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Sepali C, Gómez S, Grifoni E, Giovannini T, Cappelli C. Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling. J Phys Chem B 2024; 128:5083-5091. [PMID: 38733374 DOI: 10.1021/acs.jpcb.4c01443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
Fully atomistic multiscale polarizable quantum mechanics (QM)/molecular mechanics (MM) approaches, combined with techniques to sample the solute-solvent phase space, constitute the most accurate method to compute spectral signals in aqueous solution. Conventional sampling strategies, such as classical molecular dynamics (MD), may encounter drawbacks when the conformational space is particularly complex, and transition barriers between conformers are high. This can lead to inaccurate sampling, which can potentially impact the accuracy of spectral calculations. For this reason, in this work, we compare classical MD with enhanced sampling techniques, i.e., replica exchange MD and metadynamics. In particular, we show how the different sampling techniques affect computed UV, electronic circular dichroism, nuclear magnetic resonance shielding, and optical rotatory dispersion of N-acetylproline-amide in aqueous solution. Such a system is a model peptide characterized by complex conformational variability. Calculated values suggest that spectral properties are influenced by solute conformers, relative population, and solvent effects; therefore, particular care needs to be paid for when choosing the sampling technique.
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Affiliation(s)
- Chiara Sepali
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Emanuele Grifoni
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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2
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Adrion DM, Karunaratne WV, Lopez SA. Multiconfigurational photodynamics simulations reveal the mechanism of photodecarbonylations of cyclopropenones in explicit aqueous environments. Chem Sci 2023; 14:13205-13218. [PMID: 38023495 PMCID: PMC10664470 DOI: 10.1039/d3sc03805j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Gas-evolving photochemical reactions use light and mild conditions to access strained organic compounds irreversibly. Cyclopropenones are a class of light-responsive molecules used in bioorthogonal photoclick reactions; their excited-state decarbonylation reaction mechanisms are misunderstood due to their ultrafast (<100 femtosecond) lifetimes. We have combined multiconfigurational quantum mechanical (QM) calculations and non-adiabatic molecular dynamics (NAMD) simulations to uncover the excited-state mechanism of cyclopropenone and a photoprotected cyclooctyne-(COT)-precursor in gaseous and explicit aqueous environments. We explore the role of H-bonding with fully quantum mechanical explicitly solvated NAMD simulations for the decarbonylation reaction. The cyclopropenones pass through asynchronous conical intersections and have dynamically concerted photodecarbonylation mechanisms. The COT-precursor has a higher quantum yield of 55% than cyclopropenone (28%) because these trajectories prefer to break a σCC bond to avoid the strained trans-cyclooctene geometries. Our solvated simulations show an increased quantum yield (58%) for the systems studied here.
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Affiliation(s)
- Daniel M Adrion
- Department of Chemistry and Chemical Biology, Northeastern University Boston Massachusetts 02115 USA
| | - Waruni V Karunaratne
- Department of Chemistry and Chemical Biology, Northeastern University Boston Massachusetts 02115 USA
| | - Steven A Lopez
- Department of Chemistry and Chemical Biology, Northeastern University Boston Massachusetts 02115 USA
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3
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Tikhonov DS, Vishnevskiy YV. Describing nuclear quantum effects in vibrational properties using molecular dynamics with Wigner sampling. Phys Chem Chem Phys 2023. [PMID: 37401424 DOI: 10.1039/d3cp01007d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
In this work we discuss the generally applicable Wigner sampling and introduce a new, simplified Wigner sampling method, for computationally effective modeling of molecular properties containing nuclear quantum effects and vibrational anharmonicity. For various molecular systems test calculations of (a) vibrationally averaged rotational constants, (b) vibrational IR spectra and (c) photoelectron spectra have been performed. The performance of Wigner sampling has been assessed by comparing with experimental data and with results of other theoretical models, including harmonic and VPT2 approximations. The developed simplified Wigner sampling method shows advantages in application to large and flexible molecules.
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Affiliation(s)
- Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Yury V Vishnevskiy
- 2Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany.
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Tsuru S, Sharma B, Marx D, Hättig C. Structural Sampling and Solvation Models for the Simulation of Electronic Spectra: Pyrazine as a Case Study. J Chem Theory Comput 2023; 19:2291-2303. [PMID: 36971352 DOI: 10.1021/acs.jctc.2c01129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The impact of sampling methods on spectral broadening in the gas phase and on the convergence of spectra in aqueous solution when using microsolvation, continuum solvation, and hybrid models is studied using pyrazine as a test case. For the sake of comparing classical Maxwell-Boltzmann and Wigner samplings in the gas phase, static and time-resolved X-ray absorption spectra after photoexcitation to the lowest 1B2u(ππ*) state, as well as the static UV-vis absorption spectrum, are considered. In addition, the UV-vis absorption spectrum of pyrazine in aqueous solution is also computed in order to systematically investigate its convergence with the number of explicitly included solvent shells with and without taking bulk solvation effects into account with the conductor-like screening model to represent implicit water beyond such explicit solute complexes. Concerning the static and time-resolved X-ray absorption spectra of pyrazine at the carbon K-edge as well as its UV-vis absorption spectrum in the gas phase, we find that these spectra obtained with Wigner and Maxwell-Boltzmann samplings substantially agree. For the UV-vis absorption spectrum in the aqueous solution, only the first two energetically low-lying bands converge quickly with the size of the explicitly included solvation shells, either with or without an additional continuum solvation taken into account. In stark contrast, calculations of the higher-lying excitations relying on finite microsolvated clusters without additional continuum solvation severely suffer from unphysical charge-transfer excitations into Rydberg-like orbitals at the cluster/vacuum interface. This finding indicates that computational UV-vis absorption spectra covering sufficiently high-lying states converge only if continuum solvation of the explicitly microsolvated solutes is included in the models.
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Chakraborty P, Liu Y, McClung S, Weinacht T, Matsika S. Nonadiabatic Excited State Dynamics of Organic Chromophores: Take-Home Messages. J Phys Chem A 2022; 126:6021-6031. [PMID: 36069531 DOI: 10.1021/acs.jpca.2c04671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonadiabatic excited state dynamics are important in a variety of processes. Theoretical and experimental developments have allowed for a great progress in this area, while combining the two is often necessary and the best approach to obtain insight into the photophysical behavior of molecules. In this Feature Article we use examples of our recent work combining time-resolved photoelectron spectroscopy with theoretical nonadiabatic dynamics to highlight important lessons we learned. We compare the nonadiabatic excited state dynamics of three different organic molecules with the aim of elucidating connections between structure and dynamics. Calculations and measurements are compared for uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene. The comparison highlights the role of rigidity in influencing the dynamics and the difficulty of capturing the dynamics accurately with calculations.
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Affiliation(s)
- Pratip Chakraborty
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States.,Division of Theoretical Chemistry and Biology, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Yusong Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States.,Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Samuel McClung
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Thomas Weinacht
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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He X, Wu B, Rivlin T, Liu J, Pollak E. Transition Path Flight Times and Nonadiabatic Electronic Transitions. J Phys Chem Lett 2022; 13:6966-6974. [PMID: 35877977 PMCID: PMC9358656 DOI: 10.1021/acs.jpclett.2c01425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Transition path flight times are studied for scattering on two electronic surfaces with a single crossing. These flight times reveal nontrivial quantum effects such as resonance lifetimes and nonclassical passage times and reveal that nonadiabatic effects often increase flight times. The flight times are computed using numerically exact time propagation and compared with results obtained from the Fewest Switches Surface Hopping (FSSH) method. Comparison of the two methods shows that the FSSH method is reliable for transition path times only when the scattering is classically allowed on the relevant adiabatic surfaces. However, where quantum effects such as tunneling and resonances dominate, the FSSH method is not adequate to accurately predict the correct times and transition probabilities. These results highlight limitations in methods which do not account for quantum interference effects, and suggest that measuring flight times is important for obtaining insights from the time-domain into quantum effects in nonadiabatic scattering.
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Affiliation(s)
- Xin He
- Beijing
National Laboratory for Molecular Sciences, Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Baihua Wu
- Beijing
National Laboratory for Molecular Sciences, Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tom Rivlin
- Chemical
and Biological Physics Department, Weizmann
Institute of Science, 76100 Rehovot, Israel
| | - Jian Liu
- Beijing
National Laboratory for Molecular Sciences, Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Eli Pollak
- Chemical
and Biological Physics Department, Weizmann
Institute of Science, 76100 Rehovot, Israel
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Avagliano D, Bonfanti M, Nenov A, Garavelli M. Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM. J Comput Chem 2022; 43:1641-1655. [PMID: 35815854 PMCID: PMC9544370 DOI: 10.1002/jcc.26966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022]
Abstract
We present a series of new implementations that we recently introduced in COBRAMM, the open-source academic software developed in our group. The goal of these implementations is to offer an automatized workflow and interface to simulate time-resolved transient absorption (TA) spectra of medium-to-big chromophore embedded in a complex environment. Therefore, the excited states absorption and the stimulated emission are simulated along nonadiabatic dynamics performed with trajectory surface hopping. The possibility of treating systems from medium to big size is given by the use of time-dependent density functional theory (TD-DFT) and the presence of the environment is taken into account employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. The full implementation includes a series of auxiliary scripts to properly setup the QM/MM system, the calculation of the wavefunction overlap along the dynamics for the propagation, the evaluation of the transition dipole moment at linear response TD-DFT level, and scripts to setup, run and analyze the TA from an ensemble of trajectories. Altogether, we believe that our implementation will open the door to the easily simulate the time-resolved TA of systems so far computationally inaccessible.
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Affiliation(s)
- Davide Avagliano
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
| | - Matteo Bonfanti
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy.,Fondazione Human Technopole - Viale Rita Levi-Montalcini, 1 - Area MIND - Cargo 6 - 20157, Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
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Li J, Lopez SA. A Look Inside the Black Box of Machine Learning Photodynamics Simulations. Acc Chem Res 2022; 55:1972-1984. [PMID: 35796602 DOI: 10.1021/acs.accounts.2c00288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
ConspectusPhotochemical reactions are of great importance in chemistry, biology, and materials science because they take advantage of a renewable energy source, mild reaction conditions, and high atom economy. Light absorption can excite molecules to a higher energy electronic state of the same spin multiplicity. The following nonadiabatic processes induce molecular transformations that afford exotic molecular architectures and high-energy-isomers that are inaccessible by thermal means. Computational simulations now complement time-resolved instrumentation to reveal ultrafast excited-state mechanistic information for photochemical reactions that is essential in disentangling elusive spectroscopic features, excited-state lifetimes, and excited-state mechanistic critical points. Nonadiabatic molecular dynamics (NAMD), powered by surface hopping techniques, is among the most widely applied techniques to model the photochemical reactions of medium-sized molecules. However, the computational efficiency is limited because of the requisite thousands of multiconfigurational quantum-chemical calculations multiplied by hundreds of trajectories. Machine learning (ML) has emerged as a revolutionary force in computational chemistry to predict the outcome of the resource-intensive multiconfigurational calculations on the fly. An ML potential trained with a substantial set of quantum-chemical calculations can predict the energies and forces with errors under chemical accuracy at a negligible cost. The integration of ML potentials in NAMD dramatically extends the maximum simulation time scale by ∼10 000-fold to the nanosecond regime.In this Account, we present a comprehensive demonstration of ML photodynamics simulations and summarize our most recent applications in resolving complex photochemical reactions. First, we address three fundamental components of ML techniques for photodynamics simulations: the quantum-chemical data set, the ML potential, and NAMD. Second, we describe best practices in building training data and our procedure toward training the ML photodynamics model with our recent literature contributions. We introduce a convenient training data generation scheme combining Wigner sampling and geometrical interpolation. It trains reliable and effective ML potentials suitable for subsequent active learning to detect undersampled data. We demonstrate how active learning automatically discovers new mechanistic pathways and reproduces experimental results. We point out that atomic permutation is an essential data augmentation approach to improve the learnability of distance-based molecular descriptors for highly symmetric molecules. Third, we demonstrate the utility of ML-photodynamics by showing the results of ML photodynamics simulations of (1) photo-torquoselective 4π disrotatory electrocyclic ring closing of norbornyl cyclohexadiene, which reveals a thermal conversion from experimentally unobserved intermediates to the reactant in 1 ns; (2) [2 + 2] photocycloaddition of substituted [3]-syn-ladderdienes in competition with 4π and 6π electrocyclic ring-opening reactions, uncovering substituent effects to explain the reported increased quantum yield of substituted cubane precursors; and (3) photochemical 4π disrotatory electrocyclic reactions of fluorobenzenes in nanoseconds with XMS-CASPT2-level training data. We expect this Account to broaden understanding of ML photodynamics and inspire future developments and applications to increasingly large molecules within complex environments on long time scales.
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Affiliation(s)
- Jingbai Li
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Steven A Lopez
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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Agostini F, Curchod BFE. Chemistry without the Born-Oppenheimer approximation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200375. [PMID: 35341309 PMCID: PMC8958276 DOI: 10.1098/rsta.2020.0375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 05/20/2023]
Affiliation(s)
- Federica Agostini
- CNRS, Institut de Chimie Physique UMR8000, Université Paris-Saclay, 91405 Orsay, France
| | - Basile F. E. Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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