1
|
Pieri E, Walker AR, Zhu M, Martínez TJ. Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins. J Am Chem Soc 2024; 146:17646-17658. [PMID: 38885641 DOI: 10.1021/jacs.4c00458] [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: 06/20/2024]
Abstract
Red fluorescent protein (RFP) variants are highly sought after for in vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pretwisted chromophore conformation which provides easier access to conical intersections. The main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).
Collapse
Affiliation(s)
- Elisa Pieri
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Alice R Walker
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Mingning Zhu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| |
Collapse
|
2
|
Grobas Illobre P, Marsili M, Corni S, Stener M, Toffoli D, Coccia E. Time-Resolved Excited-State Analysis of Molecular Electron Dynamics by TDDFT and Bethe-Salpeter Equation Formalisms. J Chem Theory Comput 2021; 17:6314-6329. [PMID: 34486881 PMCID: PMC8515806 DOI: 10.1021/acs.jctc.1c00211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/16/2022]
Abstract
In this work, a theoretical and computational set of tools to study and analyze time-resolved electron dynamics in molecules, under the influence of one or more external pulses, is presented. By coupling electronic-structure methods with the resolution of the time-dependent Schrödinger equation, we developed and implemented the time-resolved induced density of the electronic wavepacket, the time-resolved formulation of the differential projection density of states (ΔPDOS), and of transition contribution map (TCM) to look at the single-electron orbital occupation and localization change in time. Moreover, to further quantify the possible charge transfer, we also defined the energy-integrated ΔPDOS and the fragment-projected TCM. We have used time-dependent density-functional theory (TDDFT), as implemented in ADF software, and the Bethe-Salpeter equation, as provided by MolGW package, for the description of the electronic excited states. This suite of postprocessing tools also provides the time evolution of the electronic states of the system of interest. To illustrate the usefulness of these postprocessing tools, excited-state populations have been computed for HBDI (the chromophore of GFP) and DNQDI molecules interacting with a sequence of two pulses. Time-resolved descriptors have been applied to study the time-resolved electron dynamics of HBDI, DNQDI, LiCN (being a model system for dipole switching upon highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) electronic excitation), and Ag22. The computational analysis tools presented in this article can be employed to help the interpretation of fast and ultrafast spectroscopies on molecular, supramolecular, and composite systems.
Collapse
Affiliation(s)
- P. Grobas Illobre
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - M. Marsili
- Dipartimento
di Scienze Chimiche, Universitá di
Padova, via Marzolo 1, Padova 35131, Italy
| | - S. Corni
- Dipartimento
di Scienze Chimiche, Universitá di
Padova, via Marzolo 1, Padova 35131, Italy
- CNR
Istituto di Nanoscienze, via Campi 213/A, Modena 41125, Italy
| | - M. Stener
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - D. Toffoli
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - E. Coccia
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Gibbard JA, Castracane E, Krylov AI, Continetti RE. Photoelectron photofragment coincidence spectroscopy of aromatic carboxylates: benzoate and p-coumarate. Phys Chem Chem Phys 2021; 23:18414-18424. [PMID: 34612382 DOI: 10.1039/d1cp02972j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoelectron-photofragment coincidence spectroscopy was used to study the dissociation dynamics of the conjugate bases of benzoic acid and p-coumaric acid. Upon photodetachment at 266 nm (4.66 eV) both aromatic carboxylates undergo decarboxylation, as well as the formation of stable carboxyl radicals. The key energetics are computed using high-level electronic structure methods. The dissociation dynamics of benzoate were dominated by a two-body DPD channel resulting in CO2 + C6H5 + e-, with a very small amount of stable C6H5CO2 showing that the radical ground state is stable and the excited states are dissociative. For p-coumarate (p-CA-) the dominant channel is photodetachment resulting in a stable radical and a photoelectron with electron kinetic energy (eKE) <2 eV. We also observed a minor two-body dissociative photodetachment (DPD) channel resulting in CO2 + HOC6H4CHCH + e-, characterized by eKE <0.8 eV. Evidence was also found for a three-body ionic photodissociation channel producing HOC6H5 + HCC- + CO2. The ion beam contained both the phenolate and carboxylate isomers of p-CA-, but DPD only occurred from the carboxylate form. For both species DPD is seen from the first and second excited states of the radical, where vibrational excitation is required for decarboxylation from the first excited radical state.
Collapse
Affiliation(s)
- J A Gibbard
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0340, USA.
| | | | | | | |
Collapse
|
5
|
Shedge SV, Zuehlsdorff TJ, Khanna A, Conley S, Isborn CM. Explicit environmental and vibronic effects in simulations of linear and nonlinear optical spectroscopy. J Chem Phys 2021; 154:084116. [PMID: 33639769 DOI: 10.1063/5.0038196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Accurately simulating the linear and nonlinear electronic spectra of condensed phase systems and accounting for all physical phenomena contributing to spectral line shapes presents a significant challenge. Vibronic transitions can be captured through a harmonic model generated from the normal modes of a chromophore, but it is challenging to also include the effects of specific chromophore-environment interactions within such a model. We work to overcome this limitation by combining approaches to account for both explicit environment interactions and vibronic couplings for simulating both linear and nonlinear optical spectra. We present and show results for three approaches of varying computational cost for combining ensemble sampling of chromophore-environment configurations with Franck-Condon line shapes for simulating linear spectra. We present two analogous approaches for nonlinear spectra. Simulated absorption spectra and two-dimensional electronic spectra (2DES) are presented for the Nile red chromophore in different solvent environments. Employing an average Franck-Condon or 2DES line shape appears to be a promising method for simulating linear and nonlinear spectroscopy for a chromophore in the condensed phase.
Collapse
Affiliation(s)
- Sapana V Shedge
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Ajay Khanna
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Stacey Conley
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| |
Collapse
|
6
|
Sen T, Ma Y, Polyakov IV, Grigorenko BL, Nemukhin AV, Krylov AI. Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang. J Phys Chem B 2021; 125:757-770. [PMID: 33411528 DOI: 10.1021/acs.jpcb.0c09221] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the results of high-level electronic structure and dynamics simulations of the photoactive protein Dreiklang. With the goal of understanding the details of the Dreiklang photocycle, we carefully characterize the excited states of the ON- and OFF-forms of Dreiklang. The key finding of our study is the existence of a low-lying excited state of a charge-transfer character in the neutral ON form and that population of this state, which is nearly isoenergetic with the locally excited bright state, initiates a series of steps that ultimately lead to the formation of the hydrated dark chromophore (OFF state). These results allow us to refine the mechanistic picture of Dreiklang's photocycle and photoactivation.
Collapse
Affiliation(s)
- Tirthendu Sen
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Yingying Ma
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
7
|
Patel AM, Henley A, Parkes MA, Assmann M, Worth GA, Anderson JC, Fielding HH. Shining light on the electronic structure and relaxation dynamics of the isolated oxyluciferin anion. Phys Chem Chem Phys 2020; 22:19022-19032. [PMID: 32808948 DOI: 10.1039/d0cp03276j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Firefly bioluminescence is exploited widely in imaging in the biochemical and biomedical sciences; however, our fundamental understanding of the electronic structure and relaxation processes of the oxyluciferin that emits the light is still rudimentary. Here, we employ photoelectron spectroscopy and quantum chemistry calculations to investigate the electronic structure and relaxation of a series of model oxyluciferin anions. We find that changing the deprotonation site has a dramatic influence on the relaxation pathway following photoexcitation of higher lying electronically excited states. The keto form of the oxyluciferin anion is found to undergo internal conversion to the fluorescent S1 state, whereas we find evidence to suggest that the enol and enolate forms undergo internal conversion to a dipole bound state, possibly via the fluorescent S1 state. Partially resolved vibrational structure points towards the involvement of out-of-plane torsional motions in internal conversion to the dipole bound state, emphasising the combined electronic and structural role that the microenvironment plays in controlling the electronic relaxation pathway in the enzyme.
Collapse
Affiliation(s)
- Anand M Patel
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | | | | | | | | | | | | |
Collapse
|
8
|
Raucci U, Perrella F, Donati G, Zoppi M, Petrone A, Rega N. Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study. J Comput Chem 2020; 41:2228-2239. [PMID: 32770577 DOI: 10.1002/jcc.26384] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/15/2022]
Abstract
Solute-solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical-physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute-solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.
Collapse
Affiliation(s)
- Umberto Raucci
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Fulvio Perrella
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Greta Donati
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy.,Dipartimento di Chimica e Biologia "Adolfo Zambelli", Università di Salerno, Fisciano, Italy
| | - Maria Zoppi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Alessio Petrone
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Nadia Rega
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy.,Center for Advanced Biomaterials for Healthcare@CRIB, Naples, Italy
| |
Collapse
|
9
|
Deng H, Yu C, Yan D, Zhu X. Dual-Self-Restricted GFP Chromophore Analogues with Significantly Enhanced Emission. J Phys Chem B 2020; 124:871-880. [PMID: 31928005 DOI: 10.1021/acs.jpcb.9b11329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The tremendous gap of fluorescence emission of synthetic green fluorescent protein (GFP) chromophore to the protein itself makes it impossible to use for applications in molecular and cellular imaging. Here, we developed an efficient methodology to enhance the photoluminescence response of synthetic GFP chromophore analogues by constructing dual-self-restricted chromophores. Single self-restricted chromophores were first generated with 2,5-dimethoxy substitution on the aromatic ring, which were further modified with phenyl or 2,5-dimethoxy phenyl to form dual-self-restricted chromophores. These two chromophores showed an obvious solvatofluorochromic color palette across blue to yellow with a maximum emission Stokes shift of 95 nm and dramatically enhanced fluorescence emission in various aprotic solvents, especially in hexane, where the QY reached around 0.6. Importantly, in acetonitrile and dimethyl sulfoxide, the fluorescence QYs of both chromophores were over 0.22, which were the highest reported so far in high polar organic solvents. Meanwhile, the fluorescence lifetimes also improved obviously with the maximum of around 4.5 ns. Theoretical calculations revealed a more favorable Mülliken atomic charge translocation over the double-bond bridge and illustrated much higher energy barriers for the Z/E photoisomerization together with larger bond orders compared with the GFP core chromophore, p-HBDI. Our work significantly improved the fluorescence emission of synthetic GFP chromophore analogues in polar solvents while reserved the multicolor emitting function, providing a solid molecular motif for engineering high-performance fluorescent probes.
Collapse
Affiliation(s)
- Hongping Deng
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Chunyang Yu
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| |
Collapse
|
10
|
Zuehlsdorff TJ, Hong H, Shi L, Isborn CM. Influence of Electronic Polarization on the Spectral Density. J Phys Chem B 2019; 124:531-543. [DOI: 10.1021/acs.jpcb.9b10250] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tim J. Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Hanbo Hong
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| |
Collapse
|
11
|
Shedge SV, Zuehlsdorff TJ, Servis MJ, Clark AE, Isborn CM. Effect of Ions on the Optical Absorption Spectra of Aqueously Solvated Chromophores. J Phys Chem A 2019; 123:6175-6184. [DOI: 10.1021/acs.jpca.9b03163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Sapana V. Shedge
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Tim J. Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Michael J. Servis
- Department of Chemistry and the Material Science and Engineering Program, Washington State University, Pullman, Washington 99164, United States
| | - Aurora E. Clark
- Department of Chemistry and the Material Science and Engineering Program, Washington State University, Pullman, Washington 99164, United States
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99164, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| |
Collapse
|
12
|
Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, London, UK
| | | |
Collapse
|
13
|
Grabarek D, Andruniów T. Assessment of Functionals for TDDFT Calculations of One- and Two-Photon Absorption Properties of Neutral and Anionic Fluorescent Proteins Chromophores. J Chem Theory Comput 2018; 15:490-508. [PMID: 30485096 DOI: 10.1021/acs.jctc.8b00769] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Performance of DFT functionals with different percentages of exact Hartree-Fock exchange energy (EX) is assessed for recovery of the CC2 reference one- (OPA) and two-photon absorption (TPA) spectra of fluorescent proteins chromophores in vacuo. The investigated DFT functionals, together with their EX contributions are BLYP (0%), B3LYP (20%), B1LYP (25%), BHandHLYP (50%), and CAM-B3LYP (19% at short range and 65% at long range). Our test set consists of anionic and neutral chromophores as naturally occurring in the fluorescent proteins. For the first time, we compare TDDFT and CC2 methods for higher excited states than the S1 state, exhibiting relatively large TPA intensity. Our TDDFT results for neutral chromophores reveal an increase in excitation energies as well as TPA and OPA intensities errors, compared to CC2-derived results, as the DFT functional contains less exact exchange. The long-range-corrected CAM-B3LYP functional performs the best, closely followed by BHandHLYP, while BLYP usually significantly underestimates all investigated spectral properties, hence being the worst in reproducing the reference CC2 results. The hybrid B3LYP and B1LYP functionals can be roughly placed in between. We propose that TDDFT may underestimate the TPA intensities for neutral chromophores of fluorescent proteins due to underestimated oscillator strengths between some excited states. In the case of anionic chromophores, we find that B3LYP and B1LYP functionals overcome others in terms of reproducing CC2 excitation energies. On the other hand, however, TPA intensity is usually significantly underestimated, and in this respect, CAM-B3LYP functional seems to be again superior. In contrast to the case of neutral chromophores, it seems that a large magnitude of excited-state dipole moments or changes in dipole moments upon excitation may be the driving force behind high TPA transition moments.
Collapse
Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering and Modelling Group , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| |
Collapse
|
14
|
Chen X, Song J, Chen ZN, Jin T, Long F, Xie H, Zheng Y, Zhuang W, Zhang L. Rational designing of 8-hydroxyquinolin-imidazolinone-based fluorescent protein mutants with dramatically red shifted emission: A computational study. J Comput Chem 2018; 39:2307-2315. [PMID: 30318750 DOI: 10.1002/jcc.25552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/11/2018] [Accepted: 07/16/2018] [Indexed: 01/17/2023]
Abstract
Engineering fluorescent proteins to be the customized in vivo labels for monitoring cellular dynamic events is critical in biochemical and biomedical studies. The design and development of novel red fluorescent proteins is one of the most important fronts in this field due to their potential of imaging the entire organism. A recent fluorescent protein mutant eqFP650-67-HqAla with the 8-hydroxyquinolin-imidazolinone (HQI) chromophore has the plausible bathochromic shift of ~30 nm in its emission spectrum wavelength comparing to the parent fluorescent protein eqFP650. However, molecular mechanism of this significant shift remains somewhat obscure. In this study, we carefully benchmarked our computational methods and performed extensive calculations to investigate various structural components' effect on the chromophore's emission energy and decipher the molecular origin of the spectral shift. The influences of conjugation size, substituent group, substituent site as well as the number of substituents have been examined by elaborately designed chromophore derivatives. Accordingly, we proposed several chromophore mutants with dramatic bathochromic shift of up to ~60 nm in their emission spectra. We further evaluated their structural stability in the protein using molecular dynamics simulations. Present theoretical study connects the structural feature of chromophore derivatives in red fluorescent proteins with their splendid performances in shifting the emission frequency and offer the molecular insight. The computational protocol and successive examination procedure to extract the structural effect utilized herein can also be widely applied to other fluorescent proteins in general. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Xian Chen
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University, Changchun, Jilin, 130012, People's Republic of China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Jian Song
- College of Physics and Materials Science, Henan Normal University, Xin Xiang, Henan, 453007, People's Republic of China
| | - Zhe-Ning Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Fengqin Long
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Hua Xie
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Yisong Zheng
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University, Changchun, Jilin, 130012, People's Republic of China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, People's Republic of China
| |
Collapse
|
15
|
Rudolph J, Jacob CR. Revisiting the Dependence of Cu K-Edge X-ray Absorption Spectra on Oxidation State and Coordination Environment. Inorg Chem 2018; 57:10591-10607. [PMID: 30113840 DOI: 10.1021/acs.inorgchem.8b01219] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
X-ray absorption spectroscopy (XAS) at the Cu K-edge is an important tool for probing the properties of copper centers in transition-metal chemistry and catalysis. However, the interpretation of experimental XAS spectra requires a detailed understanding of the dependence of spectroscopic features on the local geometric and electronic structure, which can be established by theoretical X-ray spectroscopy. Here, we present a systematic computational study of the Cu K-edge XAS spectra of selected Cu complexes based on time-dependent density-functional theory in combination with a molecular orbital analysis of the relevant transitions. For a series of Cu ammine model complexes as well as a comprehensive test set of 12 Cu(I) and 5 Cu(II) complexes, we revisit the dependence of the pre-edge region in Cu K-edge XAS spectra on oxidation state and coordination geometry. While our calculations confirm earlier experimental assignments, we can also reveal additional signatures of the ligand orbitals and identify the underlying orbital interactions. The comprehensive picture revealed by this study will provide a reliable basis for the interpretation of in situ Cu K-edge XAS spectra of catalytic intermediates.
Collapse
Affiliation(s)
- Julian Rudolph
- Institute of Physical and Theoretical Chemistry , TU Braunschweig , Gaußstraße 17 , 38106 Braunschweig , Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry , TU Braunschweig , Gaußstraße 17 , 38106 Braunschweig , Germany
| |
Collapse
|
16
|
Zuehlsdorff TJ, Napoli JA, Milanese JM, Markland TE, Isborn CM. Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. J Chem Phys 2018; 149:024107. [PMID: 30007372 DOI: 10.1063/1.5025517] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.
Collapse
Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joel M Milanese
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| |
Collapse
|
17
|
Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
| | | |
Collapse
|
18
|
Zuehlsdorff TJ, Isborn CM. Combining the ensemble and Franck-Condon approaches for calculating spectral shapes of molecules in solution. J Chem Phys 2018; 148:024110. [PMID: 29331131 DOI: 10.1063/1.5006043] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The correct treatment of vibronic effects is vital for the modeling of absorption spectra of many solvated dyes. Vibronic spectra for small dyes in solution can be easily computed within the Franck-Condon approximation using an implicit solvent model. However, implicit solvent models neglect specific solute-solvent interactions on the electronic excited state. On the other hand, a straightforward way to account for solute-solvent interactions and temperature-dependent broadening is by computing vertical excitation energies obtained from an ensemble of solute-solvent conformations. Ensemble approaches usually do not account for vibronic transitions and thus often produce spectral shapes in poor agreement with experiment. We address these shortcomings by combining zero-temperature vibronic fine structure with vertical excitations computed for a room-temperature ensemble of solute-solvent configurations. In this combined approach, all temperature-dependent broadening is treated classically through the sampling of configurations and quantum mechanical vibronic contributions are included as a zero-temperature correction to each vertical transition. In our calculation of the vertical excitations, significant regions of the solvent environment are treated fully quantum mechanically to account for solute-solvent polarization and charge-transfer. For the Franck-Condon calculations, a small amount of frozen explicit solvent is considered in order to capture solvent effects on the vibronic shape function. We test the proposed method by comparing calculated and experimental absorption spectra of Nile red and the green fluorescent protein chromophore in polar and non-polar solvents. For systems with strong solute-solvent interactions, the combined approach yields significant improvements over the ensemble approach. For systems with weak to moderate solute-solvent interactions, both the high-energy vibronic tail and the width of the spectra are in excellent agreement with experiments.
Collapse
Affiliation(s)
- T J Zuehlsdorff
- School of Natural Sciences, University of California Merced, N. Lake Road, Merced, California 95344, USA
| | - C M Isborn
- School of Natural Sciences, University of California Merced, N. Lake Road, Merced, California 95344, USA
| |
Collapse
|
19
|
Ermakova YG, Sen T, Bogdanova YA, Smirnov AY, Baleeva NS, Krylov AI, Baranov MS. Pyridinium Analogues of Green Fluorescent Protein Chromophore: Fluorogenic Dyes with Large Solvent-Dependent Stokes Shift. J Phys Chem Lett 2018; 9:1958-1963. [PMID: 29589942 DOI: 10.1021/acs.jpclett.8b00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Novel fluorogenic dyes based on the GFP chromophore are developed. The compounds contain a pyridinium ring instead of phenolate and feature large Stokes shifts and solvent-dependent variations in the fluorescence quantum yield. Electronic structure calculations explain the trends in solvatochromic behavior in terms of the increase of the dipole moment upon excited-state relaxation in polar solvents associated with the changes in bonding pattern in the excited state. A unique combination of such optical characteristics and lipophilic properties enables using one of the new dyes for imaging the membrane structure of endoplasmic reticulum. An extremely high photostability (due to a dynamic exchange between the free and absorbed states) and selectivity make this compound a promising label for this type of cellular organelles.
Collapse
Affiliation(s)
- Yulia G Ermakova
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1 , 117997 Moscow , Russia
- European Molecular Biology Laboratory , 69117 Heidelberg , Germany
| | - Tirthendu Sen
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Anna I Krylov
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1 , 117997 Moscow , Russia
| |
Collapse
|
20
|
Chen F, Zhao X, Liang W. One- and two-photon absorption spectra of the yellow fluorescent protein citrine: effects of intramolecular electron-vibrational coupling and intermolecular interactions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1426130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Fasheng Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xinyi Zhao
- Department of Science and Technology for Inspection, Xiamen Huaxia University, Xiamen, China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| |
Collapse
|
21
|
Schwanen V, Remacle F. Photoinduced Ultrafast Charge Transfer and Charge Migration in Small Gold Clusters Passivated by a Chromophoric Ligand. NANO LETTERS 2017; 17:5672-5681. [PMID: 28805392 DOI: 10.1021/acs.nanolett.7b02568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Because the development of attopulses, charge migration induced by short optical pulses has been extensively investigated. We report a computational purely electronic dynamical study of ultrafast few femtoseconds (fs) charge transfer and charge migration in realistic passivated stoichiometric Au11 and Au20 gold nanoclusters functionalized by a bipyridine ligand. We show that a net significant amount of electronic charge (0.1 to 0.4 |e| where |e| is the electron charge) is permanently transferred from the bipyridine chromophore to the gold cluster during the short 5-6 fs UV-vis strong pulse. This electron transfer to the metallic core is induced by the optical excitation of electronic states with a partial charge transfer character involving the chromophore before the onset of nuclei motion. In addition, the photoexcitation by the strong fs pulse builds a nonequilibrium electronic density that beats between the chromophore and the metallic core around the average of the transferred value. Modular systems made of a donor chromophore that can be photoexcited in the UV-vis range coupled to an efficient acceptor that could trap the charge are of interest for applications to nanodevices. Our study provides understanding on the very early, purely electronic dynamics built by the fs optical excitation and the initial charge separation step.
Collapse
Affiliation(s)
- Valérie Schwanen
- Theoretical Physical Chemistry, UR MOLSYS, University of Liège , B4000 Liège, Belgium
| | - Francoise Remacle
- Theoretical Physical Chemistry, UR MOLSYS, University of Liège , B4000 Liège, Belgium
| |
Collapse
|
22
|
Pirojsirikul T, Götz AW, Weare J, Walker RC, Kowalski K, Valiev M. Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. J Comput Chem 2017; 38:1631-1639. [PMID: 28470855 DOI: 10.1002/jcc.24804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/19/2017] [Indexed: 11/07/2022]
Abstract
Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes-NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Teerapong Pirojsirikul
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - John Weare
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Ross C Walker
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania, 19426
| | - Karol Kowalski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington, 99352
| | - Marat Valiev
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington, 99352
| |
Collapse
|
23
|
Bose S, Chakrabarty S, Ghosh D. Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach. J Phys Chem B 2017; 121:4790-4798. [DOI: 10.1021/acs.jpcb.7b02445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| |
Collapse
|
24
|
Georgieva I, Aquino AJA, Trendafilova N, Lischka H. High-level Ab Initio Absorption Spectra Simulations of Neutral, Anionic and Neutral+ Chromophore of Green Fluorescence Protein Chromophore Models in Gas Phase and Solution. Photochem Photobiol 2017; 93:1356-1367. [PMID: 28436037 DOI: 10.1111/php.12778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/29/2017] [Indexed: 12/01/2022]
Abstract
Semiclassical ab initio simulations of the absorption spectra of neutral and anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI), a model chromophore of green fluorescent protein (GFP) and of a positively charged neutral (N+)-HBDI chromophore model, were performed in gas phase with the resolution-of-identity algebraic diagrammatic construction through second-order (RI-ADC(2)) method. The calculated absorption spectra in gas phase are composed of one band centered at 3.51 eV (HBDI), 2.50 eV (HBDI- ) and 3.02 eV ((N+)-HBDI) owing to the absorption of the first 1 ππ* transition. Band maxima are redshifted by ~0.1 eV with respect to the corresponding vertical energies. The COSMO-RI-ADC(2) calculations of the first vertical excitation energy of HBDI, HBDI- and (N+)-HBDI forms in polar solution including microsolvation simulate the observed solvent redshift for neutral HBDI and the solvent blueshift of the HBDI- and (N+)-HBDI forms. The state-specific solvation approach applied to TDDFT calculations reproduced the experimental solvent shifts for the three HBDI forms, demonstrating a more accurate theoretical description as compared to the linear-response TDDFT approach.
Collapse
Affiliation(s)
- Ivelina Georgieva
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Adelia J A Aquino
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX.,School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Natasha Trendafilova
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX.,School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| |
Collapse
|
25
|
McLaughlin C, Assmann M, Parkes MA, Woodhouse JL, Lewin R, Hailes HC, Worth GA, Fielding HH. ortho and para chromophores of green fluorescent protein: controlling electron emission and internal conversion. Chem Sci 2017; 8:1621-1630. [PMID: 29780449 PMCID: PMC5933426 DOI: 10.1039/c6sc03833f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/05/2016] [Indexed: 12/22/2022] Open
Abstract
Green fluorescent protein (GFP) continues to play an important role in the biological and biochemical sciences as an efficient fluorescent probe and is also known to undergo light-induced redox transformations. Here, we employ photoelectron spectroscopy and quantum chemistry calculations to investigate how the phenoxide moiety controls the competition between electron emission and internal conversion in the isolated GFP chromophore anion, following photoexcitation with ultraviolet light in the range 400-230 nm. We find that moving the phenoxide group from the para position to the ortho position enhances internal conversion back to the ground electronic state but that adding an additional OH group to the para chromophore, at the ortho position, impedes internal conversion. Guided by quantum chemistry calculations, we interpret these observations in terms of torsions around the C-C-C bridge being enhanced by electrostatic repulsions or impeded by the formation of a hydrogen-bonded seven-membered ring. We also find that moving the phenoxide group from the para position to the ortho position reduces the energy required for detachment processes, whereas adding an additional OH group to the para chromophore at the ortho position increases the energy required for detachment processes. These results have potential applications in tuning light-induced redox processes of this biologically and technologically important fluorescent protein.
Collapse
Affiliation(s)
- Conor McLaughlin
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Mariana Assmann
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Michael A Parkes
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Joanne L Woodhouse
- 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 .
| | - Helen C Hailes
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Graham A Worth
- 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 .
| |
Collapse
|
26
|
Benda Z, Jagau TC. Communication: Analytic gradients for the complex absorbing potential equation-of-motion coupled-cluster method. J Chem Phys 2017; 146:031101. [DOI: 10.1063/1.4974094] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
27
|
Woodhouse JL, Assmann M, Parkes MA, Grounds H, Pacman SJ, Anderson JC, Worth GA, Fielding HH. Photoelectron spectroscopy of isolated luciferin and infraluciferin anions in vacuo: competing photodetachment, photofragmentation and internal conversion. Phys Chem Chem Phys 2017; 19:22711-22720. [DOI: 10.1039/c7cp04815g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The electronic structure and dynamics of luciferin and infraluciferin have been investigated using photoelectron spectroscopy and quantum chemistry calculations.
Collapse
Affiliation(s)
| | - Mariana Assmann
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
| | | | - Helen Grounds
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
| | - Steven J. Pacman
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
| | | | - Graham A. Worth
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
| | | |
Collapse
|
28
|
Bergeler M, Mizuno H, Fron E, Harvey JN. QM/MM-Based Calculations of Absorption and Emission Spectra of LSSmOrange Variants. J Phys Chem B 2016; 120:12454-12465. [DOI: 10.1021/acs.jpcb.6b09815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maike Bergeler
- Department
of Chemistry, Quantum Chemistry and Physical Chemistry
Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology
Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Hideaki Mizuno
- Department
of Chemistry, Quantum Chemistry and Physical Chemistry
Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology
Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Eduard Fron
- Department
of Chemistry, Quantum Chemistry and Physical Chemistry
Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology
Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Jeremy N. Harvey
- Department
of Chemistry, Quantum Chemistry and Physical Chemistry
Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology
Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| |
Collapse
|
29
|
Štěpánek P, Cowie TY, Šafařík M, Šebestík J, Pohl R, Bouř P. Resolving Electronic Transitions in Synthetic Fluorescent Protein Chromophores by Magnetic Circular Dichroism. Chemphyschem 2016; 17:2348-54. [PMID: 27124359 DOI: 10.1002/cphc.201600313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Indexed: 11/08/2022]
Abstract
The detailed electronic structures of fluorescent chromophores are important for their use in imaging of living cells. A series of green fluorescent protein chromophore derivatives is examined by magnetic circular dichroism (MCD) spectroscopy, which allows the resolution of more bands than plain absorption and fluorescence. Observed spectral patterns are rationalized with the aid of time-dependent density functional theory (TDDFT) computations and the sum-over-state (SOS) formalism, which also reveals a significant dependence of MCD intensities on chromophore conformation. The combination of organic and theoretical chemistry with spectroscopic techniques also appears useful in the rational design of fluorescence labels and understanding of the chromophore's properties. For example, the absorption threshold can be heavily affected by substitution on the phenyl ring but not much on the five-member ring, and methoxy groups can be used to further tune the electronic levels.
Collapse
Affiliation(s)
- Petr Štěpánek
- NMR Research Group, Faculty of Science, University of Oulu, PO Box 3000, 90014, Oulu, Finland
| | - Thomas Y Cowie
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic.
| |
Collapse
|
30
|
Deng H, Yu C, Gong L, Zhu X. Self-Restricted Green Fluorescent Protein Chromophore Analogues: Dramatic Emission Enhancement and Remarkable Solvatofluorochromism. J Phys Chem Lett 2016; 7:2935-2944. [PMID: 27404318 DOI: 10.1021/acs.jpclett.6b01251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The confinement effect of the β-barrel defines the emission profiles of the chromophores of the green fluorescent protein (GFP) family. Here, we describe the design strategy and mimicking of confinement effects via the chromophore itself, termed the self-restricted effect. By systematically tailoring the GFP core, a family of 2,5-dialkoxy-substituted GFP chromophore analogues is found to be highly emissive and show remarkable solvatofluorochromism in fluid solvents. Fluorescence quantum yield (QY) and lifetime measurements, in combination with theoretical calculations, illustrate the mechanism relying on inhibition of torsional rotation around the exocyclic CC bond. Meanwhile, theoretical calculations further reveal that the electrostatic interaction between the solvent and the imidazolinone oxygen can contribute to suppress the radiationless decay channel around the exocyclic C═C double bond. Our findings put forward a universal approach toward unlocked highly emissive GFPc analogues, potentially promoting the understanding of the photophysics and biochemical application of GFP chromophore analogues.
Collapse
Affiliation(s)
- Hongping Deng
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Chunyang Yu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Lidong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University , 850 Huanghe Road, Dalian 116029, People's Republic of China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| |
Collapse
|
31
|
Gurunathan PK, Acharya A, Ghosh D, Kosenkov D, Kaliman I, Shao Y, Krylov AI, Slipchenko LV. Extension of the Effective Fragment Potential Method to Macromolecules. J Phys Chem B 2016; 120:6562-74. [PMID: 27314461 DOI: 10.1021/acs.jpcb.6b04166] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.
Collapse
Affiliation(s)
| | - Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Debashree Ghosh
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Dmytro Kosenkov
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
- Department of Chemistry and Physics, Monmouth University , West Long Branch, New Jersey 07764, United States
| | - Ilya Kaliman
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Yihan Shao
- Q-Chem Inc. , 6601 Owens Drive, Suite 105 Pleasanton, California 94588, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| |
Collapse
|
32
|
Bose S, Chakrabarty S, Ghosh D. Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant. J Phys Chem B 2016; 120:4410-20. [DOI: 10.1021/acs.jpcb.6b03723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| |
Collapse
|
33
|
Olsen S, Baranov MS, Baleeva NS, Antonova MM, Johnson KA, Solntsev KM. pH-Sensitive fluorophores from locked GFP chromophores by a non-alternant analogue of the photochemical meta effect. Phys Chem Chem Phys 2016; 18:26703-26711. [DOI: 10.1039/c6cp02423h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis and characterization of a pH-sensitive fluorescence switch based on a conformationally-locked green fluorescent protein (GFP) chromophore.
Collapse
Affiliation(s)
- Seth Olsen
- School of Mathematics and Physics
- The University of Queensland
- Brisbane
- Australia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
- Pirogov Russian National Research Medical University
| | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
- Pirogov Russian National Research Medical University
| | - Maria M. Antonova
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
| | - Kenneth A. Johnson
- Institute for Cellular and Molecular Biology
- The University of Texas at Austin
- USA
| | | |
Collapse
|
34
|
Park JW, Rhee YM. Emission shaping in fluorescent proteins: role of electrostatics and π-stacking. Phys Chem Chem Phys 2016; 18:3944-55. [DOI: 10.1039/c5cp07535a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We obtained the fluorescence spectrum of the GFP with trajectory simulations, and revealed the role of the protein sidechains in emission shifts.
Collapse
Affiliation(s)
- Jae Woo Park
- Center for Self-assembly and Complexity
- Institute for Basic Science (IBS)
- Pohang 37673
- Korea
- Department of Chemistry
| | - Young Min Rhee
- Center for Self-assembly and Complexity
- Institute for Basic Science (IBS)
- Pohang 37673
- Korea
- Department of Chemistry
| |
Collapse
|
35
|
Faraji S, Krylov AI. On the Nature of an Extended Stokes Shift in the mPlum Fluorescent Protein. J Phys Chem B 2015; 119:13052-62. [PMID: 26402581 DOI: 10.1021/acs.jpcb.5b07724] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Far-red fluorescent proteins (FPs) enable deep-tissue in vivo imaging. Combining FPs with large and small Stokes shifts enables single-excitation/dual-emission multicolor applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the origin of an extended Stokes shift (0.2 eV) observed in mPlum, one of the most far-red-shifted FPs. We demonstrated that the red shift of emission is largely due to the excited-state relaxation of the chromophore itself. Rigid protein environment suppresses the relaxation; however, if the hydrogen-bond network around the chromophore is sufficiently flexible, it can rearrange upon electronic excitation, allowing the chromophore to relax. The reorganization of the hydrogen-bond network is driven by changes in bonding and charge distributions of the chromophore in the excited state. The ILE65 and GLU16 residues play the most important role. The MD simulations reveal two ground-state populations with the direct (Chro-ILE65···GLU16) and water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond patterns. In the excited state, both populations relax to a single emitting state with the water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond pattern, which provides a better match for the excited-state charge distribution (the acylimine's oxygen has a larger negative charge in S1 than in S0). The extended Stokes shift arises due to the conversion of the direct hydrogen-bond pattern to the water-mediated one accompanied by large structural relaxation of the electronically excited chromophore. This conclusion is supported by calculations for the GLU16LEU mutant, which has only one hydrogen-bond pattern. Consequently, no interconversion is possible, and the computed Stokes shift is small, in agreement with the experiment. Our theoretical findings provide support to a recent study of the Stokes shifts in mPlum and its mutants.
Collapse
Affiliation(s)
- Shirin Faraji
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| |
Collapse
|
36
|
Long- and Short-Range Electrostatic Fields in GFP Mutants: Implications for Spectral Tuning. Sci Rep 2015; 5:13223. [PMID: 26286372 PMCID: PMC4541067 DOI: 10.1038/srep13223] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/20/2015] [Indexed: 12/27/2022] Open
Abstract
The majority of protein functions are governed by their internal local electrostatics. Quantitative information about these interactions can shed light on how proteins work and allow for improving/altering their performance. Green fluorescent protein (GFP) and its mutation variants provide unique optical windows for interrogation of internal electric fields, thanks to the intrinsic fluorophore group formed inside them. Here we use an all-optical method, based on the independent measurements of transition frequency and one- and two-photon absorption cross sections in a number of GFP mutants to evaluate these internal electric fields. Two physical models based on the quadratic Stark effect, either with or without taking into account structural (bond-length) changes of the chromophore in varying field, allow us to separately evaluate the long-range and the total effective (short- and long-range) fields. Both types of the field quantitatively agree with the results of independent molecular dynamic simulations, justifying our method of measurement.
Collapse
|
37
|
Choosing an atomic basis set for TD-DFT, SOPPA, ADC(2), CIS(D), CC2 and EOM-CCSD calculations of low-lying excited states of organic dyes. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1676-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
38
|
Laurent AD, Adamo C, Jacquemin D. Dye chemistry with time-dependent density functional theory. Phys Chem Chem Phys 2015; 16:14334-56. [PMID: 24548975 DOI: 10.1039/c3cp55336a] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.
Collapse
Affiliation(s)
- Adèle D Laurent
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS no. 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes, Cedex 3, France.
| | | | | |
Collapse
|
39
|
Herbert JM. The Quantum Chemistry of Loosely-Bound Electrons. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
40
|
Fluorescence of a Histidine-Modified Enhanced Green Fluorescent Protein (EGFP) Effectively Quenched by Copper(II) Ions. Part II. Molecular Determinants. J Fluoresc 2015; 25:871-83. [DOI: 10.1007/s10895-015-1567-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/10/2015] [Indexed: 12/15/2022]
|
41
|
Atkins AJ, Bauer M, Jacob CR. High-resolution X-ray absorption spectroscopy of iron carbonyl complexes. Phys Chem Chem Phys 2015; 17:13937-48. [DOI: 10.1039/c5cp01045d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We apply high-energy-resolution fluorescence-detected (HERFD) X-ray absorption near-edge structure (XANES) spectroscopy to study iron carbonyl complexes.
Collapse
Affiliation(s)
- Andrew J. Atkins
- Karlsruhe Institute of Technology (KIT)
- Center for Functional Nanostructures and Institute of Physical Chemistry
- 76131 Karlsruhe
- Germany
| | - Matthias Bauer
- Universität Paderborn
- Naturwissenschaftliche Fakultät
- Department Chemie
- 33098 Paderborn
- Germany
| | - Christoph R. Jacob
- Karlsruhe Institute of Technology (KIT)
- Center for Functional Nanostructures and Institute of Physical Chemistry
- 76131 Karlsruhe
- Germany
- TU Braunschweig
| |
Collapse
|
42
|
Zuev D, Vecharynski E, Yang C, Orms N, Krylov AI. New algorithms for iterative matrix‐free eigensolvers in quantum chemistry. J Comput Chem 2014; 36:273-84. [DOI: 10.1002/jcc.23800] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/25/2014] [Accepted: 11/02/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Dmitry Zuev
- Department of ChemistryUniversity of Southern CaliforniaLos Angeles California90089‐0482
| | - Eugene Vecharynski
- Computational Research DivisionLawrence Berkeley National LaboratoryBerkeley California94720
| | - Chao Yang
- Computational Research DivisionLawrence Berkeley National LaboratoryBerkeley California94720
| | - Natalie Orms
- Department of ChemistryUniversity of Southern CaliforniaLos Angeles California90089‐0482
| | - Anna I. Krylov
- Department of ChemistryUniversity of Southern CaliforniaLos Angeles California90089‐0482
| |
Collapse
|
43
|
Ma H, Zhao Y, Liang W. Assessment of mode-mixing and Herzberg-Teller effects on two-photon absorption and resonance hyper-Raman spectra from a time-dependent approach. J Chem Phys 2014; 140:094107. [PMID: 24606353 DOI: 10.1063/1.4867273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A time-dependent approach is presented to simulate the two-photon absorption (TPA) and resonance hyper-Raman scattering (RHRS) spectra including Duschinsky rotation (mode-mixing) and Herzberg-Teller (HT) vibronic coupling effects. The computational obstacles for the excited-state geometries, vibrational frequencies, and nuclear derivatives of transition dipole moments, which enter the expressions of TPA and RHRS cross sections, are further overcome by the recently developed analytical excited-state energy derivative approaches in the framework of time-dependent density functional theory. The excited-state potential curvatures are evaluated at different levels of approximation to inspect the effects of frequency differences, mode-mixing and HT on TPA and RHRS spectra. Two types of molecules, one with high symmetry (formaldehyde, p-difluorobenzene, and benzotrifluoride) and the other with non-centrosymmetry (cis-hydroxybenzylidene-2,3-dimethylimidazolinone in the deprotonated anion state (HDBI(-))), are used as test systems. The calculated results reveal that it is crucial to adopt the exact excited-state potential curvatures in the calculations of TPA and RHRS spectra even for the high-symmetric molecules, and that the vertical gradient approximation leads to a large deviation. Furthermore, it is found that the HT contribution is evident in the TPA and RHRS spectra of HDBI(-) although its one- and two-photon transitions are strongly allowed, and its effect results in an obvious blueshift of the TPA maximum with respect to the one-photon absorption maximum. With the HT and solvent effects getting involved, the simulated blueshift of 1291 cm(-1) agrees well with the experimental measurement.
Collapse
Affiliation(s)
- HuiLi Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Institute of Fujian Provincial Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Yi Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Institute of Fujian Provincial Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Institute of Fujian Provincial Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| |
Collapse
|
44
|
Greenwood JB, Miles J, Camillis SD, Mulholland P, Zhang L, Parkes MA, Hailes HC, Fielding HH. Resonantly Enhanced Multiphoton Ionization Spectrum of the Neutral Green Fluorescent Protein Chromophore. J Phys Chem Lett 2014; 5:3588-3592. [PMID: 26278614 DOI: 10.1021/jz5019256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The photophysics of the green fluorescent protein is governed by the electronic structure of the chromophore at the heart of its β-barrel protein structure. We present the first two-color, resonance-enhanced, multiphoton ionization spectrum of the isolated neutral chromophore in vacuo with supporting electronic structure calculations. We find the absorption maximum to be 3.65 ± 0.05 eV (340 ± 5 nm), which is blue-shifted by 0.5 eV (55 nm) from the absorption maximum of the protein in its neutral form. Our results show that interactions between the chromophore and the protein have a significant influence on the electronic structure of the neutral chromophore during photoabsorption and provide a benchmark for the rational design of novel chromophores as fluorescent markers or photomanipulators.
Collapse
Affiliation(s)
- Jason B Greenwood
- †Centre for Plasma Physics, School of Maths and Physics, Queen's University Belfast, University Road, Belfast BT7 1NN, United Kingdom
| | - Jordan Miles
- †Centre for Plasma Physics, School of Maths and Physics, Queen's University Belfast, University Road, Belfast BT7 1NN, United Kingdom
| | - Simone De Camillis
- †Centre for Plasma Physics, School of Maths and Physics, Queen's University Belfast, University Road, Belfast BT7 1NN, United Kingdom
| | - Peter Mulholland
- †Centre for Plasma Physics, School of Maths and Physics, Queen's University Belfast, University Road, Belfast BT7 1NN, United Kingdom
| | - Lijuan Zhang
- ‡Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Michael A Parkes
- ‡Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Helen C Hailes
- ‡Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Helen H Fielding
- ‡Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| |
Collapse
|
45
|
Zuev D, Jagau TC, Bravaya KB, Epifanovsky E, Shao Y, Sundstrom E, Head-Gordon M, Krylov AI. Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks. J Chem Phys 2014; 141:024102. [DOI: 10.1063/1.4885056] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Thomas-C. Jagau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215-2521, USA
| | - Evgeny Epifanovsky
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Q-Chem, Inc., 6601 Owens Drive, Suite 105 Pleasanton, California 94588, USA
| | - Yihan Shao
- Q-Chem, Inc., 6601 Owens Drive, Suite 105 Pleasanton, California 94588, USA
| | - Eric Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| |
Collapse
|
46
|
Deng SHM, Kong XY, Zhang G, Yang Y, Zheng WJ, Sun ZR, Zhang DQ, Wang XB. Vibrationally Resolved Photoelectron Spectroscopy of the Model GFP Chromophore Anion Revealing the Photoexcited S1 State Being Both Vertically and Adiabatically Bound against the Photodetached D0 Continuum. J Phys Chem Lett 2014; 5:2155-2159. [PMID: 26270508 DOI: 10.1021/jz500869b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The first excited state of the model green fluorescence protein (GFP) chromophore anion (S1) and its energy level against the electron-detached neutral radical D0 state are crucial in determining the photophysics and the photoinduced dynamics of GFP. Extensive experimental and theoretical studies, particularly several very recent gas-phase investigations, concluded that S1 is a bound state in the Franck-Condon vertical region with respect to D0. However, what remains unknown and challenging is if S1 is bound adiabatically, primarily due to lack of accurate experimental measurements as well as due to the close proximity in energy for these two states that even sophisticated high-level ab initio calculations cannot reliably predict. Here, we report a negative ion photoelectron spectroscopy study on the model GFP chromophore anion, the deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI(-)) taken under low-temperature conditions with improved energy resolution. Despite the considerable size and low symmetry of the molecule, resolved vibrational structures were obtained with the 0-0 transition being the most intense peak. The adiabatic (ADE) and vertical detachment (VDE) energies therefore are determined both to be 2.73 ± 0.01 eV, indicating that the detached D0 state is 0.16 eV higher in energy than the photon excited S1 state. The accurate ADE and VDE values and the well-resolved photoelectron spectra reported here provide much needed robust benchmarks for future theoretical investigations.
Collapse
Affiliation(s)
- S H M Deng
- †Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
| | - Xiang-Yu Kong
- †Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
| | | | - Yan Yang
- †Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
- ∥State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
- ⊥State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China
| | | | - Zhen-Rong Sun
- ∥State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | | | - Xue-Bin Wang
- †Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
| |
Collapse
|
47
|
Mooney CRS, Parkes MA, Zhang L, Hailes HC, Simperler A, Bearpark MJ, Fielding HH. Competition between photodetachment and autodetachment of the 2(1)ππ* state of the green fluorescent protein chromophore anion. J Chem Phys 2014; 140:205103. [PMID: 24880334 DOI: 10.1063/1.4874643] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using a combination of photoelectron spectroscopy measurements and quantum chemistry calculations, we have identified competing electron emission processes that contribute to the 350-315 nm photoelectron spectra of the deprotonated green fluorescent protein chromophore anion, p-hydroxybenzylidene-2,3-dimethylimidazolinone. As well as direct electron detachment from S0, we observe resonant excitation of the 2(1)ππ* state of the anion followed by autodetachment. The experimental photoelectron spectra are found to be significantly broader than photoelectron spectrum calculated using the Franck-Condon method and we attribute this to rapid (∼10 fs) vibrational decoherence, or intramolecular vibrational energy redistribution, within the neutral radical.
Collapse
Affiliation(s)
- Ciarán R S Mooney
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Michael A Parkes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Lijuan Zhang
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Alexandra Simperler
- Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Michael J Bearpark
- Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Helen H Fielding
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| |
Collapse
|
48
|
Petrone A, Caruso P, Tenuta S, Rega N. On the optical absorption of the anionic GFP chromophore in vacuum, solution, and protein. Phys Chem Chem Phys 2013; 15:20536-44. [PMID: 24177429 DOI: 10.1039/c3cp52820k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In spite of the large number of experimental and theoretical studies, the optical absorption trend of the green fluorescent protein (GFP) chromophore in several environments has not been fully understood. We calculated at the same level of time dependent density functional theory the vertical excitation energy of the anionic GFP chromophore in the protein and in ethanol, dioxane, methanol and water solutions. As result, we reproduced for the first time the experimental trend of the absorption peaks with 0.015 eV as the standard deviation of the accuracy. This systematic error allowed us to analyze with confidence the relative weight of several solvation effects on the vertical excitation energy. Experimental trends not correlated with the solvent polarity were therefore explained with a fine balance of different steric and electronic effects on the photophysics of the chromophore. As an indirect and remarkable result, the present analysis confirms that the optical absorption of the chromophore in the gas phase is close to the value of 2.84 eV extrapolated by Dong et al. (J. Am. Chem. Soc., 2006, 128, 12038), and, as a consequence, that the protein environment induces a red shift of 0.23 eV.
Collapse
Affiliation(s)
- Alessio Petrone
- Dipartimento di Scienze Chimiche, Università di Napoli 'Federico II', Complesso Universitario di M. S. Angelo, via Cintia, I-80126 Napoli, Italy.
| | | | | | | |
Collapse
|
49
|
Kuś T, Mignolet B, Levine RD, Remacle F. Pump and Probe of Ultrafast Charge Reorganization in Small Peptides: A Computational Study through Sudden Ionizations. J Phys Chem A 2013; 117:10513-25. [DOI: 10.1021/jp407295t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- T. Kuś
- Department
of Chemistry, B6c, University of Liege, B4000 Liege, Belgium
| | - B. Mignolet
- Department
of Chemistry, B6c, University of Liege, B4000 Liege, Belgium
| | - R. D. Levine
- Fritz Haber Research
Centre for Molecular Dynamics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - F. Remacle
- Department
of Chemistry, B6c, University of Liege, B4000 Liege, Belgium
- Fritz Haber Research
Centre for Molecular Dynamics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| |
Collapse
|
50
|
Permanent dipole moments and energies of excited states from density functional theory compared with coupled cluster predictions: Case of para-nitroaniline. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.06.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|