1
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Clarke CJ, Verlet JRR. Dynamics of Anions: From Bound to Unbound States and Everything In Between. Annu Rev Phys Chem 2024; 75:89-110. [PMID: 38277700 DOI: 10.1146/annurev-physchem-090722-125031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Gas-phase anions present an ideal playground for the exploration of excited-state dynamics. They offer control in terms of the mass, extent of solvation, internal temperature, and conformation. The application of a range of ion sources has opened the field to a vast array of anionic systems whose dynamics are important in areas ranging from biology to star formation. Here, we review recent experimental developments in the field of anion photodynamics, demonstrating the detailed insight into photodynamical and electron-capture processes that can be uncovered. We consider the electronic and nuclear ultrafast dynamics of electronically bound excited states along entire reaction coordinates; electronically unbound states showing that photochemical concepts, such as chromophores and Kasha's rule, are transferable to electron-driven chemistry; and nonvalence states that straddle the interface between bound and unbound states. Finally, we consider likely developments that are sure to keep the field of anion dynamics buoyant and impactful.
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Affiliation(s)
- Connor J Clarke
- Department of Chemistry, Durham University, Durham, United Kingdom;
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham, United Kingdom;
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2
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Lindkvist TT, Langeland J, Kjær C, Nielsen SB. Empirical Calibration of a Cylindrical Ion Trap for Mass-Selected Gas-Phase Fluorescence Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:123-130. [PMID: 38079152 DOI: 10.1021/jasms.3c00349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The ion motion in a quadrupole ion trap of hyperbolic geometry is well described by the Mathieu equations. A simpler cylindrical ion trap has also gained significance and has been used by us for fluorescence-spectroscopy experiments. This design allows for the easy replacement of the end-cap with a mesh, enhancing the photon collection. It is crucial to obtain a firm understanding of the ion motion in cylindrical ion traps and their capability as mass spectrometers. We present here an empirical method of calibrating a cylindrical ion trap based on fluorescence detection. This can be done nearly background-free in a pulsed experiment. The ions are located at the center of the trap, where the field is primarily quadrupolar, and here an effective Mathieu description is found through an effective geometry parameter. In spectroscopy experiments, high buffer-gas pressures are needed to efficiently cool the ions, which complicates the ions' motion and hence their stability. Still, simulations show that the stability diagram closely aligns with the Mathieu diagram, albeit shifted due to collisions. We map the stability diagram for six molecular ions by fluorescence collection from four cations and two anions spanning m/z from 212 to 647. The stability diagram is parametrized through the Mathieu functions with an m/z-dependent effective geometry parameter and a q-dependent shrinkage of the diagram. Based on the calibration, we estimate the mass resolution to be +7/-3 Da for ions with masses in the hundreds of Da.
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Affiliation(s)
| | - Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
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3
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Kjær C, Vogt E, Langeland J, Christensen NF, Lindkvist TT, Kjaergaard HG, Nielsen SB. Cryogenic fluorescence spectroscopy of oxazine ions isolated in vacuo. Phys Chem Chem Phys 2023; 25:32715-32722. [PMID: 38014982 DOI: 10.1039/d3cp04615j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Recent developments in fluorescence spectroscopy have made it possible to measure both absorption and dispersed fluorescence spectra of isolated molecular ions at liquid-nitrogen temperatures. Absorption is here obtained from fluorescence-excitation experiments and does not rely on ion dissociation. One large advantage of reduced temperature compared to room-temperature spectroscopy is that spectra are narrow, and they provide information on vibronic features that can better be assigned from theoretical simulations. We report on the intrinsic spectroscopic properties of oxazine dyes cooled to about 100 K. They include six cations (crystal violet, darrow red, oxazine-1, oxazine-4, oxazine-170 and nile blue) and one anion (resorufin). Experiments were done with a home-built setup (LUNA2) where ions are stored, mass-selected, cooled, and photoexcited in a cylindrical ion trap. We find that the Stokes shifts are small (14-50 cm-1), which is ascribed to rigid geometries, that is, there are only small geometrical changes between the electronic ground and excited states. However, both the absorption and the emission spectra of darrow-red cations are broader than those of the other ionic dyes, which is likely associated with a less symmetric electronic structure and more non-zero Franck-Condon factors for the vibrational progressions. In the case of resorufin, the smallest ion under study, vibrational features are assigned based on calculated spectra.
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Affiliation(s)
- Christina Kjær
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
| | - Emil Vogt
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
| | | | | | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
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4
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Rasmusssen AP, Pedersen HB, Andersen LH. Excited-state dynamics and fluorescence lifetime of cryogenically cooled green fluorescent protein chromophore anions. Phys Chem Chem Phys 2023. [PMID: 38048068 DOI: 10.1039/d3cp04696f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Time-resolved action spectroscopy together with a fs-pump probe scheme is used in an electrostatic ion-storage ring to address lifetimes of specific vibrational levels in electronically excited states. Here we specifically consider the excited-state lifetime of cryogenically cooled green fluorescent protein (GFP) chromophore anions which is systematically measured across the S0-S1 spectral region (450-482 nm). A long lifetime of 5.2 ± 0.3 ns is measured at the S0-S1 band origin. When exciting higher vibrational levels in S1, the lifetime changes dramatically. It decreases by more than two orders of magnitude in a narrow energy region ∼250 cm-1 (31 meV) above the 0-0 transition. This is attributed to the opening of internal conversion over an excited-state energy barrier. The applied experimental technique provides a new way to uncover even small energy barriers, which are crucial for excited-state dynamics.
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Affiliation(s)
- Anne P Rasmusssen
- Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark.
| | - Henrik B Pedersen
- Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark.
| | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark.
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5
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Ashworth EK, Kao MH, Anstöter CS, Riesco-Llach G, Blancafort L, Solntsev KM, Meech SR, Verlet JRR, Bull JN. Alkylated green fluorescent protein chromophores: dynamics in the gas phase and in aqueous solution. Phys Chem Chem Phys 2023; 25:23626-23636. [PMID: 37649445 DOI: 10.1039/d3cp03250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Fluorescent labelling of macromolecular samples, including using the green fluorescent protein (GFP), has revolutionised the field of bioimaging. The ongoing development of fluorescent proteins require a detailed understanding of the photophysics of the biochromophore, and how chemical derivatisation influences the excited state dynamics. Here, we investigate the photophysical properties associated with the S1 state of three alkylated derivatives of the chromophore in GFP, in the gas phase using time-resolved photoelectron imaging, and in water using femtosecond fluorescence upconversion. The gas-phase lifetimes (1.6-10 ps), which are associated with the intrinsic (environment independent) dynamics, are substantially longer than the lifetimes in water (0.06-3 ps), attributed to stabilisation of both twisted intermediate structures and conical intersection seams in the condensed phase. In the gas phase, alkylation on the 3 and 5 positions of the phenyl ring slows the dynamics due to inertial effects, while a 'pre-twist' of the methine bridge through alkylation on the 2 and 6 positions significantly shortens the excited state lifetimes. Formation of a minor, long-lived (≫ 40 ps) excited state population in the gas phase is attributed to intersystem crossing to a triplet state, accessed because of a T1/S1 degeneracy in the so-called P-trap potential energy minimum associated with torsion of the single-bond in the bridging unit connecting to the phenoxide ring. A small amount of intersystem crossing is supported through TD-DFT molecular dynamics trajectories and MS-CASPT2 calculations. No such intersystem crossing occurs in water at T = 300 K or in ethanol at T ≈ 77 K, due to a significantly altered potential energy surface and P-trap geometry.
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Affiliation(s)
- Eleanor K Ashworth
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Min-Hsien Kao
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Cate S Anstöter
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Gerard Riesco-Llach
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/M.A. Capmany 69, 17003 Girona, Spain
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/M.A. Capmany 69, 17003 Girona, Spain
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Stephen R Meech
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK.
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6
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Zhang YR, Yuan DF, Wang LS. Probing Dipole-Bound States Using Photodetachment Spectroscopy and Resonant Photoelectron Imaging of Cryogenically Cooled Anions. J Phys Chem Lett 2023; 14:7368-7381. [PMID: 37565830 DOI: 10.1021/acs.jpclett.3c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Molecular anions with polar neutral cores can support highly diffuse dipole-bound states below their detachment thresholds due to the long-range charge-dipole interaction. Such nonvalence states constitute a special class of excited electronic states for anions and were observed in early photodetachment experiments to measure the electron affinities of organic radicals. Recent experimental advances, in particular, the ability to create cold anions using a cryogenically cooled Paul trap, have allowed the investigation of dipole-bound excited states at a new level. For the first time, the zero-point level of dipole-bound excited states can be observed via resonant two-photon detachment, and resonant photoelectron spectroscopy can be performed via the above-threshold vibrational levels (Feshbach resonances) of the dipole-bound states. This Perspective describes recent progress in the investigation of dipole-bound states in the authors' lab using an electrospray photoelectron spectroscopy apparatus equipped with a cryogenically cooled Paul trap and high-resolution photoelectron imaging.
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Affiliation(s)
- Yue-Rou Zhang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Dao-Fu Yuan
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Lai-Sheng Wang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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7
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Ashworth EK, Dezalay J, Ryan CRM, Ieritano C, Hopkins WS, Chambrier I, Cammidge AN, Stockett MH, Noble JA, Bull JN. Protomers of the green and cyan fluorescent protein chromophores investigated using action spectroscopy. Phys Chem Chem Phys 2023. [PMID: 37465988 DOI: 10.1039/d3cp02661b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The photophysics of biochromophore ions often depends on the isomeric or protomeric distribution, yet this distribution, and the individual isomer contributions to an action spectrum, can be difficult to quantify. Here, we use two separate photodissociation action spectroscopy instruments to record electronic spectra for protonated forms of the green (pHBDI+) and cyan (Cyan+) fluorescent protein chromophores. One instrument allows for cryogenic (T = 40 ± 10 K) cooling of the ions, while the other offers the ability to perform protomer-selective photodissociation spectroscopy. We show that both chromophores are generated as two protomers when using electrospray ionisation, and that the protomers have partially overlapping absorption profiles associated with the S1 ← S0 transition. The action spectra for both species span the 340-460 nm range, although the spectral onset for the pHBDI+ protomer with the proton residing on the carbonyl oxygen is red-shifted by ≈40 nm relative to the lower-energy imine protomer. Similarly, the imine and carbonyl protomers are the lowest energy forms of Cyan+, with the main band for the carbonyl protomer red-shifted by ≈60 nm relative to the lower-energy imine protomer. The present strategy for investigating protomers can be applied to a wide range of other biochromophore ions.
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Affiliation(s)
- Eleanor K Ashworth
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Jordan Dezalay
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - Christian Ieritano
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Canada
| | - Isabelle Chambrier
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Andrew N Cammidge
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Mark H Stockett
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
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8
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Andersen LH, Rasmussen AP, Pedersen HB, Beletsan OB, Bochenkova AV. High-Resolution Spectroscopy and Selective Photoresponse of Cryogenically Cooled Green Fluorescent Protein Chromophore Anions. J Phys Chem Lett 2023:6395-6401. [PMID: 37428615 DOI: 10.1021/acs.jpclett.3c01452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
By time-resolved action spectroscopy of cryogenically cooled molecular ions, we have achieved a remarkable vibrational resolution in the photoresponse of the deprotonated green fluorescent protein (GFP) chromophore, a key molecular unit in the bioimaging of living cells. We define four characteristic spectral regions of the S0-S1 band with competing electronic and nuclear decay channels. We determine the energy barrier toward internal conversion to be ∼250 cm-1. This inhibits internal conversion and hence statistical fragmentation near the S0-S1 band origin, which is identified at 481.51 ± 0.15 nm (20768 ± 6 cm-1). The origin is red-shifted by only 221 cm-1 compared to that of wild-type GFP at 77 K. This, together with a striking agreement between the vibronic profiles of the protein and its chromophore, suggests their similar photophysics. In combination with theory, the data reveal the coexistence of mutually energy-borrowing mechanisms between nuclei and electrons mediated by specific vibrational modes.
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Affiliation(s)
- Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Anne P Rasmussen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Henrik B Pedersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Oleg B Beletsan
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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9
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Tureček F. UV-vis spectroscopy of gas-phase ions. MASS SPECTROMETRY REVIEWS 2023; 42:206-226. [PMID: 34392556 DOI: 10.1002/mas.21726] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Photodissociation action spectroscopy has made a great progress in expanding investigations of gas-phase ion structures. This review deals with aspects of gas-phase ion electronic excitations that result in wavelength-dependent dissociation and light emission via fluorescence, chiefly covering the ultraviolet and visible regions of the spectrum. The principles are briefly outlined and a few examples of instrumentation are presented. The main thrust of the review is to collect and selectively present applications of UV-vis action spectroscopy to studies of stable gas-phase ion structures and combinations of spectroscopy with ion mobility, collision-induced dissociation, and ion-ion reactions leading to the generation of reactive intermediates and electronic energy transfer.
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Affiliation(s)
- František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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10
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Bochenkova AV, Andersen LH. Action-Absorption Spectroscopy at the Band Origin of the Deprotonated Green Fluorescent Protein Chromophore In Vacuo. J Phys Chem Lett 2022; 13:6683-6685. [PMID: 35848550 DOI: 10.1021/acs.jpclett.2c01791] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The application of action spectroscopy in connection with determination of the S0 to S1 band origin in the GFP anion model chromophore (deprotonated HBDI) is discussed. We specifically address the consequences of the lowest vibrational levels in S1 being located behind a potential-energy barrier that inhibits internal conversion to the S0 electronic ground state. Action spectroscopy based on consecutive absorption of two photons together with internal conversion will as a consequence reveal an apparent band origin that is significantly blue-shifted.
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Affiliation(s)
| | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
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11
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Anstöter CS, Verlet JRR. A Hückel Model for the Excited-State Dynamics of a Protein Chromophore Developed Using Photoelectron Imaging. Acc Chem Res 2022; 55:1205-1213. [PMID: 35172580 PMCID: PMC9084545 DOI: 10.1021/acs.accounts.1c00780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chemistry can be described as the movement of nuclei within molecules and the concomitant instantaneous change in electronic structure. This idea underpins the central chemical concepts of potential energy surfaces and reaction coordinates. To experimentally capture such chemical change therefore requires methods that can probe both the nuclear and electronic structure simultaneously and on the time scale of atomic motion. In this Account, we show how time-resolved photoelectron imaging can do exactly this and how it can be used to build a detailed and intuitive understanding of the electronic structure and excited-state dynamics of chromophores. The chromophore of the photoactive yellow protein (PYP) is used as a case study. This chromophore contains a para-substituted phenolate anion, where the substituent, R, can be viewed as an acrolein derivative. It is shown that the measured photoelectron angular distribution can be directly related to the electronic structure of the para-substituted phenolate anion. By incrementally considering differing R groups, it is also shown that these photoelectron angular distributions are exquisitely sensitive to the conformational flexibility of R and that when R contains a π-system the excited states of the chromophore can be viewed as a linear combination of the π* molecular orbitals on the phenolate (πPh*) and the R substituent (πR*). Such Hückel treatment shows that the S1 state of the PYP chromophore has predominantly πR* character and that it is essentially the same as the chromophore of the green fluorescent protein (GFP). The S1 excited-state dynamics of the PYP chromophore probed by time-resolved photoelectron imaging clearly reveals both structural (nuclear) dynamics through the energy spectrum and electronic dynamics through the photoelectron angular distributions. Both motions can be accurately assigned using quantum chemical calculations, and these are consistent with the intuitive Hückel treatment presented. The photoactive protein chromophores considered here are examples of where a chemists' intuitive Hückel view for ground-state chemistry appears to be transferable to the prediction of photochemical excited-state reactivity. While elegant and insightful, such models have limitations, including nonadiabatic dynamics, which is present in a related PYP chromophore, where a fraction of the S1 state population forms a nonvalence (dipole-bound) state of the anion.
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Affiliation(s)
- Cate S. Anstöter
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Jan R. R. Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
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12
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Zutterman F, Liégeois V, Champagne B. TDDFT Investigation of the Raman and Resonant Raman Spectra of Fluorescent Protein Chromophore Models. J Phys Chem B 2022; 126:3414-3424. [PMID: 35499480 DOI: 10.1021/acs.jpcb.2c01202] [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
The off-resonance and resonant Raman spectra have been simulated for models of fluorescent protein chromophores, those of the green fluorescent protein (GFP, called FP1) and of DsRed (called FP2), which presents a longer π-conjugated path, with the aim of providing a systematic investigation of structural but also computational aspects. These were performed at the (time-dependent) density functional theory [(TD)DFT] level. The off-resonance intensities have been calculated from the derivatives of the frequency-dependent polarizability with respect to the normal coordinates while the resonant ones have been evaluated using Huang-Rhys factors determined from the gradients of the excitation energies with respect to the normal coordinates. When applied with the M05 meta-GGA exchange-correlation functional, this simple computational scheme can reproduce most of the experimental Raman signatures of FP1 in its protonated and deprotonated forms, the differences of vibrational signatures of the cis (Z) and trans (E) isomers, as well as their changes as a function of the excitation wavelength. On the other hand, testing the predictions made for FP2 would require new experimental work. It was also observed that simulations with methods that inadequately predict the resonant Raman spectra could nevertheless produce a UV-vis absorption spectrum that is quite similar to the one obtained with better methods, once realistic peak broadening has been applied.
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Affiliation(s)
- Freddy Zutterman
- Laboratoire de Chimie Théorique (LCT), Unité de Chimie-Physique Théorique et Structurale (UCPTS), NISM (Namur Institute of Structured Matter), Université de Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Vincent Liégeois
- Laboratoire de Chimie Théorique (LCT), Unité de Chimie-Physique Théorique et Structurale (UCPTS), NISM (Namur Institute of Structured Matter), Université de Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Benoît Champagne
- Laboratoire de Chimie Théorique (LCT), Unité de Chimie-Physique Théorique et Structurale (UCPTS), NISM (Namur Institute of Structured Matter), Université de Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
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13
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Ashworth EK, Stockett MH, Kjær C, Bulman Page PC, Meech SR, Nielsen SB, Bull JN. Complexation of Green and Red Kaede Fluorescent Protein Chromophores by a Zwitterion to Probe Electrostatic and Induction Field Effects. J Phys Chem A 2022; 126:1158-1167. [PMID: 35138862 DOI: 10.1021/acs.jpca.1c10628] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photophysics of green fluorescent protein (GFP) and red Kaede fluorescent protein (rKFP) are defined by the intrinsic properties of the light-absorbing chromophore and its interaction with the protein binding pocket. This work deploys photodissociation action spectroscopy to probe the absorption profiles for a series of synthetic GFP and rKFP chromophores as the bare anions and as complexes with the betaine zwitterion, which is assumed as a model for dipole microsolvation. Electronic structure calculations and energy decomposition analysis using Symmetry-Adapted Perturbation Theory are used to characterize gas-phase structures and complex cohesion forces. The calculations reveal a preponderance for coordination of betaine to the phenoxide deprotonation site predominantly through electrostatic forces. Calculations using the STEOM-DLPNO-CCSD method are able to reproduce absolute and relative vertical excitation energies for the bare anions and anion-betaine complexes. On the other hand, treatment of the betaine molecule with a point-charge model, in which the charges are computed from some common electron density population analysis schemes, show that just electrostatic and point-charge induction interactions are unable to account for the betaine-induced spectral shift. The present methodology could be applied to investigate cluster forces and optical properties in other gas-phase ion-zwitterion complexes.
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Affiliation(s)
- Eleanor K Ashworth
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Mark H Stockett
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark
| | - Philip C Bulman Page
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | | | - James N Bull
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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14
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Marlton SJP, Trevitt A. Laser Photodissocation, Action Spectroscopy and Mass Spectrometry Unite to Detect and Separate Isomers. Chem Commun (Camb) 2022; 58:9451-9467. [DOI: 10.1039/d2cc02101c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The separation and detection of isomers remains a challenge for many areas of mass spectrometry. This article highlights laser photodissociation and ion mobility strategies that have been deployed to tackle...
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15
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Vogt E, Langeland J, Kjær C, Lindkvist TT, Kjaergaard HG, Nielsen SB. Effect of Freezing out Vibrational Modes on Gas-Phase Fluorescence Spectra of Small Ionic Dyes. J Phys Chem Lett 2021; 12:11346-11352. [PMID: 34780698 DOI: 10.1021/acs.jpclett.1c03259] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
While action spectroscopy of cold molecular ions is a well-established technique to provide vibrationally resolved absorption features, fluorescence experiments are still challenging. Here we report the fluorescence spectra of pyronin-Y and resorufin ions at 100 K using a newly constructed setup. Spectra narrow upon cooling, and the emission maxima blueshift. Temperature effects are attributed to the population of vibrational excited levels in S1, and that frequencies are lower in S1 than in S0. This picture is supported by calculated spectra based on a Franck-Condon model that not only predicts the observed change in maximum, but also assigns Franck-Condon active vibrations. In-plane vibrational modes that preserve the mirror plane present in both S0 and S1 of resorufin and pyronin Y account for most of the observed vibrational bands. Finally, at low temperatures, it is important to pick an excitation wavelength as far to the red as possible to not reheat the ions.
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Affiliation(s)
- Emil Vogt
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus, Denmark
| | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus, Denmark
| | | | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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16
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Zagorec-Marks W, Dodson LG, Weis P, Schneider EK, Kappes MM, Weber JM. Intrinsic Structure and Electronic Spectrum of Deprotonated Biliverdin: Cryogenic Ion Spectroscopy and Ion Mobility. J Am Chem Soc 2021; 143:17778-17785. [PMID: 34637616 DOI: 10.1021/jacs.1c08701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the structural and spectroscopic properties of singly deprotonated biliverdin anions in vacuo, using a combination of cryogenic ion spectroscopy, ion mobility spectrometry, and density functional theory. The ion mobility results show that at least two conformers are populated, with the dominant conformer at 75-90% relative abundance. The vibrational NH stretching signatures are sensitive to the tetrapyrrole structure, and they indicate that the tetrapyrrole system is in a helical conformation, consistent with simulated ion mobility collision cross sections. The vibrational spectrum in the fingerprint region of this singly deprotonated species shows that the two propionate groups share the remaining acidic proton. The S1 band of the electronic spectrum in vacuo is broad, despite ion trap temperatures of 20 K during ion preparation, with a congested Franck-Condon envelope showing partially resolved vibrational features. The vertical transition exhibits a small solvatochromic red shift (-320 cm-1) in aqueous solution.
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Affiliation(s)
- Wyatt Zagorec-Marks
- JILA and Department of Chemistry, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - Leah G Dodson
- JILA and NIST, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Erik K Schneider
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
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17
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Coughlan NJA, Stockett MH, Kjær C, Ashworth EK, Bulman Page PC, Meech SR, Brøndsted Nielsen S, Blancafort L, Hopkins WS, Bull JN. Action spectroscopy of the isolated red Kaede fluorescent protein chromophore. J Chem Phys 2021; 155:124304. [PMID: 34598549 DOI: 10.1063/5.0063258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Incorporation of fluorescent proteins into biochemical systems has revolutionized the field of bioimaging. In a bottom-up approach, understanding the photophysics of fluorescent proteins requires detailed investigations of the light-absorbing chromophore, which can be achieved by studying the chromophore in isolation. This paper reports a photodissociation action spectroscopy study on the deprotonated anion of the red Kaede fluorescent protein chromophore, demonstrating that at least three isomers-assigned to deprotomers-are generated in the gas phase. Deprotomer-selected action spectra are recorded over the S1 ← S0 band using an instrument with differential mobility spectrometry coupled with photodissociation spectroscopy. The spectrum for the principal phenoxide deprotomer spans the 480-660 nm range with a maximum response at ≈610 nm. The imidazolate deprotomer has a blue-shifted action spectrum with a maximum response at ≈545 nm. The action spectra are consistent with excited state coupled-cluster calculations of excitation wavelengths for the deprotomers. A third gas-phase species with a distinct action spectrum is tentatively assigned to an imidazole tautomer of the principal phenoxide deprotomer. This study highlights the need for isomer-selective methods when studying the photophysics of biochromophores possessing several deprotonation sites.
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Affiliation(s)
- Neville J A Coughlan
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Mark H Stockett
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark
| | - Eleanor K Ashworth
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Philip C Bulman Page
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Stephen R Meech
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | | | - Lluís Blancafort
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, C/M.A. Capmany 69, 17003 Girona, Spain
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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18
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Woodhouse JL, Henley A, Lewin R, Ward JM, Hailes HC, Bochenkova AV, Fielding HH. A photoelectron imaging study of the deprotonated GFP chromophore anion and RNA fluorescent tags. Phys Chem Chem Phys 2021; 23:19911-19922. [PMID: 34474467 DOI: 10.1039/d1cp01901e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Green fluorescent protein (GFP), together with its family of variants, is the most widely used fluorescent protein for in vivo imaging. Numerous spectroscopic studies of the isolated GFP chromophore have been aimed at understanding the electronic properties of GFP. Here, we build on earlier work [A. V. Bochenkova, C. Mooney, M. A. Parkes, J. Woodhouse, L. Zhang, R. Lewin, J. M. Ward, H. Hailes, L. H. Andersen and H. H. Fielding, Chem. Sci., 2017, 8, 3154] investigating the impact of fluorine and methoxy substituents that have been employed to tune the electronic structure of the GFP chromophore for use as fluorescent RNA tags. We present photoelectron spectra following photoexcitation over a broad range of wavelengths (364-230 nm) together with photoelectron angular distributions following photoexcitation at 364 nm, which are interpreted with the aid of quantum chemistry calculations. The results support the earlier high-level quantum chemistry calculations that predicted how fluorine and methoxy substituents tune the electronic structure and we find evidence to suggest that the methoxy substituents enhance internal conversion, most likely from the 2ππ* state which has predominantly Feshbach resonance character, to the 1ππ* state.
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Affiliation(s)
- Joanne L Woodhouse
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Alice Henley
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Ross Lewin
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | - John M Ward
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | | | - Helen H Fielding
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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19
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Paz ASP, Baleeva NS, Glover WJ. Active orbital preservation for multiconfigurational self-consistent field. J Chem Phys 2021; 155:071103. [PMID: 34418944 DOI: 10.1063/5.0058673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We introduce Active Orbital Preservation for Multiconfigurational Self-Consistent Field (AOP-MCSCF), an automated approach to improving the consistency of active space orbitals over multiple molecular configurations. Our approach is based on maximum overlap with a reference set of active space orbitals taken from a single geometry of a chromophore in the gas phase and can be used to automatically preserve the appropriate orbitals of the chromophore across multiple thermally sampled configurations, even when the chromophore is solvated by quantum-mechanically treated water molecules. In particular, using the singular value decomposition of a Molecular Orbital (MO) overlap matrix between the system and reference, we rotate the MOs of the system to align with the reference active space orbitals and use the resulting rotated orbitals as an initial guess to a MCSCF calculation. We demonstrate the approach on aqueous p-hydroxybenzylidene-imidazolinone (HBI) and find that AOP-MCSCF converges to the "correct" orbitals for over 90% of 3000 thermally sampled configurations. In addition, we compute the linear absorption spectrum and find excellent agreement with new experimental measurements up to 5.4 eV (230 nm). We show that electrostatic contributions to the solvation energy of HBI largely explain the observed state-dependent solvatochromism.
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Affiliation(s)
- Amiel S P Paz
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
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20
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Gozem S, Krylov AI. The
ezSpectra
suite: An easy‐to‐use toolkit for spectroscopy modeling. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1546] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Samer Gozem
- Department of Chemistry Georgia State University Atlanta Georgia USA
| | - Anna I. Krylov
- Department of Chemistry University of Southern California Los Angeles California USA
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21
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Zagorec-Marks W, Foreman MM, Weber JM. Tag-Free, Temperature Dependent Infrared Spectra of the GFP Chromophore: Revisiting the Question of Isomerism. J Phys Chem A 2020; 124:7827-7831. [PMID: 32866387 DOI: 10.1021/acs.jpca.0c07172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report infrared spectra of a model chromophore of green fluorescent protein, prepared in an ion trap at temperatures ranging from 30 K to room temperature. We compare the changes in the infrared spectrum with predicted infrared spectra for the Z and E isomers of this molecule, and we confirm that the molecule exists as the Z isomer at low temperatures. We revisit the question whether or not it can thermally isomerize in the temperature range of this experiment, and we find no evidence for isomerization.
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Affiliation(s)
- Wyatt Zagorec-Marks
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - Madison M Foreman
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
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22
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Zhang H, Cao W, Yuan Q, Zhou X, Valiev M, Kass SR, Wang XB. Cryogenic "Iodide-Tagging" Photoelectron Spectroscopy: A Sensitive Probe for Specific Binding Sites of Amino Acids. J Phys Chem Lett 2020; 11:4346-4352. [PMID: 32401519 DOI: 10.1021/acs.jpclett.0c01099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This work showcases cryogenic and temperature-dependent "iodide-tagging" photoelectron spectroscopy to probe specific binding sites of amino acids using the glycine-iodide complex (Gly·I-) as a case study. Multiple Gly·I- isomers were generated from ambient electrospray ionization and kinetically isolated in a cryogenic ion trap. These structures were characterized with temperature-dependent "iodide-tagging" negative ion photoelectron spectroscopy (NIPES), where iodide was used as the "messenger" to interpret electronic energetics and structural information of various Gly·I- isomers. Accompanied by theoretical computations and Franck-Condon simulations, a total of five cluster structures have been identified along with their various binding motifs. This work demonstrates that "iodide-tagging" NIPES is a powerful general means for probing specific binding interactions in biological molecules of interest.
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Affiliation(s)
- Hanhui Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Marat Valiev
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Steven R Kass
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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23
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Verlet JRR, Anstöter CS, Bull JN, Rogers JP. Role of Nonvalence States in the Ultrafast Dynamics of Isolated Anions. J Phys Chem A 2020; 124:3507-3519. [PMID: 32233436 PMCID: PMC7212518 DOI: 10.1021/acs.jpca.0c01260] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Nonvalence states
of neutral molecules (Rydberg states) play important
roles in nonadiabatic dynamics of excited states. In anions, such
nonadiabatic transitions between nonvalence and valence states have
been much less explored even though they are believed to play important
roles in electron capture and excited state dynamics of anions. The
aim of this Feature Article is to provide an overview of recent experimental
observations, based on time-resolved photoelectron imaging, of valence
to nonvalence and nonvalence to valence transitions in anions and
to demonstrate that such dynamics may be commonplace in the excited
state dynamics of molecular anions and cluster anions.
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Affiliation(s)
- Jan R R Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Cate S Anstöter
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Joshua P Rogers
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
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24
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Zagorec-Marks W, Foreman MM, Verlet JRR, Weber JM. Probing the Microsolvation Environment of the Green Fluorescent Protein Chromophore In Vacuo. J Phys Chem Lett 2020; 11:1940-1946. [PMID: 32073271 DOI: 10.1021/acs.jpclett.0c00105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present vibrational and electronic photodissociation spectra of a model chromophore of the green fluorescent protein in complexes with up to two water molecules, prepared in a cryogenic ion trap at 160-180 K. We find the band origin of the singly hydrated chromophore at 20 985 cm-1 (476.5 nm) and observe partially resolved vibrational signatures. While a single water molecule induces only a small shift of the S1 electronic band of the chromophore, without significant change of the Franck-Condon envelope, the spectrum of the dihydrate shows significant broadening and a greater blue shift of the band edge. Comparison of the vibrational spectra with predicted infrared spectra from density functional theory indicates that water molecules can interact with the oxygen atom on the phenolate group or on the imidazole moiety, respectively.
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Affiliation(s)
- Wyatt Zagorec-Marks
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - Madison M Foreman
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, U.K
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
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25
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Yuan Q, Cao W, Wang XB. Cryogenic and temperature-dependent photoelectron spectroscopy of metal complexes. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1719699] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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