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Yuan K, Rampal N, Irle S, Criscenti LJ, Lee SS, Adapa S, Stack AG. Variations in proton transfer pathways and energetics on pristine and defect-rich quartz surfaces in water: Insights into the bimodal acidities of quartz. J Colloid Interface Sci 2024; 666:232-243. [PMID: 38598996 DOI: 10.1016/j.jcis.2024.03.144] [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: 02/01/2024] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/12/2024]
Abstract
HYPOTHESIS Understanding the mechanisms of proton transfer on quartz surfaces in water is critical for a range of processes in geochemical, environmental, and materials sciences. The wide range of surface acidities (>9 pKa units) found on the ubiquitous mineral quartz is caused by the structural variations of surface silanol groups. Molecular scale simulations provide essential tools for elucidating the origin of site-specific surface acidities. SIMULATIONS We used density-functional tight-binding-based molecular dynamics combined with rare-event metadynamics simulations to probe the mechanisms of deprotonation reactions from ten representative surface silanol groups found on both pristine and defect-rich quartz (101) surfaces with Si vacancies. FINDINGS The results show that deprotonation is a highly dynamic process where both the surface hydroxyls and bridging oxygen atoms serve as the proton acceptors, in addition to water. Deprotonation of embedded silanols through intrasurface proton transfer exhibited lower pKa values with less H-bond participation and higher energy barriers, suggesting a new mechanism to explain the bimodal acidity observed on quartz surface. Defect sites, recently shown to comprise a significant portion of the quartz (101) surface, diversify the coordination and local H-bonding environments of the surface silanols, changing both the deprotonation pathways and energetics, leading to a wider range of pKa values (2.4 to 11.5) than that observed on pristine quartz surface (10.4 and 12.1).
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Affiliation(s)
- Ke Yuan
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - Nikhil Rampal
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Chemical Engineering, Columbia University, New York, NY 10027, United States
| | - Stephan Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Louise J Criscenti
- Geochemistry Department, Sandia National Laboratories, Albuquerque, NM 87185, United States
| | - Sang Soo Lee
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Sai Adapa
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Andrew G Stack
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
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2
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Elveren B, Hribernik S, Kurečič M. Fabrication of Polysaccharide-Based Halochromic Nanofibers via Needle-Less Electrospinning and Their Characterization: A Study of the Leaching Effect. Polymers (Basel) 2022; 14:polym14194239. [PMID: 36236187 PMCID: PMC9571342 DOI: 10.3390/polym14194239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022] Open
Abstract
Responsive materials, i.e., smart materials, have the ability to change their physical or chemical properties upon certain external signals. The development of nanofibrous halochromic materials, specifically combining the pH-sensitive functionality and unique nanofiber properties, could yield interesting new applications, especially when the common problem of dye leaching is successfully tackled. Therefore, in this article, we studied the fabrication process of polysaccharide-based halochromic nanofibrous materials by using a combination of various halochromic dyes (bromothymol blue, bromocresol green, and thymol blue) and cellulose acetate in a spinning solution using a one-pot strategy. The inhibition of leaching was addressed by using a complexing agent: poly-diallyl-dimethylammonium chloride (PDADMAC). The preparation of hybrid spinning solutions, their characterization, and ability to form continuous nanofibers were studied using a high production needle-less electrospinning system. The produced hybrid solutions and nanofibers were characterized, in terms of their rheological properties, chemical structure, morphology, and functionality. Fabricated nanofibrous halochromic structures show a clear color change upon exposure to different pH values, as well as the reduced leaching of dyes, upon the addition of a complexing agent. The leaching decreased by 61% in the case of bromocresol green, while, in the case of bromothymol blue and thymol blue, the leaching was reduced by 95 and 99%, respectively.
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Affiliation(s)
- Beste Elveren
- Laboratory for Characterization and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
| | - Silvo Hribernik
- Laboratory for Characterization and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
- Institute of Automation, Faculty of Electrical Engineering and Computer Science, University of Maribor, Koroska cesta 46, 2000 Maribor, Slovenia
| | - Manja Kurečič
- Laboratory for Characterization and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
- Correspondence:
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3
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Liu W, Pouvreau M, Stack AG, Yang X, Clark AE. Concentration dependent interfacial chemistry of the NaOH (aq): gibbsite interface. Phys Chem Chem Phys 2022; 24:20998-21008. [PMID: 36000443 DOI: 10.1039/d2cp01997c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Caustic conditions are often employed for dissolution of a wide variety of minerals, where ion sorption, surface diffusion, and interfacial organization impact surface reactivity. In the case of gibbsite, γ-Al(OH)3, the chemistry at the NaOH(aq) interface is deeply intertwined with industrial processing of aluminum, including metal production and the disposition of Al-containing wastes. To date, little is known about the structure, speciation, and dynamic behavior of gibbsite interfaces (and that of many other minerals) with NaOH(aq)-particularly as a function of ionic strength. Yet concentration-dependent interfacial organization and dynamics are a critical starting point to develop a fundamental understanding of the factors that influence dissolution. This work reports equilibrium molecular dynamics simulations of the γ-Al(OH)3:NaOH(aq) interface, revealing the sorption behavior and speciation of ions from 0.5-10 M [NaOH]. As inner-sphere complexes, Na+ primarily coordinates to the side of the gibbsite hexagonal cavities, while OH- accepts hydrogen-bonding from the surface-OH groups. The mobility of inner-sphere Na+ and OH- ions is significantly reduced due to a strong surface affinity in comparison to previous reports of NaCl, CaCl2, or BaCl2 electrolytes. At high [NaOH], contact ion pairing that is observed in the bulk solution is partially disrupted upon sorption to the gibbsite surface by the individual ion-surface interactions. The molecular-scale changes to surface speciation and competition between ion-surface vs. ion-ion interactions influence surface characterization of gibbsite and potential dissolution processes, providing a valuable baseline for starting conditions needed within future reactive molecular simulations.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China.
| | - Maxime Pouvreau
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA.
| | | | - Xiaoning Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China.
| | - Aurora E Clark
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA.
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4
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Smith W, Pouvreau M, Rosso K, Clark AE. pH dependent reactivity of boehmite surfaces from first principles molecular dynamics. Phys Chem Chem Phys 2022; 24:14177-14186. [PMID: 35583197 DOI: 10.1039/d2cp00534d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
pH dependent interfacial chemistry depends upon the distribution and respective pKa values of different surface active sites. This is highly relevant to the chemistry of nanoparticle morphologies that expose faces with varying surface termination. Recent synthetic advances for nanoparticles of various minerals, including AlO(OH) (boehmite), present an excellent opportunity to compare and contrast predicted surface pKa on low Miller index planes so as to reinterpret reported interfacial properties (i.e., point of zero charge - PZC) and reactivity. This work employs ab initio molecular dynamics and empirical models to predict site-specific pKa values of accurate (benchmarked) surface models of boehmite. Using the different surface site populations, the PZC is determined and the influence this has upon reported interfacial chemistry is described.
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Affiliation(s)
- William Smith
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA.
| | - Maxime Pouvreau
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA.
| | - Kevin Rosso
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Aurora E Clark
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA. .,Pacific Northwest National Laboratory, Richland, WA 99354, USA.,Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
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5
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Edeleva M, Van Steenberge PH, Sabbe MK, D’hooge DR. Connecting Gas-Phase Computational Chemistry to Condensed Phase Kinetic Modeling: The State-of-the-Art. Polymers (Basel) 2021; 13:3027. [PMID: 34577928 PMCID: PMC8467432 DOI: 10.3390/polym13183027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023] Open
Abstract
In recent decades, quantum chemical calculations (QCC) have increased in accuracy, not only providing the ranking of chemical reactivities and energy barriers (e.g., for optimal selectivities) but also delivering more reliable equilibrium and (intrinsic/chemical) rate coefficients. This increased reliability of kinetic parameters is relevant to support the predictive character of kinetic modeling studies that are addressing actual concentration changes during chemical processes, taking into account competitive reactions and mixing heterogeneities. In the present contribution, guidelines are formulated on how to bridge the fields of computational chemistry and chemical kinetics. It is explained how condensed phase systems can be described based on conventional gas phase computational chemistry calculations. Case studies are included on polymerization kinetics, considering free and controlled radical polymerization, ionic polymerization, and polymer degradation. It is also illustrated how QCC can be directly linked to material properties.
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Affiliation(s)
- Mariya Edeleva
- Laboratory for Chemical Technology (LCT), Ghent University, Technologiepark 125, 9052 Zwijnaarde, Belgium; (P.H.M.V.S.); (M.K.S.)
| | - Paul H.M. Van Steenberge
- Laboratory for Chemical Technology (LCT), Ghent University, Technologiepark 125, 9052 Zwijnaarde, Belgium; (P.H.M.V.S.); (M.K.S.)
| | - Maarten K. Sabbe
- Laboratory for Chemical Technology (LCT), Ghent University, Technologiepark 125, 9052 Zwijnaarde, Belgium; (P.H.M.V.S.); (M.K.S.)
- Industrial Catalysis and Adsorption Technology (INCAT), Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Dagmar R. D’hooge
- Laboratory for Chemical Technology (LCT), Ghent University, Technologiepark 125, 9052 Zwijnaarde, Belgium; (P.H.M.V.S.); (M.K.S.)
- Centre for Textile Science and Engineering (CTSE), Ghent University, Technologiepark 70a, 9052 Zwijnaarde, Belgium
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6
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Shiery RC, Cooper KA, Cantu DC. Computational Prediction of All Lanthanide Aqua Ion Acidity Constants. Inorg Chem 2021; 60:10257-10266. [PMID: 34214391 DOI: 10.1021/acs.inorgchem.1c00662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protonation state of lanthanide-ligand complexes, or lanthanide-containing porous materials, with many Brønsted acid sites can change due to proton loss/gain reactions with water or other heteroatom-containing compounds. Consequently, variations in the protonation state of lanthanide-containing species affect their molecular structure and desired properties. Lanthanide(III) aqua ions undergo hydrolysis and form hydroxides; they are the best characterized lanthanide-containing species with multiple Brønsted acid sites. We employed constrained ab initio molecular dynamics simulations and electronic structure calculations to determine all acidity constants of the lanthanide(III) aqua ions solely from computation. The first, second, and third acidity constants of lanthanide(III) aqua ions were predicted, on average, within 1.2, 2.5, and 4.7 absolute pKa units from experiment, respectively. A table includes our predicted pKa values alongside most experimentally measured pKa values known to date. The approach presented is particularly suitable to determine the Brønsted acidity of lanthanide-containing systems with multiple acidic sites, including those whose measured acidity constants cannot be linked to specific acid sites.
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Affiliation(s)
- Richard C Shiery
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Kyle A Cooper
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
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7
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Tirri B, Mazzone G, Ottochian A, Gomar J, Raucci U, Adamo C, Ciofini I. A combined Monte Carlo/DFT approach to simulate UV-vis spectra of molecules and aggregates: Merocyanine dyes as a case study. J Comput Chem 2021; 42:1054-1063. [PMID: 33797766 DOI: 10.1002/jcc.26505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
Abstract
The combination of a Monte Carlo (MC) sampling of the configurational space with time dependent-density functional theory (TD-DFT) to estimate vertical excitations energies has been applied to compute the absorption spectra of a family of merocyanine dyes in both their monomeric and dimeric forms. These results have been compared to those obtained using a static DFT/TD-DFT approach as well as to the available experimental spectra. Though suffering of the limitations related to the use of DFT and TD-DFT for this type of systems, our data clearly show that the classical MC sampling provides a suitable alternative to classical molecular dynamics to explore the structural flexibility of these donor-acceptor (D-π-A) chromophores enabling a realistic description of the potential energy surface of both their monomers and aggregates (here dimers) and thus of their spectra. Overall, the combination of MC sampling with quantum mechanics (TD-DFT) calculations, carried out in implicit dioxane solvent on random snapshots, provides a workable compromise to solve the combined challenge of accuracy and time-consuming problem not only for merocyanines momers, but also for their dimers, up to now less investigated. Indeed, the simulated absorption spectra fairly agree with the experimental ones, suggesting the general reliability of the method.
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Affiliation(s)
- Bernardino Tirri
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Theoretical Chemistry and Modelling, Paris, France
| | - Gloria Mazzone
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Theoretical Chemistry and Modelling, Paris, France
| | - Alistar Ottochian
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Theoretical Chemistry and Modelling, Paris, France
| | - Jerôme Gomar
- L'Oréal, Research and Innovation, Aulnay-sous-Bois, France
| | - Umberto Raucci
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Theoretical Chemistry and Modelling, Paris, France
| | - Carlo Adamo
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Theoretical Chemistry and Modelling, Paris, France.,Institut Universitaire de France, Paris, France
| | - Ilaria Ciofini
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Theoretical Chemistry and Modelling, Paris, France
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8
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Govindarajan N, Beks H, Meijer EJ. Variability of Ligand pKa during Homogeneously Catalyzed Aqueous Methanol Dehydrogenation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03907] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nitish Govindarajan
- Amsterdam Center for Multiscale Modeling and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
- Catalysis Theory Center, Department of Physics, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Hugo Beks
- Amsterdam Center for Multiscale Modeling and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Evert Jan Meijer
- Amsterdam Center for Multiscale Modeling and Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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9
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Farafonov VS, Lebed AV, Mchedlov-Petrossyan NO. Computing p Ka Shifts Using Traditional Molecular Dynamics: Example of Acid-Base Indicator Dyes in Organized Solutions. J Chem Theory Comput 2020; 16:5852-5865. [PMID: 32786914 DOI: 10.1021/acs.jctc.0c00231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A compound's acidity constant (Ka) in a given medium determines its protonation state and, thus, its behavior and physicochemical properties. Therefore, it is among the key characteristics considered during the design of new compounds for the needs of advanced technology, medicine, and biological research, a notable example being pH sensors. The computational prediction of Ka for weak acids and bases in homogeneous solvents is presently rather well developed. However, it is not the case for more complex media, such as microheterogeneous solutions. The constant-pH molecular dynamics (MD) method is a notable contribution to the solution of the problem, but it is not commonly used. Here, we develop an approach for predicting Ka changes of weak small-molecule acids upon transfer from water to colloid solutions by means of traditional classical molecular dynamics. The approach is based on free energy (ΔG) computations and requires limited experiment data input during calibration. It was successfully tested on a series of pH-sensitive acid-base indicator dyes in micellar solutions of surfactants. The difficulty of finite-size effects affecting ΔG computation between states with different total charges is taken into account by evaluating relevant corrections; their impact on the results is discussed, and it is found non-negligible (0.1-0.4 pKa units). A marked bias is found in the ΔG values of acid deprotonation, as computed from MD, which is apparently caused by force-field issues. It is hypothesized to affect the constant-pH MD and reaction ensemble MD methods as well. Consequently, for these methods, a preliminary calibration is suggested.
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Affiliation(s)
- Vladimir S Farafonov
- V. N. Karazin Kharkiv National University, 4 Svoboda Square, Kharkiv 61022, Ukraine
| | - Alexander V Lebed
- V. N. Karazin Kharkiv National University, 4 Svoboda Square, Kharkiv 61022, Ukraine
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10
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Jia M, Zhang C, Cox SJ, Sprik M, Cheng J. Computing Surface Acidity Constants of Proton Hopping Groups from Density Functional Theory-Based Molecular Dynamics: Application to the SnO 2(110)/H 2O Interface. J Chem Theory Comput 2020; 16:6520-6527. [PMID: 32794753 DOI: 10.1021/acs.jctc.0c00021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton transfer at metal oxide/water interfaces plays an important role in electrochemistry, geochemistry, and environmental science. The key thermodynamic quantity to characterize this process is the surface acidity constant. An ab initio method that combines density functional theory-based molecular dynamics (DFTMD) and free energy perturbation theory has been established for computing surface acidity constants. However, it involves a reversible proton insertion procedure in which frequent proton hopping, e.g., for strong bases and some oxide surfaces (e.g., SnO2), can cause instability issues in electronic structure calculation. In the original implementation, harmonic restraining potentials are imposed on all O-H bonds (denoted by the VrH scheme) to prevent proton hopping and thus may not be applicable for systems involving spontaneous proton hopping. In this work, we introduce an improved restraining scheme with a repulsive potential Vrep to compute the surface acidities of systems in which proton hopping is spontaneous and fast. In this Vrep scheme, a Buckingham-type repulsive potential Vrep is applied between the deprotonation site and all other protons in DFTMD simulations. We first verify the Vrep scheme by calculating the pKa values of H2O and aqueous HS- solution (i.e., strong conjugate bases) and then apply it to the SnO2(110)/H2O interface. It is found that the Vrep scheme leads to a prediction of the point of zero charge (PZC) of 4.6, which agrees well with experiment. The intrinsic individual pKa values of the terminal five-coordinated Sn site (Sn5cOH2) and bridge oxygen site (Sn2ObrH+) are 4.4 and 4.7, respectively, both being almost the same as the PZC. The similarity of the two pKa values indicates that dissociation of terminal water has almost zero free energy at this proton hopping interface (i.e., partial water dissociation), as expected from the acid-base equilibrium on SnO2.
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Affiliation(s)
- Mei Jia
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Chao Zhang
- Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, PO Box 538, Uppsala 75121, Sweden
| | - Stephen J Cox
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michiel Sprik
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jun Cheng
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
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11
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Bailleul S, Dedecker K, Cnudde P, Vanduyfhuys L, Waroquier M, Van Speybroeck V. Ab initio enhanced sampling kinetic study on MTO ethene methylation reaction. J Catal 2020. [DOI: 10.1016/j.jcat.2020.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Rossi K, Jurásková V, Wischert R, Garel L, Corminbœuf C, Ceriotti M. Simulating Solvation and Acidity in Complex Mixtures with First-Principles Accuracy: The Case of CH 3SO 3H and H 2O 2 in Phenol. J Chem Theory Comput 2020; 16:5139-5149. [PMID: 32567854 DOI: 10.1021/acs.jctc.0c00362] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We present a generally applicable computational framework for the efficient and accurate characterization of molecular structural patterns and acid properties in an explicit solvent using H2O2 and CH3SO3H in phenol as an example. To address the challenges posed by the complexity of the problem, we resort to a set of data-driven methods and enhanced sampling algorithms. The synergistic application of these techniques makes the first-principle estimation of the chemical properties feasible without renouncing to the use of explicit solvation, involving extensive statistical sampling. Ensembles of neural network (NN) potentials are trained on a set of configurations carefully selected out of preliminary simulations performed at a low-cost density functional tight-binding (DFTB) level. The energy and forces of these configurations are then recomputed at the hybrid density functional theory (DFT) level and used to train the neural networks. The stability of the NN model is enhanced by using DFTB energetics as a baseline, but the efficiency of the direct NN (i.e., baseline-free) is exploited via a multiple-time-step integrator. The neural network potentials are combined with enhanced sampling techniques, such as replica exchange and metadynamics, and used to characterize the relevant protonated species and dominant noncovalent interactions in the mixture, also considering nuclear quantum effects.
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Affiliation(s)
- Kevin Rossi
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Veronika Jurásková
- Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Raphael Wischert
- Eco-Efficient Products and Processes Laboratory, Solvay, RIC Shanghai, Shanghai 201108, China
| | - Laurent Garel
- Aroma Performance Laboratory, Solvay, RIC Lyon, 69190 Saint-Fons, France
| | - Clémence Corminbœuf
- Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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13
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Cota R, Tiwari A, Ensing B, Bakker HJ, Woutersen S. Hydration interactions beyond the first solvation shell in aqueous phenolate solution. Phys Chem Chem Phys 2020; 22:19940-19947. [DOI: 10.1039/d0cp01209b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the orientational dynamics of water molecules solvating phenolate ions using ultrafast vibrational spectroscopy and density functional theory-based molecular dynamics simulations.
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Affiliation(s)
- Roberto Cota
- Van 't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- The Netherlands
- AMOLF
| | - Ambuj Tiwari
- Van 't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- The Netherlands
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- The Netherlands
| | | | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- The Netherlands
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14
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Determination of pKa Values via ab initio Molecular Dynamics and its Application to Transition Metal-Based Water Oxidation Catalysts. INORGANICS 2019. [DOI: 10.3390/inorganics7060073] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The p K a values are important for the in-depth elucidation of catalytic processes, the computational determination of which has been challenging. The first simulation protocols employing ab initio molecular dynamics simulations to calculate p K a values appeared almost two decades ago. Since then several slightly different methods have been proposed. We compare the performance of various evaluation methods in order to determine the most reliable protocol when it comes to simulate p K a values of transition metal-based complexes, such as the here investigated Ru-based water oxidation catalysts. The latter are of high interest for sustainable solar-light driven water splitting, and understanding of the underlying reaction mechanism is crucial for their further development.
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15
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Abstract
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free energy can be computed as a function of one or more collective variables. A number of practical issues mostly around periodic boundary conditions that arise when these types of calculations are performed using PLUMED are then discussed. Later parts of the chapter discuss how PLUMED can be used to perform enhanced sampling simulations that introduce simulation biases or multiple replicas of the system and Monte Carlo exchanges between these replicas. This section is then followed by a discussion on how free-energy surfaces and associated error bars can be extracted from such simulations by using weighted histogram and block averaging techniques.
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Affiliation(s)
- Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy.
| | - Gareth A Tribello
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast, UK.
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Barroso daSilva FL, Dias LG. Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Biophys Rev 2017; 9:699-728. [PMID: 28921104 PMCID: PMC5662048 DOI: 10.1007/s12551-017-0311-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022] Open
Abstract
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.
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Affiliation(s)
- Fernando Luís Barroso daSilva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do café, s/no. - Universidade de São Paulo, BR-14040-903, Ribeirão Preto, SP, Brazil.
- UCD School of Physics, UCD Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland.
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Luis Gustavo Dias
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Av. Bandeirantes, 3900 - Universidade de São Paulo, BR-14040-901, Ribeirão Preto, SP, Brazil
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De Meyer T, Ensing B, Rogge SMJ, De Clerck K, Meijer EJ, Van Speybroeck V. Acidity Constant (pK a ) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods. Chemphyschem 2016; 17:3447-3459. [PMID: 27570194 PMCID: PMC5129556 DOI: 10.1002/cphc.201600734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 11/14/2022]
Abstract
pH‐Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH‐sensitive properties, in particular on the acidity constant (pKa). Obtaining molecular control over the factors that influence the pKa value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pKa values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules.
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Affiliation(s)
- Thierry De Meyer
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052, Zwijnaarde, Belgium.,Department of Textiles, Ghent University, Technologiepark 907, 9052, Zwijnaarde, Belgium
| | - Bernd Ensing
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Sven M J Rogge
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052, Zwijnaarde, Belgium
| | - Karen De Clerck
- Department of Textiles, Ghent University, Technologiepark 907, 9052, Zwijnaarde, Belgium
| | - Evert Jan Meijer
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
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