescales to a particular molecular process. Third, the problem lies at the interface of physics, chemistry, and molecular biology requiring an interdisciplinary toolset/approach spanning areas of Chemical Physics and Dynamics as well as Molecular Biophysics and Imaging .
In the department of chemical sciences, we are addressing the fascinating question of how thermal motions drive various protein functions such as catalysis, molecular recognition, cell signaling, and electron transfer through theory and computations. The challenging problem of visualizing protein dynamics on different timescales is being tackled using high performance computational modeling and simulations of proteins under experimental/physiological conditions. In such calculations protein structure is described at varied resolutions ranging from single atoms to entire protein domains. The motion of protein atoms, which is driven by thermal energy, is described classically when no chemical transformations (e.g breaking or forming of covalent bonds) occur. Dynamics with chemical transformations are modeled using a mixed scheme, wherein the atoms participating in the reactions obey the laws of quantum mechanics, and the rest of the protein/solvent atoms obey the laws of classical mechanics. We also build theoretical models to describe processes such as catalysis, electron transfer and optical response within a protein environment. More information about our methods and activities in this area can be found here.
Deciphering the Catalytic Activity of an Orphan P450 enzyme
A close inspection of the substrate binding pocket from the crystal structure of CYP175A1 and CYP102A1 shows that the pockets/active sites of these two enzymes are similar and mostly surrounded by hydrophobic residues. Hence, both of them would prefer hydrophobic substrates to show catalytic activity. Long chain saturated fatty acids (Lauric acid, myristic acid, palmitic acid and stearic acid) are substrates of P450BM-3. However, no substrate other than β-carotene was earlier reported for the native CYP175A1. It is known that Thermus thermophilus HB27 produces lipolytic enzymes. In the Biochemistry and Systems Biology and the Chemical Biology and Bioinorganic Chemistry groups, we systematically screened several fatty acids (saturated and monounsaturated) for their potential as substrates for CYP175A1.
The results showed that the wild type enzyme could catalyze the reaction of mono-unsaturated 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 evidences that CYP175A1 can catalyze regioselective oxygenation reaction of several monoenoic fatty acids though it cannot catalyze the oxygenation of the corresponding saturated analogues. These studies provide critical information on the nature of the enzyme pocket and on the possible natural substrate of this orphan enzyme. For further information, visit our lab website
Structure/Dynamics of Proteins and Fibrils from Solid State NMR
The Department of Chemical Sciences in TIFR has an active group in solid-state nuclear magnetic resonance spectroscopy. Nuclear magnetic resonance (NMR) of matter in solution state plays a significant role in structural and dynamics analysis. However, membrane proteins and fibril systems, which play a great role in many of the functions of human body, are not easily amenable to X-ray crystallography and solution-state NMR, as they do not yield high-quality crystals and are not easily soluble and there comes the importance of solid-state NMR. Besides, solid-state NMR has applications in zeolites, polymers, and catalysis.
The solid-state NMR group is engaged in research ranging from theory, development of methods, and applications to zeolites, catalysts, and amyloid fibrils. The theory side focuses on the development of expansion methods to solving time-dependent Schrodinger equation and the convergence of the series expansions. The methods part is on the development of radiofrequency pulse schemes for the manipulation of spins to achieve better resolution, sensitivity, and geometry information. The applications are in order to obtain structural and dynamics information of a variety of compounds in the solid state with the methods developed in the group and others in vogue.
The solid-state NMR group has access to two spectrometers in the National Facility for High-Field NMR, TIFR. They are 500 and 700 MHz spectrometers each equipped with state-of-the-art probes and other necessary accessories. The group has also access to all the standard biophysical laboratory items and other analytical methods to characterise materials.
The group has recently made significant contributions in the area of amyloid fibrils. These include understanding metal-ion binding sites, the influence of metal ions and certain biphenyl radicals on the fibrilisation pathways and their effect on toxicity, and the role of certain parts of the fibril system Aβ42 in forming the established structural motifs. More details may be found here.
Rational Design of an Artificial Peroxidase
As part of Biochemistry and Systems Biologyand the Chemical Biology and Bioinorganic Chemistry groups, we have rationally designed the heme active site of a thermostable cytochrome P450 CYP175A1 was to increase the peroxidase activity. The crystal structure of CYP175A1 shows absence of suitable amino-acid residues in the distal heme pocket that could act as acid-base catalysts as in the heme peroxidases such as HRP and CPO. The aim of the present project was to modify the active site of this thermostable P450 to introduce a residue at the distal heme pocket that could act as an acid-base catalyst and thus enhance the peroxidase activity in the mutant enzyme. This could potentially lead to the creation of a thermally stable artificial peroxidase.
In this project we have carried out molecular modeling studies and identified that the Leu80 residue in the CYP175A1 could be suitably mutated to enhance the peroxidase activity of the mutant enzyme. The high thermostability (Tm = 87oC) of CYP175A1 has the advantage to engineer this protein to create an artificial thermostable enzyme. We have studied the peroxidase activities of L80H and L80Q mutants of the enzyme at different temperatures and pH to determine the optimum conditions and results were compared with those of the archetype peroxidase, HRP. The substitution of the leucine with histidine or glutamine was indeed found to enhance the peroxidase activity of CYP175A1, which is more prominent at high temperature. For further information, visit our lab website.
Biocompatible Hydroxyapatite Nanotubes
The selective processing of inorganic structures with features on the nanometer scale has seen a great surge in interest over the last few decades. These materials are known to possess interesting and useful optical, electronic and/or magnetic properties that can subsequently be exploited in a wide variety of applications ranging from novel forms of catalysis to solar energy conversion. The choice of application is contingent on not only the chemical composition of the material but also on the overall morphology, and even more precisely on the accessible surface area. Currently, there are a myriad of methods available for fabrication of such intricate inorganic structures. However, irrespective of employing a certain fabrication method, the formation of a well-organized architecture is not trivial as various parameters have to be regulated: These include uniformity of size, stabilization against collapse, consistency in the chemical composition and growth of the overall structures with preferred morphology (thin films, spheres, fibers, helical spirals etc.).
Towards the aim of employing a synthetic approach to formation of functional materials, inevitably researchers working the area of materials science tend to resort to commercially available reactive precursors for their synthesis. These are habitually alkoxide precursors as they afford simple, innocuous by-products and the reagents are relatively easy to handle for either sol-gel synthesis for viable powders or spin-casting for thin film production. Recently, as part of the Nanoscience and Catalysis group, we have developed a generic, facile route to forming reactive precursors of a variety of elements such as titanium, zinc, bismuth, iron, vanadium and zirconium, all of which contain a simple polyol ligand. These complexes are facile in their formation and their structures have now been elucidated and can function as sophisticated precursors for generation of functional ferroelectrics, multiferroics, semiconductors and catalysts.
The figure shows single phase, stoichiometrically pure, hollow nanotubes of hydroxyapatite which have been synthesized (single-particle analysis has been performed to successfully prove the sole formation of Ca10(PO4)6(OH)2 phase). The facile synthesis involves a sol-gel process under neutral conditions in the presence of a sacrifical anodic alumina template. The structures formed are hollow nanotubes that have been characterized by XRD, SEM, TEM, SAED, EELS, EDS and BET measurements. The diameter of the resulting tubes is in the range of 140-350 nm, length is on the order of a few microns and the wall thickness of the tubes was found to be ca. 30 nm. Moreover these tubes had a large BET surface area of 115 m2/g and were found to be biocompatible. They displayed inertness in the presence of NIH 3T3 mouse fibroblast cells as dictated by an MTT assay. More information about our methods and activities in this area can be found here.
Tracking the Molecular Players in Neurodegenerative Disorders
As part of Molecular Biophysics and Imaging and the Chemical Biology and Bioinorganic Chemistry groups, we are investigating biophysically tractable yet biologically interesting systems, using (mostly) spectroscopic and imaging tools, most of which we build ourselves. Our recent focus has been on two problems: protein misfolding/aggregation, and vesicular neurotransmission. Both of these interface with the phenomenon of amyloid induced neuro-degeneration, which results in such well known and untreatable diseases such as Alzheimer’s and Parkinson’s.
Alzheimer’s Amyloid beta is a small peptide, and therefore expected to be more tractable at a molecular level compared to typical proteins. Yet it is uniquely interesting in the biological context. We have developed single molecule level fluorescence tools specifically suited for studying amyloid misfolding and aggregation. Techniques such as Fluorescence Correlation Spectroscopy, Forster Resonance Energy Transfer, Fluorescence Lifetime Imaging, Surface Enhanced Raman Scattering, and Atomic Force Microscopy are used to look at the structure-function relationship of aggregation-prone proteins.
On the other hand, vesicular neurotransmission is a multifaceted phenomena and therefore difficult to simplify beyond the level of single neurons. However, monoaminergic vesicles can be tracked with unique label-free multiphoton microscopy techniques that we have developed in the lab. We hope that a combination of these techniques, together with other tools such as solid state Nuclear Magnetic Resonance Spectroscopy and Peptide Engineering, will help us uncover the fundamental mechanisms underlying protein misfolding, aggregation and toxicity.
The work described here, undertaken in the last few years, involve different aspects of these themes. In addition, development of biophotonic instrumentation and methodology has been a frequent offshoot of this work in the lab. Some of these tools have been commercialized (e.g. http://www.holmarc.com/fcs.html), and we have also initiated training programs and annual workshops to facilitate sharing and dissemination of Biophotonic knowledge and techniques within India. The National Fluorescence Workshop (www.fcsworkshop.in), the National Photonics Fellowship of India (www.photonicsindia.org) and the Biophysics Pashchim Meetings Series (https://sites.google.com/site/biophysicspaschim/) were initiated by our lab. For further information, visit our lab website.
Formation of Functional Inorganic Structures for Energy Capture, Storage, Conversion (and also for Drug Delivery)
The architecture of inorganic structures (specially on the nanoscale) has become and important parameter (in addition to the stoichiometry) that can be manipulated in order to optimize a material for advanced applications. These structures are known to possess interesting and useful optical, electronic and/or magnetic properties that can subsequently be exploited in a wide variety of applications ranging from novel forms of catalysis to solar energy conversion. The choice of application is contingent on not only the chemical composition of the material but also on the overall morphology, and even more precisely on the accessible surface area. Currently, there are a myriad of methods available for fabrication of such intricate inorganic structures. However, irrespective of employing a certain fabrication method, the formation of well-organized materials is not trivial as various parameters have to be regulated. These include uniformity of size, stabilization against collapse, consistency in the chemical composition and growth of the overall structures with preferred morphology (thin films, spheres, fibers, helical spirals etc.). The principal aim of the research in our lab has been to augment the current understanding of the concepts in supramolecular templating of inorganic materials for formation of nanostructures. To be more precise, self-assembling amphiphilic structures (e.g. synthetic or naturally occurring surfactants, peptides, and/or block co-polymers) in the presence of diffusion-controlling media (such as gels, microemulsions, non-aqueous solvents) are used to provide a temporary ‘scaffold’. This self-assembled template provides a complex 3-dimensionsal structure which has features on the nanometer length scale. Subsequently, colloidal inorganic building blocks (sol-gel precursors and/or nanoparticles), when introduced into this media, are then organized (ideally) into the inverse replica of the template. More importantly, this template, under appropriate conditions, is able to exploit the principles of molecular recognition and in turn structure-direct and size-constrain the condensing inorganic precursors. Interestingly, cooperative assembly imparts intricate morphological characteristics to the products that were previously unattainable.
Turn-on Sensors for in vivo Imaging
Small bio-molecules, like lipids, metal ions, and carbohydrates, play vital roles in defining the physiological state of living organisms. The onset of disease is frequently associated with disturbances in homeostatic regulation of these bio-molecules, making them an obvious target when monitoring disease progression. Furthermore, the quest for unraveling fundamental biological pathways relies heavily upon the ability to precisely visualize strategic molecular players in vivo. Small molecule detection assays are usually limited to in vitro methods, during which critical information related to in vivo concentrations and states of bio-molecules is lost. The multitude of structurally and physically similar bio-molecules that might play very distinct roles in vivo makes small molecule detection both tricky and exciting. The challenge lies in designing selective, sensitive, and non-invasive molecular probes for the detection of bio-molecules.
As part of the Chemical Biology group at TIFR, we work at the interface of synthetic chemistry, molecular biology, and imaging, to develop molecular probes which give a specific ‘ON’ response only in presence of the bio-molecule of interest. This unique ‘Turn-ON’ approach helps reduce the background signal due to non-specific interactions and dramatically improves detection. The design principles for most of our sensors are based on a careful scrutiny of natural protein and nucleic acid receptors for small molecules. Our group strategically couples nature-inspired ligands to imaging agents in order to achieve the selective ‘ON’ response. The current focus is on designing probes for optical and magnetic resonance imaging modalities which provide cellular and tissue level information respectively, or both as and when required. Engineering regulatory proteins for detecting bio-molecules is also being explored.
Applying our ‘turn-on’ sensors for imaging biomarkers in vivo by choosing appropriate animal models is the ultimate aim of the group. Our current research interests lie in developing sensors for in vivo imaging of metal ions involved in neurodegeneration and phospholipids implicated in various cell signaling processes. Sensors for monitoring enzymatic oxidation of substrates in atherosclerosis and pH sensors for visualizing autophagy are underway.
We believe that using chemical insights to design sensors and applying the sensors to image bio-molecules can provide tools to expedite fundamental research in the field of biological sciences many folds. Our sensors have the potential to help decipher key links between molecular level information and physiological effects that result from the slightest homeostatic perturbation of essential bio-molecules. More information about our research activities can be found here.
Dendritic Fibrous Nanosilica for Catalysis, Energy Harvesting, Carbon Dioxide Mitigation, Drug Delivery, and Sensing
Morphology-controlled nanomaterials such as silica play a crucial role in the development of technologies for use in the fields of energy, environment (water and air pollution) and health. Since the discovery of Stöber’s silica, followed by the discovery of mesoporous silica materials, such as MCM-41 and SBA-15, a significant surge in the design and synthesis of nanosilica with various sizes, shapes, morphologies and textural properties (surface area, pore size and pore volume) has been observed in recent years.
NanoCat Group has developed next-generation nanocatalysts via the morphological control of nanomaterials, particularly dendritic fibrous nanosilica (DFNS). This material possesses a unique fibrous morphology, unlike the tubular porous structure of various conventional silica materials. It has a high surface area with improved accessibility to the internal surface, tunable pore size and pore volume, controllable particle size and importantly, improved stability. The uniqueness of DFNS is its high surface area is produced by its fibrous structure instead of the formation of pores, making the large surface area easily accessible. Our group has shown the successful utilization of DFNS in a range of important applications, including catalysis and CO2 capture. DFNS is one of the few Indian invented material which is now being explored by more than 150 reputable groups worldwide for various applications. DFNS show exceptional performance in large numbers of fields including catalysis, gas capture, solar energy harvesting, energy storage, sensors, and biomedical applications.
Reference: Facile Synthesis Protocol to Tune Size, Textural Properties & Fiber Density of Dendritic Fibrous Nanosilica (DFNS): Applications in Catalysis and CO2 Capture, A. Maity, R. Belgamwar, Vivek Polshettiwar*, Nature Protocol, 2019, 14, 2177-2204.
More information about this project can be found on the Nanocat webpage
Materials for Nanocatalysis
The chemist’s first choice for heterogeneous catalysts is often porous silica because of its high surface area. However, these surface areas are mostly due to the pores and are thus not always accessible. We have developed new kind of fibrous silica nanospheres. Such a fibrous morphology observed in these nanospheres has not been seen before in silica materials. The material exhibits excellent physical properties, including a high surface area, a fibrous surface morphology, good thermal and hydrothermal, and high mechanical stability. Its high surface area is due to these fibers and not pores (see below figure). KCC-1 will be very useful for silica-supported catalysts, wherein accessibility of active sites can be increased significantly. As part of the Nanoscience and Catalysis group, we aim to improve the properties of KCC-1 by understanding its mechanism of formation as well as exploring for various applications in catalysis as well as for gas storage.
Scanning electron microscopy (SEM) images shown in below figure (left) indicate that the KCC-1 material consists of colloidal spheres of uniform size with diameters that range from 250 nm to 450 nm. Close inspection of these images reveals that the material possesses dendrimeric fibres (angle shaped with thicknesses of 8-10 nm) arranged in three dimensions to form spheres, which can allow easy access to the available high surface area. Further structural characterization of synthesized silica nano-spheres performed by high-resolution transmission electron microscopy (HRTEM) (figure-right) reveals well-defined and ordered fibers coming out from the center of the particles and distributed uniformly in all directions.
This material was found to be very useful as a support for development of nano-catalysts such as Ru/KCC-1, Pd/KCC-1, TaH/KCC-1 etc and also as sorbents for CO2 capture. These nano-catalysts displayed superior activity which was due to the highly accessible active sites on KCC-1 support as compare to conventional MCM-41 support (see below figure). The catalysts were also stable with an excellent lifetime and no sign of deactivation, even after several days of reaction. This enhanced stability was due to the restricted Ostwald ripening and/or sintering of nanoparticles. due to fibrous nature of KCC-1.
More information about this project can be found here.
Black (nano)Gold Combat Climate Change
Global warming is a serious threat to the planet and the living beings. One of the main cause of global warming is the increase in the atmospheric CO2 level. The main source of this CO2 is from the burning of fossil fuels in our daily day life (electricity, vehicles, industry and many more).
We have developed the solution phase synthesis of dendritic plasmonic colloidosomes with varying interparticle distances between the gold NPs using a cycle-by-cycle growth approach by optimizing the nucleation-growth step. These DPCs absorbed the entire visible and near-infrared region of solar light, due to interparticle plasmonic coupling as well as the heterogeneity in the Au NP sizes, which transformed golden gold material to black gold. Raman thermometry and SERS provided information about the thermal and electromagnetic hotspots and local temperatures which was found to be dependent on the interparticle plasmonic coupling. The spatial distribution of the localized surface plasmon modes by STEM-EELS plasmon mapping confirmed the role of the interparticle distances in the SPR of the material.
We observed the significant effect of the plasmonic hotspots on the performance of these DPCs for the oxidation reaction of cinnamyl alcohol using pure oxygen as the oxidant, hydrosilylation of aldehydes as well as for temperature jump assisted protein unfolding and purification of seawater to drinkable water via steam generation.They also catalyzed CO2 to methane (fuel) conversion at atmospheric pressure and temperature, using solar energy.
This was attributed to varying interparticle distances and particle sizes in these dendritic plasmonic colloidosomes. The results indicate the synergistic effects of EM and thermal hotspots as well as hot electrons on DPC-Cx performance. Thus, DPC-Cx catalysts can effectively be utilized as Vis-NIR light photo-catalysts, and the design of new plasmonic nanocatalysts for a wide range of other chemical reactions may be possible using the concept of plasmonic coupling.
Thus, in this work, by using the techniques of nanotechnology, we transformed golden gold to black gold, by simply changing the size and gaps between gold nanoparticles. Like real trees, where they use CO2, sunlight and water to produce food, our developed black gold act like an artificial tree and use CO2, sunlight and water to produce fuel, which we can be used to run our car. Notably, black gold can also use to convert sea water into drinkable water using the heat that black gold generates after it captures sunlight.
This work is way forward to develop artificial trees which capture and convert CO2 to fuel and useful chemicals. Although at this stage, their production is low, in coming years, these challenges can be resolved and we may able to convert CO2 to fuel using sunlight at atmospheric condition, at a commercially viable scale. CO2 will then become our friend again and will become our main source of clean energy, and we will have CO2 based Civilisation.
Reference: Plasmonic Colloidosomes of Black Gold for Solar Energy Harvesting and Hotspots Directed Catalysis for CO2 to Fuel Conversion. "Cover Page” "Pick of the Week" M. Dhiman, A. Maity, A, Das, R. Belgamwar, B. Chalke, Y. Lee, Kyunjong Sim, Jwa-Min Nam and Vivek Polshettiwar*, Chemical Science, 2019, 10, 6694-6603.
More information about this project can be found on the Nanocat webpage
Single-Molecule Protein Mechanics
Mechanical forces and their influence are found in many day-to-day life examples in Nature. In spite of this, the scientific advances on the effect of mechanical forces at the molecular level in understand of chemistry and biology have been limited. This is mainly due to the lack of experimental techniques to study these phenomena in a controlled manner.
In biology, mechanical forces play a central role in ubiquitous phenomena such as protein degradation, cell-adhesion, tissue organization, and muscle function in multi-cellular organisms. The key players in these phenomena are protein molecules, which act as mechanosensors and communicate the surrounding dynamic microenvironment with the cell. Hence, studying the mechanical response of these biomolecules would provide a wealth of information about their structure, function, and chemistry. Experimental characterization of mechanical response of biomolecules has been accelerated with the adoption of optical-tweezers and atomic force microscope to study biological phenomena. These two methods have made a great deal of progress in understanding the protein mechanics, in the past two decades.
In chemistry, the bond-making and bond-breaking are central phenomena and the reactivity of bonds and the differences can be understood only by the underlying mechanistic details. In recent years, ‘force spectroscopy’ has been adopted to get the structural details of transition states with an unprecedented sub-angstrom resolution for certain solution phase reactions. This is analogous to ‘femto-second chemistry’ of gas-phase reactions.
In the Molecular Biophysics and Imaging group and the Chemical Physics and Dynamics group , we use state-of-the-art atomic force microscope (SM-AFM) to probe single molecules for studying mechano-biology and mechano-chemistry and bulk techniques, such as fluorescence spectroscopy, circular dichroism etc., for characterization. By using this novel SM-AFM technique, we can apply stretching force to a single protein molecule, measure its mechanical response and study protein mechanics. In addition, we compliment our protein mechanics experiments with steered-molecule dynamics (SMD) on proteins and peptides. We also use Monte Carlo simulations to extract free-energy surface parameters from protein mechanics experiments. More information about our methods and interesting problems we are currently investigating in our laboratory can be found here.
Perfecting Imperfection: Defected Nanosilica can transform CO2 to Fuel without any metal and ligands.
Reducing the CO2 levels in Earth’s atmosphere is key to stop further environmental degradation. CO2 conversion to methane (green fuel) using renewable hydrogen is considered as one of the best options with great potential for simultaneously resolving energy and environmental challenges, although the production of hydrogen from renewable resources also needs to be economically viable. Unfortunately, this process needs an expensive metal or complex organometallics and most of them suffer from instability and poor selectivity toward methane. In this work, using the defect engineering approach, we develop metal-free–ligand-free nanocatalysts, which convert CO2 to methane at the significant rates, scales, and stabilities
Defect-containing nanosilica was found to be an alternative catalyst to expensive noble metals as well as complex organometallic-based catalysts. In this work, we observed that by generating and tuning the defects (type, concentration, and proximity) in nanosilica, CO2 can be transformed into green fuel (methane) with good productivity and selectivity without the use of any metal nanoparticles. The optimum concentration of E′ centers, ODC, and NBOHC defect sites were needed, which allowed the defects to work synergistically to activate CO2 and dissociate hydrogen, thus converting CO2 to methane.
Unlike metal catalysts, whose activity decreases significantly with time, the loss of activity in the defect-containing silica catalysts was less significant. Notably, the regeneration of the defect-containing silica only required air (rather than hydrogen gas required for metal catalysts). Surprisingly, the catalytic activity of DNS-25 for methane production increased significantly after every regeneration cycle, reaching more than double the methane production rate (9,569 µmol g−1⋅h−1) after eight regeneration cycles as compared to the initial catalyst performance (3,810 µmol g−1⋅h−1). Also, defect-containing silica DNS-25 showed 6.6× more activity as compared to parent DFNS material, indicating the good potential of our defect-engineering approach. This activated catalyst remained stable for more than 200 h with a good formation rate and selectivity.
Thus, this magnesiothermic defect-engineering protocol may allow the development of metal-free nanocatalysts for CO2 conversion at the significant rates, scales, and stabilities required to make the process economically competitive. This metal-free approach could also have a multidisciplinary impact and may facilitate the rational design of catalysts for various other catalytic processes apart from CO2 conversion.
This work is one more tiny step towards the utilization of 30 thousand tons of CO2 in the earth's environment, and the process is far away from real use (seems unrealistic currently). However learning from this work and recent black-gold work, we hope that one day we will develop a commercially viable process by urgently required fundamental breakthrough in the field of catalysis.
More information about this project can be found on the Nanocat webpage
Supersonic Jet Spectroscopy of Weak H-bonds
Although many things around us are made up of covalently bound stable molecules, their properties are dictated by weak interactions among them. The manifestation of such forces is evident from the deviation of the ideal gas behavior of so called noble gases due to van der Waal’s forces on one hand and the variations in their physico-chemical properties due to hydrogen bonding on the other. Many of naturally occurring processes that occur at STP are also controlled by weak intermolecular forces between them. At more complicated level these forces play important roles in imparting structures to various biopolymers and also enable them to carry out many functions in living organisms under ordinary conditions that keep the biological systems ticking. These forces include electrostatic, polarization, dispersion, covalency. Hydrogen bonding interaction that is all pervading is composite of all these fundamental interactions.
Hydrogen bonding interaction involving the first row elements such as oxygen, nitrogen, and halogens has been very well studied. However, the H-bonding is not limited to these elements only. In recent past many novel H-bonding interactions have been discovered. The most important of these include CH and SH groups as Hydrogen bond donors and sulfur and carbon atoms or aromatic rings as H-bond acceptors. Some of these interactions also show unusual characteristics, e.g., the hydrogen bonding interactions in which CH acts as H-bond donor the CH stretching frequency actually shows a blue shift rather than the conventionally observed red shift. Besides, the structural data of many proteins indicate that the CH—Pi contacts constitute a large fraction of intermolecular interactions responsible for their structures.
Within the Chemical Physics and Dynamics group we have been investigating the novel hydrogen bonded systems using Supersonic Jet Spectroscopy. Supersonic jet expansion cooling method is used to form the weakly bonded clusters in the gas phase. These complexes are probed using a variety of laser spectroscopic methods in the electronic ground state, the first excited state as well as in the cationic state. Electronic excitation spectra of monomer and clusters are obtained by laser induced fluorescence (LIF). Similar information is obtained in mass gated channel by two-color resonantly enhanced multiphoton ionization (2c2p-REMPI) coupled with time of flight mass spectrometry (TOFMS). These two techniques provide the information about the S1 state. Disperser fluorescence (DF) is useful in order to obtain the information of S0 state. In this technique, the molecule is excited to a specific vibrational level in the excited state and the total fluorescence emission is dispersed by a monochromator. To characterize hydrogen bonded complex in the cationic state, zero kinetic energy (ZEKE) spectroscopy and mass analyzed threshold ionization (MATI) techniques are used. The sample is excited to the high lying Rydberg states. Thereafter the Rydberg states are extracted by applying delayed pulsed electric field which is also known as field ionization.
Usually intermolecular vibrational modes are identified by comparing the Excitation/DF spectra of monomer and the complex. The important information about the changes in the vibrational stretching frequencies of H-bond donors (e.g. O-H, N-H, SH, and C-H) upon complex formation is obtained by IR-UV double resonance spectroscopy. These are determined by resonant ion- dip infrared spectroscopy (RIDIRS) or fluorescence depletion IR spectroscopy (FDIR). In these methods, vibrational excitation is carried out by IR and the depopulation of the ground state is observed by electronic transition.
Usually the experimental data is complemented by theory and computations. Ab initio computations such as geometry optimization and frequency calculations are performed using the Gaussian09 suite of programs. Additionally, quantum theory of atoms and molecules (QTAIM), natural bonding orbital analysis (NBO), localized molecular orbital energy decomposition analysis (LMOEDA), and natural energy decomposition analysis (NEDA) are also carried out in order to get more insight about the nature of H-bonding interaction in the complexes. More information about our methods and activities in this area can be found here.