1
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Casas AM, Idris NS, Wen V, Patterson JP, Ge NH. Scattering Elimination in 2D IR Immune from Detector Artifacts. J Phys Chem B 2024; 128:8835-8845. [PMID: 39188212 DOI: 10.1021/acs.jpcb.4c04220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Highly scattering samples, such as polymer droplets or solid-state powders, are difficult to study via coherent two-dimensional infrared (2D IR) spectroscopy. Previously, researchers have employed (quasi-) phase cycling, local-oscillator chopping, and polarization control to reduce scattering, but the latter method poses a limit on polarization-dependent measurements. Here, we present a method for Scattering Elimination Immune from Detector Artifacts (SEIFDA) in pump-probe 2D IR experiments. Our method extends the negative probe delay method of removing scattering from pump-probe spectroscopy to 2D experiments. SEIFDA works well for all polarizations when combined with the optimized noise reduction scheme to remove additive and multiplicative noise. We demonstrate that our method can be employed with any polarization scheme and reliably lowers the scattering at parallel polarization to comparable levels to the conventional 8-frame phase cycling with probe chopping (8FPCPC) at perpendicular polarization. Our system can acquire artifact free spectra in parallel polarization when the signal intensity is as little as 5% of the intensity of the interference between the pump pulses scattered into the detector. It reduces the time required to characterize the scattering term by at least 50% over 8FPCPC. Through detailed analysis of detector nonlinearity, we show that the performance of 8FPCPC can be improved by incorporating nonlinear correction factors, but it is still worse than that of SEIFDA. Application of SEIFDA to study the encapsulation of Nile red in polymer droplets demonstrates that this method will be very useful for probing highly scattering systems.
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Affiliation(s)
- Anneka Miller Casas
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Nehal S Idris
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Victor Wen
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Nien-Hui Ge
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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2
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Xie Q, Zhang Y, Janzen E, Edgar JH, Xu XG. Atomic-force-microscopy-based time-domain two-dimensional infrared nanospectroscopy. NATURE NANOTECHNOLOGY 2024; 19:1108-1115. [PMID: 38750165 DOI: 10.1038/s41565-024-01670-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/02/2024] [Indexed: 05/23/2024]
Abstract
For decades, infrared (IR) spectroscopy has advanced on two distinct frontiers: enhancing spatial resolution and broadening spectroscopic information. Although atomic force microscopy (AFM)-based IR microscopy overcomes Abbe's diffraction limit and reaches sub-10 nm spatial resolutions, time-domain two-dimensional IR spectroscopy (2DIR) provides insights into molecular structures, mode coupling and energy transfers. Here we bridge the boundary between these two techniques and develop AFM-2DIR nanospectroscopy. Our method offers the spatial precision of AFM in combination with the rich spectroscopic information provided by 2DIR. This approach mechanically detects the sample's photothermal responses to a tip-enhanced femtosecond IR pulse sequence and extracts spatially resolved spectroscopic information via FFTs. In a proof-of-principle experiment, we elucidate the anharmonicity of a carbonyl vibrational mode. Further, leveraging the near-field photons' high momenta from the tip enhancement for phase matching, we photothermally probe hyperbolic phonon polaritons in isotope-enriched h10BN. Our measurements unveil an energy transfer between phonon polaritons and phonons, as well as among different polariton modes, possibly aided by scattering at interfaces. The AFM-2DIR nanospectroscopy enables the in situ investigations of vibrational anharmonicity, coupling and energy transfers in heterogeneous materials and nanostructures, especially suitable for unravelling the relaxation process in two-dimensional materials at IR frequencies.
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Affiliation(s)
- Qing Xie
- Department of Chemistry, Lehigh University, Bethlehem, PA, US
| | - Yu Zhang
- Ames National Laboratory, Iowa State University, Ames, IA, US
| | - Eli Janzen
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS, US
| | - James H Edgar
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS, US
| | - Xiaoji G Xu
- Department of Chemistry, Lehigh University, Bethlehem, PA, US.
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3
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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4
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Madzharova F, Chatterley AS, Roeters SJ, Weidner T. Probing Backbone Coupling within Hydrated Proteins with Two-Color 2D Infrared Spectroscopy. J Phys Chem Lett 2024:4933-4939. [PMID: 38686860 DOI: 10.1021/acs.jpclett.4c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The vibrational coupling between protein backbone modes and the role of water interactions are important topics in biomolecular spectroscopy. Our work reports the first study of the coupling between amide I and amide A modes within peptides and proteins with secondary structure and water contacts. We use two-color two-dimensional infrared (2D IR) spectroscopy and observe cross peaks between amide I and amide A modes. In experiments with peptides with different secondary structures and side chains, we observe that the spectra are sensitive to secondary structure. Water interactions affect the cross peaks, which may be useful as probes for the accessibility of protein sites to hydration water. Moving to two-color 2D IR spectra of proteins, the data demonstrate that the cross peaks integrate the sensitivities of both amide I and amide A spectra and that a two-color detection scheme may be a promising tool for probing secondary structures in proteins.
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Affiliation(s)
- Fani Madzharova
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Adam S Chatterley
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Steven J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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5
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Jonušas M, Bournet Q, Bonvalet A, Natile M, Guichard F, Zaouter Y, Georges P, Druon F, Hanna M, Joffre M. Chirped pulse upconversion for femtosecond mid-infrared spectroscopy at 100 kHz. OPTICS EXPRESS 2024; 32:8020-8029. [PMID: 38439469 DOI: 10.1364/oe.515291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
We demonstrate that chirped pulse up-conversion (CPU), a method routinely used with systems based on 1-kHz Titanium:Sapphire lasers, can be extended to a repetition rate of 100 kHz with an Ytterbium diode-pumped femtosecond amplifier. Individual mid-infrared spectra can thus be measured directly in the near infrared using a fast CMOS linescan camera. After an appropriate Fourier processing, a spectral resolution of 1.1 cm-1 is reported, currently limited by our spectrometer. Additionally, we demonstrate the application of CPU to a pump-probe measurement of the vibrational relaxation in carboxy-hemoglobin, and we show that the combination of fast scanning and fast acquisition enables a straightforward removal of pump scattering interference.
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6
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Procacci B, Wrathall SLD, Farmer AL, Shaw DJ, Greetham GM, Parker AW, Rippers Y, Horch M, Lynam JM, Hunt NT. Understanding the [NiFe] Hydrogenase Active Site Environment through Ultrafast Infrared and 2D-IR Spectroscopy of the Subsite Analogue K[CpFe(CO)(CN) 2] in Polar and Protic Solvents. J Phys Chem B 2024; 128:1461-1472. [PMID: 38301127 PMCID: PMC10875664 DOI: 10.1021/acs.jpcb.3c07965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
The [CpFe(CO)(CN)2]- unit is an excellent structural model for the Fe(CO)(CN)2 moiety of the active site found in [NiFe] hydrogenases. Ultrafast infrared (IR) pump-probe and 2D-IR spectroscopy have been used to study K[CpFe(CO)(CN)2] (M1) in a range of protic and polar solvents and as a dry film. Measurements of anharmonicity, intermode vibrational coupling strength, vibrational relaxation time, and solvation dynamics of the CO and CN stretching modes of M1 in H2O, D2O, methanol, dimethyl sulfoxide, and acetonitrile reveal that H-bonding to the CN ligands plays an important role in defining the spectroscopic characteristics and relaxation dynamics of the Fe(CO)(CN)2 unit. Comparisons of the spectroscopic and dynamic data obtained for M1 in solution and in a dry film with those obtained for the enzyme led to the conclusion that the protein backbone forms an important part of the bimetallic active site environment via secondary coordination sphere interactions.
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Affiliation(s)
- Barbara Procacci
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Solomon L. D. Wrathall
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Amy L. Farmer
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Daniel J. Shaw
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Yvonne Rippers
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Marius Horch
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jason M. Lynam
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Neil T. Hunt
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
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7
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Rutherford S, Hutchison CDM, Greetham GM, Parker AW, Nordon A, Baker MJ, Hunt NT. Optical Screening and Classification of Drug Binding to Proteins in Human Blood Serum. Anal Chem 2023; 95:17037-17045. [PMID: 37939225 PMCID: PMC10666086 DOI: 10.1021/acs.analchem.3c03713] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
Protein-drug interactions in the human bloodstream are important factors in applications ranging from drug design, where protein binding influences efficacy and dose delivery, to biomedical diagnostics, where rapid, quantitative measurements could guide optimized treatment regimes. Current measurement approaches use multistep assays, which probe the protein-bound drug fraction indirectly and do not provide fundamental structural or dynamic information about the in vivo protein-drug interaction. We demonstrate that ultrafast 2D-IR spectroscopy can overcome these issues by providing a direct, label-free optical measurement of protein-drug binding in blood serum samples. Four commonly prescribed drugs, known to bind to human serum albumin (HSA), were added to pooled human serum at physiologically relevant concentrations. In each case, spectral changes to the amide I band of the serum sample were observed, consistent with binding to HSA, but were distinct for each of the four drugs. A machine-learning-based classification of the serum samples achieved a total cross-validation prediction accuracy of 92% when differentiating serum-only samples from those with a drug present. Identification on a per-drug basis achieved correct drug identification in 75% of cases. These unique spectroscopic signatures of the drug-protein interaction thus enable the detection and differentiation of drug containing samples and give structural insight into the binding process as well as quantitative information on protein-drug binding. Using currently available instrumentation, the 2D-IR data acquisition required just 1 min and 10 μL of serum per sample, and so these results pave the way to fast, specific, and quantitative measurements of protein-drug binding in vivo with potentially invaluable applications for the development of novel therapies and personalized medicine.
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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, U.K.
| | - Christopher D. M. Hutchison
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Alison Nordon
- WestCHEM,
Department of Pure and Applied Chemistry and CPACT, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Matthew J. Baker
- School
of Medicine and Dentistry, University of
Central Lancashire, Fylde Rd, Preston PR1
2HE, 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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8
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Ma Z, Chen L, Xu C, Fournier JA. Two-Dimensional Infrared Spectroscopy of Isolated Molecular Ions. J Phys Chem Lett 2023; 14:9683-9689. [PMID: 37871134 DOI: 10.1021/acs.jpclett.3c02661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Two-dimensional infrared (2D IR) spectroscopy of mass-selected, cryogenically cooled molecular ions is presented. Nonlinear response pathways, encoded in the time-domain photodissociation action response of weakly bound N2 messenger tags, were isolated using pulse shaping techniques following excitation with four collinear ultrafast IR pulses. 2D IR spectra of Re(CO)3(CH3CN)3+ ions capture off-diagonal cross-peak bleach signals between the asymmetric and symmetric carbonyl stretching transitions. These cross peaks display intensity variations as a function of pump-probe delay time due to coherent coupling between the vibrational modes. Well-resolved 2D IR features in the congested fingerprint region of protonated caffeine (C8H10N4O2H+) are also reported. Importantly, intense cross-peak signals were observed at 3 ps waiting time, indicating that tag-loss dynamics are not competing with the measured nonlinear signals. These demonstrations pave the way for more precise studies of molecular interactions and dynamics that are not easily obtainable with current condensed-phase methodologies.
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Affiliation(s)
- Zifan Ma
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Liangyi Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Chuzhi Xu
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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9
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Unnikrishnan AC, Balamurugan K, Shanmugam G. Structural Insights into the Amyloid Fibril Polymorphism Using an Isotope-Edited Vibrational Circular Dichroism Study at the Amino Acid Residue Level. J Phys Chem B 2023; 127:7674-7684. [PMID: 37667494 DOI: 10.1021/acs.jpcb.3c03437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Polymorphism is common in both in vitro and in vivo amyloid fibrils formed by the same peptide/protein. However, the differences in their self-assembled structures at the amino acid level remain poorly understood. In this study, we utilized isotope-edited vibrational circular dichroism (VCD) on a well-known amyloidogenic peptide fragment (N22FGAIL27) of human islet amyloid polypeptide (IAPf) to investigate the structural polymorphism. Two individual isotope-labeled IAPf peptides were used, with a 13C label on the carbonyl group of phenylalanine (IAPf-F) and glycine (IAPf-G). We compared the amyloid-like nanofibril of IAPf induced by solvent casting (fibril B) with our previous report on the same IAPf peptide fibril but with a different fibril morphology (fibril A) formed in an aqueous buffer solution. Fibril B consisted of entangled, laterally fused amyloid-like nanofibrils with a relatively shorter diameter (15-50 nm) and longer length (several microns), while fibril A displayed nanofibrils with a higher diameter (30-60 nm) and shorter length (500 nm-2 μm). The isotope-edited VCD analysis indicated that fibrils B consisted of anti-parallel β-sheet arrangements with glycine residues in the registry and phenylalanine residues out of the registry, which was significantly different from fibrils A, where a mixture of parallel β-sheet and turn structure with the registry at phenylalanine and glycine residues was observed. The VCD analysis, therefore, suggests that polymorphism in amyloid-like fibrils can be attributed to the difference in the packing/arrangement of the individual β-strands in the β-sheet and the difference in the amino acid registry. Our findings provide insights into the structural aspects of fibril polymorphism related to various amyloid diseases and may aid in designing amyloid fibril inhibitors for therapeutic purposes.
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Affiliation(s)
- Anagha C Unnikrishnan
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research (CSIR)─Central Leather Research Institute (CLRI), Adyar, Chennai 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kanagasabai Balamurugan
- Centre for High Computing, Council of Scientific and Industrial Research (CSIR)─Central Leather Research Institute (CLRI), Adyar, Chennai 600020, India
| | - Ganesh Shanmugam
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research (CSIR)─Central Leather Research Institute (CLRI), Adyar, Chennai 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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10
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Aerts A, Jolly SW, Kockaert P, Gorza SP, Auwera JV, Vaeck N. Modulated super-Gaussian laser pulse to populate a dark rovibrational state of acetylene. J Chem Phys 2023; 159:084303. [PMID: 37638622 DOI: 10.1063/5.0160526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023] Open
Abstract
A pulse-shaping technique in the mid-infrared spectral range based on pulses with a super-Gaussian temporal profile is considered for laser control. We show a realistic and efficient path to the population of a dark rovibrational state in acetylene (C2H2). The laser-induced dynamics in C2H2 are simulated using fully experimental structural parameters. Indeed, the rotation-vibration energy structure, including anharmonicities, is defined by the global spectroscopic Hamiltonian for the ground electronic state of C2H2 built from the extensive high-resolution spectroscopy studies on the molecule, transition dipole moments from intensities, and the effects of the (inelastic) collisions that are parameterized from line broadenings using the relaxation matrix [A. Aerts, J. Vander Auwera, and N. Vaeck, J. Chem. Phys. 154, 144308 (2021)]. The approach, based on an effective Hamiltonian, outperforms today's ab initio computations both in terms of accuracy and computational cost for this class of molecules. With such accuracy, the Hamiltonian permits studying the inner mechanism of theoretical pulse shaping [A. Aerts et al., J. Chem. Phys. 156, 084302 (2022)] for laser quantum control. Here, the generated control pulse presents a number of interferences that take advantage of the control mechanism to populate the dark state. An experimental setup is proposed for in-laboratory investigation.
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Affiliation(s)
- Antoine Aerts
- Université Libre de Bruxelles, Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), 50 Avenue F. Roosevelt, C.P. 160/09, Brussels 1050, Belgium
| | - Spencer W Jolly
- Université Libre de Bruxelles, OPERA-Photonique, 50 Avenue F. Roosevelt, C.P. 194/05, Brussels 1050, Belgium
| | - Pascal Kockaert
- Université Libre de Bruxelles, OPERA-Photonique, 50 Avenue F. Roosevelt, C.P. 194/05, Brussels 1050, Belgium
| | - Simon-Pierre Gorza
- Université Libre de Bruxelles, OPERA-Photonique, 50 Avenue F. Roosevelt, C.P. 194/05, Brussels 1050, Belgium
| | - Jean Vander Auwera
- Université Libre de Bruxelles, Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), 50 Avenue F. Roosevelt, C.P. 160/09, Brussels 1050, Belgium
| | - Nathalie Vaeck
- Université Libre de Bruxelles, Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), 50 Avenue F. Roosevelt, C.P. 160/09, Brussels 1050, Belgium
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11
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Huang-Fu ZC, Qian Y, Deng GH, Zhang T, Schmidt S, Brown J, Rao Y. Development of Two-Dimensional Electronic-Vibrational Sum Frequency Generation (2D-EVSFG) for Vibronic and Solvent Couplings of Molecules at Interfaces and Surfaces. ACS PHYSICAL CHEMISTRY AU 2023; 3:374-385. [PMID: 37520317 PMCID: PMC10375875 DOI: 10.1021/acsphyschemau.3c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 08/01/2023]
Abstract
Many photoinduced excited states' relaxation processes and chemical reactions occur at interfaces and surfaces, including charge transfer, energy transfer, proton transfer, proton-coupled electron transfer, configurational dynamics, conical intersections, etc. Of them, interactions of electronic and vibrational motions, namely, vibronic couplings, are the main determining factors for the relaxation processes or reaction pathways. However, time-resolved electronic-vibrational spectroscopy for interfaces and surfaces is lacking. Here we develop interface/surface-specific two-dimensional electronic-vibrational sum frequency generation spectroscopy (2D-EVSFG) for time-dependent vibronic coupling of excited states at interfaces and surfaces. We further demonstrate the fourth-order technique by investigating vibronic coupling, solvent correlation, and time evolution of the coupling for photoexcited interface-active molecules, crystal violet (CV), at the air/water interface as an example. The two vibronic absorption peaks for CV molecules at the interface from the 2D-EVSFG experiments were found to be more prominent than their counterparts in bulk from 2D-EV. Quantitative analysis of the vibronic peaks in 2D-EVSFG suggested that a non-Condon process participates in the photoexcitation of CV at the interface. We further reveal vibrational solvent coupling for the zeroth level on the electronic state with respect to that on the ground state, which is directly related to the magnitude of its change in solvent reorganization energy. The change in the solvent reorganization energy at the interface is much smaller than that in bulk methanol. Time-dependent center line slopes (CLSs) of 2D-EVSFG also showed that kinetic behaviors of CV at the air/water interface are significantly different from those in bulk methanol. Our ultrafast 2D-EVSFG experiments not only offer vibrational information on both excited states and the ground state as compared with the traditional doubly resonant sum frequency generation and electronic-vibrational coupling but also provide vibronic coupling, dynamical solvent effects, and time evolution of vibronic coupling at interfaces.
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12
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Man VH, He X, Nguyen PH, Sagui C, Roland C, Xie XQ, Wang J. Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation. Comput Biol Med 2023; 159:106902. [PMID: 37086661 PMCID: PMC10186340 DOI: 10.1016/j.compbiomed.2023.106902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/07/2023] [Accepted: 04/09/2023] [Indexed: 04/24/2023]
Abstract
The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Phuong H Nguyen
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005, Paris, France
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC, 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC, 27695-8202, USA
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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13
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Chenchiliyan M, Kübel J, Ooi SA, Salvadori G, Mennucci B, Westenhoff S, Maj M. Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy. J Chem Phys 2023; 158:085103. [PMID: 36859103 DOI: 10.1063/5.0135268] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm-1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.
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Affiliation(s)
- Manoop Chenchiliyan
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michał Maj
- Department of Chemistry-Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
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14
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Yang H, Yuan P, Wu Y, Shi M, Caro CD, Tengeiji A, Yamanoi S, Inoue M, DeGrado WF, Condello C. EMBER multi-dimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526692. [PMID: 36778268 PMCID: PMC9915571 DOI: 10.1101/2023.02.01.526692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
In neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. However, there is a need to rapidly identify amyloid conformations in situ . Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strains in vitro , as well as Aβ deposits in different transgenic mouse models. Our EMBER (excitation multiplexed bright emission recording) imaging method rapidly identifies conformational differences in Aβ and tau deposits from Down syndrome, sporadic and familial Alzheimer's disease human brain slices. EMBER has in situ identified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick's disease. In future studies, EMBER should enable high-throughput measurements of the fidelity of strain transmission in cellular and animal neurodegenerative diseases models, time course of amyloid strain propagation, and identification of pathogenic versus benign strains. Significance In neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. There is a need to rapidly identify these amyloid conformations in situ . Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strains in vitro , as well as Aβ deposits in different transgenic mouse models. Our imaging method rapidly identifies conformational differences in Aβ and tau deposits from Down syndrome, sporadic and familial Alzheimer's disease human brain slices. We also identified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick's disease. These findings will facilitate the identification of pathogenic protein aggregates to guide research and treatment of protein misfolding diseases.
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Affiliation(s)
- Hyunjun Yang
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA 94158
| | - Peng Yuan
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA 94158
| | - Marie Shi
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
| | - Christoffer D Caro
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
| | | | | | | | - William F DeGrado
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA 94158
| | - Carlo Condello
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, CA 94143
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15
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Rutherford SH, Baker MJ, Hunt NT. 2D-IR spectroscopy of proteins in H 2O-A Perspective. J Chem Phys 2023; 158:030901. [PMID: 36681646 DOI: 10.1063/5.0129480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The form of the amide I infrared absorption band provides a sensitive probe of the secondary structure and dynamics of proteins in the solution phase. However, the frequency coincidence of the amide I band with the bending vibrational mode of H2O has necessitated the widespread use of deuterated solvents. Recently, it has been demonstrated that ultrafast 2D-IR spectroscopy allows the detection of the protein amide I band in H2O-based fluids, meaning that IR methods can now be applied to study proteins in physiologically relevant solvents. In this perspective, we describe the basis of the 2D-IR method for observing the protein amide I band in H2O and show how this development has the potential to impact areas ranging from our fundamental appreciation of protein structural dynamics to new applications for 2D-IR spectroscopy in the analytical and biomedical sciences. In addition, we discuss how the spectral response of water, rather than being a hindrance, now provides a basis for new approaches to data pre-processing, standardization of 2D-IR data collection, and signal quantification. Ultimately, we visualize a direction of travel toward the creation of 2D-IR spectral libraries that can be linked to advanced computational methods for use in high-throughput protein screening and disease diagnosis.
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Affiliation(s)
- Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Matthew J Baker
- School of Medicine, Faculty of Clinical Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, United Kingdom
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16
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Al-Mualem ZA, Chen X, Shirley JC, Xu C, Baiz CR. BoxCARS 2D IR spectroscopy with pulse shaping. OPTICS EXPRESS 2023; 31:2700-2709. [PMID: 36785278 PMCID: PMC10018786 DOI: 10.1364/oe.471984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 06/18/2023]
Abstract
BoxCARS and pump-probe geometries are common implementations of two-dimensional infrared (2D IR) spectroscopy. BoxCARS is background-free, generally offering greater signal-to-noise ratio, which enables measuring weak vibrational echo signals. Pulse shapers have been implemented in the pump-probe geometry to accelerate data collection and suppress scatter and other unwanted signals by precise control of the pump-pulse delay and carrier phase. Here, we introduce a 2D-IR optical setup in the BoxCARS geometry that implements a pulse shaper for rapid acquisition of background-free 2D IR spectra. We show a signal-to-noise improvement using this new fast-scan BoxCARS setup versus the pump-probe geometry within the same configuration.
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Affiliation(s)
- Ziareena A. Al-Mualem
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
- Authors contributed equally
| | - Xiaobing Chen
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
- Authors contributed equally
| | - Joseph C. Shirley
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
| | - Cong Xu
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, 105 E 24th Street, Austin, TX 78712, USA
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17
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Russo M, McGhee KE, Virgili T, Lidzey DG, Cerullo G, Maiuri M. Dephasing Processes in the Molecular Dye Lumogen-F Orange Characterized by Two-Dimensional Electronic Spectroscopy. Molecules 2022; 27:7095. [PMID: 36296684 PMCID: PMC9607445 DOI: 10.3390/molecules27207095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
Abstract
Molecular dyes are finding more and more applications in photonics and quantum technologies, such as polaritonic optical microcavities, organic quantum batteries and single-photon emitters for quantum sensing and metrology. For all these applications, it is of crucial importance to characterize the dephasing mechanisms. In this work we use two-dimensional electronic spectroscopy (2DES) to study the temperature dependent dephasing processes in the prototypical organic dye Lumogen-F orange. We model the 2DES maps using the Bloch equations for a two-level system and obtain a dephasing time T2 = 53 fs at room temperature, which increases to T2 = 94 fs at 86 K. Furthermore, spectral diffusion processes are observed and modeled by a combination of underdamped and overdamped Brownian oscillators. Our results provide useful design parameters for advanced optoelectronic and photonic devices incorporating dye molecules.
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Affiliation(s)
- Mattia Russo
- Physics Department, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
- Institute for Photonics and Nanotechnologies (IFN), National Research Council-CNR, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Kirsty E. McGhee
- Department of Physics and Astronomy, The University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH, UK
| | - Tersilla Virgili
- Institute for Photonics and Nanotechnologies (IFN), National Research Council-CNR, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - David G. Lidzey
- Department of Physics and Astronomy, The University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH, UK
| | - Giulio Cerullo
- Physics Department, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
- Institute for Photonics and Nanotechnologies (IFN), National Research Council-CNR, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Margherita Maiuri
- Physics Department, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
- Institute for Photonics and Nanotechnologies (IFN), National Research Council-CNR, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
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18
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Chatterjee S, Nam Y, Salimi A, Lee JY. Monitoring early-stage β-amyloid dimer aggregation by histidine site-specific two-dimensional infrared spectroscopy in a simulation study. Phys Chem Chem Phys 2022; 24:18691-18702. [PMID: 35899740 DOI: 10.1039/d2cp02479a] [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
Monitoring early-stage β-amyloid (Aβ) dimerization is a formidable challenge for understanding neurological diseases. We compared β-sheet formation and histidine site-specific two-dimensional infrared (2D IR) spectroscopic signatures of Aβ dimers with different histidine states (δ; Nδ1-H, ε; Nε2-H, or π; both protonated). Molecular dynamics (MD) simulations revealed that β-sheet formation is favored for the δδδ:δδδ and πππ:πππ tautomeric isomers showing strong couplings and frequent contacts between the central hydrophobic core and C-terminus compared with the εεε:εεε isomer. Characteristic blue-shifts in the 2D IR central bands were observed upon monomer-dimer transformation. The εεε:εεε dimer exhibited larger frequency shifts than δδδ:δδδ and πππ:πππ implying that the red-shift may have a correlation with Nδ1-H(δ) protonation. Our results support the tautomerization/protonation hypothesis that attributes Aβ misfolding to histidine tautomers as a possible primary initiator for Aβ aggregation and facilitates the application of histidine site-specific 2D IR spectroscopy for studying early-stage Aβ self-assembly.
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Affiliation(s)
| | - Yeonsig Nam
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea. .,Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea.
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea.
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19
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Aerts A, Kockaert P, Gorza SP, Brown A, Vander Auwera J, Vaeck N. Laser control of a dark vibrational state of acetylene in the gas phase—Fourier transform pulse shaping constraints and effects of decoherence. J Chem Phys 2022; 156:084302. [DOI: 10.1063/5.0080332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We propose a methodology to tackle the laser control of a non-stationary dark ro-vibrational state of acetylene (C2H2), given realistic experimental limitations in the 7.7 μm (1300 cm−1) region. Simulations are performed using the Lindblad master equation, where the so-called Lindblad parameters are used to describe the effect of the environment in the dilute gas phase. A phenomenological representation of the parameters is used, and they are extracted from high-resolution spectroscopy line broadening data. An effective Hamiltonian is used for the description of the system down to the rotational level close to experimental accuracy. The quality of both the Hamiltonian and Lindblad parameters is assessed by a comparison of a calculated infrared spectrum with the available experimental data. A single shaped laser pulse is used to perform the control, where elements of optics and pulse shaping using masks are introduced with emphasis on experimental limitations. The optimization procedure, based on gradients, explicitly takes into account the experimental constraints. Control performances are reported for shaping masks of increasing complexity. Although modest performances are obtained, mainly due to the strong pulse shaping constraints, we gain insights into the control mechanism. This work is the first step toward the conception of a realistic experiment that will allow for population characterization and manipulation of a non-stationary vibrational “dark” state. Effects of the collisions on the laser control in the dilute gas phase, leading to decoherence in the molecular system, are clearly shown.
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Affiliation(s)
- Antoine Aerts
- Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), Université Libre de Bruxelles, 50 Avenue F. Roosevelt, C.P. 160/09, B-1050 Brussels, Belgium
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pascal Kockaert
- OPERA-Photonique, Université Libre de Bruxelles, 50 Avenue F. Roosevelt, C.P. 194/05, B-1050 Brussels, Belgium
| | - Simon-Pierre Gorza
- OPERA-Photonique, Université Libre de Bruxelles, 50 Avenue F. Roosevelt, C.P. 194/05, B-1050 Brussels, Belgium
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jean Vander Auwera
- Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), Université Libre de Bruxelles, 50 Avenue F. Roosevelt, C.P. 160/09, B-1050 Brussels, Belgium
| | - Nathalie Vaeck
- Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), Université Libre de Bruxelles, 50 Avenue F. Roosevelt, C.P. 160/09, B-1050 Brussels, Belgium
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20
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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]
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21
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A polarization scheme that resolves cross-peaks with transient absorption and eliminates diagonal peaks in 2D spectroscopy. Proc Natl Acad Sci U S A 2022; 119:2117398119. [PMID: 35115405 PMCID: PMC8833161 DOI: 10.1073/pnas.2117398119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 11/18/2022] Open
Abstract
Two-dimensional (2D) optical spectroscopy contains cross-peaks that are helpful features for determining molecular structure and monitoring energy transfer, but they can be difficult to resolve from the much more intense diagonal peaks. Transient absorption (TA) spectra contain transitions similar to cross-peaks in 2D spectroscopy, but in most cases they are obscured by the bleach and stimulated emission peaks. We report a polarization scheme, <0°,0°,+θ2(t2),-θ2(t2)>, that can be easily implemented in the pump-probe beam geometry, used most frequently in 2D and TA spectroscopy. This scheme removes the diagonal peaks in 2D spectroscopies and the intense bleach/stimulated emission peaks in TA spectroscopies, thereby resolving the cross-peak features. At zero pump-probe delay, θ2 = 60° destructively interferes two Feynman paths, eliminating all signals generated by field interactions with four parallel transition dipoles, and the intense diagonal and bleach/stimulated emission peaks. At later delay times, θ2(t2) is adjusted to compensate for anisotropy caused by rotational diffusion. When implemented with TA spectroscopy or microscopy, the pump-probe spectrum is dominated by the cross-peak features. The local oscillator is also attenuated, which enhances the signal two times. This overlooked polarization scheme reduces spectral congestion by eliminating diagonal peaks in 2D spectra and enables TA spectroscopy to measure similar information given by cross-peaks in 2D spectroscopy.
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22
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Abstract
Phenol soluble modulins (PSMs) are an important class of peptides secreted by Staphylococcus aureus bacteria. The toxicity to human cells and unique ability of one such peptide, PSMα3, to aggregate into an α-helical amyloid-like structure may hold a key to a better understanding of the virulence of dangerous pathogens such as methicillin resistant S. aureus. In reporting a detailed two-dimensional infrared (2DIR) analysis of PSMα3, we found direct evidence of multiple aggregate architectures existing in equilibrium with one another. We also discovered a unique and characteristic 2DIR spectroscopic signature that unambiguously reports on the presence of the unusual and highly cytotoxic cross-α amyloid structure. The formation of ordered cross-β amyloid protein aggregates is associated with a variety of human disorders. While conventional infrared methods serve as sensitive reporters of the presence of these amyloids, the recently discovered amyloid secondary structure of cross-α fibrils presents new questions and challenges. Herein, we report results using Fourier transform infrared spectroscopy and two-dimensional infrared spectroscopy to monitor the aggregation of one such cross-α–forming peptide, phenol soluble modulin alpha 3 (PSMα3). Phenol soluble modulins (PSMs) are involved in the formation and stabilization of Staphylococcus aureus biofilms, making sensitive methods of detecting and characterizing these fibrils a pressing need. Our experimental data coupled with spectroscopic simulations reveals the simultaneous presence of cross-α and cross-β polymorphs within samples of PSMα3 fibrils. We also report a new spectroscopic feature indicative of cross-α fibrils.
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23
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Weng W, Weberg AB, Gera R, Tomson NC, Anna JM. Probing Ligand Effects on the Ultrafast Dynamics of Copper Complexes via Midinfrared Pump-Probe and 2DIR Spectroscopies. J Phys Chem B 2021; 125:12228-12241. [PMID: 34723540 DOI: 10.1021/acs.jpcb.1c06370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of ligand structural variation on the ultrafast dynamics of a series of copper coordination complexes were investigated using polarization-dependent mid-IR pump-probe spectroscopy and two-dimensional infrared (2DIR) spectroscopy. The series consists of three copper complexes [(R3P3tren)CuIIN3]BAr4F (1PR3, R3P3tren = tris[2-(phosphiniminato)ethyl]amine, BAr4F = tetrakis(pentafluorophenyl)borate) where the number of methyl and phenyl groups in the PR3 ligand are systematically varied across the series (PR3 = PMe3, PMe2Ph, PMePh2). The asymmetric stretching mode of azide in the 1PR3 series is used as a vibrational probe of the small-molecule binding site. The results of the pump-probe measurements indicate that the vibrational energy of azide dissipates through intramolecular pathways and that the bulkier phenyl groups lead to an increase in the spatial restriction of the diffusive reorientation of bound azide. From 2DIR experiments, we characterize the spectral diffusion of the azide group and find that an increase in the number of phenyl groups maps to a broader inhomogeneous frequency distribution (Δ2). This indicates that an increase in the steric bulk of the secondary coordination sphere acts to create more distinct configurations in the local environment that are accessible to the azide group. This work demonstrates how ligand structural variation affects the ultrafast dynamics of a small molecular group bound to the metal center, which could provide insight into the structure-function relationship of the copper coordination complexes and transition-metal coordination complexes in general.
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Affiliation(s)
- Wei Weng
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alexander B Weberg
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul Gera
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Neil C Tomson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jessica M Anna
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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24
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Kübel J, Westenhoff S, Maj M. Giving voice to the weak: Application of active noise reduction in transient infrared spectroscopy. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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25
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Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen H, Huang S. Allosteric Switching of Calmodulin in a
Mycobacterium smegmatis
porin A (MspA) Nanopore‐Trap. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Tiezheng Pan
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
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26
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Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen HY, Huang S. Allosteric Switching of Calmodulin in a Mycobacterium smegmatis porin A (MspA) Nanopore-Trap. Angew Chem Int Ed Engl 2021; 60:23863-23870. [PMID: 34449124 DOI: 10.1002/anie.202110545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/21/2021] [Indexed: 01/23/2023]
Abstract
Recent developments concerning large protein nanopores suggest a new approach to structure profiling of native folded proteins. In this work, the large vestibule of Mycobacterium smegmatis porin A (MspA) and calmodulin (CaM), a Ca2+ -binding protein, were used in the direct observation of the protein structure. Three conformers, including the Ca2+ -free, Ca2+ -bound, and target peptide-bound states of CaM, were unambiguously distinguished. A disease related mutant, CaM D129G was also discriminated by MspA, revealing how a single amino acid replacement can interfere with the Ca2+ -binding capacity of the whole protein. The binding capacity and aggregation effect of CaM induced by different ions (Mg2+ /Sr2+ /Ba2+ /Ca2+ /Pb2+ /Tb3+ ) were also investigated and the stability of MspA in extreme conditions was evaluated. This work demonstrates the most systematic single-molecule investigation of different allosteric conformers of CaM, acknowledging the high sensing resolution offered by the MspA nanopore trap.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Tiezheng Pan
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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27
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Agathangelou D, Javed A, Sessa F, Solinas X, Joffre M, Ogilvie JP. Phase-modulated rapid-scanning fluorescence-detected two-dimensional electronic spectroscopy. J Chem Phys 2021; 155:094201. [PMID: 34496582 DOI: 10.1063/5.0057649] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a rapid-scanning approach to fluorescence-detected two-dimensional electronic spectroscopy that combines acousto-optic phase-modulation with digital lock-in detection. This approach shifts the signal detection window to suppress 1/f laser noise and enables interferometric tracking of the time delays to allow for correction of spectral phase distortions and accurate phasing of the data. This use of digital lock-in detection enables acquisition of linear and nonlinear signals of interest in a single measurement. We demonstrate the method on a laser dye, measuring the linear fluorescence excitation spectrum as well as rephasing, non-rephasing, and absorptive fluorescence-detected two-dimensional electronic spectra.
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Affiliation(s)
- Damianos Agathangelou
- Department of Physics and Biophysics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Ariba Javed
- Department of Physics and Biophysics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Francesco Sessa
- Department of Physics and Biophysics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Xavier Solinas
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Manuel Joffre
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Jennifer P Ogilvie
- Department of Physics and Biophysics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
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28
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Tumbic GW, Hossan MY, Thielges MC. Protein Dynamics by Two-Dimensional Infrared Spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:299-321. [PMID: 34314221 PMCID: PMC8713465 DOI: 10.1146/annurev-anchem-091520-091009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.
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Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
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29
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Tiwari V. Multidimensional electronic spectroscopy in high-definition-Combining spectral, temporal, and spatial resolutions. J Chem Phys 2021; 154:230901. [PMID: 34241275 DOI: 10.1063/5.0052234] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Over the past two decades, coherent multidimensional spectroscopies have been implemented across the terahertz, infrared, visible, and ultraviolet regions of the electromagnetic spectrum. A combination of coherent excitation of several resonances with few-cycle pulses, and spectral decongestion along multiple spectral dimensions, has enabled new insights into wide ranging molecular scale phenomena, such as energy and charge delocalization in natural and artificial light-harvesting systems, hydrogen bonding dynamics in monolayers, and strong light-matter couplings in Fabry-Pérot cavities. However, measurements on ensembles have implied signal averaging over relevant details, such as morphological and energetic inhomogeneity, which are not rephased by the Fourier transform. Recent extension of these spectroscopies to provide diffraction-limited spatial resolution, while maintaining temporal and spectral information, has been exciting and has paved a way to address several challenging questions by going beyond ensemble averaging. The aim of this Perspective is to discuss the technological developments that have eventually enabled spatially resolved multidimensional electronic spectroscopies and highlight some of the very recent findings already made possible by introducing spatial resolution in a powerful spectroscopic tool.
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Affiliation(s)
- Vivek Tiwari
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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30
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Zhu J, Wang J, Wang G, Zhang J, Tao W, Liu C, Liu M, Zhang H, Xie R, Ye F, Liu Y, Fang W, Chen X, Li Y. Precise Identification of the Dimethyl Sulfoxide Triggered Tricarbonyldichlororuthenium(II) Dimer for Releasing CO. J Phys Chem Lett 2021; 12:4658-4665. [PMID: 33978423 DOI: 10.1021/acs.jpclett.1c00905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Low concentrations of carbon monoxide (CO) can play vital roles in pharmacological and physiological functions in the human body. The transition-metal carbonyl complexes of the tricarbonyldichlororuthenium(II) dimer [Ru2(CO)6Cl4 (CORM-2)] were proposed as CO-releasing molecules (CORMs) to improve the delivery efficiency of CO for therapeutic effects. The accurate identification of final products for CORMs in solution and the detailed mechanisms of the release of CO were the essential prerequisite for its effective physiological application, which have been deficient. In this study, utilizing the cutting-edge two-dimensional (2D) IR spectroscopy, with the intrinsic vibrational modes and the coupling information on dynamics of intramolecular vibrational energy redistribution (IVR), the final products of A, B, C, and E are accurately identified when CORM-2 is dissolved in dimethyl sulfoxide (DMSO). Furthermore, with the clues on intermolecular interaction and chemical exchange dynamics between different products, the transformations between different products are also directly characterized for the first time. These findings challenge the results from the classic 1D spectroscopic pattern, and they evidently demonstrated that the release of CO from CORM-2 in DMSO was slow and complicated with multiple reaction pathways. Combining with DFT simulations, the detailed mechanisms of release of CO for CORM-2 dissolved in DMSO are schematically proposed, which can significantly contribute to its drug optimization and pharmacological as well as physiological applications.
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Affiliation(s)
- Jiangrui Zhu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juanjuan Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Guosheng Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jia Zhang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Tao
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Chang Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ming Liu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Hao Zhang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ruipei Xie
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Chinese Academy of Sciences, Dongguan, Guangdong 523808, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Ying Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Weihai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xuebo Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yunliang Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Chinese Academy of Sciences, Dongguan, Guangdong 523808, China
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31
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Duan R, Mastron JN, Song Y, Kubarych KJ. Direct comparison of amplitude and geometric measures of spectral inhomogeneity using phase-cycled 2D-IR spectroscopy. J Chem Phys 2021; 154:174202. [PMID: 34241049 DOI: 10.1063/5.0043961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Two-dimensional infrared (2D-IR) spectroscopy provides access to equilibrium dynamics with the extraction of the frequency-fluctuation correlation function (FFCF) from the measured spectra. Several different methods of obtaining the FFCF from experimental spectra, such as the center line slope (CLS), ellipticity, phase slope, and nodal line slope, all depend on the geometrical nature of the 2D line shape and necessarily require spectral extent in order to achieve a measure of the FFCF. Amplitude measures, on the other hand, such as the inhomogeneity index, rely only on signal amplitudes and can, in principle, be computed using just a single point in a 2D spectrum. With a pulse shaper-based 2D-IR spectrometer, in conjunction with phase cycling, we separate the rephasing and nonrephasing signals used to determine the inhomogeneity index. The same measured data provide the absorptive spectrum, needed for the CLS. Both methods are applied to two model molecular systems: tungsten hexacarbonyl (WCO6) and methylcyclopentadienyl manganese tricarbonyl [Cp'Mn(CO)3, MCMT]. The three degenerate IR modes of W(CO)6 lack coherent modulation or noticeable intramolecular vibrational redistribution (IVR) and are used to establish a baseline comparison. The two bands of the MCMT tripod complex include intraband coherences and IVR as well as likely internal torsional motion on a few-picosecond time scale. We find essentially identical spectral diffusion, but faster, non-equilibrium dynamics lead to differences in the FFCFs extracted with the two methods. The inhomogeneity index offers an advantage in cases where spectra are complex and energy transfer can mimic line shape changes due to frequency fluctuations.
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Affiliation(s)
- Rong Duan
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Joseph N Mastron
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Yin Song
- Department of Physics, University of Michigan, 430 Church Ave., Ann Arbor, Michigan 48109, USA
| | - Kevin J Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
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32
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Krishnan-Schmieden M, Konold PE, Kennis JTM, Pandit A. The molecular pH-response mechanism of the plant light-stress sensor PsbS. Nat Commun 2021; 12:2291. [PMID: 33863895 PMCID: PMC8052336 DOI: 10.1038/s41467-021-22530-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/12/2021] [Indexed: 11/12/2022] Open
Abstract
Plants need to protect themselves from excess light, which causes photo-oxidative damage and lowers the efficiency of photosynthesis. Photosystem II subunit S (PsbS) is a pH sensor protein that plays a crucial role in plant photoprotection by detecting thylakoid lumen acidification in excess light conditions via two lumen-faced glutamates. However, how PsbS is activated under low-pH conditions is unknown. To reveal the molecular response of PsbS to low pH, here we perform an NMR, FTIR and 2DIR spectroscopic analysis of Physcomitrella patens PsbS and of the E176Q mutant in which an active glutamate has been replaced. The PsbS response mechanism at low pH involves the concerted action of repositioning of a short amphipathic helix containing E176 facing the lumen and folding of the luminal loop fragment adjacent to E71 to a 310-helix, providing clear evidence of a conformational pH switch. We propose that this concerted mechanism is a shared motif of proteins of the light-harvesting family that may control thylakoid inter-protein interactions driving photoregulatory responses.
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Affiliation(s)
| | - Patrick E Konold
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
| | - Anjali Pandit
- Dept. of Solid-State NMR, Leiden Inst. of Chemistry, Leiden University, Leiden, The Netherlands.
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33
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Brünker P, Domenianni LI, Fleck N, Lindner J, Schiemann O, Vöhringer P. Intramolecular O-H⋯S hydrogen bonding in threefold symmetry: Line broadening dynamics from ultrafast 2DIR-spectroscopy and ab initio calculations. J Chem Phys 2021; 154:134305. [PMID: 33832237 DOI: 10.1063/5.0047885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dynamics of intramolecular hydrogen-bonding involving sulfur atoms as acceptors is studied using two-dimensional infrared (2DIR) spectroscopy. The molecular system is a tertiary alcohol whose donating hydroxy group is embedded in a hydrogen-bond potential with torsional C3-symmetry about the carbon-oxygen bond. The linear and 2DIR-spectra recorded in the OH-stretching region of the alcohol can be simulated very well using Kubo's line shape theory based on the cumulant expansion for evaluating the linear and nonlinear optical response functions. The correlation function for OH-stretching frequency fluctuations reveals an ultrafast component decaying with a time constant of 700 fs, which is in line with the apparent decay of the center line slopes averaged over absorption and bleach/emission signals. In addition, a quasi-static inhomogeneity is detected, which prevents the 2DIR line shape to fully homogenize within the observation window of 4 ps. The experimental data were then analyzed in more detail using a full ab initio approach that merges time-dependent structural information from classical molecular dynamics (MD) simulations with an OH-stretching frequency map derived from density functional theory (DFT). The latter method was also used to obtain a complementary transition dipole map to account for non-Condon effects. The 2DIR-spectra obtained from the MD/DFT method are in good agreement with the experimental data at early waiting delays, thereby corroborating an assignment of the fast decay of the correlation function to the dynamics of hydrogen-bond breakage and formation.
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Affiliation(s)
- Paul Brünker
- Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Luis I Domenianni
- Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Nico Fleck
- Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Jörg Lindner
- Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Peter Vöhringer
- Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
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34
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Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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35
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Price DA, Hill TD, Hutson KA, Rightnowar BW, Moran SD. Membrane-dependent amyloid aggregation of human BAX α9 (173-192). Protein Sci 2021; 30:1072-1080. [PMID: 33641228 DOI: 10.1002/pro.4053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/08/2021] [Accepted: 02/24/2021] [Indexed: 11/07/2022]
Abstract
Mitochondrial outer membrane permeabilization, which is a critical step in apoptosis, is initiated upon transmembrane insertion of the C-terminal α-helix (α9) of the proapoptotic Bcl-2 family protein BAX. The isolated α9 fragment (residues 173-192) is also competent to disrupt model membranes, and the structures of its membrane-associated oligomers are of interest in understanding the potential roles of this sequence in apoptosis. Here, we used ultrafast two-dimensional infrared (2D IR) spectroscopy, thioflavin T binding, and transmission electron microscopy to show that the synthetic BAX α9 peptide (α9p) forms amyloid aggregates in aqueous environments and on the surfaces of anionic small unilamellar vesicles. Its inherent amyloidogenicity was predicted by sequence analysis, and 2D IR spectra reveal that vesicles modulate the β-sheet structures of insoluble aggregates, motivating further examination of the formation or suppression of BAX amyloids in apoptosis.
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Affiliation(s)
- David A Price
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Tayler D Hill
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Kaitlyn A Hutson
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Blaze W Rightnowar
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
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36
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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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37
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Grafton AB, Dunkelberger AD, Simpkins BS, Triana JF, Hernández FJ, Herrera F, Owrutsky JC. Excited-state vibration-polariton transitions and dynamics in nitroprusside. Nat Commun 2021; 12:214. [PMID: 33431901 PMCID: PMC7801531 DOI: 10.1038/s41467-020-20535-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/02/2020] [Indexed: 01/31/2023] Open
Abstract
Strong cavity coupling to molecular vibrations creates vibration-polaritons capable of modifying chemical reaction kinetics, product branching ratios, and charge transfer equilibria. However, the mechanisms impacting these molecular processes remain elusive. Furthermore, even basic elements determining the spectral properties of polaritons, such as selection rules, transition moments, and lifetimes are poorly understood. Here, we use two-dimensional infrared and filtered pump–probe spectroscopy to report clear spectroscopic signatures and relaxation dynamics of excited vibration-polaritons formed from the cavity-coupled NO band of nitroprusside. We apply an extended multi-level quantum Rabi model that predicts transition frequencies and strengths that agree well with our experiment. Notably, the polariton features decay ~3–4 times slower than the polariton dephasing time, indicating that they support incoherent population, a consequence of their partial matter character. Here the authors report spectroscopy and dynamics of cavity coupled NO band of sodium nitroprusside using 2D infrared and transient spectroscopy employing pump-probe technique. They find signatures of third-order nonlinearity, incoherent and strong coupling effects of vibrational polaritons.
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Affiliation(s)
- Andrea B Grafton
- National Research Council Post-Doctoral Scholar, Washington, DC, USA
| | | | - Blake S Simpkins
- Chemistry Division, Naval Research Laboratory, Washington, DC, USA
| | - Johan F Triana
- Department of Physics, Universidad de Santiago de Chile, Santiago, Chile
| | - Federico J Hernández
- Department of Chemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Felipe Herrera
- Department of Physics, Universidad de Santiago de Chile, Santiago, Chile
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38
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Hoffman DJ, Fica-Contreras SM, Pan J, Fayer MD. Pulse-shaped chopping: Eliminating and characterizing heat effects in ultrafast infrared spectroscopy. J Chem Phys 2020; 153:204201. [DOI: 10.1063/5.0031581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David J. Hoffman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Junkun Pan
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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39
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Farrell KM, Ostrander JS, Jones AC, Yakami BR, Dicke SS, Middleton CT, Hamm P, Zanni MT. Shot-to-shot 2D IR spectroscopy at 100 kHz using a Yb laser and custom-designed electronics. OPTICS EXPRESS 2020; 28:33584-33602. [PMID: 33115018 PMCID: PMC7679191 DOI: 10.1364/oe.409360] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 05/29/2023]
Abstract
The majority of 2D IR spectrometers operate at 1-10 kHz using Ti:Sapphire laser technology. We report a 2D IR spectrometer designed around Yb:KGW laser technology that operates shot-to-shot at 100 kHz. It includes a home-built OPA, a mid-IR pulse shaper, and custom-designed electronics with optional on-chip processing. We report a direct comparison between Yb:KGW and Ti:Sapphire based 2D IR spectrometers. Even though the mid-IR pulse energy is much lower for the Yb:KGW driven system, there is an 8x improvement in signal-to-noise over the 1 kHz Ti:Sapphire driven spectrometer to which it is compared. Experimental data is shown for sub-millimolar concentrations of amides. Advantages and disadvantages of the design are discussed, including thermal background that arises at high repetition rates. This fundamental spectrometer design takes advantage of newly available Yb laser technology in a new way, providing a straightforward means of enhancing sensitivity.
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Affiliation(s)
- Kieran M. Farrell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Josh S. Ostrander
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Currently with the Department of Chemistry, Indiana Wesleyan University, Marion, Indiana 46953, USA
| | - Andrew C. Jones
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Currently with the Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Albuquerque, New Mexico 87185, USA
| | - Baichhabi R. Yakami
- PhaseTech Spectroscopy, 2810 Crossroads Drive, Suite 4000 Madison, Wisconsin 53718, USA
| | - Sidney S. Dicke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Chris T. Middleton
- PhaseTech Spectroscopy, 2810 Crossroads Drive, Suite 4000 Madison, Wisconsin 53718, USA
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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40
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Lloyd LT, Wood RE, Allodi MA, Sohoni S, Higgins JS, Otto JP, Engel GS. Leveraging scatter in two-dimensional spectroscopy: passive phase drift correction enables a global phasing protocol. OPTICS EXPRESS 2020; 28:32869-32881. [PMID: 33114962 DOI: 10.1364/oe.404601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Phase stability between pulse pairs defining Fourier-transform time delays can limit resolution and complicates development and adoption of multidimensional coherent spectroscopies. We demonstrate a data processing procedure to correct the long-term phase drift of the nonlinear signal during two-dimensional (2D) experiments based on the relative phase between scattered excitation pulses and a global phasing procedure to generate fully absorptive 2D electronic spectra of wafer-scale monolayer MoS2. Our correction results in a ∼30-fold increase in effective long-term signal phase stability, from ∼λ/2 to ∼λ/70 with negligible extra experimental time and no additional optical components. This scatter-based drift correction should be applicable to other interferometric techniques as well, significantly lowering the practical experimental requirements for this class of measurements.
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41
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Munoz MF, Medina A, Autry TM, Moody G, Siemens ME, Bristow AD, Cundiff ST, Li H. Fast phase cycling in non-collinear optical two-dimensional coherent spectroscopy. OPTICS LETTERS 2020; 45:5852-5855. [PMID: 33057301 DOI: 10.1364/ol.405196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
As optical two-dimensional coherent spectroscopy (2DCS) is extended to a broader range of applications, it is critical to improve the detection sensitivity of optical 2DCS. We developed a fast phase-cycling scheme in a non-collinear optical 2DCS implementation by using liquid crystal phase retarders to modulate the phases of two excitation pulses. The background in the signal can be eliminated by combining either two or four interferograms measured with a proper phase configuration. The effectiveness of this method was validated in optical 2DCS measurements of an atomic vapor. This fast phase-cycling scheme will enable optical 2DCS in novel emerging applications that require enhanced detection sensitivity.
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42
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Grieco C, Kohl FR, Hanes AT, Kohler B. Probing the heterogeneous structure of eumelanin using ultrafast vibrational fingerprinting. Nat Commun 2020; 11:4569. [PMID: 32917892 PMCID: PMC7486937 DOI: 10.1038/s41467-020-18393-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/18/2020] [Indexed: 11/25/2022] Open
Abstract
Eumelanin is a brown-black biological pigment with sunscreen and radical scavenging functions important to numerous organisms. Eumelanin is also a promising redox-active material for energy conversion and storage, but the chemical structures present in this heterogeneous pigment remain unknown, limiting understanding of the properties of its light-responsive subunits. Here, we introduce an ultrafast vibrational fingerprinting approach for probing the structure and interactions of chromophores in heterogeneous materials like eumelanin. Specifically, transient vibrational spectra in the double-bond stretching region are recorded for subsets of electronic chromophores photoselected by an ultrafast excitation pulse tuned through the UV-visible spectrum. All subsets show a common vibrational fingerprint, indicating that the diverse electronic absorbers in eumelanin, regardless of transition energy, contain the same distribution of IR-active functional groups. Aggregation of chromophores diverse in oxidation state is the key structural property underlying the universal, ultrafast deactivation behavior of eumelanin in response to photoexcitation with any wavelength.
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Affiliation(s)
- Christopher Grieco
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, USA
| | - Forrest R Kohl
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, USA
| | - Alex T Hanes
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, USA
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, USA.
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Malm C, Prädel LA, Marekha BA, Grechko M, Hunger J. Composition-Dependent Hydrogen-Bonding Motifs and Dynamics in Brønsted Acid-Base Mixtures. J Phys Chem B 2020; 124:7229-7238. [PMID: 32701282 PMCID: PMC7443859 DOI: 10.1021/acs.jpcb.0c04714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
recent years the interaction of organophosphates and imines,
which is at the core of Brønsted acid organocatalysis, has been
established to be based on strong ionic hydrogen bonds. Yet, besides
the formation of homodimers consisting of two acid molecules and heterodimers
consisting of one acid and one base, also multimeric molecular aggregates
are formed in solution. These multimeric aggregates consist of one
base and several acid molecules. The details of the intermolecular
bonding in such aggregates, however, have remained elusive. To characterize
composition-dependent bonding and bonding dynamics in these aggregates,
we use linear and nonlinear infrared (IR) spectroscopy at varying
molar ratios of diphenyl phosphoric acid and quinaldine. We identify
the individual aggregate species, giving rise to the structured, strong,
and very broad infrared absorptions, which span more than 1000 cm–1. Linear infrared spectra and density functional theory
calculations of the proton transfer potential show that doubly ionic
intermolecular hydrogen bonds between the acid and the base lead to
absorptions which peak at ∼2040 cm–1. The
contribution of singly ionic hydrogen bonds between an acid anion
and an acid molecule is observed at higher frequencies. As common
to such strong hydrogen bonds, ultrafast IR spectroscopy reveals rapid,
∼ 100 fs, dissipation of energy from the proton transfer coordinate.
Yet, the full dissipation of the excess energy occurs on a ∼0.8–1.1
ps time scale, which becomes longer when multimers dominate. Our results
thus demonstrate the coupling and collectivity of the hydrogen bonds
within these complexes, which enable efficient energy transfer.
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Affiliation(s)
- Christian Malm
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Leon A Prädel
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Bogdan A Marekha
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Maksim Grechko
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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44
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Fields CR, Dicke SS, Petti MK, Zanni MT, Lomont JP. A Different hIAPP Polymorph Is Observed in Human Serum Than in Aqueous Buffer: Demonstration of a New Method for Studying Amyloid Fibril Structure Using Infrared Spectroscopy. J Phys Chem Lett 2020; 11:6382-6388. [PMID: 32706257 PMCID: PMC7968077 DOI: 10.1021/acs.jpclett.0c01345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
There is enormous interest in measuring amyloid fibril structures, but most structural studies measure fibril formation in vitro using aqueous buffer. Ideally, one would like to measure fibril structure and mechanism under more physiological conditions. Toward this end, we have developed a method for studying amyloid fibril structure in human serum. Our approach uses isotope labeling, antibody depletion of the most abundant proteins (albumin and IgG), and infrared spectroscopy to measure aggregation in human serum with reduced protein content. Reducing the nonamyloid protein content enables the measurements by decreasing background signals but retains the full composition of salts, sugars, metal ions, etc. that are naturally present but usually missing from in vitro studies. We demonstrate the method by measuring the two-dimensional infrared (2D IR) spectra of isotopically labeled human islet amyloid polypeptide (hIAPP or amylin). We find that the fibril structure of hIAPP formed in serum differs from that formed via aggregation in aqueous buffer at residues Gly24 and Ala25, which reside in the putative "amyloidogenic core" or FGAIL region of the sequence. The spectra are consistent with extended parallel stacks of strands consistent with β-sheet-like structure, rather than a partially disordered loop that forms in aqueous buffer. These experiments provide a new method for using infrared spectroscopy to monitor the structure of proteins under physiological conditions and reveal the formation of a significantly different polymorph structure in the most important region of hIAPP.
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Affiliation(s)
- Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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46
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Silori Y, Seliya P, De AK. Ultrafast Excited-State Dynamics of Tricarbocyanine Dyes Probed by Two-Dimensional Electronic Spectroscopy: Polar Solvation vs Photoisomerization. J Phys Chem B 2020; 124:6825-6834. [DOI: 10.1021/acs.jpcb.0c01333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yogita Silori
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140 306, India
| | - Pankaj Seliya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140 306, India
| | - Arijit K. De
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140 306, India
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47
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Greetham GM, Clark IP, Young B, Fritsch R, Minnes L, Hunt NT, Towrie M. Time-Resolved Temperature-Jump Infrared Spectroscopy at a High Repetition Rate. APPLIED SPECTROSCOPY 2020; 74:720-727. [PMID: 32114769 DOI: 10.1177/0003702820913636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Time-resolved temperature-jump infrared absorption spectroscopy at a 0.5 to 1 kHz repetition rate is presented. A 1 kHz neodymium-doped yttrium aluminum garnet (Nd:YAG) laser pumping an optical parametric oscillator provided >70 µJ, 3.75 µm pump pulses, which delivered a temperature jump via excitation of the O-D stretch of a D2O solution. A 10 kHz train of mid-infrared probe pulses was used to monitor spectral changes following the temperature jump. Calibration with trifluoroacetic acid solution showed that a temperature jump of 10 K lasting for tens of microseconds was achieved, sufficient to observe fast processes in functionally relevant biomolecular mechanisms. Modeling of heating profiles across ≤10 µm path length cells and subsequent cooling dynamics are used to describe the initial <100 ns cooling at the window surface and subsequent, >10 µs cooling dynamics of the bulk solution.
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Affiliation(s)
- Gregory M Greetham
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
| | - Ian P Clark
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
| | - Benjamin Young
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
| | - Robby Fritsch
- Department of Physics, SUPA, University of Strathclyde, Glasgow, UK
| | - Lucy Minnes
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
- Department of Physics, SUPA, University of Strathclyde, Glasgow, UK
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York, UK
| | - Mike Towrie
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, UK
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48
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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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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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50
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Patrizi B, Cozza C, Pietropaolo A, Foggi P, Siciliani de Cumis M. Synergistic Approach of Ultrafast Spectroscopy and Molecular Simulations in the Characterization of Intramolecular Charge Transfer in Push-Pull Molecules. Molecules 2020; 25:E430. [PMID: 31968694 PMCID: PMC7024558 DOI: 10.3390/molecules25020430] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 11/28/2022] Open
Abstract
The comprehensive characterization of Intramolecular Charge Transfer (ICT) stemming in push-pull molecules with a delocalized π-system of electrons is noteworthy for a bespoke design of organic materials, spanning widespread applications from photovoltaics to nanomedicine imaging devices. Photo-induced ICT is characterized by structural reorganizations, which allows the molecule to adapt to the new electronic density distribution. Herein, we discuss recent photophysical advances combined with recent progresses in the computational chemistry of photoactive molecular ensembles. We focus the discussion on femtosecond Transient Absorption Spectroscopy (TAS) enabling us to follow the transition from a Locally Excited (LE) state to the ICT and to understand how the environment polarity influences radiative and non-radiative decay mechanisms. In many cases, the charge transfer transition is accompanied by structural rearrangements, such as the twisting or molecule planarization. The possibility of an accurate prediction of the charge-transfer occurring in complex molecules and molecular materials represents an enormous advantage in guiding new molecular and materials design. We briefly report on recent advances in ultrafast multidimensional spectroscopy, in particular, Two-Dimensional Electronic Spectroscopy (2DES), in unraveling the ICT nature of push-pull molecular systems. A theoretical description at the atomistic level of photo-induced molecular transitions can predict with reasonable accuracy the properties of photoactive molecules. In this framework, the review includes a discussion on the advances from simulation and modeling, which have provided, over the years, significant information on photoexcitation, emission, charge-transport, and decay pathways. Density Functional Theory (DFT) coupled with the Time-Dependent (TD) framework can describe electronic properties and dynamics for a limited system size. More recently, Machine Learning (ML) or deep learning approaches, as well as free-energy simulations containing excited state potentials, can speed up the calculations with transferable accuracy to more complex molecules with extended system size. A perspective on combining ultrafast spectroscopy with molecular simulations is foreseen for optimizing the design of photoactive compounds with tunable properties.
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Affiliation(s)
- Barbara Patrizi
- National Institute of Optics-National Research Council (INO-CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (B.P.); (P.F.)
- European Laboratory for Non-Linear Spectroscopy (LENS),Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Concetta Cozza
- Dipartimento di Scienze della Salute, Università di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.C.); (A.P.)
| | - Adriana Pietropaolo
- Dipartimento di Scienze della Salute, Università di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.C.); (A.P.)
| | - Paolo Foggi
- National Institute of Optics-National Research Council (INO-CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (B.P.); (P.F.)
- European Laboratory for Non-Linear Spectroscopy (LENS),Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
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