Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

scholarly journals Two-photon sensitive protecting groups operating via intramolecular electron transfer: uncaging of GABA and tryptophan

2015 ◽  
Vol 6 (4) ◽  
pp. 2419-2426 ◽  
Author(s):  
Karolina A. Korzycka ◽  
Philip M. Bennett ◽  
Eduardo Jose Cueto-Diaz ◽  
Geoffrey Wicks ◽  
Mikhail Drobizhev ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Photoinduced Electron Transfer ◽  
High Sensitivity ◽  
Protecting Groups ◽  
Intramolecular Electron Transfer ◽  
Modular Approach ◽  
Two Photon ◽  
Photon Excitation ◽  
Two Photon Excitation

We present a modular approach to photo-labile protecting groups based on photoinduced electron transfer, providing high sensitivity to two-photon excitation.

scholarly journals DFT Study of Binding and Electron Transfer from a Metal-Free Dye with Carboxyl, Hydroxyl, and Sulfonic Anchors to a Titanium Dioxide Nanocluster

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Corneliu I. Oprea ◽  
Petre Panait ◽  
Jeanina Lungu ◽  
Daniela Stamate ◽  
Anca Dumbravă ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Density Functional ◽  
Dye Sensitized Solar Cells ◽  
Disodium Salt ◽  
Carboxyl Group ◽  
Functional Theory ◽  
Metal Free ◽  
Anchor Group ◽  
Sensitized Solar Cells

We report results of density functional theory (DFT) calculations of a metal-free dye, 5-(4-sulfophenylazo)salicylic acid disodium salt, known as Mordant Yellow 10 (MY-10), used as sensitizer for TiO2dye-sensitized solar cells (DSSCs). Given the need to better understand the behavior of the dyes adsorbed on the TiO2nanoparticle, we studied various single and double deprotonated forms of the dye bound to a TiO2cluster, taking advantage of the presence of the carboxyl, hydroxyl, and sulfonic groups as possible anchors. We discuss various binding configurations to the TiO2substrate and the charge transfer from the pigment to the oxide by means of DFT calculations. In agreement with other reports, we find that the carboxyl group tends to bind in bidentate bridging configurations. The salicylate uses both the carboxyl and hydroxyl substituent groups for either a tridentate binding to adjacent Ti(IV) ions or a bidentate Ti-O binding together with an O-H-O binding, due to the rotation of the carboxyl group out of the plane of the dye. The sulfonic group prefers a tridentate binding. We analyze the propensity for electron transfer of the various dyes and find that for MY-10, as a function of the anchor group, the DSSC performance decreases in the order hydroxyl + carboxyl > carboxyl > sulfonate.

A Carbon-Based DNA Framework Nano–Bio Interface for Biosensing with High Sensitivity and a High Signal-to-Noise Ratio

ACS Sensors ◽  
2020 ◽  
Vol 5 (12) ◽  
pp. 3979-3987
Author(s):  
Jing Su ◽  
Wenhan Liu ◽  
Shixing Chen ◽  
Wangping Deng ◽  
Yanzhi Dou ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
High Sensitivity ◽  
High Signal ◽  
Signal To Noise ◽  
Noise Ratio ◽  
Carbon Based

scholarly journals Polydopamine and eumelanin molecular structures investigated with ab initio calculations

2017 ◽  
Vol 8 (2) ◽  
pp. 1631-1641 ◽  
Author(s):  
Chun-Teh Chen ◽  
Francisco J. Martin-Martinez ◽  
Gang Seob Jung ◽  
Markus J. Buehler
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Molecular Structures ◽  
Brute Force ◽  
Functional Theory

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

scholarly journals Direct estimation of the transfer integral for photoinduced electron transfer from TD DFT calculations

2017 ◽  
Vol 19 (46) ◽  
pp. 31007-31010 ◽  
Author(s):  
Lluís Blancafort ◽  
Alexander A. Voityuk
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Charge Separation ◽  
Photoinduced Electron Transfer ◽  
Simple Approach ◽  
Electronic Coupling ◽  
Td Dft ◽  
Photoinduced Charge Separation ◽  
Transfer Integral ◽  
Photoinduced Charge

A simple approach to estimate the electronic coupling for photoinduced charge separation in materials and biomolecules is proposed.

Simulating Surfactant-Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics

2019 ◽  
Author(s):  
Carlos Ayestaran Latorre ◽  
James Ewen ◽  
Chiara Gattinoni ◽  
Daniele Dini
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Iron Oxide ◽  
Dft Calculations ◽  
Density Functional ◽  
Md Simulations ◽  
Oxide Surfaces ◽  
Interaction Energies ◽  
Functional Theory ◽  
Oxide Interfaces

<div>Understanding the behaviour of surfactant molecules on iron oxide surfaces is important for many industrial applications. Molecular dynamics (MD) simulations of such systems have been limited by the absence of a force-feild (FF) which accurately describes the molecule-surface interactions. In this study, interaction energies from density functional theory (DFT) + U calculations with a van der Waals functional are used to parameterize a classical FF for MD simulations of amide surfactants on iron oxide surfaces. The Original FF, which was derived using mixing rules and surface Lennard-Jones (LJ) parameters developed for nonpolar molecules, were shown to signi cantly underestimate the adsorption energy and overestimate the equilibrium adsorption distance compared to DFT. Conversely, the Optimized FF showed excellent agreement with the interaction energies obtained from DFT calculations for a wide range of surface coverages and molecular conformations near to and adsorbed on a-Fe2O3(0001). This was facilitated through the use of a Morse potential for strong chemisorption interactions, modi fied LJ parameters for weaker physisorption interactions, and adjusted partial charges for the electrostatic interactions. The Original FF and Optimized FF were compared in classical nonequilibrium molecular dynamics (NEMD) simulations of amide molecules con fined between iron oxide surfaces. When the Optimized FF was employed, the amide molecules were pulled closer to the surface and the orientation of the headgroups was more similar to that observed in the DFT calculations compared to the Original FF. The Optimized FF proposed here facilitates classical MD simulations of amide-iron oxide interfaces in which the interactions are representative of accurate DFT calculations.</div>

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