1
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Vallejos A, Katona G, Neutze R. Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:044302. [PMID: 39056073 PMCID: PMC11272219 DOI: 10.1063/4.0000258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
With the development of serial crystallography at both x-ray free electron laser and synchrotron radiation sources, time-resolved x-ray crystallography is increasingly being applied to study conformational changes in macromolecules. A successful time-resolved serial crystallography study requires the growth of microcrystals, a mechanism for synchronized and homogeneous excitation of the reaction of interest within microcrystals, and tools for structural interpretation. Here, we utilize time-resolved serial femtosecond crystallography data collected from microcrystals of bacteriorhodopsin to compare results from partial occupancy structural refinement and refinement against extrapolated data. We illustrate the domain wherein the amplitude of refined conformational changes is inversely proportional to the activated state occupancy. We illustrate how resampling strategies allow coordinate uncertainty to be estimated and demonstrate that these two approaches to structural refinement agree within coordinate errors. We illustrate how singular value decomposition of a set of difference Fourier electron density maps calculated from resampled data can minimize phase bias in these maps, and we quantify residual densities for transient water molecules by analyzing difference Fourier and Polder omit maps from resampled data. We suggest that these tools may assist others in judging the confidence with which observed electron density differences may be interpreted as functionally important conformational changes.
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Affiliation(s)
- Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
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2
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Wega J, Zhang KF, Lacour J, Vauthey E. Controlling Symmetry-Breaking Charge Separation in Pyrene Bichromophores. J Phys Chem Lett 2024:2834-2840. [PMID: 38442038 DOI: 10.1021/acs.jpclett.4c00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
So far, symmetry-breaking charge separation (SB-CS) has been observed with a limited number of chromophores and is usually inhibited by the formation of an excimer. , We show here that thanks to of fine-tuning of the interchromophore coupling via structural control, SB-CS can be operative with pyrene, despite its high propensity to form an excimer. This is realized with a bichromophoric system consisting of two pyrenes attached to a crown ether macrocycle, which can bind cations of different sizes. By combining stationary and time-resolved spectroscopy together with molecular dynamics simulations, we demonstrate that the excited-state dynamics can be totally changed depending on the binding cation. Whereas strong coupling leads to rapid excimer formation, too weak coupling results in noninteracting chromophores. However, intermediate coupling, achieved upon binding of Mg2+, allows for SB-CS to be operative.
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3
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Ma L, Jiang L. Intelligently optimized global analysis of time resolved spectra with particle swarm optimization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123685. [PMID: 38039640 DOI: 10.1016/j.saa.2023.123685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/01/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Time-resolved spectroscopy, especially transient absorption spectroscopy (TAS), provides valuable insights to excited state dynamics. Analyzing TAS data involves fitting complex kinetic traces at various probe wavelengths using different rate equations. Conventional TAS global fitting methods require domain experts to establish physically valid models and provide good initial guesses to generate converged solutions. This poses challenges for non-experts who seek to utilize TAS, thus limiting its broader application and impact. To address this problem, we propose an intelligent optimization framework based on the particle swarm optimization (PSO) algorithm. In the proposed method, the PSO algorithm acts as the global fitting method to find the optimal values of the target variables or unknown parameters in the kinetics models. The target solution is optimized by iteratively updating candidate solutions with respect to an objective feedback signal. We demonstrated the effectiveness of the proposed PSO-based global fitting method with both synthetic and experimental datasets. The results show that our proposed method can successfully find the optimal target values in the global fitting process automatically, thus eliminating the iterative manual labor traditionally required. The proposed intelligent optimization framework provides a novel approach for automatic global fitting of TAS data, which significantly enhances the accessibility and utilization of the TAS methodology.
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Affiliation(s)
- Lin Ma
- School of Physics and Optoelectronic Engineering, Guangdong Provincial Key Laboratory of Information Photonics Technology, Guangdong University of Technology, Guangzhou 510006, China.
| | - Lianlian Jiang
- Institute for Infocomm Research (I2R), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #21-01, Connexis South Tower 138632, Singapore.
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4
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Lininger A, Palermo G, Guglielmelli A, Nicoletta G, Goel M, Hinczewski M, Strangi G. Chirality in Light-Matter Interaction. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2107325. [PMID: 35532188 DOI: 10.1002/adma.202107325] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/07/2022] [Indexed: 06/14/2023]
Abstract
The scientific effort to control the interaction between light and matter has grown exponentially in the last 2 decades. This growth has been aided by the development of scientific and technological tools enabling the manipulation of light at deeply sub-wavelength scales, unlocking a large variety of novel phenomena spanning traditionally distant research areas. Here, the role of chirality in light-matter interactions is reviewed by providing a broad overview of its properties, materials, and applications. A perspective on future developments is highlighted, including the growing role of machine learning in designing advanced chiroptical materials to enhance and control light-matter interactions across several scales.
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Affiliation(s)
- Andrew Lininger
- Department of Physics, Case Western Reserve University, 2076 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Giovanna Palermo
- Department of Physics, NLHT-Lab, University of Calabria and CNR-NANOTEC Istituto di Nanotecnologia, Rende, 87036, Italy
| | - Alexa Guglielmelli
- Department of Physics, NLHT-Lab, University of Calabria and CNR-NANOTEC Istituto di Nanotecnologia, Rende, 87036, Italy
| | - Giuseppe Nicoletta
- Department of Physics, NLHT-Lab, University of Calabria and CNR-NANOTEC Istituto di Nanotecnologia, Rende, 87036, Italy
| | - Madhav Goel
- Department of Physics, Case Western Reserve University, 2076 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, 2076 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Giuseppe Strangi
- Department of Physics, Case Western Reserve University, 2076 Adelbert Rd, Cleveland, OH, 44106, USA
- Department of Physics, NLHT-Lab, University of Calabria and CNR-NANOTEC Istituto di Nanotecnologia, Rende, 87036, Italy
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5
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Chen Q, Maslarova D, Wang J, Li S, Umstadter D. Injection of electron beams into two laser wakefields and generation of electron rings. Phys Rev E 2022; 106:055202. [PMID: 36559382 DOI: 10.1103/physreve.106.055202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Mutual injection of electron beams into two laser plasma wakefields was observed experimentally when driving laser pulses interfered in plasma at a small crossing angle and were slightly relatively delayed, approximately by one pulse duration. Particle-in-cell simulations revealed that the mutual injection was sensitive to the spatial overlap of the laser pulses, which therefore could be used to control the mutual injection. The dual synchronized, femtosecond electron beams are potentially useful for pump-probe experiments in ultrafast science. In addition, out-of-axis ring-shaped electron beams were detected in both experiments and simulations.
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Affiliation(s)
- Q Chen
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Dominika Maslarova
- Institute of Plasma Physics of the Czech Academy of Sciences, Za Slovankou 1782/3, 182 00 Prague, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Brehová 78/7, 115 19 Prague, Czech Republic
| | - J Wang
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - S Li
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - D Umstadter
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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6
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Symmetry Breaking Charge Transfer in DNA-Templated Perylene Dimer Aggregates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196612. [PMID: 36235149 PMCID: PMC9571668 DOI: 10.3390/molecules27196612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022]
Abstract
Molecular aggregates are of interest to a broad range of fields including light harvesting, organic optoelectronics, and nanoscale computing. In molecular aggregates, nonradiative decay pathways may emerge that were not present in the constituent molecules. Such nonradiative decay pathways may include singlet fission, excimer relaxation, and symmetry-breaking charge transfer. Singlet fission, sometimes referred to as excitation multiplication, is of great interest to the fields of energy conversion and quantum information. For example, endothermic singlet fission, which avoids energy loss, has been observed in covalently bound, linear perylene trimers and tetramers. In this work, the electronic structure and excited-state dynamics of dimers of a perylene derivative templated using DNA were investigated. Specifically, DNA Holliday junctions were used to template the aggregation of two perylene molecules covalently linked to a modified uracil nucleobase through an ethynyl group. The perylenes were templated in the form of monomer, transverse dimer, and adjacent dimer configurations. The electronic structure of the perylene monomers and dimers were characterized via steady-state absorption and fluorescence spectroscopy. Initial insights into their excited-state dynamics were gleaned from relative fluorescence intensity measurements, which indicated that a new nonradiative decay pathway emerges in the dimers. Femtosecond visible transient absorption spectroscopy was subsequently used to elucidate the excited-state dynamics. A new excited-state absorption feature grows in on the tens of picosecond timescale in the dimers, which is attributed to the formation of perylene anions and cations resulting from symmetry-breaking charge transfer. Given the close proximity required for symmetry-breaking charge transfer, the results shed promising light on the prospect of singlet fission in DNA-templated molecular aggregates.
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7
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Saida Y, Shikata R, En-Ya K, Ohmura S, Nishina Y, Hada M. Development of a Multitimescale Time-Resolved Electron Diffraction Setup: Photoinduced Dynamics of Oxygen Radicals on Graphene Oxide. J Phys Chem A 2022; 126:6301-6308. [PMID: 36063425 DOI: 10.1021/acs.jpca.2c04075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed a multitimescale time-resolved electron diffraction setup by electrically synchronizing a nanosecond laser with our table-top picosecond time-resolved electron diffractometer. The setup covers the photoinduced structural dynamics of target materials at timescales ranging from picoseconds to submilliseconds. Using this setup, we sequentially observed the ultraviolet (UV) photoinduced bond dissociation, radical formation, and relaxation dynamics of the oxygen atoms in the epoxy functional group on the basal plane of graphene oxide (GO). The results show that oxygen radicals formed via UV photoexcitation on the basal plane of GO in several tens of picoseconds and then relaxed back to the initial state on the microsecond timescale. The results of first-principles calculations also support the formation of oxygen radicals in the excited state on an early timescale. These results are essential for the further discussion of the reactivities on the basal plane of GO, such as catalytic reactions and antibacterial and antiviral activities. The results also suggest that the multitimescale time-resolved electron diffraction system is a promising tool for laboratory-based molecular dynamics studies of materials and chemical systems.
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Affiliation(s)
- Yuri Saida
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8573, Japan
| | - Ryo Shikata
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8573, Japan
| | - Kaito En-Ya
- College of Engineering Sciences, University of Tsukuba, Tsukuba 305-8573, Japan
| | - Satoshi Ohmura
- Faculty of Engineering, Hiroshima Institute of Technology, Hiroshima 731-5193, Japan
| | - Yuta Nishina
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama 700-8530, Japan
| | - Masaki Hada
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8573, Japan.,Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8573, Japan
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8
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Kotsina N, Brahms C, Jackson S, Travers JC, Townsend D. Spectroscopic application of few-femtosecond deep-ultraviolet laser pulses from resonant dispersive wave emission in a hollow capillary fibre. Chem Sci 2022; 13:9586-9594. [PMID: 36091901 PMCID: PMC9400683 DOI: 10.1039/d2sc02185d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022] Open
Abstract
We exploit the phenomenon of resonant dispersive wave (RDW) emission in gas-filled hollow capillary fibres (HCFs) to realize time-resolved photoelectron imaging (TRPEI) measurements with an extremely short temporal resolution. By integrating the output end of an HCF directly into a vacuum chamber assembly we demonstrate two-colour deep ultraviolet (DUV)-infrared instrument response functions of just 10 and 11 fs at central pump wavelengths of 250 and 280 nm, respectively. This result represents an advance in the current state of the art for ultrafast photoelectron spectroscopy. We also present an initial TRPEI measurement investigating the excited-state photochemical dynamics operating in the N-methylpyrrolidine molecule. Given the substantial interest in generating extremely short and highly tuneable DUV pulses for many advanced spectroscopic applications, we anticipate our first demonstration will stimulate wider uptake of the novel RDW-based approach for studying ultrafast photochemistry – particularly given the relatively compact and straightforward nature of the HCF setup. We exploit the phenomenon of resonant dispersive wave emission in gas-filled hollow capillary fibres to realize time-resolved photoelectron imaging measurements with an extremely short temporal resolution.![]()
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Affiliation(s)
- Nikoleta Kotsina
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Christian Brahms
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Sebastian L. Jackson
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - John C. Travers
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Dave Townsend
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
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9
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Heisler IA, Meech SR. Altered relaxation dynamics of excited state reactions by confinement in reverse micelles probed by ultrafast fluorescence up-conversion. Chem Soc Rev 2021; 50:11486-11502. [PMID: 34661209 DOI: 10.1039/d1cs00516b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chemical reactions in confined environments are important in areas as diverse as heterogenous catalysis, environmental chemistry and biochemistry, yet they are much less well understood than the equivalent reactions in either the gas phase or in free solution. The understanding of chemical reactions in solution was greatly enhanced by real time studies of model reactions, through ultrafast spectroscopy (especially when supported by molecular dynamics simulation). Here we review some of the efforts that have been made to adapt this approach to the investigation of reactions in confined media. Specifically, we review the application of ultrafast fluorescence spectroscopy to measure reaction dynamics in the nanoconfined water phase of reverse micelles, as a function of the droplet radius and the charge on the interface. Methods of measurement and modelling of the reactions are outlined. In all of the cases studied (which are focused on ultrafast intramolecular reactions) the effect of confinement was to suppress the reaction. Even in the largest micelles the result in the bulk aqueous phase was not usually recovered, suggesting an important role for specific interactions between reactant and environment, for example at the interface. There was no simple one-to-one correspondence with direct measures of the dynamics of the confined phase. Thus, understanding the effect of confinement on reaction rate appears to require not only knowledge of the dynamics of the reaction in solutions and the effect of confinement on the medium, but also of the interaction between reactant and confining medium.
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Affiliation(s)
- Ismael A Heisler
- Departamento de Física, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK.
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10
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Li D, Zhu Y, Li S, Shu C, Liu P. Post‐Functionalization of Supramolecular Polymers on Surface and the Chiral Assembly‐Induced Enantioselective Reaction. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Deng‐Yuan Li
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center Frontiers Science Center for Materiobiology and Dynamic Chemistry State Key Laboratory of Chemical Engineering School of Chemistry and Molecular Engineering East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
| | - Ya‐Cheng Zhu
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center Frontiers Science Center for Materiobiology and Dynamic Chemistry State Key Laboratory of Chemical Engineering School of Chemistry and Molecular Engineering East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
| | - Shi‐Wen Li
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center Frontiers Science Center for Materiobiology and Dynamic Chemistry State Key Laboratory of Chemical Engineering School of Chemistry and Molecular Engineering East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
| | - Chen‐Hui Shu
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center Frontiers Science Center for Materiobiology and Dynamic Chemistry State Key Laboratory of Chemical Engineering School of Chemistry and Molecular Engineering East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
| | - Pei‐Nian Liu
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center Frontiers Science Center for Materiobiology and Dynamic Chemistry State Key Laboratory of Chemical Engineering School of Chemistry and Molecular Engineering East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
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11
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Li DY, Zhu YC, Li SW, Shu CH, Liu PN. Post-Functionalization of Supramolecular Polymers on Surface and the Chiral Assembly-Induced Enantioselective Reaction. Angew Chem Int Ed Engl 2021; 60:11370-11377. [PMID: 33630356 DOI: 10.1002/anie.202016395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/22/2021] [Indexed: 11/07/2022]
Abstract
Although post-functionalization is extensively used to introduce diverse functional groups into supramolecular polymers (SPs) in solution, post-functionalization of SPs on surfaces still remains unexplored. Here we achieved the on-surface post-functionalization of two SPs derived from 5,10,15-tri-(4-pyridyl)-20-bromophenyl porphyrin (Br-TPyP) via cross-coupling reactions on Au(111). The ladder-shaped, Cu-coordinated SPs preformed from Br-TPyP were functionalized through Heck reaction with 4-vinyl-1,1'-biphenyl. In the absence of Cu, Br-TPyP formed chiral SPs as two enantiomers via self-assembly, which were functionalized via divergent cross-coupling reaction with 4-isocyano-1,1'-biphenyl (ICBP). Surprisingly, this reaction was discovered as an enantioselective on-surface reaction induced by the chirality of SPs. Mechanistic analysis and DFT calculations indicated that after debromination of Br-TPyP and the first addition of ICBP, only one attack direction of ICBP to the chiral SP intermediate is permissive in the second addition step due to the steric hindrance, which guaranteed the high enantioselectivity of the reaction.
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Affiliation(s)
- Deng-Yuan Li
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ya-Cheng Zhu
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Shi-Wen Li
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Chen-Hui Shu
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Pei-Nian Liu
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai, 200237, China
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12
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Ghosh A, Ghosh S, Ghosh G, Patra A. Implications of relaxation dynamics of collapsed conjugated polymeric nanoparticles for light-harvesting applications. Phys Chem Chem Phys 2021; 23:14549-14563. [DOI: 10.1039/d1cp01618k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The mechanism of the formation of nanoparticles (collapsed state) from the extended state of polymers and their ultrafast excited state relaxation dynamics are illustrated.
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Affiliation(s)
- Arnab Ghosh
- School of Materials Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Srijon Ghosh
- School of Materials Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Goutam Ghosh
- School of Materials Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Amitava Patra
- School of Materials Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
- Institute of Nano Science and Technology
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13
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Qi H, Lian Z, Fei D, Chen Z, Hu Z. Manipulation of matter with shaped-pulse light field and its applications. ADVANCES IN PHYSICS: X 2021. [DOI: 10.1080/23746149.2021.1949390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Hongxia Qi
- Institute of Atomic and Molecular Physics, Jilin University, Changchun, China
- Advanced Light Field and Modern Medical Treatment Science and Technology Innovation Center of Jilin Province, Jilin University, Changchun, China
| | - Zhenzhong Lian
- Institute of Atomic and Molecular Physics, Jilin University, Changchun, China
| | - Dehou Fei
- Institute of Atomic and Molecular Physics, Jilin University, Changchun, China
| | - Zhou Chen
- Institute of Atomic and Molecular Physics, Jilin University, Changchun, China
- Advanced Light Field and Modern Medical Treatment Science and Technology Innovation Center of Jilin Province, Jilin University, Changchun, China
| | - Zhan Hu
- Advanced Light Field and Modern Medical Treatment Science and Technology Innovation Center of Jilin Province, Jilin University, Changchun, China
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14
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Kotsina N, Townsend D. Improved insights in time-resolved photoelectron imaging. Phys Chem Chem Phys 2021; 23:10736-10755. [DOI: 10.1039/d1cp00933h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review new light source developments and data analysis considerations relevant to the time-resolved photoelectron imaging technique. Case studies illustrate how these themes may enhance understanding in studies of excited state molecular dynamics.
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Affiliation(s)
- Nikoleta Kotsina
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Dave Townsend
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
- Institute of Chemical Sciences
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15
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Supramolecular chlorophyll aggregates inspired from specific light-harvesting antenna “chlorosome”: Static nanostructure, dynamic construction process, and versatile application. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2020.100385] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Paterson MJ, Townsend D. Rydberg-to-valence evolution in excited state molecular dynamics. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1815389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Dave Townsend
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, UK
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17
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Adachi J, Mori T, Inoue R, Naito M, Le NHT, Kawamorita S, Hill JP, Naota T, Ariga K. Emission Control by Molecular Manipulation of Double-Paddled Binuclear Pt II Complexes at the Air-Water Interface. Chem Asian J 2020; 15:406-414. [PMID: 31922659 DOI: 10.1002/asia.201901691] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/19/2019] [Indexed: 12/19/2022]
Abstract
Molecular functions depend on conformations and motions of the corresponding molecular species. An air-water interface is a suitable asymmetric field for the control of molecular conformations and motions under a small applied force. In this work, double-paddled binuclear PtII complexes containing pyrazole rings linked by alkyl spacers were synthesized and their orientations and emission properties dynamically manipulated at the air-water interface. The complexes emerge from water with concurrent variation of interface orientation of the planes of the PtII complexes from perpendicular to parallel during mechanical compression suggesting a unique 'submarine emission'. Phosphorescence of the complexes is quenched at the air-water interface prior to monolayer formation with intensities subsequently rapidly increasing during monolayer compression. These results indicate that asymmetric reactions and motions might be controlled by applying mechanical force at the air-water interface.
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Affiliation(s)
- Junya Adachi
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Taizo Mori
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, 277-0827, Japan.,International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Ryo Inoue
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Masaya Naito
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Ngoc Ha-Thu Le
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Soichiro Kawamorita
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Jonathan P Hill
- International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Takeshi Naota
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Katsuhiko Ariga
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, 277-0827, Japan.,International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan
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18
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Kotsina N, Candelaresi M, Saalbach L, Zawadzki MM, Crane SW, Sparling C, Townsend D. Short-wavelength probes in time-resolved photoelectron spectroscopy: an extended view of the excited state dynamics in acetylacetone. Phys Chem Chem Phys 2020; 22:4647-4658. [DOI: 10.1039/d0cp00068j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved photoelectron spectroscopy using a vacuum ultraviolet probe brings new insight to the excited state dynamics operating in acetylacetone.
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Affiliation(s)
- Nikoleta Kotsina
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Marco Candelaresi
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Lisa Saalbach
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | | | - Stuart W. Crane
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Chris Sparling
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Dave Townsend
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
- Institute of Chemical Sciences
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19
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Naz Z, Moin ST, Hofer TS. Hydration of Closely Related Manganese and Magnesium Porphyrins in Aqueous Solutions: Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation Study. J Phys Chem B 2019; 123:10769-10779. [PMID: 31738566 DOI: 10.1021/acs.jpcb.9b07639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To the best of our knowledge, the current study based on ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) is the first to explore the difference in the hydration behavior between Mn(II)- and Mg(II)-associated porphyrins (Mn(II)-POR and Mg(II)-POR) in aqueous solution. The simulation study highlights similar and dissimilar characteristics of the structural, dynamical, and thermodynamical properties of these closely related metals bound to porphyrins in aqueous solution. The structural analysis is based on radial and angular distribution functions, coordination number distributions, and angular-radial distributions. Both hydrated systems demonstrate similar pentacoordinated structures formed via the axial coordination of one water molecule to the metal ion in addition to the four nitrogen atoms of the porphyrin ring. However, in the case of Mn(II)-POR, the formation of a distorted square pyramidal geometry was observed. It was envisaged as a weak coordination of the water molecule to the Mn(II) atom and thus higher atomic fluctuation for all atoms in contrast to that for the hydrated Mg(II)-POR. The dynamical data in terms of the mean residence times, velocity autocorrelation function, free energy, and other parameters revealed the difference in the metal binding effect because the Mn(II) atom was observed to inhibit H-bond formation more than the presence of Mg(II) atoms in the core of the porphyrin. The current study thus highlights the significant differences in the structural and dynamical properties of Mn(II)- and Mg(II)-associated porphyrin systems.
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Affiliation(s)
- Zobia Naz
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences , University of Karachi , Karachi 75270 , Pakistan
| | - Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences , University of Karachi , Karachi 75270 , Pakistan
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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20
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Maiuri M, Garavelli M, Cerullo G. Ultrafast Spectroscopy: State of the Art and Open Challenges. J Am Chem Soc 2019; 142:3-15. [DOI: 10.1021/jacs.9b10533] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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21
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Aster A, Licari G, Zinna F, Brun E, Kumpulainen T, Tajkhorshid E, Lacour J, Vauthey E. Tuning symmetry breaking charge separation in perylene bichromophores by conformational control. Chem Sci 2019; 10:10629-10639. [PMID: 34040711 PMCID: PMC8133027 DOI: 10.1039/c9sc03913a] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Understanding structure-property relationships in multichromophoric molecular architectures is a crucial step in establishing new design principles in organic electronics as well as to fully understand how nature exploits solar energy. Here, we study the excited state dynamics of three bichromophores consisting of two perylene chromophores linked to three different crown-ether backbones, using stationary and ultrafast electronic spectroscopy combined with molecular dynamics simulations. The conformational space available to the bichromophores depends on the structure and geometry of the crown-ether and can be significantly changed upon cation binding, strongly affecting the excited-state dynamics. We show that, depending on the conformational restrictions and the local environment, the nature of the excited state varies greatly, going from an excimer to a symmetry-broken charge separated state. These results can be rationalised in terms of a structure-property relationship that includes the effect of the local environment.
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Affiliation(s)
- Alexander Aster
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Giuseppe Licari
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois USA.,Department of Biochemistry, Center for Biophysics and Quantitative Biology Urbana Illinois USA
| | - Francesco Zinna
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Elodie Brun
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Tatu Kumpulainen
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois USA.,Department of Biochemistry, Center for Biophysics and Quantitative Biology Urbana Illinois USA
| | - Jérôme Lacour
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
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22
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Aleksandrov A. A Molecular Mechanics Model for Flavins. J Comput Chem 2019; 40:2834-2842. [DOI: 10.1002/jcc.26061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/03/2019] [Accepted: 08/04/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Alexey Aleksandrov
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique IP Paris, 91128 Palaiseau France
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23
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Abstract
After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Lausanne Centre for Ultrafast Science (LACUS), FSB, Station 6, CH-1015 Lausanne, Switzerland.
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24
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Analytical Theory of Attosecond Transient Absorption Spectroscopy of Perturbatively Dressed Systems. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9071350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A theoretical description of attosecond transient absorption spectroscopy for temporally and spatially overlapping XUV and optical pulses is developed, explaining the signals one can obtain in such an experiment. To this end, we employ a two-stage approach based on perturbation theory, which allows us to give an analytical expression for the transient absorption signal. We focus on the situation in which the attosecond XUV pulse is used to create a coherent superposition of electronic states. As we explain, the resulting dynamics can be detected in the spectrum of the transmitted XUV pulse by manipulating the electronic wave packet using a carrier-envelope-phase-stabilized optical dressing pulse. In addition to coherent electron dynamics triggered by the attosecond pulse, the transmitted XUV spectrum encodes information on electronic states made accessible by the optical dressing pulse. We illustrate these concepts through calculations performed for a few-level model.
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25
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Kotsina N, Belli F, Gao SF, Wang YY, Wang P, Travers JC, Townsend D. Ultrafast Molecular Spectroscopy Using a Hollow-Core Photonic Crystal Fiber Light Source. J Phys Chem Lett 2019; 10:715-720. [PMID: 30694062 DOI: 10.1021/acs.jpclett.8b03777] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We demonstrate, for the first time, the application of rare-gas-filled hollow-core photonic crystal fibers (HC-PCFs) as tunable ultraviolet light sources in femtosecond pump-probe spectroscopy. A critical requirement here is excellent output stability over extended periods of data acquisition, and we show this can be readily achieved. The time-resolved photoelectron imaging technique reveals nonadiabatic dynamical processes operating on three distinct time scales in the styrene molecule following excitation over the 242-258 nm region. These include ultrafast (<100 fs) internal conversion between the S2(ππ*) and S1(ππ*) electronic states and subsequent intramolecular vibrational energy redistribution within S1(ππ*). Compact, cost-effective, and highly efficient benchtop HC-PCF sources have huge potential to open up many exciting new avenues for ultrafast spectroscopy in the ultraviolet and vacuum ultraviolet spectral regions. We anticipate that our initial validation of this approach will generate important impetus in this area.
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Affiliation(s)
- Nikoleta Kotsina
- Institute of Photonics & Quantum Sciences , Heriot-Watt University , Edinburgh EH14 4AS , U.K
| | - Federico Belli
- Institute of Photonics & Quantum Sciences , Heriot-Watt University , Edinburgh EH14 4AS , U.K
| | - Shou-Fei Gao
- Beijing Engineering Research Centre of Laser Technology, Institute of Laser Engineering , Beijing University of Technology , 100124 Beijing , China
| | - Ying-Ying Wang
- Beijing Engineering Research Centre of Laser Technology, Institute of Laser Engineering , Beijing University of Technology , 100124 Beijing , China
| | - Pu Wang
- Beijing Engineering Research Centre of Laser Technology, Institute of Laser Engineering , Beijing University of Technology , 100124 Beijing , China
| | - John C Travers
- Institute of Photonics & Quantum Sciences , Heriot-Watt University , Edinburgh EH14 4AS , U.K
| | - Dave Townsend
- Institute of Photonics & Quantum Sciences , Heriot-Watt University , Edinburgh EH14 4AS , U.K
- Institute of Chemical Sciences , Heriot-Watt University , Edinburgh EH14 4AS , U.K
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26
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Mak A, Shamuilov G, Salén P, Dunning D, Hebling J, Kida Y, Kinjo R, McNeil BWJ, Tanaka T, Thompson N, Tibai Z, Tóth G, Goryashko V. Attosecond single-cycle undulator light: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:025901. [PMID: 30572315 DOI: 10.1088/1361-6633/aafa35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Research at modern light sources continues to improve our knowledge of the natural world, from the subtle workings of life to matter under extreme conditions. Free-electron lasers, for instance, have enabled the characterization of biomolecular structures with sub-ångström spatial resolution, and paved the way to controlling the molecular functions. On the other hand, attosecond temporal resolution is necessary to broaden our scope of the ultrafast world. Here we discuss attosecond pulse generation beyond present capabilities. Furthermore, we review three recently proposed methods of generating attosecond x-ray pulses. These novel methods exploit the coherent radiation of microbunched electrons in undulators and the tailoring of the emitted wavefronts. The computed pulse energy outperforms pre-existing technologies by three orders of magnitude. Specifically, our simulations of the proposed Soft X-ray Laser at MAX IV (Lund, Sweden) show that a pulse duration of 50-100 as and a pulse energy up to 5 [Formula: see text]J is feasible with the novel methods. In addition, the methods feature pulse shape control, enable the incorporation of orbital angular momentum, and can be used in combination with modern compact free-electron laser setups.
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Affiliation(s)
- Alan Mak
- FREIA Laboratory, Uppsala University, Uppsala, Sweden
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27
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Do thermal treatments influence the ultrafast opto-thermal processes of eumelanin? EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:153-160. [DOI: 10.1007/s00249-018-1342-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/12/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
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28
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Hummert J, Reitsma G, Mayer N, Ikonnikov E, Eckstein M, Kornilov O. Femtosecond Extreme Ultraviolet Photoelectron Spectroscopy of Organic Molecules in Aqueous Solution. J Phys Chem Lett 2018; 9:6649-6655. [PMID: 30388021 DOI: 10.1021/acs.jpclett.8b02937] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Time-resolved valence photoelectron spectroscopy is an established tool for studies of ultrafast molecular dynamics in the gas phase. Here we demonstrate time-resolved XUV photoelectron spectroscopy from dilute aqueous solutions of organic molecules, paving the way to application of this method to photodynamics studies of organic molecules in natural environments, which so far have only been accessible to all-optical transient spectroscopies. We record static and time-resolved photoelectron spectra of a sample molecule, quinoline yellow WS, analyze its electronic structure, and follow the relaxation dynamics upon excitation with 400 nm pulses. The dynamics exhibit three time scales, of which a 250 ± 70 fs time scale is attributed to solvent rearrangement. The two longer time scales of 1.3 ± 0.4 and 90 ± 20 ps can be correlated to the recently proposed ultrafast excited-state intramolecular proton transfer in a closely related molecule, quinophthalone.
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Affiliation(s)
- Johan Hummert
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy , Max-Born-Strasse 2a , 12489 Berlin , Germany
| | - Geert Reitsma
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy , Max-Born-Strasse 2a , 12489 Berlin , Germany
| | - Nicola Mayer
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy , Max-Born-Strasse 2a , 12489 Berlin , Germany
| | - Evgenii Ikonnikov
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy , Max-Born-Strasse 2a , 12489 Berlin , Germany
| | - Martin Eckstein
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy , Max-Born-Strasse 2a , 12489 Berlin , Germany
| | - Oleg Kornilov
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy , Max-Born-Strasse 2a , 12489 Berlin , Germany
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29
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Abstract
Resonance energy transfer (RET) is a complex phenomenon where energy is transferred between two nonequivalent molecules. In the Förster picture, that applies to the weak coupling regime, RET occurs from the energy donor molecule in the relaxed excited state toward the acceptor, in an energy-conserving process. However, energy dissipation is crucial for a more general picture of RET that also applies to the strong coupling regime. Here we present a dynamical, nonadiabatic model for RET also accounting for energy relaxation. We exploit the essential state formalism to set up a model for the RET pair that yields an accurate picture of the relevant physics, accounting for just a few electronic states and a single coupled vibrational coordinate per molecule. Molecular vibrations are treated in a nonadiabatic approach, and energy dissipation is dealt within the Redfield formalism. The approach is first validated on an isolated dye, demonstrating that a very simple relaxation model, defined in terms of a single relaxation parameter, properly describes the different regimes of energy dissipation expected for a molecule, with a fast (fs time window) internal conversion to the lowest excited state and a slow relaxation toward the ground state (ns time window). The same approach is then applied to follow the real time dynamics of a RET pair. In line with the Förster model, in the weak coupling regime the internal conversion of the donor molecule is completed before energy transfer takes place. Our approach also applies to the strong coupling regime, where we observe ultrafast energy transfer occurring well before the internal relaxation of the energy donor is completed.
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Affiliation(s)
- Francesco Di Maiolo
- Department of Chemistry, Life Science and Environmental Sustainability , Università di Parma , 43124 Parma , Italy
| | - Anna Painelli
- Department of Chemistry, Life Science and Environmental Sustainability , Università di Parma , 43124 Parma , Italy
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30
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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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31
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Ultraviolet Transient Absorption Spectrometer with Sub-20-fs Time Resolution. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8060989] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Bai X, Qiu J, Wang L. An efficient solution to the decoherence enhanced trivial crossing problem in surface hopping. J Chem Phys 2018; 148:104106. [PMID: 29544303 DOI: 10.1063/1.5020693] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We provide an in-depth investigation of the time interval convergence when both trivial crossing and decoherence corrections are applied to Tully's fewest switches surface hopping (FSSH) algorithm. Using one force-based and one energy-based decoherence strategies as examples, we show decoherence corrections intrinsically enhance the trivial crossing problem. We propose a restricted decoherence (RD) strategy and incorporate it into the self-consistent (SC) fewest switches surface hopping algorithm [L. Wang and O. V. Prezhdo, J. Phys. Chem. Lett. 5, 713 (2014)]. The resulting SC-FSSH-RD approach is applied to general Hamiltonians with different electronic couplings and electron-phonon couplings to mimic charge transport in tens to hundreds of molecules. In all cases, SC-FSSH-RD allows us to use a large time interval of 0.1 fs for convergence and the simulation time is reduced by over one order of magnitude. Both the band and hopping mechanisms of charge transport have been captured perfectly. SC-FSSH-RD makes surface hops in the adiabatic representation and can be implemented in both diabatic and locally diabatic representations for wave function propagation. SC-FSSH-RD can potentially describe general nonadiabatic dynamics of electrons and excitons in organics and other materials.
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Affiliation(s)
- Xin Bai
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Jing Qiu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Linjun Wang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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33
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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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34
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Shimizu T, Hashimoto K, Hada M, Miyazaki M, Fujii M. A theoretical study on the size-dependence of ground-state proton transfer in phenol-ammonia clusters. Phys Chem Chem Phys 2018; 20:3265-3276. [PMID: 29134211 DOI: 10.1039/c7cp05247b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Geometries and infrared (IR) spectra in the mid-IR region of phenol-(ammonia)n (PhOH-(NH3)n) (n = 0-10) clusters have been studied using density functional theory (DFT) to investigate the critical number of solvent molecules necessary to promote ground-state proton transfer (GSPT). For n ≤ 8 clusters, the most stable isomer is a non-proton-transferred (non-PT) structure, and all isomers found within 1.5 kcal mol-1 from it are also non-PT structures. For n = 9, the most stable isomer is also a non-PT structure; however, the second stable isomer is a PT structure, whose relative energy is within the experimental criterion of population (0.7 kcal mol-1). For n = 10, the PT structure is the most stable one. We can therefore estimate that the critical size of GSPT is n = 9. This is confirmed by the fact that these calculated IR spectra are in good accordance with our previous experimental results of mid-IR spectra. It is demonstrated that characteristic changes of the ν9a and ν12 bands in the skeletal vibrational region provide clear information that the GSPT reaction has occurred. It was also found that the shortest distance between the π-ring and the solvent moiety is a good indicator of the PT reaction.
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Affiliation(s)
- Toshihiko Shimizu
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan.
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35
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Kaplan M, Yoo B, Tang J, Karam TE, Liao B, Majumdar D, Baltimore D, Jensen GJ, Zewail AH. Photon‐Induced Near‐Field Electron Microscopy of Eukaryotic Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mohammed Kaplan
- Physical Biology Center for Ultrafast Science and Technology Arthur Amos Noyes Laboratory of Chemical Physics California Institute of Technology Pasadena CA 91125 USA
| | - Byung‐Kuk Yoo
- Physical Biology Center for Ultrafast Science and Technology Arthur Amos Noyes Laboratory of Chemical Physics California Institute of Technology Pasadena CA 91125 USA
| | - Jau Tang
- Physical Biology Center for Ultrafast Science and Technology Arthur Amos Noyes Laboratory of Chemical Physics California Institute of Technology Pasadena CA 91125 USA
| | - Tony E. Karam
- Physical Biology Center for Ultrafast Science and Technology Arthur Amos Noyes Laboratory of Chemical Physics California Institute of Technology Pasadena CA 91125 USA
| | - Bolin Liao
- Physical Biology Center for Ultrafast Science and Technology Arthur Amos Noyes Laboratory of Chemical Physics California Institute of Technology Pasadena CA 91125 USA
| | - Devdoot Majumdar
- Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA
| | - David Baltimore
- Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA
| | - Grant J. Jensen
- California Institute of Technology Pasadena CA 91125 USA
- Howard Hughes Medical Institute Pasadena CA 91125 USA
| | - Ahmed H. Zewail
- Physical Biology Center for Ultrafast Science and Technology Arthur Amos Noyes Laboratory of Chemical Physics California Institute of Technology Pasadena CA 91125 USA
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36
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Ehn A, Bood J, Li Z, Berrocal E, Aldén M, Kristensson E. FRAME: femtosecond videography for atomic and molecular dynamics. LIGHT, SCIENCE & APPLICATIONS 2017; 6:e17045. [PMID: 30167293 PMCID: PMC6062331 DOI: 10.1038/lsa.2017.45] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 05/18/2023]
Abstract
Many important scientific questions in physics, chemistry and biology require effective methodologies to spectroscopically probe ultrafast intra- and inter-atomic/molecular dynamics. However, current methods that extend into the femtosecond regime are capable of only point measurements or single-snapshot visualizations and thus lack the capability to perform ultrafast spectroscopic videography of dynamic single events. Here we present a laser-probe-based method that enables two-dimensional videography at ultrafast timescales (femtosecond and shorter) of single, non-repetitive events. The method is based on superimposing a structural code onto the illumination to encrypt a single event, which is then deciphered in a post-processing step. This coding strategy enables laser probing with arbitrary wavelengths/bandwidths to collect signals with indiscriminate spectral information, thus allowing for ultrafast videography with full spectroscopic capability. To demonstrate the high temporal resolution of our method, we present videography of light propagation with record high 200 femtosecond temporal resolution. The method is widely applicable for studying a multitude of dynamical processes in physics, chemistry and biology over a wide range of time scales. Because the minimum frame separation (temporal resolution) is dictated by only the laser pulse duration, attosecond-laser technology may further increase video rates by several orders of magnitude.
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Affiliation(s)
- Andreas Ehn
- Division of Combustion Physics, Department of Physics, Lund University, Lund SE-223 63, Sweden
| | - Joakim Bood
- Division of Combustion Physics, Department of Physics, Lund University, Lund SE-223 63, Sweden
| | - Zheming Li
- Division of Combustion Physics, Department of Physics, Lund University, Lund SE-223 63, Sweden
| | - Edouard Berrocal
- Division of Combustion Physics, Department of Physics, Lund University, Lund SE-223 63, Sweden
| | - Marcus Aldén
- Division of Combustion Physics, Department of Physics, Lund University, Lund SE-223 63, Sweden
| | - Elias Kristensson
- Division of Combustion Physics, Department of Physics, Lund University, Lund SE-223 63, Sweden
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37
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Kuramochi H, Fujisawa T, Takeuchi S, Tahara T. Broadband stimulated Raman spectroscopy in the deep ultraviolet region. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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Razjivin AP, Lukashev EP, Kompanets VO, Kozlovsky VS, Ashikhmin AA, Chekalin SV, Moskalenko AA, Paschenko VZ. Excitation energy transfer from the bacteriochlorophyll Soret band to carotenoids in the LH2 light-harvesting complex from Ectothiorhodospira haloalkaliphila is negligible. PHOTOSYNTHESIS RESEARCH 2017; 133:289-295. [PMID: 28205063 DOI: 10.1007/s11120-017-0341-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
Pathways of intramolecular conversion and intermolecular electronic excitation energy transfer (EET) in the photosynthetic apparatus of purple bacteria remain subject to debate. Here we experimentally tested the possibility of EET from the bacteriochlorophyll (BChl) Soret band to the singlet S2 level of carotenoids using femtosecond pump-probe measurements and steady-state fluorescence excitation and absorption measurements in the near-ultraviolet and visible spectral ranges. The efficiency of EET from the Soret band of BChl to S2 of the carotenoids in light-harvesting complex LH2 from the purple bacterium Ectothiorhodospira haloalkaliphila appeared not to exceed a few percent.
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Affiliation(s)
- A P Razjivin
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991.
| | - E P Lukashev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - V O Kompanets
- Institute of Spectroscopy, Russian Academy of Sciences, Troitsk, Moscow, Russia, 142190
| | - V S Kozlovsky
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - A A Ashikhmin
- Institute of Fundamental Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia, 142290
| | - S V Chekalin
- Institute of Spectroscopy, Russian Academy of Sciences, Troitsk, Moscow, Russia, 142190
| | - A A Moskalenko
- Institute of Fundamental Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia, 142290
| | - V Z Paschenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
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39
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Kaplan M, Yoo BK, Tang J, Karam TE, Liao B, Majumdar D, Baltimore D, Jensen GJ, Zewail AH. Photon-Induced Near-Field Electron Microscopy of Eukaryotic Cells. Angew Chem Int Ed Engl 2017; 56:11498-11501. [PMID: 28736869 DOI: 10.1002/anie.201706120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Indexed: 11/09/2022]
Abstract
Photon-induced near-field electron microscopy (PINEM) is a technique to produce and then image evanescent electromagnetic fields on the surfaces of nanostructures. Most previous applications of PINEM have imaged surface plasmon-polariton waves on conducting nanomaterials. Here, the application of PINEM on whole human cancer cells and membrane vesicles isolated from them is reported. We show that photons induce time-, orientation-, and polarization-dependent evanescent fields on the surfaces of A431 cancer cells and isolated membrane vesicles. Furthermore, the addition of a ligand to the major surface receptor on these cells and vesicles (epidermal growth factor receptor, EGFR) reduces the intensity of these fields in both preparations. We propose that in the absence of plasmon waves in biological samples, these evanescent fields reflect the changes in EGFR kinase domain polarization upon ligand binding.
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Affiliation(s)
- Mohammed Kaplan
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Byung-Kuk Yoo
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jau Tang
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Tony E Karam
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bolin Liao
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Devdoot Majumdar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grant J Jensen
- California Institute of Technology, Pasadena, CA, 91125, USA.,Howard Hughes Medical Institute, Pasadena, CA, 91125, USA
| | - Ahmed H Zewail
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, 91125, USA
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40
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Debus B, Orio M, Rehault J, Burdzinski G, Ruckebusch C, Sliwa M. Fusion of Ultraviolet-Visible and Infrared Transient Absorption Spectroscopy Data to Model Ultrafast Photoisomerization. J Phys Chem Lett 2017; 8:3530-3535. [PMID: 28696118 DOI: 10.1021/acs.jpclett.7b01255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultrafast photoisomerization reactions generally start at a higher excited state with excess of internal vibrational energy and occur via conical intersections. This leads to ultrafast dynamics which are difficult to investigate with a single transient absorption spectroscopy technique, be it in the ultraviolet-visible (UV-vis) or infrared (IR) domain. On one hand, the information available in the UV-vis domain is limited as only slight spectral changes are observed for different isomers. On the other hand, the interpretation of vibrational spectra is strongly hindered by intramolecular relaxation and vibrational cooling. These limitations can be circumvented by fusing UV-vis and IR transient absorption spectroscopy data in a multiset multivariate curve resolution analysis. We apply this approach to describe the spectrodynamics of the ultrafast cis-trans photoisomerization around the C-N double bond observed for aromatic Schiff bases. Twisted intermediate states could be elucidated, and isomerization was shown to occur through a continuous complete rotation. More broadly, data fusion can be used to rationalize a vast range of ultrafast photoisomerization processes of interest in photochemistry.
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Affiliation(s)
- Bruno Debus
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, Lille 59000, France
| | - Maylis Orio
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, Lille 59000, France
- Aix Marseille Univ , CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Julien Rehault
- University of Zurich , Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Gotard Burdzinski
- Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University in Poznan , 85 Umultowska, Poznan 61-614, Poland
| | - Cyril Ruckebusch
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, Lille 59000, France
| | - Michel Sliwa
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, Lille 59000, France
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41
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Moin ST, Hofer TS. Zinc- and copper-porphyrins in aqueous solution - two similar complexes with strongly contrasting hydration. MOLECULAR BIOSYSTEMS 2017; 12:2288-2295. [PMID: 27194391 DOI: 10.1039/c6mb00133e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present detailed analysis of the hydration behavior of zinc and copper bound porphyrins treated via ab initio quantum mechanical charge field molecular dynamics which agrees well with available experimental data. The computed metal-water coordination in the case of zinc bound porphyrin demonstrates a strong association of water with zinc compared to the copper-water interaction which correlates well with the calculated free energy of binding. The H-bond dynamics in these hydrated systems yield weaker H-bond interactions as compared to that observed in the case of metal-free porphyrin; nevertheless, the effect of metal association with porphyrin resulted in shifts in the vibrational frequencies. These characteristic data suggest a contrasting behavior between these metalloporphyrins in solution which could also serve to correlate with the properties of biological systems.
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Affiliation(s)
- Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
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42
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Chiba Y, Liu M, Tachibana Y, Fujihara T, Tsuji Y, Terao J. Hetero Face-to-Face Porphyrin Array with Cooperative Effects of Coordination and Host-Guest Complexation. Chem Asian J 2017; 12:1900-1904. [DOI: 10.1002/asia.201700738] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Yusuke Chiba
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering, Kyoto University; Kyoto 615-8510 Japan
| | - Maning Liu
- School of Engineering; RMIT University; Bundoora VIC 3083 Australia
| | | | - Tetsuaki Fujihara
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering, Kyoto University; Kyoto 615-8510 Japan
| | - Yasushi Tsuji
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering, Kyoto University; Kyoto 615-8510 Japan
| | - Jun Terao
- Department of Basic Science, Graduate School of Arts and Sciences; The University of Tokyo; Tokyo 153-8902 Japan
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43
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Baker LA, Habershon S. Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport. Proc Math Phys Eng Sci 2017; 473:20170112. [PMID: 28588417 PMCID: PMC5454362 DOI: 10.1098/rspa.2017.0112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/04/2017] [Indexed: 02/01/2023] Open
Abstract
Photosynthetic pigment-protein complexes (PPCs) are a vital component of the light-harvesting machinery of all plants and photosynthesizing bacteria, enabling efficient transport of the energy of absorbed light towards the reaction centre, where chemical energy storage is initiated. PPCs comprise a set of chromophore molecules, typically bacteriochlorophyll species, held in a well-defined arrangement by a protein scaffold; this relatively rigid distribution leads to a viewpoint in which the chromophore subsystem is treated as a network, where chromophores represent vertices and inter-chromophore electronic couplings represent edges. This graph-based view can then be used as a framework within which to interrogate the role of structural and electronic organization in PPCs. Here, we use this network-based viewpoint to compare excitation energy transfer (EET) dynamics in the light-harvesting complex II (LHC-II) system commonly found in higher plants and the Fenna-Matthews-Olson (FMO) complex found in green sulfur bacteria. The results of our simple network-based investigations clearly demonstrate the role of network connectivity and multiple EET pathways on the efficient and robust EET dynamics in these PPCs, and highlight a role for such considerations in the development of new artificial light-harvesting systems.
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Affiliation(s)
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK
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44
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Morisue M, Hoshino Y, Shimizu M, Nakanishi T, Hasegawa Y, Hossain MA, Sakurai S, Sasaki S, Uemura S, Matsui J. Supramolecular Polymer of Near-Infrared Luminescent Porphyrin Glass. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00316] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | | | | | - Takayuki Nakanishi
- Graduate
School of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo 060-8628, Japan
| | - Yasuchika Hasegawa
- Graduate
School of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo 060-8628, Japan
| | | | | | | | - Shinobu Uemura
- Department
of Advanced Materials Science, Kagawa University, Hayashi-cho, Takamatsu 761-0396, Japan
| | - Jun Matsui
- Department
of Material and Biological Chemistry, Faculty of Science, Yamagata University, Kojirakawa-cho, Yamagata 990-8560, Japan
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45
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Malý P, Ravensbergen J, Kennis JTM, van Grondelle R, Croce R, Mančal T, van Oort B. Polarization-controlled optimal scatter suppression in transient absorption spectroscopy. Sci Rep 2017; 7:43484. [PMID: 28262765 PMCID: PMC5337968 DOI: 10.1038/srep43484] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/24/2017] [Indexed: 12/19/2022] Open
Abstract
Ultrafast transient absorption spectroscopy is a powerful technique to study fast photo-induced processes, such as electron, proton and energy transfer, isomerization and molecular dynamics, in a diverse range of samples, including solid state materials and proteins. Many such experiments suffer from signal distortion by scattered excitation light, in particular close to the excitation (pump) frequency. Scattered light can be effectively suppressed by a polarizer oriented perpendicular to the excitation polarization and positioned behind the sample in the optical path of the probe beam. However, this introduces anisotropic polarization contributions into the recorded signal. We present an approach based on setting specific polarizations of the pump and probe pulses, combined with a polarizer behind the sample. Together, this controls the signal-to-scatter ratio (SSR), while maintaining isotropic signal. We present SSR for the full range of polarizations and analytically derive the optimal configuration at angles of 40.5° between probe and pump and of 66.9° between polarizer and pump polarizations. This improves SSR by (or compared to polarizer parallel to probe). The calculations are validated by transient absorption experiments on the common fluorescent dye Rhodamine B. This approach provides a simple method to considerably improve the SSR in transient absorption spectroscopy.
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Affiliation(s)
- Pavel Malý
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands.,Institute of Physics, Faculty of Mathematics and Physics, Charles University, Czech Republic
| | - Janneke Ravensbergen
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - John T M Kennis
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Rienk van Grondelle
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Roberta Croce
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Tomáš Mančal
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Czech Republic
| | - Bart van Oort
- Biophysics of Photosynthesis, Department of Physics and Astronomy, Faculty of Sciences, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
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46
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Triphenylamine corrole dyads: Synthesis, characterization and substitution effect on photophysical properties. J CHEM SCI 2017. [DOI: 10.1007/s12039-016-1219-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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47
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Kotsina N, Townsend D. Relative detection sensitivity in ultrafast spectroscopy: state lifetime and laser pulse duration effects. Phys Chem Chem Phys 2017; 19:29409-29417. [DOI: 10.1039/c7cp05426b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excited state lifetime and laser pulse duration have important implications for effective relative detection sensitivity in time-resolved spectroscopy.
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Affiliation(s)
- Nikoleta Kotsina
- Institute of Photonics & Quantum Sciences, Heriot-Watt University
- Edinburgh
- UK
| | - Dave Townsend
- Institute of Photonics & Quantum Sciences, Heriot-Watt University
- Edinburgh
- UK
- Institute of Chemical Sciences
- Heriot-Watt University
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48
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Abramczyk H, Brozek-Pluska B, Surmacki J, Tondusson M, Freysz E. Photostability of biological systems—Femtosecond dynamics of zinc tetrasulfonated phthalocyanine at cancerous and noncancerous human Breast tissues. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2016.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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49
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Kottke T, Lórenz-Fonfría VA, Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J Phys Chem B 2016; 121:335-350. [PMID: 28100053 DOI: 10.1021/acs.jpcb.6b09222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
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50
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Shimizu T, Miyazaki M, Fujii M. Theoretical Study on the Size Dependence of Ground-State Proton Transfer in 1-Naphthol–Ammonia Clusters. J Phys Chem A 2016; 120:7167-74. [DOI: 10.1021/acs.jpca.6b07079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshihiko Shimizu
- Laboratory
for Chemistry
and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Mitsuhiko Miyazaki
- Laboratory
for Chemistry
and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory
for Chemistry
and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
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