1
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Huang-Fu ZC, Tkachenko NV, Qian Y, Zhang T, Brown JB, Harutyunyan A, Chen G, Rao Y. Conical Intersections at Interfaces Revealed by Phase-Cycling Interface-Specific Two-Dimensional Electronic Spectroscopy (i2D-ES). J Am Chem Soc 2024. [PMID: 39037260 DOI: 10.1021/jacs.4c06035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Conical intersections (CIs) hold significant stake in manipulating and controlling photochemical reaction pathways of molecules at interfaces and surfaces by affecting molecular dynamics therein. Currently, there is no tool for characterizing CIs at interfaces and surfaces. To this end, we have developed phase-cycling interface-specific two-dimensional electronic spectroscopy (i2D-ES) and combined it with advanced computational modeling to explore nonadiabatic CI dynamics of molecules at the air/water interface. Specifically, we integrated the phase locked pump pulse pair with an interface-specific electronic probe to obtain the two-dimensional interface-specific responses. We demonstrate that the nonadiabatic transitions of an interface-active azo dye molecule that occur through the CIs at the interface have different kinetic pathways from those in the bulk water. Upon photoexcitation, two CIs are present: one from an intersection of an optically active S2 state with a dark S1 state and the other from the intersection of the progressed S1 with the ground state S0. We find that the molecular conformations in the ground state are different for interfacial molecules. The interfacial molecules are intimately correlated with the locally populated excited state S2 being farther away from the CI region. This leads to slower nonadiabatic dynamics at the interface than in bulk water. Moreover, we show that the nonadiabatic transition from the S1 dark state to the ground state is significantly longer at the interface than that in the bulk, which is likely due to the orientationally restricted configuration of the excited state at the interface. Our findings suggest that orientational configurations of molecules manipulate reaction pathways at interfaces and surfaces.
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Affiliation(s)
- Zhi-Chao Huang-Fu
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Nikolay V Tkachenko
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Yuqin Qian
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Tong Zhang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Jesse B Brown
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Avetik Harutyunyan
- Honda Research Institute, USA, Inc., San Jose, California 95134, United States
| | - Gugang Chen
- Honda Research Institute, USA, Inc., San Jose, California 95134, United States
| | - Yi Rao
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
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2
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Thomassen AB, Jansen TLC, Weidner T. The secondary structure of diatom silaffin peptide R5 determined by two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2024; 26:18538-18546. [PMID: 38888161 DOI: 10.1039/d4cp00970c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Diatoms, unicellular marine organisms, harness short peptide repeats of the protein silaffin to transform silicic acid into biosilica nanoparticles. This process has been a white whale for material scientists due to its potential in biomimetic applications, ranging from medical to microelectronic fields. Replicating diatom biosilicification will depend on a thorough understanding of the silaffin peptide structure during the reaction, yet existing models in the literature offer conflicting views on peptide folding during silicification. In our study, we employed two-dimensional infrared spectroscopy (2DIR) within the amide I region to determine the secondary structure of the silaffin repeat unit 5 (R5), both pre- and post-interaction with silica. The 2DIR experiments are complemented by molecular dynamics (MD) simulations of pure R5 reacting with silicate. Subsequently, theoretical 2DIR spectra calculated from these MD trajectories allowed us to compare calculated spectra with experimental data, and to determine the diverse structural poses of R5. Our findings indicate that unbound R5 predominantly forms β-strand structures alongside various atypical secondary structures. Post-silicification, there's a noticeable shift: a decrease in β-strands coupled with an increase in turn-type and bend-type configurations. We theorize that this structural transformation stems from silicate embedding within R5's hydrogen-bond network, prompting the peptide backbone to contract and adapt around the biosilica precursors.
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Affiliation(s)
- Asger Berg Thomassen
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark.
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark.
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3
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Hung ST, Roget SA, Fayer MD. Effects of Nanoconfinement on Dynamics in Concentrated Aqueous Magnesium Chloride Solutions. J Phys Chem B 2024; 128:5513-5527. [PMID: 38787935 DOI: 10.1021/acs.jpcb.4c01639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Water behavior in various natural and manufactured settings is influenced by confinement in organic or inorganic frameworks and the presence of solutes. Here, the effects on dynamics from both confinement and the addition of solutes are examined. Specifically, water and ion dynamics in concentrated (2.5-4.2 m) aqueous magnesium chloride solutions confined in mesoporous silica (2.8 nm pore diameter) were investigated using polarization selective pump-probe and 2D infrared spectroscopies. Fitting the rotational and spectral diffusion dynamics measured by the vibrational probe, selenocyanate, with a previously developed two-state model revealed distinct behaviors at the interior of the silica pores (core state) and near the wall of the confining framework (shell state). The shell dynamics are noticeably slower than the bulk, or core, dynamics. The concentration-dependent slowing of the dynamics aligns with behavior in the bulk solutions, but the spectrally separated water-associated and Mg2+-associated forms of the selenocyanate probe exhibit different responses to confinement. The disparity in the complete reorientation times is larger upon confinement, but the spectral diffusion dynamics become more similar near the silica surface. The length scales that characterize the transition from surface-influenced to bulk-like behavior for the salt solutions in the pores are discussed and compared to those of pure water and an organic solvent confined in the same pores. These comparisons offer insights into how confinement modulates the properties of different liquids.
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Affiliation(s)
- Samantha T Hung
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Sean A Roget
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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4
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Felsted RG, Graham TR, Zhao Y, Bazak JD, Nienhuis ET, Pauzauskie PJ, Joly AG, Pearce CI, Wang Z, Rosso KM. Anionic Effects on Concentrated Aqueous Lithium Ion Dynamics. J Phys Chem Lett 2024:5076-5087. [PMID: 38708887 DOI: 10.1021/acs.jpclett.4c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
The dynamics, orientational anisotropy, diffusivity, viscosity, and density were measured for concentrated lithium salt solutions, including lithium chloride (LiCl), lithium bromide (LiBr), lithium nitrite (LiNO2), and lithium nitrate (LiNO3), with methyl thiocyanate as an infrared vibrational probe molecule, using two-dimensional infrared spectroscopy (2D IR), nuclear magnetic resonance (NMR) spectroscopy, and viscometry. The 2D IR, NMR, and viscosity results show that LiNO2 exhibits longer correlation times, lower diffusivity, and nearly 4 times greater viscosity compared to those of the other lithium salt solutions of the same concentration, suggesting that nitrite anions may strongly facilitate structure formation via strengthening water-ion network interactions, directly impacting bulk solution properties at sufficiently high concentrations. Additionally, the LiNO2 and LiNO3 solutions show significantly weakened chemical interactions between the lithium cations and the methyl thiocyanate when compared with those of the lithium halide salts.
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Affiliation(s)
- Robert G Felsted
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Trent R Graham
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yatong Zhao
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - J David Bazak
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Emily T Nienhuis
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Peter J Pauzauskie
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Materials Science and Engineering Department, University of Washington, Seattle, Washington 98195, United States
| | - Alan G Joly
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Carolyn I Pearce
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164, United States
| | - Zheming Wang
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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5
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Barclay MS, Wright ND, Cavanaugh P, Pensack RD, Martin EW, Turner DB. Ultrabroadband two-dimensional electronic spectroscopy in the pump-probe geometry using conventional optics. OPTICS LETTERS 2024; 49:2065-2068. [PMID: 38621077 DOI: 10.1364/ol.519387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/14/2024] [Indexed: 04/17/2024]
Abstract
We report ultrabroadband two-dimensional electronic spectroscopy (2D ES) measurements obtained in the pump-probe geometry using conventional optics. A phase-stabilized Michelson interferometer provides the pump-pulse delay interval, τ1, necessary to obtain the excitation-frequency dimension. Spectral resolution of the probe beam provides the detection-frequency dimension, ω3. The interferometer incorporates active phase stabilization via a piezo stage and feedback from interference of a continuous-wave reference laser detected in quadrature. To demonstrate the method, we measured a well-characterized laser dye sample and obtained the known peak structure. The vibronic peaks are modulated as a function of the waiting time, τ2, by vibrational wave packets. The interferometer simplifies ultrabroadband 2D ES measurements and analysis.
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6
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Sanders SE, Zhang M, Javed A, Ogilvie JP. Expanding the bandwidth of fluorescence-detected two-dimensional electronic spectroscopy using a broadband continuum probe pulse pair. OPTICS EXPRESS 2024; 32:8887-8902. [PMID: 38571135 DOI: 10.1364/oe.516963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/16/2024] [Indexed: 04/05/2024]
Abstract
We demonstrate fluorescence-detected two-dimensional electronic spectroscopy (F-2DES) with a broadband, continuum probe pulse pair in the pump-probe geometry. The approach combines a pump pulse pair generated by an acousto-optic pulse-shaper with precise control of the relative pump pulse phase and time delay with a broadband, continuum probe pulse pair created using the Translating Wedge-based Identical pulses eNcoding System (TWINS). The continuum probe expands the spectral range of the detection axis and lengthens the waiting times that can be accessed in comparison to implementations of F-2DES using a single pulse-shaper. We employ phase-cycling of the pump pulse pair and take advantage of the separation of signals in the frequency domain to isolate rephasing and non-rephasing signals and optimize the signal-to-noise ratio. As proof of principle, we demonstrate broadband F-2DES on a laser dye and bacteriochlorophyll a.
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7
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Cai MR, Zhang X, Cheng ZQ, Yan TF, Dong H. Extracting double-quantum coherence in two-dimensional electronic spectroscopy under pump-probe geometry. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:033006. [PMID: 38497835 DOI: 10.1063/5.0198255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
Two-dimensional electronic spectroscopy (2DES) can be implemented with different geometries, e.g., BOXCARS, collinear, and pump-probe geometries. The pump-probe geometry has the advantage of overlapping only two beams and reducing phase cycling steps. However, its applications are typically limited to observing the dynamics with single-quantum coherence and population, leaving the challenge to measure the dynamics of the double-quantum (2Q) coherence, which reflects the many-body interactions. We demonstrate an experimental technique in 2DES under pump-probe geometry with a designed pulse sequence and the signal processing method to extract 2Q coherence. In the designed pulse sequence, with the probe pulse arriving earlier than the pump pulses, our measured signal includes the 2Q signal as well as the zero-quantum signal. With phase cycling and data processing using causality enforcement, we extract the 2Q signal. The proposal is demonstrated with rubidium atoms. We observe the collective resonances of two-body dipole-dipole interactions in both the D1 and D2 lines.
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Affiliation(s)
- Mao-Rui Cai
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Xue Zhang
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Zi-Qian Cheng
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Teng-Fei Yan
- School of Microelectronics, Shanghai University, Shanghai 200444, China
| | - Hui Dong
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
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8
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Procacci B, Wrathall SLD, Farmer AL, Shaw DJ, Greetham GM, Parker AW, Rippers Y, Horch M, Lynam JM, Hunt NT. Understanding the [NiFe] Hydrogenase Active Site Environment through Ultrafast Infrared and 2D-IR Spectroscopy of the Subsite Analogue K[CpFe(CO)(CN) 2] in Polar and Protic Solvents. J Phys Chem B 2024; 128:1461-1472. [PMID: 38301127 PMCID: PMC10875664 DOI: 10.1021/acs.jpcb.3c07965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
The [CpFe(CO)(CN)2]- unit is an excellent structural model for the Fe(CO)(CN)2 moiety of the active site found in [NiFe] hydrogenases. Ultrafast infrared (IR) pump-probe and 2D-IR spectroscopy have been used to study K[CpFe(CO)(CN)2] (M1) in a range of protic and polar solvents and as a dry film. Measurements of anharmonicity, intermode vibrational coupling strength, vibrational relaxation time, and solvation dynamics of the CO and CN stretching modes of M1 in H2O, D2O, methanol, dimethyl sulfoxide, and acetonitrile reveal that H-bonding to the CN ligands plays an important role in defining the spectroscopic characteristics and relaxation dynamics of the Fe(CO)(CN)2 unit. Comparisons of the spectroscopic and dynamic data obtained for M1 in solution and in a dry film with those obtained for the enzyme led to the conclusion that the protein backbone forms an important part of the bimetallic active site environment via secondary coordination sphere interactions.
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Affiliation(s)
- Barbara Procacci
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Solomon L. D. Wrathall
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Amy L. Farmer
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Daniel J. Shaw
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Yvonne Rippers
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Marius Horch
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jason M. Lynam
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Neil T. Hunt
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
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9
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Faitz ZM, Im D, Zanni MT. Femtosecond pulse shaper built into a prism compressor. OPTICS EXPRESS 2024; 32:6092-6103. [PMID: 38439320 DOI: 10.1364/oe.510551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/17/2024] [Indexed: 03/06/2024]
Abstract
We present a frequency domain, AOM-based pulse shaper that utilizes Brewster prisms rather than the current standard of gratings. In doing so, we demonstrate a three-fold increase in efficiency and the ability to compensate for temporal dispersion created by the acousto-optic modulator that filters the pulse spectrum. The shaper is tested between the wavelengths of 520-660 and 840-1170 nm, creating sub-50 fs pulses for each, and used to collect a 2D white-light spectrum of a thin film of semiconducting carbon nanotubes.
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10
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Dong T, Yu P, Zhao J, Wang J. Site specifically probing the unfolding process of human telomere i-motif DNA using vibrationally enhanced alkynyl stretch. Phys Chem Chem Phys 2024; 26:3857-3868. [PMID: 38224126 DOI: 10.1039/d3cp05328h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The microscopic unfolding process of a cytosine-rich DNA forming i-motif by hemi-protonated base pairs is related to gene regulation. However, the detailed thermal unfolding mechanism and the protonation/deprotonation status of site-specific cytosine in DNA in a physiological environment are still obscure. To address this issue, a vibration-enhanced CC probe tagged on 5'E terminal cytosine of human telomere i-motif DNA was examined using linear and nonlinear infrared (IR) spectroscopies and quantum-chemistry calculations. The CC probe extended into the major groove of the i-motif was found using nonlinear IR results only to introduce a minor steric effect on both steady-state structure and local structure dynamics; however, its IR absorption profile effectively reports the cleavage of the hemi-protonated base pair of C1-C13 upon the unfolding with C1 remaining protonated. The temperature mid-point (Tm) of the local transition reported using the CC tag was slightly lower than the Tm of global transition, and the enthalpy of the former exceeds 60% of the global transition. It is shown that the base-pair unraveling is noncooperative, with outer base pairs breaking first and being likely the rate limiting step. Our results offered an in-depth understanding of the macroscopic unfolding characteristics of the i-motif DNA and provided a nonlinear IR approach to monitoring the local structural transition and dynamics of DNA and its complexes.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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11
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Cai MR, Zhang X, Cheng ZQ, Yan TF, Dong H. Cross-phase modulation in two-dimensional spectroscopy. OPTICS EXPRESS 2024; 32:2929-2941. [PMID: 38297529 DOI: 10.1364/oe.503686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/31/2023] [Indexed: 02/02/2024]
Abstract
Developing from transient absorption (TA) spectroscopy, two-dimensional (2D) spectroscopy with pump-probe geometry has emerged as a versatile approach for alleviating the difficulty in implementing 2D spectroscopy with other geometries. However, the presence of cross-phase modulation (XPM) in TA spectroscopy introduces significant spectral distortions, particularly when the pump and probe pulses overlap. We demonstrate that this phenomenon is extended to the 2D spectroscopy with pump-probe geometry and the XPM is induced by the interference of the two pump pulses. We present the oscillatory behavior of XPM in the 2D spectrum and its displacement with respect to the waiting time delay through both experimental measurements and numerical simulations. Additionally, we explore the influence of probe pulse chirp on XPM and discover that by compressing the chirp, the impact of XPM on the desired signal can be reduced.
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12
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Yan C, Wang C, Wagner JC, Ren J, Lee C, Wan Y, Wang SE, Xiong W. Multidimensional Widefield Infrared-Encoded Spontaneous Emission Microscopy: Distinguishing Chromophores by Ultrashort Infrared Pulses. J Am Chem Soc 2024; 146:1874-1886. [PMID: 38085547 PMCID: PMC10811677 DOI: 10.1021/jacs.3c07251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 01/25/2024]
Abstract
Photoluminescence (PL) imaging has broad applications in visualizing biological activities, detecting chemical species, and characterizing materials. However, the chemical information encoded in the PL images is often limited by the overlapping emission spectra of chromophores. Here, we report a PL microscopy based on the nonlinear interactions between mid-infrared and visible excitations on matters, which we termed MultiDimensional Widefield Infrared-encoded Spontaneous Emission (MD-WISE) microscopy. MD-WISE microscopy can distinguish chromophores that possess nearly identical emission spectra via conditions in a multidimensional space formed by three independent variables: the temporal delay between the infrared and the visible pulses (t), the wavelength of visible pulses (λvis), and the frequencies of the infrared pulses (ωIR). This method is enabled by two mechanisms: (1) modulating the optical absorption cross sections of molecular dyes by exciting specific vibrational functional groups and (2) reducing the PL quantum yield of semiconductor nanocrystals, which was achieved through strong field ionization of excitons. Importantly, MD-WISE microscopy operates under widefield imaging conditions with a field of view of tens of microns, other than the confocal configuration adopted by most nonlinear optical microscopies, which require focusing the optical beams tightly. By demonstrating the capacity of registering multidimensional information into PL images, MD-WISE microscopy has the potential of expanding the number of species and processes that can be simultaneously tracked in high-speed widefield imaging applications.
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Affiliation(s)
- Chang Yan
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Center
for Ultrafast Science and Technology, School of Chemistry and Chemical
Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang
Institute for Advanced Study, Shanghai Jiao
Tong University, Shanghai 200240, China
| | - Chenglai Wang
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Jackson C. Wagner
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Jianyu Ren
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Carlynda Lee
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Yuhao Wan
- Department
of Pathology, University of California San
Diego, La Jolla, California 92093, United States
| | - Shizhen E. Wang
- Department
of Pathology, University of California San
Diego, La Jolla, California 92093, United States
| | - Wei Xiong
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Materials
Science and Engineering Program, University
of California San Diego, La Jolla, California 92093, United States
- Department
of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
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13
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Baiz C, Bredenbeck J, Cho M, Jansen T, Krummel A, Roberts S. Celebrating 25 years of 2D IR spectroscopy. J Chem Phys 2024; 160:010401. [PMID: 38165102 DOI: 10.1063/5.0190809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024] Open
Affiliation(s)
- Carlos Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
| | - Jens Bredenbeck
- Institute of Biophysics, Department of Physics, Goethe-University, Max von Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Thomas Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 6 9747 AG Groningen, The Netherlands
| | - Amber Krummel
- Colorado State University, Department of Chemistry, Fort Collins, Colorado 80523, USA
| | - Sean Roberts
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
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14
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Hunt NT. Biomolecular infrared spectroscopy: making time for dynamics. Chem Sci 2024; 15:414-430. [PMID: 38179520 PMCID: PMC10763549 DOI: 10.1039/d3sc05223k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.
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Affiliation(s)
- Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York Heslington York YO10 5DD UK
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15
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Whaley-Mayda L, Guha A, Tokmakoff A. Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. I. Response function theory. J Chem Phys 2023; 159:194201. [PMID: 37966137 DOI: 10.1063/5.0171939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/19/2023] [Indexed: 11/16/2023] Open
Abstract
Fluorescence-encoded infrared (FEIR) spectroscopy is an emerging technique for performing vibrational spectroscopy in solution with detection sensitivity down to single molecules. FEIR experiments use ultrashort pulses to excite a fluorescent molecule's vibrational and electronic transitions in a sequential, time-resolved manner, and are therefore sensitive to intervening vibrational dynamics on the ground state, vibronic coupling, and the relative orientation of vibrational and electronic transition dipole moments. This series of papers presents a theoretical treatment of FEIR spectroscopy that describes these phenomena and examines their manifestation in experimental data. This first paper develops a nonlinear response function description of Fourier-transform FEIR experiments for a two-level electronic system coupled to multiple vibrations, which is then applied to interpret experimental measurements in the second paper [L. Whaley-Mayda et al., J. Chem. Phys. 159, 194202 (2023)]. Vibrational coherence between pairs of modes produce oscillatory features that interfere with the vibrations' population response in a manner dependent on the relative signs of their respective Franck-Condon wavefunction overlaps, leading to time-dependent distortions in FEIR spectra. The orientational response of population and coherence contributions are analyzed and the ability of polarization-dependent experiments to extract relative transition dipole angles is discussed. Overall, this work presents a framework for understanding the full spectroscopic information content of FEIR measurements to aid data interpretation and inform optimal experimental design.
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Affiliation(s)
- Lukas Whaley-Mayda
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Abhirup Guha
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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16
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Dean JLS, Winkler VS, Boyer MA, Sibert EL, Fournier JA. Investigating Intramolecular H Atom Transfer Dynamics in β-Diketones with Ultrafast Infrared Spectroscopies and Theoretical Modeling. J Phys Chem A 2023; 127:9258-9272. [PMID: 37882618 DOI: 10.1021/acs.jpca.3c05417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
The vibrational signatures and ultrafast dynamics of the intramolecular H-bond in a series of β-diketones are investigated with 2D IR spectroscopy and computational modeling. The chosen β-diketones exhibit a range of H atom donor-acceptor distances and asymmetry along the H atom transfer coordinate that tunes the intramolecular H-bond strength. The species with the strongest H-bonds are calculated to have very soft H atom potentials, resulting in highly red-shifted OH stretch fundamental frequencies and dislocation of the H atom upon vibrational excitation. These soft potentials lead to significant coupling to the other normal mode coordinates and give rise to the very broad vibrational signatures observed experimentally. The 2D IR spectra in both the OH and OD stretch regions of the light and deuterated isotopologues reveal broadened and long-lived ground-state bleach signatures of the vibrationally hot molecules. Polarization-sensitive transient absorption measurements in the OH and OD stretch regions reveal notable isotopic differences in orientational dynamics. Orientational relaxation was measured to occur on ∼600 fs and ∼2 ps time scales for the light and deuterated isotopologues, respectively. The orientational dynamics are interpreted in terms of activated H/D atom transfer events driven by collective intramolecular structural rearrangements.
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Affiliation(s)
- Jessika L S Dean
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Valerie S Winkler
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mark A Boyer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin Madison, Madison, Wisconsin 53706, United States
| | - Edwin L Sibert
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin Madison, Madison, Wisconsin 53706, United States
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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17
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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18
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Harel E. Parameter estimation in ultrafast spectroscopy using probability theory. J Chem Phys 2023; 159:124101. [PMID: 38127370 DOI: 10.1063/5.0160631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/01/2023] [Indexed: 12/23/2023] Open
Abstract
Ultrafast spectroscopy is a powerful technique that utilizes short pulses on the femtosecond time scale to generate and probe coherent responses in molecular systems. While the specific ultrafast methodologies vary, the most common data analysis tools rely on discrete Fourier transformation for recovering coherences that report on electronic or vibrational states and multi-exponential fitting for probing population dynamics, such as excited-state relaxation. These analysis tools are widely used due to their perceived reliability in estimating frequencies and decay rates. Here, we demonstrate that such "black box" methods for parameter estimation often lead to inaccurate results even in the absence of noise. To address this issue, we propose an alternative approach based on Bayes probability theory that simultaneously accounts for both population and coherence contributions to the signal. This Bayesian inference method offers accurate parameter estimations across a broad range of experimental conditions, including scenarios with high noise and data truncation. In contrast to traditional methods, Bayesian inference incorporates prior information about the measured signal and noise, leading to improved accuracy. Moreover, it provides estimator error bounds, enabling a systematic statistical framework for interpreting confidence in the results. By employing Bayesian inference, all parameters of a realistic model system may be accurately recovered, even in extremely challenging scenarios where Fourier and multi-exponential fitting methods fail. This approach offers a more reliable and comprehensive analysis tool for time-resolved coherent spectroscopy, enhancing our understanding of molecular systems and enabling a better interpretation of experimental data.
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Affiliation(s)
- Elad Harel
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48864, USA
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19
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Aerts A, Jolly SW, Kockaert P, Gorza SP, Auwera JV, Vaeck N. Modulated super-Gaussian laser pulse to populate a dark rovibrational state of acetylene. J Chem Phys 2023; 159:084303. [PMID: 37638622 DOI: 10.1063/5.0160526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023] Open
Abstract
A pulse-shaping technique in the mid-infrared spectral range based on pulses with a super-Gaussian temporal profile is considered for laser control. We show a realistic and efficient path to the population of a dark rovibrational state in acetylene (C2H2). The laser-induced dynamics in C2H2 are simulated using fully experimental structural parameters. Indeed, the rotation-vibration energy structure, including anharmonicities, is defined by the global spectroscopic Hamiltonian for the ground electronic state of C2H2 built from the extensive high-resolution spectroscopy studies on the molecule, transition dipole moments from intensities, and the effects of the (inelastic) collisions that are parameterized from line broadenings using the relaxation matrix [A. Aerts, J. Vander Auwera, and N. Vaeck, J. Chem. Phys. 154, 144308 (2021)]. The approach, based on an effective Hamiltonian, outperforms today's ab initio computations both in terms of accuracy and computational cost for this class of molecules. With such accuracy, the Hamiltonian permits studying the inner mechanism of theoretical pulse shaping [A. Aerts et al., J. Chem. Phys. 156, 084302 (2022)] for laser quantum control. Here, the generated control pulse presents a number of interferences that take advantage of the control mechanism to populate the dark state. An experimental setup is proposed for in-laboratory investigation.
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Affiliation(s)
- Antoine Aerts
- Université Libre de Bruxelles, Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), 50 Avenue F. Roosevelt, C.P. 160/09, Brussels 1050, Belgium
| | - Spencer W Jolly
- Université Libre de Bruxelles, OPERA-Photonique, 50 Avenue F. Roosevelt, C.P. 194/05, Brussels 1050, Belgium
| | - Pascal Kockaert
- Université Libre de Bruxelles, OPERA-Photonique, 50 Avenue F. Roosevelt, C.P. 194/05, Brussels 1050, Belgium
| | - Simon-Pierre Gorza
- Université Libre de Bruxelles, OPERA-Photonique, 50 Avenue F. Roosevelt, C.P. 194/05, Brussels 1050, Belgium
| | - Jean Vander Auwera
- Université Libre de Bruxelles, Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), 50 Avenue F. Roosevelt, C.P. 160/09, Brussels 1050, Belgium
| | - Nathalie Vaeck
- Université Libre de Bruxelles, Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), 50 Avenue F. Roosevelt, C.P. 160/09, Brussels 1050, Belgium
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20
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Lüttig J, Mueller S, Malý P, Krich JJ, Brixner T. Higher-Order Multidimensional and Pump-Probe Spectroscopies. J Phys Chem Lett 2023; 14:7556-7573. [PMID: 37589504 DOI: 10.1021/acs.jpclett.3c01694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Transient absorption and coherent two-dimensional spectroscopy are widely established methods for the investigation of ultrafast dynamics in quantum systems. Conventionally, they are interpreted in the framework of perturbation theory at the third order of interaction. Here, we discuss the potential of higher-(than-third-)order pump-probe and multidimensional spectroscopy to provide insight into excited multiparticle states and their dynamics. We focus on recent developments from our group. In particular, we demonstrate how phase cycling can be used in fluorescence-detected two-dimensional spectroscopy to isolate higher-order spectra that provide information about highly excited states such as the correlation of multiexciton states. We discuss coherently detected fifth-order 2D spectroscopy and its power to track exciton diffusion. Finally, we show how to extract higher-order signals even from ordinary pump-probe experiments, providing annihilation-free signals at high excitation densities and insight into multiexciton interactions.
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Affiliation(s)
- Julian Lüttig
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefan Mueller
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Pavel Malý
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague, Czech Republic
| | - Jacob J Krich
- Department of Physics, University of Ottawa, Ottawa K1N 6N5, Canada
- School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa K1N 6N5, Canada
| | - 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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21
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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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22
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Gross N, Kuhs CT, Ostovar B, Chiang WY, Wilson KS, Volek TS, Faitz ZM, Carlin CC, Dionne JA, Zanni MT, Gruebele M, Roberts ST, Link S, Landes CF. Progress and Prospects in Optical Ultrafast Microscopy in the Visible Spectral Region: Transient Absorption and Two-Dimensional Microscopy. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:14557-14586. [PMID: 37554548 PMCID: PMC10406104 DOI: 10.1021/acs.jpcc.3c02091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/24/2023] [Indexed: 08/10/2023]
Abstract
Ultrafast optical microscopy, generally employed by incorporating ultrafast laser pulses into microscopes, can provide spatially resolved mechanistic insight into scientific problems ranging from hot carrier dynamics to biological imaging. This Review discusses the progress in different ultrafast microscopy techniques, with a focus on transient absorption and two-dimensional microscopy. We review the underlying principles of these techniques and discuss their respective advantages and applicability to different scientific questions. We also examine in detail how instrument parameters such as sensitivity, laser power, and temporal and spatial resolution must be addressed. Finally, we comment on future developments and emerging opportunities in the field of ultrafast microscopy.
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Affiliation(s)
- Niklas Gross
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Christopher T. Kuhs
- Army
Research Laboratory-South, U.S. Army DEVCOM, Houston, Texas 77005, United States
| | - Behnaz Ostovar
- Department
of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Wei-Yi Chiang
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Kelly S. Wilson
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Tanner S. Volek
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Zachary M. Faitz
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Claire C. Carlin
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
| | - Jennifer A. Dionne
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
- Department
of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, California 94305, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Martin Gruebele
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sean T. Roberts
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Stephan Link
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
- Department
of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Christy F. Landes
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
- Department
of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
- Department
of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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23
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Donaldson PM, Greetham GM, Middleton CT, Luther BM, Zanni MT, Hamm P, Krummel AT. Breaking Barriers in Ultrafast Spectroscopy and Imaging Using 100 kHz Amplified Yb-Laser Systems. Acc Chem Res 2023; 56:2062-2071. [PMID: 37429010 PMCID: PMC10809409 DOI: 10.1021/acs.accounts.3c00152] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Indexed: 07/12/2023]
Abstract
ConspectusUltrafast spectroscopy and imaging have become tools utilized by a broad range of scientists involved in materials, energy, biological, and chemical sciences. Commercialization of ultrafast spectrometers including transient absorption spectrometers, vibrational sum frequency generation spectrometers, and even multidimensional spectrometers have put these advanced spectroscopy measurements into the hands of practitioners originally outside the field of ultrafast spectroscopy. There is now a technology shift occurring in ultrafast spectroscopy, made possible by new Yb-based lasers, that is opening exciting new experiments in the chemical and physical sciences. Amplified Yb-based lasers are not only more compact and efficient than their predecessors but also, most importantly, operate at many times the repetition rate with improved noise characteristics in comparison to the previous generation of Ti:sapphire amplifier technologies. Taken together, these attributes are enabling new experiments, generating improvements to long-standing techniques, and affording the transformation of spectroscopies to microscopies. This Account aims to show that the shift to 100 kHz lasers is a transformative step in nonlinear spectroscopy and imaging, much like the dramatic expansion that occurred with the commercialization of Ti:sapphire laser systems in the 1990s. The impact of this technology will be felt across a great swath of scientific communities. We first describe the technology landscape of amplified Yb-based laser systems used in conjunction with 100 kHz spectrometers operating with shot-to-shot pulse shaping and detection. We also identify the range of different parametric conversion and supercontinuum techniques which now provide a path to making pulses of light optimal for ultrafast spectroscopy. Second, we describe specific instances from our laboratories of how the amplified Yb-based light sources and spectrometers are transformative. For multiple probe time-resolved infrared and transient 2D IR spectroscopy, the gain in temporal span and signal-to-noise enables dynamical spectroscopy measurements from femtoseconds to seconds. These gains widen the applicability of time-resolved infrared techniques across a range of topics in photochemistry, photocatalysis, and photobiology as well as lower the technical barriers to implementation in a laboratory. For 2D visible spectroscopy and microscopy with white light, as well as 2D IR imaging, the high repetition rates of these new Yb-based light sources allow one to spatially map 2D spectra while maintaining high signal-to-noise in the data. To illustrate the gains, we provide examples of imaging applications in the study of photovoltaic materials and spectroelectrochemistry.
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Affiliation(s)
- Paul M. Donaldson
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Greg M. Greetham
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Chris T. Middleton
- PhaseTech
Spectroscopy, Inc., 4916
East Broadway, Suite 125, Madison, Wisconsin 53716, United States
| | - Bradley M. Luther
- Colorado
State University, Department of Chemistry, 200 W. Lake Street, Fort Collins, Colorado 80523, United States
| | - Martin T. Zanni
- University
of Wisconsin, Department of Chemistry, Room 8361, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Peter Hamm
- University
of Zurich, Department of Chemistry, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Amber T. Krummel
- Colorado
State University, Department of Chemistry, 200 W. Lake Street, Fort Collins, Colorado 80523, United States
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24
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Perosa G, Wätzel J, Garzella D, Allaria E, Bonanomi M, Danailov MB, Brynes A, Callegari C, De Ninno G, Demidovich A, Di Fraia M, Di Mitri S, Giannessi L, Manfredda M, Novinec L, Pal N, Penco G, Plekan O, Prince KC, Simoncig A, Spampinati S, Spezzani C, Zangrando M, Berakdar J, Feifel R, Squibb RJ, Coffee R, Hemsing E, Roussel E, Sansone G, McNeil BWJ, Ribič PR. Femtosecond Polarization Shaping of Free-Electron Laser Pulses. PHYSICAL REVIEW LETTERS 2023; 131:045001. [PMID: 37566861 DOI: 10.1103/physrevlett.131.045001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/13/2023] [Indexed: 08/13/2023]
Abstract
We demonstrate the generation of extreme-ultraviolet (XUV) free-electron laser (FEL) pulses with time-dependent polarization. To achieve polarization modulation on a femtosecond timescale, we combine two mutually delayed counterrotating circularly polarized subpulses from two cross-polarized undulators. The polarization profile of the pulses is probed by angle-resolved photoemission and above-threshold ionization of helium; the results agree with solutions of the time-dependent Schrödinger equation. The stability limit of the scheme is mainly set by electron-beam energy fluctuations, however, at a level that will not compromise experiments in the XUV. Our results demonstrate the potential to improve the resolution and element selectivity of methods based on polarization shaping and may lead to the development of new coherent control schemes for probing and manipulating core electrons in matter.
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Affiliation(s)
- Giovanni Perosa
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
- Department of Physics, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Jonas Wätzel
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - David Garzella
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Enrico Allaria
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Matteo Bonanomi
- Politecnico di Milano, 20133 Milano, Italy
- Istituto di Fotonica e Nanotecnologie, 20133 Milano, Italy
| | | | | | - Carlo Callegari
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Giovanni De Ninno
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
- Laboratory of Quantum Optics, University of Nova Gorica, 5001 Nova Gorica, Slovenia
| | | | - Michele Di Fraia
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, 34149 Basovizza, Italy
| | - Simone Di Mitri
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
- Department of Physics, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Luca Giannessi
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
- ENEA C.R. Frascati, 00044 Frascati (Roma), Italy
| | | | - Luka Novinec
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Nitish Pal
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Giuseppe Penco
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Oksana Plekan
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | | | | | - Carlo Spezzani
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Marco Zangrando
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, 34149 Basovizza, Italy
| | - Jamal Berakdar
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 41133 Gothenburg, Sweden
| | - Richard J Squibb
- Department of Physics, University of Gothenburg, 41133 Gothenburg, Sweden
| | - Ryan Coffee
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Erik Hemsing
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Eléonore Roussel
- Université de Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Giuseppe Sansone
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Brian W J McNeil
- University of Strathclyde (SUPA), Glasgow G4 0NG, United Kingdom
- Cockcroft Institute, Warrington WA4 4AD, United Kingdom
- ASTeC, STFC Daresbury Laboratory, Warrington WA4 4AD, United Kingdom
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25
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Huang-Fu ZC, Qian Y, Deng GH, Zhang T, Schmidt S, Brown J, Rao Y. Development of Two-Dimensional Electronic-Vibrational Sum Frequency Generation (2D-EVSFG) for Vibronic and Solvent Couplings of Molecules at Interfaces and Surfaces. ACS PHYSICAL CHEMISTRY AU 2023; 3:374-385. [PMID: 37520317 PMCID: PMC10375875 DOI: 10.1021/acsphyschemau.3c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 08/01/2023]
Abstract
Many photoinduced excited states' relaxation processes and chemical reactions occur at interfaces and surfaces, including charge transfer, energy transfer, proton transfer, proton-coupled electron transfer, configurational dynamics, conical intersections, etc. Of them, interactions of electronic and vibrational motions, namely, vibronic couplings, are the main determining factors for the relaxation processes or reaction pathways. However, time-resolved electronic-vibrational spectroscopy for interfaces and surfaces is lacking. Here we develop interface/surface-specific two-dimensional electronic-vibrational sum frequency generation spectroscopy (2D-EVSFG) for time-dependent vibronic coupling of excited states at interfaces and surfaces. We further demonstrate the fourth-order technique by investigating vibronic coupling, solvent correlation, and time evolution of the coupling for photoexcited interface-active molecules, crystal violet (CV), at the air/water interface as an example. The two vibronic absorption peaks for CV molecules at the interface from the 2D-EVSFG experiments were found to be more prominent than their counterparts in bulk from 2D-EV. Quantitative analysis of the vibronic peaks in 2D-EVSFG suggested that a non-Condon process participates in the photoexcitation of CV at the interface. We further reveal vibrational solvent coupling for the zeroth level on the electronic state with respect to that on the ground state, which is directly related to the magnitude of its change in solvent reorganization energy. The change in the solvent reorganization energy at the interface is much smaller than that in bulk methanol. Time-dependent center line slopes (CLSs) of 2D-EVSFG also showed that kinetic behaviors of CV at the air/water interface are significantly different from those in bulk methanol. Our ultrafast 2D-EVSFG experiments not only offer vibrational information on both excited states and the ground state as compared with the traditional doubly resonant sum frequency generation and electronic-vibrational coupling but also provide vibronic coupling, dynamical solvent effects, and time evolution of vibronic coupling at interfaces.
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26
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Buhrke D, Lahav Y, Rao A, Ruf J, Schapiro I, Hamm P. Transient 2D IR Spectroscopy and Multiscale Simulations Reveal Vibrational Couplings in the Cyanobacteriochrome Slr1393-g3. J Am Chem Soc 2023. [PMID: 37450891 DOI: 10.1021/jacs.3c00896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Cyanobacteriochromes are bistable photoreceptor proteins with desirable photochemical properties for biotechnological applications, such as optogenetics or fluorescence microscopy. Here, we investigate Slr1393-g3, a cyanobacteriochrome that reversibly photoswitches between a red-absorbing (Pr) and green-absorbing (Pg) form. We applied advanced IR spectroscopic methods to track the sequence of intermediates during the photocycle over many orders of magnitude in time. In the conversion from Pg to Pr, we have revealed a new intermediate with distinct spectroscopic features in the IR, which precedes Pr formation using transient IR spectroscopy. In addition, stationary and transient 2D IR experiments measured the vibrational couplings between different groups of the chromophore and the protein in these intermediate states, as well as their structural disorder. Anharmonic QM/MM calculations predict spectra in good agreement with experimental 2D IR spectra of the initial and final states of the photocycle. They facilitate the assignment of the IR spectra that serve as a basis for the interpretation of the spectroscopic results and suggest structural changes of the intermediates along the photocycle.
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Affiliation(s)
- David Buhrke
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
- Institute of Biology, Humboldt University Berlin, 10115 Berlin, Germany
| | - Yigal Lahav
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
- MIGAL - Galilee Research Institute, 1101602 Kiryat Shmona, Israel
| | - Aditya Rao
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Jeannette Ruf
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Peter Hamm
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
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27
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Lüttig J, Rose PA, Malý P, Turkin A, Bühler M, Lambert C, Krich JJ, Brixner T. High-order pump-probe and high-order two-dimensional electronic spectroscopy on the example of squaraine oligomers. J Chem Phys 2023; 158:234201. [PMID: 37326161 DOI: 10.1063/5.0139090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/06/2023] [Indexed: 06/17/2023] Open
Abstract
Time-resolved spectroscopy is commonly used to study diverse phenomena in chemistry, biology, and physics. Pump-probe experiments and coherent two-dimensional (2D) spectroscopy have resolved site-to-site energy transfer, visualized electronic couplings, and much more. In both techniques, the lowest-order signal, in a perturbative expansion of the polarization, is of third order in the electric field, which we call a one-quantum (1Q) signal because in 2D spectroscopy it oscillates in the coherence time with the excitation frequency. There is also a two-quantum (2Q) signal that oscillates in the coherence time at twice the fundamental frequency and is fifth order in the electric field. We demonstrate that the appearance of the 2Q signal guarantees that the 1Q signal is contaminated by non-negligible fifth-order interactions. We derive an analytical connection between an nQ signal and (2n + 1)th-order contaminations of an rQ (with r < n) signal by studying Feynman diagrams of all contributions. We demonstrate that by performing partial integrations along the excitation axis in 2D spectra, we can obtain clean rQ signals free of higher-order artifacts. We exemplify the technique using optical 2D spectroscopy on squaraine oligomers, showing clean extraction of the third-order signal. We further demonstrate the analytical connection with higher-order pump-probe spectroscopy and compare both techniques experimentally. Our approach demonstrates the full power of higher-order pump-probe and 2D spectroscopy to investigate multi-particle interactions in coupled systems.
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Affiliation(s)
- Julian Lüttig
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Peter A Rose
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Pavel Malý
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Arthur Turkin
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Michael Bühler
- 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
| | - Jacob J Krich
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - 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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28
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Donaldson PM, Howe RF, Hawkins AP, Towrie M, Greetham GM. Ultrafast 2D-IR spectroscopy of intensely optically scattering pelleted solid catalysts. J Chem Phys 2023; 158:114201. [PMID: 36948842 DOI: 10.1063/5.0139103] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Solid, powdered samples are often prepared for infrared (IR) spectroscopy analysis in the form of compressed pellets. The intense scattering of incident light by such samples inhibits applications of more advanced IR spectroscopic techniques, such as two-dimensional (2D)-IR spectroscopy. We describe here an experimental approach that enables the measurement of high-quality 2D-IR spectra from scattering pellets of zeolites, titania, and fumed silica in the OD-stretching region of the spectrum under flowing gas and variable temperature up to ∼500 ◦C. In addition to known scatter suppression techniques, such as phase cycling and polarization control, we demonstrate how a bright probe laser beam comparable in strength with the pump beam provides effective scatter suppression. The possible nonlinear signals arising from this approach are discussed and shown to be limited in consequence. In the intense focus of 2D-IR laser beams, a free-standing solid pellet may become elevated in temperature compared with its surroundings. The effects of steady state and transient laser heating effects on practical applications are discussed.
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Affiliation(s)
- Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Russell F Howe
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Alexander P Hawkins
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Mike Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
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29
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Chenchiliyan M, Kübel J, Ooi SA, Salvadori G, Mennucci B, Westenhoff S, Maj M. Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy. J Chem Phys 2023; 158:085103. [PMID: 36859103 DOI: 10.1063/5.0135268] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm-1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.
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Affiliation(s)
- Manoop Chenchiliyan
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michał Maj
- Department of Chemistry-Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
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30
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Li X, Guan J, Shen C, Yu Z, Zheng J. Direct observation of conformations of a high-mobility n-type low-bandgap copolymer in solutions and solid films. J Chem Phys 2023; 158:064202. [PMID: 36792510 DOI: 10.1063/5.0134807] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The aggregation morphologies of conjugated polymers in solutions and solid films are important for their optoelectronic applications. Due to the amorphous state of the polymers, it remains a great challenge to determine their conformations in either liquids or solids. Herein, a ps/fs synchronized 2D IR technique is applied to investigate the molecular conformations of a high-mobility n-type low-bandgap copolymer, N2200, dissolved in CHCl3 and CCl4, and in solid films cast from both solutions by the vibrational cross-angle method. In CCl4, the polymer forms more aggregates and folds more and the backbone dihedral angle of C-C(NDI)/C-S(Thiophene) of its average conformation is about 10° more distorted than that in CHCl3 and the most stable conformation for a free molecule. Anti-intuitively, the solid films cast from both solutions have the same molecular conformation, and the conformation is similar to that of the polar CHCl3 rather than the conformation of the less polar CCl4. The results imply that the interaction between the polymer backbones is probably stronger than its interaction with CCl4, which can naturally guide the rearrangement of polymer chains during the evaporation of solvent molecules. This work also implies that the balance and competition between the polymer/polymer interaction and the polymer/solvent interaction seem to be the dominant factors responsible for what morphology can form in a solid film cast from solution. It is not always true that different molecular conformations must exist in solid films grown from different solutions with different polarity or different extents of aggregates with different conformations.
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Affiliation(s)
- Xinmao Li
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Jianxin Guan
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Chengzhen Shen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Zhihao Yu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Junrong Zheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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31
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Tsubouchi M, Ishii N, Kagotani Y, Shimizu R, Fujita T, Adachi M, Itakura R. Beat-frequency-resolved two-dimensional electronic spectroscopy: disentangling vibrational coherences in artificial fluorescent proteins with sub-10-fs visible laser pulses. OPTICS EXPRESS 2023; 31:6890-6906. [PMID: 36823935 DOI: 10.1364/oe.480505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
We perform a beat-frequency-resolved analysis for two-dimensional electronic spectroscopy using a high-speed and stable 2D electronic spectrometer and few-cycle visible laser pulses to disentangle the vibrational coherences in an artificial fluorescent protein. We develop a highly stable ultrashort light source that generates 5.3-fs visible pulses with a pulse energy of 4.7 µJ at a repetition rate of 10 kHz using multi-plate pulse compression and laser filamentation in a gas cell. The above-5.3-fs laser pulses together with a high-speed multichannel detector enable us to measure a series of 2D electronic spectra, which are resolved in terms of beat frequency related to vibrational coherence. We successfully extract the discrete vibrational peaks behind the inhomogeneous broadening in the absorption spectra and the vibrational quantum beats of the excited electronic state behind the strong incoherent population background in the typical 2D electronic spectra.
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32
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Complete Elimination of Pump Scattering in Transient Absorption Spectroscopy Using Phase and Amplitude Modulation. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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33
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Rutherford SH, Baker MJ, Hunt NT. 2D-IR spectroscopy of proteins in H 2O-A Perspective. J Chem Phys 2023; 158:030901. [PMID: 36681646 DOI: 10.1063/5.0129480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The form of the amide I infrared absorption band provides a sensitive probe of the secondary structure and dynamics of proteins in the solution phase. However, the frequency coincidence of the amide I band with the bending vibrational mode of H2O has necessitated the widespread use of deuterated solvents. Recently, it has been demonstrated that ultrafast 2D-IR spectroscopy allows the detection of the protein amide I band in H2O-based fluids, meaning that IR methods can now be applied to study proteins in physiologically relevant solvents. In this perspective, we describe the basis of the 2D-IR method for observing the protein amide I band in H2O and show how this development has the potential to impact areas ranging from our fundamental appreciation of protein structural dynamics to new applications for 2D-IR spectroscopy in the analytical and biomedical sciences. In addition, we discuss how the spectral response of water, rather than being a hindrance, now provides a basis for new approaches to data pre-processing, standardization of 2D-IR data collection, and signal quantification. Ultimately, we visualize a direction of travel toward the creation of 2D-IR spectral libraries that can be linked to advanced computational methods for use in high-throughput protein screening and disease diagnosis.
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Affiliation(s)
- Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Matthew J Baker
- School of Medicine, Faculty of Clinical Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, United Kingdom
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34
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Al-Mualem ZA, Chen X, Shirley JC, Xu C, Baiz CR. BoxCARS 2D IR spectroscopy with pulse shaping. OPTICS EXPRESS 2023; 31:2700-2709. [PMID: 36785278 PMCID: PMC10018786 DOI: 10.1364/oe.471984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 06/18/2023]
Abstract
BoxCARS and pump-probe geometries are common implementations of two-dimensional infrared (2D IR) spectroscopy. BoxCARS is background-free, generally offering greater signal-to-noise ratio, which enables measuring weak vibrational echo signals. Pulse shapers have been implemented in the pump-probe geometry to accelerate data collection and suppress scatter and other unwanted signals by precise control of the pump-pulse delay and carrier phase. Here, we introduce a 2D-IR optical setup in the BoxCARS geometry that implements a pulse shaper for rapid acquisition of background-free 2D IR spectra. We show a signal-to-noise improvement using this new fast-scan BoxCARS setup versus the pump-probe geometry within the same configuration.
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Affiliation(s)
- Ziareena A. Al-Mualem
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
- Authors contributed equally
| | - Xiaobing Chen
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
- Authors contributed equally
| | - Joseph C. Shirley
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
| | - Cong Xu
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
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35
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Dong T, Yu P, Zhao J, Wang J. Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching. Phys Chem Chem Phys 2022; 24:29988-29998. [PMID: 36472165 DOI: 10.1039/d2cp03920f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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36
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Askelson PG, Meloni SL, Hoffnagle AM, Anna JM. Resolving the Impact of Hydrogen Bonding on the Phylloquinone Cofactor through Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2022; 126:10120-10135. [PMID: 36444999 DOI: 10.1021/acs.jpcb.2c03556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional infrared spectroscopy (2DIR) was applied to phylloquinone (PhQ), an important biological cofactor, to elucidate the impact of hydrogen bonding on the ultrafast dynamics and energetics of the carbonyl stretching modes. 2DIR measurements were performed on PhQ dissolved in hexanol, which served as the hydrogen bonding solvent, and hexane, which served as a non-hydrogen bonding control. Molecular dynamics simulations and quantum chemical calculations were performed to aid in spectral assignment and interpretation. From the position of the peaks in the 2DIR spectra, we extracted the transition frequencies for the fundamental, overtone, and combination bands of hydrogen bonded and non-hydrogen bonded carbonyl groups of PhQ in the 1635-1680 cm-1 region. We find that hydrogen bonding to a single carbonyl group acts to decouple the two carbonyl units of PhQ. Through analysis of the time-resolved 2DIR data, we find that hydrogen bonding leads to faster vibrational relaxation as well as an increase in the inhomogeneous broadening of the carbonyl groups. Overall, this work demonstrates how hydrogen bonding to the carbonyl groups of PhQ presents in the 2DIR spectra, laying the groundwork to use PhQ as a 2DIR probe to characterize the ultrafast fluctuations in the local environment of natural photosynthetic complexes.
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Affiliation(s)
- Phoebe G Askelson
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Stephen L Meloni
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Alexander M Hoffnagle
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Jessica M Anna
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
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37
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Dephasing Processes in the Molecular Dye Lumogen-F Orange Characterized by Two-Dimensional Electronic Spectroscopy. Molecules 2022; 27:molecules27207095. [PMID: 36296684 PMCID: PMC9607445 DOI: 10.3390/molecules27207095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
Abstract
Molecular dyes are finding more and more applications in photonics and quantum technologies, such as polaritonic optical microcavities, organic quantum batteries and single-photon emitters for quantum sensing and metrology. For all these applications, it is of crucial importance to characterize the dephasing mechanisms. In this work we use two-dimensional electronic spectroscopy (2DES) to study the temperature dependent dephasing processes in the prototypical organic dye Lumogen-F orange. We model the 2DES maps using the Bloch equations for a two-level system and obtain a dephasing time T2 = 53 fs at room temperature, which increases to T2 = 94 fs at 86 K. Furthermore, spectral diffusion processes are observed and modeled by a combination of underdamped and overdamped Brownian oscillators. Our results provide useful design parameters for advanced optoelectronic and photonic devices incorporating dye molecules.
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38
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Chatterley AS, Laity P, Holland C, Weidner T, Woutersen S, Giubertoni G. Broadband Multidimensional Spectroscopy Identifies the Amide II Vibrations in Silkworm Films. Molecules 2022; 27:molecules27196275. [PMID: 36234809 PMCID: PMC9571984 DOI: 10.3390/molecules27196275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
We used two-dimensional infrared spectroscopy to disentangle the broad infrared band in the amide II vibrational regions of Bombyx mori native silk films, identifying the single amide II modes and correlating them to specific secondary structure. Amide I and amide II modes have a strong vibrational coupling, which manifests as cross-peaks in 2D infrared spectra with frequencies determined by both the amide I and amide II frequencies of the same secondary structure. By cross referencing with well-known amide I assignments, we determined that the amide II (N-H) absorbs at around 1552 and at 1530 cm–1 for helical and β-sheet structures, respectively. We also observed a peak at 1517 cm−1 that could not be easily assigned to an amide II mode, and instead we tentatively assigned it to a Tyrosine sidechain. These results stand in contrast with previous findings from linear infrared spectroscopy, highlighting the ability of multidimensional spectroscopy for untangling convoluted spectra, and suggesting the need for caution when assigning silk amide II spectra.
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Affiliation(s)
| | - Peter Laity
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Chris Holland
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Sander Woutersen
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Giulia Giubertoni
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Correspondence:
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Sil S, Tilluck RW, Mohan T M N, Leslie CH, Rose JB, Domínguez-Martín MA, Lou W, Kerfeld CA, Beck WF. Excitation energy transfer and vibronic coherence in intact phycobilisomes. Nat Chem 2022; 14:1286-1294. [PMID: 36123451 DOI: 10.1038/s41557-022-01026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 07/21/2022] [Indexed: 11/09/2022]
Abstract
The phycobilisome is an oligomeric chromoprotein complex that serves as the principal mid-visible light-harvesting system in cyanobacteria. Here we report the observation of excitation-energy-transfer pathways involving delocalized optical excitations of the bilin (linear tetrapyrrole) chromophores in intact phycobilisomes isolated from Fremyella diplosiphon. By using broadband multidimensional electronic spectroscopy with 6.7-fs laser pulses, we are able to follow the progress of excitation energy from the phycoerythrin disks at the ends of the phycobilisome's rods to the C-phycocyanin disks along their length in <600 fs. Oscillation maps show that coherent wavepacket motions prominently involving the hydrogen out-of-plane vibrations of the bilins mediate non-adiabatic relaxation of a manifold of vibronic exciton states. However, the charge-transfer character of the bilins in the allophycocyanin-containing segments localizes the excitations in the core of the phycobilisome, yielding a kinetic bottleneck that enables photoregulatory mechanisms to operate efficiently on the >10-ps timescale.
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Affiliation(s)
- Sourav Sil
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Ryan W Tilluck
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Nila Mohan T M
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Chase H Leslie
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Justin B Rose
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | | | - Wenjing Lou
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Warren F Beck
- Department of Chemistry, Michigan State University, East Lansing, MI, USA.
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40
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Cai MR, Ye C, Dong H, Li Y. Enantiodetection of Chiral Molecules via Two-Dimensional Spectroscopy. PHYSICAL REVIEW LETTERS 2022; 129:103201. [PMID: 36112446 DOI: 10.1103/physrevlett.129.103201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/14/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Enantiodetection of chiral molecules is important to chemical reaction control and biological function designs. Traditional optical methods of enantiodetection rely on the weak magnetic-dipole or electric-quadrupole interactions, and in turn suffer from the weak signal and low sensitivity. We propose a new optical enantiodetection method to determine the enantiomeric excess via two-dimensional (2D) spectroscopy of the chiral mixture driven by three electromagnetic fields. The quantities of left- and right-handed chiral molecules are reflected by the intensities of different peaks on the 2D spectrum, separated by the chirality-dependent frequency shifts resulting from the relative strong electric-dipole interactions between the chiral molecules and the driving fields. Thus, the enantiomeric excess can be determined via the intensity ratio of the peaks for the two enantiomers.
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Affiliation(s)
- Mao-Rui Cai
- Beijing Computational Science Research Center, Beijing 100193, China
- Graduate School of China Academy of Engineering Physics, No. 10 Xibeiwang East Road, Haidian District, Beijing 100193, China
| | - Chong Ye
- Beijing Key Laboratory of Nanophotonics and Ultrafine Optoelectronic Systems School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Hui Dong
- Graduate School of China Academy of Engineering Physics, No. 10 Xibeiwang East Road, Haidian District, Beijing 100193, China
| | - Yong Li
- Beijing Computational Science Research Center, Beijing 100193, China
- Center for Theoretical Physics and School of Science, Hainan University, Haikou 570228, China
- Synergetic Innovation Center for Quantum Effects and Applications, Hunan Normal University, Changsha 410081, China
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41
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Bohlmann Kunz M, Podorova Y, Armstrong ZT, Zanni MT. Time-Domain Photothermal AFM Spectroscopy via Femtosecond Pulse Shaping. Anal Chem 2022; 94:12374-12382. [PMID: 36040762 DOI: 10.1021/acs.analchem.2c01920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A time-domain version of photothermal microscopy using an atomic force microscope (AFM) is reported, which we call Fourier transform photothermal (FTPT) spectroscopy, where the delay between two laser pulses is varied and the Fourier transform is computed. An acousto-optic modulator-based pulse shaper sets the delay and phases of the pulses shot-to-shot at 100 kHz, enabling background subtraction and data collection in the rotating frame. The pulse shaper is also used to flatten the pulse spectrum, thereby eliminating the need for normalization by the laser spectrum. We demonstrate the method on 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-Pn) microcrystals and Mn-phthalocyanine islands, confirming subdiffraction spatial resolution, and providing new spectroscopic insights likely linked to structural defects in the crystals.
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Affiliation(s)
- Miriam Bohlmann Kunz
- , Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Yulia Podorova
- , Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Zachary T Armstrong
- , Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- , Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
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42
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Chatterley AS, Golbek TW, Weidner T. Measuring Protein Conformation at Aqueous Interfaces with 2D Infrared Spectroscopy of Emulsions. J Phys Chem Lett 2022; 13:7191-7196. [PMID: 35905449 DOI: 10.1021/acs.jpclett.2c01324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Determining the secondary and tertiary structures of proteins at aqueous interfaces is crucial for understanding their function, but measuring these structures selectively at the interface is challenging. Here we demonstrate that two-dimensional infrared (2D-IR) spectroscopy of protein stabilized emulsions offers a new route to measuring interfacial protein structure with high levels of detail. We prepared hexadecane/water oil-in-water emulsions stabilized by model LK peptides that are known to fold into either α-helix or β-sheet conformations at hydrophobic interfaces and measured 2D-IR spectra in a transmission geometry. We saw clear spectral signatures of the peptides folding at the interface, with no detectable residue from remaining bulk peptides. Using 2D spectroscopy gives us access to correlation and dynamics data, which enables structural assignment in cases where linear spectroscopy fails. Using the emulsions allows one to study interfacial spectra with standard transmission geometry spectrometers, bringing the richness of 2D-IR to the interface with no additional optical complexity.
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Affiliation(s)
| | | | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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43
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Praturi A, Schrod S, Singh BP, Vasa P. White-Light Spectral Interferometry for Characterizing Inhomogeneity in Solutions and Nanocolloids. ACS NANOSCIENCE AU 2022; 2:486-493. [PMID: 37101849 PMCID: PMC10125346 DOI: 10.1021/acsnanoscienceau.2c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022]
Abstract
We demonstrate the use of white-light spectral interferometry as an effective technique involving only linear optical interactions and a partially coherent light source to measure the complex transmission response function of optical resonance and to determine the corresponding variation in the refractive index relative to a reference. We also discuss experimental arrangements to increase the accuracy and sensitivity of the technique. The superiority of the technique over single-beam absorption measurements is demonstrated by the accurate determination of the response function of the chlorophyll-a solution. The technique is then applied to chlorophyll-a solutions of varying concentrations and gold nanocolloids to characterize inhomogeneous broadening. Results on the inhomogeneity of gold nanocolloids are also supported by transmission electron micrographs, showing distributions of the size and shape of the constituent gold nanorods.
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Affiliation(s)
- Aparna Praturi
- Department of Physics, Indian Institute of Technology Bombay, 400076 Mumbai, India
| | - Stefan Schrod
- Department of Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Bhanu Pratap Singh
- Department of Physics, Indian Institute of Technology Bombay, 400076 Mumbai, India
| | - Parinda Vasa
- Department of Physics, Indian Institute of Technology Bombay, 400076 Mumbai, India
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44
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Farrell KM, Zanni MT. Phase stable, shot-to-shot measurement of third- and fifth-order two-quantum correlation spectra using a pulse shaper in the pump-probe geometry. J Chem Phys 2022; 157:014203. [PMID: 35803806 PMCID: PMC9262413 DOI: 10.1063/5.0097019] [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
We demonstrate the first phase stable measurement of a third-order 2Q spectrum using a pulse shaper in the pump-probe geometry. This measurement was achieved by permuting the time-ordering of the pump pulses, thus rearranging the signal pathways that are emitted in the probe direction. The third-order 2Q spectrum is self-heterodyned by the probe pulse. Using this method, one can interconvert between a 1Q experiment and a 2Q experiment by simply reprogramming a pulse shaper or delay stage. We also measure a fifth-order absorptive 2Q spectrum in the pump-probe geometry, which contains similar information as a third-order experiment but does not suffer from dispersive line shapes. To do so, we introduce methods to minimize saturation-induced artifacts of the pulse shaper, improving fifth-order signals. These techniques add new capabilities for 2D spectrometers that use pulse shapers in the pump-probe beam geometry.
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Affiliation(s)
- Kieran M Farrell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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45
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Dicke SS, Maj M, Fields CR, Zanni MT. Metastable intermediate during hIAPP aggregation catalyzed by membranes as detected with 2D IR spectroscopy. RSC Chem Biol 2022; 3:931-940. [PMID: 35866164 PMCID: PMC9257649 DOI: 10.1039/d2cb00028h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
The aggregation of human islet amyloid polypeptide (hIAPP) into amyloid fibrils involves formation of oligomeric intermediates that are thought to be the cytotoxic species responsible for β-cell dysfunction in type 2 diabetes. hIAPP oligomers permeating or disrupting the cellular membrane may be one mechanism of toxicity and so measuring the structural kinetics of aggregation in the presence of membranes is of much interest. In this study, we use 2D IR spectroscopy and 13C18O isotope labeling to study the secondary structure of the oligomeric intermediates formed in solution and in the presence of phospholipid vesicles at sites L12A13, L16V17, G24A25 and V32G33. Pairs of labels monitor the couplings between associated polypeptides and the dihedral angles between adjacent residues. In solution, the L12A13 residues form an oligomeric β-sheet in addition to an α-helix whereas with the phospholipid vesicles they are α-helical throughout the aggregation process. In both solution and with DOPC vesicles, L16V17 and V32G33 have disordered structures until fibrils are formed. Similarly, under both conditions, G24A25 exhibits 3-state kinetics, created by an oligomeric intermediate with a well-defined β-sheet structure. Amyloid fibril formation is often thought to involve intermediates with exceedingly low populations that are difficult to detect experimentally. These experiments establish that amyloid fibril formation of hIAPP when catalyzed by membranes includes a metastable intermediate and that this intermediate has a similar structure at G24A25 in the FGAIL region as the corresponding intermediate in solution, thought to be the toxic species. 2D IR and 13C18O isotope labeling establish that amyloid formation of hIAPP catalyzed by membranes includes a metastable intermediate with a similar structure at G24A25 in the FGAIL region as the corresponding intermediate in solution.![]()
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Affiliation(s)
- Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA .,Formally at Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
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46
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Gerken F, Posske T, Mukamel S, Thorwart M. Unique Signatures of Topological Phases in Two-Dimensional THz Spectroscopy. PHYSICAL REVIEW LETTERS 2022; 129:017401. [PMID: 35841546 DOI: 10.1103/physrevlett.129.017401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/12/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
We develop a microscopic theory for the two-dimensional (2D) spectroscopy of one-dimensional topological superconductors. We consider a ring geometry of an archetypal topological superconductor with periodic boundary conditions, bypassing energy-specific differences caused by topologically protected or trivial boundary modes that are hard to distinguish. We show numerically and analytically that the cross-peak structure of the 2D spectra carries unique signatures of the topological phases of the chain. Our work reveals how 2D spectroscopy can identify topological phases in bulk properties.
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Affiliation(s)
- Felix Gerken
- I. Institut für Theoretische Physik, Universität Hamburg, Notkestraße 9, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thore Posske
- I. Institut für Theoretische Physik, Universität Hamburg, Notkestraße 9, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Shaul Mukamel
- Departments of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697-2025, USA
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Notkestraße 9, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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47
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Al-Mualem ZA, Baiz CR. Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra. J Phys Chem A 2022; 126:3816-3825. [PMID: 35668543 DOI: 10.1021/acs.jpca.2c02605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ultrafast spectroscopy often involves measuring weak signals and long data acquisition times. Spectra are typically collected as a "pump-probe" spectrum by measuring differences in intensity across laser shots. Shot-to-shot intensity fluctuations are most often the primary source of noise in ultrafast spectroscopy. Here, we present a novel approach for denoising ultrafast two-dimensional infrared (2D IR) spectra using conditional generative adversarial neural networks (cGANNs). The cGANN approach is able to eliminate shot-to-shot noise and reconstruct the line shapes present in the noisy input spectrum. We present a general approach for training the cGANN using matched pairs of noisy and clean synthetic 2D IR spectra based on the Kubo-line shape model for a three-level system. Experimental shot-to-shot laser noise is added to synthetic spectra to recreate the noise profile present in measured experimental spectra. The cGANNs can recover line shapes from synthetic 2D IR spectra with signal-to-noise ratios as low as 2:1, while largely preserving the key features such as center frequencies, line widths, and diagonal elongation. In addition, we benchmark the performance of the cGANN using experimental 2D IR spectra of an ester carbonyl vibrational probe and demonstrate that, by applying the cGANN denoising approach, we can extract the frequency-frequency time correlation function (FFCF) from reconstructed spectra using a nodal-line slope analysis. Finally, we provide a set of practical guidelines for extending the denoising method to other coherent multidimensional spectroscopies.
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Affiliation(s)
- Ziareena A Al-Mualem
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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48
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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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49
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Considerations in upconversion: A practical guide to sum-frequency generation spectrometer design and implementation. Biointerphases 2022; 17:021201. [PMID: 35473296 DOI: 10.1116/6.0001817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In this tutorial review, we discuss how the choice of upconversion pulse shape in broadband vibrational sum-frequency generation (SFG) spectrometer design impacts the chemical or physical insights one can obtain from a set of measurements. A time-domain picture of a vibrational coherence being mapped by a second optical field is described and the implications of how this mapping, or upconversion process, takes place are given in the context of several popular and emerging approaches found in the literature. Emphasis is placed on broadband frequency-domain measurements, where the choice of upconversion pulse enhances or limits the information contained in the SFG spectrum. We conclude with an outline for a flexible approach to SFG upconversion using pulse-shaping methods and a simple guide to design and optimize the associated instrumentation.
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50
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MAREKHA B, Hunger J. A single methyl group drastically changes urea's hydration dynamics. J Chem Phys 2022; 156:164504. [DOI: 10.1063/5.0085461] [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
The amphiphilicity and denaturation efficiency of urea can be tuned via alkylation. Although the interaction of alkylureas with water and proteins has been studied in detail, the hydration of 1-methylurea has remained elusive, precluding the isolation of the effect of an individual methyl group. Here, we study water dynamics in the hydration shell of 1-methylurea (1-MU) using infrared absorption and ultrafast infrared spectroscopies. We find that 1-MU hardly affects the hydrogen-bond distribution of water as probed by the OD stretching vibration of HOD molecules. Polarization resolved infrared pump-probe experiments reveal that 1-MU slows down the rotational dynamics of up to 3 water molecules in its hydration shell. Comparison to earlier results for other alkylureas suggests that further alkylation does not necessarily slow down the rotational dynamics of additional water molecules. Two-dimensional infrared experiments show that 1-MU markedly slows down the hydrogen-bond fluctuation dynamics of water, yet similar to what has been found for urea and dimethylureas. Remarkably, (alkyl-) ureas that share a similar effect on water's hydrogen-bond fluctuation dynamics share a similar (modest) protein denaturation tendency. As such, not only the hydrophobicity but also hydration of hydrophilic fragments of alkylureas may be relevant to explain their function towards biomolecules.
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Affiliation(s)
- Bogdan MAREKHA
- Max-Planck-Institute for Medical Research Department of Biomolecular Mechanisms, Germany
| | - Johannes Hunger
- Molecular Spectroscopy, Max Planck Institute for Polymer Research, Germany
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