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Hawkins AP, Edmeades AE, Hutchison CDM, Towrie M, Howe RF, Greetham GM, Donaldson PM. Laser induced temperature-jump time resolved IR spectroscopy of zeolites. Chem Sci 2024; 15:3453-3465. [PMID: 38455000 PMCID: PMC10915812 DOI: 10.1039/d3sc06128k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
Combining pulsed laser heating and time-resolved infrared (TR-IR) absorption spectroscopy provides a means of initiating and studying thermally activated chemical reactions and diffusion processes in heterogeneous catalysts on timescales from nanoseconds to seconds. To this end, we investigated single pulse and burst laser heating in zeolite catalysts under realistic conditions using TR-IR spectroscopy. 1 ns, 70 μJ, 2.8 μm laser pulses from a Nd:YAG-pumped optical parametric oscillator were observed to induce temperature-jumps (T-jumps) in zeolite pellets in nanoseconds, with the sample cooling over 1-3 ms. By adopting a tightly focused beam geometry, T-jumps as large as 145 °C from the starting temperature were achieved, demonstrated through comparison of the TR-IR spectra with temperature dependent IR absorption spectra and three dimensional heat transfer modelling using realistic experimental parameters. The simulations provide a detailed understanding of the temperature distribution within the sample and its evolution over the cooling period, which we observe to be bi-exponential. These results provide foundations for determining the magnitude of a T-jump in a catalyst/adsorbate system from its absorption spectrum and physical properties, and for applying T-jump TR-IR spectroscopy to the study of reactive chemistry in heterogeneous catalysts.
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Affiliation(s)
- Alexander P Hawkins
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Amy E Edmeades
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Christopher D M Hutchison
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Russell F Howe
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE UK
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
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2
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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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3
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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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Howe CP, Greetham GM, Procacci B, Parker AW, Hunt NT. Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy. J Phys Chem B 2023; 127:1586-1597. [PMID: 36787177 PMCID: PMC9969394 DOI: 10.1021/acs.jpcb.2c08709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Time-resolved temperature-jump/drop infrared (IR) spectroscopy has been used to measure the impact of stem base sequence on the melting and refolding dynamics of ribonucleic acid (RNA) tetraloops. A series of three 12-nucleotide RNA hairpin sequences were studied, each featuring a UACG tetraloop motif and a double-stranded stem containing four base pairs. In each case, the stem comprised three GC pairs plus a single AU base pair inserted at the closing point of the loop (RNAloop), in the middle of the stem (RNAmid), or at the stem terminus (RNAend). Results from analogous DNA tetraloop (TACG) sequences were also obtained. Inclusion of AU or AT base pairs in the stem leads to faster melting of the stem-loop structure compared to a stem sequence featuring four GC base pairs while refolding times were found to be slower, consistent with a general reduction in stem-loop stability caused by the AU/AT pair. Independent measurement of the dynamic timescales for melting and refolding of ring vibrational modes of guanine (GR) and adenine (AR) provided position-specific insight into hairpin dynamics. The GR-derived data showed that DNA sequences melted more quickly (0.5 ± 0.1 to 0.7 ± 0.1 μs at 70 °C) than analogous RNA sequences (4.3 ± 0.4 to 4.4 ± 0.3 μs at 70 °C). Position-sensitive data from the AR modes suggests that DNA hairpins begin melting from the terminal end of the stem toward the loop while RNA sequences begin melting from the loop. Refolding timescales for both RNA and DNA hairpins were found to be similar (250 ± 50 μs at 70 °C) except for RNAend and DNAloop which refolded much more slowly (746 ± 36 and 430 ± 31 μs, respectively), showing that the refolding pathway is significantly impaired by the placement of AU/AT pairs at different points in the stem. We conclude that conformational changes of analogous pairs of RNA and DNA tetraloops proceed by different mechanisms.
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Affiliation(s)
- C P Howe
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - G M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, Oxon, U.K
| | - B Procacci
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - A W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, Oxon, U.K
| | - N T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
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Howe CP, Greetham GM, Procacci B, Parker AW, Hunt NT. Measuring RNA UNCG Tetraloop Refolding Dynamics Using Temperature-Jump/Drop Infrared Spectroscopy. J Phys Chem Lett 2022; 13:9171-9176. [PMID: 36166668 PMCID: PMC9549515 DOI: 10.1021/acs.jpclett.2c02338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Determining the structural dynamics of RNA and DNA is essential to understanding their cellular function, but direct measurement of strand association or folding remains experimentally challenging. Here we illustrate a temperature-jump/drop method able to reveal refolding dynamics. Time-resolved temperature-jump/drop infrared spectroscopy is used to measure the melting and refolding dynamics of a 12-nucleotide RNA sequence comprising a UACG tetraloop and a four-base-pair double-stranded GC stem, comparing them to an equivalent DNA (TACG) sequence. Stem-loop melting occurred an order of magnitude more slowly in RNA than DNA (6.0 ± 0.1 μs versus 0.8 ± 0.1 μs at 70 °C). In contrast, the refolding dynamics of both sequences occurred on similar time scales (200 μs). While the melting and refolding dynamics of RNA and DNA hairpins both followed Arrhenius temperature dependences, refolding was characterized by an apparent negative activation energy, consistent with a mechanism involving multiple misfolded intermediates prior to zipping of the stem base pairs.
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Affiliation(s)
- C. P. Howe
- Department
of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
| | - G. M. Greetham
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory,
Harwell Oxford, Didcot, Oxon OX11 0QX, U.K.
| | - B. Procacci
- Department
of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
| | - A. W. Parker
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory,
Harwell Oxford, Didcot, Oxon OX11 0QX, U.K.
| | - N. T. Hunt
- Department
of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
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Cole-Filipiak NC, Knepper R, Wood M, Ramasesha K. Mode-Selective Vibrational Energy Transfer Dynamics in 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) Thin Films. J Phys Chem A 2021; 125:7788-7802. [PMID: 34464533 DOI: 10.1021/acs.jpca.1c04800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The coupling of inter- and intramolecular vibrations plays a critical role in initiating chemistry during the shock-to-detonation transition in energetic materials. Herein, we report on the subpicosecond to subnanosecond vibrational energy transfer (VET) dynamics of the solid energetic material 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) by using broadband, ultrafast infrared transient absorption spectroscopy. Experiments reveal VET occurring on three distinct time scales: subpicosecond, 5 ps, and 200 ps. The ultrafast appearance of signal at all probed modes in the mid-infrared suggests strong anharmonic coupling of all vibrations in the solid, whereas the long-lived evolution demonstrates that VET is incomplete, and thus thermal equilibrium is not attained, even on the 100 ps time scale. Density functional theory and classical molecular dynamics simulations provide valuable insights into the experimental observations, revealing compression-insensitive time scales for the initial VET dynamics of high-frequency vibrations and drastically extended relaxation times for low-frequency phonon modes under lattice compression. Mode selectivity of the longest dynamics suggests coupling of the N-N and axial NO2 stretching modes with the long-lived, excited phonon bath.
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Affiliation(s)
- Neil C Cole-Filipiak
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Robert Knepper
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Mitchell Wood
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Krupa Ramasesha
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
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Dale J, Howe CP, Toncrova H, Fritzsch R, Greetham GM, Clark IP, Towrie M, Parker AW, McLeish TC, Hunt NT. Combining steady state and temperature jump IR spectroscopy to investigate the allosteric effects of ligand binding to dsDNA. Phys Chem Chem Phys 2021; 23:15352-15363. [PMID: 34254612 DOI: 10.1039/d1cp02233d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Changes in the structural dynamics of double stranded (ds)DNA upon ligand binding have been linked to the mechanism of allostery without conformational change, but direct experimental evidence remains elusive. To address this, a combination of steady state infrared (IR) absorption spectroscopy and ultrafast temperature jump IR absorption measurements has been used to quantify the extent of fast (∼100 ns) fluctuations in (ds)DNA·Hoechst 33258 complexes at a range of temperatures. Exploiting the direct link between vibrational band intensities and base stacking shows that the absolute magnitude of the change in absorbance caused by fast structural fluctuations following the temperature jump is only weakly dependent on the starting temperature of the sample. The observed fast dynamics are some two orders of magnitude faster than strand separation and associated with all points along the 10-base pair duplex d(GCATATATCC). Binding the Hoechst 33258 ligand causes a small but consistent reduction in the extent of these fast fluctuations of base pairs located outside of the ligand binding region. These observations point to a ligand-induced reduction in the flexibility of the dsDNA near the binding site, consistent with an estimated allosteric propagation length of 15 Å, about 5 base pairs, which agrees well with both molecular simulation and coarse-grained statistical mechanics models of allostery leading to cooperative ligand binding.
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Affiliation(s)
- Jessica Dale
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK.
| | - C Peter Howe
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK.
| | - Hedvika Toncrova
- Department of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Robby Fritzsch
- Department of Physics, SUPA, University of Strathclyde, Glasgow, G4 0NG, UK
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Ian P Clark
- 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
| | - Thomas C McLeish
- Department of Physics, University of York, Heslington, York YO10 5DD, UK.
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK.
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Edington SC, Liu S, Baiz CR. Infrared spectroscopy probes ion binding geometries. Methods Enzymol 2021; 651:157-191. [PMID: 33888203 DOI: 10.1016/bs.mie.2020.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Stephanie Liu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States.
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