1
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Turi L, Baranyi B, Madarász Á. 2-in-1 Phase Space Sampling for Calculating the Absorption Spectrum of the Hydrated Electron. J Chem Theory Comput 2024; 20:4265-4277. [PMID: 38727675 PMCID: PMC11137824 DOI: 10.1021/acs.jctc.4c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024]
Abstract
The investigation of vibrational effects on absorption spectrum calculations often employs Wigner sampling or thermal sampling. While Wigner sampling incorporates zero-point energy, it may not be suitable for flexible systems. Thermal sampling is applicable to anharmonic systems yet treats nuclei classically. The application of generalized smoothed trajectory analysis (GSTA) as a postprocessing method allows for the incorporation of nuclear quantum effects (NQEs), combining the advantages of both sampling methods. We demonstrate this approach in computing the absorption spectrum of a hydrated electron. Theoretical exploration of the hydrated electron and its embryonic forms, such as water cluster anions, poses a significant challenge due to the diffusivity of the excess electron and the continuous motion of water molecules. In many previous studies, the wave nature of atomic nuclei is often neglected, despite the substantial impact of NQEs on thermodynamic and spectroscopic properties, particularly for hydrogen atoms. In our studies, we examine these NQEs for the excess electrons in various water systems. We obtained structures from mixed classical-quantum simulations for water cluster anions and the hydrated electron by incorporating the quantum effects of atomic nuclei with the filtration of the classical trajectories. Absorption spectra were determined at different theoretical levels. Our results indicate significant NQEs, red shift, and broadening of the spectra for hydrated electron systems. This study demonstrates the applicability of GSTA to complex systems, providing insights into NQEs on energetic and structural properties.
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Affiliation(s)
- László Turi
- Institute
of Chemistry, ELTE, Eötvös
Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Bence Baranyi
- Institute
of Chemistry, ELTE, Eötvös
Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Ádám Madarász
- Research
Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
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2
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Chen Z, Bononi FC, Sievers CA, Kong WY, Donadio D. UV-Visible Absorption Spectra of Solvated Molecules by Quantum Chemical Machine Learning. J Chem Theory Comput 2022; 18:4891-4902. [PMID: 35913220 DOI: 10.1021/acs.jctc.1c01181] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Predicting UV-visible absorption spectra is essential to understand photochemical processes and design energy materials. Quantum chemical methods can deliver accurate calculations of UV-visible absorption spectra, but they are computationally expensive, especially for large systems or when one computes line shapes from thermal averages. Here, we present an approach to predict UV-visible absorption spectra of solvated aromatic molecules by quantum chemistry (QC) and machine learning (ML). We show that a ML model, trained on the high-level QC calculation of the excitation energy of a set of aromatic molecules, can accurately predict the line shape of the lowest-energy UV-visible absorption band of several related molecules with less than 0.1 eV deviation with respect to reference experimental spectra. Applying linear decomposition analysis on the excitation energies, we unveil that our ML models probe vertical excitations of these aromatic molecules primarily by learning the atomic environment of their phenyl rings, which align with the physical origin of the π →π* electronic transition. Our study provides an effective workflow that combines ML with quantum chemical methods to accelerate the calculations of UV-visible absorption spectra for various molecular systems.
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Affiliation(s)
- Zekun Chen
- Department of Chemistry, University of California Davis 95616, California, United States
| | - Fernanda C Bononi
- Department of Chemistry, University of California Davis 95616, California, United States
| | - Charles A Sievers
- Department of Chemistry, University of California Davis 95616, California, United States
| | - Wang-Yeuk Kong
- Department of Chemistry, University of California Davis 95616, California, United States
| | - Davide Donadio
- Department of Chemistry, University of California Davis 95616, California, United States
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3
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Borrego-Sánchez A, Zemmouche M, Carmona-García J, Francés-Monerris A, Mulet P, Navizet I, Roca-Sanjuán D. Multiconfigurational Quantum Chemistry Determinations of Absorption Cross Sections (σ) in the Gas Phase and Molar Extinction Coefficients (ε) in Aqueous Solution and Air-Water Interface. J Chem Theory Comput 2021; 17:3571-3582. [PMID: 33974417 PMCID: PMC8444339 DOI: 10.1021/acs.jctc.0c01083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Indexed: 11/29/2022]
Abstract
Theoretical determinations of absorption cross sections (σ) in the gas phase and molar extinction coefficients (ε) in condensed phases (water solution, interfaces or surfaces, protein or nucleic acids embeddings, etc.) are of interest when rates of photochemical processes, J = ∫ ϕ(λ) σ(λ) I(λ) dλ, are needed, where ϕ(λ) and I(λ) are the quantum yield of the process and the irradiance of the light source, respectively, as functions of the wavelength λ. Efficient computational strategies based on single-reference quantum-chemistry methods have been developed enabling determinations of line shapes or, in some cases, achieving rovibrational resolution. Developments are however lacking for strongly correlated problems, with many excited states, high-order excitations, and/or near degeneracies between states of the same and different spin multiplicities. In this work, we define and compare the performance of distinct computational strategies using multiconfigurational quantum chemistry, nuclear sampling of the chromophore (by means of molecular dynamics, ab initio molecular dynamics, or Wigner sampling), and conformational and statistical sampling of the environment (by means of molecular dynamics). A new mathematical approach revisiting previous absolute orientation algorithms is also developed to improve alignments of geometries. These approaches are benchmarked through the nπ* band of acrolein not only in the gas phase and water solution but also in a gas-phase/water interface, a common situation for instance in atmospheric chemistry. Subsequently, the best strategy is used to compute the absorption band for the adduct formed upon addition of an OH radical to the C6 position of uracil and compared with the available experimental data. Overall, quantum Wigner sampling of the chromophore with molecular dynamics sampling of the environment with CASPT2 electronic-structure determinations arise as a powerful methodology to predict meaningful σ(λ) and ε(λ) band line shapes with accurate absolute intensities.
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Affiliation(s)
- Ana Borrego-Sánchez
- Instituto
Andaluz de Ciencias de la Tierra, CSIC-University
of Granada, Av. de las
Palmeras 4, 18100 Armilla, Granada, Spain
| | - Madjid Zemmouche
- MSME,
Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris-Est Créteil 8208, F-77454 Marne-la-Vallée, France
| | - Javier Carmona-García
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, València, Spain
| | - Antonio Francés-Monerris
- Université
de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
- Departamento
de Química Física, Universitat
de València, C/Dr.
Moliner 50, 46100 Burjassot, Spain
| | - Pep Mulet
- Departamento
de Matemáticas Área de Matemática Aplicada Facultad
de Matemáticas C/Dr. Moliner, 50 46100 Burjassot, Spain
| | - Isabelle Navizet
- MSME,
Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris-Est Créteil 8208, F-77454 Marne-la-Vallée, France
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, València, Spain
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4
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Bononi FC, Chen Z, Rocca D, Andreussi O, Hullar T, Anastasio C, Donadio D. Bathochromic Shift in the UV–Visible Absorption Spectra of Phenols at Ice Surfaces: Insights from First-Principles Calculations. J Phys Chem A 2020; 124:9288-9298. [DOI: 10.1021/acs.jpca.0c07038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Fernanda C. Bononi
- Department of Chemistry, University of California Davis, Davis, California 95616-5270, United States
| | - Zekun Chen
- Department of Chemistry, University of California Davis, Davis, California 95616-5270, United States
| | - Dario Rocca
- Université de Lorraine, CNRS, LPTC, F-54000 Nancy, France
| | - Oliviero Andreussi
- Department of Physics, University of North Texas Denton, Texas 76203, United States
| | - Ted Hullar
- Department of Land, Air and Water Resources, University of California Davis Davis, California 95616-8627, United States
| | - Cort Anastasio
- Department of Land, Air and Water Resources, University of California Davis Davis, California 95616-8627, United States
| | - Davide Donadio
- Department of Chemistry, University of California Davis, Davis, California 95616-5270, United States
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5
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Hullar T, Bononi FC, Chen Z, Magadia D, Palmer O, Tran T, Rocca D, Andreussi O, Donadio D, Anastasio C. Photodecay of guaiacol is faster in ice, and even more rapid on ice, than in aqueous solution. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:1666-1677. [PMID: 32671365 DOI: 10.1039/d0em00242a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Snowpacks contain a wide variety of inorganic and organic compounds, including some that absorb sunlight and undergo direct photoreactions. How the rates of these reactions in, and on, ice compare to rates in water is unclear: some studies report similar rates, while others find faster rates in/on ice. Further complicating our understanding, there is conflicting evidence whether chemicals react more quickly at the air-ice interface compared to in liquid-like regions (LLRs) within the ice. To address these questions, we measured the photodegradation rate of guaiacol (2-methoxyphenol) in various sample types, including in solution, in ice, and at the air-ice interface of nature-identical snow. Compared to aqueous solution, we find modest rate constant enhancements (increases of 3- to 6-fold) in ice LLRs, and much larger enhancements (of 17- to 77-fold) at the air-ice interface of nature-identical snow. Our computational modeling suggests the absorption spectrum for guaiacol red-shifts and increases on ice surfaces, leading to more light absorption, but these changes explain only a small portion (roughly 2 to 9%) of the observed rate constant enhancements in/on ice. This indicates that increases in the quantum yield are primarily responsible for the increased photoreactivity of guaiacol on ice; relative to solution, our results suggest that the quantum yield is larger by a factor of roughly 3-6 in liquid-like regions and 12-40 at the air-ice interface.
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Affiliation(s)
- Ted Hullar
- Department of Land, Air and Water Resources, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
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6
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Rusishvili M, Grisanti L, Laporte S, Micciarelli M, Rosa M, Robbins RJ, Collins T, Magistrato A, Baroni S. Unraveling the molecular mechanisms of color expression in anthocyanins. Phys Chem Chem Phys 2019; 21:8757-8766. [PMID: 30968901 DOI: 10.1039/c9cp00747d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Anthocyanins are a broad family of natural dyes, increasingly finding application as substitutes for artificial colorants in the food industry. In spite of their importance and ubiquity, the molecular principles responsible for their extreme color variability are poorly known. We address these mechanisms by computer simulations and photoabsorption experiments of cyanidin-3-O-glucoside in water solution, as a proxy for more complex members of the family. Experimental results are presented in the range of pH 1-9, accompanied by a comprehensive systematic computational study across relevant charge states and tautomers. The computed spectra are in excellent agreement with the experiments, providing unprecedented insight into the complex behavior underlying color expression in these molecules. Besides confirming the importance of the molecule's charge state, we also unveil the hitherto unrecognized role of internal distortions in the chromophore, which affect its degree of conjugation, modulating the optical gap and in turn the color. This entanglement of structural and electronic traits is also shared by other members of the anthocyanin family (e.g. pelargonidin and delphinidin) highlighting a common mechanism for color expression across this important family of natural dyes.
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Affiliation(s)
- Mariami Rusishvili
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34125 Trieste, Italy. and International Center for Theoretical Physics, Condensed Matter and Statistical Physics, 34151 Trieste, Italy
| | - Luca Grisanti
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34125 Trieste, Italy.
| | - Sara Laporte
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34125 Trieste, Italy.
| | - Marco Micciarelli
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34125 Trieste, Italy.
| | - Marta Rosa
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34125 Trieste, Italy.
| | - Rebecca J Robbins
- Mars Wrigley Confectionery R&D, 1132 W. Blackhawk St., Chicago, IL 60642, USA
| | - Tom Collins
- Mars Wrigley Confectionery R&D, 800 High St., Hackettstown, NJ 07840, USA
| | | | - Stefano Baroni
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34125 Trieste, Italy. and CNR-IOM DEMOCRITOS, SISSA, Trieste, Italy
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7
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Heid E, Hunt PA, Schröder C. Evaluating excited state atomic polarizabilities of chromophores. Phys Chem Chem Phys 2018. [PMID: 29542743 PMCID: PMC5885803 DOI: 10.1039/c7cp08549d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ground and excited state atomic polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine and coumarin 153 have been evaluated via quantum mechanics.
Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered.
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Affiliation(s)
- Esther Heid
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 19, A-1090 Vienna, Austria.
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8
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Micciarelli M, Curchod BFE, Bonella S, Altucci C, Valadan M, Rothlisberger U, Tavernelli I. Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory. J Phys Chem A 2017; 121:3909-3917. [PMID: 28467074 DOI: 10.1021/acs.jpca.6b12799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime (LR-TDDFT) to a set of different wave-function-based methods for excited states, namely perturbed coupled cluster (CC2), algebraic diagrammatic construction method to second order (ADC(2)), and perturbed configuration interaction (CIS(D)). 5BU has been used to investigate DNA base-amino acid interactions. In particular, it served as a model of protein-DNA photoinduced cross-linking. While LR-TDDFT is computationally the most efficient first-principles approach for static and dynamic simulations of this bichromophoric system, its accuracy is difficult to assess due to the presence of excited states with charge transfer character. In this work, the performance of different exchange correlation functionals is compared against accurate benchmarks obtained either from high level wave-function-based methods or directly from experimental absorption spectra. Our investigation shows that accurate results for the excitation energies can be obtained using the hybrid meta-GGA functional M06. In view of dynamical studies of the relaxation of 5BU after photoexcitation, we also show that the PBE functional, while failing in the Franck-Condon region, provides qualitatively good results for the characterisation of a possible photocyclization path.
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Affiliation(s)
- M Micciarelli
- Department of Physics, University of Rome "La Sapienza" , Ple A. Moro 5, 00185 Rome, Italy
| | | | | | - C Altucci
- Department of Physics, University of Naples "Federico II" , Via Cintia, 26-80126 Napoli, Italy
| | - M Valadan
- Department of Physics, University of Naples "Federico II" , Via Cintia, 26-80126 Napoli, Italy
| | | | - I Tavernelli
- Zurich Research Laboratory, IBM Research GmbH , 8803 Rüschlikon, Switzerland
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9
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Pagliai M, Mancini G, Carnimeo I, De Mitri N, Barone V. Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach. J Comput Chem 2017; 38:319-335. [PMID: 27910109 PMCID: PMC6680224 DOI: 10.1002/jcc.24683] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 01/06/2023]
Abstract
The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Marco Pagliai
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
| | | | - Ivan Carnimeo
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
- Compunet, Istituto Italiano di Tecnologia (IIT)via Morego 30GenovaI‐16163Italy
| | - Nicola De Mitri
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
- Present address:
Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWU.K.
| | - Vincenzo Barone
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
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10
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Low-lying electronic excitations of a water-soluble BODIPY: from the gas phase to the solvated molecule. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2011-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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