Department of Chemistry

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Author: search.filters.author.Pati, Avik K.Has files: No

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    Organic fluorophores for studying lipid membrane structures and dynamics
    (Wiley, 2025-09) Pati, Avik K.
    Biomembranes act as boundaries between cells and their outside environment and between intracellular compartments, playing integral roles in cellular signaling and communications. A vast body of research has shown that biomembranes are dynamic and heterogeneous, and that they largely vary in lipid compositions and their organizations, governing a plethora of membrane-associated biological processes. Fluorescent tools, including fluorescent contrast agents (fluorophores) and fluorescence imaging modalities, have been demonstrated to be powerful in studying lipid membrane structures and dynamics. Here, we review recent progress in lipid membrane probes based on organic fluorophore designs and their uses in studying lipid membrane properties in plasma membranes and various organelle membranes. In this context, we also highlight applications of these fluorescent membrane probes in diverse fluorescence-based imaging settings that advance lipid membrane research.
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    Microsolvation-driven hours-long spectral dynamics in phenoxazine dyes
    (ACS, 2024-12) Pati, Avik K.
    The phenoxazine class of dyes has found widespread applications in chemistry and biology for more than a century, particularly for lipid membrane studies. Here, we report a general phenomenon on the ensemble spectral stability of traditional phenoxazine class of dyes (nile red, cresyl violet, and nile blue) that exhibit hours-long microstructural transitions reflected through systematic changes of electronic spectra over an hour. Mechanistic investigations reveal that such spectral dynamics of the dyes can be mitigated by tuning microenvironments, where microsolvation plays an underlying role. These microsolvation-induced microstructural changes in a single dye species tend to follow zeroth-order kinetics. The half-life values of such processes systematically vary with solvent hydrogen bonding strength and ionic radius of the dyes’ counteranions. In so doing, using a model lipid membrane, we demonstrate that the spectral response of a phenoxazine dye must be utilized appropriately for studying membrane properties. These findings of the phenoxazine class of dyes are of high significance for their careful applications in chemistry and biology
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    Search for improved triplet-state quenchers for fluorescence imaging: a computational framework incorporating excited-state Baird-aromaticity
    (RSC, 2025-03) Pati, Avik K.
    Fluorescence imaging is crucial for studying biology. Triplet state quenchers (TSQs), especially cyclooctatetraene (COT), can dramatically improve fluorophore performance, particularly when linked intramolecularly so as to enable “self-healing”. Leveraging knowledge revealed through investigations of the self-healing mechanism enabled by COT, we computationally screened for cyclic 8π-electron species, and their annulated derivatives, with efficient triplet–triplet energy transfer potential, high photostability, and strong spin–orbit coupling (SOC) between the lowest triplet state to the singlet ground state. Here, we report theory-based analyses of a broad array of candidates that demonstrate various extents of triplet state Baird-aromaticity, indicating self-healing potential. We identify specific candidates with 7-membered ring structures predicted to exhibit favorable enhancements in fluorophore performance spanning the visible spectrum, with several possessing estimated intersystem crossing (ISC) rates up to 4 × 106 times faster than that of COT, the current benchmark for the self-healing strategy.
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    Diverse fluorescent probe concepts for detection and monitoring of reactive oxygen species
    (Wiley, 2025-02) Pati, Avik K.
    World-wide research on reactive oxygen species (ROS) continues to reveal new information about the role and impact of ROS on human health and disease. ROS are generated in live cells as a byproduct of aerobic metabolism. Physiological concentrations of cellular ROS are important for signaling and homeostasis, but excessive generation of ROS causes apoptotic and necrotic cell death and various health disorders. Fluorescence technology is a powerful tool to detect, monitor, and image cellular ROS. The present review provides an overview of diverse organic dye-based fluorescent probe concepts that involve modifications of traditional fluorescent dyes utilizing basic principles of dye chemistry and photophysics. Fluorescence responses of the probes and their specificity towards ROS are discussed through analyses of their photophysical and photochemical parameters. We also provide an outlook on future directions of ROS-responsive fluorescent dyes, which could enable the design and development of advanced probes for gaining deeper insights into redox biology.
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    BPS2025 - Dissecting the mechanism of aminoglycoside-induced miscoding with spatially multiplexed single-molecule FRET
    (Elsevier, 2025-02) Pati, Avik K.
    The kinetic mechanism of mRNA decoding has been established through ensemble kinetic investigations using purified translation components from Escherichia coli. Pre-steady state single-molecule fluorescence resonance energy transfer (smFRET) measurements have directly revealed insights into the movement of aminoacyl-tRNA (aa-tRNA) within the A site of the ribosome and their mRNA codon-dependencies. Here, we have interrogated the conformational dynamics of aa-tRNA on the ribosome during mRNA decoding using a multiplexed smFRET approach that facilitates side-by-side comparisons of multiple samples under identical experimental conditions. We demonstrate the utility of this approach by simultaneously examining the process of elongation factor-Tu (EF-Tu) facilitated Phe-tRNAPhe incorporation into 4 distinct initiation complexes bearing either cognate or near-cognate codons in the A site. As expected from prior ensemble investigations, our results show that the cognate Phe codons, UUU and UUC, exhibit distinctions in the rates of tRNA selection and those near-cognate codons (CUC and UCC) efficiently reject Phe-tRNAPhe during early steps of tRNA selection prior to GTP hydrolysis. We then examined the impacts of the miscoding antibiotic streptomycin on mRNA decoding. Prior ensemble investigations report that streptomycin slows cognate tRNA selection and accelerates near-cognate tRNA selection during intermediate steps of mRNA decoding to homogenize the rates of GTP hydrolysis and peptide bond formation. Our findings show that the primary impact of streptomycin is to accelerate the rates of mRNA decoding for both cognate and near-cognate ribosome complexes, while slowing the rates of aa-tRNA binding to the A site of the ribosome. These data are consistent with streptomycin favoring “closed” conformational states of the small subunit shoulder domain prior to aa-tRNA binding that inhibit early codon recognition steps where the tRNA anticodon is escorted by EF-Tu into the A site decoding region on the small ribosomal subunit.
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    Deciphering the Photophysical Role of Conjugated Diyne in Butadiynyl Fluorophores: Synthesis, Photophysical and Theoretical Study
    (ACS, 2013-07) Pati, Avik K.
    The present work focuses on the current interest in diyne bridged chromophores necessitating a clearer understanding of the photophysics of such molecules. The significance of the diyne moiety in the photophysics has been investigated by synthesizing simple substituted diphenyl butadiynyl derivatives following a quick and efficient microwave assisted Eglinton coupling of terminal alkynes. Emission of the fluorophores is observed from the usual locally excited (LE) state and intramolecular charge transfer (ICT) state. Separation of pure ICT emission from pure LE emission has been carried out by Gaussian/Lorentzian curve fitting. The vibronic coupling in the local transitions appears to be confined to the normal mode involving the C–C triple bond stretching of the diyne moiety. This implies that the LE transition involves the diyne moiety, a conclusion supported by quantum chemical calculations. The resolved ICT emission follows double linear dependence on ET(30) solvent polarity scale. The important role of the diyne moiety in the photophysics of this class of molecules is clearly discernible in this study.
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    Photoinduced solid state keto–enol tautomerization of 2-(2-(3-nitrophenyl)-4,5-diphenyl-1H-imidazol-1-yloxy)-1-phenylethanone
    (RSC, 2014) Pati, Avik K.
    Excited state intramolecular proton transfer (ESIPT) plays an important role in biological systems and has also recently found applications in electronic devices such as transducers, switches etc. In this paper we report the synthesis and solid state photochromic behavior of 2-(2-(3-nitrophenyl)-4,5-diphenyl-1H-imidazol-1-yloxy)-1-phenylethanone (II) due to ESIPT. Compound II exhibits yellow color in dark and red color in light, with the yellow form attributed to the keto derivative and the red form assigned to its enol derivative The color change in the presence of light is thus attributed to the keto–enol tautomerism through ESIPT. The color change from yellow to red is a photochemical process which thermally decays to the yellow form in the dark. The solid state stability of the enol form upon phototautomerization of the keto form is a noteworthy phenomenon, and its stability has been substantiated by our experimental findings. In the solution state, the yellow form (keto) is stable in chloroform while the red form (enol) is stable in DMSO. Theoretical calculations have been performed to understand the geometries and electronic transitions of the keto and enol forms. In addition, ground and excited state equilibrium constants for the keto–enol tautomerism were calculated.
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    Substituted diphenyl butadiynes: a computational study of geometries and electronic transitions using DFT/TD-DFT
    (RSC, 2014) Pati, Avik K.
    This work is aimed at theoretical understanding of electronic absorption and emission energies of a series of substituted diphenyl butadiynes through an assessment of several TDDFT functionals and a detailed study of solvent effects on their ground and excited state structures and properties. Out of a series of functionals examined, the coulomb attenuated DFT functional CAM-B3LYP is found to be most successful in predicting charge transfer absorption and emission energies of such derivatives. However, TDDFT potential energy surfaces obtained from hybrid functionals such as B3LYP and PBE0 are found to give a good description of the stability of locally excited (LE) and intramolecular charge transfer (ICT) states as a function of torsional angle, for the butadiynyl fluorophores. Interesting structural variations are observed in the ground and excited state optimized geometries of the fluorophores. The ICT emission of the butadiynyl fluorophores is observed to originate from the twisted state where the two phenyl rings in the diphenyl butadiyne get twisted around the butadiyne moiety. A bending of the butadiyne moiety is noted for some of the butadiynyl derivatives in the ICT emissive state. In addition, the direction of absorption and emission transition dipole moment vectors of the butadiynyl fluorophores is found to depend on the nature of substituents present at the periphery of the diphenyl butadiyne moiety.
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    Meta Effect of Absorption Energy in Donor–Acceptor Substituted Benzenoids: A Computational Study of Its Dependence on Acceptor Strength, Solvent Polarity, and Conjugation Length
    (ACS, 2014-08) Pati, Avik K.
    The present work focuses on theoretical understanding of electronic absorption energies of N,N-dimethylaniline with different ortho-, meta-, and para-substituted acceptor groups. The meta isomers exhibit the lowest absorption energy compared to the ortho and para derivatives. This unusual behavior of absorption energies of the meta isomers is related to the “meta effect” well-known in organic photochemical reactions. The meta effect of absorption energy of the derivatives is found to depend on the strength of acceptors, solvent polarity, and conjugation length. The meta derivatives with strong acceptor groups generally exhibit the lowest absorption energy over the other isomers irrespective of solvent polarity. However, the meta isomers with weak acceptor groups exhibit the meta effect only in highly polar solvents. The trend of the lowest absorption energies of the meta isomers is observed to change if the acceptor group is bridged through π conjugation unit (n) with the core moiety. The normal pattern of absorption energy that is the para isomer is of lowest energy is observed to occur for the derivatives where the repeated conjugation units (n) are between 2 and 4. The normal pattern of absorption energy is continued to observe from n > 4 for all the derivatives.
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    On the photophysics of butadiyne bridged pyrene–phenyl molecular conjugates: multiple emissive pathways through locally excited, intramolecular charge transfer and excimer states
    (RSC, 2015-01) Pati, Avik K.
    The present work describes the photophysical properties of a group of butadiyne bridged pyrene–phenyl molecular hybrids having different substitutions with varying donor and acceptor abilities. In addition to emission from the locally excited (LE) state originating from the pyrene moiety, intramolecular charge transfer (ICT) emissions were observed in molecules with donor–acceptor character. The positions of the ICT emission maxima varied over a wide range of wavelengths (475–600 nm). Pyrene behaved as a donor when a strong acceptor group (–CN) was attached to the phenyl ring and it behaved as an acceptor when the phenyl group contained a strong donor group (–NMe2). In mixed aqueous solvents at higher percentages of water (80–99%), the derivatives showed emissions from the aggregate state in addition to the LE and ICT states. Emissions from the aggregate states of the derivatives were centred in the range 510–560 nm. The aggregate state emissions were found to originate from static excimers involving pyrene moieties. A detailed structure–property relationship of the butadiynyl derivatives was revealed in this study.