1
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Sirimatayanant S, Andruniów T. Tuning Two-Photon Absorption in Rhodopsin Chromophore via Backbone Modification: The Story Told by CC2 and TD-DFT. J Chem Theory Comput 2024. [PMID: 39269133 DOI: 10.1021/acs.jctc.4c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
We investigate here a systematic way to tune two-photon transition strengths (δ2PA) and two-photon absorption (2PA) cross sections (σ2PA) of the rhodopsin's chromophore 11-cis-retinal protonated Schiff base (RPSB) via the modulation of the methyl groups pattern along its polyene chain. Our team employed the resolution of identity, coupled cluster approximate second order (RI-CC2) method with Dunning's aug-cc-pVDZ basis set, to determine the structural impact on δ2PA, as well as its correlation to both transition dipole moments and permanent electric dipole moments. Seven structures were probed in vacuo, including five-double-bond-conjugated model of the native chromophore, shortened by the β-ionone ring (RPSB5), and its de/methylated analogues: 9-methyl, 13-methyl, planar and twisted models of 9,10-dimethyl and 9,10,13-trimethyl. Our results demonstrate that the magnitude of δ2PA is dictated by both the position and number of methylated groups attached to its polyene chain as well as the degree of dihedral twist that is introduced due to the de/methylation. In fact, a strong correlation between δ2PA enhancement and the presence of a C13-methyl group in the planar RPSB5 species is found. Trends in δ2PA values follow the trends observed in their corresponding changes in the permanent dipole moment upon the S0-S1 excitation nearly exactly. The assessment of four DFT functionals, i.e., M11, MN15, CAM-B3LYP, and BHandHLYP, previously found most successful in predicting 2PA properties in biological chromophores, points to a long-range-corrected hybrid meta-GGA M11 as the top-performing functional, albeit still delivering underestimated δ2PA and σ2PA values by a factor of 3.3-5.3 with respect to the CC2 results. In the case of global-hybrid meta-NGA (MN15), as well as CAM-B3LYP and BHandHLYP functionals, this factor deteriorates significantly to 6.7-20.9 and is mostly related to significantly lower quality of the ground- and excited-state dipole moments.
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Affiliation(s)
- Saruti Sirimatayanant
- Institute of Advanced Materials, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspiańskiego 27, Wrocław 50-370, Poland
| | - Tadeusz Andruniów
- Institute of Advanced Materials, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspiańskiego 27, Wrocław 50-370, Poland
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2
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Elayan IA, Brown A. Non-Degenerate Two-Photon Absorption of Fluorescent Protein Chromophores. J Phys Chem A 2024; 128:7511-7523. [PMID: 39192559 DOI: 10.1021/acs.jpca.3c08402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Two-photon absorption (2PA), where a pair of photons are absorbed simultaneously, is recognized as a potent bioimaging technique, which depends on the quantified 2PA probability, defined as cross-section (σ2PA). The absorbed photons either have equivalent (ω1 = ω2) or different frequencies (ω1 ≠ ω2), where the former is degenerate 2PA (D-2PA) and the latter is nondegenerate 2PA (ND-2PA). ND-2PA is of particular interest since it is a promising imaging technology with flexibility of photon frequencies and enhanced cross sections, however, it remains a relatively unexplored area compared to D-2PA. This work utilizes time-dependent density functional theory (TD-DFT) and second-order approximate coupled-cluster with the resolution-of-identity approximation (RI-CC2), for the excitation from S0 to S1, to investigate σD-2PA and σND-2PA of FP chromophore models. Interestingly, comparing CAM-B3LYP with the RI-CC2 computations shows qualitative and, in fact, near quantitative agreement in the computed improvements of σND-2PA for comparable (relative) frequency detunings, despite the known underestimations of 2PA cross sections, for TD-DFT results relative to RI-CC2 values. As expected from the 2-state model, the computed values of σND-2PA are quantitatively larger than σD-2PA, where chromophores with the largest values of σD-2PA show greater potential for σND-2PA improvement. Anionic chromophores demonstrated improvements up to 14%, while substantial enhancements were observed in neutral chromophores with some achieving a 30% increase. This work investigates the ND-2PA photophysical characteristics of FP chromophores and identifies qualitative patterns in the computed properties of ND-2PA relative to D-2PA.
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Affiliation(s)
- Ismael A Elayan
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
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3
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Elayan IA, Rib L, A Mendes R, Brown A. Beyond Explored Functionals: A Computational Journey of Two-Photon Absorption. J Chem Theory Comput 2024; 20:3879-3893. [PMID: 38648613 DOI: 10.1021/acs.jctc.4c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We present a thorough investigation into the efficacy of 19 density functional theory (DFT) functionals, relative to RI-CC2 results, for computing two-photon absorption (2PA) cross sections (σ2PA) and key dipole moments (|μ00|, |μ11|, |Δμ|, |μ01|) for a series of coumarin dyes in the gas-phase. The functionals include different categories, including local density approximation (LDA), generalized gradient approximation (GGA), hybrid-GGA (H-GGA), range-separated hybrid-GGA (RSH-GGA), meta-GGA (M-GGA), and hybrid M-GGA (HM-GGA), with 14 of them being subjected to analysis for the first time with respect to predicting σ2PA values. Analysis reveals that functionals integrating both short-range (SR) and long-range (LR) corrections, particularly those within the RSH-GGA and HM-GGA classes, outperform the others. Furthermore, the range-separation approach was found more impactful compared to the varying percentages of Hartree-Fock exchange (HF Ex) within different functionals. The functionals traditionally recommended for 2PA do not appear among the top 9 in our study, which is particularly interesting, as these top-performing functionals have not been previously investigated in this context. This list is dominated by M11, QTP variants, ωB97X, ωB97X-V, and M06-2X, surpassing the performance of other functionals, including the commonly used CAM-B3LYP.
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Affiliation(s)
- Ismael A Elayan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Laura Rib
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Rodrigo A Mendes
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Departamento de Química, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso 78060-900, Brazil
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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4
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Ahmadzadeh K, Li X, Rinkevicius Z, Norman P, Zaleśny R. Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation. J Phys Chem Lett 2024; 15:969-974. [PMID: 38252270 PMCID: PMC10839899 DOI: 10.1021/acs.jpclett.3c03513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.
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Affiliation(s)
- Karan Ahmadzadeh
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Xin Li
- PDC
Center for High Performance Computing, KTH
Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Zilvinas Rinkevicius
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- Department
of Physics, Faculty of Mathematics and Natural Sciences, Kaunas University of Technology, Kaunas LT-51368, Lithuania
| | - Patrick Norman
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Robert Zaleśny
- Faculty
of Chemistry, Wrocław University of
Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
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5
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Moztarzadeh O, Jamshidi M, Taherpour AA, Babuska V. Molecular modelling of fullerene C 60 functionalized by nitric oxide for use in biological environment. Sci Rep 2024; 14:2565. [PMID: 38297014 PMCID: PMC10831047 DOI: 10.1038/s41598-024-53050-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/27/2024] [Indexed: 02/02/2024] Open
Abstract
The unique potential of fullerene C60 for various biological applications has ignited significant interest. However, its inherent non-polarity poses a critical challenge for its effective integration within biological systems. This study delves into the intricate physicochemical characteristics of the innovative [C60 + NO] complex using density functional theory and time-dependent density functional theory. The computational analyses encompass molecular charge, surface electrostatic potential, and dipole moment evaluations. Impressively, the dipole moment of the [C60 + NO] complex significantly increases to 12.92 D. Meticulous surface analysis reveals a subtle interplay between molecular structures, indicating weak interactions. The analysis of the absorption spectrum unveils a noteworthy red-shift of 200 nm subsequent to complex formation. To elucidate the electron transfer mechanisms, we explore photo-induced electron transfer through CAM-B3LYP. This exploration elucidates intricate pathways governing electron transfer, with complementary insights gleaned from Marcus theory's outputs, especially the Gibbs free energy of electron transfer. Changes in the physicochemical properties of approaching C60 and NO molecules reveal interesting results compared to separate molecules. These findings resonate profoundly in the context of potential biological and pharmaceutical utilization. With implications for the biomedical area, the outcomes linked to the [C60 + NO] complex kindle optimism for pioneering biomedical applications.
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Affiliation(s)
- Omid Moztarzadeh
- Department of Stomatology, University Hospital Pilsen, Faculty of Medicine in Pilsen, Charles University, 323 00, Pilsen, Czech Republic
- Department of Anatomy, Faculty of Medicine in Pilsen, Charles University, 323 00, Pilsen, Czech Republic
| | - Morteza Jamshidi
- Young Researchers and Elite Club, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | | | - Vaclav Babuska
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine in Pilsen, Charles University, 323 00, Pilsen, Czech Republic.
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6
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Elayan IA, Brown A. Degenerate and non-degenerate two-photon absorption of coumarin dyes. Phys Chem Chem Phys 2023. [PMID: 37318284 DOI: 10.1039/d3cp00723e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Two-photon absorption (2PA) spectroscopy is a robust bioimaging tool that depends on the determined cross-sections (σ2PA). The absorption of both photons occurs simultaneously with equivalent (degenerate) or different (non-degenerate) photon energies, D-2PA and ND-2PA, respectively. The former has been investigated experimentally and computationally for many systems, while the latter remains relatively unexplored computationally and limited experimentally. In this study, response theory using time-dependent density functional theory (TD-DFT) and the 2-state model (2SM) have been utilized to investigate σD-2PA and σND-2PA for the excitation to the lowest energy singlet state (S1) of coumarin, coumarin 6, coumarin 120, coumarin 307, and coumarin 343. Solvents involved were methanol (MeOH), chloroform (ClForm), and dimethylsulfoxide (DMSO), where the latter leads to the largest σ2PA. Values of σ2PA are largest for coumarin 6 and lowest for coumarin, which illustrates the effect of substituents. The 2SM clarifies how the largest cross-sections correspond to molecules with the largest transition dipole moments, μ01. In general, σD-2SM computations agree with σD-2PA. Moreover, σND-2SM are in qualitative agreement with σND-2PA with comparable enhancement relative to σD-2PA. Overall, σND-2PA are larger than σD-2PA where the increase is in the range of 22% to 49%, depending on the coumarin as well as the relative energies of the two photons. This work aids in future investigations into various fluorophores to understand their photophysical properties for ND-2PA.
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Affiliation(s)
- Ismael A Elayan
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2.
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2.
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7
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Sirimatayanant S, Andruniów T. Benchmarking two-photon absorption strengths of rhodopsin chromophore models with CC3 and CCSD methodologies: An assessment of popular density functional approximations. J Chem Phys 2023; 158:094106. [PMID: 36889953 DOI: 10.1063/5.0135594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
This work presents the investigations of the impact of an increasing electron correlation in the hierarchy of coupled-cluster methods, i.e., CC2, CCSD, and CC3, on two-photon absorption (2PA) strengths for the lowest excited state of the minimal rhodopsin's chromophore model-cis-penta-2,4-dieniminium cation (PSB3). For a larger chromophore's model [4-cis-hepta-2,4,6-trieniminium cation (PSB4)], CC2 and CCSD calculations of 2PA strengths were performed. Additionally, 2PA strengths predicted by some popular density functional theory (DFT) functionals differing in HF exchange contribution were assessed against the reference CC3/CCSD data. For PSB3, the accuracy of 2PA strengths increases in the following order: CC2 < CCSD < CC3, with the CC2 deviation from both higher-level methods exceeding 10% at 6-31+G* basis sets and 2% at aug-cc-pVDZ basis set. However, for PSB4, this trend is reversed and CC2-based 2PA strength is larger than the corresponding CCSD value. Among the DFT functionals investigated, CAM-B3LYP and BHandHLYP provide 2PA strengths in best compliance with reference data, however, with the error approaching an order of magnitude.
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Affiliation(s)
- Saruti Sirimatayanant
- Institute of Advanced Materials, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Tadeusz Andruniów
- Institute of Advanced Materials, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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8
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de Wergifosse M, Beaujean P, Grimme S. Ultrafast Evaluation of Two-Photon Absorption with Simplified Time-Dependent Density Functional Theory. J Phys Chem A 2022; 126:7534-7547. [PMID: 36201255 DOI: 10.1021/acs.jpca.2c02395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work presents the theoretical background to evaluate two-photon absorption (2PA) cross-sections in the framework of simplified time-dependent density functional theory (sTD-DFT). Our new implementation allows the ultrafast evaluation of 2PA cross-sections for large molecules based on a regular DFT ground-state determinant as well as a variant employing our tight-binding sTD-DFT-xTX flavor for very large systems. The method is benchmarked against higher-level calculations for trans-stilbene and typical fluorescent protein chromophores. For eGFP, a quadrupolar chromophore and its branched version, the flavine mono-nucleotide, and the iLOV protein, we compare sTD-DFT 2PA spectra to experimental ones. This includes extension and testing of our all-atom quantum chemistry methodology for the evaluation of 2PA for a system of ∼2000 atoms, providing striking agreement with the experimental spectrum.
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Affiliation(s)
- Marc de Wergifosse
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115Bonn, Germany
| | - Pierre Beaujean
- Laboratory of Theoretical Chemistry, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000Namur, Belgium
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115Bonn, Germany
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9
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Grabarek D, Andruniów T. Quantum chemistry study of the multiphoton absorption in enhanced green fluorescent protein at the single amino acid residue level. Chemphyschem 2022; 23:e202200335. [PMID: 35875840 DOI: 10.1002/cphc.202200335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/17/2022] [Indexed: 11/11/2022]
Abstract
The chromophore (CRO) of fluorescent proteins (FPs) is embedded in a complex environment that is a source of specific interactions with the CRO. Understanding how these interactions influence FPs spectral properties is important for a directed design of novel markers with desired characteristics. In this work, we apply computational chemistry methods to gain insight into one-, two- and three-photon absorption (1PA, 2PA, 3PA) tuning in enhanced green fluorescent protein (EGFP). To achieve this goal, we built EGFP models differing in: i) number and position of hydrogen-bonds (h-bonds) donors to the CRO and ii) the electric field, as approximated by polarizable force field, acting on the CRO. We find that h-bonding to the CRO's phenolate oxygen results in stronger one- and multiphoton absorption. The brighter absorption can be also achieved by creating more positive electric field near the CRO's phenolate moiety. Interestingly, while individual CRO-environment h-bonds usually enhance 1PA and 2PA, it takes a few h-bond donors to enhance 3PA. Clearly, response of the absorption intensity to many-body effects depends on the excitation mechanism. We further employ symmetry-adapted perturbation theory (SAPT) to reveal excellent (2PA) and good (3PA) correlation of multiphoton intensity with electrostatic and induction interaction energies. This points to importance of accounting for mutual CRO-environment polarization in quantitative calculations of absorption spectra in FPs.
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Affiliation(s)
| | - Tadeusz Andruniów
- Wroclaw University of Science and Technology, Chemistry, Wyb. Wyspianskiego, 30-516, Wroclaw, POLAND
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10
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Knysh I, Jassar MB, Osmialowsk B, Zalesny R, Jacquemin D. IN SILICO SCREENING OF TWO‐PHOTON ABSORPTION PROPERTIES OF A LARGE SET OF BIS‐DIFLUOROBORATE‐DYES. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Iryna Knysh
- Nantes University: Universite de Nantes CEISAM Lab FRANCE
| | | | | | - Robert Zalesny
- Wroclaw University of Technology: Politechnika Wroclawska Department of Chemistr FRANCE
| | - Denis Jacquemin
- Université de Nantes CEISAM 2, rue de la Houssinière 44322 Nantes FRANCE
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11
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Liang W, Pei Z, Mao Y, Shao Y. Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges. J Chem Phys 2022; 156:210901. [PMID: 35676148 PMCID: PMC9162785 DOI: 10.1063/5.0088271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/15/2022] [Indexed: 01/04/2023] Open
Abstract
Time-dependent density functional theory (TDDFT) based approaches have been developed in recent years to model the excited-state properties and transition processes of the molecules in the gas-phase and in a condensed medium, such as in a solution and protein microenvironment or near semiconductor and metal surfaces. In the latter case, usually, classical embedding models have been adopted to account for the molecular environmental effects, leading to the multi-scale approaches of TDDFT/polarizable continuum model (PCM) and TDDFT/molecular mechanics (MM), where a molecular system of interest is designated as the quantum mechanical region and treated with TDDFT, while the environment is usually described using either a PCM or (non-polarizable or polarizable) MM force fields. In this Perspective, we briefly review these TDDFT-related multi-scale models with a specific emphasis on the implementation of analytical energy derivatives, such as the energy gradient and Hessian, the nonadiabatic coupling, the spin-orbit coupling, and the transition dipole moment as well as their nuclear derivatives for various radiative and radiativeless transition processes among electronic states. Three variations of the TDDFT method, the Tamm-Dancoff approximation to TDDFT, spin-flip DFT, and spin-adiabatic TDDFT, are discussed. Moreover, using a model system (pyridine-Ag20 complex), we emphasize that caution is needed to properly account for system-environment interactions within the TDDFT/MM models. Specifically, one should appropriately damp the electrostatic embedding potential from MM atoms and carefully tune the van der Waals interaction potential between the system and the environment. We also highlight the lack of proper treatment of charge transfer between the quantum mechanics and MM regions as well as the need for accelerated TDDFT modelings and interpretability, which calls for new method developments.
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Affiliation(s)
- 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, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Zheng Pei
- 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, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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12
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ZHU ZHE, Higashi M, Saito S. Excited states of chlorophyll a and b in solution by time-dependent density functional theory. J Chem Phys 2022; 156:124111. [DOI: 10.1063/5.0083395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ground state and excited state electronic properties of chlorophyll (Chl) a and Chl b in diethyl ether, acetone, and ethanol solutions are investigated using quantum mechanical and molecular mechanical calculations with density functional theory (DFT) and time-dependent DFT (TDDFT). Although the DFT/TDDFT methods are widely used, the electronic structures of molecules, especially large molecules, calculated with these methods are known to be strongly dependent on the functionals and the parameters used in functionals. Here, we optimize the range-separated parameter, µ, of the CAM-B3LYP functional of Chl a and Chl b to reproduce the experimental excitation energy differences of these Chl molecules in solution. The optimal values of µ for Chl a and Chl b are smaller than the default value of µ and that for bacteriochlorophyll a, indicating the change in electronic distribution, i.e., an increase in electron delocalization, within the molecule. We find that the electronic distribution of Chl b with an extra formyl group is different from that of Chl a. We also find that the polarity of solution and hydrogen bond cause the decrease in the excitation energies and the increase in the widths of excitation energy distributions of Chl a and Chl b. The present results are expected to be useful for understanding the electronic properties of each pigment molecule in a local heterogeneous environment, which will play an important role in the excitation energy transfer in light-harvesting complex II.
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Affiliation(s)
| | - Masahiro Higashi
- Department of Molecular Engineering, Kyoto University - Katsura Campus, Japan
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
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13
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Grabarek D, Andruniów T. The role of hydrogen bonds and electrostatic interactions in enhancing two-photon absorption in green and yellow fluorescent proteins. Chemphyschem 2022; 23:e202200003. [PMID: 35130370 DOI: 10.1002/cphc.202200003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Indexed: 11/07/2022]
Abstract
The spectral properties of fluorescent proteins (FPs) depend on the protein environment of the chromophore (CRO). A deeper understanding of the CRO - environment interactions in terms of FPs spectral characteristics will allow for a rational design of novel markers with desired properties. Here, we are taking a step towards achieving this important goal. With the time-dependent density functional theory (TDDFT), we calculate one- and two-photon absorption (OPA and TPA) spectra for 5 green FPs (GFPs) and 3 yellow FPs (YFPs) differing in amino acid sequence. The goal is to reveal a role of: (i) electrostatic interactions, (ii) hydrogen-bonds (h-bonds), and (iii) h-bonds together with distant electrostatic field in absorption spectra tuning. Our results point to design hypothesis towards FPs optimised for TPA-based applications. Both h-bonds and electrostatic interactions co-operate in enhancing TPA cross-section (σ TPA ) for the S 0 ->S 1 transition in GFPs. Furthermore, it seems that details of h-bonds network in the CRO's vicinity influences σ TPA response to CRO - environment electrostatic interactions in YFPs. We postulate that engineering FPs with more hydrophilic CRO's environment can lead to greater σ TPA . We also find that removing h-bonds formed with the CRO's phenolate leads to TPA enhancement for transition to higher excited states than S 1 . Particularly Y145 and T203 residues are important in this regard.
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Affiliation(s)
- Dawid Grabarek
- Department of Chemistry, Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Tadeusz Andruniów
- Department of Chemistry, Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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14
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Chołuj M, Alam MM, Beerepoot MTP, Sitkiewicz SP, Matito E, Ruud K, Zaleśny R. Choosing Bad versus Worse: Predictions of Two-Photon-Absorption Strengths Based on Popular Density Functional Approximations. J Chem Theory Comput 2022; 18:1046-1060. [PMID: 35080389 PMCID: PMC8830054 DOI: 10.1021/acs.jctc.1c01056] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We present a benchmark
study of density functional approximation
(DFA) performances in predicting the two-photon-absorption strengths
in π-conjugated molecules containing electron-donating/-accepting
moieties. A set of 48 organic molecules is chosen for this purpose,
for which the two-photon-absorption (2PA) parameters are evaluated
using different DFAs, including BLYP, PBE, B3LYP, PBE0, CAM-B3LYP,
LC-BLYP, and optimally tuned LC-BLYP. Minnesota functionals and ωB97X-D
are also used, applying the two-state approximation, for a subset
of molecules. The efficient resolution-of-identity implementation
of the coupled-cluster CC2 model (RI-CC2) is used as a reference for
the assessment of the DFAs. Two-state models within the framework
of both DFAs and RI-CC2 are used to gain a deeper insight into the
performance of different DFAs. Our results give a clear picture of
the performance of the density functionals in describing the two-photon
activity in dipolar π-conjugated systems. The results show that
global hybrids are best suited to reproduce the absolute values of
2PA strengths of donor–acceptor molecules. The range-separated
functionals CAM-B3LYP and optimally tuned LC-BLYP, however, show the
highest linear correlations with the reference RI-CC2 results. Hence,
we recommend the latter DFAs for structure–property studies
across large series of dipolar compounds.
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Affiliation(s)
- Marta Chołuj
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
| | - Md Mehboob Alam
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh 492015, India
| | - Maarten T P Beerepoot
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Sebastian P Sitkiewicz
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 Donostia, Euskadi, Spain.,Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), 20080 Donostia, Euskadi, Spain
| | - Eduard Matito
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 Donostia, Euskadi, Spain.,Ikerbasque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Euskadi, Spain
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Robert Zaleśny
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
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15
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E/ Z Molecular Photoswitches Activated by Two-Photon Absorption: Comparison between Different Families. Molecules 2021; 26:molecules26237379. [PMID: 34885961 PMCID: PMC8659108 DOI: 10.3390/molecules26237379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Nonlinear optical techniques as two-photon absorption (TPA) have raised relevant interest within the last years due to the capability to excite chromophores with photons of wavelength equal to only half of the corresponding one-photon absorption energy. At the same time, its probability being proportional to the square of the light source intensity, it allows a better spatial control of the light-induced phenomenon. Although a consistent number of experimental studies focus on increasing the TPA cross section, very few of them are devoted to the study of photochemical phenomena induced by TPA. Here, we show a design strategy to find suitable E/Z photoswitches that can be activated by TPA. A theoretical approach is followed to predict the TPA cross sections related to different excited states of various photoswitches’ families, finally concluding that protonated Schiff-bases (retinal)-like photoswitches outperform compared to the others. The donor-acceptor substitution effect is therefore rationalized for the successful TPA activatable photoswitch, in order to maximize its properties, finally also forecasting a possible application in optogenetics. Some experimental measurements are also carried out to support our conclusions.
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16
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Grabarek D, Andruniów T. Removing artifacts in polarizable embedding calculations of one- and two-photon absorption spectra of fluorescent proteins. J Chem Phys 2021; 153:215102. [PMID: 33291919 DOI: 10.1063/5.0023434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The multiscale calculations involving excited states may suffer from the electron spill-out (ESO) problem. This seems to be especially the case when the environment of the core region, described with the electronic structure method, is approximated by a polarizable force field. The ESO effect often leads to incorrect physical character of electronic excitations, spreading outside the quantum region, which, in turn, results in erroneous absorption spectra. In this work, we investigate means to remove the artifacts in one-photon absorption (OPA) and two-photon absorption (TPA) spectra of green and yellow fluorescent protein representatives. This includes (i) using different basis sets, (ii) extending the core subsystem beyond the chromophore, (iii) modification of polarization interaction between the core region and its environment, and (iv) including the Pauli repulsion through effective core potentials (ECPs). Our results clearly show that ESO is observed when diffuse functions are used to assemble the multielectron wave function regardless of the exchange-correlation functional used. Furthermore, extending the core region, thus accounting for exchange interactions between the chromophore and its environment, leads to even more spurious excited states. Also, damping the interactions between the core subsystem and the polarizable force field is hardly helpful. In contrast, placing ECPs in the position of sites creating the embedding potential leads to the removal of artificious excited states that presumably should not be observed in the OPA and TPA spectra. We prove that it is a reliable and cost-effective approach for systems where the covalent bond(s) between the core region and its environment must be cut.
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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
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17
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Bourne Worster S, Feighan O, Manby FR. Reliable transition properties from excited-state mean-field calculations. J Chem Phys 2021; 154:124106. [DOI: 10.1063/5.0041233] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Susannah Bourne Worster
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Oliver Feighan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Frederick R. Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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18
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Lehtola S, Dimitrova M, Fliegl H, Sundholm D. Benchmarking Magnetizabilities with Recent Density Functionals. J Chem Theory Comput 2021; 17:1457-1468. [PMID: 33599491 PMCID: PMC8023670 DOI: 10.1021/acs.jctc.0c01190] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Indexed: 12/21/2022]
Abstract
We have assessed the accuracy of the magnetic properties of a set of 51 density functional approximations, including both recently published and already established functionals. The accuracy assessment considers a series of 27 small molecules and is based on comparing the predicted magnetizabilities to literature reference values calculated using coupled-cluster theory with full singles and doubles and perturbative triples [CCSD(T)] employing large basis sets. The most accurate magnetizabilities, defined as the smallest mean absolute error, are obtained with the BHandHLYP functional. Three of the six studied Berkeley functionals and the three range-separated Florida functionals also yield accurate magnetizabilities. Also, some older functionals like CAM-B3LYP, KT1, BHLYP (BHandH), B3LYP, and PBE0 perform rather well. In contrast, unsatisfactory performance is generally obtained with Minnesota functionals, which are therefore not recommended for calculations of magnetically induced current density susceptibilities and related magnetic properties such as magnetizabilities and nuclear magnetic shieldings. We also demonstrate that magnetizabilities can be calculated by numerical integration of magnetizability density; we have implemented this approach as a new feature in the gauge-including magnetically induced current (GIMIC) method. Magnetizabilities can be calculated from magnetically induced current density susceptibilities within this approach even when analytical approaches for magnetizabilities as the second derivative of the energy have not been implemented. The magnetizability density can also be visualized, providing additional information that is not otherwise easily accessible on the spatial origin of magnetizabilities.
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Affiliation(s)
- Susi Lehtola
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FI-00014 University
of Helsinki, Finland
- Molecular
Sciences Software Institute, Blacksburg, Virginia 24061, United States
| | - Maria Dimitrova
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FI-00014 University
of Helsinki, Finland
| | - Heike Fliegl
- Institute
of Nanotechnology, KIT, Hermann-von-Helmholtz Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Dage Sundholm
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FI-00014 University
of Helsinki, Finland
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19
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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.
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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
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20
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Sokolovski SG, Zherebtsov EA, Kar RK, Golonka D, Stabel R, Chichkov NB, Gorodetsky A, Schapiro I, Möglich A, Rafailov EU. Two-photon conversion of a bacterial phytochrome. Biophys J 2021; 120:964-974. [PMID: 33545103 DOI: 10.1016/j.bpj.2021.01.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/20/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
In nature, sensory photoreceptors underlie diverse spatiotemporally precise and generally reversible biological responses to light. Photoreceptors also serve as genetically encoded agents in optogenetics to control by light organismal state and behavior. Phytochromes represent a superfamily of photoreceptors that transition between states absorbing red light (Pr) and far-red light (Pfr), thus expanding the spectral range of optogenetics to the near-infrared range. Although light of these colors exhibits superior penetration of soft tissue, the transmission through bone and skull is poor. To overcome this fundamental challenge, we explore the activation of a bacterial phytochrome by a femtosecond laser emitting in the 1 μm wavelength range. Quantum chemical calculations predict that bacterial phytochromes possess substantial two-photon absorption cross sections. In line with this notion, we demonstrate that the photoreversible Pr ↔ Pfr conversion is driven by two-photon absorption at wavelengths between 1170 and 1450 nm. The Pfr yield was highest for wavelengths between 1170 and 1280 nm and rapidly plummeted beyond 1300 nm. By combining two-photon activation with bacterial phytochromes, we lay the foundation for enhanced spatial resolution in optogenetics and unprecedented penetration through bone, skull, and soft tissue.
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Affiliation(s)
- Serge G Sokolovski
- Optoelectronics and Biomedical Photonics Group, AIPT, Aston University, Birmingham, United Kingdom
| | - Evgeny A Zherebtsov
- Optoelectronics and Measurement Techniques, University of Oulu, Oulu, Finland; Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Golonka
- Photobiochemistry, University of Bayreuth, Bayreuth, Germany
| | - Robert Stabel
- Photobiochemistry, University of Bayreuth, Bayreuth, Germany
| | - Nikolai B Chichkov
- Optoelectronics and Biomedical Photonics Group, AIPT, Aston University, Birmingham, United Kingdom
| | - Andrei Gorodetsky
- ITMO University, St. Petersburg, Russia; Department of Chemistry, Imperial College London, London, United Kingdom; School of Physics and Astronomy, University of Birmingham, Birmingham, United Kingdom
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andreas Möglich
- Photobiochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Edik U Rafailov
- Optoelectronics and Biomedical Photonics Group, AIPT, Aston University, Birmingham, United Kingdom.
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21
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Grabarek D, Andruniów T. What is the Optimal Size of the Quantum Region in Embedding Calculations of Two-Photon Absorption Spectra of Fluorescent Proteins? J Chem Theory Comput 2020; 16:6439-6455. [PMID: 32862643 PMCID: PMC7586329 DOI: 10.1021/acs.jctc.0c00602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
We
systematically investigate an impact of the size and content
of a quantum (QM) region, treated at the density functional theory
level, in embedding calculations on one- (OPA) and two-photon absorption
(TPA) spectra of the following fluorescent proteins (FPs) models: Aequorea victoria green FP (avGFP) with neutral (avGFP-n)
and anionic (avGFP-a) chromophore as well as Citrine FP. We find that
amino acid (a.a.) residues as well as water molecules hydrogen-bonded
(h-bonded) to the chromophore usually boost both OPA and TPA processes
intensity. The presence of hydrophobic a.a. residues in the quantum
region also non-negligibly affects both absorption spectra but decreases
absorption intensity. We conclude that to reach a quantitative description
of OPA and TPA spectra in multiscale modeling of FPs, the quantum
region should consist of a chromophore and most of a.a. residues and
water molecules in a radius
of 0.30–0.35 nm (ca. 200–230 atoms)
when the remaining part of the system is approximated by the electrostatic
point-charges. The optimal size of the QM region can be reduced to
80–100 atoms by utilizing a more advanced polarizable embedding
model. We also find components of the QM region that are specific
to a FP under study. We propose that the F165 a.a. residue is important
in tuning the TPA spectrum of avGFP-n but not other investigated FPs.
In the case of Citrine, Y203 and M69 a.a. residues must definitely
be part of the QM subsystem. Furthermore, we find that long-range
electrostatic interactions between the QM region and the rest of the
protein cannot be neglected even for the most extensive QM regions
(ca. 350 atoms).
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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
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22
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Suellen C, Freitas RG, Loos PF, Jacquemin D. Cross-Comparisons between Experiment, TD-DFT, CC, and ADC for Transition Energies. J Chem Theory Comput 2019; 15:4581-4590. [DOI: 10.1021/acs.jctc.9b00446] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Cinthia Suellen
- Departamento de Quimica, Laboratorio Computacional de Materiais, Universidade Federal de Mato Grosso, Cuiaba, Mato Grosso 78060, Brazil
| | - Renato Garcia Freitas
- Departamento de Quimica, Laboratorio Computacional de Materiais, Universidade Federal de Mato Grosso, Cuiaba, Mato Grosso 78060, Brazil
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31062 Cedex 9 Toulouse, France
| | - Denis Jacquemin
- Laboratoire CEISAM—UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Cedex 3 Nantes, France
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23
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Rossano-Tapia M, Brown A. Determination of Two-Photon-Absorption Cross Sections Using Time-Dependent Density Functional Theory Tight Binding: Application to Fluorescent Protein Chromophores. J Chem Theory Comput 2019; 15:3153-3161. [DOI: 10.1021/acs.jctc.9b00082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maria Rossano-Tapia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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