1
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Gan Z, Gloor CJ, Yan L, Zhong X, You W, Moran AM. Elucidating phonon dephasing mechanisms in layered perovskites with coherent Raman spectroscopies. J Chem Phys 2024; 161:074202. [PMID: 39158047 DOI: 10.1063/5.0216472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/29/2024] [Indexed: 08/20/2024] Open
Abstract
Organic-inorganic hybrid perovskite quantum wells exhibit electronic structures with properties intermediate between those of inorganic semiconductors and molecular crystals. In these systems, periodic layers of organic spacer molecules occupy the interstitial spaces between perovskite sheets, thereby confining electronic excitations to two dimensions. Here, we investigate spectroscopic line broadening mechanisms for phonons coupled to excitons in lead-iodide layered perovskites with phenyl ethyl ammonium (PEA) and azobenzene ethyl ammonium (AzoEA) spacer cations. Using a modified Elliot line shape analysis for the absorbance and photoluminescence spectra, polaron binding energies of 11.2 and 17.5 meV are calculated for (PEA)2PbI4 and (AzoEA)2PbI4, respectively. To determine whether the polaron stabilization processes influence the dephasing mechanisms of coupled phonons, five-pulse coherent Raman spectroscopies are applied to the two systems under electronically resonant conditions. The prominence of inhomogeneous line broadening mechanisms detected in (AzoEA)2PbI4 suggests that thermal fluctuations involving the deformable organic phase broaden the distributions of phonon frequencies within the quantum wells. In addition, our data indicate that polaron stabilization primarily involves photoinduced reorganization of the organic phases for both systems, whereas the impulsively excited phonons represent less than 10% of the total polaron binding energy. The signal generation mechanisms associated with our fifth-order coherent Raman experiments are explored with a perturbative model in which cumulant expansions are used to account for time-coincident vibrational dephasing and polaron stabilization processes.
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Affiliation(s)
- Zijian Gan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Camryn J Gloor
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Liang Yan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xiaowei Zhong
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Wei You
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Andrew M Moran
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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2
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Zhong K, Nguyen HL, Do TN, Tan HS, Knoester J, Jansen TLC. Coarse-Grained Approach to Simulate Signatures of Excitation Energy Transfer in Two-Dimensional Electronic Spectroscopy of Large Molecular Systems. J Chem Theory Comput 2024; 20:6111-6124. [PMID: 38996082 PMCID: PMC11270824 DOI: 10.1021/acs.jctc.4c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024]
Abstract
Two-dimensional electronic spectroscopy (2DES) has proven to be a highly effective technique in studying the properties of excited states and the process of excitation energy transfer in complex molecular assemblies, particularly in biological light-harvesting systems. However, the accurate simulation of 2DES for large systems still poses a challenge because of the heavy computational demands it entails. In an effort to overcome this limitation, we devised a coarse-grained 2DES method. This method encompasses the treatment of the entire system by dividing it into distinct weakly coupled segments, which are assumed to communicate predominantly through incoherent exciton transfer. We first demonstrate the efficiency of this method through simulation on a model dimer system, which demonstrates a marked improvement in calculation efficiency, with results that exhibit good concordance with reference spectra calculated with less approximate methods. Additionally, the application of this method to the light-harvesting antenna 2 (LH2) complex of purple bacteria showcases its advantages, accuracy, and limitations. Furthermore, simulating the anisotropy decay in LH2 induced by energy transfer and its comparison with experiments confirm that the method is capable of accurately describing dynamical processes in a biologically relevant system. This method presented lends itself to an extension that accounts for the effect of intrasegment relaxation processes on the 2DES spectra, which for computational efficiency are ignored in the implementation reported here. It is envisioned that the method will be employed in the future to accurately and efficiently calculate 2D spectra of more extensive systems, such as photosynthetic supercomplexes.
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Affiliation(s)
- Kai Zhong
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Hoang Long Nguyen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Thanh Nhut Do
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Howe-Siang Tan
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Jasper Knoester
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- Faculty
of Science, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
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3
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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4
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Barclay MS, Wright ND, Cavanaugh P, Pensack RD, Martin EW, Turner DB. Ultrabroadband two-dimensional electronic spectroscopy in the pump-probe geometry using conventional optics. OPTICS LETTERS 2024; 49:2065-2068. [PMID: 38621077 DOI: 10.1364/ol.519387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/14/2024] [Indexed: 04/17/2024]
Abstract
We report ultrabroadband two-dimensional electronic spectroscopy (2D ES) measurements obtained in the pump-probe geometry using conventional optics. A phase-stabilized Michelson interferometer provides the pump-pulse delay interval, τ1, necessary to obtain the excitation-frequency dimension. Spectral resolution of the probe beam provides the detection-frequency dimension, ω3. The interferometer incorporates active phase stabilization via a piezo stage and feedback from interference of a continuous-wave reference laser detected in quadrature. To demonstrate the method, we measured a well-characterized laser dye sample and obtained the known peak structure. The vibronic peaks are modulated as a function of the waiting time, τ2, by vibrational wave packets. The interferometer simplifies ultrabroadband 2D ES measurements and analysis.
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5
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McDonnell RP, Oram K, Boyer MA, Kohler DD, Meyer KA, Sibert Iii EL, Wright JC. Direct Probe of Vibrational Fingerprint and Combination Band Coupling. J Phys Chem Lett 2024; 15:3975-3981. [PMID: 38569133 DOI: 10.1021/acs.jpclett.4c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Vibrational fingerprints and combination bands are a direct measure of couplings that control molecular properties. However, most combination bands possess small transition dipoles. Here we use multiple, ultrafast coherent infrared pulses to resolve vibrational coupling between CH3CN fingerprint modes at 918 and 1039 cm-1 and combination bands in the 2750-6100 cm-1 region via doubly vibrationally enhanced (DOVE) coherent multidimensional spectroscopy (CMDS). This approach provides a direct probe of vibrational coupling between fingerprint modes and near-infrared combination bands of large and small transition dipoles in a molecular system over a large frequency range.
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Affiliation(s)
- Ryan P McDonnell
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Kelson Oram
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Mark A Boyer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Daniel D Kohler
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Kent A Meyer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Edwin L Sibert Iii
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - John C Wright
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
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6
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Zazubovich V, Jankowiak R. High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes. Int J Mol Sci 2024; 25:3850. [PMID: 38612659 PMCID: PMC11011720 DOI: 10.3390/ijms25073850] [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: 02/23/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Photosystem I (PSI) is one of the two main pigment-protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI3), PSI3 mutants, and PSI3-IsiA18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure-function relationship. We will focus on the so-called "red antenna states" of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI3 and PSI3-IsiA18 supercomplexes allowed us to make inferences about EET from the IsiA18 ring to the PSI3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA18 ring to the PSI3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.
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Affiliation(s)
- Valter Zazubovich
- Department of Physics, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
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7
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Kaufman E, Kohler DD, Sunden KF, Wright JC. Strategies for phase matching control in a multidimensional Floquet state spectroscopy. OPTICS LETTERS 2024; 49:610-613. [PMID: 38300071 DOI: 10.1364/ol.511808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024]
Abstract
Floquet state spectroscopy is an optical analogue of multiple quantum coherence nuclear magnetic resonance (MQC-NMR). Tunable ultrafast excitation pulses resonantly excite multiple states in a sample to form the Floquet state. The Floquet state emits multiple coherent beams at frequencies and in directions that conserve energy and momenta. The different output beams differ in the time ordering and coherences created by the excitation beams. They correspond to the different methodologies in the NMR family. Isolating a specific beam and monitoring the output intensity as a function of excitation frequencies creates multidimensional spectra containing cross-peaks between coupled states. The frequency range of the multidimensional spectra is limited by phase matching constraints. This paper presents a new, to the best of our knowledge, active phase matching strategy that increases the versatility of multidimensional Floquet state spectroscopy through both longer sample path lengths and larger spectral ranges.
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8
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Sayer T, Montoya-Castillo A. Efficient formulation of multitime generalized quantum master equations: Taming the cost of simulating 2D spectra. J Chem Phys 2024; 160:044108. [PMID: 38270238 DOI: 10.1063/5.0185578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024] Open
Abstract
Modern 4-wave mixing spectroscopies are expensive to obtain experimentally and computationally. In certain cases, the unfavorable scaling of quantum dynamics problems can be improved using a generalized quantum master equation (GQME) approach. However, the inclusion of multiple (light-matter) interactions complicates the equation of motion and leads to seemingly unavoidable cubic scaling in time. In this paper, we present a formulation that greatly simplifies and reduces the computational cost of previous work that extended the GQME framework to treat arbitrary numbers of quantum measurements. Specifically, we remove the time derivatives of quantum correlation functions from the modified Mori-Nakajima-Zwanzig framework by switching to a discrete-convolution implementation inspired by the transfer tensor approach. We then demonstrate the method's capabilities by simulating 2D electronic spectra for the excitation-energy-transfer dimer model. In our method, the resolution of data can be arbitrarily coarsened, especially along the t2 axis, which mirrors how the data are obtained experimentally. Even in a modest case, this demands O(103) fewer data points. We are further able to decompose the spectra into one-, two-, and three-time correlations, showing how and when the system enters a Markovian regime where further measurements are unnecessary to predict future spectra and the scaling becomes quadratic. This offers the ability to generate long-time spectra using only short-time data, enabling access to timescales previously beyond the reach of standard methodologies.
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Affiliation(s)
- Thomas Sayer
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
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9
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Ryan M, Gao L, Valiyaveetil FI, Kananenka AA, Zanni MT. Water inside the Selectivity Filter of a K + Ion Channel: Structural Heterogeneity, Picosecond Dynamics, and Hydrogen Bonding. J Am Chem Soc 2024; 146:1543-1553. [PMID: 38181505 PMCID: PMC10797622 DOI: 10.1021/jacs.3c11513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
Water inside biological ion channels regulates the key properties of these proteins, such as selectivity, ion conductance, and gating. In this article, we measure the picosecond spectral diffusion of amide I vibrations of an isotope-labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100-2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope-labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D line shapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent or nonadjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations was observed on a picosecond timescale. These dynamics are in stark contrast with liquid water, which remains highly dynamic even in the presence of ions at high concentrations.
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Affiliation(s)
- Matthew
J. Ryan
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lujia Gao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Francis I. Valiyaveetil
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Alexei A. Kananenka
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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10
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Toutounji M. Homogeneous Dephasing in Photosynthetic Bacterial Reaction Centers: Time Correlation Function Approach. Chemphyschem 2024; 25:e202300335. [PMID: 37953408 DOI: 10.1002/cphc.202300335] [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: 05/09/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
A new tractable linear electronic transition dipole moment time correlation function (ETDMTCF) that accurately accounts for electronic dephasing, asymmetry, and width of 1-phonon profile, which the zero-phonon line (ZPL) contributes to it, in Rhodopseudomonas viridis bacterial reaction center is derived. This time correlation function proves to be superior to other frequency-domain expressions in case of strong electron-phonon coupling (which is often the case in bacterial RCs and pigment-protein complexes), many vibrational modes involved, and high temperature, whereby more vibronic and electronic (sequence) transitions would arise. The Fourier transform of this ETDMTCF leads to asymmetric multiphonon profiles composed of Lorentzian distribution and Gaussian distribution on the high- and low-energy sides, respectively, whereby the overtone widths fold themselves with that of the one-phonon profile. This ETDMTCF also features expedient computation in large systems using asymmetric phonon profiles to account correctly for dephasing and pigment-protein interaction (electron-phonon coupling). The derived ETDMTCF allows computing all nonlinear optical signals in both time and frequency domains, through the nonlinear dipole moment time correlation functions (as guided by nonlinear optical response theory) in line with the eight Liouville space pathways. The linear transition dipole moment time correlation function is of a central value as the nonlinear transition dipole moment time correlation function is expressed in terms of the linear transition dipole moment time correlation function, derived herein. One of the great advantages of presenting this ETDMTCF is its applicability to nonlinear transition dipole moment time correlation functions in line with the eight Liouville space pathways needed in computing nonlinear signals. As such, there is more to the utility and applicability of the presented ETDMTCF besides computational expediency and efficiency. Results show good agreement with the reported literature. The intimate connection between a one-phonon profile and the corresponding bath spectral density in photosynthetic complexes is discussed.
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Affiliation(s)
- Mohamad Toutounji
- College of Science, Department of Chemistry, P. O. Box 15551, UAE University, Al-Ain, United Arab Emirate
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11
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Wiethorn ZR, Hunter KE, Zuehlsdorff TJ, Montoya-Castillo A. Beyond the Condon limit: Condensed phase optical spectra from atomistic simulations. J Chem Phys 2023; 159:244114. [PMID: 38153146 DOI: 10.1063/5.0180405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
While dark transitions made bright by molecular motions determine the optoelectronic properties of many materials, simulating such non-Condon effects in condensed phase spectroscopy remains a fundamental challenge. We derive a Gaussian theory to predict and analyze condensed phase optical spectra beyond the Condon limit. Our theory introduces novel quantities that encode how nuclear motions modulate the energy gap and transition dipole of electronic transitions in the form of spectral densities. By formulating the theory through a statistical framework of thermal averages and fluctuations, we circumvent the limitations of widely used microscopically harmonic theories, allowing us to tackle systems with generally anharmonic atomistic interactions and non-Condon fluctuations of arbitrary strength. We show how to calculate these spectral densities using first-principles simulations, capturing realistic molecular interactions and incorporating finite-temperature, disorder, and dynamical effects. Our theory accurately predicts the spectra of systems known to exhibit strong non-Condon effects (phenolate in various solvents) and reveals distinct mechanisms for electronic peak splitting: timescale separation of modes that tune non-Condon effects and spectral interference from correlated energy gap and transition dipole fluctuations. We further introduce analysis tools to identify how intramolecular vibrations, solute-solvent interactions, and environmental polarization effects impact dark transitions. Moreover, we prove an upper bound on the strength of cross correlated energy gap and transition dipole fluctuations, thereby elucidating a simple condition that a system must follow for our theory to accurately predict its spectrum.
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Affiliation(s)
- Zachary R Wiethorn
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Kye E Hunter
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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12
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Malik R, Chandra A, Das B, Chandra A. Theoretical Study of the Two-Dimensional Vibrational Sum Frequency Generation Spectroscopy of the Air-Water Interface at Varying Temperature and Its Connections to the Interfacial Structure and Dynamics. J Phys Chem B 2023; 127:10880-10895. [PMID: 38055625 DOI: 10.1021/acs.jpcb.3c03205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We performed a theoretical study of the temperature variation of two-dimensional vibrational sum frequency generation (2D-VSFG) spectra of the OH stretch modes at air-water interfaces in the mid-IR region. The calculations are performed at four different temperatures from 250 to 325 K by using a combination of techniques involving response function formalism of nonlinear spectroscopy, electronic structure calculations, and molecular dynamics simulations. Also, the calculations are performed for isotopically dilute solutions so that the intra- and intermolecular coupling between the vibrational modes of interest can be ignored. We have established the connections of temperature variation of various frequency- and time-dependent features of the calculated spectra to the changes in the underlying structure and dynamics of the interfaces. The results reveal that interfacial water is dynamically more heterogeneous than bulk water, with three dominant dynamical processes exhibiting their corresponding time-dependent features in the 2D-VSFG spectrum. These are the spectral diffusion of hydrogen-bonded OH groups at the interface, conversion of an initially hydrogen-bonded OH group to a dangling OH which is a stable state for surface water, unlike the bulk water, and the third one, which involves the conversion of an initially free or dangling OH group to its hydrogen-bonded state at the interface. The temporal appearance of the cross peaks corresponding to interconversion of the hydrogen-bonded state to the dangling state or vice versa of an interfacial OH group is found to take place at a slower rate than the dynamics of spectral diffusion of hydrogen-bonded molecules at the interface, which, in turn, is slower than the corresponding spectral diffusion of bulk water molecules. The temperature variation of these dynamic processes can be linked to the decay of appropriate hydrogen-bond and non-hydrogen-bond time correlation functions of interfacial water molecules for the different air-water systems studied in this work.
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Affiliation(s)
- Ravi Malik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Abhilash Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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13
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Ryan MJ, Gao L, Valiyaveetil FI, Kananenka AA, Zanni MT. Water inside the selectivity filter of a K + ion channel: structural heterogeneity, picosecond dynamics, and hydrogen-bonding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567415. [PMID: 38014355 PMCID: PMC10680850 DOI: 10.1101/2023.11.16.567415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Water inside biological ion channels regulates the key properties of these proteins such as selectivity, ion conductance, and gating. In this Article we measure the picosecond spectral diffusion of amide I vibrations of an isotope labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100 - 2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D lineshapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent, or non-adjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations were observed on a picosecond timescale. These dynamics are in stark contrast with liquid water that remains highly dynamic even in the presence of ions at high concentrations.
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Affiliation(s)
- Matthew J. Ryan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lujia Gao
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Francis I. Valiyaveetil
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexei A. Kananenka
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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14
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Lim C, Jeon J, Park K, Liang C, Chae Y, Kwak K, Cho M. Revisiting Ultrafast Dynamics in Carbonate-Based Electrolytes for Li-Ion Batteries: Clarifying 2D-IR Cross-Peak Interpretation. J Phys Chem B 2023; 127:9566-9574. [PMID: 37905968 DOI: 10.1021/acs.jpcb.3c05480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Understanding chemical exchange in carbonate-based electrolytes employed in Li-ion batteries (LIBs) is crucial for elucidating ion transport mechanisms. Ultrafast two-dimensional (2D) IR spectroscopy has been widely used to investigate the solvation structure and dynamics of Li-ions in organic carbonate-based electrolytes. However, the interpretation of cross-peaks observed in picosecond carbonyl stretch 2D-IR spectra has remained contentious. These cross-peaks could arise from various phenomena, including vibrational couplings between neighboring carbonyl groups in the first solvation shell around Li-ions, vibrational excitation transfers between carbonyl groups in distinct solvation environments, and local heating effects. Therefore, it is imperative to resolve the interpretation of 2D-IR cross-peaks to avoid misinterpretations regarding ultrafast dynamics found in LIB carbonate-based electrolytes. In this study, we have taken a comprehensive investigation of carbonate-based electrolytes utilizing 2D-IR spectroscopy and molecular dynamics (MD) simulations. Through meticulous analyses and interpretations, we have identified that the cross-peaks observed in the picosecond 2D-IR spectra of LIB electrolytes predominantly arise from intermolecular vibrational excitation transfer processes between the carbonyl groups of Li-bound and free carbonate molecules. We further discuss the limitations of employing a picosecond 2D-IR spectroscopic technique to study chemical exchange and intermolecular vibrational excitation transfer processes, particularly when the effects of the molecular photothermal process cannot be ignored. Our findings shed light on the dynamics of LIB electrolytes and resolve the controversy related to 2D-IR cross-peaks. By discerning the origin of these features, we could provide valuable insights for the design and optimization of next-generation Li-ion batteries.
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Affiliation(s)
- Chaiho Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jonggu Jeon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
| | - Kwanghee Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Chungwen Liang
- Creyon Bio Inc., San Diego, California 92121, United States
| | - Yeongseok Chae
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
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15
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Ma Z, Chen L, Xu C, Fournier JA. Two-Dimensional Infrared Spectroscopy of Isolated Molecular Ions. J Phys Chem Lett 2023; 14:9683-9689. [PMID: 37871134 DOI: 10.1021/acs.jpclett.3c02661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Two-dimensional infrared (2D IR) spectroscopy of mass-selected, cryogenically cooled molecular ions is presented. Nonlinear response pathways, encoded in the time-domain photodissociation action response of weakly bound N2 messenger tags, were isolated using pulse shaping techniques following excitation with four collinear ultrafast IR pulses. 2D IR spectra of Re(CO)3(CH3CN)3+ ions capture off-diagonal cross-peak bleach signals between the asymmetric and symmetric carbonyl stretching transitions. These cross peaks display intensity variations as a function of pump-probe delay time due to coherent coupling between the vibrational modes. Well-resolved 2D IR features in the congested fingerprint region of protonated caffeine (C8H10N4O2H+) are also reported. Importantly, intense cross-peak signals were observed at 3 ps waiting time, indicating that tag-loss dynamics are not competing with the measured nonlinear signals. These demonstrations pave the way for more precise studies of molecular interactions and dynamics that are not easily obtainable with current condensed-phase methodologies.
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Affiliation(s)
- Zifan Ma
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Liangyi Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Chuzhi Xu
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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16
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Brüggemann J, Chekmeneva M, Wolter M, Jacob CR. Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra. J Phys Chem Lett 2023; 14:9257-9264. [PMID: 37812580 PMCID: PMC10591501 DOI: 10.1021/acs.jpclett.3c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.
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Affiliation(s)
- Julia Brüggemann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Maria Chekmeneva
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
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17
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Yang J, Cong Y, Li Y, Li H. Machine Learning Approach Based on a Range-Corrected Deep Potential Model for Efficient Vibrational Frequency Computation. J Chem Theory Comput 2023; 19:6366-6374. [PMID: 37652890 DOI: 10.1021/acs.jctc.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
As an ensemble average result, vibrational spectrum simulation can be time-consuming with high accuracy methods. We present a machine learning approach based on the range-corrected deep potential (DPRc) model to improve the computing efficiency. The DPRc method divides the system into "probe region" and "solvent region"; "solvent-solvent" interactions are not counted in the neural network. We applied the approach to two systems: formic acid C═O stretching and MeCN C≡N stretching vibrational frequency shifts in water. All data sets were prepared using the quantum vibration perturbation approach. Effects of different region divisions, one-body correction, cut range, and training data size were tested. The model with a single-molecule "probe region" showed stable accuracy; it ran roughly 10 times faster than regular deep potential and reduced the training time by about four. The approach is efficient, easy to apply, and extendable to calculating various spectra.
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Affiliation(s)
- Jitai Yang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Yang Cong
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - You Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
| | - Hui Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, P. R. China
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18
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Malik R, Chandra A. Counteracting Effects of Trimethylamine N-Oxide against Urea in Aqueous Solutions: Insights from Theoretical Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2023; 127:7372-7383. [PMID: 37566900 DOI: 10.1021/acs.jpcb.3c03864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
The study of small osmolytes in their aqueous solutions has gained significant attention because of their relevance to structure and thermodynamics of proteins in aqueous media. Special attention has been given to the binary and ternary aqueous solutions of urea and trimethylamine N-oxide (TMAO). Urea is a well-known protein denaturant, while TMAO protects proteins in their native states. Interestingly, TMAO counteracts urea's ability to denature proteins when present in solutions with approximately half of the concentration of urea. Vibrational spectroscopy can improve our understanding of the molecular origin of this counteracting effect because of its sensitivity to local structure and dynamics. We present results of theoretical linear vibrational and two-dimensional infrared (2DIR) spectroscopy of water in the binary and ternary aqueous solutions of TMAO and urea. The 2DIR spectra are calculated using the electronic structure/molecular dynamics approach. The non-Condon effects in spectral transitions are incorporated in the theoretical calculations of 2DIR spectra. It is found that TMAO disrupts the local structure of water, while urea leaves it essentially unaffected. The 2DIR results show that both TMAO and urea slow down the dynamics of spectral diffusion of water. The extent of slowing down is found to be particularly significant for both hydration and bulk water in the presence of TMAO which can be attributed to strong hydrogen bonds between the water and TMAO molecules. The water molecules present in the hydration layer of the solutes in the ternary solutions are found to relax at even slower rates compared to that in their binary solutions in water. The hydrogen bonds between TMAO and urea are found to be not stable. Thus, the counteracting effect of TMAO against urea is seen to take place mainly through water-mediated interactions. Such TMAO-induced effects giving rise to more structured and slower hydrogen-bonded network are successfully captured through 2DIR spectroscopic calculations.
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Affiliation(s)
- Ravi Malik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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19
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Gross N, Kuhs CT, Ostovar B, Chiang WY, Wilson KS, Volek TS, Faitz ZM, Carlin CC, Dionne JA, Zanni MT, Gruebele M, Roberts ST, Link S, Landes CF. Progress and Prospects in Optical Ultrafast Microscopy in the Visible Spectral Region: Transient Absorption and Two-Dimensional Microscopy. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:14557-14586. [PMID: 37554548 PMCID: PMC10406104 DOI: 10.1021/acs.jpcc.3c02091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/24/2023] [Indexed: 08/10/2023]
Abstract
Ultrafast optical microscopy, generally employed by incorporating ultrafast laser pulses into microscopes, can provide spatially resolved mechanistic insight into scientific problems ranging from hot carrier dynamics to biological imaging. This Review discusses the progress in different ultrafast microscopy techniques, with a focus on transient absorption and two-dimensional microscopy. We review the underlying principles of these techniques and discuss their respective advantages and applicability to different scientific questions. We also examine in detail how instrument parameters such as sensitivity, laser power, and temporal and spatial resolution must be addressed. Finally, we comment on future developments and emerging opportunities in the field of ultrafast microscopy.
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Affiliation(s)
- Niklas Gross
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Christopher T. Kuhs
- Army
Research Laboratory-South, U.S. Army DEVCOM, Houston, Texas 77005, United States
| | - Behnaz Ostovar
- Department
of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Wei-Yi Chiang
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Kelly S. Wilson
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Tanner S. Volek
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Zachary M. Faitz
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Claire C. Carlin
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
| | - Jennifer A. Dionne
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
- Department
of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, California 94305, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Martin Gruebele
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sean T. Roberts
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Stephan Link
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
- Department
of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Christy F. Landes
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
- Department
of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
- Department
of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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20
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Chen MS, Mao Y, Snider A, Gupta P, Montoya-Castillo A, Zuehlsdorff TJ, Isborn CM, Markland TE. Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure. J Phys Chem Lett 2023; 14:6610-6619. [PMID: 37459252 DOI: 10.1021/acs.jpclett.3c01444] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. We show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Andrew Snider
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Prachi Gupta
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Andrés Montoya-Castillo
- Department of Chemistry, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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21
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Gu B, Sun S, Chen F, Mukamel S. Photoelectron spectroscopy with entangled photons; enhanced spectrotemporal resolution. Proc Natl Acad Sci U S A 2023; 120:e2300541120. [PMID: 37186860 PMCID: PMC10214152 DOI: 10.1073/pnas.2300541120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
In this theoretical study, we show how photoelectron signals generated by time-energy entangled photon pairs can monitor ultrafast excited state dynamics of molecules with high joint spectral and temporal resolutions, not limited by the Fourier uncertainty of classical light. This technique scales linearly, rather than quadratically, with the pump intensity, allowing the study of fragile biological samples with low photon fluxes. Since the spectral resolution is achieved by electron detection and the temporal resolution by a variable phase delay, this technique does not require scanning the pump frequency and the entanglement times, which significantly simplifies the experimental setup, making it feasible with current instrumentation. Application is made to the photodissociation dynamics of pyrrole calculated by exact nonadiabatic wave packet simulations in a reduced two nuclear coordinate space. This study demonstrates the unique advantages of ultrafast quantum light spectroscopy.
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Affiliation(s)
- Bing Gu
- Department of Chemistry, School of Science, Westlake University, Hangzhou, Zhejiang310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang310024, China
| | - Shichao Sun
- Department of Chemistry, University of California, Irvine, CA92697
- Department of Physics and Astronomy, University of California, Irvine, CA92697
| | - Feng Chen
- Department of Chemistry, University of California, Irvine, CA92697
- Department of Physics and Astronomy, University of California, Irvine, CA92697
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, CA92697
- Department of Physics and Astronomy, University of California, Irvine, CA92697
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22
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Malik R, Das B, Chandra A. Theoretical Two Dimensional Infrared Spectroscopy of Aqueous Solutions of tert-Butyl Alcohol: Variation of the Dynamics of Spectral Diffusion along the Percolation Transition. J Phys Chem B 2023; 127:4099-4111. [PMID: 37126459 DOI: 10.1021/acs.jpcb.2c08916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Binary mixtures of water and tert-butyl alcohol (TBA) are known to exhibit the so-called percolation transition where small clusters of TBA molecules span into large aggregates beyond a threshold concentration of the alcohol. In the present study, we have investigated the linear and two-dimensional infrared spectral features of aqueous solutions of TBA for varying concentration of the alcohol along the percolation transition. The percolation transition is characterized through calculations of intermolecular radial distribution functions and average size of the largest cluster of TBA molecules. It is found that, with variation of alcohol concentration, the radial distribution functions of the central carbon atoms of TBA molecules show a nonmonotonic change in the height of the first peak and also the size of the largest cluster of TBA molecules show a jump in the increase of its size for TBA mole fraction between 0.04 and 0.06 corresponding to a transition from smaller clusters to larger spanning aggregates. However, it is found that the linear infrared spectrum of water does not exhibit any noticeable changes on variation of TBA concentration along the percolation transition. Subsequently, two-dimensional infrared (2DIR) spectra and vibrational frequency time correlation function of water are calculated for all the TBA-water solutions considered in this study. The spectral diffusion of water calculated from 2DIR is found to slow down with increase of the TBA concentration. The time scales of spectral diffusion of water, as characterized by the relaxation of frequency time correlation function, 2DIR metric of central line slope, and also the hydrogen bond time correlation functions, are found to exhibit a noticeable jump along the percolation transition. The hydrophilic group of TBA is found to retard the water dynamics more effectively than the hydrophobic groups. Also, the jump in the dynamical slowdown along the percolation transition is found to be more significant for water molecules at the hydrophilic sites.
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Affiliation(s)
- Ravi Malik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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23
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Hedse A, Kalaee AAS, Wacker A, Pullerits T. Pulse overlap artifacts and double quantum coherence spectroscopy. J Chem Phys 2023; 158:141104. [PMID: 37061484 DOI: 10.1063/5.0146148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
The double quantum coherence (DQC) signal in nonlinear spectroscopy gives information about the many-body correlation effects not easily available by other methods. The signal is short-lived, consequently, a significant part of it is generated during the pulse overlap. Since the signal is at two times the laser frequency, one may intuitively expect that the pulse overlap-related artifacts are filtered out by the Fourier transform. Here, we show that this is not the case. We perform explicit calculations of phase-modulated two-pulse experiments of a two-level system where the DQC is impossible. Still, we obtain a significant signal at the modulation frequency, which corresponds to the DQC, while the Fourier transform over the pulse delay shows a double frequency. We repeat the calculations with a three-level system where the true DQC signal occurs. We conclude that with realistic dephasing times, the pulse-overlap artifact can be significantly stronger than the DQC signal. Our results call for great care when analyzing such experiments. As a rule of thumb, we recommend that only delays larger than 1.5 times the pulse length should be used.
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Affiliation(s)
- Albin Hedse
- Chemical Physics and NanoLund, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | | | - Andreas Wacker
- Mathematical Physics and NanoLund, Lund University, P.O. Box 118, 22100 Lund, Sweden
| | - Tõnu Pullerits
- Chemical Physics and NanoLund, Lund University, P.O. Box 124, 22100 Lund, Sweden
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24
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Kim T, Feng Y, O'Connor JP, Stoddart JF, Young RM, Wasielewski MR. Coherent Vibronic Wavepackets Show Structure-Directed Charge Flow in Host-Guest Donor-Acceptor Complexes. J Am Chem Soc 2023. [PMID: 37018535 DOI: 10.1021/jacs.2c13576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Designing and controlling charge transfer (CT) pathways in organic semiconductors are important for solar energy applications. To be useful, a photogenerated, Coulombically bound CT exciton must further separate into free charge carriers; direct observations of the detailed CT relaxation pathways, however, are lacking. Here, photoinduced CT and relaxation dynamics in three host-guest complexes, where a perylene (Per) electron donor guest is incorporated into two symmetric and one asymmetric extended viologen cyclophane acceptor hosts, are presented. The central ring in the extended viologen is either p-phenylene (ExV2+) or electron-rich 2,5-dimethoxy-p-phenylene (ExMeOV2+), resulting in two symmetric cyclophanes with unsubstituted or methoxy-substituted central rings, ExBox4+ and ExMeOBox4+, respectively, and an asymmetric cyclophane with one of the central viologen rings being methoxylated ExMeOVBox4+. Upon photoexcitation, the asymmetric host-guest ExMeOVBox4+ ⊃ Per complex exhibits directional CT toward the energetically unfavorable methoxylated side due to structural restrictions that facilitate strong interactions between the Per donor and the ExMeOV2+ side. The CT state relaxation pathways are probed using ultrafast optical spectroscopy by focusing on coherent vibronic wavepackets, which are used to identify CT relaxations along charge localization and vibronic decoherence coordinates. Specific low- and high-frequency nuclear motions are direct indicators of a delocalized CT state and the degree of CT character. Our results show that the CT pathway can be controlled by subtle chemical modifications of the acceptor host in addition to illustrating how coherent vibronic wavepackets can be used to probe the nature and time evolution of the CT states.
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Affiliation(s)
- Taeyeon Kim
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Yuanning Feng
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - James P O'Connor
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - J Fraser Stoddart
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Ryan M Young
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Michael R Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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25
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Malik R, Chandra A, Das B, Chandra A. Temperature Dependence of Non-Condon Effects in Two-Dimensional Vibrational Spectroscopy of Water. J Phys Chem B 2023; 127:2488-2498. [PMID: 36893383 DOI: 10.1021/acs.jpcb.2c06794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Non-Condon effects in vibrational spectroscopy refers to the dependence of a molecule's vibrational transition dipole and polarizability on the coordinates of the surrounding environment. Earlier studies have shown that such effects can be pronounced for hydrogen-bonded systems like liquid water. Here, we present a theoretical study of two-dimensional vibrational spectroscopy under the non-Condon and Condon approximations at varying temperatures. We have performed calculations of both two-dimensional infrared and two-dimensional vibrational Raman spectra to gain insights into the temperature dependence of non-Condon effects in nonlinear vibrational spectroscopy. The two-dimensional spectra are calculated for the OH vibration of interest in the isotopic dilution limit where the coupling between the oscillators is ignored. Generally, both the infrared and Raman line shapes undergo red shifts with decrease in temperature due to strengthening of hydrogen bonds and decrease in the fraction of OH modes with weaker or no hydrogen bonds. The infrared line shape is further red-shifted under the non-Condon effects at a given temperature, while the Raman line shape does not show any such red shift due to non-Condon effects. The spectral dynamics becomes slower on decrease of temperature due to slower hydrogen bond relaxation and, for a given temperature, the spectral diffusion occurs at a faster rate upon inclusion of non-Condon effects. The time scales of spectral diffusion extracted from different metrics agree well with each other and also with experiments. The changes in the spectrum due to non-Condon effects are found to be more significant at lower temperatures.
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Affiliation(s)
- Ravi Malik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Abhilash Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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26
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Stingel AM, Leemans J, Hens Z, Geiregat P, Petersen PB. Narrow homogeneous linewidths and slow cooling dynamics across infrared intra-band transitions in n-doped HgSe colloidal quantum dots. J Chem Phys 2023; 158:114202. [PMID: 36948807 DOI: 10.1063/5.0139795] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Intra-band transitions in colloidal quantum dots (QDs) are promising for opto-electronic applications in the mid-IR spectral region. However, such intra-band transitions are typically very broad and spectrally overlapping, making the study of individual excited states and their ultrafast dynamics very challenging. Here, we present the first full spectrum two-dimensional continuum infrared (2D CIR) spectroscopy study of intrinsically n-doped HgSe QDs, which exhibit mid-infrared intra-band transitions in their ground state. The obtained 2D CIR spectra reveal that underneath the broad absorption line shape of ∼500 cm-1, the transitions exhibit surprisingly narrow intrinsic linewidths with a homogeneous broadening of 175-250 cm-1. Furthermore, the 2D IR spectra are remarkably invariant, with no sign of spectral diffusion dynamics at waiting times up to 50 ps. Accordingly, we attribute the large static inhomogeneous broadening to the distribution of size and doping level of the QDs. In addition, the two higher-lying P-states of the QDs can be clearly identified in the 2D IR spectra along the diagonal with a cross-peak. However, there is no indication of cross-peak dynamics indicating that, despite the strong spin-orbit coupling in HgSe, transitions between the P-states must be longer than our maximum waiting time of 50 ps. This study illustrates a new frontier of 2D IR spectroscopy enabling the study of intra-band carrier dynamics in nanocrystalline materials across the entire mid-infrared spectrum.
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Affiliation(s)
- Ashley M Stingel
- Physical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Jari Leemans
- Physics and Chemistry of Nanostructures Group, Department of Chemistry, Faculty of Sciences, Ghent University, 9000 Gent, Belgium
| | - Zeger Hens
- Physics and Chemistry of Nanostructures Group, Department of Chemistry, Faculty of Sciences, Ghent University, 9000 Gent, Belgium
| | - Pieter Geiregat
- Physics and Chemistry of Nanostructures Group, Department of Chemistry, Faculty of Sciences, Ghent University, 9000 Gent, Belgium
| | - Poul B Petersen
- Physical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Bochum, Germany
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27
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Garrett P, Shirley JC, Baiz CR. Forced Interactions: Ionic Polymers at Charged Surfactant Interfaces. J Phys Chem B 2023; 127:2829-2836. [PMID: 36926899 DOI: 10.1021/acs.jpcb.2c08636] [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
Characterizing electrostatic interactions at heterogeneous interfaces is critical for developing a fundamental description of the dynamic processes at charged interfaces. Water-in-oil reverse micelles (RMs) offer a high degree of tunability across composition, polarity, and temperature, making them ideal systems for studying interactions at heterogeneous liquid-liquid interfaces. In the present study, we use a combination of ultrafast two-dimensional infrared spectroscopy and molecular dynamics (MD) simulations to determine the picosecond interfacial dynamics in RMs containing binary compositions of sorbitan monostearate and anionic or cationic cosurfactants, which are used to tune the ratio of charged to nonionic surfactants at the interface. The positively charged polyethylenimine (PEI) polymer is encapsulated within the RMs, and the carbonyl stretching mode of sorbitan monostearate reports on the interfacial hydrogen-bond populations and dynamics. The results show that hydrogen-bond populations are altered through the inclusion of both negatively and positively charged cosurfactants. Charged surfactants increase interfacial water penetration into the surfactant layer, and the surface localization of polymers decreases water penetration. Local hydrogen-bond dynamics undergo a slowdown with the inclusion of charged surfactants, and the encapsulation of polymers results in similar effects, irrespective of the charge.
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Affiliation(s)
- Paul Garrett
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Joseph C Shirley
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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28
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Atsango AO, Montoya-Castillo A, Markland TE. An accurate and efficient Ehrenfest dynamics approach for calculating linear and nonlinear electronic spectra. J Chem Phys 2023; 158:074107. [PMID: 36813724 DOI: 10.1063/5.0138671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Linear and nonlinear electronic spectra provide an important tool to probe the absorption and transfer of electronic energy. Here, we introduce a pure state Ehrenfest approach to obtain accurate linear and nonlinear spectra that is applicable to systems with large numbers of excited states and complex chemical environments. We achieve this by representing the initial conditions as sums of pure states and unfolding multi-time correlation functions into the Schrödinger picture. By doing this, we show that one can obtain significant improvements in accuracy over the previously used projected Ehrenfest approach and that these benefits are particularly pronounced in cases where the initial condition is a coherence between excited states. While such initial conditions do not arise when calculating linear electronic spectra, they play a vital role in capturing multidimensional spectroscopies. We demonstrate the performance of our method by showing that it is able to quantitatively capture the exact linear, 2D electronic spectroscopy, and pump-probe spectra for a Frenkel exciton model in slow bath regimes and is even able to reproduce the main spectral features in fast bath regimes.
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Affiliation(s)
- Austin O Atsango
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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29
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Xu Y, Liu C, Ma H. Hierarchical Mapping for Efficient Simulation of Strong System-Environment Interactions. J Chem Theory Comput 2023; 19:426-435. [PMID: 36626721 DOI: 10.1021/acs.jctc.2c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Quantum dynamics (QD) simulation is a powerful tool for interpreting ultrafast spectroscopy experiments and unraveling their microscopic mechanism in out-of-equilibrium excited state behaviors in various chemical, biological, and material systems. Although state-of-the-art numerical QD approaches such as the time-dependent density matrix renormalization group (TD-DMRG) already greatly extended the solvable system size of general linearly coupled exciton-phonon models with up to a few hundred phonon modes, the accurate simulation of larger system sizes or strong system-environment interactions is still computationally highly challenging. Based on quantum information theory (QIT), in this work, we realize that only a small number of effective phonon modes couple to the excitonic system directly regardless of a large or even infinite number of modes in the condensed phase environment. On top of the identified small number of direct effective modes, we propose a hierarchical mapping (HM) approach through performing block Lanczos transformations on the remaining indirect modes, which transforms the Hamiltonian matrix to a nearly block-tridiagonal form and eliminates the long-range interactions. Numerical tests on model spin-boson systems and realistic singlet fission models in a rubrene crystal environment with up to 7000 modes and strong system-environment interactions indicate HM can reduce the system size by 1-2 orders of magnitude and accelerate the calculation by ∼80% without losing accuracy.
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Affiliation(s)
- Yihe Xu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haibo Ma
- Qingdao Institute for Theoretical and Computational Sciences, Qingdao Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
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30
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Giubertoni G, Rombouts G, Caporaletti F, Deblais A, van Diest R, Reek JNH, Bonn D, Woutersen S. Infrared Diffusion-Ordered Spectroscopy Reveals Molecular Size and Structure. Angew Chem Int Ed Engl 2023; 62:e202213424. [PMID: 36259515 PMCID: PMC10107201 DOI: 10.1002/anie.202213424] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Indexed: 11/07/2022]
Abstract
Inspired by ideas from NMR, we have developed Infrared Diffusion-Ordered Spectroscopy (IR-DOSY), which simultaneously characterizes molecular structure and size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient and tracking its equilibration in an IR-frequency resolved manner. Analogous to NMR-DOSY, a two-dimensional IR-DOSY spectrum has IR frequency along one axis and diffusion coefficient (or equivalently, size) along the other, so the chemical structure and the size of a compound are characterized simultaneously. In an IR-DOSY spectrum of a mixture, molecules with different sizes are nicely separated into distinct sets of IR peaks. Extending this idea to higher dimensions, we also perform 3D-IR-DOSY, in which we combine the conformation sensitivity of femtosecond multi-dimensional IR spectroscopy with size sensitivity.
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Affiliation(s)
- Giulia Giubertoni
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Gijs Rombouts
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Federico Caporaletti
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands.,Institute of Physics, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Antoine Deblais
- Institute of Physics, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Rianne van Diest
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Joost N H Reek
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Daniel Bonn
- Institute of Physics, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Sander Woutersen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
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31
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Gelin MF, Chen L, Domcke W. Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals. Chem Rev 2022; 122:17339-17396. [PMID: 36278801 DOI: 10.1021/acs.chemrev.2c00329] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system-field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.
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Affiliation(s)
- Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Lipeng Chen
- Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching,Germany
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32
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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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33
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Giubertoni G, Caporaletti F, Roeters SJ, Chatterley AS, Weidner T, Laity P, Holland C, Woutersen S. In Situ Identification of Secondary Structures in Unpurified Bombyx mori Silk Fibrils Using Polarized Two-Dimensional Infrared Spectroscopy. Biomacromolecules 2022; 23:5340-5349. [PMID: 36437734 DOI: 10.1021/acs.biomac.2c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanical properties of biomaterials are dictated by the interactions and conformations of their building blocks, typically proteins. Although the macroscopic behavior of biomaterials is widely studied, our understanding of the underlying molecular properties is generally limited. Among the noninvasive and label-free methods to investigate molecular structures, infrared spectroscopy is one of the most commonly used tools because the absorption bands of amide groups strongly depend on protein secondary structure. However, spectral congestion usually complicates the analysis of the amide spectrum. Here, we apply polarized two-dimensional (2D) infrared spectroscopy (IR) to directly identify the protein secondary structures in native silk films cast from Bombyx mori silk feedstock. Without any additional peak fitting, we find that the initial effect of hydration is an increase of the random coil content at the expense of the helical content, while the β-sheet content is unchanged and only increases at a later stage. This paper demonstrates that 2D-IR can be a valuable tool for characterizing biomaterials.
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Affiliation(s)
- Giulia Giubertoni
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - Federico Caporaletti
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XHAmsterdam, The Netherlands
| | - Steven J Roeters
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands.,Department of Chemistry, Aarhus University, 8000Aarhus C, Denmark
| | | | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000Aarhus C, Denmark
| | - Peter Laity
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, SheffieldS1 3JD, U.K
| | - Chris Holland
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, SheffieldS1 3JD, U.K
| | - Sander Woutersen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XHAmsterdam, The Netherlands
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34
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Askelson PG, Meloni SL, Hoffnagle AM, Anna JM. Resolving the Impact of Hydrogen Bonding on the Phylloquinone Cofactor through Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2022; 126:10120-10135. [PMID: 36444999 DOI: 10.1021/acs.jpcb.2c03556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional infrared spectroscopy (2DIR) was applied to phylloquinone (PhQ), an important biological cofactor, to elucidate the impact of hydrogen bonding on the ultrafast dynamics and energetics of the carbonyl stretching modes. 2DIR measurements were performed on PhQ dissolved in hexanol, which served as the hydrogen bonding solvent, and hexane, which served as a non-hydrogen bonding control. Molecular dynamics simulations and quantum chemical calculations were performed to aid in spectral assignment and interpretation. From the position of the peaks in the 2DIR spectra, we extracted the transition frequencies for the fundamental, overtone, and combination bands of hydrogen bonded and non-hydrogen bonded carbonyl groups of PhQ in the 1635-1680 cm-1 region. We find that hydrogen bonding to a single carbonyl group acts to decouple the two carbonyl units of PhQ. Through analysis of the time-resolved 2DIR data, we find that hydrogen bonding leads to faster vibrational relaxation as well as an increase in the inhomogeneous broadening of the carbonyl groups. Overall, this work demonstrates how hydrogen bonding to the carbonyl groups of PhQ presents in the 2DIR spectra, laying the groundwork to use PhQ as a 2DIR probe to characterize the ultrafast fluctuations in the local environment of natural photosynthetic complexes.
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Affiliation(s)
- Phoebe G Askelson
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Stephen L Meloni
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Alexander M Hoffnagle
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Jessica M Anna
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
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35
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Hu R, Ding X, Yu P, He X, Watts A, Zhao X, Wang J. Ultrafast Two-Dimensional Infrared Spectroscopy Resolved a Structured Lysine 159 on the Cytoplasmic Surface of the Microbial Photoreceptor Bacteriorhodopsin. J Am Chem Soc 2022; 144:22083-22092. [PMID: 36399663 DOI: 10.1021/jacs.2c09435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacteriorhodopsin (bR) is a light-driven microbial receptor, and lysine 159 (K159) is a charged residue on the cytoplasmic (CP) side of its E-F loop. However, its conformation and function remain unknown due to fast surface dynamics. By utilizing a 13C, 15N-labeled lysine (K) as an isotope probe, we created a network of site-specific amide-I vibrational signatures (backbone carbonyl stretch) to identify the frequency contribution of the labeled residues to the amide-I excitonic band structure. Thus, the red-shifted amide-I frequency in the 13C, 15N-lysine-labeled bR (uK-bR) to the unlabeled bR (WT-bR) could be differentiated and examined by ultrafast two-dimensional vibrational echo infrared (2D IR) spectroscopy. Our results showed that the backbone carbonyl of K159 is located at a high frequency of ca. 1693 cm-1 and has a vibrational excited-state relaxation time shorter than the bulk helical amide-I mode at the same frequency, suggesting that K159 may possess a hydrogen-bonded γ-turn structure with E161, one of the carboxylate residues on the CP surface of bR. The 2D solid-state NMR study of uK-bR also revealed conformational dependent lysine residues, from which K159 was found to involve the turn motif. This γ-turn structure maintained by K159 may help to stabilize the E-F loop and support E161 in attracting protons from the bulk during the late stage of the bR photocycle. The combined spectroscopic approach illustrated in this work may be applied to map residue-specific local structures and dynamics of other receptors and large proteins.
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Affiliation(s)
- Rong Hu
- Molecular Reaction Dynamics Laboratory, 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
| | - Xiaoyan Ding
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China.,Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, 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
| | - Xuemei He
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Xin Zhao
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, 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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36
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Chatterley AS, Laity P, Holland C, Weidner T, Woutersen S, Giubertoni G. Broadband Multidimensional Spectroscopy Identifies the Amide II Vibrations in Silkworm Films. Molecules 2022; 27:6275. [PMID: 36234809 PMCID: PMC9571984 DOI: 10.3390/molecules27196275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
We used two-dimensional infrared spectroscopy to disentangle the broad infrared band in the amide II vibrational regions of Bombyx mori native silk films, identifying the single amide II modes and correlating them to specific secondary structure. Amide I and amide II modes have a strong vibrational coupling, which manifests as cross-peaks in 2D infrared spectra with frequencies determined by both the amide I and amide II frequencies of the same secondary structure. By cross referencing with well-known amide I assignments, we determined that the amide II (N-H) absorbs at around 1552 and at 1530 cm-1 for helical and β-sheet structures, respectively. We also observed a peak at 1517 cm-1 that could not be easily assigned to an amide II mode, and instead we tentatively assigned it to a Tyrosine sidechain. These results stand in contrast with previous findings from linear infrared spectroscopy, highlighting the ability of multidimensional spectroscopy for untangling convoluted spectra, and suggesting the need for caution when assigning silk amide II spectra.
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Affiliation(s)
| | - Peter Laity
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Chris Holland
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Giulia Giubertoni
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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37
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Chen L, Bennett DIG, Eisfeld A. Calculating non-linear response functions for multi-dimensional electronic spectroscopy using dyadic non-Markovian quantum state diffusion. J Chem Phys 2022; 157:114104. [DOI: 10.1063/5.0107925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a methodology for simulating multi-dimensional electronic spectra of molecular aggregates with coupling of electronic excitation to a structured environment using the stochastic non-Markovian quantum state diffusion (NMQSD) method in combination with perturbation theory for the response functions. A crucial aspect of our approach is that we propagate the NMQSD equation in a doubled system Hilbert space, but with the same noise. We demonstrate that our approach shows fast convergence with respect to the number of stochastic trajectories, providing a promising technique for numerical calculation of two-dimensional electronic spectra of large molecular aggregates.
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Affiliation(s)
- Lipeng Chen
- Department of Chemistry, Max-Planck-Institute for the Physics of Complex Systems, Germany
| | - Doran I. G Bennett
- Chemistry, Southern Methodist University Department of Chemistry, United States of America
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38
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Parker KA, Schultz JD, Singh N, Wasielewski MR, Beratan DN. Mapping Simulated Two-Dimensional Spectra to Molecular Models Using Machine Learning. J Phys Chem Lett 2022; 13:7454-7461. [PMID: 35930790 DOI: 10.1021/acs.jpclett.2c01913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Two-dimensional (2D) spectroscopy encodes molecular properties and dynamics into expansive spectral data sets. Translating these data into meaningful chemical insights is challenging because of the many ways chemical properties can influence the spectra. To address the task of extracting chemical information from 2D spectroscopy, we study the capacity of simple feedforward neural networks (NNs) to map simulated 2D electronic spectra to underlying physical Hamiltonians. We examined hundreds of simulated 2D spectra corresponding to monomers and dimers with varied Franck-Condon active vibrations and monomer-monomer electronic couplings. We find the NNs are able to correctly characterize most Hamiltonian parameters in this study with an accuracy above 90%. Our results demonstrate that NNs can aid in interpreting 2D spectra, leading from spectroscopic features to underlying effective Hamiltonians.
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Affiliation(s)
- Kelsey A Parker
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jonathan D Schultz
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Niven Singh
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael R Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
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39
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Lai Y, Geva E. Electronic Absorption Spectra from Off-Diagonal Quantum Master Equations. J Chem Phys 2022; 157:104115. [DOI: 10.1063/5.0106888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Quantum master equations (QMEs) provide a general framework for describing electronic dynamics within a complex molecular system. Off-diagonal QMEs (OD-QMEs) correspond to a family of QMEs that describe the electronic dynamics in the interaction picture based on treating the off-diagonal coupling terms between electronic states as a small perturbation within the framework of second-order perturbation theory. The fact that OD-QMEs are given in terms of the interaction picture makes it non-trivial to obtain Schrodinger picture electronic coherences from them. A key experimental quantity that relies on the ability to obtain accurate Schrodinger picture electronic coherences is the absorption spectrum. In this paper, we propose using a recently introduced procedure for extracting Schrodinger picture electronic coherences from interaction picture inputs to calculate electronic absorption spectra from electronic dynamics generated by OD-QMEs. The accuracy of the absorption spectra obtained in this way is studied in the context of a biexciton benchmark model, by comparing spectra calculated based on time-local and time-nonlocal OD-QMEs to spectra calculated based on a Redfield-type QME and the non-perturbative and quantum-mechanically exact hierarchical equations of motion (HEOM) method.
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Affiliation(s)
- Yifan Lai
- Chemistry, University of Michigan, United States of America
| | - Eitan Geva
- Department of Chemistry, University of Michigan Department of Chemistry, United States of America
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40
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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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41
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Li H, Shah SA, Bittner E, Piryatinski A, Silva C. Stochastic exciton-scattering theory of optical lineshapes: Renormalized many-body contributions. J Chem Phys 2022; 157:054103. [DOI: 10.1063/5.0095575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Spectral line-shapes provide a window into the local environment coupled to a quantum transition in the condensed phase. In this paper, we build upon a stochastic model to account for non-stationary background processes produced by broad-band pulsed laser stimulation. In particular, we consider the contribution of pair-fluctuations arising from the full bosonic many-body Hamiltonian within a mean-field approximation, treating the coupling to the system as a stochastic noise term. Using the It{\^o} transformation, we consider two limiting cases for our model which lead to a connection between the observed spectral fluctuations and the spectral density of the environment. In the first case, we consider a Brownian environment and show that this produces spectral dynamics that relax to form dressed excitonic states and recover an Anderson-Kubo-like form for the spectral correlations. In the second case, we assume that the spectrum is Anderson-Kubo like, and invert to determine the corresponding background. Using the Jensen inequality, we obtain an upper limit for the spectral density of the background. The results presented here provide the technical tools for applying the stochastic model to a broad range of problems.
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Affiliation(s)
- Hao Li
- Chemistry, University of Houston, United States of America
| | - S. A. Shah
- University of Houston, United States of America
| | - Eric Bittner
- chemistry, University of Houston, United States of America
| | - Andrei Piryatinski
- Theoretical Division, Los Alamos National Laboratory, United States of America
| | - Carlos Silva
- School of Chemistry and Biochemistry, Georgia Institute of Technology, United States of America
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42
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Kim T, Lin C, Schultz JD, Young RM, Wasielewski MR. π-Stacking-Dependent Vibronic Couplings Drive Excited-State Dynamics in Perylenediimide Assemblies. J Am Chem Soc 2022; 144:11386-11396. [PMID: 35699940 DOI: 10.1021/jacs.2c03993] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Vibronic coupling, the interplay of electronic and nuclear vibrational motion, is considered a critical mechanism in photoinduced reactions such as energy transfer, charge transfer, and singlet fission. However, our understanding of how particular vibronic couplings impact excited-state dynamics is lacking due to the limited number of experimental studies of model molecular systems. Herein, we use two-dimensional electronic spectroscopy (2DES) to launch and interrogate a range of vibronic coherences in two distinct types of perylenediimide slip stacks─along the short and long molecular axes, which form either an excimer or a mixed state between the Frenkel exciton (FE) and charge transfer states. We explore the functionality of these vibronic coherences using quantum beatmaps, which display the Fourier amplitude signal oscillations as a function of pump and probe frequencies, along with knowledge of the characteristic signatures of the FE, ionic, and excimer species. We find that a low-frequency vibrational mode of the short-axis slip stack appears concomitantly with the formation of the excimer state, survives 2-fold longer than in the FE state in the reference monomer, and shows a phase shift compared to other modes. For the long-axis slip stacks, a pair of low-frequency modes coupled to a high-frequency coordinate of the FE state were found to play a critical role in mixed-state generation. Our findings thus experimentally reveal the complex and varying roles of vibronic couplings in tightly packed multimers undergoing a range of photoinduced processes.
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Affiliation(s)
- Taeyeon Kim
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Chenjian Lin
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Jonathan D Schultz
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Ryan M Young
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Michael R Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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43
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Solowan HP, Malý P, Brixner T. Direct comparison of molecular-beam versus liquid-phase pump-probe and two-dimensional spectroscopy on the example of azulene. J Chem Phys 2022; 157:044201. [DOI: 10.1063/5.0088365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although azulene's anomalous fluorescence originating from S2 rather than from S1 is the textbook example for the violation of Kasha's rule, the understanding of the underlying processes is still a subject of investigation. Here, we use action-based coherent two-dimensional electronic spectroscopy (2DES) to measure a single Liouville-space response pathway from S0 via S1 to the S2 state of azulene. We directly compare this sequential excitation in liquid phase detecting S2 fluorescence and in a molecular beam detecting photoionized cations, using the S2 anomalous emission to our advantage. We complement the 2DES study by pump-probe measurements of S1 excitation dynamics, including vibrational relaxation and passage through a conical intersection. The direct comparison of liquid and gas phase allows us to assess the effect of the solvent and the interplay of intra- and inter-molecular energy relaxation.
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Affiliation(s)
| | - Pavel Malý
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-Universität Würzburg, Germany
| | - Tobias Brixner
- Institut fuer Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Germany
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44
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Cho D, Gu B, Mukamel S. Optical Cavity Manipulation and Nonlinear UV Molecular Spectroscopy of Conical Intersections in Pyrazine. J Am Chem Soc 2022; 144:7758-7767. [PMID: 35404593 DOI: 10.1021/jacs.2c00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Optical cavities provide a versatile platform for manipulating the excited-state dynamics of molecules via strong light-matter coupling. We employ optical absorption and two-multidimensional electronic spectroscopy simulations to investigate the effect of optical cavity coupling in the nonadiabatic dynamics of photoexcited pyrazine. We observe the emergence of a novel polaritonic conical intersection (PCI) between the electronic dark state and photonic surfaces as the cavity frequency is tuned. The PCI could significantly change the nonadiabatic dynamics of pyrazine by doubling the decay rate constant of the S2 state population. Moreover, the absorption spectrum and excited-state dynamics could be systematically manipulated by tuning the strong light-matter interaction, e.g., the cavity frequency and cavity coupling strength. We propose that a tunable optical cavity-molecule system may provide promising approaches for manipulating the photophysical properties of molecules.
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Affiliation(s)
- Daeheum Cho
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, South Korea
| | - Bing Gu
- Department of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
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45
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Garrett P, Baiz CR. Dynamic effect of polymers at the surfactant-water interface: an ultrafast study. SOFT MATTER 2022; 18:1793-1800. [PMID: 35170620 DOI: 10.1039/d1sm01651b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Interfaces play a role in controlling the rates and outcomes of chemical processes. Characterizing the interactions at heterogeneous interfaces is critical to developing a comprehensive model of the role of interfaces and confinement in modulating chemical reactions. Reverse micelles are an ideal model system for exploring the effect of encapsulated species on interfacial environments. Here, we use a combination of ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics (MD) simulations to characterize the picosecond interfacial dynamics in reverse micelles (RMs) containing acrylamide monomers and polyacrylamide polymers within the aqueous phase. The ester carbonyl vibrations of the sorbitan monostearate surfactants are examined to extract interfacial hydrogen-bonding populations and dynamics. Hydrogen bond populations at the ester carbonyl positions remain unchanged with the inclusion of either polymer or monomer species. Hydrogen-bond dynamics are not altered with the addition of monomer but are slowed down twofold in the presence of encapsulated polyacrylamide polymer species as a result of polymer chains partially localizing to the interface. These findings imply that kinetics of reactions that occur at interfaces or in confined environments could be modulated by interfacial localization of the different components.
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Affiliation(s)
- Paul Garrett
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA.
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA.
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46
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Sparapassi G, Cavaletto SM, Tollerud J, Montanaro A, Glerean F, Marciniak A, Giusti F, Mukamel S, Fausti D. Transient measurement of phononic states with covariance-based stochastic spectroscopy. LIGHT, SCIENCE & APPLICATIONS 2022; 11:44. [PMID: 35228519 PMCID: PMC8885707 DOI: 10.1038/s41377-022-00727-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/17/2022] [Accepted: 01/26/2022] [Indexed: 05/09/2023]
Abstract
We present a novel approach to transient Raman spectroscopy, which combines stochastic probe pulses and a covariance-based detection to measure stimulated Raman signals in alpha-quartz. A coherent broadband pump is used to simultaneously impulsively excite a range of different phonon modes, and the phase, amplitude, and energy of each mode are independently recovered as a function of the pump-probe delay by a noisy-probe and covariance-based analysis. Our experimental results and the associated theoretical description demonstrate the feasibility of 2D-Raman experiments based on the stochastic-probe schemes, with new capabilities not available in equivalent mean-value-based 2D-Raman techniques. This work unlocks the gate for nonlinear spectroscopies to capitalize on the information hidden within the noise and overlooked by a mean-value analysis.
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Affiliation(s)
- Giorgia Sparapassi
- Physics Department, University of Trieste, Trieste, Italy
- Elettra-Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Stefano M Cavaletto
- Department of Chemistry and Department of Physics & Astronomy, University of California, Irvine, CA, USA
| | - Jonathan Tollerud
- Optical Sciences Centre, Swinburne University, Melbourne, Australia.
| | - Angela Montanaro
- Physics Department, University of Trieste, Trieste, Italy
- Elettra-Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Filippo Glerean
- Physics Department, University of Trieste, Trieste, Italy
- Elettra-Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Alexandre Marciniak
- Physics Department, University of Trieste, Trieste, Italy
- Elettra-Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Fancesca Giusti
- Physics Department, University of Trieste, Trieste, Italy
- Elettra-Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics & Astronomy, University of California, Irvine, CA, USA
| | - Daniele Fausti
- Physics Department, University of Trieste, Trieste, Italy.
- Elettra-Sincrotrone Trieste S.C.p.A., Trieste, Italy.
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47
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Dostál J. Nonresonant coherent two-dimensional spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120441. [PMID: 34678717 DOI: 10.1016/j.saa.2021.120441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Coherent electronic two-dimensional spectroscopy is nowadays a matured experimental technique that monitors the time evolution of the studied sample after its resonant optical excitation. However, the experimental experience shows that even nonresonant interactions can provide detectable spectral contributions. These are often present as a weak parasitic signals originating in the solvent and/or cuvette walls underlying the resonant spectrum of the actual sample and as such they are usually discarded from the analysis. In this work, we adapt the formalism of double-sided Feynman diagrams for the needs of coherent two-dimensional spectroscopy in the nonresonant regime. We analytically calculate the third-order polarization of a two-level and several variants of three-level systems. As a result, we demonstrate the typical appearance of the optical Kerr-effect, cross-phase modulation, excited-state coherence, two-photon absorption and stimulated Raman scattering in the 2D spectrum. This provides a framework for studying these effects by means of coherent two-dimensional spectroscopy.
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Affiliation(s)
- Jakub Dostál
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 121 16, Czech Republic; ELI Beamlines, Institute of Physics, Czech Academy of Sciences, Za Radnicí 835, Dolní Břežany 252 41, Czech Republic.
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48
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Long F, Xie H, Zhuang W. Identification of Trans- and Cis-2-Methylcyclopropanecarboxylic acid using EVV 2DIR spectroscopy: A theoretical study. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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Han NS, Kim J, Yoon TH, Cho M. Time-resolved spectroscopy of thioflavin T solutions: Asynchronous optical sampling method with two frequency-upconverted mode-locked lasers. J Chem Phys 2022; 156:064201. [DOI: 10.1063/5.0077756] [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] Open
Affiliation(s)
- Noh Soo Han
- Korea University, Korea, Republic of (South Korea)
| | - JunWoo Kim
- Department of Chemistry, Princeton University, United States of America
| | - Tai Hyun Yoon
- Department of Physics, Korea University, Korea, Republic of (South Korea)
| | - Minhaeng Cho
- Chemistry, Korea University, Korea, Republic of (South Korea)
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50
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Yb-Doped Fiber Chirped Pulse Amplification System Delivering 1 mJ, 231 fs at 1 kHz Repetition Rate. PHOTONICS 2022. [DOI: 10.3390/photonics9020067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this paper a single-channel chirped pulse amplification laser system based on Yb-doped photonic crystal fiber was constructed, which achieved a pulse energy output of 1 mJ with a beam quality close to the diffraction limit. Pulsed synchronous pumping was used to suppress amplified spontaneous emission at a repetition rate of 1 kHz. The de-chirped pulse width of 231 fs was achieved by precise systematic dispersion control, and the corresponding peak power reached 3.85 GW.
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