1
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Wu F, Huang Y, Yang G, Ye S, Mukamel S, Jiang J. Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model. Proc Natl Acad Sci U S A 2024; 121:e2409257121. [PMID: 38917009 PMCID: PMC11228460 DOI: 10.1073/pnas.2409257121] [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: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Dynamic protein structures are crucial for deciphering their diverse biological functions. Two-dimensional infrared (2DIR) spectroscopy stands as an ideal tool for tracing rapid conformational evolutions in proteins. However, linking spectral characteristics to dynamic structures poses a formidable challenge. Here, we present a pretrained machine learning model based on 2DIR spectra analysis. This model has learned signal features from approximately 204,300 spectra to establish a "spectrum-structure" correlation, thereby tracing the dynamic conformations of proteins. It excels in accurately predicting the dynamic content changes of various secondary structures and demonstrates universal transferability on real folding trajectories spanning timescales from microseconds to milliseconds. Beyond exceptional predictive performance, the model offers attention-based spectral explanations of dynamic conformational changes. Our 2DIR-based pretrained model is anticipated to provide unique insights into the dynamic structural information of proteins in their native environments.
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Affiliation(s)
- Fan Wu
- Key Laboratory of Precision and Intelligent Chemistry, Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei230026, Anhui, China
| | - Yan Huang
- Key Laboratory of Precision and Intelligent Chemistry, Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei230026, Anhui, China
| | - Guokun Yang
- Key Laboratory of Precision and Intelligent Chemistry, Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei230026, Anhui, China
| | - Sheng Ye
- Anhui Provincial Engineering Research Center for Unmanned System and Intelligent Technology, School of Artificial Intelligence, Anhui University, Hefei230601, Anhui, China
| | - Shaul Mukamel
- Department of Chemistry and of Physics & Astronomy, University of California, Irvine, CA92697
| | - Jun Jiang
- Key Laboratory of Precision and Intelligent Chemistry, Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei230026, Anhui, China
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2
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Cuk T. Phenomenology of Intermediate Molecular Dynamics at Metal-Oxide Interfaces. Annu Rev Phys Chem 2024; 75:457-481. [PMID: 38941530 DOI: 10.1146/annurev-physchem-062123-022921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Reaction intermediates buried within a solid-liquid interface are difficult targets for physiochemical measurements. They are inherently molecular and locally dynamic, while their surroundings are extended by a periodic lattice on one side and the solvent dielectric on the other. Challenges compound on a metal-oxide surface of varied sites and especially so at its aqueous interface of many prominent reactions. Recently, phenomenological theory coupled with optical spectroscopy has become a more prominent tool for isolating the intermediates and their molecular dynamics. The following article reviews three examples of the SrTiO3-aqueous interface subject to the oxygen evolution from water: reaction-dependent component analyses of time-resolved intermediates, a Fano resonance of a mode at the metal-oxide-water interface, and reaction isotherms of metastable intermediates. The phenomenology uses parameters to encase what is unknown at a microscopic level to then circumscribe the clear and macroscopically tuned trends seen in the spectroscopic data.
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Affiliation(s)
- Tanja Cuk
- Department of Chemistry, Materials Science and Engineering Program, and Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado, USA;
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3
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Chen X, Al-Mualem ZA, Baiz CR. Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity. Annu Rev Phys Chem 2024; 75:283-305. [PMID: 38382566 DOI: 10.1146/annurev-physchem-090722-010230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Cell membranes are incredibly complex environments containing hundreds of components. Despite substantial advances in the past decade, fundamental questions related to lipid-lipid interactions and heterogeneity persist. This review explores the complexity of lipid membranes, showcasing recent advances in vibrational spectroscopy to characterize the structure, dynamics, and interactions at the membrane interface. We include an overview of modern techniques such as surface-enhanced infrared spectroscopy as a steady-state technique with single-bilayer sensitivity, two-dimensional sum-frequency generation spectroscopy, and two-dimensional infrared spectroscopy to measure time-evolving structures and dynamics with femtosecond time resolution. Furthermore, we discuss the potential of multiscale molecular dynamics (MD) simulations, focusing on recently developed simulation algorithms, which have emerged as a powerful approach to interpret complex spectra. We highlight the ongoing challenges in studying heterogeneous environments in multicomponent membranes via current vibrational spectroscopic techniques and MD simulations. Overall, this review provides an up-to-date comprehensive overview of the powerful combination of vibrational spectroscopy and simulations, which has great potential to illuminate lipid-lipid, lipid-protein, and lipid-water interactions in the intricate conformational landscape of cell membranes.
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Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA;
| | | | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA;
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4
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Kwac K, Yang N, Ryan MJ, Zanni MT, Cho M. Molecular dynamics simulation study of water structure and dynamics on the gold electrode surface with adsorbed 4-mercaptobenzonitrile. J Chem Phys 2024; 160:064701. [PMID: 38341780 PMCID: PMC11219078 DOI: 10.1063/5.0189122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/16/2024] [Indexed: 02/13/2024] Open
Abstract
Understanding water dynamics at charged interfaces is of great importance in various fields, such as catalysis, biomedical processes, and solar cell materials. In this study, we implemented molecular dynamics simulations of a system of pure water interfaced with Au electrodes, on one side of which 4-mercaptobenzonitrile (4-MBN) molecules are adsorbed. We calculated time correlation functions of various dynamic quantities, such as the hydrogen bond status of the N atom of the adsorbed 4-MBN molecules, the rotational motion of the water OH bond, hydrogen bonds between 4-MBN and water, and hydrogen bonds between water molecules in the interface region. Using the Luzar-Chandler model, we analyzed the hydrogen bond dynamics between a 4-MBN and a water molecule. The dynamic quantities we calculated can be divided into two categories: those related to the collective behavior of interfacial water molecules and the H-bond interaction between a water molecule and the CN group of 4-MBN. We found that these two categories of dynamic quantities exhibit opposite trends in response to applied potentials on the Au electrode. We anticipate that the present work will help improve our understanding of the interfacial dynamics of water in various electrolyte systems.
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Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
| | - Nan Yang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Matthew J. Ryan
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Minhaeng Cho
- Authors to whom correspondence should be addressed: or
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5
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Ye S, Zhong K, Huang Y, Zhang G, Sun C, Jiang J. Artificial Intelligence-based Amide-II Infrared Spectroscopy Simulation for Monitoring Protein Hydrogen Bonding Dynamics. J Am Chem Soc 2024; 146:2663-2672. [PMID: 38240637 DOI: 10.1021/jacs.3c12258] [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: 02/01/2024]
Abstract
The structurally sensitive amide II infrared (IR) bands of proteins provide valuable information about the hydrogen bonding of protein secondary structures, which is crucial for understanding protein dynamics and associated functions. However, deciphering protein structures from experimental amide II spectra relies on time-consuming quantum chemical calculations on tens of thousands of representative configurations in solvent water. Currently, the accurate simulation of amide II spectra for whole proteins remains a challenge. Here, we present a machine learning (ML)-based protocol designed to efficiently simulate the amide II IR spectra of various proteins with an accuracy comparable to experimental results. This protocol stands out as a cost-effective and efficient alternative for studying protein dynamics, including the identification of secondary structures and monitoring the dynamics of protein hydrogen bonding under different pH conditions and during protein folding process. Our method provides a valuable tool in the field of protein research, focusing on the study of dynamic properties of proteins, especially those related to hydrogen bonding, using amide II IR spectroscopy.
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Affiliation(s)
- Sheng Ye
- School of Artificial Intelligence, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Kai Zhong
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747AG, Netherlands
| | - Yan Huang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Guozhen Zhang
- Hefei National Research Center of Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
| | - Changyin Sun
- School of Artificial Intelligence, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Jun Jiang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
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6
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Bodine M, Rozyyev V, Elam JW, Tokmakoff A, Lewis NHC. Vibrational Probe at the Electrochemical Interface: Dependence on Plasmon Coupling and Potential of the Lineshape in Two-Dimensional Infrared Spectroscopy. J Phys Chem Lett 2023:11092-11099. [PMID: 38051916 DOI: 10.1021/acs.jpclett.3c02987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Two-dimensional infrared spectroscopy of vibrational probes at an electrode surface shows promise for studying the structural dynamics at an active electrochemical interface. This interface is a complex environment where the solution structures in response to the applied potential. A strategy for achieving the necessary monolayer sensitivity is to use a plasmonically active electrode, which enhances the electromagnetic fields that produce the spectroscopic response. Here, we show how the coupling between the plasmon and the vibrations of the molecular monolayer impacts the FTIR and 2D IR spectroscopy, with an emphasis on the electrochemical potential difference spectra. We show how mixing between the vibrational and plasmonic states gives rise to the distortions that are observed in these measurements. This provides an important step toward 2D IR measurements of vibrational probes at the electrochemical interface as a tool for probing the structural dynamics in the double layer.
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Affiliation(s)
- Melissa Bodine
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vepa Rozyyev
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
- Applied Materials Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Jeffrey W Elam
- Applied Materials Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Nicholas H C Lewis
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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7
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Litman Y, Lan J, Nagata Y, Wilkins DM. Fully First-Principles Surface Spectroscopy with Machine Learning. J Phys Chem Lett 2023; 14:8175-8182. [PMID: 37671886 PMCID: PMC10510433 DOI: 10.1021/acs.jpclett.3c01989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023]
Abstract
Our current understanding of the structure and dynamics of aqueous interfaces at the molecular level has grown substantially due to the continuous development of surface-specific spectroscopies, such as vibrational sum-frequency generation (VSFG). As in other vibrational spectroscopies, we must turn to atomistic simulations to extract all of the information encoded in the VSFG spectra. The high computational cost associated with existing methods means that they have limitations in representing systems with complex electronic structure or in achieving statistical convergence. In this work, we combine high-dimensional neural network interatomic potentials and symmetry-adapted Gaussian process regression to overcome these constraints. We show that it is possible to model VSFG signals with fully ab initio accuracy using machine learning and illustrate the versatility of our approach on the water/air interface. Our strategy allows us to identify the main sources of theoretical inaccuracy and establish a clear pathway toward the modeling of surface-sensitive spectroscopy of complex interfaces.
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Affiliation(s)
- Yair Litman
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jinggang Lan
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Simons
Center for Computational Physical Chemistry at New York University, New York, New York 10003, United States
| | - Yuki Nagata
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - David M. Wilkins
- Centre
for Quantum Materials and Technologies School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
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8
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Zhang Y, Jin J, Xue Y, Zhao Y, Luo Q, Mao L, Wang F. Molecular unravelling of the mechanism of overpotential change at the carbon nanotubes-modified gold electrode surface. Chem Commun (Camb) 2023. [PMID: 37326456 DOI: 10.1039/d3cc01818k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Using liquid secondary ion mass spectrometry, we in situ unraveled that the single walled carbon nanotubes-modified gold electrode surface is free of a dense adsorption phase and abundant in water molecules, which facilitated the electro-oxidation reaction of ascorbate. Such an understanding will expedite the knowledge-based development of electrochemical interfaces.
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Affiliation(s)
- Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jing Jin
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifei Xue
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Donaldson PM, Howe RF, Hawkins AP, Towrie M, Greetham GM. Ultrafast 2D-IR spectroscopy of intensely optically scattering pelleted solid catalysts. J Chem Phys 2023; 158:114201. [PMID: 36948842 DOI: 10.1063/5.0139103] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Solid, powdered samples are often prepared for infrared (IR) spectroscopy analysis in the form of compressed pellets. The intense scattering of incident light by such samples inhibits applications of more advanced IR spectroscopic techniques, such as two-dimensional (2D)-IR spectroscopy. We describe here an experimental approach that enables the measurement of high-quality 2D-IR spectra from scattering pellets of zeolites, titania, and fumed silica in the OD-stretching region of the spectrum under flowing gas and variable temperature up to ∼500 ◦C. In addition to known scatter suppression techniques, such as phase cycling and polarization control, we demonstrate how a bright probe laser beam comparable in strength with the pump beam provides effective scatter suppression. The possible nonlinear signals arising from this approach are discussed and shown to be limited in consequence. In the intense focus of 2D-IR laser beams, a free-standing solid pellet may become elevated in temperature compared with its surroundings. The effects of steady state and transient laser heating effects on practical applications are discussed.
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Affiliation(s)
- Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Russell F Howe
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Alexander P Hawkins
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Mike Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
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10
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Glotz G, Püschmann S, Haas M, Gescheidt G. Direct detection of photo-induced reactions by IR: from Brook rearrangement to photo-catalysis. Photochem Photobiol Sci 2023:10.1007/s43630-023-00406-4. [PMID: 36933157 DOI: 10.1007/s43630-023-00406-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
In situ IR detection of photoreactions induced by the light of LEDs at appropriate wavelengths provides a simple, cost-effective, and versatile method to get insight into mechanistic details. In particular, conversions of functional groups can be selectively followed. Overlapping UV-Vis bands or fluorescence from the reactants and products and the incident light do not obstruct IR detection. Compared with in situ photo-NMR, our setup does not require tedious sample preparation (optical fibers) and offers a selective detection of reactions, even at positions where 1H-NMR lines overlap or 1H resonances are not clear-cut. We illustrate the applicability of our setup following the photo-Brook rearrangement of (adamant-1-yl-carbonyl)-tris(trimethylsilyl)silane, address photo-induced α-bond cleavage (1-hydroxycyclohexyl phenyl ketone), study photoreduction using tris(bipyridine)ruthenium(II), investigate photo-oxygenation of double bonds with molecular oxygen and the fluorescent 2,4,6-triphenylpyrylium photocatalyst, and address photo-polymerization. With the LED/FT-IR combination, reactions can be qualitatively followed in fluid solution, (highly) viscous environments, and in the solid state. Viscosity changes during the reaction (e.g., during a polymerization) do not obstruct the method.
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Affiliation(s)
- Gabriel Glotz
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010, Graz, Austria.
| | - Sabrina Püschmann
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Michael Haas
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Georg Gescheidt
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010, Graz, Austria
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11
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Xiong W. Molecular Vibrational Polariton Dynamics: What Can Polaritons Do? Acc Chem Res 2023; 56:776-786. [PMID: 36930582 PMCID: PMC10077590 DOI: 10.1021/acs.accounts.2c00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
ConspectusWhen molecular vibrational modes strongly couple to virtual states of photonic modes, new molecular vibrational polariton states are formed, along with a large population of dark reservoir modes. The polaritons are much like the bonding and antibonding molecular orbitals when atomic orbitals form molecular bonds, while the dark modes are like nonbonding orbitals. Because the polariton states are half-matter and half-light, whose energy is shifted from the parental states, polaritons are predicted to modify chemistry under thermally activated conditions, leading to an exciting and emerging field known as polariton chemistry that could potentially shift paradigms in chemistry. Despite several published results supporting this concept, the chemical physics and mechanism of polariton chemistry remain elusive. One reason for this challenge is that previous works cannot differentiate polaritons from dark modes. This limitation makes delineating the contributions to chemistry from polaritons and dark states difficult. However, this level of insight is critical for developing a solid mechanism for polariton chemistry to design and predict the outcome of strong coupling with any given reaction. My group addressed the challenge of differentiating the dynamics of polaritons and dark modes by ultrafast two-dimensional infrared (2D IR) spectroscopy. Specifically, (1) we found that polaritons can facilitate intra- and intermolecular vibrational energy transfer, opening a pathway to control vibrational energy flow in liquid-phase molecular systems, and (2) by studying a single-step isomerization event, we verified that indeed polaritons can modify chemical dynamics under strong coupling conditions, but in contrast, the dark modes behave like uncoupled molecules and do not change the dynamics. This finding confirmed the central concept of polariton chemistry: polaritons modify the potential energy landscape of reactions. The result also clarified the role of dark modes, which lays a critical foundation for designing cavities for future polariton chemistry. Aside from using 2D IR spectroscopy to study polariton chemistry, we also used the same technique to develop molecular polaritons into a potential quantum simulation platform. We demonstrated that polaritons have Rabi oscillations, and using a checkerboard cavity design, we showed that polaritons could have large nonlinearity across space. We further used the checkerboard polaritons to simulate coherence transfer and visualize it. A unidirectional coherence transfer was observed, indicating non-Hermitian dynamics. The highlighted efforts in this Account provide a solid understanding of the capability of polaritons for chemistry and quantum information science. I conclude this Account by discussing a few challenges for moving polariton chemistry toward being predictable and making the polariton quantum platform a complement to existing systems.
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Affiliation(s)
- Wei Xiong
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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12
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Yang N, Ryan MJ, Son M, Mavrič A, Zanni MT. Voltage-Dependent FTIR and 2D Infrared Spectroscopies within the Electric Double Layer Using a Plasmonic and Conductive Electrode. J Phys Chem B 2023; 127:2083-2091. [PMID: 36821845 DOI: 10.1021/acs.jpcb.2c08431] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Strong electric fields exist between the electric double layer and charged surfaces. These fields impact molecular structures and chemistry at interfaces. We have developed a transparent electrode with infrared plasmonic enhancement sufficient to measure FTIR and two-dimensional infrared spectra at submonolayer coverages on the surface to which a voltage can be applied. Our device consists of an infrared transparent substrate, a 10-20 nm layer of conductive indium tin oxide (ITO), an electrically resistive layer of 3-5 nm Al2O3, and a 3 nm layer of nonconductive plasmonic gold. The materials and thicknesses are set to maximize the surface number density of the monolayer molecules, electrical conductivity, and plasmonic enhancement while minimizing background signals and avoiding Fano line shape distortions. The design was optimized by iteratively characterizing the material roughness and thickness with atomic force microscopy and electron microscopy and by monitoring the plasmon resonance enhancement with spectroscopy. The design is robust to repeated fabrication. This new electrode is tested on nitrile functional groups using a monolayer of 4-mercaptobenzonitrile as well as on CO and CC stretching modes using 4-mercaptobenzoic acid methyl ester. A voltage-dependent Stark shift is observed on both monolayers. We also observe that the transition dipole strength of the CN mode scales linearly with the applied voltage, providing a second way of measuring the surface electric field strength. We anticipate that this cell will enable many new voltage-dependent infrared experiments under applied voltages.
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Affiliation(s)
- Nan Yang
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Matthew J Ryan
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Minjung Son
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Andraž Mavrič
- University of Nova Gorica, Materials Research Laboratory, Vipavska 13, SI-5000 Nova Gorica, Slovenia
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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13
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Brüggemann J, Wolter M, Jacob CR. Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. J Chem Phys 2022; 157:244107. [PMID: 36586972 DOI: 10.1063/5.0135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.
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Affiliation(s)
- Julia Brüggemann
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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14
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Su HS, Chang X, Xu B. Surface-enhanced vibrational spectroscopies in electrocatalysis: Fundamentals, challenges, and perspectives. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(22)64157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Wu Z, Xiong W. Neumann's principle based eigenvector approach for deriving non-vanishing tensor elements for nonlinear optics. J Chem Phys 2022; 157:134702. [PMID: 36209027 PMCID: PMC9531997 DOI: 10.1063/5.0118711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/05/2022] [Indexed: 11/14/2022] Open
Abstract
Physical properties are commonly represented by tensors, such as optical susceptibilities. The conventional approach of deriving non-vanishing tensor elements of symmetric systems relies on the intuitive consideration of positive/negative sign flipping after symmetry operations, which could be tedious and prone to miscalculation. Here, we present a matrix-based approach that gives a physical picture centered on Neumann's principle. The principle states that symmetries in geometric systems are adopted by their physical properties. We mathematically apply the principle to the tensor expressions and show a procedure with clear physical intuition to derive non-vanishing tensor elements based on eigensystems. The validity of the approach is demonstrated by examples of commonly known second and third-order nonlinear susceptibilities of chiral/achiral surfaces, together with complicated scenarios involving symmetries such as D6 and Oh symmetries. We then further applied this method to higher-rank tensors that are useful for 2D and high-order spectroscopy. We also extended our approach to derive nonlinear tensor elements with magnetization, which is critical for measuring spin polarization on surfaces for quantum information technologies. A Mathematica code based on this generalized approach is included that can be applied to any symmetry and higher order nonlinear processes.
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Affiliation(s)
- Zishan Wu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California 92093, USA
| | - Wei Xiong
- Authors to whom correspondence should be addressed: and
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16
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Chatterley AS, Golbek TW, Weidner T. Measuring Protein Conformation at Aqueous Interfaces with 2D Infrared Spectroscopy of Emulsions. J Phys Chem Lett 2022; 13:7191-7196. [PMID: 35905449 DOI: 10.1021/acs.jpclett.2c01324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Determining the secondary and tertiary structures of proteins at aqueous interfaces is crucial for understanding their function, but measuring these structures selectively at the interface is challenging. Here we demonstrate that two-dimensional infrared (2D-IR) spectroscopy of protein stabilized emulsions offers a new route to measuring interfacial protein structure with high levels of detail. We prepared hexadecane/water oil-in-water emulsions stabilized by model LK peptides that are known to fold into either α-helix or β-sheet conformations at hydrophobic interfaces and measured 2D-IR spectra in a transmission geometry. We saw clear spectral signatures of the peptides folding at the interface, with no detectable residue from remaining bulk peptides. Using 2D spectroscopy gives us access to correlation and dynamics data, which enables structural assignment in cases where linear spectroscopy fails. Using the emulsions allows one to study interfacial spectra with standard transmission geometry spectrometers, bringing the richness of 2D-IR to the interface with no additional optical complexity.
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Affiliation(s)
| | | | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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17
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Ahsan MS, Kochetov V, Hein D, Bokarev SI, Wilkinson I. Probing the molecular structure of aqueous triiodide via X-ray photoelectron spectroscopy and correlated electron phenomena. Phys Chem Chem Phys 2022; 24:15540-15555. [PMID: 35713286 DOI: 10.1039/d1cp05840a] [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
Liquid-microjet-based X-ray photoelectron spectroscopy was applied to aqueous triiodide solutions, I3-(aq.), to investigate the anion's valence- and core-level electronic structure, ionization dynamics, associated electron-correlation effects, and nuclear geometric structure. The roles of multi-active-electron (shake-up) ionization processes - with noted sensitivity to the solute geometric structure - were investigated through I3-(aq.) solution valence, I 4d, and I 3d core-level measurements. The experimental spectra were interpreted with the aid of simulated photoelectron spectra, built upon multi-reference ab initio electronic structure calculations associated with different I3-(aq.) molecular geometries. A comparison of the single-to-multi-active-electron ionization signal ratios extracted from the experimental and theoretical core-level photoemission spectra suggests that the ground state of the solute adopts a near-linear average geometry in aqueous solutions. This contrasts with the interpretation of time-resolved X-ray solution scattering studies, but is found to be fully consistent with the rest of the solution-phase I3-(aq.) literature. Comparing the results of low- and high-photon-energy photoemission measurements, we further suggest that the aqueous anion adopts a more asymmetric geometry at the aqueous-solution-gas interface than in the aqueous bulk.
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Affiliation(s)
- Md Sabbir Ahsan
- Department of Locally-Sensitive and Time-Resolved Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany. .,Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Vladislav Kochetov
- Institut für Physik, Universität Rostock, Albert Einstein Str. 23-24, D-18059 Rostock, Germany
| | - Dennis Hein
- Operando Interfacial Photochemistry, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-platz. 1, D-14109 Berlin, Germany.,Department of Physics, Humboldt-Universität zu Berlin, Newtonstrasse 15, D-12489 Berlin, Germany
| | - Sergey I Bokarev
- Institut für Physik, Universität Rostock, Albert Einstein Str. 23-24, D-18059 Rostock, Germany
| | - Iain Wilkinson
- Department of Locally-Sensitive and Time-Resolved Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany.
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18
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Charboneau DJ, Hazari N, Huang H, Uehling MR, Zultanski SL. Homogeneous Organic Electron Donors in Nickel-Catalyzed Reductive Transformations. J Org Chem 2022; 87:7589-7609. [PMID: 35671350 DOI: 10.1021/acs.joc.2c00462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many contemporary organic transformations, such as Ni-catalyzed cross-electrophile coupling (XEC), require a reductant. Typically, heterogeneous reductants, such as Zn0 or Mn0, are used as the electron source in these reactions. Although heterogeneous reductants are highly practical for preparative-scale batch reactions, they can lead to complications in performing reactions on process scale and are not easily compatible with modern applications, such as flow chemistry. In principle, homogeneous organic reductants can address some of the challenges associated with heterogeneous reductants and also provide greater control of the reductant strength, which can lead to new reactivity. Nevertheless, homogeneous organic reductants have rarely been used in XEC. In this Perspective, we summarize recent progress in the use of homogeneous organic electron donors in Ni-catalyzed XEC and related reactions, discuss potential synthetic and mechanistic benefits, describe the limitations that inhibit their implementation, and outline challenges that need to be solved in order for homogeneous organic reductants to be widely utilized in synthetic chemistry. Although our focus is on XEC, our discussion of the strengths and weaknesses of different methods for introducing electrons is general to other reductive transformations.
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Affiliation(s)
- David J Charboneau
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Nilay Hazari
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Haotian Huang
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Mycah R Uehling
- Discovery Chemistry, HTE and Lead Discovery Capabilities, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Susan L Zultanski
- Department of Process Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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19
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Efficient generation of few-cycle pulses beyond 10 μm from an optical parametric amplifier pumped by a 1-µm laser system. Sci Rep 2022; 12:5082. [PMID: 35332211 PMCID: PMC8948267 DOI: 10.1038/s41598-022-08964-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/08/2022] [Indexed: 12/30/2022] Open
Abstract
Nonlinear vibrational spectroscopy profits from broadband sources emitting in the molecular fingerprint region. Yet, broadband lasers operating at wavelengths above 7 μm have been lacking, while traditional cascaded parametric frequency down-conversion schemes suffer from exceedingly low conversion efficiencies. Here we present efficient, direct frequency down-conversion of femtosecond 100-kHz, 1.03-μm pulses to the mid-infrared from 7.5 to 13.3 μm in a supercontinuum-seeded, tunable, single-stage optical parametric amplifier based on the wide-bandgap material Cd0.65Hg0.35Ga2S4. The amplifier delivers near transform-limited, few-cycle pulses with an average power > 30 mW at center wavelengths between 8.8 and 10.6 μm, at conversion efficiencies far surpassing that of optical parametric amplification followed by difference-frequency generation or intrapulse difference-frequency generation. The pulse duration at 10.6 μm is 101 fs corresponding to 2.9 optical cycles with a spectral coverage of 760–1160 cm−1. CdxHg1−xGa2S4 is an attractive alternative to LiGaS2 and BaGa4S7 in small-scale, Yb-laser-pumped, few-cycle mid-infrared optical parametric amplifiers and offers a much higher nonlinear figure of merit compared to those materials. Leveraging the inherent spatial variation of composition in CdxHg1−xGa2S4, an approach is proposed to give access to a significant fraction of the molecular fingerprint region using a single crystal at a fixed phase matching angle.
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20
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Wang Y, Chen D. Application of Advanced Vibrational Spectroscopy in Revealing Critical Chemical Processes and Phenomena of Electrochemical Energy Storage and Conversion. ACS APPLIED MATERIALS & INTERFACES 2022; 14:23033-23055. [PMID: 35130433 DOI: 10.1021/acsami.1c20893] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The future of the energy industry and green transportation critically relies on exploration of high-performance, reliable, low-cost, and environmentally friendly energy storage and conversion materials. Understanding the chemical processes and phenomena involved in electrochemical energy storage and conversion is the premise of a revolutionary materials discovery. In this article, we review the recent advancements of application of state-of-the-art vibrational spectroscopic techniques in unraveling the nature of electrochemical energy, including bulk energy storage, dynamics of liquid electrolytes, interfacial processes, etc. Technique-wise, the review covers a wide range of spectroscopic methods, including classic vibrational spectroscopy (direct infrared absorption and Raman scattering), external field enhanced spectroscopy (surface enhanced Raman and IR, tip enhanced Raman, and near-field IR), and two-photon techniques (2D infrared absorption, stimulated Raman, and vibrational sum frequency generation). Finally, we provide perspectives on future directions in refining vibrational spectroscopy to contribute to the research frontier of electrochemical energy storage and conversion.
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Affiliation(s)
- You Wang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Dongchang Chen
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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21
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Yu Z, Li JQ, Wang YH, Su JQ, Fu JY, Zou JW, Zheng JF, Shao Y, Zhou XS. Visualizing an Electrochemically Induced Radical Cation of Bipyridine at Au(111)/Ionic Liquid Interfaces toward a Single-Molecule Switch. Anal Chem 2022; 94:1823-1830. [PMID: 35020360 DOI: 10.1021/acs.analchem.1c04707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Room-temperature ionic liquids (RTILs) emerged as ideal solvents, and bipyridine as one of the most used ligands have been widely employed in surface science, catalysis, and molecular electronics. Herein, in situ shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) and STM break junction (STM-BJ) technique has been employed to probe the electrochemical process of bipyridine at Au(111)/IL interfaces. It is interestingly found that these molecules undertake a redox process with a pair of well-defined reversible peaks in cyclic voltammograms (CVs). The spectroscopic evidence shows a radical cation generated with rising new Raman peaks related to parallel CC stretching of a positively charged pyridyl ring. Furthermore, these electrochemically charged bipyridine is also confirmed by electrochemical STM-BJ at the single-molecule level, which displays a binary conductance switch ratio of about 400% at the redox potentials. This present work offers a molecular-level insight into the pyridine-mediated reaction process and electron transport in RTILs.
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Affiliation(s)
- Zhou Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Jie-Qiong Li
- Henan Engineering Center of New Energy Battery Materials, Henan D&A Engineering Center of Advanced Battery Materials, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Ya-Hao Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Jun-Qing Su
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Ying Fu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Wei Zou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Ju-Fang Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Xiao-Shun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, China
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22
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Limits in the Enhancement Factor in Near-Brewster Angle Reflection Pump-Probe Two-Dimensional Infrared Spectroscopy. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2111234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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23
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Vinogradov I, Singh S, Lyle H, Paolino M, Mandal A, Rossmeisl J, Cuk T. Free energy difference to create the M-OH * intermediate of the oxygen evolution reaction by time-resolved optical spectroscopy. NATURE MATERIALS 2022; 21:88-94. [PMID: 34725518 DOI: 10.1038/s41563-021-01118-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Theoretical descriptors differentiate the catalytic activity of materials for the oxygen evolution reaction by the strength of oxygen binding in the reactive intermediate created upon electron transfer. Recently, time-resolved spectroscopy of a photo-electrochemically driven oxygen evolution reaction followed the vibrational and optical spectra of this intermediate, denoted M-OH*. However, these inherently kinetic experiments have not been connected to the relevant thermodynamic quantities. Here we discover that picosecond optical spectra of the Ti-OH* population on lightly doped SrTiO3 are ordered by the surface hydroxylation. A Langmuir isotherm as a function of pH extracts an effective equilibrium constant relatable to the free energy difference of the first oxygen evolution reaction step. Thus, time-resolved spectroscopy of the catalytic surface reveals both kinetic and energetic information of elementary reaction steps, which provides a critical new connection between theory and experiment by which to tailor the pathway of water oxidation and other surface reactions.
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Affiliation(s)
- Ilya Vinogradov
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, Boulder, CO, USA
| | - Suryansh Singh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, Boulder, CO, USA
- Materials Science and Engineering Program, University of Colorado, Boulder, Boulder, CO, USA
| | - Hanna Lyle
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, Boulder, CO, USA
- Materials Science and Engineering Program, University of Colorado, Boulder, Boulder, CO, USA
| | - Michael Paolino
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, Boulder, CO, USA
| | - Aritra Mandal
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, Boulder, CO, USA.
| | - Jan Rossmeisl
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Tanja Cuk
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, Boulder, CO, USA.
- Materials Science and Engineering Program, University of Colorado, Boulder, Boulder, CO, USA.
- Department of Chemistry, University of Colorado, Boulder, Boulder, CO, USA.
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24
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Lewis NHC, Tokmakoff A. Lineshape Distortions in Internal Reflection Two-Dimensional Infrared Spectroscopy: Tuning across the Critical Angle. J Phys Chem Lett 2021; 12:11843-11849. [PMID: 34871004 PMCID: PMC8686116 DOI: 10.1021/acs.jpclett.1c03432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Reflection mode two-dimensional infrared spectroscopy (R-2DIR) has recently emerged as a tool that expands the utility of ultrafast IR spectroscopy toward a broader class of materials. The impact of experimental configurations on the potential distortions of the transient reflectance (TR) spectra has not been fully explored, particularly in the vicinity of the critical angle θc and through the crossover from total internal reflection to partial reflection. Here we study the impact on the spectral lineshape of a dilute bulk solution as θc is varied across the incident angle by tuning the refractive index of the solvent. We demonstrate the significance of several distortions, including the appearance of phase twisted lineshapes and apparent changes in the spectral inhomogeneity, and show how these distortions impact the interpretation of the TR and R-2DIR spectroscopies.
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25
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Barry E, Burns R, Chen W, De Hoe GX, De Oca JMM, de Pablo JJ, Dombrowski J, Elam JW, Felts AM, Galli G, Hack J, He Q, He X, Hoenig E, Iscen A, Kash B, Kung HH, Lewis NHC, Liu C, Ma X, Mane A, Martinson ABF, Mulfort KL, Murphy J, Mølhave K, Nealey P, Qiao Y, Rozyyev V, Schatz GC, Sibener SJ, Talapin D, Tiede DM, Tirrell MV, Tokmakoff A, Voth GA, Wang Z, Ye Z, Yesibolati M, Zaluzec NJ, Darling SB. Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport. Chem Rev 2021; 121:9450-9501. [PMID: 34213328 DOI: 10.1021/acs.chemrev.1c00069] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure, chemistry, and charge of interfaces between materials and aqueous fluids play a central role in determining properties and performance of numerous water systems. Sensors, membranes, sorbents, and heterogeneous catalysts almost uniformly rely on specific interactions between their surfaces and components dissolved or suspended in the water-and often the water molecules themselves-to detect and mitigate contaminants. Deleterious processes in these systems such as fouling, scaling (inorganic deposits), and corrosion are also governed by interfacial phenomena. Despite the importance of these interfaces, much remains to be learned about their multiscale interactions. Developing a deeper understanding of the molecular- and mesoscale phenomena at water/solid interfaces will be essential to driving innovation to address grand challenges in supplying sufficient fit-for-purpose water in the future. In this Review, we examine the current state of knowledge surrounding adsorption, reactivity, and transport in several key classes of water/solid interfaces, drawing on a synergistic combination of theory, simulation, and experiments, and provide an outlook for prioritizing strategic research directions.
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Affiliation(s)
- Edward Barry
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Raelyn Burns
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Wei Chen
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Guilhem X De Hoe
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Joan Manuel Montes De Oca
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Juan J de Pablo
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - James Dombrowski
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Jeffrey W Elam
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Alanna M Felts
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Giulia Galli
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - John Hack
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Qiming He
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Xiang He
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Eli Hoenig
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Aysenur Iscen
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Benjamin Kash
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Harold H Kung
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Nicholas H C Lewis
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Chong Liu
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Xinyou Ma
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Anil Mane
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Alex B F Martinson
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Karen L Mulfort
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Julia Murphy
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Kristian Mølhave
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, Kgs. Lyngby, Lyngby, Hovedstaden 2800, DK Denmark
| | - Paul Nealey
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Yijun Qiao
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Vepa Rozyyev
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - George C Schatz
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Steven J Sibener
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Dmitri Talapin
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - David M Tiede
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Matthew V Tirrell
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Andrei Tokmakoff
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Gregory A Voth
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Zhongyang Wang
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Zifan Ye
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Murat Yesibolati
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, Kgs. Lyngby, Lyngby, Hovedstaden 2800, DK Denmark
| | - Nestor J Zaluzec
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Photon Sciences Directorate, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Seth B Darling
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
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26
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Watson MD, Lee JC. Coupling chemical biology and vibrational spectroscopy for studies of amyloids in vitro and in cells. Curr Opin Chem Biol 2021; 64:90-97. [PMID: 34186291 DOI: 10.1016/j.cbpa.2021.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 01/21/2023]
Abstract
Amyloid diseases are characterized by the aggregation of various proteins to form insoluble β-sheet-rich fibrils leading to cell death. Vibrational spectroscopies have emerged as attractive methods to study this process because of the rich structural information that can be extracted without large, perturbative probes. Importantly, specific vibrations such as the amide-I band directly report on secondary structure changes, which are key features of amyloid formation. Beyond intrinsic vibrations, the incorporation of unnatural vibrational probes can improve sensitivity for secondary structure determination (e.g. isotopic labeling), can provide residue-specific information of the surrounding polarity (e.g. unnatural amino acid), and are translatable into cellular studies. Here, we review the latest studies that have leveraged tools from chemical biology for the incorporation of novel vibrational probes into amyloidogenic proteins for both mechanistic and cellular studies.
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Affiliation(s)
- Matthew D Watson
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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27
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Zhang Y, Tang J, Ni Z, Zhao Y, Jia F, Luo Q, Mao L, Zhu Z, Wang F. Real-Time Characterization of the Fine Structure and Dynamics of an Electrical Double Layer at Electrode-Electrolyte Interfaces. J Phys Chem Lett 2021; 12:5279-5285. [PMID: 34061525 DOI: 10.1021/acs.jpclett.1c01134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The chemisorption of an electrolyte species on electrode surfaces is ubiquitous and affects the dynamics and mechanism of various electrochemical reactions. Understanding of the chemical structure and property of the resulting electrical double layer is vital but limited. Herein, we operando probed the electrochemical interface between a gold electrode surface and a common electrolyte, phosphate buffer, using our newly developed in situ liquid secondary ion mass spectrometry. We surprisingly found that, on the positively charged gold electrode surface, sodium cations were anchored in the Stern layer in a partially dehydrated form by a formation of compact ion pairs with the accumulated phosphate anions. The resulting strong adsorption phase was further revealed to retard the electro-oxidation reaction of ascorbate. This finding addressed one major gap in the fundamental science of electrode-electrolyte interfaces, namely, where and how cations reside in the double layer to impose effects on electrochemical reactions, providing insights into the engineering of better electrochemical systems.
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Affiliation(s)
- Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jilin Tang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Ni
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Feifei Jia
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihua Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland 99354, Washington, United States
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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28
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Noriega R. Measuring the Multiscale Dynamics, Structure, and Function of Biomolecules at Interfaces. J Phys Chem B 2021; 125:5667-5675. [PMID: 34042455 DOI: 10.1021/acs.jpcb.1c01546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The individual and collective structure and properties of biomolecules can change dramatically when they are localized at an interface. However, the small spatial extent of interfacial regions poses challenges to the detailed characterization of multiscale processes that dictate the structure and function of large biological units such as peptides, proteins, or nucleic acids. This Perspective surveys a broad set of tools that provide new opportunities to probe complex, dynamic interfaces across the vast range of temporal regimes that connect molecular-scale events to macroscopic observables. An emphasis is placed on the integration over multiple time scales, the use of complementary techniques, and the incorporation of external stimuli to control interfacial properties with spatial, temporal, and chemical specificity.
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Affiliation(s)
- Rodrigo Noriega
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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29
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Kiefer LM, Michocki LB, Kubarych KJ. Transmission Mode 2D-IR Spectroelectrochemistry of In Situ Electrocatalytic Intermediates. J Phys Chem Lett 2021; 12:3712-3717. [PMID: 33835814 DOI: 10.1021/acs.jpclett.1c00504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Unraveling electrocatalytic mechanisms, as well as fundamental structural dynamics of intermediates, requires spectroscopy with high time and frequency resolution that can account for nonequilibrium in situ concentration changes inherent to electrochemistry. Two-dimensional infrared (2D-IR) spectroscopy is an ideal candidate, but several technical challenges have hindered development of this powerful tool for spectroelectrochemistry (SEC). We demonstrate a transmission-mode, optically transparent thin-layer electrochemical (OTTLE) cell adapted to 2D-IR-SEC to monitor the important Re(bpy)(CO)3Cl CO2-reduction electrocatalyst. 2D-IR-SEC reveals pronounced differences in both spectral diffusion time scales and spectral inhomogeneity in the singly reduced catalyst, [Re(bpy)(CO)3Cl]•-, relative to the starting Re(bpy)(CO)3Cl. Cross-peaks between well-resolved symmetric vibrations and congested low-frequency bands enable direct assignment of all distinct species during the electrochemical reaction. With this information, 2D-IR-SEC provides new mechanistic insights regarding unproductive, catalyst-degrading dimerization. 2D-IR-SEC opens new experimental windows into the electrocatalysis foundation of future energy conversion and greenhouse gas reduction.
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Affiliation(s)
- Laura M Kiefer
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Lindsay B Michocki
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Kevin J Kubarych
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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30
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Procacci B, Rutherford SH, Greetham GM, Towrie M, Parker AW, Robinson CV, Howle CR, Hunt NT. Differentiation of bacterial spores via 2D-IR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119319. [PMID: 33360210 DOI: 10.1016/j.saa.2020.119319] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Ultrafast 2D-IR spectroscopy is a powerful tool for understanding the spectroscopy and dynamics of biological molecules in the solution phase. A number of recent studies have begun to explore the utility of the information-rich 2D-IR spectra for analytical applications. Here, we report the application of ultrafast 2D-IR spectroscopy for the detection and classification of bacterial spores. 2D-IR spectra of Bacillus atrophaeus and Bacillus thuringiensis spores as dry films on CaF2 windows were obtained. The sporulated nature of the bacteria was confirmed using 2D-IR diagonal and off-diagonal peaks arising from the calcium dipicolinate CaDP·3H2O biomarker for sporulation. Distinctive peaks, in the protein amide I region of the spectrum were used to differentiate the two types of spore. The identified marker modes demonstrate the potential for the use of 2D-IR methods as a direct means of spore classification. We discuss these new results in perspective with the current state of analytical 2D-IR measurements, showing that the potential exists to apply 2D-IR spectroscopy to detect the spores on surfaces and in suspensions as well as in dry films. The results demonstrate how applying 2D-IR screening methodologies to spores would enable the creation of a library of spectra for classification purposes.
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Affiliation(s)
- Barbara Procacci
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Samantha H Rutherford
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Camilla V Robinson
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Christopher R Howle
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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31
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Versatility of Reverse Micelles: From Biomimetic Models to Nano (Bio)Sensor Design. Processes (Basel) 2021. [DOI: 10.3390/pr9020345] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
This paper presents an overview of the principal structural and dynamics characteristics of reverse micelles (RMs) in order to highlight their structural flexibility and versatility, along with the possibility to modulate their parameters in a controlled manner. The multifunctionality in a large range of different scientific fields is exemplified in two distinct directions: a theoretical model for mimicry of the biological microenvironment and practical application in the field of nanotechnology and nano-based sensors. RMs represent a convenient experimental approach that limits the drawbacks of the conventionally biological studies in vitro, while the particular structure confers them the status of simplified mimics of cells by reproducing a complex supramolecular organization in an artificial system. The biological relevance of RMs is discussed in some particular cases referring to confinement and a crowded environment, as well as the molecular dynamics of water and a cell membrane structure. The use of RMs in a range of applications seems to be more promising due to their structural and compositional flexibility, high efficiency, and selectivity. Advances in nanotechnology are based on developing new methods of nanomaterial synthesis and deposition. This review highlights the advantages of using RMs in the synthesis of nanoparticles with specific properties and in nano (bio)sensor design.
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32
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Kelsheimer CJ, Garrett-Roe S. Intramolecular Vibrational Energy Relaxation of CO 2 in Cross-Linked Poly(ethylene glycol) Diacrylate-Based Ion Gels. J Phys Chem B 2021; 125:1402-1415. [PMID: 32955891 DOI: 10.1021/acs.jpcb.0c06685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast two-dimensional infrared spectroscopy (2D-IR) and Fourier transform infrared spectroscopy (FTIR) were used to measure carbon dioxide (CO2) in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf2N]), cross-linked low-molecular-weight poly(ethylene glycol) diacrylate (PEGDA), and an ion gel composed of a 50 vol % blend of the two. The center frequency of the antisymmetric stretch, ν3, of CO2 shifts monotonically to lower wavenumbers with increasing polymer content, with the largest line width in the ion gel (6 cm-1). Increasing polymer content slows both spectral diffusion and vibrational energy relaxation (VER) rates. An unexpected excited-state absorbance peak appears in the 2D-IR of cross-linked PEGDA due to VER from the antisymmetric stretch into the bending mode, ν2. Thirty-two response functions are necessary to describe the observed features in the 2D-IR spectra. Nonlinear least-squares fitting extracts both spectral diffusion and VER rates. In the ion gel, CO2 exhibits spectral diffusion dynamics that lie between that of the pure compounds. The kinetics of VER reflect both fast excitation and de-excitation of the bending mode, similar to the ionic liquid (IL), and slow overall vibrational population relaxation, similar to the cross-linked polymer. The IL-like and polymer-like dynamics suggest that the CO2 resides at the interface of the two components in the ion gel.
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Affiliation(s)
- C J Kelsheimer
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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33
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Ye S, Zhong K, Zhang J, Hu W, Hirst JD, Zhang G, Mukamel S, Jiang J. A Machine Learning Protocol for Predicting Protein Infrared Spectra. J Am Chem Soc 2020; 142:19071-19077. [PMID: 33126795 DOI: 10.1021/jacs.0c06530] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive quantum-mechanical calculations in a fluctuating environment. Herein we present a novel machine learning protocol that uses a few key structural descriptors to rapidly predict amide I IR spectra of various proteins and agrees well with experiment. Its transferability enabled us to distinguish protein secondary structures, probe atomic structure variations with temperature, and monitor protein folding. This approach offers a cost-effective tool to model the relationship between protein spectra and their biological/chemical properties.
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Affiliation(s)
- Sheng Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Kai Zhong
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jinxiao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Wei Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Guozhen Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Shaul Mukamel
- Departments of Chemistry, and Physics & Astronomy, University of California, Irvine, California 92697, United States
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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34
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Heiner Z, Petrov V, Mero M. Efficient, sub-4-cycle, 1-µm-pumped optical parametric amplifier at 10 µm based on BaGa 4S 7. OPTICS LETTERS 2020; 45:5692-5695. [PMID: 33057261 DOI: 10.1364/ol.403856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
We report on a microjoule-scale mid-infrared optical parametric amplifier (OPA) based on the recently developed wide-bandgap orthorhombic crystal, BaGa4S7 (BGS) and directly compare its performance to that of LiGaS2 (LGS) in the same OPA setup. The source is based on a single OPA stage amplifying supercontinuum seed pulses with a quantum efficiency of 29% at an idler wavelength of 10 µm, featuring nominally carrier-envelope phase-stable pulses. As a result of pumping the OPA directly at 1 µm, the overall conversion efficiency far exceeds that of traditional schemes based on OPAs followed by difference frequency generation. Chirp compensation using bulk germanium resulted in 126 fs pulses covering the 7.6-11.5 µm spectral range. BGS holds great promise for power scaling due to its availability in larger single-crystal sizes than LGS.
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35
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36
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Chuntonov L, Rubtsov IV. Surface-enhanced ultrafast two-dimensional vibrational spectroscopy with engineered plasmonic nano-antennas. J Chem Phys 2020; 153:050902. [DOI: 10.1063/5.0013956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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37
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Tek G, Hamm P. A Correction Scheme for Fano Line Shapes in Two-Dimensional Infrared Spectroscopy. J Phys Chem Lett 2020; 11:6185-6190. [PMID: 32659094 DOI: 10.1021/acs.jpclett.0c01752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The asymmetry of Fano line shapes observed for metal-adsorbate systems is reflected in two-dimensional infrared (2D IR) spectroscopy as a distorted spectrum. A phenomenological correction scheme is proposed that transforms distorted 2D IR spectra into conventional spectra. To that end, a phase correction factor is first derived from the IR absorption spectrum of the sample by symmetrizing the asymmetric line shape and subsequently applied to the distorted 2D IR spectra. The concept is illustrated for a model system consisting of an organic molecule (p-mercaptobenzonitrile) adsorbed on a sputter-coated metal layer (Au). The correction scheme reveals conventional, easily interpretable 2D IR spectra.
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Affiliation(s)
- Gökçen Tek
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
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38
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Zhou L, Tian L, Zhang WK. Experimental consideration of two-dimensional Fourier transform spectroscopy. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2007125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Lie Tian
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Wen-kai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
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39
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Lesnicki D, Zhang Z, Bonn M, Sulpizi M, Backus EHG. Oberflächenladungen an der CaF
2
‐Wasser‐Grenzfläche erlauben eine sehr schnelle intermolekulare Übertragung von Schwingungsenergie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Dominika Lesnicki
- Institut für Physik Johannes Gutenberg Universität Mainz Staudingerweg 7 55099 Mainz Deutschland
| | - Zhen Zhang
- Abteilung für molekulare Spektroskopie Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Abteilung für molekulare Spektroskopie Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Marialore Sulpizi
- Institut für Physik Johannes Gutenberg Universität Mainz Staudingerweg 7 55099 Mainz Deutschland
| | - Ellen H. G. Backus
- Abteilung für molekulare Spektroskopie Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Fachbereich für Physikalische Chemie Universität Wien Währinger Strasse 42 1090 Vienna Österreich
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40
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Wang YL, Li B, Sarman S, Mocci F, Lu ZY, Yuan J, Laaksonen A, Fayer MD. Microstructural and Dynamical Heterogeneities in Ionic Liquids. Chem Rev 2020; 120:5798-5877. [PMID: 32292036 PMCID: PMC7349628 DOI: 10.1021/acs.chemrev.9b00693] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Ionic liquids (ILs) are a special category of molten salts solely composed of ions with varied molecular symmetry and charge delocalization. The versatility in combining varied cation-anion moieties and in functionalizing ions with different atoms and molecular groups contributes to their peculiar interactions ranging from weak isotropic associations to strong, specific, and anisotropic forces. A delicate interplay among intra- and intermolecular interactions facilitates the formation of heterogeneous microstructures and liquid morphologies, which further contributes to their striking dynamical properties. Microstructural and dynamical heterogeneities of ILs lead to their multifaceted properties described by an inherent designer feature, which makes ILs important candidates for novel solvents, electrolytes, and functional materials in academia and industrial applications. Due to a massive number of combinations of ion pairs with ion species having distinct molecular structures and IL mixtures containing varied molecular solvents, a comprehensive understanding of their hierarchical structural and dynamical quantities is of great significance for a rational selection of ILs with appropriate properties and thereafter advancing their macroscopic functionalities in applications. In this review, we comprehensively trace recent advances in understanding delicate interplay of strong and weak interactions that underpin their complex phase behaviors with a particular emphasis on understanding heterogeneous microstructures and dynamics of ILs in bulk liquids, in mixtures with cosolvents, and in interfacial regions.
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Affiliation(s)
- Yong-Lei Wang
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Bin Li
- School
of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, P. R. China
| | - Sten Sarman
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Francesca Mocci
- Department
of Chemical and Geological Sciences, University
of Cagliari, I-09042 Monserrato, Italy
| | - Zhong-Yuan Lu
- State
Key Laboratory of Supramolecular Structure and Materials, Institute
of Theoretical Chemistry, Jilin University, Changchun 130021, P. R. China
| | - Jiayin Yuan
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Aatto Laaksonen
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- State
Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 210009, P. R. China
- Centre of
Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry Aleea Grigore Ghica-Voda, 41A, 700487 Iasi, Romania
- Department
of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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41
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Lesnicki D, Zhang Z, Bonn M, Sulpizi M, Backus EHG. Surface Charges at the CaF 2 /Water Interface Allow Very Fast Intermolecular Vibrational-Energy Transfer. Angew Chem Int Ed Engl 2020; 59:13116-13121. [PMID: 32239715 PMCID: PMC7496624 DOI: 10.1002/anie.202004686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Indexed: 01/15/2023]
Abstract
We investigate the dynamics of water in contact with solid calcium fluoride, where at low pH, localized charges can develop upon fluorite dissolution. We use 2D surface‐specific vibrational spectroscopy to quantify the heterogeneity of the interfacial water (D2O) molecules and provide information about the sub‐picosecond vibrational‐energy‐relaxation dynamics at the buried solid/liquid interface. We find that strongly H‐bonded OD groups, with a vibrational frequency below 2500 cm−1, display very rapid spectral diffusion and vibrational relaxation; for weakly H‐bonded OD groups, above 2500 cm−1, the dynamics slows down substantially. Atomistic simulations based on electronic‐structure theory reveal the molecular origin of energy transport through the local H‐bond network. We conclude that strongly oriented H‐bonded water molecules in the adsorbed layer, whose orientation is pinned by the localized charge defects, can exchange vibrational energy very rapidly due to the strong collective dipole, compensating for a partially missing solvation shell.
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Affiliation(s)
- Dominika Lesnicki
- Institute of Physics, JohannesGutenberg University MainzStaudingerweg 755099MainzGermany
| | - Zhen Zhang
- Department for Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Mischa Bonn
- Department for Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Marialore Sulpizi
- Institute of Physics, JohannesGutenberg University MainzStaudingerweg 755099MainzGermany
| | - Ellen H. G. Backus
- Department for Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Department of Physical ChemistryUniversity of ViennaWähringer Strasse 421090ViennaAustria
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42
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Wu B, Breen JP, Xing X, Fayer MD. Controlling the Dynamics of Ionic Liquid Thin Films via Multilayer Surface Functionalization. J Am Chem Soc 2020; 142:9482-9492. [PMID: 32349470 DOI: 10.1021/jacs.0c03044] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The structural dynamics of planar thin films of an ionic liquid (IL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimNTf2) as a function of surface charge density and thickness were investigated using two-dimensional infrared (2D IR) spectroscopy. The films were made by spin coating a methanol solution of the IL on silica substrates that were functionalized with alkyl chains containing head groups that mimic the IL cation. The thicknesses of the ionic liquid films ranged from ∼50 to ∼250 nm. The dynamics of the films are slower than those in the bulk IL, becoming increasingly slow as the films become thinner. Control of the dynamics of the IL films can be achieved by adjusting the charge density on substrates through multilayer network surface functionalization. The charge density of the surface (number of positively charged groups in the network bound to the surface per unit area) is controlled by the duration of the functionalization reaction. As the charge density is increased, the IL dynamics become slower. For comparison, the surface was functionalized with three different neutral groups. Dynamics of the IL films on the functionalized neutral surfaces are faster than on any of the ionic surfaces but still slower than the bulk IL, even for the thickest films. These results can have implications in applications that employ ILs that have electrodes, such as batteries, as the electrode surface charge density will influence properties like diffusion close to the surface.
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Affiliation(s)
- Boning Wu
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - John P Breen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Xiangyu Xing
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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43
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Petti MK, Ostrander JS, Birdsall ER, Kunz MB, Armstrong ZT, Alperstein AM, Zanni MT. A Proposed Method to Obtain Surface Specificity with Pump-Probe and 2D Spectroscopies. J Phys Chem A 2020; 124:3471-3483. [PMID: 32255629 PMCID: PMC7993518 DOI: 10.1021/acs.jpca.9b11791] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Surfaces and interfaces are ubiquitous in nature. From cell membranes, to photovoltaic thin films, surfaces have important function in both biological and materials systems. Spectroscopic techniques have been developed to probe systems like these, such as sum frequency generation (SFG) spectroscopies. The advantage of SFG spectroscopy, a second-order spectroscopy, is that it can distinguish between signals produced from molecules in the bulk versus on the surface. We propose a polarization scheme for third-order spectroscopy experiments, such as pump-probe and 2D spectroscopy, to select for surface signals and not bulk signals. This proposed polarization condition uses one pulse perpendicular compared to the other three to isolate cross-peaks arising from molecules with polar and uniaxial (i.e., biaxial) order at a surface, while removing the signal from bulk isotropic molecules. In this work, we focus on two of these cases: XXXY and YYYX, which differ by the sign of the cross-peak they create. We compare this technique to SFG spectroscopy and vibrational circular dichroism to provide insight to the behavior of the cross-peak signal. We propose that these singularly cross-polarized schemes provide odd-ordered spectroscopies the surface-specificity typically associated with even-ordered techniques.
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Affiliation(s)
- Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Erin R Birdsall
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Miriam Bohlmann Kunz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Zachary T Armstrong
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ariel M Alperstein
- 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
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44
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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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45
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Dong X, Wang S, Yu P, Yang F, Zhao J, Wu LZ, Tung CH, Wang J. Ultrafast Vibrational Energy Transfer through the Covalent Bond and Intra- and Intermolecular Hydrogen Bonds in a Supramolecular Dimer by Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2020; 124:544-555. [PMID: 31873023 DOI: 10.1021/acs.jpcb.9b10431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, the structural fluctuations and vibrational energy transfer dynamics in a supramolecular homodimer model, which is composed of 2-(9-anthracene)ureido-6-(1-undecyl)-4[1H]-pyrimidinone (UPAn) with quadruple intermolecular and single intramolecular hydrogen bonds (HBs), have been examined using ultrafast two-dimensional infrared (2D IR) and steady-state IR spectroscopies. A less structurally fluctuating intermolecular HB is found between the pyrimidinone C═O and ureido N-H groups. However, a larger structurally fluctuating intramolecular HB is suggested by the equilibrium and dynamical line-shape measurements of the ureido C═O stretch. Further, dynamical time-dependent 2D IR diagonal and off-diagonal signals show that intra- and intermolecular vibrational energy transfer processes occur on the picosecond timescale, where the latter is more efficient due to intermolecular hydrogen bonding interaction and through-space interaction.
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Affiliation(s)
- Xueqian Dong
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Sumin Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials , Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,School of Materials and Chemical Engineering , Xi'an Technological University , Xi'an 710021 , P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Li-Zhu Wu
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China.,Key Laboratory of Photochemical Conversion and Optoelectronic Materials , Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Chen-Ho Tung
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China.,Key Laboratory of Photochemical Conversion and Optoelectronic Materials , Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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46
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Mackin RT, Cohn B, Chuntonov L, Rubtsov IV. Intense-field interaction regime with weak laser pulses and localized plasmonic enhancement: Reference-free demonstration by 3rd- and 5th-order infrared spectroscopies. J Chem Phys 2019; 151:121103. [DOI: 10.1063/1.5120531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Robert T. Mackin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Bar Cohn
- Schulich Faculty of Chemistry, and Solid State Institute, Technion, Haifa, Israel
| | - Lev Chuntonov
- Schulich Faculty of Chemistry, and Solid State Institute, Technion, Haifa, Israel
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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47
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Kas R, Ayemoba O, Firet NJ, Middelkoop J, Smith WA, Cuesta A. In-Situ Infrared Spectroscopy Applied to the Study of the Electrocatalytic Reduction of CO 2 : Theory, Practice and Challenges. Chemphyschem 2019; 20:2904-2925. [PMID: 31441195 DOI: 10.1002/cphc.201900533] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 08/22/2019] [Indexed: 11/11/2022]
Abstract
The field of electrochemical CO2 conversion is undergoing significant growth in terms of the number of publications and worldwide research groups involved. Despite improvements of the catalytic performance, the complex reaction mechanisms and solution chemistry of CO2 have resulted in a considerable amount of discrepancies between theoretical and experimental studies. A clear identification of the reaction mechanism and the catalytic sites are of key importance in order to allow for a qualitative breakthrough and, from an experimental perspective, calls for the use of in-situ or operando spectroscopic techniques. In-situ infrared spectroscopy can provide information on the nature of intermediate species and products in real time and, in some cases, with relatively high time resolution. In this contribution, we review key theoretical aspects of infrared reflection spectroscopy, followed by considerations of practical implementation. Finally, recent applications to the electrocatalytic reduction of CO2 are reviewed, including challenges associated with the detection of reaction intermediates.
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Affiliation(s)
- Recep Kas
- Department of Chemical Engineering, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Onagie Ayemoba
- School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK
| | - Nienke J Firet
- Department of Chemical Engineering, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Joost Middelkoop
- Department of Chemical Engineering, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Wilson A Smith
- Department of Chemical Engineering, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Angel Cuesta
- School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK
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48
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Hanson-Heine MW, George MW, Besley NA. Electronically excited state geometries and vibrational frequencies calculated using the algebraic diagrammatic construction scheme for the polarization propagator. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.04.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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49
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Ge A, Rudshteyn B, Videla PE, Miller CJ, Kubiak CP, Batista VS, Lian T. Heterogenized Molecular Catalysts: Vibrational Sum-Frequency Spectroscopic, Electrochemical, and Theoretical Investigations. Acc Chem Res 2019; 52:1289-1300. [PMID: 31056907 DOI: 10.1021/acs.accounts.9b00001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rhenium and manganese bipyridyl tricarbonyl complexes have attracted intense interest for their promising applications in photocatalytic and electrocatalytic CO2 reduction in both homogeneous and heterogenized systems. To date, there have been extensive studies on immobilizing Re catalysts on solid surfaces for higher catalytic efficiency, reduced catalyst loading, and convenient product separation. However, in order for the heterogenized molecular catalysts to achieve the combination of the best aspects of homogeneous and heterogeneous catalysts, it is essential to understand the fundamental physicochemical properties of such heterogeneous systems, such as surface-bound structures of Re/Mn catalysts, substrate-adsorbate interactions, and photoinduced or electric-field-induced effects on Re/Mn catalysts. For example, the surface may act to (un)block substrates, (un)trap charges, (de)stabilize particular intermediates (and thus affect scaling relations), and shift potentials in different directions, just as protein environments do. The close collaboration between the Lian, Batista, and Kubiak groups has resulted in an integrated approach to investigate how the semiconductor or metal surface affects the properties of the attached catalyst. Synthetic strategies to achieve stable and controlled attachment of Re/Mn molecular catalysts have been developed. Steady-state, time-resolved, and electrochemical vibrational sum-frequency generation (SFG) spectroscopic studies have provided insight into the effects of interfacial structures, ultrafast vibrational energy relaxation, and electric field on the Re/Mn catalysts, respectively. Various computational methods utilizing density functional theory (DFT) have been developed and applied to determine the molecular orientation by direct comparison to spectroscopy, unravel vibrational energy relaxation mechanisms, and quantify the interfacial electric field strength of the Re/Mn catalyst systems. This Account starts with a discussion of the recent progress in determining the surface-bound structures of Re catalysts on semiconductor and Au surfaces by a combined vibrational SFG and DFT study. The effects of crystal facet, length of anchoring ligands, and doping of the semiconductor on the bound structures of Re catalysts and of the substrate itself are discussed. This is followed by a summary of the progress in understanding the vibrational relaxation (VR) dynamics of Re catalysts covalently adsorbed on semiconductor and metal surfaces. The VR processes of Re catalysts on TiO2 films and TiO2 single crystals and a Re catalyst tethered on Au, particularly the role of electron-hole pair (EHP)-induced coupling on the VR of the Re catalyst bound on Au, are discussed. The Account also summarizes recent studies in quantifying the electric field strength experienced by the catalytically active site of the Re/Mn catalyst bound on a Au electrode based on a combined electrochemical SFG and DFT study of the Stark tuning of the CO stretching modes of these catalysts. Finally, future research directions on surface-immobilized molecular catalyst systems are discussed.
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Affiliation(s)
- Aimin Ge
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Benjamin Rudshteyn
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - Pablo E. Videla
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - Christopher J. Miller
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093, United States
| | - Clifford P. Kubiak
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093, United States
| | - Victor S. Batista
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093, United States
| | - Tianquan Lian
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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50
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Ghosh A, Prasad AK, Chuntonov L. Two-Dimensional Infrared Spectroscopy Reveals Molecular Self-Assembly on the Surface of Silver Nanoparticles. J Phys Chem Lett 2019; 10:2481-2486. [PMID: 30978284 DOI: 10.1021/acs.jpclett.9b00530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The conformation of molecules, peptides, and proteins, self-assembled into structured monolayers on the surface of metal nanoparticles (NPs), can strongly affect their properties and use in chemical or nanobiomedical applications. Elucidating molecular conformations on the NP surface is highly challenging, and the microscopic details mostly remain elusive. Using polarization-selective third-order two-dimensional ultrafast infrared spectroscopy, we revealed the highly ordered intermolecular structure of γ-tripeptide glutathione on the surface of silver NPs in aqueous solution. Glutathione is an antioxidant thiol abundant in living cells; it is extensively used in NP chemistry and related research. We identified conditions where the interaction of glutathione with the NP surface facilitates formation of a β-sheet-like structure enclosing the NPs. A spectroscopic signature associated with the assembly of β-sheets into an amyloid fibril-like structure was also observed. Remarkably, the interaction with the metal surface promotes formation of a fibril-like structure by a small peptide involving only two amino acids.
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Affiliation(s)
- Anup Ghosh
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Amit K Prasad
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
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