1
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Sun K, Vasquez L, Borrelli R, Chen L, Zhao Y, Gelin MF. Interconnection between Polarization-Detected and Population-Detected Signals: Theoretical Results and Ab Initio Simulations. J Chem Theory Comput 2024. [PMID: 39185737 DOI: 10.1021/acs.jctc.4c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Most of spectroscopic signals are specified by the nonlinear laser-induced polarization. In recent years, population-detection of signals becomes a trend in femtosecond spectroscopy. Polarization-detected (PD) and population-detected signals are fundamentally different, because they are determined by photoinduced processes acting on disparate time scales. In this work, we consider the fluorescence-detected (FD) N-wave-mixing (NWM) signal as a representative example of population-detected signals, derive a rigorous expression for this signal, and discuss its approximate variants suitable for numerical simulations. This leads us to the definition of the phenomenological FD (PFD) signal, which contains as a special case all definitions of FD signals available in the literature. Then we formulate and prove the population-polarization equivalence (PPE) theorem, which states that PFD NWM signals produced by (possibly strong) laser pulses can be evaluated as conventional PD signals in which the effective polarization is determined by the PFD transition dipole moment operator. We use the PPE theorem for the construction of the ab initio protocol for the simulation of PFD 4WM signals. As an example, we calculate electronic two-dimensional (2D) PFD spectra of the gas-phase pyrazine and compare them with the corresponding PD 2D spectra.
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Affiliation(s)
- Kewei Sun
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Luis Vasquez
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | | | | | - Yang Zhao
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
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2
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Gustin I, Kim CW, McCamant DW, Franco I. Mapping electronic decoherence pathways in molecules. Proc Natl Acad Sci U S A 2023; 120:e2309987120. [PMID: 38015846 PMCID: PMC10710033 DOI: 10.1073/pnas.2309987120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.
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Affiliation(s)
- Ignacio Gustin
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Chang Woo Kim
- Department of Chemistry, Chonnam National University, Gwangju61186, South Korea
| | - David W. McCamant
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Ignacio Franco
- Department of Chemistry, University of Rochester, Rochester, NY14627
- Department of Physics, University of Rochester, Rochester, NY14627
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3
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Yang J, Gelin MF, Chen L, Šanda F, Thyrhaug E, Hauer J. Two-dimensional fluorescence excitation spectroscopy: A novel technique for monitoring excited-state photophysics of molecular species with high time and frequency resolution. J Chem Phys 2023; 159:074201. [PMID: 37581414 DOI: 10.1063/5.0156297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
We propose a novel UV/Vis femtosecond spectroscopic technique, two-dimensional fluorescence-excitation (2D-FLEX) spectroscopy, which combines spectral resolution during the excitation process with exclusive monitoring of the excited-state system dynamics at high time and frequency resolution. We discuss the experimental feasibility and realizability of 2D-FLEX, develop the necessary theoretical framework, and demonstrate the high information content of this technique by simulating the 2D-FLEX spectra of a model four-level system and the Fenna-Matthews-Olson antenna complex. We show that the evolution of 2D-FLEX spectra with population time directly monitors energy transfer dynamics and can thus yield direct qualitative insight into the investigated system. This makes 2D-FLEX a highly efficient instrument for real-time monitoring of photophysical processes in polyatomic molecules and molecular aggregates.
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Affiliation(s)
- Jianmin Yang
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | | | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, 12116 Prague, Czech Republic
| | - Erling Thyrhaug
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Jürgen Hauer
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
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4
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Liu H, Chen L, Zhang H, Yang Z, Ye J, Zhou P, Fang C, Xu W, Shi J, Liu J, Yang Y, Hong W. Single-molecule photoelectron tunnelling spectroscopy. NATURE MATERIALS 2023; 22:1007-1012. [PMID: 37349394 DOI: 10.1038/s41563-023-01591-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/25/2023] [Indexed: 06/24/2023]
Abstract
Experimental mapping of transmission is essential for understanding and controlling charge transport through molecular devices and materials. Here we developed a single-molecule photoelectron tunnelling spectroscopy approach for mapping transmission beyond the HOMO-LUMO gap of the single diketopyrrolopyrrole molecule junction using an ultrafast-laser combined scanning tunnelling microscope-based break junction set-up at room temperature. Two resonant transport channels of ultrafast photocurrent are found by our photoelectron tunnelling spectroscopy, ranging from 1.31 eV to 1.77 eV, consistent with the LUMO + 1 and LUMO + 2 in the transmission spectrum obtained by density functional theory calculations. Moreover, we observed the modulation of resonant peaks by varying bias voltages, which demonstrates the ability to quantitatively characterize the effect of the electric field on frontier molecular orbitals. Our single-molecule photoelectron tunnelling spectroscopy offers an avenue that allows us to explore the nature of energy-dependent charge transport through single-molecule junctions.
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Affiliation(s)
- Haojie Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Lijue Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Hao Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Zhangqiang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Jingyao Ye
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Ping Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Chao Fang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Wei Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Ye Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, China.
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5
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Jakob LA, Deacon WM, Zhang Y, de Nijs B, Pavlenko E, Hu S, Carnegie C, Neuman T, Esteban R, Aizpurua J, Baumberg JJ. Giant optomechanical spring effect in plasmonic nano- and picocavities probed by surface-enhanced Raman scattering. Nat Commun 2023; 14:3291. [PMID: 37280203 DOI: 10.1038/s41467-023-38124-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 04/17/2023] [Indexed: 06/08/2023] Open
Abstract
Molecular vibrations couple to visible light only weakly, have small mutual interactions, and hence are often ignored for non-linear optics. Here we show the extreme confinement provided by plasmonic nano- and pico-cavities can sufficiently enhance optomechanical coupling so that intense laser illumination drastically softens the molecular bonds. This optomechanical pumping regime produces strong distortions of the Raman vibrational spectrum related to giant vibrational frequency shifts from an optical spring effect which is hundred-fold larger than in traditional cavities. The theoretical simulations accounting for the multimodal nanocavity response and near-field-induced collective phonon interactions are consistent with the experimentally-observed non-linear behavior exhibited in the Raman spectra of nanoparticle-on-mirror constructs illuminated by ultrafast laser pulses. Further, we show indications that plasmonic picocavities allow us to access the optical spring effect in single molecules with continuous illumination. Driving the collective phonon in the nanocavity paves the way to control reversible bond softening, as well as irreversible chemistry.
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Affiliation(s)
- Lukas A Jakob
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - William M Deacon
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Yuan Zhang
- Henan Key Laboratory of Diamond Optoelectronic Materials and Devices, Key Laboratory of Material Physics, Ministry of Education, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, 450052, China.
| | - Bart de Nijs
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Elena Pavlenko
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Shu Hu
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Cloudy Carnegie
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Tomas Neuman
- Center for Material Physics (CSIC-UPV/EHU and DIPC), Paseo Manuel de Lardizabal 5, Donostia-San Sebastian Gipuzkoa, 20018, Spain
| | - Ruben Esteban
- Center for Material Physics (CSIC-UPV/EHU and DIPC), Paseo Manuel de Lardizabal 5, Donostia-San Sebastian Gipuzkoa, 20018, Spain
| | - Javier Aizpurua
- Center for Material Physics (CSIC-UPV/EHU and DIPC), Paseo Manuel de Lardizabal 5, Donostia-San Sebastian Gipuzkoa, 20018, Spain.
| | - Jeremy J Baumberg
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.
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6
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Fersch D, Malý P, Rühe J, Lisinetskii V, Hensen M, Würthner F, Brixner T. Single-Molecule Ultrafast Fluorescence-Detected Pump-Probe Microscopy. J Phys Chem Lett 2023:4923-4932. [PMID: 37207316 DOI: 10.1021/acs.jpclett.3c00839] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce fluorescence-detected pump-probe microscopy by combining a wavelength-tunable ultrafast laser with a confocal scanning fluorescence microscope, enabling access to the femtosecond time scale on the micrometer spatial scale. In addition, we obtain spectral information from Fourier transformation over excitation pulse-pair time delays. We demonstrate this new approach on a model system of a terrylene bisimide (TBI) dye embedded in a PMMA matrix and acquire the linear excitation spectrum as well as time-dependent pump-probe spectra simultaneously. We then push the technique toward single TBI molecules and analyze the statistical distribution of their excitation spectra. Furthermore, we demonstrate the ultrafast transient evolution of several individual molecules, highlighting their different behavior in contrast to the ensemble due to their individual local environment. By correlating the linear and nonlinear spectra, we assess the effect of the molecular environment on the excited-state energy.
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Affiliation(s)
- Daniel Fersch
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Pavel Malý
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague, Czech Republic
| | - Jessica Rühe
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Victor Lisinetskii
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Matthias Hensen
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Frank Würthner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
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7
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Single-exonuclease nanocircuits reveal the RNA degradation dynamics of PNPase and demonstrate potential for RNA sequencing. Nat Commun 2023; 14:552. [PMID: 36725855 PMCID: PMC9892577 DOI: 10.1038/s41467-023-36278-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
The degradation process of RNA is decisive in guaranteeing high-fidelity translation of genetic information in living organisms. However, visualizing the single-base degradation process in real time and deciphering the degradation mechanism at the single-enzyme level remain formidable challenges. Here, we present a reliable in-situ single-PNPase-molecule dynamic electrical detector based on silicon nanowire field-effect transistors with ultra-high temporal resolution. These devices are capable of realizing real-time and label-free monitoring of RNA analog degradation with single-base resolution, including RNA analog binding, single-nucleotide hydrolysis, and single-base movement. We discover a binding event of the enzyme (near the active site) with the nucleoside, offering a further understanding of the RNA degradation mechanism. Relying on systematic analyses of independent reads, approximately 80% accuracy in RNA nucleoside sequencing is achieved in a single testing process. This proof-of-concept sets up a Complementary Metal Oxide Semiconductor (CMOS)-compatible playground for the development of high-throughput detection technologies toward mechanistic exploration and single-molecule sequencing.
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8
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Gelin MF, Chen L, Domcke W. Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals. Chem Rev 2022; 122:17339-17396. [PMID: 36278801 DOI: 10.1021/acs.chemrev.2c00329] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system-field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.
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Affiliation(s)
- Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Lipeng Chen
- Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching,Germany
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9
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Masullo LA, Szalai AM, Lopez LF, Pilo-Pais M, Acuna GP, Stefani FD. An alternative to MINFLUX that enables nanometer resolution in a confocal microscope. LIGHT, SCIENCE & APPLICATIONS 2022; 11:199. [PMID: 35773265 PMCID: PMC9247048 DOI: 10.1038/s41377-022-00896-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 05/31/2023]
Abstract
Localization of single fluorescent emitters is key for physicochemical and biophysical measurements at the nanoscale and beyond ensemble averaging. Examples include single-molecule tracking and super-resolution imaging by single-molecule localization microscopy. Among the numerous localization methods available, MINFLUX outstands for achieving a ~10-fold improvement in resolution over wide-field camera-based approaches, reaching the molecular scale at moderate photon counts. Widespread application of MINFLUX and related methods has been hindered by the technical complexity of the setups. Here, we present RASTMIN, a single-molecule localization method based on raster scanning a light pattern comprising a minimum of intensity. RASTMIN delivers ~1-2 nm localization precision with usual fluorophores and is easily implementable on a standard confocal microscope with few modifications. We demonstrate the performance of RASTMIN in localization of single molecules and super-resolution imaging of DNA origami structures.
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Affiliation(s)
- Luciano A Masullo
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Alan M Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Lucía F Lopez
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Mauricio Pilo-Pais
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg, CH-1700, Switzerland
| | - Guillermo P Acuna
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg, CH-1700, Switzerland
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
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10
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Dodin A, Provazza J, Coker DF, Willard AP. Trajectory Ensemble Methods Provide Single-Molecule Statistics for Quantum Dynamical Systems. J Chem Theory Comput 2022; 18:2047-2061. [PMID: 35230105 DOI: 10.1021/acs.jctc.1c00477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emergence of experiments capable of probing quantum dynamics at the single-molecule level requires the development of new theoretical tools capable of simulating and analyzing these dynamics beyond an ensemble-averaged description. In this article, we present an efficient method for sampling and simulating the dynamics of the individual quantum systems that make up an ensemble and apply it to study the nonequilibrium dynamics of the ubiquitous spin-boson model. We generate an ensemble of single-system trajectories, and we analyze this trajectory ensemble using tools from classical statistical mechanics. Our results demonstrate that the dynamics of quantum coherence is highly heterogeneous at the single-system level due to variations in the initial bath configuration, which significantly affects the transient exchange of coherence between the system and its bath. We observe that single systems tend to retain coherence over time scales longer than that of the ensemble. We also compute a novel thermodynamic entanglement entropy that quantifies a thermodynamic driving force favoring system-bath entanglement.
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Affiliation(s)
- Amro Dodin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Justin Provazza
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - David F Coker
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Dodin A, Willard AP. Nonequilibrium Work Relations and Response Theories in Ensemble Quantum Systems. J Phys Chem Lett 2021; 12:11151-11157. [PMID: 34757738 DOI: 10.1021/acs.jpclett.1c01315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We develop a nonequilibrium response theory for macroscopic quantum systems that separates the contributions of ensemble heterogeneity and intrinsic quantum uncertainty. To accomplish this, we describe systems with a quantum P-ensemble, which goes beyond the standard density matrix description by explicitly specifying the classical heterogeneity between individual quantum systems in an ensemble. We use the P-ensemble formalism to present quantum generalizations of linear response theory and the Jarzynski nonequilibrium work relation. We derive these generalizations from a Bochkov-Kuzovlev generating functional for quantum P-ensembles, which can be further utilized to derive all orders of response theory that apply to ensemble quantum systems. We contrast these developments with their ρ-ensemble analogs, and we discuss how these P-ensemble theories provide a guide for an effective application of single molecule experiments.
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Affiliation(s)
- Amro Dodin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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12
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Grobas Illobre P, Marsili M, Corni S, Stener M, Toffoli D, Coccia E. Time-Resolved Excited-State Analysis of Molecular Electron Dynamics by TDDFT and Bethe-Salpeter Equation Formalisms. J Chem Theory Comput 2021; 17:6314-6329. [PMID: 34486881 PMCID: PMC8515806 DOI: 10.1021/acs.jctc.1c00211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/16/2022]
Abstract
In this work, a theoretical and computational set of tools to study and analyze time-resolved electron dynamics in molecules, under the influence of one or more external pulses, is presented. By coupling electronic-structure methods with the resolution of the time-dependent Schrödinger equation, we developed and implemented the time-resolved induced density of the electronic wavepacket, the time-resolved formulation of the differential projection density of states (ΔPDOS), and of transition contribution map (TCM) to look at the single-electron orbital occupation and localization change in time. Moreover, to further quantify the possible charge transfer, we also defined the energy-integrated ΔPDOS and the fragment-projected TCM. We have used time-dependent density-functional theory (TDDFT), as implemented in ADF software, and the Bethe-Salpeter equation, as provided by MolGW package, for the description of the electronic excited states. This suite of postprocessing tools also provides the time evolution of the electronic states of the system of interest. To illustrate the usefulness of these postprocessing tools, excited-state populations have been computed for HBDI (the chromophore of GFP) and DNQDI molecules interacting with a sequence of two pulses. Time-resolved descriptors have been applied to study the time-resolved electron dynamics of HBDI, DNQDI, LiCN (being a model system for dipole switching upon highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) electronic excitation), and Ag22. The computational analysis tools presented in this article can be employed to help the interpretation of fast and ultrafast spectroscopies on molecular, supramolecular, and composite systems.
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Affiliation(s)
- P. Grobas Illobre
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - M. Marsili
- Dipartimento
di Scienze Chimiche, Universitá di
Padova, via Marzolo 1, Padova 35131, Italy
| | - S. Corni
- Dipartimento
di Scienze Chimiche, Universitá di
Padova, via Marzolo 1, Padova 35131, Italy
- CNR
Istituto di Nanoscienze, via Campi 213/A, Modena 41125, Italy
| | - M. Stener
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - D. Toffoli
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - E. Coccia
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
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13
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Xiang L, Chen K, Xu K. Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy. ACS NANO 2021; 15:12483-12496. [PMID: 34304562 PMCID: PMC8789943 DOI: 10.1021/acsnano.1c04708] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.
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14
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Carbajo S. Light by design: emerging frontiers in ultrafast photon sciences and light–matter interactions. JPHYS PHOTONICS 2021. [DOI: 10.1088/2515-7647/ac015e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract
Photon sciences and technologies establish the building blocks for myriad scientific and engineering frontiers in life and energy sciences. Because of their overarching functionality, the developmental roadmap and opportunities underpinned by photonics are often semiotically mediated by the delineation of subject areas of application. In this perspective article, we map current and emerging linkages between three intersecting areas of research stewarded by advanced photonics technologies, namely light by design, outlined as (a) quantum and structured photonics, (b) light–matter interactions in accelerators and accelerator-based light sources, and (c) ultrafast sciences and quantum molecular dynamics. In each section, we will concentrate on state-of-the-art achievements and present prospective applications in life sciences, biochemistry, quantum optics and information sciences, and environmental and chemical engineering, all founded on a broad range of photon sources and methodologies. We hope that this interconnected mapping of challenges and opportunities seeds new concepts, theory, and experiments in the advancement of ultrafast photon sciences and light–matter interactions. Through this mapping, we hope to inspire a critically interdisciplinary approach to the science and applications of light by design.
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15
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Copp SM, Gonzàlez-Rosell A. Large-scale investigation of the effects of nucleobase sequence on fluorescence excitation and Stokes shifts of DNA-stabilized silver clusters. NANOSCALE 2021; 13:4602-4613. [PMID: 33605954 PMCID: PMC8043073 DOI: 10.1039/d0nr08300c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DNA-stabilized silver clusters (AgN-DNAs) exhibit diverse sequence-programmed fluorescence, making these tunable nanoclusters promising sensors and bioimaging probes. Recent advances in the understanding of AgN-DNA structures and optical properties have largely relied on detailed characterization of single species isolated by chromatography. Because most AgN-DNAs are unstable under chromatography, such studies do not fully capture the diversity of these clusters. As an alternative method, we use high-throughput synthesis and spectroscopy to measure steady state Stokes shifts of hundreds of AgN-DNAs. Steady state Stokes shift is of interest because its magnitude is determined by energy relaxation processes which may be sensitive to specific cluster geometry, attachment to the DNA template, and structural engagement of solvent molecules. We identify 305 AgN-DNA samples with single-peaked emission and excitation spectra, a characteristic of pure solutions and single emitters, which thus likely contain a dominant emissive AgN-DNA species. Steady state Stokes shifts of these samples vary widely, are in agreement with values reported for purified clusters, and are several times larger than for typical organic dyes. We then examine how DNA sequence selects AgN-DNA excitation energies and Stokes shifts, comment on possible mechanisms for energy relaxation processes in AgN-DNAs, and discuss how differences in AgN-DNA structure and DNA conformation may result in the wide distribution of optical properties observed here. These results may aid computational studies seeking to understand the fluorescence process in AgN-DNAs and the relations of this process to AgN-DNA structure.
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Affiliation(s)
- Stacy M Copp
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697-2585, USA. and Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA and Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-2580, USA
| | - Anna Gonzàlez-Rosell
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697-2585, USA.
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16
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Xiong H, Min W. Combining the best of two worlds: Stimulated Raman excited fluorescence. J Chem Phys 2020; 153:210901. [PMID: 33291903 PMCID: PMC7986273 DOI: 10.1063/5.0030204] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/06/2020] [Indexed: 11/14/2022] Open
Abstract
The pursuit of a hybrid spectroscopy that combines the superb sensitivity of fluorescence and the high chemical specificity of Raman scattering has lasted for 40 years, with multiple experimental and theoretical attempts in the literature. It was only recently that the stimulated Raman excited fluorescence (SREF) process was successfully observed in a broad range of fluorophores. SREF allows single-molecule vibrational spectroscopy and imaging in the optical far field without relying on plasmonic enhancement. In this perspective, we will first review the historical efforts that lead to the successful excitation and detection of SREF, followed by the underlying physical principles, then the remaining technical challenges will be discussed, and, at last, the future opportunities in this old but yet newly emerged spectroscopy are outlined.
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Affiliation(s)
- Hanqing Xiong
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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17
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Coccia E, Fregoni J, Guido CA, Marsili M, Pipolo S, Corni S. Hybrid theoretical models for molecular nanoplasmonics. J Chem Phys 2020; 153:200901. [PMID: 33261492 DOI: 10.1063/5.0027935] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The multidisciplinary nature of the research in molecular nanoplasmonics, i.e., the use of plasmonic nanostructures to enhance, control, or suppress properties of molecules interacting with light, led to contributions from different theory communities over the years, with the aim of understanding, interpreting, and predicting the physical and chemical phenomena occurring at molecular- and nano-scale in the presence of light. Multiscale hybrid techniques, using a different level of description for the molecule and the plasmonic nanosystems, permit a reliable representation of the atomistic details and of collective features, such as plasmons, in such complex systems. Here, we focus on a selected set of topics of current interest in molecular plasmonics (control of electronic excitations in light-harvesting systems, polaritonic chemistry, hot-carrier generation, and plasmon-enhanced catalysis). We discuss how their description may benefit from a hybrid modeling approach and what are the main challenges for the application of such models. In doing so, we also provide an introduction to such models and to the selected topics, as well as general discussions on their theoretical descriptions.
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Affiliation(s)
- E Coccia
- Dipartimento di Scienze Chimiche e Farmaceutiche, Universit di Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
| | - J Fregoni
- Dipartimento di Scienze Fisiche, Informatiche e Matematiche, Universit di Modena e Reggio Emilia, via Campi 213/A, 41125 Modena, Italy
| | - C A Guido
- Dipartimento di Scienze Chimiche, Universit di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - M Marsili
- Dipartimento di Scienze Chimiche, Universit di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - S Pipolo
- Université de Lille, CNRS, Centrale Lille, ENSCL, Université d'Artois UMR 8181-UCCS Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - S Corni
- Istituto Nanoscienze-CNR, via Campi 213/A, 41125 Modena, Italy
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18
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Dall'Osto G, Coccia E, Guido CA, Corni S. Investigating ultrafast two-pulse experiments on single DNQDI fluorophores: a stochastic quantum approach. Phys Chem Chem Phys 2020; 22:16734-16746. [PMID: 32658228 DOI: 10.1039/d0cp02557g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ultrafast two-pulse experiments on single molecules are invaluable tools to investigate the microscopic dynamics of a fluorophore. The first pulse generates electronic or vibronic coherence and the second pulse probes the time-evolution of the coherence. A protocol that is able to simulate ultrafast experiments on single molecules is applied in this study. It is based on a coupled quantum-mechanical description of the fluorophore and real-time dynamics of the system vibronic wave packet interacting with an electric field, described by means of the stochastic Schrödinger equation within the Markovian limit. This approach is applied to the DNQDI fluorophore, previously investigated experimentally [D. Brinks et al., Nature, 2010, 465, 905-908]. We find this to be in good agreement with the experimental outcomes and provide microscopic and atomistic interpretation.
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Affiliation(s)
- Giulia Dall'Osto
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, Italy.
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19
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Han Y, Nickle C, Zhang Z, Astier HPAG, Duffin TJ, Qi D, Wang Z, Del Barco E, Thompson D, Nijhuis CA. Electric-field-driven dual-functional molecular switches in tunnel junctions. NATURE MATERIALS 2020; 19:843-848. [PMID: 32483243 DOI: 10.1038/s41563-020-0697-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/28/2020] [Indexed: 05/24/2023]
Abstract
To avoid crosstalk and suppress leakage currents in resistive random access memories (RRAMs), a resistive switch and a current rectifier (diode) are usually combined in series in a one diode-one resistor (1D-1R) RRAM. However, this complicates the design of next-generation RRAM, increases the footprint of devices and increases the operating voltage as the potential drops over two consecutive junctions1. Here, we report a molecular tunnel junction based on molecules that provide an unprecedented dual functionality of diode and variable resistor, resulting in a molecular-scale 1D-1R RRAM with a current rectification ratio of 2.5 × 104 and resistive on/off ratio of 6.7 × 103, and a low drive voltage of 0.89 V. The switching relies on dimerization of redox units, resulting in hybridization of molecular orbitals accompanied by directional ion migration. This electric-field-driven molecular switch operating in the tunnelling regime enables a class of molecular devices where multiple electronic functions are preprogrammed inside a single molecular layer with a thickness of only 2 nm.
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Affiliation(s)
- Yingmei Han
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Cameron Nickle
- Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Ziyu Zhang
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | | | - Thorin J Duffin
- Department of Chemistry, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Dongchen Qi
- Centre for Materials Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Zhe Wang
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Enrique Del Barco
- Department of Physics, University of Central Florida, Orlando, FL, USA.
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland.
| | - Christian A Nijhuis
- Department of Chemistry, National University of Singapore, Singapore, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore.
- Centre for Advanced 2D Materials and Graphene Research Center, National University of Singapore, Singapore, Singapore.
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20
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Affiliation(s)
- E. Coccia
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Trieste, Italy
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21
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Quantum dissipation driven by electron transfer within a single molecule investigated with atomic force microscopy. Nat Commun 2020; 11:1337. [PMID: 32165626 PMCID: PMC7067884 DOI: 10.1038/s41467-020-15054-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/17/2020] [Indexed: 11/26/2022] Open
Abstract
Intramolecular charge transfer processes play an important role in many biological, chemical and physical processes including photosynthesis, redox chemical reactions and electron transfer in molecular electronics. These charge transfer processes are frequently influenced by the dynamics of their molecular or atomic environments, and they are accompanied with energy dissipation into this environment. The detailed understanding of such processes is fundamental for their control and possible exploitation in future technological applications. Most of the experimental studies of the intramolecular charge transfer processes so far have been carried out using time-resolved optical spectroscopies on large molecular ensembles. This hampers detailed understanding of the charge transfer on the single molecular level. Here we build upon the recent progress in scanning probe microscopy, and demonstrate the control of mixed valence state. We report observation of single electron transfer between two ferrocene redox centers within a single molecule and the detection of energy dissipation associated with the single electron transfer. Here, the authors use atomic force microscopy under ultra-high vacuum conditions to study intramolecular single electron transfer within a single molecule. This allows them to investigate energy dissipation process related to the electron transfer as a function of temperature.
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22
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Schedlbauer J, Wilhelm P, Grabenhorst L, Federl ME, Lalkens B, Hinderer F, Scherf U, Höger S, Tinnefeld P, Bange S, Vogelsang J, Lupton JM. Ultrafast Single-Molecule Fluorescence Measured by Femtosecond Double-Pulse Excitation Photon Antibunching. NANO LETTERS 2020; 20:1074-1079. [PMID: 31869232 DOI: 10.1021/acs.nanolett.9b04354] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Most measurements of fluorescence lifetimes on the single-molecule level are carried out using avalanche photon diodes (APDs). These single-photon counters are inherently slow, and their response shows a strong dependence on photon energy, which can make reconvolution of the instrument response function (IRF) challenging. An ultrafast time resolution in single-molecule fluorescence is crucial, e.g., in determining donor lifetimes in donor-acceptor couples which undergo energy transfer, or in plasmonic antenna structures, where the radiative rate and non-radiative rates are enhanced. We introduce a femtosecond double-excitation (FeDEx) photon correlation technique, which measures the degree of photon antibunching as a function of time delay between two excitation pulses. In this boxcar integration, the time resolution of fluorescence transients is limited solely by the laser pulse length and is independent of the detector IRF. The versatility of the technique is demonstrated with a custom-made donor-acceptor complex with one donor and two acceptors and with single dye molecules positioned accurately between two gold nanoparticles using DNA origami. The latter structures show ∼75-fold radiative-rate enhancement and fluorescence lifetimes down to 19 ps, which is measured without the need for any reconvolution. With the potential of measuring subpicosecond fluorescence lifetimes, plasmonic antenna structures can now be optimized further.
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Affiliation(s)
- J Schedlbauer
- Institut für Experimentelle und Angewandte Physik , Universität Regensburg , Universitätsstrasse 31 , 93040 Regensburg , Germany
| | - P Wilhelm
- Institut für Experimentelle und Angewandte Physik , Universität Regensburg , Universitätsstrasse 31 , 93040 Regensburg , Germany
| | - L Grabenhorst
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universität München , Butenandtstrasse 5-13 , 81377 München , Germany
| | - M E Federl
- Institut für Experimentelle und Angewandte Physik , Universität Regensburg , Universitätsstrasse 31 , 93040 Regensburg , Germany
| | - B Lalkens
- Institute of Semiconductor Technology, LENA Laboratory for Emerging Nanometrology , Technische Universität Braunschweig , Langer Kamp 6a , 38106 Braunschweig , Germany
| | - F Hinderer
- Kekulé-Institut für Organische Chemie und Biochemie , Universität Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany
| | - U Scherf
- Macromolecular Chemistry Group, Chemistry Department and IfP , Bergische Universität Wuppertal , Gauss-Strasse 20 , 42097 Wuppertal , Germany
| | - S Höger
- Kekulé-Institut für Organische Chemie und Biochemie , Universität Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany
| | - P Tinnefeld
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universität München , Butenandtstrasse 5-13 , 81377 München , Germany
| | - S Bange
- Institut für Experimentelle und Angewandte Physik , Universität Regensburg , Universitätsstrasse 31 , 93040 Regensburg , Germany
| | - J Vogelsang
- Institut für Experimentelle und Angewandte Physik , Universität Regensburg , Universitätsstrasse 31 , 93040 Regensburg , Germany
| | - J M Lupton
- Institut für Experimentelle und Angewandte Physik , Universität Regensburg , Universitätsstrasse 31 , 93040 Regensburg , Germany
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23
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Marcus M, Knee GC, Datta A. Towards a spectroscopic protocol for unambiguous detection of quantum coherence in excitonic energy transport. Faraday Discuss 2020; 221:110-132. [DOI: 10.1039/c9fd00068b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We propose a witness for quantum coherence in EET that can be extracted directly from two-pulse pump–probe spectroscopy experimental data.
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Affiliation(s)
- Max Marcus
- Department of Physics
- University of Warwick
- Coventry
- UK
| | | | - Animesh Datta
- Department of Physics
- University of Warwick
- Coventry
- UK
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24
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Dodin A, Willard AP. State space distribution and dynamical flow for closed and open quantum systems. J Chem Phys 2019. [DOI: 10.1063/1.5100736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Amro Dodin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Adam P. Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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25
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Xiong H, Shi L, Wei L, Shen Y, Long R, Zhao Z, Min W. Stimulated Raman Excited Fluorescence Spectroscopy and Imaging. NATURE PHOTONICS 2019; 13:412-417. [PMID: 32607124 PMCID: PMC7326316 DOI: 10.1038/s41566-019-0396-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Powerful optical tools have revolutionized science and technology. The prevalent fluorescence detection offers superb sensitivity down to single molecules but lacks sufficient chemical information1-3. In contrast, Raman-based vibrational spectroscopy provides exquisite chemical specificity about molecular structure, dynamics and coupling, but is notoriously insensitive3-5. Here we report a hybrid technique of Stimulated Raman Excited Fluorescence (SREF) that integrates superb detection sensitivity and fine chemical specificity. Through stimulated Raman pumping to an intermediate vibrational eigenstate followed by an upconversion to an electronic fluorescent state, SREF encodes vibrational resonance into the excitation spectrum of fluorescence emission. By harnessing narrow vibrational linewidth, we demonstrated multiplexed SREF imaging in cells, breaking the "color barrier" of fluorescence. By leveraging superb sensitivity of SREF, we achieved all-far-field single-molecule Raman spectroscopy and imaging without plasmonic enhancement, a long-sought-after goal in photonics. Thus, through merging Raman and fluorescence spectroscopy, SERF would be a valuable tool for chemistry and biology.
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26
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Zhou H, Qin C, Chen R, Liu Y, Zhou W, Zhang G, Gao Y, Xiao L, Jia S. Quantum Coherent Modulation-Enhanced Single-Molecule Imaging Microscopy. J Phys Chem Lett 2019; 10:223-228. [PMID: 30599135 DOI: 10.1021/acs.jpclett.8b03606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In fluorescence imaging and detection, undesired fluorescence interference (such as autofluorescence) often hampers the contrast of the image and even prevents the identification of structures of interest. Here, we develop a quantum coherent modulation-enhanced (QCME) single-molecule imaging microscopy (SMIM) to substantially eliminate the strong fluorescence interference, based on manipulation of the excited-state population probability of a single molecule. By periodically modulating the phase difference between the ultrashort pulse pairs and performing a discrete Fourier transform of the arrival time of emitted photons, the decimation of single molecules from strong interference in QCME-SMIM has been clearly determined, where the signal-to-interference ratio is enhanced by more than 2 orders of magnitude. This technique, confirmed to be universal to organic dyes and linked with biomacromolecules, paves the way to high-contrast bioimaging under unfavorable conditions.
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Affiliation(s)
- Haitao Zhou
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Chengbing Qin
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Ruiyun Chen
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Yaoming Liu
- Scientific Instrument Center , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Wenjin Zhou
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Guofeng Zhang
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Yan Gao
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Liantuan Xiao
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Suotang Jia
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
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27
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Kunsel T, Tiwari V, Matutes YA, Gardiner AT, Cogdell RJ, Ogilvie JP, Jansen TLC. Simulating Fluorescence-Detected Two-Dimensional Electronic Spectroscopy of Multichromophoric Systems. J Phys Chem B 2019; 123:394-406. [PMID: 30543283 PMCID: PMC6345114 DOI: 10.1021/acs.jpcb.8b10176] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Indexed: 11/28/2022]
Abstract
We present a theory for modeling fluorescence-detected two-dimensional electronic spectroscopy of multichromophoric systems. The theory is tested by comparison of the predicted spectra of the light-harvesting complex LH2 with experimental data. A qualitative explanation of the strong cross-peaks as compared to conventional two-dimensional electronic spectra is given. The strong cross-peaks are attributed to the clean ground-state signal that is revealed when the annihilation of exciton pairs created on the same LH2 complex cancels oppositely signed signals from the doubly excited state. This annihilation process occurs much faster than the nonradiative relaxation. Furthermore, the line shape difference is attributed to slow dynamics, exciton delocalization within the bands, and intraband exciton-exciton annihilation. This is in line with existing theories presented for model systems. We further propose the use of time-resolved fluorescence-detected two-dimensional spectroscopy to study state-resolved exciton-exciton annihilation.
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Affiliation(s)
- Tenzin Kunsel
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Vivek Tiwari
- Department
of Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yassel Acosta Matutes
- Department
of Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Richard J. Cogdell
- Institute
for Molecular Biology, University of Glasgow, Glasgow G12 8TA, U.K.
| | - Jennifer P. Ogilvie
- Department
of Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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28
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Gelin MF, Palacino-González E, Chen L, Domcke W. Monitoring of Nonadiabatic Effects in Individual Chromophores by Femtosecond Double-Pump Single-Molecule Spectroscopy: A Model Study. Molecules 2019; 24:E231. [PMID: 30634541 PMCID: PMC6359062 DOI: 10.3390/molecules24020231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/01/2019] [Accepted: 01/07/2019] [Indexed: 12/03/2022] Open
Abstract
We explore, by theoretical modeling and computer simulations, how nonadiabatic couplings of excited electronic states of a polyatomic chromophore manifest themselves in single-molecule signals on femtosecond timescales. The chromophore is modeled as a system with three electronic states (the ground state and two non-adiabatically coupled excited states) and a Condon-active vibrational mode which, in turn, is coupled to a harmonic oscillator heat bath. For this system, we simulate double-pump single-molecule signals with fluorescence detection for different system-field interaction strengths, from the weak-coupling regime to the strong-coupling regime. While the signals are determined by the coherence of the electronic density matrix in the weak-coupling regime, they are determined by the populations of the electronic density matrix in the strong-coupling regime. As a consequence, the signals in the strong coupling regime allow the monitoring of nonadiabatic electronic population dynamics and are robust with respect to temporal inhomogeneity of the optical gap, while signals in the weak-coupling regime are sensitive to fluctuations of the optical gap and do not contain information on the electronic population dynamics.
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Affiliation(s)
- Maxim F Gelin
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany.
| | | | - Lipeng Chen
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany.
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29
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Beane G, Devkota T, Brown BS, Hartland GV. Ultrafast measurements of the dynamics of single nanostructures: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:016401. [PMID: 30485256 DOI: 10.1088/1361-6633/aaea4b] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The ability to study single particles has revolutionized nanoscience. The advantage of single particle spectroscopy measurements compared to conventional ensemble studies is that they remove averaging effects from the different sizes and shapes that are present in the samples. In time-resolved experiments this is important for unraveling homogeneous and inhomogeneous broadening effects in lifetime measurements. In this report, recent progress in the development of ultrafast time-resolved spectroscopic techniques for interrogating single nanostructures will be discussed. The techniques include far-field experiments that utilize high numerical aperture (NA) microscope objectives, near-field scanning optical microscopy (NSOM) measurements, ultrafast electron microscopy (UEM), and time-resolved x-ray diffraction experiments. Examples will be given of the application of these techniques to studying energy relaxation processes in nanoparticles, and the motion of plasmons, excitons and/or charge carriers in different types of nanostructures.
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Affiliation(s)
- Gary Beane
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States of America
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30
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Crampton KT, Fast A, Potma EO, Apkarian VA. Junction Plasmon Driven Population Inversion of Molecular Vibrations: A Picosecond Surface-Enhanced Raman Spectroscopy Study. NANO LETTERS 2018; 18:5791-5796. [PMID: 30064221 DOI: 10.1021/acs.nanolett.8b02438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular surface-enhanced Raman spectra recorded at single plasmonic nanojunctions using a 7 ps pulse train exhibit vibrational up-pumping and population inversion. The process is assigned to plasmon-driven, dark, impulsive electron-vibration (e-v) excitation. Both optical (Raman) pumping and hot-electron mediated excitation can be rejected by the characteristic spectra, which allow the simultaneous measurement of vibrational temperature of the molecules and electronic temperature of the metal. Vibrational populations are determined from anti-Stokes to Stokes intensity ratios, while the electron temperature is obtained from the anti-Stokes branch of the electronic Raman scattering continuum. Population inversion survives in high-frequency vibrations that effectively decouple from the metal.
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Affiliation(s)
- Kevin T Crampton
- Department of Chemistry , University of California Irvine , Irvine , California 92697 , United States
| | - Alexander Fast
- Department of Chemistry , University of California Irvine , Irvine , California 92697 , United States
| | - Eric O Potma
- Department of Chemistry , University of California Irvine , Irvine , California 92697 , United States
| | - V Ara Apkarian
- Department of Chemistry , University of California Irvine , Irvine , California 92697 , United States
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31
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Chen L, Gelin MF, Domcke W, Zhao Y. Simulation of Femtosecond Phase-Locked Double-Pump Signals of Individual Light-Harvesting Complexes LH2. J Phys Chem Lett 2018; 9:4488-4494. [PMID: 30037231 DOI: 10.1021/acs.jpclett.8b01887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recent phase-locked femtosecond double-pump experiments on individual light-harvesting complexes LH2 of purple bacteria at ambient temperature revealed undamped oscillatory responses on a time scale of at least 400 fs [ Hildner et al. Science 2013 , 340 , 1448 ]. Using an excitonic Hamiltonian for LH2 available in the literature, we simulate these signals numerically by a method that treats excitonic couplings and exciton-phonon couplings in a nonperturbative manner. The simulations provide novel insights into the origin of coherent dynamics in individual LH2 complexes.
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Affiliation(s)
- Lipeng Chen
- Department of Chemistry , Technische Universität München , D-85747 Garching , Germany
- Division of Materials Science , Nanyang Technological University , Singapore 639798 , Singapore
| | - Maxim F Gelin
- Department of Chemistry , Technische Universität München , D-85747 Garching , Germany
| | - Wolfgang Domcke
- Department of Chemistry , Technische Universität München , D-85747 Garching , Germany
| | - Yang Zhao
- Division of Materials Science , Nanyang Technological University , Singapore 639798 , Singapore
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32
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Zhang H, Liu Y, Zhang K, Ji J, Liu J, Liu B. Single Molecule Fluorescent Colocalization of Split Aptamers for Ultrasensitive Detection of Biomolecules. Anal Chem 2018; 90:9315-9321. [PMID: 30003776 DOI: 10.1021/acs.analchem.8b01916] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single-molecule fluorescence imaging is a promising strategy for biomolecule detection. However, the accuracy of single-molecule method is often compromised by the false-positive events at the ultralow sample levels that are caused by the nonspecific adsorption of the fluorescent labeled probe and other fluorescent impurities on the imaging surface. Here, we demonstrate an ultrasensitive single molecule detection assay based on dual-color fluorescent colocalization of spilt aptamers that was implemented to the measurement of adenosine triphosphate (ATP). The ATP aptamer was split into two fragments and labeled with green and red dye molecules, respectively. When the two probes of split aptamers were brought together by the target ATP molecule, the two colors of fluorescence of two probes were simultaneously detected through two channels and projected to the correlated locations in the two halves of image. The colocalizaiton imaging of two split apatamer probes greatly excluded the false detection of biomolecules that was usually caused by the fluorescent noise of single nonbound aptamer probes and impurities, and further improved the accuracy of measurement. The assay showed excellent selectivity and high sensitivity for ATP detection with linear range of 1 pM to 5 nM and a detection limit of 100 fM. This versatile protocol of single molecule colocalization of split apatamer can be widely applied to the ultrasensitive and highly accurate detection of many types of biomolecules in basic research and biomedical applications.
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Affiliation(s)
- Hongding Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Yujie Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Kun Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Ji Ji
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Jianwei Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
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33
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Introduction to State-of-the-Art Multidimensional Time-Resolved Spectroscopy Methods. Top Curr Chem (Cham) 2018; 376:28. [DOI: 10.1007/s41061-018-0206-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 10/28/2022]
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34
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Coccia E, Troiani F, Corni S. Probing quantum coherence in ultrafast molecular processes: Anab initioapproach to open quantum systems. J Chem Phys 2018; 148:204112. [DOI: 10.1063/1.5022976] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Emanuele Coccia
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, Italy
- CNR Institute of Nanoscience, via Campi 213/A, Modena, Italy
| | - Filippo Troiani
- CNR Institute of Nanoscience, via Campi 213/A, Modena, Italy
| | - Stefano Corni
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, Italy
- CNR Institute of Nanoscience, via Campi 213/A, Modena, Italy
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35
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Malý P, Gardiner AT, Cogdell RJ, van Grondelle R, Mančal T. Robust light harvesting by a noisy antenna. Phys Chem Chem Phys 2018; 20:4360-4372. [PMID: 29368769 PMCID: PMC5901068 DOI: 10.1039/c7cp06139k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/13/2017] [Indexed: 01/26/2023]
Abstract
Photosynthetic light harvesting can be very efficient in solar energy conversion while taking place in a highly disordered and noisy physiological environment. This efficiency is achieved by the ultrafast speed of the primary photosynthetic processes, which is enabled by a delicate interplay of quantum effects, thermodynamics and environmental noise. The primary processes take place in light-harvesting antennas built from pigments bound to a fluctuating protein scaffold. Here, we employ ultrafast single-molecule spectroscopy to follow fluctuations of the femtosecond energy transfer times in individual LH2 antenna complexes of purple bacteria. By combining single molecule results with ensemble spectroscopy through a unified theoretical description of both, we show how the protein fluctuations alter the excitation energy transfer dynamics. We find that from the thirteen orders of magnitude of possible timescales from picoseconds to minutes, the relevant fluctuations occur predominantly on a biological timescale of seconds, i.e. in the domain of slow protein motion. The measured spectra and dynamics can be explained by the protein modulating pigment excitation energies only. Moreover, we find that the small spread of pigment mean energies allows for excitation delocalization between the coupled pigments to survive. These unique features provide fast energy transport even in the presence of disorder. We conclude that this is the mechanism that enables LH2 to operate as a robust light-harvester, in spite of its intrinsically noisy biological environment.
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Affiliation(s)
- Pavel Malý
- Department of Biophysics , Faculty of Sciences , Vrije Universiteit Amsterdam , De Boeleaan 1081 , 1081HV Amsterdam , The Netherlands .
- Faculty of Mathematics and Physics , Charles University , Ke Karlovu 3 , 121 16 Prague , Czech Republic
| | - Alastair T. Gardiner
- Institute of Molecular , Cellular and Systems Biology , College of Medical , Veterinary and Life Sciences , University of Glasgow , Glasgow G128QQ , UK
| | - Richard J. Cogdell
- Institute of Molecular , Cellular and Systems Biology , College of Medical , Veterinary and Life Sciences , University of Glasgow , Glasgow G128QQ , UK
| | - Rienk van Grondelle
- Department of Biophysics , Faculty of Sciences , Vrije Universiteit Amsterdam , De Boeleaan 1081 , 1081HV Amsterdam , The Netherlands .
| | - Tomáš Mančal
- Faculty of Mathematics and Physics , Charles University , Ke Karlovu 3 , 121 16 Prague , Czech Republic
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36
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Chen L, Palacino-González E, Gelin MF, Domcke W. Nonperturbative response functions: A tool for the interpretation of four-wave-mixing signals beyond third order. J Chem Phys 2017; 147:234104. [DOI: 10.1063/1.5004763] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lipeng Chen
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | | | - Maxim F. Gelin
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
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37
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Vapaavuori J, Bazuin CG, Pellerin C. Taming Macromolecules with Light: Lessons Learned from Vibrational Spectroscopy. Macromol Rapid Commun 2017; 39. [DOI: 10.1002/marc.201700430] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/20/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Jaana Vapaavuori
- Département de chimieUniversité de Montréal Montréal Québec H3C 3J7 Canada
| | | | - Christian Pellerin
- Département de chimieUniversité de Montréal Montréal Québec H3C 3J7 Canada
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38
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Nairat M, Webb M, Esch MP, Lozovoy VV, Levine BG, Dantus M. Time-resolved signatures across the intramolecular response in substituted cyanine dyes. Phys Chem Chem Phys 2017; 19:14085-14095. [PMID: 28518192 DOI: 10.1039/c7cp00119c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The optically populated excited state wave packet propagates along multidimensional intramolecular coordinates soon after photoexcitation. This action occurs alongside an intermolecular response from the surrounding solvent. Disentangling the multidimensional convoluted signal enables the possibility to separate and understand the initial intramolecular relaxation pathways over the excited state potential energy surface. Here we track the initial excited state dynamics by measuring the fluorescence yield from the first excited state as a function of time delay between two color femtosecond pulses for several cyanine dyes having different substituents. We find that when the high frequency pulse precedes the low frequency one and for timescales up to 200 fs, the excited state population can be depleted through stimulated emission with efficiency that is dependent on the molecular electronic structure. A similar observation at even shorter times was made by scanning the chirp (frequencies ordering) of a femtosecond pulse. The changes in depletion reflect the rate at which the nuclear coordinates of the excited state leave the Franck-Condon (FC) region and progress towards achieving equilibrium. Through functional group substitution, we explore these dynamic changes as a function of dipolar change following photoexcitation. Density functional theory calculations were performed to provide greater insight into the experimental spectroscopic observations. Complete active space (CAS) self-consistent field and CAS second order perturbation theory calculated potential energy surfaces tracking twisting and pyramidalization confirm that the steeper potential at the FC region leads to the observation of faster wave packet dynamics.
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Affiliation(s)
- Muath Nairat
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA.
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39
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Chu JW, Yang H. Identifying the structural and kinetic elements in protein large-amplitude conformational motions. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1283885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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40
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Accanto N, de Roque PM, Galvan-Sosa M, Christodoulou S, Moreels I, van Hulst NF. Rapid and robust control of single quantum dots. LIGHT, SCIENCE & APPLICATIONS 2017; 6:e16239. [PMID: 30167237 PMCID: PMC6062170 DOI: 10.1038/lsa.2016.239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 09/07/2016] [Accepted: 09/26/2016] [Indexed: 06/01/2023]
Abstract
The combination of single particle detection and ultrafast laser pulses is an instrumental method to track dynamics at the femtosecond time scale in single molecules, quantum dots and plasmonic nanoparticles. Optimal control of the extremely short-lived coherences of these individual systems has so far remained elusive, yet its successful implementation would enable arbitrary external manipulation of otherwise inaccessible nanoscale dynamics. In ensemble measurements, such control is often achieved by resorting to a closed-loop optimization strategy, where the spectral phase of a broadband laser field is iteratively optimized. This scheme needs long measurement times and strong signals to converge to the optimal solution. This requirement is in conflict with the nature of single emitters whose signals are weak and unstable. Here we demonstrate an effective closed-loop optimization strategy capable of addressing single quantum dots at room temperature, using as feedback observable the two-photon photoluminescence induced by a phase-controlled broadband femtosecond laser. Crucial to the optimization loop is the use of a deterministic and robust-against-noise search algorithm converging to the theoretically predicted solution in a reduced amount of steps, even when operating at the few-photon level. Full optimization of the single dot luminescence is obtained within ~100 trials, with a typical integration time of 100 ms per trial. These times are faster than the typical photobleaching times in single molecules at room temperature. Our results show the suitability of the novel approach to perform closed-loop optimizations on single molecules, thus extending the available experimental toolbox to the active control of nanoscale coherences.
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Affiliation(s)
- Nicolò Accanto
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - Pablo M de Roque
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | | | - Sotirios Christodoulou
- Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Physics, University of Genova, 16146 Genova, Italy
| | - Iwan Moreels
- Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Niek F van Hulst
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
- ICREA - Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
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41
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Roeding S, Klimovich N, Brixner T. Optimizing sparse sampling for 2D electronic spectroscopy. J Chem Phys 2017; 146:084201. [DOI: 10.1063/1.4976309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Sebastian Roeding
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Nikita Klimovich
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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42
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Draeger S, Roeding S, Brixner T. Rapid-scan coherent 2D fluorescence spectroscopy. OPTICS EXPRESS 2017; 25:3259-3267. [PMID: 28241542 DOI: 10.1364/oe.25.003259] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We developed pulse-shaper-assisted coherent two-dimensional (2D) electronic spectroscopy in liquids using fluorescence detection. A customized pulse shaper facilitates shot-to-shot modulation at 1 kHz and is employed for rapid scanning over all time delays. A full 2D spectrum with 15 × 15 pixels is obtained in approximately 6 s of measurement time (plus further averaging if needed). Coherent information is extracted from the incoherent fluorescence signal via 27-step phase cycling. We exemplify the technique on cresyl violet in ethanol and recover literature-known oscillations as a function of population time. Signal-to-noise behavior is analyzed as a function of the amount of averaging. Rapid scanning provides a 2D spectrum with a root-mean-square error of < 0.05 after 1 min of measurement time.
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43
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Kondo T, Chen WJ, Schlau-Cohen GS. Single-Molecule Fluorescence Spectroscopy of Photosynthetic Systems. Chem Rev 2017; 117:860-898. [DOI: 10.1021/acs.chemrev.6b00195] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Toru Kondo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Wei Jia Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
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44
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Palacino-González E, Gelin MF, Domcke W. Theoretical aspects of femtosecond double-pump single-molecule spectroscopy. II. Strong-field regime. Phys Chem Chem Phys 2017; 19:32307-32319. [DOI: 10.1039/c7cp04810f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate femtosecond double-pump single-molecule signals in the strong-field regime, which is characterized by nonlinear scaling of the signal with the intensity of the pump pulses.
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Affiliation(s)
| | - Maxim F. Gelin
- Department of Chemistry
- Technische Universität München
- Garching
- Germany
| | - Wolfgang Domcke
- Department of Chemistry
- Technische Universität München
- Garching
- Germany
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45
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Palacino-González E, Gelin MF, Domcke W. Theoretical aspects of femtosecond double-pump single-molecule spectroscopy. I. Weak-field regime. Phys Chem Chem Phys 2017; 19:32296-32306. [DOI: 10.1039/c7cp04809b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a theoretical description of double-pump femtosecond single-molecule signals with fluorescence detection.
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Affiliation(s)
| | - Maxim F. Gelin
- Department of Chemistry
- Technische Universität München
- Garching
- Germany
| | - Wolfgang Domcke
- Department of Chemistry
- Technische Universität München
- Garching
- Germany
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46
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Song K, Bai S, Shi Q. Effect of Pulse Shaping on Observing Coherent Energy Transfer in Single Light-Harvesting Complexes. J Phys Chem B 2016; 120:11637-11643. [PMID: 27749066 DOI: 10.1021/acs.jpcb.6b07025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent experimental and theoretical studies have revealed that quantum coherence plays an important role in the excitation energy transfer in photosynthetic light-harvesting (LH) complexes. Inspired by the recent single-molecule two-color double-pump experiment, we theoretically investigate the effect of pulse shaping on observing coherent energy transfer in the single bacterial LH2 complex. It is found that quantum coherent energy transfer can be observed when the time delay and phase difference between the two laser pulses are controlled independently. However, when the two-color pulses are generated using the pulse-shaping method, how the laser pulses are prepared is crucial to the observation of quantum coherent energy transfer in single photosynthetic complexes.
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Affiliation(s)
- Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences , Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Shuming Bai
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences , Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences , Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
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47
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Abstract
Organic (opto)electronic materials have received considerable attention due to their applications in thin-film-transistors, light-emitting diodes, solar cells, sensors, photorefractive devices, and many others. The technological promises include low cost of these materials and the possibility of their room-temperature deposition from solution on large-area and/or flexible substrates. The article reviews the current understanding of the physical mechanisms that determine the (opto)electronic properties of high-performance organic materials. The focus of the review is on photoinduced processes and on electronic properties important for optoelectronic applications relying on charge carrier photogeneration. Additionally, it highlights the capabilities of various experimental techniques for characterization of these materials, summarizes top-of-the-line device performance, and outlines recent trends in the further development of the field. The properties of materials based both on small molecules and on conjugated polymers are considered, and their applications in organic solar cells, photodetectors, and photorefractive devices are discussed.
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Affiliation(s)
- Oksana Ostroverkhova
- Department of Physics, Oregon State University , Corvallis, Oregon 97331, United States
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48
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Single molecule fluorescence spectroscopy for quantitative biological applications. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0083-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Tao MJ, Ai Q, Deng FG, Cheng YC. Proposal for probing energy transfer pathway by single-molecule pump-dump experiment. Sci Rep 2016; 6:27535. [PMID: 27277702 PMCID: PMC4899753 DOI: 10.1038/srep27535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 12/25/2022] Open
Abstract
The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex had long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices.
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Affiliation(s)
- Ming-Jie Tao
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Qing Ai
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Fu-Guo Deng
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Yuan-Chung Cheng
- Department of Chemistry, Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan
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50
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Abstract
Energy relaxation in light-harvesting complexes has been extensively studied by various ultrafast spectroscopic techniques, the fastest processes being in the sub-100-fs range. At the same time, much slower dynamics have been observed in individual complexes by single-molecule fluorescence spectroscopy (SMS). In this work, we use a pump-probe-type SMS technique to observe the ultrafast energy relaxation in single light-harvesting complexes LH2 of purple bacteria. After excitation at 800 nm, the measured relaxation time distribution of multiple complexes has a peak at 95 fs and is asymmetric, with a tail at slower relaxation times. When tuning the excitation wavelength, the distribution changes in both its shape and position. The observed behavior agrees with what is to be expected from the LH2 excited states structure. As we show by a Redfield theory calculation of the relaxation times, the distribution shape corresponds to the expected effect of Gaussian disorder of the pigment transition energies. By repeatedly measuring few individual complexes for minutes, we find that complexes sample the relaxation time distribution on a timescale of seconds. Furthermore, by comparing the distribution from a single long-lived complex with the whole ensemble, we demonstrate that, regarding the relaxation times, the ensemble can be considered ergodic. Our findings thus agree with the commonly used notion of an ensemble of identical LH2 complexes experiencing slow random fluctuations.
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