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Kiataki MB, Coutinho K, Varella MTDN. Toward a numerically efficient description of bulk-solvated anionic states. J Chem Phys 2024; 161:034301. [PMID: 39007383 DOI: 10.1063/5.0203247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute-solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute-solvent and solvent-solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.
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Affiliation(s)
- Matheus B Kiataki
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
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Kiataki MB, Varella MTDN, Coutinho K, Rabilloud F. Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules. J Chem Theory Comput 2024; 20:4893-4900. [PMID: 38783835 DOI: 10.1021/acs.jctc.4c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
When low-energy electrons interact with molecules, they can give rise to transient anion states commonly known as resonances. These states are formed through vertical electron attachment processes and have the potential to induce various forms of DNA lesions, including base damage, single- and double-strand breaks, cross-links, and clustered lesions that are challenging to repair. So far, most experimental and theoretical studies have investigated the formation of resonances of (bio)molecules in the gas phase or in microsolvated environments. Since cellular environments are mainly composed of water molecules, it is crucial to understand how bulk water affects the resonances of (bio)molecules. Given the existing gap in studies on resonances of bulk-solvated molecules, we propose a novel theoretical-computational approach to address this void. Our approach combines the multibasis-set (time-dependent-)density functional theory and self-consistent sequential quantum mechanics/molecular mechanics polarizable electrostatic embedding methods. We apply this combined methodology to predict the vertical electron attachment energies of 1-methyl-5-nitroimidazole (1M5NI), a well-known radiosensitizer model, in bulk water. In addition, we analyze the rapid mutual polarization between the resonances (both shape- and core-excited) of 1M5NI and the surrounding bulk water environment. For comparison, we also studied the isolated and microsolvated 1M5NI. Overall, while the polarization of the environment is clearly sensitive to the solute charge, causing a significant impact on the vertical electron affinity and consequently on the attachment electron energies, it does not have a significant impact on the excitation energies of the anion.
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Affiliation(s)
- Matheus B Kiataki
- Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Villeurbanne F-69100, France
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, São Paulo 05508-090, São Paulo, Brazil
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, São Paulo 05508-090, São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, São Paulo 05508-090, São Paulo, Brazil
| | - Franck Rabilloud
- Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Villeurbanne F-69100, France
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Zhang J, Li L, Li H. Adsorption-Controlled Wettability and Self-Cleaning of TiO 2. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:6188-6200. [PMID: 37073727 DOI: 10.1021/acs.langmuir.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular adsorption on solids is inevitable and has significant influences on the wettability of materials, while the tuning mechanism of the wettability from molecular adsorption is yet to be understood. Using molecular dynamics (MD) simulations, we comprehensively studied the relation between the wettability of the TiO2 surface and the adsorption of water and carboxylic acid molecules. Our results reveal that the increasing amount of surface hydroxyl groups from the decomposition adsorption of H2O increases the hydrophilicity of TiO2, providing molecular-level evidence for the previously proposed mechanism of photo-induced hydrophilicity. By contrast, the surface wettability becomes tunable with water contact angles changing from 0 to ∼130° through length adjustment of the adsorbed carboxylic acids. The TiO2 surface is hydrophilic with the adsorption of short-alkyl-chain carboxylic acids (e.g., HCOOH) and becomes hydrophobic when longer-alkyl-chain carboxylic acids (H(CH2)nCOOH, n > 2) are present. Furthermore, long-alkyl-chain acids also increase surface oleophilicity, while the adsorption of HCOOH and CH3COOH significantly enhances the oleophobicity of TiO2. Water molecules can also more easily penetrate the space between oily contaminants and adsorbed short acid molecules, thereby further increasing its self-cleaning capacity. The present simulations not only reveal the mechanism of wettability caused by molecular adsorption but also provide a promising method to create materials with controllable wettability and high self-cleaning efficiency.
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Affiliation(s)
- Jingyan Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemistry Technology, Beijing 100029, China
| | - Lei Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemistry Technology, Beijing 100029, China
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Das S, Samanta K. Recent Advances in the Study of Negative-Ion Resonances Using Multiconfigurational Propagator and a Complex Absorbing Potential. Chemphyschem 2023; 24:e202200546. [PMID: 36223261 DOI: 10.1002/cphc.202200546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/12/2022] [Indexed: 02/03/2023]
Abstract
The transient resonances are a challenge to bound state quantum mechanics. These states lie in the continuum part of the spectrum of the Hamiltonian. For this, one has to treat a continuum problem due to electron-molecule scattering and the many-electron correlation problem simultaneously. Moreover, the description of a resonance requires a wavefunction that bridges the part that resembles a bound state with another that resembles a continuum state such that the continuity of the wavefunction and its first derivative with respect to the distance between the incoming projectile and the target is maintained. A review of the recent advances in the theoretical investigation of the negative-ion resonances (NIR) is presented. The NIRs are ubiquitous in nature. They result from the scattering of electrons off of an atomic or molecular target. They are important for numerous chemical processes in upper atmosphere, space and even biological systems. A contextual background of the existing theoretical methods as well as the newly-developed multiconfigurational propagator tools based on a complex absorbing potential are discussed.
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Affiliation(s)
- Subhasish Das
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Kansapada, Argul, 752050, India
| | - Kousik Samanta
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Kansapada, Argul, 752050, India
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Cornetta LM, Coutinho K, Varella MTDN. Solvent effects on the π* shape resonances of uracil. J Chem Phys 2020; 152:084301. [DOI: 10.1063/1.5139459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- L. M. Cornetta
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
| | - K. Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
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Sieradzka A, Gorfinkiel JD. Theoretical study of resonance formation in microhydrated molecules. I. Pyridine-(H2O)n, n = 1,2,3,5. J Chem Phys 2017; 147:034302. [DOI: 10.1063/1.4993941] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Agnieszka Sieradzka
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Jimena D. Gorfinkiel
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
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Sieradzka A, Gorfinkiel JD. Theoretical study of resonance formation in microhydrated molecules. II. Thymine-(H2O)n, n = 1,2,3,5. J Chem Phys 2017; 147:034303. [DOI: 10.1063/1.4993946] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Agnieszka Sieradzka
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Jimena D. Gorfinkiel
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
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Kossoski F, Varella MTDN. Precursor anion states in dissociative electron attachment to chlorophenol isomers. J Chem Phys 2016; 145:044310. [DOI: 10.1063/1.4959229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- F. Kossoski
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, São Paulo, Brazil
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Murdachaew G, Nathanson GM, Benny Gerber R, Halonen L. Deprotonation of formic acid in collisions with a liquid water surface studied by molecular dynamics and metadynamics simulations. Phys Chem Chem Phys 2016; 18:29756-29770. [DOI: 10.1039/c6cp06071d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formic acid has a lower barrier to deprotonation at the air–water interface than in bulk liquid water.
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Affiliation(s)
- Garold Murdachaew
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
| | | | - R. Benny Gerber
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
- Institute of Chemistry and the Fritz Haber Research Center
| | - Lauri Halonen
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
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de Oliveira EM, Freitas TC, Coutinho K, do N. Varella MT, Canuto S, Lima MAP, Bettega MHF. Communication: Transient anion states of phenol…(H2O)n (n = 1, 2) complexes: Search for microsolvation signatures. J Chem Phys 2014; 141:051105. [DOI: 10.1063/1.4892066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Eliane M. de Oliveira
- Instituto de Física “Gleb Wataghin”, Universidade Estadual de Campinas, 13083-859 Campinas, SP, Brazil
| | - Thiago C. Freitas
- Tecnologia em Luteria, Universidade Federal do Paraná, 81520-260 Curitiba, PR, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP, Brazil
| | | | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP, Brazil
| | - Marco A. P. Lima
- Instituto de Física “Gleb Wataghin”, Universidade Estadual de Campinas, 13083-859 Campinas, SP, Brazil
| | - Márcio H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, PR, Brazil
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Smyth M, Kohanoff J, Fabrikant II. Electron-induced hydrogen loss in uracil in a water cluster environment. J Chem Phys 2014; 140:184313. [DOI: 10.1063/1.4874841] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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