A5046826497- Protein Structure and Dynamics
- Molecular Junctions and Nanostructures
- Advanced biosensing and bioanalysis techniques
- Enzyme Structure and Function
- DNA and Nucleic Acid Chemistry
- Force Microscopy Techniques and Applications
- RNA and protein synthesis mechanisms
- Spectroscopy and Quantum Chemical Studies
- Photoreceptor and optogenetics research
- Photochemistry and Electron Transfer Studies
- Peptidase Inhibition and Analysis
- Electrochemical Analysis and Applications
- Mass Spectrometry Techniques and Applications
- Molecular Sensors and Ion Detection
- Photosynthetic Processes and Mechanisms
- Alzheimer's disease research and treatments
- Cancer-related Molecular Pathways
- Microtubule and mitosis dynamics
- Computational Drug Discovery Methods
- Click Chemistry and Applications
- Supramolecular Self-Assembly in Materials
- Biotin and Related Studies
- Ubiquitin and proteasome pathways
- Diabetes Treatment and Management
- Spectroscopy and Laser Applications
Tata Institute of Fundamental Research
2016-2025
University of Pennsylvania
2007-2017
University of Mumbai
2016
Duke University
2008-2014
Center for Child and Family Health
2008-2010
Carnegie Mellon University
2009-2010
University of Pittsburgh
2009-2010
Temple University
2010
University of Rochester
2002-2005
University of California, Irvine
2005
We report 250–800 nm UV-Vis monomeric protein absorption originating from backbone–sidechain and sidechain–sidechain charge transfer transitions involving Lys/Glu residues.
The effects of structural fluctuations on charge transfer in double-stranded DNA and peptide nucleic acid (PNA) are investigated. A palindromic sequence with two guanine bases that play the roles hole donor acceptor, separated by a bridge adenine bases, was analyzed using combined molecular dynamics (MD) quantum-chemical methods. Surprisingly, electronic structure calculations individual MD snapshots show significant frontier orbital population ∼10% structures. Electron-density...
In molecular electronics, the linker group, which attaches functional core to electrode, plays a crucial role in determining overall conductivity of junction. While much focus has been placed on optimizing conductivity, there have relatively few attempts at designing optimal groups metallic or semiconducting electrodes. The vast majority electronic studies use thiol groups; work probing alternative amine systems only recently explored. Here, we probe single-molecule conductances...
This study examines quantitative correlations between molecular conductances and standard electrochemical rate constants for alkanes peptide nucleic acid (PNA) oligomers as a function of the length, structure, charge transport mechanism. The experimental data show power-law relationship transfer rates within given class molecules with same bridge chemistry, lack correlation when more diverse group is compared, in contrast some theoretical predictions. Surprisingly, PNA duplexes exhibit...
Light energy absorbed by molecules can be harnessed to activate chemical bonds with extraordinary speed. However, excitation redistribution within various molecular degrees of freedom prohibits bond-selective chemistry. Inspired enzymes, we devised a new photocatalytic scheme that preorganizes and polarizes target inside water-soluble cationic nanocavities engineer selective functionalization. Specifically, present route photoactivate weakly polarized sp
A theoretical framework is presented to describe and understand the observed relationship between molecular conductances charge transfer rates across bridges as a function of length, structure, mechanism. The approach uses reduced density matrix formulation with phenomenological treatment system–bath couplings kinetics Green's based Landauer–Buttiker method steady-state currents. Application independent transport regime includes bath-induced decoherence effects. This model shows that follows...
A water-soluble, cell-permeable, turn-on Mn 2+ sensor visualizes dynamics live and provides an estimate for endogenous labile in a living mammalian cell.
Predictive approaches and rules to connect combine molecular circuit components are required realize the potential of electronics develop miniaturized integrated circuits. To this end, we have recently demonstrated a bis(terpyridine)-based breadboard with four conductance states formed by superposition five 2–5 ring Here, generic analytical/statistical model describe break-junction data use it extract embedded circuits in bis-terpyridine-based junction. The can be used experimentally verify...
We present evidence for a near-resonant mechanism of charge transfer in short peptide nucleic acid (PNA) duplexes obtained through electrochemical, STM break junction (STM-BJ), and computational studies. A seven base pair (7-bp) PNA duplex with the sequence (TA)3-(XY)-(TA)3 was studied, which XY is complementary nucleobase pair. The experiments showed that heterogeneous rate constant (k0) single-molecule conductance (σ) correlate oxidation potential purine electrochemical measurements...
Umbrella sampling (US) is a widely used biased simulation technique to generate projections of free energy surfaces (FES) chemical and biomolecular processes along reaction coordinate (RC). US results are sensitive the choice discretization RC which bias applied as well lengths. Furthermore, combination comparison FES slices from multiple runs remains poorly understood. Here, we address these issues through redefined scheme based on recent statistical insights in equilibration convergence...
Self-assembled monolayers of single-stranded (ss) peptide nucleic acids (PNAs) containing seven nucleotides (TTTXTTT), a C-terminus cysteine, and an N-terminus ferrocene redox group were formed on gold electrodes. The PNA monomer (X) was selected to be either cytosine (C), thymine (T), adenine (A), guanine (G), or methyl (Bk). charge transfer rate through the oligonucleotides found correlate with oxidation potential X. Kinetic measurements computational studies ss-PNA fragments show that...
Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those a γ-methylated (γ-PNA). The common aeg-PNA is achiral molecule flexible structure, whereas γ-PNA chiral significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through bridging unit twice unit. Theoretical calculations of PNA electronic properties, which based on molecular dynamics structural ensemble,...
The third-order optical response of two coupled anharmonic vibrations interacting with a Brownian oscillator bath that induces energy level fluctuations arbitrary time scales and degree correlation is calculated. Two-dimensional plots show distinct signatures these in the various possible three pulse, infrared, femtosecond techniques.
Controlling charge flow in single molecule circuits with multiple electrical contacts and conductance pathways is a much sought after goal molecular electronics. In this joint experimental theoretical study, we advance the possibility of creating breadboard through an analysis bis-terpyridine based (TP1). The TP1 can adopt conformations relative rotations 7 aromatic rings attach to electrodes 61 possible multi-terminal configurations 6 pyridyl groups. Despite complexity, show that it extract...
Decoupling conformational changes from aggregation will help us understand amyloids better. Here we attach Alzheimer's amyloid-β(1-40) monomers to silver nanoparticles, preventing their aggregation, and study conformation under aggregation-favoring conditions using SERS. Surprisingly, the α-helical character of peptide remains unchanged between pH 10.5 5.5, while solubility >100×. Amyloid can therefore start without significant changes.
Optically triggered twisted intramolecular charge transfer (TICT) states in donor–acceptor chromophores form the molecular basis for designing bioimaging probes that sense polarity, microviscosity, and pH vivo. However, a lack of predictive understanding "twist" localization precludes rational design TICT-based dyes. Here, using femtosecond stimulated Raman spectroscopy, we reveal distinct signature TICT state stilbazolium-class mitochondrial staining dye. Resonance-selective probing...
The absorption of light by proteins can induce charge transfer (CT) transitions in the UV-visible range electromagnetic spectrum. Metal-ligand complexes or active site prosthetic groups which absorb visible region exhibit prominent CT transitions. Furthermore, protein backbone also exhibits far UV range. In this manuscript, we present a detailed computational study new near that involve amino acids with charged side chains. Specifically, using time dependent density functional theory...
Metalloproteins carry out diverse biological functions including metal transport, electron transfer, and catalysis. At present, the influence of cofactors on metalloprotein stability is not well understood. Here, we report mechanical unfolding pathway azurin, a cupredoxin family protein with β-barrel topology type I copper-binding centre. Single-molecule force spectroscopy (SMFS) experiments reveal 2-state 3-state pathways for apo-azurin. The intermediate in occurs at an contour length 7.5...
Cyclooctatetraene (COT) is predicted to have a planar aromatic triplet state. Using femtosecond-to-microsecond transient absorption spectroscopy, we show that acene chromophore-fused COT dyes also ring in their states, although they are not aromatic.