1
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Zhong K, Nguyen HL, Do TN, Tan HS, Knoester J, Jansen TLC. Coarse-Grained Approach to Simulate Signatures of Excitation Energy Transfer in Two-Dimensional Electronic Spectroscopy of Large Molecular Systems. J Chem Theory Comput 2024. [PMID: 38996082 DOI: 10.1021/acs.jctc.4c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Two-dimensional electronic spectroscopy (2DES) has proven to be a highly effective technique in studying the properties of excited states and the process of excitation energy transfer in complex molecular assemblies, particularly in biological light-harvesting systems. However, the accurate simulation of 2DES for large systems still poses a challenge because of the heavy computational demands it entails. In an effort to overcome this limitation, we devised a coarse-grained 2DES method. This method encompasses the treatment of the entire system by dividing it into distinct weakly coupled segments, which are assumed to communicate predominantly through incoherent exciton transfer. We first demonstrate the efficiency of this method through simulation on a model dimer system, which demonstrates a marked improvement in calculation efficiency, with results that exhibit good concordance with reference spectra calculated with less approximate methods. Additionally, the application of this method to the light-harvesting antenna 2 (LH2) complex of purple bacteria showcases its advantages, accuracy, and limitations. Furthermore, simulating the anisotropy decay in LH2 induced by energy transfer and its comparison with experiments confirm that the method is capable of accurately describing dynamical processes in a biologically relevant system. This method presented lends itself to an extension that accounts for the effect of intrasegment relaxation processes on the 2DES spectra, which for computational efficiency are ignored in the implementation reported here. It is envisioned that the method will be employed in the future to accurately and efficiently calculate 2D spectra of more extensive systems, such as photosynthetic supercomplexes.
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Affiliation(s)
- Kai Zhong
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Hoang Long Nguyen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Thanh Nhut Do
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Howe-Siang Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Jasper Knoester
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
- Faculty of Science, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
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2
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Thomassen AB, Jansen TLC, Weidner T. The secondary structure of diatom silaffin peptide R5 determined by two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2024; 26:18538-18546. [PMID: 38888161 DOI: 10.1039/d4cp00970c] [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
Diatoms, unicellular marine organisms, harness short peptide repeats of the protein silaffin to transform silicic acid into biosilica nanoparticles. This process has been a white whale for material scientists due to its potential in biomimetic applications, ranging from medical to microelectronic fields. Replicating diatom biosilicification will depend on a thorough understanding of the silaffin peptide structure during the reaction, yet existing models in the literature offer conflicting views on peptide folding during silicification. In our study, we employed two-dimensional infrared spectroscopy (2DIR) within the amide I region to determine the secondary structure of the silaffin repeat unit 5 (R5), both pre- and post-interaction with silica. The 2DIR experiments are complemented by molecular dynamics (MD) simulations of pure R5 reacting with silicate. Subsequently, theoretical 2DIR spectra calculated from these MD trajectories allowed us to compare calculated spectra with experimental data, and to determine the diverse structural poses of R5. Our findings indicate that unbound R5 predominantly forms β-strand structures alongside various atypical secondary structures. Post-silicification, there's a noticeable shift: a decrease in β-strands coupled with an increase in turn-type and bend-type configurations. We theorize that this structural transformation stems from silicate embedding within R5's hydrogen-bond network, prompting the peptide backbone to contract and adapt around the biosilica precursors.
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Affiliation(s)
- Asger Berg Thomassen
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark.
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark.
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3
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Betti E, Saraceno P, Cignoni E, Cupellini L, Mennucci B. Insights into Energy Transfer in Light-Harvesting Complex II Through Machine-Learning Assisted Simulations. J Phys Chem B 2024; 128:5188-5200. [PMID: 38761151 DOI: 10.1021/acs.jpcb.4c01494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Light-harvesting complex II (LHCII) is the major antenna of higher plants. Energy transfer processes taking place inside its aggregate of chlorophylls have been experimentally investigated with time-resolved techniques, but a complete understanding of the most relevant energy transfer pathways and relative characteristic times remains elusive. Theoretical models to disentangle experimental data in LHCII have long been challenged by the large size and complex nature of the system. Here, we show that a fully first-principles approach combining molecular dynamics and machine learning can be successfully used to reproduce transient absorption spectra and characterize the EET pathways and the involved times.
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Affiliation(s)
- Elena Betti
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Piermarco Saraceno
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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4
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Erić V, Li X, Dsouza L, Huijser A, Holzwarth AR, Buda F, Sevink GJA, de Groot HJM, Jansen TLC. Observation of Dark States in Two-Dimensional Electronic Spectra of Chlorosomes. J Phys Chem B 2024; 128:3575-3584. [PMID: 38569137 PMCID: PMC11033866 DOI: 10.1021/acs.jpcb.4c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
Observations of low-lying dark states in several photosynthetic complexes challenge our understanding of the mechanisms behind their efficient energy transfer processes. Computational models are necessary for providing novel insights into the nature and function of dark states, especially since these are not directly accessible in spectroscopy experiments. Here, we will focus on signatures of dark-type states in chlorosomes, a light-harvesting complex from green sulfur bacteria well-known for uniting a broad absorption band with very efficient energy transfer. In agreement with experiments, our simulations of two-dimensional electronic spectra capture the ultrafast exciton transfer occurring in 100s of femtoseconds within a single chlorosome cylinder. The sub-100 fs process corresponds to relaxation within the single-excitation manifold in a single chlorosome tube, where all initially created populations in the bright exciton states are quickly transferred to dark-type exciton states. Structural inhomogeneities on the local scale cause a redistribution of the oscillator strength, leading to the emergence of these dark-type exciton states, which dominate ultrafast energy transfer. The presence of the dark-type exciton states suppresses energy loss from an isolated chlorosome via fluorescence quenching, as observed experimentally. Our results further question whether relaxation to dark-exciton states is a leading process or merely competes with transfer to the baseplate within the photosynthetic apparatus of green sulfur bacteria.
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Affiliation(s)
- Vesna Erić
- Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Xinmeng Li
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Sem Sælands vei 26, 0315 Oslo, Norway
| | - Lolita Dsouza
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Annemarie Huijser
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan
5, 7522 NB Enschede, The Netherlands
| | - Alfred R. Holzwarth
- Department
of Biophysical Chemistry, Max Planck Institute
for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim, Germany
| | - Francesco Buda
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Huub J. M. de Groot
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
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5
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Xu C, Lin C, Peng J, Zhang J, Lin S, Gu FL, Gelin MF, Lan Z. On-the-fly simulation of time-resolved fluorescence spectra and anisotropy. J Chem Phys 2024; 160:104109. [PMID: 38477337 DOI: 10.1063/5.0201204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
We combine on-the-fly trajectory surface hopping simulations and the doorway-window representation of nonlinear optical response functions to create an efficient protocol for the evaluation of time- and frequency-resolved fluorescence (TFRF) spectra and anisotropies of the realistic polyatomic systems. This approach gives the effective description of the proper (e.g., experimental) pulse envelopes, laser field polarizations, and the proper orientational averaging of TFRF signals directly from the well-established on-the-fly nonadiabatic dynamic simulations without extra computational cost. To discuss the implementation details of the developed protocol, we chose cis-azobenzene as a prototype to simulate the time evolution of the TFRF spectra governed by its nonadiabatic dynamics. The results show that the TFRF is determined by the interplay of several key factors, i.e., decays of excited-state populations, evolution of the transition dipole moments along with the dynamic propagation, and scaling factor of the TFRF signals associated with the cube of emission frequency. This work not only provides an efficient and effective approach to simulate the TFRF and anisotropies of realistic polyatomic systems but also discusses the important relationship between the TFRF signals and the underlining nonadiabatic dynamics.
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Affiliation(s)
- Chao Xu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety; School of Environment, South China Normal University, Guangzhou 510006, People's Republic of China
| | - Congru Lin
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety; School of Environment, South China Normal University, Guangzhou 510006, People's Republic of China
| | - Jiawei Peng
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety; School of Environment, South China Normal University, Guangzhou 510006, People's Republic of China
| | - Juanjuan Zhang
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety; School of Environment, South China Normal University, Guangzhou 510006, People's Republic of China
| | - Shichen Lin
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety; School of Environment, South China Normal University, Guangzhou 510006, People's Republic of China
| | - Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Zhenggang Lan
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety; School of Environment, South China Normal University, Guangzhou 510006, People's Republic of China
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6
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Pios SV, Gelin MF, Ullah A, Dral PO, Chen L. Artificial-Intelligence-Enhanced On-the-Fly Simulation of Nonlinear Time-Resolved Spectra. J Phys Chem Lett 2024; 15:2325-2331. [PMID: 38386692 DOI: 10.1021/acs.jpclett.4c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Time-resolved spectroscopy is an important tool for unraveling the minute details of structural changes in molecules of biological and technological significance. The nonlinear femtosecond signals detected for such systems must be interpreted, but it is a challenging task for which theoretical simulations are often indispensable. Accurate simulations of transient absorption or two-dimensional electronic spectra are, however, computationally very expensive, prohibiting the wider adoption of existing first-principles methods. Here, we report an artificial-intelligence-enhanced protocol to drastically reduce the computational cost of simulating nonlinear time-resolved electronic spectra, which makes such simulations affordable for polyatomic molecules of increasing size. The protocol is based on the doorway-window approach for the on-the-fly surface-hopping simulations. We show its applicability for the prototypical molecule of pyrazine for which it produces spectra with high precision with respect to ab initio reference while cutting the computational cost by at least 95% compared to pure first-principles simulations.
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Affiliation(s)
- Sebastian V Pios
- Zhejiang Laboratory, Hangzhou, Zhejiang 311100, People's Republic of China
| | - Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Arif Ullah
- School of Physics and Optoelectronic Engineering, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Lipeng Chen
- Zhejiang Laboratory, Hangzhou, Zhejiang 311100, People's Republic of China
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7
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Maity S, Daskalakis V, Jansen TLC, Kleinekathöfer U. Electric Field Susceptibility of Chlorophyll c Leads to Unexpected Excitation Dynamics in the Major Light-Harvesting Complex of Diatoms. J Phys Chem Lett 2024; 15:2499-2510. [PMID: 38410961 PMCID: PMC10926154 DOI: 10.1021/acs.jpclett.3c03241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Diatoms are one of the most abundant photosynthetic organisms on earth and contribute largely to atmospheric oxygen production. They contain fucoxanthin and chlorophyll-a/c binding proteins (FCPs) as light-harvesting complexes with a remarkable adaptation to the fluctuating light on ocean surfaces. To understand the basis of the photosynthetic process in diatoms, the excitation energy funneling within FCPs must be probed. A state-of-the-art multiscale analysis within a quantum mechanics/molecular mechanics framework has been employed. To this end, the chlorophyll (Chl) excitation energies within the FCP complex from the diatom Phaeodactylum tricornutum have been determined. The Chl-c excitation energies were found to be 5-fold more susceptible to electric fields than those of Chl-a pigments and thus are significantly lower in FCP than in organic solvents. This finding challenges the general belief that the excitation energy of Chl-c is always higher than that of Chl-a in FCP proteins and reveals that Chl-c molecules are much more sensitive to electric fields within protein scaffolds than in Chl-a pigments. The analysis of the linear absorption spectrum and the two-dimensional electronic spectra of the FCP complex strongly supports these findings and allows us to study the excitation transfer within the FCP complex.
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Affiliation(s)
- Sayan Maity
- School
of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Vangelis Daskalakis
- Department
of Chemical Engineering, School of Engineering,
University of Patras, Patras 26504, Greece
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
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8
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Bruschi M, Gallina F, Fresch B. A Quantum Algorithm from Response Theory: Digital Quantum Simulation of Two-Dimensional Electronic Spectroscopy. J Phys Chem Lett 2024; 15:1484-1492. [PMID: 38295347 DOI: 10.1021/acs.jpclett.3c03499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Multidimensional optical spectroscopies are powerful techniques to investigate energy transfer pathways in natural and artificial systems. Because of the high information content of the spectra, numerical simulations of the optical response are of primary importance to assist the interpretation of spectral features. However, the increasing complexity of the investigated systems and their quantum dynamics call for the development of novel simulation strategies. In this work, we consider using digital quantum computers. By combining quantum dynamical simulation and nonlinear response theory, we present a quantum algorithm for computing the optical response of molecular systems. The quantum advantage stems from the efficient quantum simulation of the dynamics governed by the molecular Hamiltonian, and it is demonstrated by explicitly considering exciton-vibrational coupling. The protocol is tested on a near-term quantum device, providing the digital quantum simulation of the linear and nonlinear response of simple molecular models.
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Affiliation(s)
- Matteo Bruschi
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, Padua 35131, Italy
| | - Federico Gallina
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, Padua 35131, Italy
| | - Barbara Fresch
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, Padua 35131, Italy
- Padua Quantum Technologies Research Center, Università degli Studi di Padova, via Gradenigo 6/A, Padua 35131, Italy
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9
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Mitoli D, Maul J, Erba A. First-Principles Anharmonic Infrared and Raman Vibrational Spectra of Materials: Fermi Resonance in Dry Ice. J Phys Chem Lett 2024; 15:888-894. [PMID: 38241167 DOI: 10.1021/acs.jpclett.3c03372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
We introduce a computational tool for the quantum-mechanical simulation of anharmonic infrared and Raman vibrational spectra of materials. The approach, implemented in the CRYSTAL software, stems from Taylor's expansion of the potential energy surface (PES) on the basis of normal modes up to cubic and quartic terms. The PES can be sampled with four different numerical schemes at the level of density functional theory (DFT), with local, generalized-gradient, and hybrid density functional approximations. Anharmonic states are obtained by solving Shrödinger's nuclear equation with either the vibrational self-consistent field (VSCF) or vibrational configuration interaction (VCI) methods. Nuclear quantum effects (NQEs) are thus fully accounted for. Infrared intensities are computed numerically through a Berry phase approach or analytically through a coupled-perturbed (CP) approach. Raman intensities are computed analytically via the CP approach. A variety of anharmonic features of vibrational spectra of materials can be simulated, including band shifts, combination bands, overtones, resonances (first-order Fermi, second-order Darling-Dennison), and hot bands. We showcase the effectiveness of the approach on the description of a first-order Fermi resonance (FR) in CO2 dry ice: a challenging test-case given that the FR occurs in the Raman spectrum, requires NQEs, and involves two- and three-mode couplings. Fundamental mechanistic differences with respect to the well-known FR in molecular CO2 are addressed. This application represents the first quantum-mechanical, periodic description of FR in dry ice.
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Affiliation(s)
- Davide Mitoli
- Dipartimento di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jefferson Maul
- Dipartimento di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Alessandro Erba
- Dipartimento di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
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10
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Sayer T, Montoya-Castillo A. Efficient formulation of multitime generalized quantum master equations: Taming the cost of simulating 2D spectra. J Chem Phys 2024; 160:044108. [PMID: 38270238 DOI: 10.1063/5.0185578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024] Open
Abstract
Modern 4-wave mixing spectroscopies are expensive to obtain experimentally and computationally. In certain cases, the unfavorable scaling of quantum dynamics problems can be improved using a generalized quantum master equation (GQME) approach. However, the inclusion of multiple (light-matter) interactions complicates the equation of motion and leads to seemingly unavoidable cubic scaling in time. In this paper, we present a formulation that greatly simplifies and reduces the computational cost of previous work that extended the GQME framework to treat arbitrary numbers of quantum measurements. Specifically, we remove the time derivatives of quantum correlation functions from the modified Mori-Nakajima-Zwanzig framework by switching to a discrete-convolution implementation inspired by the transfer tensor approach. We then demonstrate the method's capabilities by simulating 2D electronic spectra for the excitation-energy-transfer dimer model. In our method, the resolution of data can be arbitrarily coarsened, especially along the t2 axis, which mirrors how the data are obtained experimentally. Even in a modest case, this demands O(103) fewer data points. We are further able to decompose the spectra into one-, two-, and three-time correlations, showing how and when the system enters a Markovian regime where further measurements are unnecessary to predict future spectra and the scaling becomes quadratic. This offers the ability to generate long-time spectra using only short-time data, enabling access to timescales previously beyond the reach of standard methodologies.
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Affiliation(s)
- Thomas Sayer
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
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11
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López X, Sánchez-Mansilla A, Sousa C, Straatsma TP, Broer R, de Graaf C. Comparison of Computational Strategies for the Calculation of the Electronic Coupling in Intermolecular Energy and Electron Transport Processes. J Phys Chem A 2023; 127:10717-10731. [PMID: 38084088 PMCID: PMC10749449 DOI: 10.1021/acs.jpca.3c05998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023]
Abstract
Electronic couplings in intermolecular electron and energy transfer processes calculated by six different existing computational techniques are compared to nonorthogonal configuration interaction for fragments (NOCI-F) results. The paper addresses the calculation of the electronic coupling in diketopyrrolopyrol, tetracene, 5,5'-difluoroindigo, and benzene-Cl for hole and electron transport, as well as the local exciton and singlet fission coupling. NOCI-F provides a rigorous computational scheme to calculate these couplings, but its computational cost is rather elevated. The here-considered ab initio Frenkel-Davydov (AIFD), Dimer projection (DIPRO), transition dipole moment coupling, Michl-Smith, effective Hamiltonian, and Mulliken-Hush approaches are computationally less demanding, and the comparison with the NOCI-F results shows that the NOCI-F results in the couplings for hole and electron transport are rather accurately predicted by the more approximate schemes but that the NOCI-F exciton transfer and singlet fission couplings are more difficult to reproduce.
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Affiliation(s)
- Xavier López
- Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili, C. Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Aitor Sánchez-Mansilla
- Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili, C. Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Carmen Sousa
- Departament
de Ciència de Materials i Química Física and
Institut de Química Teòrica i Computacional, Universitat de Barcelona, C. Martí i Franquès, 08028 Barcelona, Spain
| | - Tjerk P. Straatsma
- National
Center for Computational Sciences, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831-6373, United States
- Department
of Chemistry and Biochemistry, University
of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | - Ria Broer
- Zernike
Institute of Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Coen de Graaf
- Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili, C. Marcel·lí Domingo 1, 43007 Tarragona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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12
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Erić V, Castro JL, Li X, Dsouza L, Frehan SK, Huijser A, Holzwarth AR, Buda F, Sevink GJA, de Groot HJM, Jansen TLC. Ultrafast Anisotropy Decay Reveals Structure and Energy Transfer in Supramolecular Aggregates. J Phys Chem B 2023; 127:7487-7496. [PMID: 37594912 PMCID: PMC10476209 DOI: 10.1021/acs.jpcb.3c04719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/20/2023] [Indexed: 08/20/2023]
Abstract
Chlorosomes from green bacteria perform the most efficient light capture and energy transfer, as observed among natural light-harvesting antennae. Hence, their unique functional properties inspire developments in artificial light-harvesting and molecular optoelectronics. We examine two distinct organizations of the molecular building blocks as proposed in the literature, demonstrating how these organizations alter light capture and energy transfer, which can serve as a mechanism that the bacteria utilize to adapt to changes in light conditions. Spectral simulations of polarization-resolved two-dimensional electronic spectra unravel how changes in the helicity of chlorosomal aggregates alter energy transfer. We show that ultrafast anisotropy decay presents a spectral signature that reveals contrasting energy pathways in different chlorosomes.
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Affiliation(s)
- Vesna Erić
- Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Jorge Luis Castro
- Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Xinmeng Li
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Sem Sælands vei 26, 0315 Oslo, Norway
| | - Lolita Dsouza
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Sean K. Frehan
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Annemarie Huijser
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Alfred R. Holzwarth
- Department
of Biophysical Chemistry, Max Planck Institute
for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim, Germany
| | - Francesco Buda
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Huub J. M. de Groot
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
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13
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López X, Straatsma TP, Sánchez-Mansilla A, de Graaf C. Non-orthogonal Configuration Interaction Study on the Effect of Thermal Distortions on the Singlet Fission Process in Photoexcited Pure and B,N-Doped Pentacene Crystals. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:16249-16258. [PMID: 37811311 PMCID: PMC10552079 DOI: 10.1021/acs.jpcc.3c02083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/29/2023] [Indexed: 10/10/2023]
Abstract
The present computational work analyzes singlet fission (SF) as a pathway for multiplication of photogenerated excitons in crystalline polyacenes. Our study explores the well-known crystalline pentacene (C22H14) and the prospective and potentially interesting doped B,N-pentacene (BC20NH14). At the molecular level, the singlet fission process involves a pair of neighboring molecules and is based on the coupling between an excited singlet state (S1S0) and two singlet-coupled triplets (1T1T1), which, typically, is influenced by an intermolecular charge transfer state. Taking data from periodic density functional theory and ab initio wave function calculations, we applied the non-orthogonal configuration interaction method to determine electronic coupling parameters. The comparison of the results for both equilibrium structures reveal smaller SF coupling for pentacene than for B,N-pentacene by a factor of ∼5. Introduction of the dynamic behavior to the crystals (vibrations, thermal motion) provides a more realistic picture of the effect of the disorder at the molecular level on the SF efficiency. The coupling values associated to out-of-equilibrium structures show that most of the S1S0/1T1T1 couplings remain virtually constant or slightly increase for pentacene when molecular disorder is introduced. Homologous calculations on B,N-pentacene show a generalized decrease in the coupling values, notably if large phonon displacements are considered. A few of the structures analyzed feature much larger SF coupling if some distortion results in (nearly) degenerate charge transfer and excited singlet and triplet states. For these particular situations, an acceleration of the SF process could occur although in competition with electron-hole separation as an alternative pathway.
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Affiliation(s)
- Xavier López
- Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Tjerk P. Straatsma
- National
Center for Computational Sciences, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831-6373, United States of America
- Department
of Chemistry and Biochemistry, University
of Alabama, Tuscaloosa, Alabama 35487-0336, United States of America
| | - Aitor Sánchez-Mansilla
- Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Coen de Graaf
- Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA). Passeig Lluís Companys 23, 08010 Barcelona, Spain
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14
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Yang J, Gelin MF, Chen L, Šanda F, Thyrhaug E, Hauer J. Two-dimensional fluorescence excitation spectroscopy: A novel technique for monitoring excited-state photophysics of molecular species with high time and frequency resolution. J Chem Phys 2023; 159:074201. [PMID: 37581414 DOI: 10.1063/5.0156297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
We propose a novel UV/Vis femtosecond spectroscopic technique, two-dimensional fluorescence-excitation (2D-FLEX) spectroscopy, which combines spectral resolution during the excitation process with exclusive monitoring of the excited-state system dynamics at high time and frequency resolution. We discuss the experimental feasibility and realizability of 2D-FLEX, develop the necessary theoretical framework, and demonstrate the high information content of this technique by simulating the 2D-FLEX spectra of a model four-level system and the Fenna-Matthews-Olson antenna complex. We show that the evolution of 2D-FLEX spectra with population time directly monitors energy transfer dynamics and can thus yield direct qualitative insight into the investigated system. This makes 2D-FLEX a highly efficient instrument for real-time monitoring of photophysical processes in polyatomic molecules and molecular aggregates.
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Affiliation(s)
- Jianmin Yang
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | | | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, 12116 Prague, Czech Republic
| | - Erling Thyrhaug
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Jürgen Hauer
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
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15
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Zhan S, Gelin MF, Huang X, Sun K. Ab initio simulation of peak evolutions and beating maps for electronic two-dimensional signals of a polyatomic chromophore. J Chem Phys 2023; 158:2890773. [PMID: 37191214 DOI: 10.1063/5.0150387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023] Open
Abstract
By employing the doorway-window (DW) on-the-fly simulation protocol, we performed ab initio simulations of peak evolutions and beating maps of electronic two-dimensional (2D) spectra of a polyatomic molecule in the gas phase. As the system under study, we chose pyrazine, which is a paradigmatic example of photodynamics dominated by conical intersections (CIs). From the technical perspective, we demonstrate that the DW protocol is a numerically efficient methodology suitable for simulations of 2D spectra for a wide range of excitation/detection frequencies and population times. From the information content perspective, we show that peak evolutions and beating maps not only reveal timescales of transitions through CIs but also pinpoint the most relevant coupling and tuning modes active at these CIs.
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Affiliation(s)
- Siying Zhan
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Xiang Huang
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Kewei Sun
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
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16
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Palacino-González E, Jansen TLC. Modeling the Effect of Disorder in the Two-Dimensional Electronic Spectroscopy of Poly-3-hexyltiophene in an Organic Photovoltaic Blend: A Combined Quantum/Classical Approach. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:6793-6801. [PMID: 37081993 PMCID: PMC10108354 DOI: 10.1021/acs.jpcc.3c01080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 02/28/2023] [Indexed: 05/03/2023]
Abstract
We introduce a first-principles model of the 12-mer poly-3-hexyltiophene (P3HT) polymer system in the realistic description of an organic photovoltaic blend environment. We combine Molecular Dynamics (MD) simulations of a thin-film blend of P3HT and phenyl-C61-butyric acid methyl ester (PCBM) to model the interactions with a fluctuating environment with Time-Dependent Density Functional Theory (TDDFT) calculations to parametrize the effect of the torsional flexibility in the polymer and construct an exciton-type Hamiltonian that describes the photoexcitation of the polymer. This allows us to reveal the presence of different flexibility patterns governed by the torsional angles along the polymer chain which, in the interacting fluctuating environment, control the broadening of the spectral observables. We identify the origin of the homogeneous and inhomogeneous line shape of the simulated optical signals. This is paramount to decipher the spectroscopic nature of the ultrafast electron-transfer process occurring in organic photovoltaic (OPV) materials.
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17
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Maity S, Kleinekathöfer U. Recent progress in atomistic modeling of light-harvesting complexes: a mini review. PHOTOSYNTHESIS RESEARCH 2023; 156:147-162. [PMID: 36207489 PMCID: PMC10070314 DOI: 10.1007/s11120-022-00969-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
In this mini review, we focus on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Because of their size and sophisticated electronic structures, multiscale methods are required to investigate the dynamical and spectroscopic properties of such complexes. The excitation energies, in this context also known as site energies, excitonic couplings, and spectral densities are key quantities which usually need to be extracted to be able to determine the exciton dynamics and spectroscopic properties. The recently developed multiscale approach based on the numerically efficient density functional tight-binding framework followed by excited state calculations has been shown to be superior to the scheme based on pure classical molecular dynamics simulations. The enhanced approach, which improves the description of the internal vibrational dynamics of the pigment molecules, yields spectral densities in good agreement with the experimental counterparts for various bacterial and plant LH systems. Here, we provide a brief overview of those results and described the theoretical foundation of the multiscale protocol.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany.
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18
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Glotz G, Püschmann S, Haas M, Gescheidt G. Direct detection of photo-induced reactions by IR: from Brook rearrangement to photo-catalysis. Photochem Photobiol Sci 2023:10.1007/s43630-023-00406-4. [PMID: 36933157 DOI: 10.1007/s43630-023-00406-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
In situ IR detection of photoreactions induced by the light of LEDs at appropriate wavelengths provides a simple, cost-effective, and versatile method to get insight into mechanistic details. In particular, conversions of functional groups can be selectively followed. Overlapping UV-Vis bands or fluorescence from the reactants and products and the incident light do not obstruct IR detection. Compared with in situ photo-NMR, our setup does not require tedious sample preparation (optical fibers) and offers a selective detection of reactions, even at positions where 1H-NMR lines overlap or 1H resonances are not clear-cut. We illustrate the applicability of our setup following the photo-Brook rearrangement of (adamant-1-yl-carbonyl)-tris(trimethylsilyl)silane, address photo-induced α-bond cleavage (1-hydroxycyclohexyl phenyl ketone), study photoreduction using tris(bipyridine)ruthenium(II), investigate photo-oxygenation of double bonds with molecular oxygen and the fluorescent 2,4,6-triphenylpyrylium photocatalyst, and address photo-polymerization. With the LED/FT-IR combination, reactions can be qualitatively followed in fluid solution, (highly) viscous environments, and in the solid state. Viscosity changes during the reaction (e.g., during a polymerization) do not obstruct the method.
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Affiliation(s)
- Gabriel Glotz
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010, Graz, Austria.
| | - Sabrina Püschmann
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Michael Haas
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Georg Gescheidt
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010, Graz, Austria
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19
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van Hengel CDN, van Adrichem KE, Jansen TLC. Simulation of two-dimensional infrared Raman spectroscopy with application to proteins. J Chem Phys 2023; 158:064106. [PMID: 36792507 DOI: 10.1063/5.0138958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by β-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra.
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Affiliation(s)
- Carleen D N van Hengel
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kim E van Adrichem
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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20
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Cignoni E, Cupellini L, Mennucci B. Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes. J Chem Theory Comput 2023; 19:965-977. [PMID: 36701385 PMCID: PMC9933434 DOI: 10.1021/acs.jctc.2c01044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We propose a machine learning (ML)-based strategy for an inexpensive calculation of excitonic properties of light-harvesting complexes (LHCs). The strategy uses classical molecular dynamics simulations of LHCs in their natural environment in combination with ML prediction of the excitonic Hamiltonian of the embedded aggregate of pigments. The proposed ML model can reproduce the effects of geometrical fluctuations together with those due to electrostatic and polarization interactions between the pigments and the protein. The training is performed on the chlorophylls of the major LHC of plants, but we demonstrate that the model is able to extrapolate well beyond the initial training set. Moreover, the accuracy in predicting the effects of the environment is tested on the simulation of the small changes observed in the absorption spectra of the wild-type and a mutant of a minor LHC.
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21
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Erić V, Li X, Dsouza L, Frehan SK, Huijser A, Holzwarth AR, Buda F, Sevink GJA, de Groot HJM, Jansen TLC. Manifestation of Hydrogen Bonding and Exciton Delocalization on the Absorption and Two-Dimensional Electronic Spectra of Chlorosomes. J Phys Chem B 2023; 127:1097-1109. [PMID: 36696537 PMCID: PMC9923760 DOI: 10.1021/acs.jpcb.2c07143] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Chlorosomes are supramolecular aggregates that contain thousands of bacteriochlorophyll molecules. They perform the most efficient ultrafast excitation energy transfer of all natural light-harvesting complexes. Their broad absorption band optimizes light capture. In this study, we identify the microscopic sources of the disorder causing the spectral width and reveal how it affects the excited state properties and the optical response of the system. We combine molecular dynamics, quantum chemical calculations, and response function calculations to achieve this goal. The predicted linear and two-dimensional electronic spectra are found to compare well with experimental data reproducing all key spectral features. Our analysis of the microscopic model reveals the interplay of static and dynamic disorder from the molecular perspective. We find that hydrogen bonding motifs are essential for a correct description of the spectral line shape. Furthermore, we find that exciton delocalization over tens to hundreds of molecules is consistent with the two-dimensional electronic spectra.
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Affiliation(s)
- Vesna Erić
- University
of Groningen, Zernike Institute
for Advanced Materials, 9747
AG Groningen, The Netherlands
| | - Xinmeng Li
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Sem Sælands vei 26, 0315 Oslo, Norway
| | - Lolita Dsouza
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Sean K. Frehan
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Annemarie Huijser
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Alfred R. Holzwarth
- Department
of Biophysical Chemistry, Max Planck Institute
for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim, Germany
| | - Francesco Buda
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Huub J. M. de Groot
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas L. C. Jansen
- University
of Groningen, Zernike Institute
for Advanced Materials, 9747
AG Groningen, The Netherlands,
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22
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Gelin MF, Chen L, Domcke W. Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals. Chem Rev 2022; 122:17339-17396. [PMID: 36278801 DOI: 10.1021/acs.chemrev.2c00329] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system-field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.
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Affiliation(s)
- Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Lipeng Chen
- Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching,Germany
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23
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O'Neill N, Lima TA, Ferreira FF, Thursch L, Alvarez N, Schweitzer-Stenner R. Forbidden Secondary Structures Found in Gel-Forming Fibrils of Glycylphenylalanylglycine. J Phys Chem B 2022; 126:8080-8093. [PMID: 36194765 DOI: 10.1021/acs.jpcb.2c05010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The zwitterionic l-tripeptide glycylphenylalanylglycine self-assembles into very long crystalline fibrils in an aqueous solution, which causes the formation of an exceptionally strong gel phase (G' ∼ 5 × 106 Pa). The Rietveld refinement analysis of its powder X-ray diffraction (PXRD) pattern reveals a unit cell with four peptides forming a P212121 space group and adopting an inverse polyproline II conformation, that is, a right-handed helical structure that occupies the "forbidden" region of the Ramachandran plot. This unusual structure is stabilized by a plethora of intermolecular interactions facilitated by the large number of different functional groups of the unblocked tripeptide. Comparisons of simulated and experimental Fourier transform infrared and vibrational circular dichroism (VCD) amide I' profiles corroborate the PXRD structure. Our experimental setup reduces the sample to a quasi-two-dimensional network of fibrils. We exploited the influence of this reduced dimensionality on the amide I VCD to identify the main fibril axis. We demonstrate that PXRD, vibrational spectroscopy, and amide I simulations provide a powerful toolset for secondary structure and fibril axis determination.
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Affiliation(s)
- Nichole O'Neill
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States.,Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Thamires A Lima
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Fabio Furlan Ferreira
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Av. Dos Estados, 5001, S622-3, Santo André, São Paulo09210-580, Brazil
| | - Lavenia Thursch
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Nicolas Alvarez
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
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24
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Cignoni E, Cupellini L, Mennucci B. A fast method for electronic couplings in embedded multichromophoric systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:304004. [PMID: 35552268 DOI: 10.1088/1361-648x/ac6f3c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Electronic couplings are key to understanding exciton delocalization and transport in natural and artificial light harvesting processes. We develop a method to compute couplings in multichromophoric aggregates embedded in complex environments without running expensive quantum chemical calculations. We use a transition charge approximation to represent the quantum mechanical transition densities of the chromophores and an atomistic and polarizable classical model to describe the environment atoms. We extend our framework to estimate transition charges directly from the chromophore geometry, i.e., bypassing completely the quantum mechanical calculations using a regression approach. The method allows to rapidly compute accurate couplings for a large number of geometries along molecular dynamics trajectories.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
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25
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Sánchez-Mansilla A, Sousa C, Kathir RK, Broer R, Straatsma TP, de Graaf C. On the role of dynamic electron correlation in non-orthogonal configuration interaction with fragments. Phys Chem Chem Phys 2022; 24:11931-11944. [PMID: 35521680 DOI: 10.1039/d2cp00772j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two different approaches have been implemented to include the effect of dynamic electron correlation in the Non-Orthogonal Configuration Interaction for Fragments (NOCI-F) method. The first is based on shifting the diagonal matrix elements of the NOCI matrix, while the second incorporates the dynamic correlation explicitly in the fragment wave functions used to construct the many-electron basis functions of the NOCI. The two approaches are illustrated for the calculation of the electronic coupling relevant in singlet fission and the coupling of spin moments in organic radicals. Comparison of the calculated diabatic couplings, the NOCI energies and wave functions shows that dynamic electron correlation is not only efficiently but also effectively incorporated by the shifting approach and can largely affect the coupling between electronic states. Also, it brings the NOCI coupling of the spin moments in close agreement with benchmark calculations.
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Affiliation(s)
- A Sánchez-Mansilla
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - C Sousa
- Departament de Ciència de Materials i Química Física and Institut de Química Teòrica i Computacional, Universitat de Barcelona, Spain.
| | - R K Kathir
- Zernike Institute of Advanced Materials, University of Groningen, The Netherlands
| | - R Broer
- Zernike Institute of Advanced Materials, University of Groningen, The Netherlands
| | - T P Straatsma
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373, USA.,Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - C de Graaf
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain.,Zernike Institute of Advanced Materials, University of Groningen, The Netherlands.,ICREA, Pg. Lluís Companys 23, Barcelona, Spain.
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26
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van Adrichem KE, Jansen TLC. AIM: A Mapping Program for Infrared Spectroscopy of Proteins. J Chem Theory Comput 2022; 18:3089-3098. [PMID: 35387451 PMCID: PMC9097285 DOI: 10.1021/acs.jctc.2c00113] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Here, we present
a new analysis program, AIM, that allows extracting
the vibrational amide-I Hamiltonian using molecular dynamics trajectories
for protein infrared spectroscopy modeling. The constructed Hamiltonians
can be used as input for spectral calculations allowing the calculation
of infrared absorption spectra, vibrational circular dichroism, and
two-dimensional infrared spectra. These spectroscopies allow the study
of the structure and dynamics of proteins. We will explain the essence
of how AIM works and give examples of the information and spectra
that can be obtained with the program using the Trypsin Inhibitor
as an example. AIM is freely available from GitHub, and the package
contains a demonstration allowing easy introduction to the use of
the program.
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Affiliation(s)
- Kim E van Adrichem
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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27
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Cignoni E, Slama V, Cupellini L, Mennucci B. The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol. J Chem Phys 2022; 156:120901. [DOI: 10.1063/5.0086275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Slama
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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28
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Searching for a Unique Exciton Model of Photosynthetic Pigment–Protein Complexes: Photosystem II Reaction Center Study by Differential Evolution. MATHEMATICS 2022. [DOI: 10.3390/math10060959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Studying the optical properties of photosynthetic pigment–protein complexes (PPCs) in the visible light range, both experimentally and theoretically, is one of the ways of gaining knowledge about the function of the photosynthetic machinery of living species. To simulate the PPC optical response, it is necessary to use semiclassical theories describing the effect of external fields–matter interaction, energy migration in molecular crystals, and electron–phonon coupling. In this paper, we report the results of photosystem II reaction center (PSIIRC) linear optical response simulations. Applying the multimode Brownian oscillator model and the theory of molecular excitons, we have demonstrated that the absorption, circular and linear dichroism, and steady-state fluorescence of PSIIRC can be accurately fitted with the help of differential evolution (DE), the multiparametric evolutionary optimization algorithm. To explore the effectiveness of DE, we used the simulated experimental data as the target functions instead of those actually measured. Only 2 of 10 DE strategies have shown the best performance of the optimization algorithm. With the best tuning parameters of DE/rand-to-best/1/exp strategy determined from the strategy tests, we found the exact solution for the PSIIRC exciton model and fitted the spectra with a reasonable convergence rate.
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29
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Saxena V, Steendam R, Jansen TLC. Distinguishing islet amyloid polypeptide fibril structures with infrared isotope-label spectroscopy. J Chem Phys 2022; 156:055101. [DOI: 10.1063/5.0082322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Vishesh Saxena
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ruben Steendam
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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