Stability and Copper-binding properties of Azurin and its variants probed using optical spectroscopy
Materials Simulation From First-Principles: Fundamental Challenges and Importance of Finite Temperature Modeling
The discovery of the extraordinary activity in catalysis exhibited by small clusters has stimulated considerable research interest. However, in heterogeneous catalysis, materials property changes under operational environment (i.e. at a finite temperature (T) and pressure (p) in an atmosphere of reactive molecules). Therefore, a solid theoretical understanding at a realistic (T, p) is essential in order to address the underlying phenomena.
This talk is, therefore, driven by the vision of computational design of materials at a finite (T, p). Here, I shall introduce a robust methodological approach that integrates various levels of theories combined into one multi-scale simulation to address the environmental effect to predict the properties of materials at a finite T, p. Our approach employs density-functional theory (DFT) combined with ab initio atomistic thermodynamics. In order to quantitatively account the contribution of anharmonic vibrational free energy to the configurational entropy, we have evaluated the excess free energy of selected clusters numerically by thermodynamic integration method with DFT inputs. We further establish the necessity of this finite temperature modeling as DFT (with appropriate exchange and correlation functionals) fails to predict the stable phases even at a moderately low temperature. We have successfully applied our finite temperature modeling approach in various inter-disciplinary fields viz. (i) catalysis[2-3], (ii) defects in semi-conductor, (iii) energy materials[5-6], etc. I shall discuss in details one application of this methodology in addressing (T, p) dependence on the composition, structure, thermodynamic stability of metal hydride clusters in a reactive atmosphere in the context of designing energy materials.
1.S. Bhattacharya, S. Levchenko, L. Ghiringhelli, M. Scheffler Phys. Rev. Lett. 111, 135501 (2013).
2.S. Bhattacharya, D. Berger, K. Reuter, L. Ghiringhelli, S. Levchenko Phys. Rev. Materials (Rapid Commun.) 1, 071601(R) (2017).
3.S. Saini, D. Sarker, P. Basera, S. Levchenko, L. Ghiringhelli, S. Bhattacharya J. Phys. Chem. C 122, 16788 (2018).
4.A. Bhattacharya, S. Bhattacharya Phys. Rev. B 94, 094305 (2016).
5.E. Arora, S. Saini, P. Basera, M. Kumar, A. Singh, S. Bhattacharya J. Phys. Chem. C (article ASAP), DOI: 10.1021/acs.jpcc.8b08687.
6.A. Bhattacharya, S. Bhattacharya J. Phys. Chem. Lett. 6, 3726 (2015).
Computational Design of Nano-clusters by Property-Based Cascade Genetic Algorithms: Tuning the Electronic Properties of (TiO2)n Clusters
For complex open systems such as atomic clusters, defected surfaces, structured over-layers adsorbed on inorganic surfaces, human intuition for predicting relevant structures is likely incomplete or even misleading. Thus, an unbiased algorithm is required for the global optimization. In order to obtain both extensive and accurate sampling of the configurational space - we have developed a massively parallel cascade genetic algorithm (cGA)[1-3]. The term “cascade” refers to a multi-stepped procedure involving increasing levels of accuracy for the evaluation of the globally-optimized quantity (usually total energy of the system). Typically, a cGA starts with classical force field and goes up to density functional theory (DFT) with hybrid functionals. This development has already been applied and successful in various inter-disciplinary fields in materials science[4-6].
Recently, we have extended our cGA-implementation to property based potential energy surface (PES)-scanning to address the famous “inverse problem” of materials science, i.e. how to computationally design materials/structures with the desired electronic properties as opposed to calculating the properties of the given material/structure. In this talk, I shall discuss the fundamental challenges behind this implementation in the context of computational design of cluster-based nano-catalysts.
1.S. Bhattacharya, S. Levchenko, L. Ghiringhelli, M. Scheffler New J. Phys. 16, 123016 (2014).
2.F. Curtis, X. Li, T. Rose, A. Mayagoitia, S. Bhattacharya, L. Ghiringhelli, N. Marom J. Chem. Theory Comput. 14, 2246 (2018).
3.M. Reilly, R. I. Cooper, C. S. Adjiman, S. Bhattacharya et al. Acta Cryst. B 72, 439 (2016).
4.Bhattacharya, S. Bhattacharya J. Phys. Chem. Lett. 6, 3726 (2015).
5.X. Zhao, X. Shao, Y. Fujimori, S. Bhattacharya, L. M. Ghiringhelli, H. Freund, M Sterrer, N. Nilius, S. V. Levchenko J. Phys. Chem. Lett. 6, 1204 (2015).
6.S. Bhattacharya, D. Berger, K. Reuter, L. Ghiringhelli, S. Levchenko Phys. Rev. Materials (Rapid Commun.) 1, 071601(R) (2017).
7.S. Bhattacharya, B. H. Sonin, C. J. Jumonville, L. M. Ghiringhelli, N. Marom Phys. Rev. B (Rapid Commun.) 91, 241115(R) (2015).
Probing Charge Transfer Reaction Coordinate in Supramolecular Donor-Acceptor Frameworks
Enzymes: an Emerging Puzzle of Mechanobiology and Active Matter
The traditional view that enzyme kinetics is only a matter of catalyzing chemical reactions is challenged by recent experiments and theory showing that catalysis enhances enzyme mobility. This is significant to programming spatio-temporal patterns of molecular response to chemical stimulus. This talk will report that the enhanced diffusivity of enzymes is a “run-and-tumble” process analogous to that performed by swimming microorganisms, executed in this situation by molecules that lack the decision-making machinery of microorganisms. One consequence is that enzymes migrate in the direction of lesser reactant concentration when they turn over substrate; they display “anti-chemotaxis.” This run-and-tumble process offers the possible biological function to homogenize product concentration, which could be significant in situations when the reactant concentration varies from spot to spot. Attempts will be made to place these and our related recent findings in the context of larger puzzles in the active matter intellectual community.
About the Speaker:
Steve Granick is a member of the U.S. National Academy of Sciences and American Academy of Arts and Sciences. Among his other major awards are the Paris-Sciences Medal, APS national Polymer Physics Prize, and ACS national Colloid and Surface Chemistry Prize. Holding and having held Honorary and Visiting Positions at multiple universities in Europe and Asia, he has core experience in science globalization.
Structural Biochemistry: A versatile tool to study biological reactions
Structural biochemistry employs structure in conjunction with biochemical and biophysical tools to understand molecular mechanism in biological system. Here, we study two major problems of importance to the Indian scenario; first towards understanding and devising strategies towards combating antibiotic resistance and second in development of biosensors for water quality monitoring. The first problem pertains towards combating the problem of antibiotic resistance. Here, we take a two-fold approach, first, towards discovery of novel enzymes that are divergent between human and pathogens as potential new targets and second focuses on understanding why do pathogens become resistant to existing drugs? Towards the first approach we have selected nucleobase deaminases as model systems to search for alternative therapies. These deaminases are essential enzymes and are structurally very different between humans and bacteria. This difference has already lead them to be used as prodrug-enzyme systems for cancer therapy and now we are exploiting them towards developing therapies for antimicrobial resistance. The problem pertaining to origins of antibiotic resistance involves unearthing molecular mechanisms that promote it. Two prominent systems have been undertaken, the tetracycline efflux pump regulators that activate efflux pumps that deplete antibiotic concentrations in the cells and ribosomal modifying enzymes with focus on methyltransferases that cause a steric clash with certain antibiotics thus result in evading their action. By solving a series of crystal structures of antibiotic efflux pump regulators as well as ribosomal methytransferases with and without DNA and complimenting these studies with biochemical and fluorescence spectroscopy we have delineated strategies to combat antibiotic resistance.
Towards developing biosensors,NtrC transcription regulators that activate sigma 54 class of polymerases and facilitate transcription of stress and virulence combating genes were selected for study. This is because these proteins have a self contained sensor and readout domain on a single polypeptide and thus pose as an efficient sensing-readout system. In this regards the class of sensors that we focused pertain to aromatic xenobiotics like phenol, benzene etc which are prominent pollutants from petroleum, dye and petrochemical industries. The crystal structure of the phenol sensing domain solved by us for this class of enzymes opened the doors towards design of a battery of specific sensors for both phenol as well as benzene group of compounds. The detection of these compounds was further optimized to low ppb levels and the shelf life, stability and sensitivity optimized to yield sensors that are potentially compatible in a commercial setting. Their xenobiotic sensing potential was further exploited by employing a combination of structure based design as well as mutagenesis created biosensors for not only phenol but xyenols, benzene derivatives and other aromatic pollutants. The sensor design has been translated to a chip based design where, the protein has been immobilized onto mesoporous silica nanoparticles. The aim is to create cheap and effective biosensor units that can detect these pollutants insitu.
Quantum Dot Antennae for Photovoltaics
The low-cost third-generation photovoltaic devices with semiconductor quantum dot (QD) absorbers are becoming popular due to the QDs having band gap tunability, high absorption coefficient, solution processability, multiple exciton generation and stability.1-8 Nonetheless owing to the inherent drawback of abundant surface trap states in QDs, the propensity of interfacial charge recombination have always limited their power conversion efficiencies (PCE). In spite of such challenges, QD sensitized solar cells (QDSSCs) have emerged as the newest technology in the NREL chart and CsPbI3 happen to be the new QD leader in 2017 with PCE of 13.4%. This lecture at first will discuss our efforts to improve the photoanode performance of liquid junction QDSSCs with core-shell II-VI and I-III-VI QD absorbers,4-6 along with the counter electrode strategies.7 The second part of this lecture will deal with few of our approaches to fabricate relatively stable all-inorganic lead perovskite QD sensitized solar cells.9,10 Our approach has been validated by transient absorption spectroscopy which shows lesser abundance of trap states and enhanced charge carrier recombination lifetime.
(1) Halder, G.; Ghosh, D.; Ali, Md. Y.; Sahasrabudhe, A.; Bhattacharyya, S. Langmuir 2018, 34, 10197-10216. (Invited Feature Article)
(2) Ghosh, D.; Halder, G.; Sahasrabudhe, A.; Bhattacharyya, S. Nanoscale 2016, 8, 10632-10641.
(3) Sahasrabudhe, A.; Kapri, S.; Bhattacharyya, S. Carbon 2016, 107, 395-404.
(4) Sahasrabudhe, A.; Bhattacharyya, S. Chem. Mater. 2015, 27, 4848-4859.
(5) Halder, G.; Bhattacharyya, S. J. Mater. Chem. A 2017, 5, 11746-11755.
(6) Halder, G.; Ghosh, A.; Parvin, S.; Bhattacharyya, S. Chem. Mater. 2018, DOI: 10.1021/acs.chemmater.8b03743.
(7) Ghosh, D.; Ghosh, A.; Ali, Md. Y.; Bhattacharyya, S. Chem. Mater. 2018, 30, 6071-6081.
(8) Halder, G.; Bhattacharyya, S. J. Phys. Chem. C 2015, 119, 13404-13412.
(9) Ghosh, D.; Ali, Md. Y.; Chaudhary, D. K.; Bhattacharyya, S. Sol. Energy Mater. Sol. Cells 2018, 185, 28-35.
(10) Unpublished results.
Synthesis and Photophysical Quenching study of Chromophores Covalently linked with TEMPO Free Radical
N-H...N Hydrogen Bonded Complexes of Benzimidazole and Indole: Excited and Cationic State Characterization and Proton Transfer Energetics and Dynamics
Hydrogen Production from Water (via Photoelectrochemical Water Splitting) and Biomass Derivatives (via Aqueous Phase Reforming)
Hydrogen production from renewable sources such as water and biomass derivatives, is a promising and sustainable way of storing energy in the form of chemical fuel on a large-scale. In this regard, photoelectrochemical (PEC) water splitting has been found to be a potential approach and therefore, has been extensively studied in recent years. The desired efficiency of > 10% (STH) has already been achieved in laboratory scale. However, the stability of most of the suitable semiconductors (absorber layer in photoelectrodes) is a major issue due to the existence of corrosion potentials within the bandgap.
This talk presents the development of stable photocathode (for H2 evolution) and photoanode (for O2 evolution) devices based on Cu2O and CdS as the light absorber respectively. Inherent in the above statement is the development of low-cost, efficient, and robust protective layers for the devices in both substrate (device on Au-coated glass) and superstrate (device on F-doped SnO2, FTO-coated glass) configurations. Photoinduced conducting atomic force microscopy (c-AFM) reveals shunts and sub-bandgap states at the grain boundaries of the electrodeposited Cu2O. To minimize shunting, we developed a method to obtain larger grains of Cu2O via electrodeposition (two-step deposition) method. The Cu2O photocathodes were protected with electron selective layers of ALD-TiO2 (~ 10 nm) and CVD-Graphene, resulting in higher photocurrent (3 mA cm-2), twice that of a bare Cu2O electrode at 0.0 V vs RHE. The protected device shows a slow decay till 5-6 min and later, it generates stable photocurrent till 35 min of the experiment.
The photoanode was fabricated via a low-cost solution processing method in a core-shell structure for effective charge separation. The core, ZnO nanorods were optimized to grow sparsely such that the active absorber material, CdS can be loaded more in the interspace of the nanorods. A mesoporous (m-) NiO layer on top led to the mitigation of photocorrosion, acted as a cocatalyst to enhance the kinetics of oxygen evolution reaction, and provided a larger surface area at the electrode-electrolyte interface. The m-NiO coated photoanode resulted in a stable photocurrent of 2.15 mA cm-2 at 1.23 V vs RHE.
Apart from the above projects, this talk also includes the synthesis of an active and stable catalyst for Aqueous Phase Reforming (APR) of diol and polyol for H2 production in fixed-bed and batch reactors. Pt, Ru on Al2O3 and Ac-Carbon shows good activity. However, the metal nanoparticles agglomerate within a short period of time in the reaction condition, thereby slowing down the conversion rate. Use of m-Carbon as support may be a major focus of future study.
Conformation, dynamics and cellular interaction of amyloid peptides
Organic Photocatalysis inside Water-Soluble Supramolecular Cages
Nanoparticles in Fundamental and Applied Research
Local probing of nanoscopic matter by spectroscopy and spectromicroscopy is reviewed. Targets are free nanoparticles in the gas phase, nanoscopic matter in liquid microdroplets, deposited nanosystems, and nanoscopic matter in biological surroundings. The experimental studies are primarily performed by tunable soft X-rays, in the infrared regime, as well as complimentary radiation sources, including free electron lasers and laboratory-based laser sources.
Properties of free nanoparticles prepared in a narrow beam are investigated by soft X-rays. This approach has the advantage that single particles without any contact to a substrate are probed and radiation damage and charging effects are efficiently suppressed. The emission of electrons or ions is probed as a function of photon energy. Especially photoemission studies reveal distinct information on the surface composition of heterogeneous nanoparticles, indicating segregation phenomena . Characteristic asymmetries in photoelectron angular distributions have been probed yielding detailed information on photoelectron elastic scattering processes allowing for a quantification of the number of elastic scattering events the photoelectrons have undergone prior to leaving the sample . The dynamics of photoemission from free nanoparticles leading to processes occurring in the femto- and atto-second regimes will be briefly mentioned. This requires the use of free electron lasers and ultra-short laser pulses .
Nanoscopic matter can also be formed in levitated supersaturated and supercooled microdroplets for investigating nucleation processes in metastable liquids. Structural properties of pre-nucleation clusters are identified by a combination of near-edge spectroscopy and molecular dynamics calculations . In the role of excess charges on the nucleation of liquid microdroplets has been evaluated, since these influence massively the nucleation processes .
Finally, topical drug delivery into skin probed by label-free spectromicroscopy is reported. The role of drug formulations and polymeric nanocarriers as efficient drug transport vehicles is evaluated regarding their penetration into deeper skin layers [6, 7]. Selective and high spatial resolution detection of drugs and drug nanocarriers is accomplished by X-ray microscopy and complementary methods, such as atomic force microscopy-based spectroscopic approaches in the infrared regime [8, 9] and stimulated Raman microscopy . Recent results on the penetration of the anti-inflammatory drug dexamethasone are reported, where the drug is topically applied to human and murine skin samples ex vivo, reaching a spatial resolution below 10 nm.
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Emerging Photovoltaics: Bounds and Challenges
Shockley-Queisser (S-Q) model gives the upper limit for light to electrical power conversion efficiency (PCE) of a single junction photovoltaic cell. The efficiency of a real-world single junction solar cell will always be below the S-Q limit as real material properties come into the play. In this seminar, I will present a common formalism that considers factors beyond the S-Q model and enables us to analyze the performance of all kinds of solid-state single junction solar cell. This is relevant in the present époque since it gives a chance to compare the disparate and technology-focussed strands of PV research. I will discuss the material and cell properties that are needed for a high-performing solar cell. There have been remarkable developments, most notably in organic-photovoltaics and perovskite photovoltaics. I will explain what has been done in the past half-decade to improve the cell performances and what to look forward.
I will present a novel way of electronic doping of organic semiconductors which is essential for realizing high-performance organic-based and perovskite-based optoelectronic devices, particularly the solar cells. I will discuss the mechanism of the doping process and its application in devices. This dart cheap method makes the existing expensive commercial p-type dopants obsolete and opens up new avenues of electronic doping.
Intriguing formation pathways of metal halide perovskites and their impact
Metal halide perovskites-based optoelectronic devices have shown remarkable progress in the last several years. However, despite their success in the device performances, there remain many open questions about their fundamental properties. Single crystals are often seen as the model for understanding the fundamental properties and assessing the limits and possibilities of these materials. In addition to delivering high-quality crystals, the nature of the crystallization is closely related to the crystallization of perovskites in thin films, and proper understanding of the mechanism enables a critically needed advance in the reproducibility and quality of both thin films and single crystals for optoelectronic devices.
In this seminar, I will unveil the reasons behind the observed rapid crystallization in metal halide perovskites. I will show the applications of the newly found information towards the preparation of high-quality thin films, single crystals, and solar cells. To consolidate the electronic properties of these hybrid materials, I will present a comparative study on single crystals and polycrystalline thin films. I will then discuss the impact of heterovalent doping in halide perovskites which is contrary to earlier conclusions. These findings are of central importance to enabling the continued advancement of perovskite optoelectronics and to the improved reproducibility, homogeneity and eventual manufacturability of these technologies. In passing, I will discuss the role of interfacial chemistry in the development of semi-transparent and flexible perovskite-based solar cells.