1
|
Schmid SY, Lachowski K, Chiang HT, Pozzo L, De Yoreo J, Zhang S. Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309725. [PMID: 37702227 DOI: 10.1002/anie.202309725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.
Collapse
Affiliation(s)
- Sakshi Yadav Schmid
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kacper Lachowski
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | - Huat Thart Chiang
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Lilo Pozzo
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Jim De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| |
Collapse
|
2
|
Glotz G, Püschmann S, Haas M, Gescheidt G. Direct detection of photo-induced reactions by IR: from Brook rearrangement to photo-catalysis. Photochem Photobiol Sci 2023:10.1007/s43630-023-00406-4. [PMID: 36933157 DOI: 10.1007/s43630-023-00406-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
In situ IR detection of photoreactions induced by the light of LEDs at appropriate wavelengths provides a simple, cost-effective, and versatile method to get insight into mechanistic details. In particular, conversions of functional groups can be selectively followed. Overlapping UV-Vis bands or fluorescence from the reactants and products and the incident light do not obstruct IR detection. Compared with in situ photo-NMR, our setup does not require tedious sample preparation (optical fibers) and offers a selective detection of reactions, even at positions where 1H-NMR lines overlap or 1H resonances are not clear-cut. We illustrate the applicability of our setup following the photo-Brook rearrangement of (adamant-1-yl-carbonyl)-tris(trimethylsilyl)silane, address photo-induced α-bond cleavage (1-hydroxycyclohexyl phenyl ketone), study photoreduction using tris(bipyridine)ruthenium(II), investigate photo-oxygenation of double bonds with molecular oxygen and the fluorescent 2,4,6-triphenylpyrylium photocatalyst, and address photo-polymerization. With the LED/FT-IR combination, reactions can be qualitatively followed in fluid solution, (highly) viscous environments, and in the solid state. Viscosity changes during the reaction (e.g., during a polymerization) do not obstruct the method.
Collapse
Affiliation(s)
- Gabriel Glotz
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010, Graz, Austria.
| | - Sabrina Püschmann
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Michael Haas
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Georg Gescheidt
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010, Graz, Austria
| |
Collapse
|
3
|
Hashimoto K, Nakamura T, Kageyama T, Badarla VR, Shimada H, Horisaki R, Ideguchi T. Upconversion time-stretch infrared spectroscopy. LIGHT, SCIENCE & APPLICATIONS 2023; 12:48. [PMID: 36869075 PMCID: PMC9984475 DOI: 10.1038/s41377-023-01096-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/24/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
High-speed measurement confronts the extreme speed limit when the signal becomes comparable to the noise level. In the context of broadband mid-infrared spectroscopy, state-of-the-art ultrafast Fourier-transform infrared spectrometers, in particular dual-comb spectrometers, have improved the measurement rate up to a few MSpectra s-1, which is limited by the signal-to-noise ratio. Time-stretch infrared spectroscopy, an emerging ultrafast frequency-swept mid-infrared spectroscopy technique, has shown a record-high rate of 80 MSpectra s-1 with an intrinsically higher signal-to-noise ratio than Fourier-transform spectroscopy by more than the square-root of the number of spectral elements. However, it can measure no more than ~30 spectral elements with a low resolution of several cm-1. Here, we significantly increase the measurable number of spectral elements to more than 1000 by incorporating a nonlinear upconversion process. The one-to-one mapping of a broadband spectrum from the mid-infrared to the near-infrared telecommunication region enables low-loss time-stretching with a single-mode optical fiber and low-noise signal detection with a high-bandwidth photoreceiver. We demonstrate high-resolution mid-infrared spectroscopy of gas-phase methane molecules with a high resolution of 0.017 cm-1. This unprecedentedly high-speed vibrational spectroscopy technique would satisfy various unmet needs in experimental molecular science, e.g., measuring ultrafast dynamics of irreversible phenomena, statistically analyzing a large amount of heterogeneous spectral data, or taking broadband hyperspectral images at a high frame rate.
Collapse
Affiliation(s)
- Kazuki Hashimoto
- Institute for Photon Science and Technology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takuma Nakamura
- Institute for Photon Science and Technology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takahiro Kageyama
- Department of Physics, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Venkata Ramaiah Badarla
- Institute for Photon Science and Technology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyuki Shimada
- Institute for Photon Science and Technology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ryoich Horisaki
- Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Takuro Ideguchi
- Institute for Photon Science and Technology, The University of Tokyo, Tokyo, 113-0033, Japan.
- Department of Physics, The University of Tokyo, Tokyo, 113-0033, Japan.
| |
Collapse
|
4
|
Grills DC, Layne BH, Wishart JF. Coupling Pulse Radiolysis with Nanosecond Time-Resolved Step-Scan Fourier Transform Infrared Spectroscopy: Broadband Mid-Infrared Detection of Radiolytically Generated Transients. APPLIED SPECTROSCOPY 2022; 76:1142-1153. [PMID: 35414202 DOI: 10.1177/00037028221097429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We describe the first implementation of broadband, nanosecond time-resolved step-scan Fourier transform infrared (S2-FT-IR) spectroscopy at a pulse radiolysis facility. This new technique allows the rapid acquisition of nano- to microsecond time-resolved infrared (TRIR) spectra of transient species generated by pulse radiolysis of liquid samples at a pulsed electron accelerator. Wide regions of the mid-infrared can be probed in a single experiment, which often takes < 20-30 min to complete. It is therefore a powerful method for rapidly locating the IR absorptions of short-lived, radiation-induced species in solution, and for directly monitoring their subsequent reactions. Time-resolved step-scan FT-IR detection for pulse radiolysis thus complements our existing narrowband quantum cascade laser-based pulse radiolysis-TRIR detection system, which is more suitable for acquiring single-shot kinetics and narrowband TRIR spectra on small-volume samples and in strongly absorbing solvents, such as water. We have demonstrated the application of time-resolved step-scan FT-IR spectroscopy to pulse radiolysis by probing the metal carbonyl and organic carbonyl vibrations of the one-electron-reduced forms of two Re-based CO2 reduction catalysts in acetonitrile solution. Transient IR absorption bands with amplitudes on the order of 1 × 10-3 are easily detected on the sub-microsecond timescale using electron pulses as short as 250 ns.
Collapse
Affiliation(s)
- David C Grills
- Chemistry Division, 8099Brookhaven National Laboratory, Upton, NY, USA
| | - Bobby H Layne
- Chemistry Division, 8099Brookhaven National Laboratory, Upton, NY, USA
| | - James F Wishart
- Chemistry Division, 8099Brookhaven National Laboratory, Upton, NY, USA
| |
Collapse
|
5
|
Schubert L, Langner P, Ehrenberg D, Lorenz-Fonfria VA, Heberle J. Protein conformational changes and protonation dynamics probed by a single shot using quantum-cascade-laser-based IR spectroscopy. J Chem Phys 2022; 156:204201. [PMID: 35649857 DOI: 10.1063/5.0088526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mid-IR spectroscopy is a powerful and label-free technique to investigate protein reactions. In this study, we use quantum-cascade-laser-based dual-comb spectroscopy to probe protein conformational changes and protonation events by a single-shot experiment. By using a well-characterized membrane protein, bacteriorhodopsin, we provide a comparison between dual-comb spectroscopy and our homebuilt tunable quantum cascade laser (QCL)-based scanning spectrometer as tools to monitor irreversible reactions with high time resolution. In conclusion, QCL-based infrared spectroscopy is demonstrated to be feasible for tracing functionally relevant protein structural changes and proton translocations by single-shot experiments. Thus, we envisage a bright future for applications of this technology for monitoring the kinetics of irreversible reactions as in (bio-)chemical transformations.
Collapse
Affiliation(s)
- Luiz Schubert
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Pit Langner
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - David Ehrenberg
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Victor A Lorenz-Fonfria
- Institute of Molecular Science, Universitat de Valencia, Catedrático José Beltrán Martínez, No. 2, 46980 Paterna, Spain
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| |
Collapse
|
6
|
Time-resolved infrared absorption spectroscopy applied to photoinduced reactions: how and why. Photochem Photobiol Sci 2022; 21:557-584. [DOI: 10.1007/s43630-022-00180-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
|
7
|
Weigel A, Jacob P, Gröters D, Buberl T, Huber M, Trubetskov M, Heberle J, Pupeza I. Ultra-rapid electro-optic sampling of octave-spanning mid-infrared waveforms. OPTICS EXPRESS 2021; 29:20747-20764. [PMID: 34266157 DOI: 10.1364/oe.423818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
We demonstrate ultra-rapid electro-optic sampling (EOS) of octave-spanning mid-infrared pulses centered at 9 μm, implemented by mechanically scanning a mirror with a sonotrode resonating at 19 kHz (forward and backward acquisition at 38 kHz). The instrument records the infrared waveform with a spectral intensity dynamic range of 1.6 × 105 for a single scan over a 1.6-ps delay range, acquired within 26 μs. The purely reflective nature of the delay scanning technique is compatible with broad optical bandwidths, short pulse durations (16 fs, centered at 1030 nm) and high average powers (Watt-level). Interferometric tracking of the sonotrode motion in combination with a predictor-corrector algorithm allows for delay-axis determination with down to single-digit attosecond precision. Ultra-rapid mid-infrared EOS will advance applications such as molecular fingerprinting of static samples as well as tracking of biological processes and chemical reactions and is likely to find new fields of application such as infrared-spectroscopic flow cytometry.
Collapse
|
8
|
Norahan MJ, Horvath R, Woitzik N, Jouy P, Eigenmann F, Gerwert K, Kötting C. Microsecond-Resolved Infrared Spectroscopy on Nonrepetitive Protein Reactions by Applying Caged Compounds and Quantum Cascade Laser Frequency Combs. Anal Chem 2021; 93:6779-6783. [PMID: 33881816 DOI: 10.1021/acs.analchem.1c00666] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Infrared spectroscopy is ideally suited for the investigation of protein reactions at the atomic level. Many systems were investigated successfully by applying Fourier transform infrared (FTIR) spectroscopy. While rapid-scan FTIR spectroscopy is limited by time resolution (about 10 ms with 16 cm-1 resolution), step-scan FTIR spectroscopy reaches a time resolution of about 10 ns but is limited to cyclic reactions that can be repeated hundreds of times under identical conditions. Consequently, FTIR with high time resolution was only possible with photoactivable proteins that undergo a photocycle. The huge number of nonrepetitive reactions, e.g., induced by caged compounds, were limited to the millisecond time domain. The advent of dual-comb quantum cascade laser now allows for a rapid reaction monitoring in the microsecond time domain. Here, we investigate the potential to apply such an instrument to the huge class of G-proteins. We compare caged-compound-induced reactions monitored by FTIR and dual-comb spectroscopy by applying the new technique to the α subunit of the inhibiting Gi protein and to the larger protein-protein complex of Gαi with its cognate regulator of G-protein signaling (RGS). We observe good data quality with a 4 μs time resolution with a wavelength resolution comparable to FTIR. This is more than three orders of magnitude faster than any FTIR measurement on G-proteins in the literature. This study paves the way for infrared spectroscopic studies in the so far unresolvable microsecond time regime for nonrepetitive biological systems including all GTPases and ATPases.
Collapse
Affiliation(s)
- Mohamad Javad Norahan
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, 44801 Bochum, Germany.,Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | | | - Nathalie Woitzik
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, 44801 Bochum, Germany.,Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Pierre Jouy
- IRsweep AG, Laubisruetistrasse 44, 8712 Staefa, Switzerland
| | | | - Klaus Gerwert
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, 44801 Bochum, Germany.,Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Carsten Kötting
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, 44801 Bochum, Germany.,Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| |
Collapse
|
9
|
Abstract
AbstractThis work reports a multispectral tomography technique in transmission mode (called 3DITI for 3D Infrared Thermospectroscopic Imaging) based on a middle wavelength infrared (MWIR) focal plane array. This technique relies on an MWIR camera (1.5 to 5.5 μm) used in combination with a multispectral IR monochromator (400 nm to 20 μm), and a sample mounted on a rotary stage for the measurement of its transmittance at several angular positions. Based on the projections expressed in terms of a sinogram, spatial three-dimensional (3D) cubes (proper emission and absorptivity) are reconstructed using a back-projection method based on inverse Radon transform. As a validation case, IR absorptivity tomography of a reflective metallic screw is performed within a very short time, i.e., shorter than 1 min, to monitor 72 angular positions of the sample. Then, the absorptivity and proper emission tomographies of a butane-propane-air burner flame and microfluidic perfluoroalkoxy (PFA) tubing filled with water and ethanol are obtained. These unique data evidence that 3D thermo-chemical information in complex semi-transparent media can be obtained using the proposed 3DITI method. Moreover, this measurement technique presents new problems in the acquisition, storage and processing of big data. In fact, the quantity of reconstructed data can reach several TB (a tomographic sample cube of 1.5 × 1.5 × 3 cm3 is composed of more than 1 million pixels per wavelength).
Collapse
|
10
|
Gorzelanny C, Mess C, Schneider SW, Huck V, Brandner JM. Skin Barriers in Dermal Drug Delivery: Which Barriers Have to Be Overcome and How Can We Measure Them? Pharmaceutics 2020; 12:E684. [PMID: 32698388 PMCID: PMC7407329 DOI: 10.3390/pharmaceutics12070684] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/11/2020] [Accepted: 07/14/2020] [Indexed: 12/13/2022] Open
Abstract
Although, drugs are required in the various skin compartments such as viable epidermis, dermis, or hair follicles, to efficiently treat skin diseases, drug delivery into and across the skin is still challenging. An improved understanding of skin barrier physiology is mandatory to optimize drug penetration and permeation. The various barriers of the skin have to be known in detail, which means methods are needed to measure their functionality and outside-in or inside-out passage of molecules through the various barriers. In this review, we summarize our current knowledge about mechanical barriers, i.e., stratum corneum and tight junctions, in interfollicular epidermis, hair follicles and glands. Furthermore, we discuss the barrier properties of the basement membrane and dermal blood vessels. Barrier alterations found in skin of patients with atopic dermatitis are described. Finally, we critically compare the up-to-date applicability of several physical, biochemical and microscopic methods such as transepidermal water loss, impedance spectroscopy, Raman spectroscopy, immunohistochemical stainings, optical coherence microscopy and multiphoton microscopy to distinctly address the different barriers and to measure permeation through these barriers in vitro and in vivo.
Collapse
Affiliation(s)
| | | | | | | | - Johanna M. Brandner
- Department of Dermatology and Venerology, Center for Internal Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (C.G.); (C.M.); (S.W.S.); (V.H.)
| |
Collapse
|
11
|
Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
Collapse
|
12
|
Vöhringer P. Vibrations tell the tale. A time-resolved mid-infrared perspective of the photochemistry of iron complexes. Dalton Trans 2020; 49:256-266. [DOI: 10.1039/c9dt04165f] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Time-resolved infrared spectroscopies are used to elucidate multiscalar photochemical processes of iron complexes.
Collapse
Affiliation(s)
- Peter Vöhringer
- Abteilung für Molekulare Physikalische Chemie
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| |
Collapse
|
13
|
Jacob P, Weigel A, Gröters D, Buberl T, Trubetskov M, Huber M, Heberle J, Pupeza I. Mid-infrared waveform measurement by rapid mechanical scanning. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202024316002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
14
|
Ritter E, Puskar L, Kim SY, Park JH, Hofmann KP, Bartl F, Hegemann P, Schade U. Féry Infrared Spectrometer for Single-Shot Analysis of Protein Dynamics. J Phys Chem Lett 2019; 10:7672-7677. [PMID: 31763851 DOI: 10.1021/acs.jpclett.9b03099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Current submillisecond time-resolved broad-band infrared spectroscopy, one of the most frequently used techniques for studying structure-function relationships in life sciences, is typically limited to fast-cycling reactions that can be repeated thousands of times with high frequency. Notably, a majority of chemical and biological processes do not comply with this requirement. For example, the activation of vertebrate rhodopsin, a prototype of many protein receptors in biological organisms that mediate basic functions of life, including vision, smell, and taste, is irreversible. Here we present a dispersive single-shot Féry spectrometer setup that extends such spectroscopy to irreversible and slow-cycling systems by exploiting the unique properties of brilliant synchrotron infrared light combined with an advanced focal plane detector array embedded in a dispersive optical concept. We demonstrate our single-shot method on microbial actinorhodopsin with a slow photocycle and on vertebrate rhodopsin with irreversible activation.
Collapse
Affiliation(s)
- Eglof Ritter
- Humboldt-Universität zu Berlin , Experimentelle Biophysik , 10115 Berlin , Germany
- Humboldt-Universität zu Berlin , Biophysikalische Chemie , 10115 Berlin , Germany
| | - Ljiljana Puskar
- Helmholtz-Zentrum Berlin für Materialien und Energie , 12498 Berlin , Germany
| | - So Young Kim
- Chonbuk National University , Division of Biotechnology, Advanced Institute of Environment and Bioscience , 54596 Iksan , Republic of Korea
| | - Jung Hee Park
- Chonbuk National University , Division of Biotechnology, Advanced Institute of Environment and Bioscience , 54596 Iksan , Republic of Korea
| | | | - Franz Bartl
- Humboldt-Universität zu Berlin , Biophysikalische Chemie , 10115 Berlin , Germany
| | - Peter Hegemann
- Humboldt-Universität zu Berlin , Experimentelle Biophysik , 10115 Berlin , Germany
| | - Ulrich Schade
- Helmholtz-Zentrum Berlin für Materialien und Energie , 12498 Berlin , Germany
| |
Collapse
|
15
|
Hashimoto K, Badarla VR, Kawai A, Ideguchi T. Complementary vibrational spectroscopy. Nat Commun 2019; 10:4411. [PMID: 31562337 PMCID: PMC6764968 DOI: 10.1038/s41467-019-12442-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/10/2019] [Indexed: 01/24/2023] Open
Abstract
Vibrational spectroscopy, comprised of infrared absorption and Raman scattering spectroscopy, is widely used for label-free optical sensing and imaging in various scientific and industrial fields. The two molecular spectroscopy methods are sensitive to different types of vibrations and provide complementary vibrational spectra, but obtaining complete vibrational information with a single spectroscopic device is challenging due to the large wavelength discrepancy between the two methods. Here, we demonstrate simultaneous infrared absorption and Raman scattering spectroscopy that allows us to measure the complete broadband vibrational spectra in the molecular fingerprint region with a single instrument based on an ultrashort pulsed laser. The system is based on dual-modal Fourier-transform spectroscopy enabled by efficient use of nonlinear optical effects. Our proof-of-concept experiment demonstrates rapid, broadband and high spectral resolution measurements of complementary spectra of organic liquids for precise and accurate molecular analysis.
Collapse
Affiliation(s)
- Kazuki Hashimoto
- Department of Physics, The University of Tokyo, Tokyo, 113-0033, Japan
- Aeronautical Technology Directorate, Japan Aerospace Exploration Agency, Tokyo, 181-0015, Japan
| | - Venkata Ramaiah Badarla
- Institute for Photon Science and Technology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Akira Kawai
- Department of Physics, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takuro Ideguchi
- Institute for Photon Science and Technology, The University of Tokyo, Tokyo, 113-0033, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, 332-0012, Japan.
| |
Collapse
|
16
|
Yu M, Okawachi Y, Griffith AG, Lipson M, Gaeta AL. Microfluidic mid-infrared spectroscopy via microresonator-based dual-comb source. OPTICS LETTERS 2019; 44:4259-4262. [PMID: 31465377 DOI: 10.1364/ol.44.004259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Over the past decade, microresonator-based soliton combs based on photonic integration have broadened the scope of applications in sensing, ranging, and imaging. The large comb line spacing on the order of hundreds of gigahertz allows for rapid acquisition of absorption spectra in the condensed matter phase without aliasing via a dual-comb interferometer. We present a proof-of-principle demonstration of high-throughput label-free microresonator-based dual-comb spectroscopy in a microfluidic chip that dynamically probes the linear absorption of liquid acetone in the mid-infrared wavelength regime. We measure the flow dynamics of an acetone droplet with a spectral acquisition rate of 25 kHz (40 μs per spectrum) covering a spectral range from 2900 to 2990 nm. Combining microfluidics and silicon-photonic technology would potentially enable a compact time-resolved spectroscopy system for a wide range of applications such as chemical synthesis, biological cell-sorting, and lab-on-a-chip.
Collapse
|
17
|
Hashimoto K, Ideguchi T. Phase-controlled Fourier-transform spectroscopy. Nat Commun 2018; 9:4448. [PMID: 30361645 PMCID: PMC6202327 DOI: 10.1038/s41467-018-06956-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/28/2018] [Indexed: 01/17/2023] Open
Abstract
Fourier-transform spectroscopy (FTS) has been widely used as a standard analytical technique over the past half-century. FTS is an autocorrelation-based technique that is compatible with both temporally coherent and incoherent light sources, and functions as an active or passive spectrometer. However, it has been mostly used for static measurements due to the low scan rate imposed by technological restrictions. This has impeded its application to continuous rapid measurements, which would be of significant interest for a variety of fields, especially when monitoring of non-repeating or transient complex dynamics is desirable. Here, we demonstrate highly efficient FTS operating at a high spectral acquisition rate with a simple delay line based on a dynamic phase-control technique. The independent adjustability of phase and group delays allows us to achieve the Nyquist-limited spectral acquisition rate over 10,000 spectra per second, while maintaining a large spectral bandwidth and high resolution. We also demonstrate passive spectroscopy with an incoherent light source.
Collapse
Affiliation(s)
- Kazuki Hashimoto
- Department of Physics, The University of Tokyo, Tokyo, 113-0033, Japan
- Aeronautical Technology Directorate, Japan Aerospace Exploration Agency, Tokyo, 181-0015, Japan
| | - Takuro Ideguchi
- Department of Physics, The University of Tokyo, Tokyo, 113-0033, Japan.
- PRESTO, Japan Science and Technology Agency, Tokyo, 113-0033, Japan.
| |
Collapse
|
18
|
Abstract
The development of a spectroscopy device on a chip that could realize real-time fingerprinting with label-free and high-throughput detection of trace molecules represents one of the big challenges in sensing. Dual-comb spectroscopy (DCS) in the mid-infrared is a powerful technique offering high acquisition rates and signal-to-noise ratios through use of only a single detector with no moving parts. Here, we present a nanophotonic silicon-on-insulator platform designed for mid-infrared (mid-IR) DCS. A single continuous-wave low-power pump source generates two mutually coherent mode-locked frequency combs spanning from 2.6 to 4.1 μm in two silicon microresonators. A proof-of-principle experiment of vibrational absorption DCS in the liquid phase is achieved acquiring spectra of acetone spanning from 2900 to 3100 nm at 127-GHz (4.2-cm−1) resolution. These results represent a significant step towards a broadband, mid-IR spectroscopy instrument on a chip for liquid/condensed matter phase studies. Dual-comb spectroscopy is a powerful tool for realizing rapid spectroscopic measurements with high sensitivity and selectivity. Here, Yu et al. demonstrate silicon microresonator-based dual comb spectroscopy in the mid-infrared region, where strong vibrational resonances of many liquids exist.
Collapse
|
19
|
Design Considerations for Integration of Terahertz Time-Domain Spectroscopy in Microfluidic Platforms. PHOTONICS 2018. [DOI: 10.3390/photonics5010005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Microfluidic platforms have received much attention in recent years. In particular, there is interest in combining spectroscopy with microfluidic platforms. This work investigates the integration of microfluidic platforms and terahertz time-domain spectroscopy (THz-TDS) systems. A semiclassical computational model is used to simulate the emission of THz radiation from a GaAs photoconductive THz emitter. This model incorporates white noise with increasing noise amplitude (corresponding to decreasing dynamic range values). White noise is selected over other noise due to its contributions in THz-TDS systems. The results from this semiclassical computational model, in combination with defined sample thicknesses, can provide the maximum measurable absorption coefficient for a microfluidic-based THz-TDS system. The maximum measurable frequencies for such systems can be extracted through the relationship between the maximum measurable absorption coefficient and the absorption coefficient for representative biofluids. The sample thickness of the microfluidic platform and the dynamic range of the THz-TDS system play a role in defining the maximum measurable frequency for microfluidic-based THz-TDS systems. The results of this work serve as a design tool for the development of such systems.
Collapse
|
20
|
Schultz BJ, Mohrmann H, Lorenz-Fonfria VA, Heberle J. Protein dynamics observed by tunable mid-IR quantum cascade lasers across the time range from 10ns to 1s. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:666-674. [PMID: 28110813 DOI: 10.1016/j.saa.2017.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
We have developed a spectrometer based on tunable quantum cascade lasers (QCLs) for recording time-resolved absorption spectra of proteins in the mid-infrared range. We illustrate its performance by recording time-resolved difference spectra of bacteriorhodopsin in the carboxylic range (1800-1700cm-1) and on the CO rebinding reaction of myoglobin (1960-1840cm-1), at a spectral resolution of 1cm-1. The spectrometric setup covers the time range from 4ns to nearly a second with a response time of 10-15ns. Absorption changes as low as 1×10-4 are detected in single-shot experiments at t>1μs, and of 5×10-6 in kinetics obtained after averaging 100 shots. While previous time-resolved IR experiments have mostly been conducted on hydrated films of proteins, we demonstrate here that the brilliance of tunable quantum cascade lasers is superior to perform ns time-resolved experiments even in aqueous solution (H2O).
Collapse
Affiliation(s)
- Bernd-Joachim Schultz
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Hendrik Mohrmann
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Victor A Lorenz-Fonfria
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany; Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain; Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| |
Collapse
|
21
|
Mezzetti A, Leibl W. Time-resolved infrared spectroscopy in the study of photosynthetic systems. PHOTOSYNTHESIS RESEARCH 2017; 131:121-144. [PMID: 27678250 DOI: 10.1007/s11120-016-0305-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
Time-resolved (TR) infrared (IR) spectroscopy in the nanosecond to second timescale has been extensively used, in the last 30 years, in the study of photosynthetic systems. Interesting results have also been obtained at lower time resolution (minutes or even hours). In this review, we first describe the used techniques-dispersive IR, laser diode IR, rapid-scan Fourier transform (FT)IR, step-scan FTIR-underlying the advantages and disadvantages of each of them. Then, the main TR-IR results obtained so far in the investigation of photosynthetic reactions (in reaction centers, in light-harvesting systems, but also in entire membranes or even in living organisms) are presented. Finally, after the general conclusions, the perspectives in the field of TR-IR applied to photosynthesis are described.
Collapse
Affiliation(s)
- Alberto Mezzetti
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7197, Laboratoire de Réactivité de Surfaces, 4 Pl. Jussieu, 75005, Paris, France.
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
| | - Winfried Leibl
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| |
Collapse
|
22
|
Müller P, Hermans I. Applications of Modulation Excitation Spectroscopy in Heterogeneous Catalysis. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.6b04855] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Philipp Müller
- Department of Chemistry & Department of Chemical Engineering, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ive Hermans
- Department of Chemistry & Department of Chemical Engineering, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
23
|
Kottke T, Lórenz-Fonfría VA, Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J Phys Chem B 2016; 121:335-350. [PMID: 28100053 DOI: 10.1021/acs.jpcb.6b09222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.
Collapse
Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
| |
Collapse
|