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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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2
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Bournet Q, Jonusas M, Zheng A, Guichard F, Natile M, Zaouter Y, Joffre M, Bonvalet A, Druon F, Hanna M, Georges P. Inline amplification of mid-infrared intrapulse difference frequency generation. OPTICS LETTERS 2022; 47:4885-4888. [PMID: 36181142 DOI: 10.1364/ol.467792] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
We demonstrate an ultrafast mid-infrared source architecture that implements both intrapulse difference frequency generation (iDFG) and further optical parametric amplification (OPA), in an all-inline configuration. The source is driven by a nonlinearly compressed high-energy Yb-doped-fiber amplifier delivering 7.4 fs pulses at a central wavelength of 1030 nm, at a repetition rate of 250 kHz. It delivers 1 µJ, 73 fs pulses at a central wavelength of 8 µm, tunable over more than one octave. By enrolling all the pump photons in the iDFG process and recycling the long wavelength pump photons amplified in the iDFG in the subsequent OPA, we obtain an unprecedented overall optical efficiency of 2%. These performances, combining high energy and repetition rate in a very simple all-inline setup, make this technique ideally suited for a growing number of applications, such as high harmonic generation in solids or two-dimensional infrared spectroscopy experiments.
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3
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Rutherford SH, Greetham GM, Towrie M, Parker AW, Kharratian S, Krauss TF, Nordon A, Baker MJ, Hunt NT. Detection of paracetamol binding to albumin in blood serum using 2D-IR spectroscopy. Analyst 2022; 147:3464-3469. [DOI: 10.1039/d2an00978a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-Dimensional Infrared (2D-IR) spectroscopy is used to detect binding of paracetamol with proteins in blood serum. Quantitative peak patterns are observed indicating structural changes of the albumins' secondary structure when paracetamol bound.
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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, UK
| | - Gregory M. Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Anthony W. Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Soheila Kharratian
- Department of Chemistry and York Biomedical Institute, University of York, Heslington, York, YO10 5DD, UK
- School of Physics, Engineering and Technology and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - Thomas F. Krauss
- School of Physics, Engineering and Technology and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - Alison Nordon
- WestCHEM, Department of Pure and Applied Chemistry and CPACT, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Matthew J. Baker
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
- Dxcover Ltd, Suite RC534, 204 George Street, Glasgow, G1 1XL, UK
| | - Neil T. Hunt
- Department of Chemistry and York Biomedical Institute, University of York, Heslington, York, YO10 5DD, UK
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4
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Valentine ML, Al-Mualem ZA, Baiz CR. Pump Slice Amplitudes: A Simple and Robust Method for Connecting Two-Dimensional Infrared and Fourier Transform Infrared Spectra. J Phys Chem A 2021; 125:6498-6504. [PMID: 34259508 DOI: 10.1021/acs.jpca.1c04558] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast two-dimensional infrared (2D IR) spectroscopy and Fourier transform infrared (FTIR) spectroscopy are often performed in tandem, with FTIR typically used to interpret and provide hypotheses for 2D IR experiments. Comparisons between 2D IR and FTIR spectra can also be used to examine the structure and orientation in systems of coupled vibrational chromophores. The most common method for comparing 2D IR and FTIR lineshapes, the diagonal slice method, contains significant artifacts when applied to oscillators with low anharmonicities. Here, we introduce a new technique, the pump slice amplitude (PSA) method, for relating 2D IR lineshapes to FTIR lineshapes and compare PSAs against diagonal slices using theoretical and experimental spectra. We find that PSAs are significantly more similar to FTIR lineshapes than diagonal slices in systems with low anharmonicity.
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Affiliation(s)
- Mason L Valentine
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
| | - Ziareena A Al-Mualem
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
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5
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Muntean CM, Ştefan R, Tǎbǎran A, Tripon C, Bende A, Fǎlǎmaş A, Colobǎţiu LM, Olar LE. The Influence of UV Femtosecond Laser Pulses on Bacterial DNA Structure, as Proved by Fourier Transform Infrared (FT‐IR) Spectroscopy. ChemistrySelect 2021. [DOI: 10.1002/slct.202102097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Cristina M. Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies 67-103 Donat Str. 400293 Cluj-Napoca Romania
| | - Rǎzvan Ştefan
- University of Agricultural Sciences and Veterinary Medicine Faculty of Veterinary Medicine 3–5 Calea Manastur Str. 400372 Cluj-Napoca Romania
| | - Alexandra Tǎbǎran
- University of Agricultural Sciences and Veterinary Medicine Faculty of Veterinary Medicine 3–5 Calea Manastur Str. 400372 Cluj-Napoca Romania
| | - Carmen Tripon
- National Institute for Research & Development of Isotopic and Molecular Technologies 67-103 Donat Str. 400293 Cluj-Napoca Romania
| | - Attila Bende
- National Institute for Research & Development of Isotopic and Molecular Technologies 67-103 Donat Str. 400293 Cluj-Napoca Romania
| | - Alexandra Fǎlǎmaş
- National Institute for Research & Development of Isotopic and Molecular Technologies 67-103 Donat Str. 400293 Cluj-Napoca Romania
| | - Liora M. Colobǎţiu
- Iuliu Haţieganu University of Medicine and Pharmacy Faculty of Pharmacy 8 Victor Babeş Str. 400012 Cluj-Napoca Romania
| | - Loredana E. Olar
- University of Agricultural Sciences and Veterinary Medicine Faculty of Veterinary Medicine 3–5 Calea Manastur Str. 400372 Cluj-Napoca Romania
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6
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Procacci B, Rutherford SH, Greetham GM, Towrie M, Parker AW, Robinson CV, Howle CR, Hunt NT. Differentiation of bacterial spores via 2D-IR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119319. [PMID: 33360210 DOI: 10.1016/j.saa.2020.119319] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Ultrafast 2D-IR spectroscopy is a powerful tool for understanding the spectroscopy and dynamics of biological molecules in the solution phase. A number of recent studies have begun to explore the utility of the information-rich 2D-IR spectra for analytical applications. Here, we report the application of ultrafast 2D-IR spectroscopy for the detection and classification of bacterial spores. 2D-IR spectra of Bacillus atrophaeus and Bacillus thuringiensis spores as dry films on CaF2 windows were obtained. The sporulated nature of the bacteria was confirmed using 2D-IR diagonal and off-diagonal peaks arising from the calcium dipicolinate CaDP·3H2O biomarker for sporulation. Distinctive peaks, in the protein amide I region of the spectrum were used to differentiate the two types of spore. The identified marker modes demonstrate the potential for the use of 2D-IR methods as a direct means of spore classification. We discuss these new results in perspective with the current state of analytical 2D-IR measurements, showing that the potential exists to apply 2D-IR spectroscopy to detect the spores on surfaces and in suspensions as well as in dry films. The results demonstrate how applying 2D-IR screening methodologies to spores would enable the creation of a library of spectra for classification purposes.
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Affiliation(s)
- Barbara Procacci
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Samantha H Rutherford
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Camilla V Robinson
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Christopher R Howle
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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7
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Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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8
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Rutherford SH, Greetham GM, Donaldson PM, Towrie M, Parker AW, Baker MJ, Hunt NT. Detection of Glycine as a Model Protein in Blood Serum Using 2D-IR Spectroscopy. Anal Chem 2021; 93:920-927. [PMID: 33295755 DOI: 10.1021/acs.analchem.0c03567] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycine (Gly) is used as a model system to evaluate the ability of ultrafast two-dimensional infrared (2D-IR) spectroscopy to detect and quantify the low-molecular-weight proteinaceous components of blood serum. Combining data acquisition schemes to suppress absorption bands of H2O that overlap with the protein amide I band with analysis of peak patterns appearing in the off-diagonal region of the 2D-IR spectrum allows separation of the Gly spectral signature from that of the dominant protein fraction of serum in a transmission-mode 2D-IR measurement without any sample manipulation, e.g., filtration or drying. 2D-IR spectra of blood serum samples supplemented with varying concentrations of Gly were obtained, and a range of data analysis methods compared, leading to a detection limit of ∼3 mg/mL for Gly. The reported methodology provides a platform for a critical assessment of the sensitivity of 2D-IR for measuring the concentrations of amino acids, peptides, and low-molecular-weight proteins present in serum samples. We conclude that, in the case of several clinically relevant diagnostic molecules and their combinations, the potential exists for 2D-IR to complement IR absorption methods as the benefits of the second frequency dimension offered by 2D-IR spectroscopy outweigh the added technical complexity of the measurement.
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Affiliation(s)
- Samantha H Rutherford
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Paul M Donaldson
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Michael Towrie
- 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
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, U.K
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
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9
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Pérez RD, Leani JJ, Robledo JI, Sánchez HJ. First characterization of chemical environments using energy dispersive inelastic x-ray scattering induced by an x-ray tube. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:013102. [PMID: 33514261 DOI: 10.1063/5.0026061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
Energy Dispersive Inelastic X-ray Scattering (EDIXS) is a reliable technique for the discrimination and characterization of local chemical environments. By means of this methodology, the speciation of samples has been attained in a variety of samples and experimental conditions, such as total reflection, grazing incidence, and confocal setups. Until now, due to the requirement of a monochromatic and intense exciting beam, this tool had been applied using exclusively synchrotron radiation sources. We present, for the first time, results of test measurements using EDIXS for chemical characterization implemented in a conventional x-ray tube based laboratory. The results show good discrimination between different iron compounds under study, suggesting the real possibility of rutinary chemical state characterizations of samples by means of EDIXS using a conventional x-ray tube.
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Affiliation(s)
- Roberto Daniel Pérez
- IFEG, National Scientific and Technical Research Council (CONICET), X5000HUA Córdoba, Argentina and FaMAF, Universidad Nacional de Córdoba (UNC), X5000HUA Córdoba, Argentina
| | - Juan José Leani
- IFEG, National Scientific and Technical Research Council (CONICET), X5000HUA Córdoba, Argentina and FaMAF, Universidad Nacional de Córdoba (UNC), X5000HUA Córdoba, Argentina
| | - José Ignacio Robledo
- IFEG, National Scientific and Technical Research Council (CONICET), X5000HUA Córdoba, Argentina and FaMAF, Universidad Nacional de Córdoba (UNC), X5000HUA Córdoba, Argentina
| | - Héctor Jorge Sánchez
- IFEG, National Scientific and Technical Research Council (CONICET), X5000HUA Córdoba, Argentina and FaMAF, Universidad Nacional de Córdoba (UNC), X5000HUA Córdoba, Argentina
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10
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Zhang XX, Brantley SL, Corcelli SA, Tokmakoff A. DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site. Commun Biol 2020; 3:525. [PMID: 32963293 PMCID: PMC7508854 DOI: 10.1038/s42003-020-01241-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/13/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the dynamic interactions of ligands to DNA is important in DNA-based nanotechnologies. By structurally tracking the dissociation of Hoechst 33258-bound DNA (d(CGCAAATTTGCG)2) complex (H-DNA) with T-jump 2D-IR spectroscopy, the ligand is found to strongly disturb the stability of the three C:G base pairs adjacent to A:T the binding site, with the broken base pairs being more than triple at 100 ns. The strong stabilization effect of the ligand on DNA duplex makes this observation quite striking, which dramatically increases the melting temperature and dissociation time. MD simulations demonstrate an important role of hydration water and counter cations in maintaining the separation of terminal base pairs. The hydrogen bonds between the ligand and thymine carbonyls are crucial in stabilizing H-DNA, whose breaking signal appearing prior to the complete dissociation. Thermodynamic analysis informs us that H-DNA association is a concerted process, where H cooperates with DNA single strands in forming H-DNA.
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Affiliation(s)
- Xin-Xing Zhang
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA.
| | - Shelby L Brantley
- Department of Chemistry and Biochemistry, University of Norte Dame, Notre Dame, IN, 46556, USA
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Norte Dame, Notre Dame, IN, 46556, USA.
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
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11
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Fritzsch R, Hume S, Minnes L, Baker MJ, Burley GA, Hunt NT. Two-dimensional infrared spectroscopy: an emerging analytical tool? Analyst 2020; 145:2014-2024. [PMID: 32051976 DOI: 10.1039/c9an02035g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ultrafast two-dimensional infrared (2D-IR) spectroscopy has provided valuable insights into biomolecular structure and dynamics, but recent progress in laser technology and data analysis methods have demonstrated the potential for high throughput 2D-IR measurements and analytical applications. Using 2D-IR as an analytical tool requires a different approach to data collection and analysis compared to pure research applications however and, in this review, we highlight progress towards usage of 2D-IR spectroscopy in areas relevant to biomedical, pharmaceutical and analytical molecular science. We summarise the technical and methodological advances made to date and discuss the challenges that still face 2D-IR spectroscopy as it attempts to transition from the state-of-the-art laser laboratory to the standard suite of analytical tools.
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Affiliation(s)
- Robby Fritzsch
- Department of Physics, SUPA, University of Strathclyde, Glasgow, G4 0NG, UK
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12
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Hume S, Greetham GM, Donaldson PM, Towrie M, Parker AW, Baker MJ, Hunt NT. 2D-Infrared Spectroscopy of Proteins in Water: Using the Solvent Thermal Response as an Internal Standard. Anal Chem 2020; 92:3463-3469. [PMID: 31985198 PMCID: PMC7145279 DOI: 10.1021/acs.analchem.9b05601] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Ultrafast
two-dimensional infrared (2D-IR) spectra can now be obtained
in a matter of seconds, opening up the possibility of high-throughput
screening applications of relevance to the biomedical and pharmaceutical
sectors. Determining quantitative information from 2D-IR spectra recorded
on different samples and different instruments is however made difficult
by variations in beam alignment, laser intensity, and sample conditions.
Recently, we demonstrated that 2D-IR spectroscopy of the protein amide
I band can be performed in aqueous (H2O) rather than deuterated
(D2O) solvents, and we now report a method that uses the
magnitude of the associated thermal response of H2O as
an internal normalization standard for 2D-IR spectra. Using the water
response, which is temporally separated from the protein signal, to
normalize the spectra allows significant reduction of the impact of
measurement-to-measurement fluctuations on the data. We demonstrate
that this normalization method enables creation of calibration curves
for measurement of absolute protein concentrations and facilitates
reproducible difference spectroscopy methodologies. These advances
make significant progress toward the robust data handling strategies
that will be essential for the realization of automated spectral analysis
tools for large scale 2D-IR screening studies of protein-containing
solutions and biofluids.
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Affiliation(s)
- Samantha Hume
- Department of Physics, SUPA , University of Strathclyde , 107 Rottenrow East , Glasgow G4 0NG , U.K
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Paul M Donaldson
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Michael Towrie
- 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
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry , University of Strathclyde , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , U.K
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13
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Kübel J, Lee G, Ooi SA, Westenhoff S, Han H, Cho M, Maj M. Ultrafast Chemical Exchange Dynamics of Hydrogen Bonds Observed via Isonitrile Infrared Sensors: Implications for Biomolecular Studies. J Phys Chem Lett 2019; 10:7878-7883. [PMID: 31794222 DOI: 10.1021/acs.jpclett.9b03144] [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: 05/13/2023]
Abstract
Local probes are indispensable to study protein structure and dynamics with site-specificity. The isonitrile functional group is a highly sensitive and H-bonding interaction-specific probe. Isonitriles exhibit large spectral shifts and transition dipole moment changes upon H-bonding while being weakly affected by solvent polarity. These unique properties allow a clear separation of distinct subpopulations of interacting species and an elucidation of their ultrafast dynamics with two-dimensional infrared (2D-IR) spectroscopy. Here, we apply 2D-IR to quantify the picosecond chemical exchange dynamics of solute-solvent complexes forming between isonitrile-derivatized alanine and fluorinated ethanol, where the degree of fluorination controls their H-bond-donating ability. We show that the molecules undergo faster exchange in the presence of more acidic H-bond donors, indicating that the exchange process is primarily dependent on the nature of solvent-solvent interactions. We foresee isonitrile as a highly promising probe for studying of H-bonds dynamics in the active site of enzymes.
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Affiliation(s)
- Joachim Kübel
- Department of Chemistry and Molecular Biology , University of Gothenburg , 40530 Gothenburg , Sweden
| | - Giseong Lee
- Department of Chemistry , Korea University , Seoul 02841 , South Korea
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology , University of Gothenburg , 40530 Gothenburg , Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology , University of Gothenburg , 40530 Gothenburg , Sweden
| | - Hogyu Han
- Department of Chemistry , Korea University , Seoul 02841 , South Korea
| | - Minhaeng Cho
- Department of Chemistry , Korea University , Seoul 02841 , South Korea
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science , Seoul 02841 , South Korea
| | - Michał Maj
- Department of Chemistry and Molecular Biology , University of Gothenburg , 40530 Gothenburg , Sweden
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14
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Fritzsch R, Greetham GM, Clark IP, Minnes L, Towrie M, Parker AW, Hunt NT. Monitoring Base-Specific Dynamics during Melting of DNA-Ligand Complexes Using Temperature-Jump Time-Resolved Infrared Spectroscopy. J Phys Chem B 2019; 123:6188-6199. [PMID: 31268327 DOI: 10.1021/acs.jpcb.9b04354] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ultrafast time-resolved infrared spectroscopy employing nanosecond temperature-jump initiation has been used to study the melting of double-stranded (ds)DNA oligomers in the presence and absence of minor groove-binding ligand Hoechst 33258. Ligand binding to ds(5'-GCAAATTTCC-3'), which binds Hoechst 33258 in the central A-tract region with nanomolar affinity, causes a dramatic increase in the timescales for strand melting from 30 to ∼250 μs. Ligand binding also suppresses premelting disruption of the dsDNA structure, which takes place on 100 ns timescales and includes end-fraying. In contrast, ligand binding to the ds(5'-GCATATATCC-3') sequence, which exhibits an order of magnitude lower affinity for Hoechst 33258 than the A-tract motif, leads to an increase by only a factor of 5 in melting timescales and reduced suppression of premelting sequence perturbation and end-fraying. These results demonstrate a dynamic impact of the minor groove ligand on the dsDNA structure that correlates with binding strength and thermodynamic stabilization of the duplex. Moreover, the ability of the ligand to influence base pairs distant from the binding site has potential implications for allosteric communication mechanisms in dsDNA.
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Affiliation(s)
- Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , U.K
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , U.K
| | - Michael Towrie
- 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
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , U.K
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Hume S, Hithell G, Greetham GM, Donaldson PM, Towrie M, Parker AW, Baker MJ, Hunt NT. Measuring proteins in H 2O with 2D-IR spectroscopy. Chem Sci 2019; 10:6448-6456. [PMID: 31341597 PMCID: PMC6611063 DOI: 10.1039/c9sc01590f] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/13/2019] [Indexed: 02/06/2023] Open
Abstract
The amide I infrared band of proteins is highly sensitive to secondary structure, but studies under physiological conditions are prevented by strong, overlapping water absorptions, motivating the widespread use of deuterated solutions. H/D exchange raises fundamental questions regarding the impact of increased mass on protein dynamics, while deuteration is impractical for biomedical or commercial applications of protein IR spectroscopy. We show that 2D-IR spectroscopy can avoid this problem because the 2D-IR amide I signature of proteins dominates that of water even at sub-millimolar protein concentrations. Using equine blood serum as a test system, we investigate the significant implications of being able to measure the spectroscopy and dynamics of proteins in water, demonstrating relevance in areas ranging from fundamental science to the clinic. Measurements of vibrational relaxation dynamics of serum proteins reveals that deuteration slows down the rate of amide I vibrational relaxation by >10%, indicating a dynamic impact of isotopic exchange in some proteins. The unique link between protein secondary structure and 2D-IR amide I lineshape allows differentiation of signals due to albumin and globulin protein fractions in serum leading to measurements of the biomedically-important albumin to globulin ratio (AGR) with an accuracy of ±4% across a clinically-relevant range. Furthermore, we demonstrate that 2D-IR spectroscopy enables differentiation of the structurally similar globulin proteins IgG, IgA and IgM, opening up a straightforward spectroscopic approach to measuring levels of serum proteins that are currently only accessible via biomedical laboratory testing.
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Affiliation(s)
- Samantha Hume
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK
| | - Gordon Hithell
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK
| | - Gregory M Greetham
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX , UK
| | - Paul M Donaldson
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX , UK
| | - Michael Towrie
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX , UK
| | - Anthony W Parker
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX , UK
| | - Matthew J Baker
- WestCHEM , Department of Pure and Applied Chemistry , University of Strathclyde , Technology and Innovation Centre , 99 George Street , Glasgow , G1 1RD , UK
| | - Neil T Hunt
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
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