1
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Pios SV, Gelin MF, Luis Vasquez, Hauer J, Chen L. On-the-Fly Simulation of Two-Dimensional Fluorescence-Excitation Spectra. J Phys Chem Lett 2024; 15:8728-8735. [PMID: 39162319 DOI: 10.1021/acs.jpclett.4c01842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Two-dimensional (2D) fluorescence-excitation (2D-FLEX) spectroscopy is a recently proposed nonlinear femtosecond technique for the detection of photoinduced dynamics. The method records a time-resolved fluorescence signal in its excitation- and detection-frequency dependence and hence combines the exclusive detection of excited state dynamics (fluorescence) with signals resolved in both excitation and emission frequencies (2D electronic spectroscopy). In this work, we develop an on-the-fly protocol for the simulation of 2D-FLEX spectra of molecular systems, which is based on interfacing the classical doorway-window representation of spectroscopic responses with trajectory surface hopping simulations. Applying this methodology to gas-phase pyrazine, we show that femtosecond 2D-FLEX spectra can deliver detailed information that is otherwise obtainable via attosecond spectroscopy.
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Affiliation(s)
| | - Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Luis Vasquez
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Jürgen Hauer
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
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2
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Presswala Z, Acharya S, Shah S. Addressing barriers in diffuse intrinsic pontine glioma: the transformative role of lipid nanoparticulate drug delivery. ADMET AND DMPK 2024; 12:403-429. [PMID: 39091904 PMCID: PMC11289511 DOI: 10.5599/admet.2214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 06/27/2024] [Indexed: 08/04/2024] Open
Abstract
Background and purpose The brainstem tumour known as diffuse intrinsic pontine glioma (DIPG), also known as pontine glioma, infiltrative brainstem glioma is uncommon and virtually always affects children. A pontine glioma develops in the brainstem's most vulnerable region (the "pons"), which regulates a number of vital processes like respiration and blood pressure. It is particularly challenging to treat due to its location and how it invades healthy brain tissue. The hunt for a solution is continually advancing thanks to advances in modern medicine, but the correct approach is still elusive. With a particular focus on brain tumours that are incurable or recur, research is ongoing to discover fresh, practical approaches to target particular areas of the brain. Experimental approach To successfully complete this task, a thorough literature search was carried out in reputable databases like Google Scholar, PubMed, and ScienceDirect. Key results The present article provides a comprehensive analysis of the notable advantages of lipid nanoparticles compared to alternative nanoparticle formulations. The article delves into the intricate realm of diverse lipid-based nanoparticulate delivery systems, which are used in Diffuse Intrinsic Pontine Glioma (DIPG) which thoroughly examines preclinical and clinical studies, providing a comprehensive analysis of the effectiveness and potential of lipid nanoparticles in driving therapeutic advancements for DIPG. Conclusion There is strong clinical data to support the promising method of using lipid-based nanoparticulate drug delivery for brain cancer treatment, which shows improved outcomes.
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Affiliation(s)
| | - Sheetal Acharya
- Department of Pharmaceutical Technology, L.J Institute of Pharmacy, Lok Jagruti University, L.J Campus, Near Sarkhej-Sanand Circle, Off. S.G. Road, Ahmedabad-382 210, India
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3
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Marcus AH, Matsika S, Heussman D, Sorour MI, Maurer J, Albrecht CS, Enkhbaatar L, Herbert P, Kistler KA, von Hippel PH. Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA. ARXIV 2024:arXiv:2403.16251v2. [PMID: 38584614 PMCID: PMC10996769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.
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Affiliation(s)
- Andrew H. Marcus
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Dylan Heussman
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Mohammed I. Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Jack Maurer
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Claire S. Albrecht
- Center for Optical, Molecular and Quantum Science, Department of Physics, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Physics, and University of Oregon, Eugene, Oregon 97403
| | - Lulu Enkhbaatar
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Patrick Herbert
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Kurt A. Kistler
- Department of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, Pennsylvania 19063
| | - Peter H. von Hippel
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
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4
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Yang J, Gelin MF, Chen L, Šanda F, Thyrhaug E, Hauer J. Two-dimensional fluorescence excitation spectroscopy: A novel technique for monitoring excited-state photophysics of molecular species with high time and frequency resolution. J Chem Phys 2023; 159:074201. [PMID: 37581414 DOI: 10.1063/5.0156297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
We propose a novel UV/Vis femtosecond spectroscopic technique, two-dimensional fluorescence-excitation (2D-FLEX) spectroscopy, which combines spectral resolution during the excitation process with exclusive monitoring of the excited-state system dynamics at high time and frequency resolution. We discuss the experimental feasibility and realizability of 2D-FLEX, develop the necessary theoretical framework, and demonstrate the high information content of this technique by simulating the 2D-FLEX spectra of a model four-level system and the Fenna-Matthews-Olson antenna complex. We show that the evolution of 2D-FLEX spectra with population time directly monitors energy transfer dynamics and can thus yield direct qualitative insight into the investigated system. This makes 2D-FLEX a highly efficient instrument for real-time monitoring of photophysical processes in polyatomic molecules and molecular aggregates.
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Affiliation(s)
- Jianmin Yang
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | | | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, 12116 Prague, Czech Republic
| | - Erling Thyrhaug
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Jürgen Hauer
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
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5
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Zhan S, Gelin MF, Huang X, Sun K. Ab initio simulation of peak evolutions and beating maps for electronic two-dimensional signals of a polyatomic chromophore. J Chem Phys 2023; 158:2890773. [PMID: 37191214 DOI: 10.1063/5.0150387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023] Open
Abstract
By employing the doorway-window (DW) on-the-fly simulation protocol, we performed ab initio simulations of peak evolutions and beating maps of electronic two-dimensional (2D) spectra of a polyatomic molecule in the gas phase. As the system under study, we chose pyrazine, which is a paradigmatic example of photodynamics dominated by conical intersections (CIs). From the technical perspective, we demonstrate that the DW protocol is a numerically efficient methodology suitable for simulations of 2D spectra for a wide range of excitation/detection frequencies and population times. From the information content perspective, we show that peak evolutions and beating maps not only reveal timescales of transitions through CIs but also pinpoint the most relevant coupling and tuning modes active at these CIs.
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Affiliation(s)
- Siying Zhan
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Xiang Huang
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Kewei Sun
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
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6
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Gelin MF, Chen L, Domcke W. Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals. Chem Rev 2022; 122:17339-17396. [PMID: 36278801 DOI: 10.1021/acs.chemrev.2c00329] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system-field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.
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Affiliation(s)
- Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Lipeng Chen
- Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching,Germany
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7
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Li Z, Li X, Cai Z, Jin G, Ahn DU, Huang X. Immunomodulatory Effects of Chicken Soups Prepared with the Native Cage-free Chickens and the Commercial Caged Broilers. Poult Sci 2022; 101:102053. [PMID: 35986946 PMCID: PMC9411684 DOI: 10.1016/j.psj.2022.102053] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/29/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022] Open
Abstract
The objective of this study was to compare the immunomodulatory effects of the chicken soups prepared with the native free-range chickens and the commercial caged broilers in the immunosuppressive mice. The immunosuppressive mice model was established by the intraperitoneal injection of 100 mg of cyclophosphamide (CTX) per kg body weight. The powders of Gushi Chicken Soup (GCS), Honglashan Chicken Soup (HCS), and Cobb Broiler Soup (CBS) were prepared by high-pressure stewing followed by spray drying. The chicken soups' nutrient content and the effects of three chicken soups on the body weight, organ index, blood index, and serum cytokine and immunoglobulin contents in the immunosuppressive mice were determined. The three chicken soups promoted the recovery of immunosuppressive mice, but the expression mechanisms were different. The GCS was more effective than the HCS and CBS in restoring blood index, promoting cytokine secretion, and increasing immunoglobulin content (P < 0.05). The HCS stimulated the Th1-type immune response and promoted immunoglobulin secretion (P < 0.05), while the CBS increased the production of CD4+ and promoted the T-cell functions better than other soups (P < 0.05). Although soups from the native free-range chickens and the commercial caged broilers showed distinctly different mechanisms in promoting immunity, both could be used as potential immunomodulators.
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Affiliation(s)
- Zuyue Li
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiaomeng Li
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zhaoxia Cai
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Guofeng Jin
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Dong Uk Ahn
- Animal Science Department, Iowa State University, Ames, USA
| | - Xi Huang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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8
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High-resolution two-dimensional electronic spectroscopy reveals the homogeneous line profile of chromophores solvated in nanoclusters. Nat Commun 2022; 13:3350. [PMID: 35688839 PMCID: PMC9187667 DOI: 10.1038/s41467-022-31021-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Doped clusters in the gas phase provide nanoconfined model systems for the study of system-bath interactions. To gain insight into interaction mechanisms between chromophores and their environment, the ensemble inhomogeneity has to be lifted and the homogeneous line profile must be accessed. However, such measurements are very challenging at the low particle densities and low signal levels in cluster beam experiments. Here, we dope cryogenic rare-gas clusters with phthalocyanine molecules and apply action-detected two-dimensional electronic spectroscopy to gain insight into the local molecule-cluster environment for solid and superfluid cluster species. The high-resolution homogeneous linewidth analysis provides a benchmark for the theoretical modelling of binding configurations and shows a promising route for high-resolution molecular two-dimensional spectroscopy. Understanding the interaction of single chromophores with nanoparticles remains a challenging task in nanoscience. Here the authors provide insight into the interaction between isolated base-free phthalocyanine molecules and He and Ne nanoclusters in the gas phase using high-resolution two-dimensional spectroscopy.
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9
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Solowan HP, Malý P, Brixner T. Direct comparison of molecular-beam versus liquid-phase pump-probe and two-dimensional spectroscopy on the example of azulene. J Chem Phys 2022; 157:044201. [DOI: 10.1063/5.0088365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although azulene's anomalous fluorescence originating from S2 rather than from S1 is the textbook example for the violation of Kasha's rule, the understanding of the underlying processes is still a subject of investigation. Here, we use action-based coherent two-dimensional electronic spectroscopy (2DES) to measure a single Liouville-space response pathway from S0 via S1 to the S2 state of azulene. We directly compare this sequential excitation in liquid phase detecting S2 fluorescence and in a molecular beam detecting photoionized cations, using the S2 anomalous emission to our advantage. We complement the 2DES study by pump-probe measurements of S1 excitation dynamics, including vibrational relaxation and passage through a conical intersection. The direct comparison of liquid and gas phase allows us to assess the effect of the solvent and the interplay of intra- and inter-molecular energy relaxation.
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Affiliation(s)
| | - Pavel Malý
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-Universität Würzburg, Germany
| | - Tobias Brixner
- Institut fuer Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Germany
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10
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Bera A, Nag P, Pandey D, Vennapusa SR. Theoretical approach to modeling the early nonadiabatic events of ESIPT originating from three-state conical intersection in quinophthalone. Photochem Photobiol Sci 2022; 21:1287-1298. [PMID: 35403961 DOI: 10.1007/s43630-022-00220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/25/2022] [Indexed: 11/30/2022]
Abstract
We explore the excited-state intramolecular proton transfer process of quinophthalone theoretically. This molecule possesses three low-lying singlet excited states ([Formula: see text] and [Formula: see text]) in a narrow energy gap of less than the N-H stretching frequency. Dynamics simulations show nonadiabatic wavepacket transfer to [Formula: see text] and [Formula: see text] upon initiating the wavepacket on [Formula: see text]. Multiple accessible conical intersections that lie in the Franck-Condon region facilitate the nonadiabatic wavepacket transfer. Nuclear densities associated with the proton transfer promoting vibrations would start accumulating on [Formula: see text] and [Formula: see text] within a few tens of femtoseconds, validating the involvement of these vibrations in the nonadiabatic events that occur before the proton transfer process. Our findings emphasize the necessity of refined kinetic models for assigning the time constants of ultrafast transient spectroscopy measurements due to the simultaneous evolution of nonadiabatic events and proton transfer kinetics in quinophthalone.
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Affiliation(s)
- Anshuman Bera
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, 695551, India
| | - Probal Nag
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, 695551, India
| | - Diksha Pandey
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, 695551, India
| | - Sivaranjana Reddy Vennapusa
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, 695551, India.
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11
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Dostál J. Nonresonant coherent two-dimensional spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120441. [PMID: 34678717 DOI: 10.1016/j.saa.2021.120441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Coherent electronic two-dimensional spectroscopy is nowadays a matured experimental technique that monitors the time evolution of the studied sample after its resonant optical excitation. However, the experimental experience shows that even nonresonant interactions can provide detectable spectral contributions. These are often present as a weak parasitic signals originating in the solvent and/or cuvette walls underlying the resonant spectrum of the actual sample and as such they are usually discarded from the analysis. In this work, we adapt the formalism of double-sided Feynman diagrams for the needs of coherent two-dimensional spectroscopy in the nonresonant regime. We analytically calculate the third-order polarization of a two-level and several variants of three-level systems. As a result, we demonstrate the typical appearance of the optical Kerr-effect, cross-phase modulation, excited-state coherence, two-photon absorption and stimulated Raman scattering in the 2D spectrum. This provides a framework for studying these effects by means of coherent two-dimensional spectroscopy.
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Affiliation(s)
- Jakub Dostál
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 121 16, Czech Republic; ELI Beamlines, Institute of Physics, Czech Academy of Sciences, Za Radnicí 835, Dolní Břežany 252 41, Czech Republic.
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12
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Biswas S, Kim J, Zhang X, Scholes GD. Coherent Two-Dimensional and Broadband Electronic Spectroscopies. Chem Rev 2022; 122:4257-4321. [PMID: 35037757 DOI: 10.1021/acs.chemrev.1c00623] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Over the past few decades, coherent broadband spectroscopy has been widely used to improve our understanding of ultrafast processes (e.g., photoinduced electron transfer, proton transfer, and proton-coupled electron transfer reactions) at femtosecond resolution. The advances in femtosecond laser technology along with the development of nonlinear multidimensional spectroscopy enabled further insights into ultrafast energy transfer and carrier relaxation processes in complex biological and material systems. New discoveries and interpretations have led to improved design principles for optimizing the photophysical properties of various artificial systems. In this review, we first provide a detailed theoretical framework of both coherent broadband and two-dimensional electronic spectroscopy (2DES). We then discuss a selection of experimental approaches and considerations of 2DES along with best practices for data processing and analysis. Finally, we review several examples where coherent broadband and 2DES were employed to reveal mechanisms of photoinitiated ultrafast processes in molecular, biological, and material systems. We end the review with a brief perspective on the future of the experimental techniques themselves and their potential to answer an even greater range of scientific questions.
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Affiliation(s)
- Somnath Biswas
- Department of Chemistry, Princeton University, Princeton, New Jersey 08 544, United States
| | - JunWoo Kim
- Department of Chemistry, Princeton University, Princeton, New Jersey 08 544, United States
| | - Xinzi Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08 544, United States
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08 544, United States
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13
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Krueger TD, Fang C. Elucidating Inner Workings of Naturally Sourced Organic Optoelectronic Materials with Ultrafast Spectroscopy. Chemistry 2021; 27:17736-17750. [PMID: 34545971 DOI: 10.1002/chem.202102766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 01/18/2023]
Abstract
Recent advances in sustainable optoelectronics including photovoltaics, light-emitting diodes, transistors, and semiconductors have been enabled by π-conjugated organic molecules. A fundamental understanding of light-matter interactions involving these materials can be realized by time-resolved electronic and vibrational spectroscopies. In this Minireview, the photoinduced mechanisms including charge/energy transfer, electronic (de)localization, and excited-state proton transfer are correlated with functional properties encompassing optical absorption, fluorescence quantum yield, conductivity, and photostability. Four naturally derived molecules (xylindein, dimethylxylindein, alizarin, indigo) with ultrafast spectral insights showcase efficient energy dissipation involving H-bonding networks and proton motions, which yield high photostability. Rational design principles derived from such investigations could increase the efficiency for light harvesting, triplet formation, and photosensitivity for improved and versatile optoelectronic performance.
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Affiliation(s)
- Taylor D Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331-4003, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331-4003, USA
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14
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Maiti KS. Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein. Molecules 2021; 26:molecules26226893. [PMID: 34833985 PMCID: PMC8618531 DOI: 10.3390/molecules26226893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.
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Affiliation(s)
- Kiran Sankar Maiti
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; ; Tel.: +49-89-289-54056
- Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Coulombwall 1, 85748 Garching, Germany
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15
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Boulanger SA, Chen C, Myasnyanko IN, Sokolov AI, Baranov MS, Fang C. Excited-State Dynamics of a meta-Dimethylamino Locked GFP Chromophore as a Fluorescence Turn-on Water Sensor †. Photochem Photobiol 2021; 98:311-324. [PMID: 34714942 DOI: 10.1111/php.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022]
Abstract
Strategic incorporation of a meta-dimethylamino (-NMe2 ) group on the conformationally locked green fluorescent protein (GFP) model chromophore (m-NMe2 -LpHBDI) has drastically altered molecular electronic properties, counterintuitively enhancing fluorescence of only the neutral and cationic chromophores in aqueous solution. A ˜200-fold decrease in fluorescence quantum yield of m-NMe2 -LpHBDI in alcohols (e.g., MeOH, EtOH and 2-PrOH) supports this GFP-derived compound as a fluorescence turn-on water sensor, with large fluorescence intensity differences between H2 O and ROH emissions in various H2 O/ROH binary mixtures. A combination of steady-state electronic spectroscopy, femtosecond transient absorption, ground-state femtosecond stimulated Raman spectroscopy (FSRS) and quantum calculations elucidates an intermolecular hydrogen-bonding chain between a solvent -OH group and the chromophore phenolic ring -NMe2 and -OH functional groups, wherein fluorescence differences arise from an extended hydrogen-bonding network beyond the first solvation shell, as opposed to fluorescence quenching via a dark twisted intramolecular charge-transfer state. The absence of a meta-NMe2 group twisting coordinate upon electronic excitation was corroborated by experiments on control samples without the meta-NMe2 group or with both meta-NMe2 and para-OH groups locked in a six-membered ring. These deep mechanistic insights stemming from GFP chromophore scaffold will enable rational design of organic, compact and environmentally friendly water sensors.
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Affiliation(s)
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, OR
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, OR
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16
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Zhang C, Xue Y, Wang L, Wu Q, Fang B, Sheng Y, Bai H, Peng B, Yang N, Li L. Progress on the Physiological Function of Mitochondrial DNA and Its Specific Detection and Therapy. Chembiochem 2021; 23:e202100474. [PMID: 34661371 DOI: 10.1002/cbic.202100474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/16/2021] [Indexed: 11/10/2022]
Abstract
Mitochondrial DNA (mtDNA) is the genetic information of mitochondrion, and its structure is circular double-stranded. Despite the diminutive size of the mitochondrial genome, mtDNA mutations are an important cause of mitochondrial diseases which are characterized by defects in oxidative phosphorylation (OXPHOS). Mitochondrial diseases are involved in multiple systems, particularly in the organs that are highly dependent on aerobic metabolism. The diagnosis of mitochondrial disease is more complicated since mtDNA mutations can cause various clinical symptoms. To realize more accurate diagnosis and treatment of mitochondrial diseases, the detection of mtDNA and the design of drugs acting on it are extremely important. Over the past few years, many probes and therapeutic drugs targeting mtDNA have been developed, making significant contributions to fundamental research including elucidation of the mechanisms of mitochondrial diseases at the genetic level. In this review, we summarize the structure, function, and detection approaches for mtDNA. The most current topics in this field, such as mechanistic exploration and treatment of mtDNA mutation-related disorders, are also reviewed. Specific attention is given to discussing the design and development of these probes and drugs for mtDNA. We hope that this review will provide readers with a comprehensive understanding of the importance of mtDNA, and promote the development of effective molecules for theragnosis of mtDNA mutation-related diseases.
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Affiliation(s)
- Congcong Zhang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Yufei Xue
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Lan Wang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Bin Fang
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Yu Sheng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Naidi Yang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China.,The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, Fujian, P. R. China
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17
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Zhou Y, Qin Z, Yuan P, Ma J, Xie G. 2-MW peak-power pulses from a dispersion-managed fluoride fiber amplifier at 2.8 µm. OPTICS LETTERS 2021; 46:5104-5107. [PMID: 34653126 DOI: 10.1364/ol.440029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
We report on a scheme of pulse amplification and simultaneous self-compression in fluoride fiber for generating a high-peak-power pulse at 2.8-µm wavelength. We find dispersion management plays a key role for the amplification and self-compression process. Through dispersion management with a Ge rod, pulse amplification and simultaneous pulse self-compression were realized in the small anomalous dispersion region. A 2-MW peak-power pulse was achieved through amplification and self-compression in Er:ZBLAN fiber, with pulse energy of 101 nJ and pulse duration of 49 fs. To the best of our knowledge, this is the highest peak power obtained from fluoride fiber at 2.8 µm, and will benefit a series of applications.
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18
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M J C, Nag P, Vennapusa SR. Surface hopping dynamics reveal ultrafast triplet generation promoted by S 1-T 2-T 1 spin-vibronic coupling in 2-mercaptobenzothiazole. Phys Chem Chem Phys 2021; 23:20183-20192. [PMID: 34473155 DOI: 10.1039/d1cp02587b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the T1 formation upon populating the optically "bright" S2 in 2-mercaptobenzothiazole to interpret the underlying relaxation pathways associated with the experimental decay constants reported by D. Koyama and A. J. Orr-Ewing, Phys. Chem. Chem. Phys., 2016, 18, 26224-26235. Energetics, electronic populations and geometries of various stationary points of low-lying electronic states are computed using the semi-classical ab initio surface hopping dynamics simulations. Estimated decay constants of S2-S1 internal conversion (IC) and S1-T2 intersystem crossing (ISC) are in excellent agreement with the experiment. The observed ultrafast ISC is analyzed based on the S1-T2-T1 spin-vibronic coupling mechanism. In contrast to the previous assignment of 6 ps to the T2-T1 IC, our findings enable us to attribute this decay constant to the combined events of T2-T1 IC followed by relaxation of vibrationally hot T1.
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Affiliation(s)
- Chithra M J
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala PO, Vithura, Thiruvananthapuram 695551, Kerala, India.
| | - Probal Nag
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala PO, Vithura, Thiruvananthapuram 695551, Kerala, India.
| | - Sivaranjana Reddy Vennapusa
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala PO, Vithura, Thiruvananthapuram 695551, Kerala, India.
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19
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Valentine ML, Al-Mualem ZA, Baiz CR. Pump Slice Amplitudes: A Simple and Robust Method for Connecting Two-Dimensional Infrared and Fourier Transform Infrared Spectra. J Phys Chem A 2021; 125:6498-6504. [PMID: 34259508 DOI: 10.1021/acs.jpca.1c04558] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast two-dimensional infrared (2D IR) spectroscopy and Fourier transform infrared (FTIR) spectroscopy are often performed in tandem, with FTIR typically used to interpret and provide hypotheses for 2D IR experiments. Comparisons between 2D IR and FTIR spectra can also be used to examine the structure and orientation in systems of coupled vibrational chromophores. The most common method for comparing 2D IR and FTIR lineshapes, the diagonal slice method, contains significant artifacts when applied to oscillators with low anharmonicities. Here, we introduce a new technique, the pump slice amplitude (PSA) method, for relating 2D IR lineshapes to FTIR lineshapes and compare PSAs against diagonal slices using theoretical and experimental spectra. We find that PSAs are significantly more similar to FTIR lineshapes than diagonal slices in systems with low anharmonicity.
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Affiliation(s)
- Mason L Valentine
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
| | - Ziareena A Al-Mualem
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
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20
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Procacci B, Rutherford SH, Greetham GM, Towrie M, Parker AW, Robinson CV, Howle CR, Hunt NT. Differentiation of bacterial spores via 2D-IR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119319. [PMID: 33360210 DOI: 10.1016/j.saa.2020.119319] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Ultrafast 2D-IR spectroscopy is a powerful tool for understanding the spectroscopy and dynamics of biological molecules in the solution phase. A number of recent studies have begun to explore the utility of the information-rich 2D-IR spectra for analytical applications. Here, we report the application of ultrafast 2D-IR spectroscopy for the detection and classification of bacterial spores. 2D-IR spectra of Bacillus atrophaeus and Bacillus thuringiensis spores as dry films on CaF2 windows were obtained. The sporulated nature of the bacteria was confirmed using 2D-IR diagonal and off-diagonal peaks arising from the calcium dipicolinate CaDP·3H2O biomarker for sporulation. Distinctive peaks, in the protein amide I region of the spectrum were used to differentiate the two types of spore. The identified marker modes demonstrate the potential for the use of 2D-IR methods as a direct means of spore classification. We discuss these new results in perspective with the current state of analytical 2D-IR measurements, showing that the potential exists to apply 2D-IR spectroscopy to detect the spores on surfaces and in suspensions as well as in dry films. The results demonstrate how applying 2D-IR screening methodologies to spores would enable the creation of a library of spectra for classification purposes.
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Affiliation(s)
- Barbara Procacci
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Samantha H Rutherford
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Camilla V Robinson
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Christopher R Howle
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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21
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Ladaycia A, Loretz B, Passirani C, Lehr CM, Lepeltier E. Microbiota and cancer: In vitro and in vivo models to evaluate nanomedicines. Adv Drug Deliv Rev 2021; 170:44-70. [PMID: 33388279 DOI: 10.1016/j.addr.2020.12.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/23/2020] [Accepted: 12/27/2020] [Indexed: 02/08/2023]
Abstract
Nanomedicine implication in cancer treatment and diagnosis studies witness huge attention, especially with the promising results obtained in preclinical studies. Despite this, only few nanomedicines succeeded to pass clinical phase. The human microbiota plays obvious roles in cancer development. Nanoparticles have been successfully used to modulate human microbiota and notably tumor associated microbiota. Taking the microbiota involvement under consideration when testing nanomedicines for cancer treatment might be a way to improve the poor translation from preclinical to clinical trials. Co-culture models of bacteria and cancer cells, as well as animal cancer-microbiota models offer a better representation for the tumor microenvironment and so potentially better platforms to test nanomedicine efficacy in cancer treatment. These models would allow closer representation of human cancer and might smoothen the passage from preclinical to clinical cancer studies for nanomedicine efficacy.
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22
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Decoding ultrafast polarization responses in lead halide perovskites by the two-dimensional optical Kerr effect. Proc Natl Acad Sci U S A 2021; 118:2022268118. [PMID: 33558241 DOI: 10.1073/pnas.2022268118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ultrafast polarization response to incident light and ensuing exciton/carrier generation are essential to outstanding optoelectronic properties of lead halide perovskites (LHPs). A large number of mechanistic studies in the LHP field to date have focused on contributions to polarizability from organic cations and the highly polarizable inorganic lattice. For a comprehensive understanding of the ultrafast polarization response, we must additionally account for the nearly instantaneous hyperpolarizability response to the propagating light field itself. While light propagation is pivotal to optoelectronics and photonics, little is known about this in LHPs in the vicinity of the bandgap where stimulated emission, polariton condensation, superfluorescence, and photon recycling may take place. Here we develop two-dimensional optical Kerr effect (2D-OKE) spectroscopy to energetically dissect broadband light propagation and dispersive nonlinear polarization responses in LHPs. In contrast to earlier interpretations, the below-bandgap OKE responses in both hybrid CH3NH3PbBr3 and all-inorganic CsPbBr3 perovskites are found to originate from strong hyperpolarizability and highly anisotropic dispersions. In both materials, the nonlinear mixing of anisotropically propagating light fields results in convoluted oscillatory polarization dynamics. Based on a four-wave mixing model, we quantitatively derive dispersion anisotropies, reproduce 2D-OKE frequency correlations, and establish polarization-dressed light propagation in single-crystal LHPs. Moreover, our findings highlight the importance of distinguishing the often-neglected anisotropic light propagation from underlying coherent quasiparticle responses in various forms of ultrafast spectroscopy.
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23
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Nag P, Vennapusa SR. Role of Skeletal and O-H Vibrational Motions in the Ultrafast Excited-State Relaxation Dynamics of Alizarin. J Phys Chem A 2020; 124:10989-10996. [PMID: 33331785 DOI: 10.1021/acs.jpca.0c09454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of two skeletal (C═C and C═O stretch) and O-H vibrational motions in the internal conversion dynamics associated with the coupled S1(ππ*, A') -S2(nπ*, A″) potential energy surfaces of alizarin are investigated theoretically. Quantum wavepacket dynamics simulations reveal a nonadiabatic population transfer from the "bright" S1(ππ*, A') to "dark" S2(nπ*, A″) state on a time scale of 10 fs. A detailed analysis of computed structural parameters, energetics, and time-dependent observables suggest that these vibrations promote the nonadiabatic dynamics before initiating the proton transfer process. We also discuss how the simultaneous evolution of multidimensional dynamics involving several vibrational degrees of freedom would increase the complexity, while analyzing the spectral and kinetic data of time-resolved spectroscopy measurements.
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Affiliation(s)
- Probal Nag
- Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Sivaranjana Reddy Vennapusa
- Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
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24
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Sardjan AS, Westerman FP, Ogilvie JP, Jansen TLC. Observation of Ultrafast Coherence Transfer and Degenerate States with Polarization-Controlled Two-Dimensional Electronic Spectroscopy. J Phys Chem B 2020; 124:9420-9427. [PMID: 32990439 PMCID: PMC7586392 DOI: 10.1021/acs.jpcb.0c08126] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Optical
spectroscopy is a powerful tool to interrogate quantum
states of matter. We present simulation results for the cross-polarized
two-dimensional electronic spectra of the light-harvesting system
LH2 of purple bacteria. We identify a spectral feature on the diagonal,
which we assign to ultrafast coherence transfer between degenerate
states. The implication for the interpretation of previous experiments
on different systems and the potential use of this feature are discussed.
In particular, we foresee that this kind of feature will be useful
for identifying mixed degenerate states and for identifying the origin
of symmetry breaking disorder in systems like LH2. Furthermore, this
may help identify both vibrational and electronic states in biological
systems such as proteins and solid-state materials such as hybrid
perovskites.
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Affiliation(s)
- Andy S Sardjan
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Floris P Westerman
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jennifer P Ogilvie
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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25
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Dostál J, Alster J. Interplay between coherence-time undersampling and scattered light in two-dimensional electronic spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:093103. [PMID: 33003825 DOI: 10.1063/5.0009513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Scanning pulse delays in multi-pulse non-linear optical spectroscopy experiments is a major contributor to lengthy data acquisition. Using large steps for the scan can significantly speed up the experiment. However, an improper choice of step length can cause distortions to the resulting spectra, especially if the light scattered on the sample is mixed into the signal. In this work, we identify potential sources of such distortions and suggest appropriate countermeasures to avoid them while maintaining a faster data collection.
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Affiliation(s)
- Jakub Dostál
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic
| | - Jan Alster
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic
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26
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Apolonski A, Roy S, Lampe R, Sankar Maiti K. Molecular identification of bio-fluids in gas phase using infrared spectroscopy. APPLIED OPTICS 2020; 59:E36-E41. [PMID: 32543511 DOI: 10.1364/ao.388362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Bio-fluids are the source of a large number of metabolites. Identification and quantification of them can be an efficient step for understanding the internal chemistry of the body as well as for developing objective diagnostics of diseases. Several techniques have been developed so far; however, their metabolite identification and/or quantification are not reliable enough for acceptance by clinicians. As another promising step in this direction, we push infrared spectroscopy of bio-fluids in gas phase. Here we discuss features of breath and urine headspace realized with Fourier transform infrared spectroscopy. Molecular identification procedures based on component analysis of gas samples are proposed. In this paper, we show that aggregate data from different bio-fluids in gas phase can strengthen the diagnostics of the body state and disease.
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27
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Abstract
The microscopic origin and timescale of the fluctuations of the energies of electronic states has a significant impact on the properties of interest of electronic materials, with implication in fields ranging from photovoltaic devices to quantum information processing. Spectroscopic investigations of coherent dynamics provide a direct measurement of electronic fluctuations. Modern multidimensional spectroscopy techniques allow the mapping of coherent processes along multiple time or frequency axes and thus allow unprecedented discrimination between different sources of electronic dephasing. Exploiting modern abilities in coherence mapping in both amplitude and phase, we unravel dissipative processes of electronic coherences in the model system of CdSe quantum dots (QDs). The method allows the assignment of the nature of the observed coherence as vibrational or electronic. The expected coherence maps are obtained for the coherent longitudinal optical (LO) phonon, which serves as an internal standard and confirms the sensitivity of the technique. Fast dephasing is observed between the first two exciton states, despite their shared electron state and common environment. This result is contrary to predictions of the standard effective mass model for these materials, in which the exciton levels are strongly correlated through a common size dependence. In contrast, the experiment is in agreement with ab initio molecular dynamics of a single QD. Electronic dephasing in these materials is thus dominated by the realistic electronic structure arising from fluctuations at the atomic level rather than static size distribution. The analysis of electronic dephasing thereby uniquely enables the study of electronic fluctuations in complex materials.
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28
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Petti MK, Ostrander JS, Birdsall ER, Kunz MB, Armstrong ZT, Alperstein AM, Zanni MT. A Proposed Method to Obtain Surface Specificity with Pump-Probe and 2D Spectroscopies. J Phys Chem A 2020; 124:3471-3483. [PMID: 32255629 PMCID: PMC7993518 DOI: 10.1021/acs.jpca.9b11791] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Surfaces and interfaces are ubiquitous in nature. From cell membranes, to photovoltaic thin films, surfaces have important function in both biological and materials systems. Spectroscopic techniques have been developed to probe systems like these, such as sum frequency generation (SFG) spectroscopies. The advantage of SFG spectroscopy, a second-order spectroscopy, is that it can distinguish between signals produced from molecules in the bulk versus on the surface. We propose a polarization scheme for third-order spectroscopy experiments, such as pump-probe and 2D spectroscopy, to select for surface signals and not bulk signals. This proposed polarization condition uses one pulse perpendicular compared to the other three to isolate cross-peaks arising from molecules with polar and uniaxial (i.e., biaxial) order at a surface, while removing the signal from bulk isotropic molecules. In this work, we focus on two of these cases: XXXY and YYYX, which differ by the sign of the cross-peak they create. We compare this technique to SFG spectroscopy and vibrational circular dichroism to provide insight to the behavior of the cross-peak signal. We propose that these singularly cross-polarized schemes provide odd-ordered spectroscopies the surface-specificity typically associated with even-ordered techniques.
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Affiliation(s)
- Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Erin R Birdsall
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Miriam Bohlmann Kunz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Zachary T Armstrong
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ariel M Alperstein
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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29
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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30
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Fritzsch R, Hume S, Minnes L, Baker MJ, Burley GA, Hunt NT. Two-dimensional infrared spectroscopy: an emerging analytical tool? Analyst 2020; 145:2014-2024. [PMID: 32051976 DOI: 10.1039/c9an02035g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ultrafast two-dimensional infrared (2D-IR) spectroscopy has provided valuable insights into biomolecular structure and dynamics, but recent progress in laser technology and data analysis methods have demonstrated the potential for high throughput 2D-IR measurements and analytical applications. Using 2D-IR as an analytical tool requires a different approach to data collection and analysis compared to pure research applications however and, in this review, we highlight progress towards usage of 2D-IR spectroscopy in areas relevant to biomedical, pharmaceutical and analytical molecular science. We summarise the technical and methodological advances made to date and discuss the challenges that still face 2D-IR spectroscopy as it attempts to transition from the state-of-the-art laser laboratory to the standard suite of analytical tools.
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Affiliation(s)
- Robby Fritzsch
- Department of Physics, SUPA, University of Strathclyde, Glasgow, G4 0NG, UK
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31
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Zhu XL, Weng SM, Chen M, Sheng ZM, Zhang J. Efficient generation of relativistic near-single-cycle mid-infrared pulses in plasmas. LIGHT, SCIENCE & APPLICATIONS 2020; 9:46. [PMID: 32218917 PMCID: PMC7083853 DOI: 10.1038/s41377-020-0282-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Ultrashort intense optical pulses in the mid-infrared (mid-IR) region are very important for broad applications ranging from super-resolution spectroscopy to attosecond X-ray pulse generation and particle acceleration. However, currently, it is still difficult to produce few-cycle mid-IR pulses of relativistic intensities using standard optical techniques. Here, we propose and numerically demonstrate a novel scheme to produce these mid-IR pulses based on laser-driven plasma optical modulation. In this scheme, a plasma wake is first excited by an intense drive laser pulse in an underdense plasma, and a signal laser pulse initially at the same wavelength (1 micron) as that of the drive laser is subsequently injected into the plasma wake. The signal pulse is converted to a relativistic multi-millijoule near-single-cycle mid-IR pulse with a central wavelength of ~5 microns via frequency-downshifting, where the energy conversion efficiency is as high as approximately 30% when the drive and signal laser pulses are both at a few tens of millijoules at the beginning. Our scheme can be realized with terawatt-class kHz laser systems, which may bring new opportunities in high-field physics and ultrafast science.
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Affiliation(s)
- Xing-Long Zhu
- Key Laboratory for Laser Plasmas (MOE), School of Physics and Astronomy, Shanghai Jiao Tong University, 200240 Shanghai, China
- Collaborative Innovation Center of IFSA, Shanghai Jiao Tong University, 200240 Shanghai, China
- SUPA, Department of Physics, University of Strathclyde, Glasgow, G4 0NG UK
| | - Su-Ming Weng
- Key Laboratory for Laser Plasmas (MOE), School of Physics and Astronomy, Shanghai Jiao Tong University, 200240 Shanghai, China
- Collaborative Innovation Center of IFSA, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Min Chen
- Key Laboratory for Laser Plasmas (MOE), School of Physics and Astronomy, Shanghai Jiao Tong University, 200240 Shanghai, China
- Collaborative Innovation Center of IFSA, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Zheng-Ming Sheng
- Key Laboratory for Laser Plasmas (MOE), School of Physics and Astronomy, Shanghai Jiao Tong University, 200240 Shanghai, China
- Collaborative Innovation Center of IFSA, Shanghai Jiao Tong University, 200240 Shanghai, China
- SUPA, Department of Physics, University of Strathclyde, Glasgow, G4 0NG UK
- Cockcroft Institute, Sci-Tech Daresbury, Cheshire, WA4 4AD UK
- Tsung-Dao Lee Institute, 200240 Shanghai, China
| | - Jie Zhang
- Key Laboratory for Laser Plasmas (MOE), School of Physics and Astronomy, Shanghai Jiao Tong University, 200240 Shanghai, China
- Collaborative Innovation Center of IFSA, Shanghai Jiao Tong University, 200240 Shanghai, China
- Institute of Physics, Chinese Academy of Sciences, 100190 Beijing, China
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32
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Palato S, Seiler H, Baker H, Sonnichsen C, Brosseau P, Kambhampati P. Investigating the electronic structure of confined multiexcitons with nonlinear spectroscopies. J Chem Phys 2020; 152:104710. [DOI: 10.1063/1.5142180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- S. Palato
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 0B8, Canada
| | - H. Seiler
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 0B8, Canada
| | - H. Baker
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 0B8, Canada
| | - C. Sonnichsen
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 0B8, Canada
| | - P. Brosseau
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 0B8, Canada
| | - P. Kambhampati
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Montréal, Québec H3A 0B8, Canada
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33
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Fang C, Tang L. Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy. Annu Rev Phys Chem 2020; 71:239-265. [PMID: 32075503 DOI: 10.1146/annurev-physchem-071119-040154] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The structure-function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences.
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Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA;
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34
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Tapping PC, Song Y, Kobayashi Y, Scholes GD, Kee TW. Two-Dimensional Electronic Spectroscopy Using Rotating Optical Flats. J Phys Chem A 2020; 124:1053-1061. [DOI: 10.1021/acs.jpca.0c00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Patrick C. Tapping
- Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Yin Song
- Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109, United States
| | - Yoichi Kobayashi
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Gregory D. Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Tak W. Kee
- Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
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35
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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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36
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Fang C, Tang L, Chen C. Unveiling coupled electronic and vibrational motions of chromophores in condensed phases. J Chem Phys 2019; 151:200901. [PMID: 31779327 DOI: 10.1063/1.5128388] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.
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Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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37
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Malý P, Lüttig J, Turkin A, Dostál J, Lambert C, Brixner T. From wavelike to sub-diffusive motion: exciton dynamics and interaction in squaraine copolymers of varying length. Chem Sci 2019; 11:456-466. [PMID: 34084345 PMCID: PMC8146531 DOI: 10.1039/c9sc04367e] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/15/2020] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
Exciton transport and exciton-exciton interactions in molecular aggregates and polymers are of great importance in natural photosynthesis, organic electronics, and related areas of research. Both the experimental observation and theoretical description of these processes across time and length scales, including the transition from the initial wavelike motion to the following long-range exciton transport, are highly challenging. Therefore, while exciton dynamics at small scales are often treated explicitly, long-range exciton transport is typically described phenomenologically by normal diffusion. In this work, we study the transition from wavelike to diffusive motion of interacting exciton pairs in squaraine copolymers of varying length. To this end we use a combination of the recently introduced exciton-exciton-interaction two-dimensional (EEI2D) electronic spectroscopy and microscopic theoretical modelling. As we show by comparison with the model, the experimentally observed kinetics include three phases, wavelike motion dominated by immediate exciton-exciton annihilation (10-100 fs), sub-diffusive behavior (0.1-10 ps), and excitation relaxation (0.01-1 ns). We demonstrate that the key quantity for the transition from wavelike to diffusive dynamics is the exciton delocalization length relative to the length of the polymer: while in short polymers wavelike motion of rapidly annihilating excitons dominates, in long polymers the excitons become locally trapped and exhibit sub-diffusive behavior. Our findings indicate that exciton transport through conjugated systems emerging from the excitonic structure is generally not governed by normal diffusion. Instead, to characterize the material transport properties, the diffusion presence and character should be determined.
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Affiliation(s)
- Pavel Malý
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Julian Lüttig
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Arthur Turkin
- Institut für Organische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Jakub Dostál
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Christoph Lambert
- Institut für Organische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
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38
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Kwac K, Cho M. Differential evolution algorithm approach for describing vibrational solvatochromism. J Chem Phys 2019; 151:134112. [PMID: 31594319 DOI: 10.1063/1.5120777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We model the solvation-induced vibrational frequency shifts of the amide I and amide II modes of N-methylacetamide in water and the nitrile stretch mode of acetonitrile in water by expressing the frequency shift as a polynomial function expanded by the inverse power of interatomic distances. The coefficients of the polynomial are optimized to minimize the deviation between the predicted frequency shifts and those calculated with quantum chemistry methods. Here, we show that a differential evolution algorithm combined with singular value decomposition is useful to find the optimum set of coefficients of polynomial terms. The differential evolution optimization shows that only a few terms in the polynomial are dominant in the contribution to the vibrational frequency shifts. We anticipate that the present work paves the way for further developing different genetic algorithms and machine learning schemes for their applications to vibrational spectroscopic studies.
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Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
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39
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Gijón A, Lasanta A, Hernández ER. Paths towards equilibrium in molecular systems: The case of water. Phys Rev E 2019; 100:032103. [PMID: 31639902 DOI: 10.1103/physreve.100.032103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 06/10/2023]
Abstract
We consider the problem of how a condensed molecular system approaches equilibrium, focusing on the particular case of water. We show, by means of extensive molecular dynamics simulations, that the existence of different types of degrees of freedom affects the dynamics of equilibration, and this influence is made most obvious in the system's temperature. When equipartition of energy does not hold in the initial, nonequilibrium state, the instantaneous temperature can be up to a few degrees lower than that observed under equipartition conditions, resulting in a Mpemba-like effect. Though our study considers water in particular, our findings apply more generally to condensed molecular systems.
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Affiliation(s)
- A Gijón
- Instituto de Ciencia de Materiales de Madrid (ICMM-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - A Lasanta
- G. Millán Institute, Fluid Dynamics, Nanoscience and Industrial Mathematics, Department of Materials Science and Engineering and Chemical Engineering, Universidad Carlos III de Madrid, Leganés, Spain
| | - E R Hernández
- Instituto de Ciencia de Materiales de Madrid (ICMM-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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40
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Toa ZSD, deGolian MH, Jumper CC, Hiller RG, Scholes GD. Consistent Model of Ultrafast Energy Transfer in Peridinin Chlorophyll-a Protein Using Two-Dimensional Electronic Spectroscopy and Förster Theory. J Phys Chem B 2019; 123:6410-6420. [DOI: 10.1021/acs.jpcb.9b04324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zi S. D. Toa
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
| | - Mary H. deGolian
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
| | - Chanelle C. Jumper
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
| | - Roger G. Hiller
- Department of Biology, Faculty of Science and Engineering, Macquarie University, Sydney NSW 2109, Australia
| | - Gregory D. Scholes
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08540, United States
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41
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Tang L, Fang C. Nitration of Tyrosine Channels Photoenergy through a Conical Intersection in Water. J Phys Chem B 2019; 123:4915-4928. [PMID: 31094198 DOI: 10.1021/acs.jpcb.9b03464] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nitration of tyrosine occurs under oxidative stress in vivo. The product, 3-nitrotyrosine (3NY), has a dramatically decreased quantum yield and can be used as a molecular ruler. In this study, femtosecond transient absorption spectroscopy and quantum calculations were implemented to elucidate the photoinduced relaxation processes of anionic 3NY in water. Upon 400 nm excitation into an excited electronic state with notable charge-transfer (CT) character, a barrierless nitro-twisting motion rapidly (<100 fs) guides the chromophore into an adjacent twisted intramolecular CT state, therein reaching a sloped S1/S0 conical intersection on the ∼100 fs time scale. Once in the hot ground state, excess energy is further released through vibrational cooling with biexponential time constants of ∼140 and 680 fs in water. Nitro back-twisting occurs on longer time scales (∼1.1 and 9 ps in water), returning the system to original ground state. Systematic evaluations of excited-state potential energies of anionic 3NY were performed by density functional theory (DFT) and time-dependent DFT calculations, showing that intersystem crossing (ISC) from the first singlet state (S1) to the first or second triplet state (T1 or T2) is unlikely. Inclusion of an explicit water molecule in calculations leads to improved mapping of the excited-state energy ordering of the second singlet state (S2) and T2, further diminishing ISC probability from S1 and favoring an ultrafast internal conversion to S0. These results provide deep insights into the highly efficient nonradiative decay of anionic 3NY in aqueous solution, with nitro-site-specific information that can help infer the characterization and potential optogenetic control of 3NY in protein environment.
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Affiliation(s)
- Longteng Tang
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97331-4003 , United States
| | - Chong Fang
- Department of Chemistry , Oregon State University , 153 Gilbert Hall , Corvallis , Oregon 97331-4003 , United States
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42
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Kalaee AAS, Damtie F, Karki KJ. Differentiation of True Nonlinear and Incoherent Mixing of Linear Signals in Action-Detected 2D Spectroscopy. J Phys Chem A 2019; 123:4119-4124. [DOI: 10.1021/acs.jpca.9b01129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | - Fikeraddis Damtie
- Mathematical Physics and NanoLund, Lund University, P.O. Box 118, 22100 Lund, Sweden
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43
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Borrego-Varillas R, Nenov A, Ganzer L, Oriana A, Manzoni C, Tolomelli A, Rivalta I, Mukamel S, Garavelli M, Cerullo G. Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules. Chem Sci 2019. [DOI: 10.1039/c9sc03871j] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Two-dimensional ultraviolet spectroscopy has the potential to deliver rich structural and dynamical information on biomolecules such as DNA and proteins.
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Affiliation(s)
| | - A. Nenov
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - L. Ganzer
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - A. Oriana
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - C. Manzoni
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - A. Tolomelli
- Dipartimento di Chimica
- Universitá degli Studi di Bologna
- I-40126 Bologna
- Italy
| | - I. Rivalta
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - S. Mukamel
- Department of Chemistry
- Department of Physics and Astronomy
- University of California
- Irvine
- USA
| | - M. Garavelli
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - G. Cerullo
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
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44
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Agathangelou D, El-Khoury Y, Brazard J, Crégut O, Haacke S, Cerullo G, Léonard J. Towards broadband two-Dimensional electronic spectroscopy with ~8 fs phase-locked pulses at 400 nm. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920503006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce a two-dimensional spectroscopy setup based on a pair of near-UV-blue (360 - 430 nm), 8.4-fs, phase-locked, collinear excitation pulses and a nearly collinear UV-Vis supercontinuum probe pulse.
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45
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Bruder L, Bangert U, Binz M, Uhl D, Vexiau R, Bouloufa-Maafa N, Dulieu O, Stienkemeier F. Coherent multidimensional spectroscopy of dilute gas-phase nanosystems. Nat Commun 2018; 9:4823. [PMID: 30446649 PMCID: PMC6240067 DOI: 10.1038/s41467-018-07292-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/25/2018] [Indexed: 12/20/2022] Open
Abstract
Two-dimensional electronic spectroscopy (2DES) is one of the most powerful spectroscopic techniques with unique sensitivity to couplings, coherence properties and real-time dynamics of a quantum system. While successfully applied to a variety of condensed phase samples, high precision experiments on isolated systems in the gas phase have been so far precluded by insufficient sensitivity. However, such experiments are essential for a precise understanding of fundamental mechanisms and to avoid misinterpretations. Here, we solve this issue by extending 2DES to isolated nanosystems in the gas phase prepared by helium nanodroplet isolation in a molecular beam-type experiment. This approach uniquely provides high flexibility in synthesizing tailored, quantum state-selected model systems of single and many-body character. In a model study of weakly-bound Rb2 and Rb3 molecules we demonstrate the method's unique capacity to elucidate interactions and dynamics in tailored quantum systems, thereby also bridging the gap to experiments in ultracold quantum science.
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Affiliation(s)
- Lukas Bruder
- Institute of Physics, University of Freiburg, 79104, Freiburg, Germany.
| | - Ulrich Bangert
- Institute of Physics, University of Freiburg, 79104, Freiburg, Germany
| | - Marcel Binz
- Institute of Physics, University of Freiburg, 79104, Freiburg, Germany
| | - Daniel Uhl
- Institute of Physics, University of Freiburg, 79104, Freiburg, Germany
| | - Romain Vexiau
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Nadia Bouloufa-Maafa
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Olivier Dulieu
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Frank Stienkemeier
- Institute of Physics, University of Freiburg, 79104, Freiburg, Germany.,Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg, Albertstr. 19, 79194, Freiburg, Germany
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46
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Maiti KS. Ultrafast N–H vibrational dynamics of hydrogen-bonded cyclic amide reveal by 2DIR spectroscopy. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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47
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Valentine ML, Cardenas AE, Elber R, Baiz CR. Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface. Biophys J 2018; 115:1541-1551. [PMID: 30269885 PMCID: PMC6260210 DOI: 10.1016/j.bpj.2018.08.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/20/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023] Open
Abstract
Phospholipids can interact strongly with ions at physiological concentrations, and these interactions can alter membrane properties. Here, we describe the effects of calcium ions on the dynamics in phospholipid membranes. We used a combination of time-resolved ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations. We found that millimolar Ca2+ concentrations lead to slower fluctuations in the local environment at the lipid-water interface of membranes with phosphatidylserine. The effect was only observed in bilayers containing anionic phosphatidylserine; membranes composed of only zwitterionic phosphatidylcholine did not experience a slowdown. Local water dynamics were measured using the ester groups as label-free probes and were found to be up to 50% slower with 2.5 mM Ca2+. Molecular dynamics simulations show that Ca2+ primarily binds to the carboxylate group of phosphatidylserines. These findings have implications for apoptotic and diseased cells in which phosphatidylserine is exposed to extracellular calcium and for the biophysical effects of divalent cations on lipid bilayers.
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Affiliation(s)
- Mason L Valentine
- Department of Chemistry, University of Texas at Austin, Austin, Texas
| | - Alfredo E Cardenas
- Department of Chemistry, University of Texas at Austin, Austin, Texas; Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, Texas; Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas.
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48
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Deb P, Jin GY, Singh SK, Moon J, Kwon H, Das A, Bagchi S, Kim YS. Interconverting Hydrogen-Bonding and Weak n → π* Interactions in Aqueous Solution: A Direct Spectroscopic Evidence. J Phys Chem Lett 2018; 9:5425-5429. [PMID: 30149713 DOI: 10.1021/acs.jpclett.8b02398] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular structure and function depend on myriad noncovalent interactions. However, the weak and transient nature of noncovalent interactions in solution makes them challenging to study. Information on weak interactions is typically derived from theory and indirect structural data. Solvent fluctuations, not revealed by structure analysis, further complicate the study of these interactions. Using 2D infrared spectroscopy, we show that the strong hydrogen bond and the weak n → π* interaction coexist and interconvert in aqueous solution. We found that the kinetics of these interconverting interactions becomes faster with increasing water content. This experimental observation provides a new perspective on the existence of weak noncovalent interactions in aqueous solution.
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Affiliation(s)
- Pranab Deb
- Physical and Materials Chemistry Division , CSIR-National Chemical Laboratory (CSIR-NCL) , Dr. Homi Bhabha Road , Pune 411008 , India
- Academy of Scientific & Innovative Research (AcSIR) , CSIR-National Chemical Laboratory (CSIR-NCL) , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Geun Young Jin
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
- Department of NanoFusion Technology , Pusan National University , Busan 46241 , Republic of Korea
| | - Santosh K Singh
- Department of Chemistry , Indian Institute of Science Education and Research (IISER) , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Juran Moon
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
| | - Hyejin Kwon
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
| | - Aloke Das
- Department of Chemistry , Indian Institute of Science Education and Research (IISER) , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division , CSIR-National Chemical Laboratory (CSIR-NCL) , Dr. Homi Bhabha Road , Pune 411008 , India
- Academy of Scientific & Innovative Research (AcSIR) , CSIR-National Chemical Laboratory (CSIR-NCL) , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Yung Sam Kim
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
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Marroux HJB, Fidler AP, Neumark DM, Leone SR. Multidimensional spectroscopy with attosecond extreme ultraviolet and shaped near-infrared pulses. SCIENCE ADVANCES 2018; 4:eaau3783. [PMID: 30276268 PMCID: PMC6162074 DOI: 10.1126/sciadv.aau3783] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/22/2018] [Indexed: 05/16/2023]
Abstract
Dynamics following excitation with attosecond extreme ultraviolet (XUV) pulses arise from enormous numbers of accessible excited states, complicating the retrieval of state-specific time evolutions. We develop attosecond XUV multidimensional spectroscopy here to separate interfering pathways on a near-infrared (NIR) energy axis, retrieving single state dynamics in argon atoms in a two-dimensional (2D) XUV-NIR spectrum. In this experiment, we measure four-wave mixing signal arising from the interaction of XUV attosecond pulses centered around 15 eV with two few-cycle NIR pulses. The 2D spectrum is created by measuring the emitted XUV signal field spectrum while applying narrowband amplitude and phase modulations to one of the NIR pulses. Application of such a technique to systems of high dimensionality will provide for the observation of state-resolved pure electronic dynamics, in direct analogy to phenomena unraveled by multidimensional spectroscopies at optical frequencies.
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Affiliation(s)
- Hugo J. B. Marroux
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ashley P. Fidler
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel M. Neumark
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen R. Leone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
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Excited State Structural Evolution of a GFP Single-Site Mutant Tracked by Tunable Femtosecond-Stimulated Raman Spectroscopy. Molecules 2018; 23:molecules23092226. [PMID: 30200474 PMCID: PMC6225354 DOI: 10.3390/molecules23092226] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022] Open
Abstract
Tracking vibrational motions during a photochemical or photophysical process has gained momentum, due to its sensitivity to the progression of reaction and change of environment. In this work, we implemented an advanced ultrafast vibrational technique, femtosecond-stimulated Raman spectroscopy (FSRS), to monitor the excited state structural evolution of an engineered green fluorescent protein (GFP) single-site mutant S205V. This mutation alters the original excited state proton transfer (ESPT) chain. By strategically tuning the Raman pump to different wavelengths (i.e., 801, 539, and 504 nm) to achieve pre-resonance with transient excited state electronic bands, the characteristic Raman modes of the excited protonated (A*) chromophore species and intermediate deprotonated (I*) species can be selectively monitored. The inhomogeneous distribution/population of A* species go through ESPT with a similar ~300 ps time constant, confirming that bridging a water molecule to protein residue T203 in the ESPT chain is the rate-limiting step. Some A* species undergo vibrational cooling through high-frequency motions on the ~190 ps time scale. At early times, a portion of the largely protonated A* species could also undergo vibrational cooling or return to the ground state with a ~80 ps time constant. On the photoproduct side, a ~1330 cm−1 delocalized motion is observed, with dispersive line shapes in both the Stokes and anti-Stokes FSRS with a pre-resonance Raman pump, which indicates strong vibronic coupling, as the mode could facilitate the I* species to reach a relatively stable state (e.g., the main fluorescent state) after conversion from A*. Our findings disentangle the contributions of various vibrational motions active during the ESPT reaction, and offer new structural dynamics insights into the fluorescence mechanisms of engineered GFPs and other analogous autofluorescent proteins.
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