Theory of high bias Coulomb Blockade in ultrashort molecules

We point out that single electron charging effects such as Coulomb Blockade (CB) and high-bias staircases play a crucial role in transport through single ultrashort molecules. A treatment of Coulomb Blockade through a prototypical molecule, benzene, is developed using a master-equation in its complete many-electron Fock space, evaluated through exact diagonalization or full Configuration Interaction (CI). This approach can explain a whole class of non-trivial experimental features including vanishing zero bias conductances, sharp current onsets followed by ohmic current rises, and gateable current levels and conductance structures, most of which cannot be captured even qualitatively within the traditional Self Consistent Field (SCF) approach coupled with perturbative transport theories. By comparing the two approaches, namely SCF and CB, in the limit of weak coupling to the electrode, we establish that the inclusion of strong-correlations within the molecule becomes critical in addressing the above experiments. Our approach includes on-bridge-correlations fully, and is therefore well-suited for describing transport through short molecules in the limit of weak coupling to electrodes.Comment: 19 pages 5 figure

White Light Emission in Butadiyne Bridged Pyrene–Phenyl Hybrid Fluorophore: Understanding the Photophysical Importance of Diyne Spacer and Utilizing the Excited-State Photophysics for Vapor Detection

Generation of white light emission (WLE) from a single organic fluorophore is challenging because of the need to get fluorescence covering the visible region (400–700 nm) upon excitation of the dye at near-ultraviolet wavelength. Herein, we report WLE from a butadiyne bridged pyrene–phenyl hybrid fluorophore in mixed-aqueous solvents as well as in polymer film matrices. The ability of the butadiynyl dye to emit from multiple excited states such as locally excited (LE; 400–500 nm), aggregate (excimer type; 475–600 nm), and charge transfer (CT; 500–750 nm) states spanning the emission almost throughout the visible range has made the generation of the white light to be possible. In highly polar solvent such as acetonitrile, the butadiynyl dye emits from the LE and CT states, and the WLE is achieved through a control of the dye concentration such that intermolecular CT (exciplex type) contributes along with the intramolecular CT and LE emissions. In mixed-aqueous systems such as water–acetonitrile and water–<i>N</i>,<i>N</i>-dimethylformamide, the CT emission is red-shifted (because of the high dielctric constant of water), and the contribution of the aggregate emission (originated because of the poor solvent water) is important in maintaining the relative distribution of the fluorescence intensities (LE, excimer, and CT) in the entire visible region. The significance of the diyne spacer in achieving the WLE is delineated through a control study with a single acetylenic analogue. The LE, aggregate, and CT emissions are involved in generating bluish-white light in a poly­(vinyl alcohol) film matrix of the butadiynyl dye. Blue emission is noted in a poly­(methyl methacrylate) (PMMA) film matrix of the dye with a major contribution from the LE and a minor contribution from the aggregate state. Exposure of the PMMA film of the dye to polar aprotic vapors assists in gaining the CT state emission such that the LE, aggregate, CT emissions cover the entire visible region to produce the WLE. This opens a new strategy for selective vapor sensing

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein.

Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limitations in the time scales of MD simulations and the time resolution of single-molecule measurements have challenged efforts to obtain overlapping temporal regimes required for close quantitative comparisons. Achieving such overlap has the potential to provide novel theories, hypotheses, and interpretations that can inform idealized experimental designs that maximize the detection of the desired reaction coordinate. Here, we report MD simulations at time scales overlapping with in vitro single-molecule Förster (fluorescence) resonance energy transfer (smFRET) measurements of the amino acid binding protein LIV-BPSS at sub-millisecond resolution. Computationally efficient all-atom structure-based simulations, calibrated against explicit solvent simulations, were employed for sampling multiple cycles of LIV-BPSS clamshell-like conformational changes on the time scale of seconds, examining the relationship between these events and those observed by smFRET. The MD simulations agree with the smFRET measurements and provide valuable information on local dynamics of fluorophores at their sites of attachment on LIV-BPSS and the correlations between fluorophore motions and large-scale conformational changes between LIV-BPSS domains. We further utilize the MD simulations to inform the interpretation of smFRET data, including Förster radius (R0) and fluorophore orientation factor (κ2) determinations. The approach we describe can be readily extended to distinct biochemical systems, allowing for the interpretation of any FRET system conjugated to protein or ribonucleoprotein complexes, including those with more conformational processes, as well as those implementing multi-color smFRET

Photophysics of Diphenylbutadiynes in Water, Acetonitrile–Water, and Acetonitrile Solvent Systems: Application to Single Component White Light Emission

Diacetylenes have been the subject of current research because of their interesting optoelectronic properties. Herein, we report that substituted diphenylbutadiynes exhibit locally excited (LE) and excimer emissions in water and multiple emissions from the LE, excimer, and intramolecular charge transfer (ICT) states in acetonitrile–water solvent systems. The LE, excimer, and ICT emissions are clearly distinguishable for a diphenylbutadiynyl derivative with push (−NMe₂)–pull (−CN) substituents and those are closely overlapped for non-push–pull analogues. In neat acetonitrile, the excimer emission disappears and the LE and ICT emissions predominate. In the case of the push (−NMe₂)–pull (−CN) diphenylbutadiyne, the intensity of the ICT emission increases with increasing the fluorophore concentration. This suggests that the ICT emission accompanies with intermolecular CT emission which is of exciplex type. As the LE and exciplex emissions of the push–pull diphenylbutadiyne together cover the visible region (400–700 nm) in acetonitrile, a control of the fluorophore concentration makes the relative intensities of the LE and exciplex emissions such that pure white light emission is achieved. The white light emission is not observed in those diphenylbutadiynyl analogues in which the peripheral substituents of the phenyl rings do not possess strong push–pull character

Deciphering the Photophysical Role of Conjugated Diyne in Butadiynyl Fluorophores: Synthesis, Photophysical and Theoretical Study

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 E_T(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

Tuning the Baird aromatic triplet-state energy of cyclooctatetraene to maximize the self-healing mechanism in organic fluorophores

Bright, photostable, and nontoxic fluorescent contrast agents are critical for biological imaging. "Self-healing" dyes, in which triplet states are intramolecularly quenched, enable fluorescence imaging by increasing fluorophore brightness and longevity, while simultaneously reducing the generation of reactive oxygen species that promote phototoxicity. Here, we systematically examine the self-healing mechanism in cyanine-class organic fluorophores spanning the visible spectrum. We show that the Baird aromatic triplet-state energy of cyclooctatetraene can be physically altered to achieve order of magnitude enhancements in fluorophore brightness and signal-to-noise ratio in both the presence and absence of oxygen. We leverage these advances to achieve direct measurements of large-scale conformational dynamics within single molecules at submillisecond resolution using wide-field illumination and camera-based detection methods. These findings demonstrate the capacity to image functionally relevant conformational processes in biological systems in the kilohertz regime at physiological oxygen concentrations and shed important light on the multivariate parameters critical to self-healing organic fluorophore design

Abstracts of National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020

This book presents the abstracts of the papers presented to the Online National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020 (RDMPMC-2020) held on 26th and 27th August 2020 organized by the Department of Metallurgical and Materials Science in Association with the Department of Production and Industrial Engineering, National Institute of Technology Jamshedpur, Jharkhand, India. Conference Title: National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020Conference Acronym: RDMPMC-2020Conference Date: 26–27 August 2020Conference Location: Online (Virtual Mode)Conference Organizer: Department of Metallurgical and Materials Engineering, National Institute of Technology JamshedpurCo-organizer: Department of Production and Industrial Engineering, National Institute of Technology Jamshedpur, Jharkhand, IndiaConference Sponsor: TEQIP-