1
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Cascella M, Bore SL, Eisenstein O. The fellowship of the Grignard: 21st century computational tools for hundred-year-old chemistry. Chem Sci 2025; 16:8196-8216. [PMID: 40308958 PMCID: PMC12039541 DOI: 10.1039/d5sc01078k] [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: 02/11/2025] [Accepted: 04/10/2025] [Indexed: 05/02/2025] Open
Abstract
This perspective begins with the discovery of the Grignard reaction by a graduate student in the last years of the 19th century, followed by describing why it has remained largely unexplained for more than a century. From the summary of what has been achieved, focusing on the computational aspects, it is now clear that further studies of the chemistry of any chemical species that is highly sensitive to solvents, such as Group I and II elements, require a holistic approach that includes the solute and the solvent together. Ab initio molecular dynamics, which meets these requirements, has produced some results but has hit hard limits due to its relatively high computational costs. In these days, it is becoming clear that data-driven methods, including machine learning potentials and simulations driven by quantitative on-the-fly calculation of relevant observables, have the potential to better and more completely explore the very large chemical space associated with the presence of a large number of species in solution. These methodologies have the chance to give the keys to enter the challenging and still poorly explored world of chemical species whose behaviour and reactivity are strongly influenced by the solvent and the experimental conditions.
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Affiliation(s)
- Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo PO Box 1033 Blindern 0315 Oslo Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo PO Box 1033 Blindern 0315 Oslo Norway
| | - Odile Eisenstein
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo PO Box 1033 Blindern 0315 Oslo Norway
- ICGM, Univ. Montpellier, CNRS, ENSCM Montpellier 34293 France
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2
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Creazzo F, Sivula K, Luber S. DFT-metadynamics insights on the origin of the oxygen evolution kinetics at the (100)-WSe 2 surface. iScience 2025; 28:112045. [PMID: 40124514 PMCID: PMC11930373 DOI: 10.1016/j.isci.2025.112045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 01/02/2025] [Accepted: 02/13/2025] [Indexed: 03/25/2025] Open
Abstract
Water oxidation or oxygen evolution reaction (OER) in electrochemical cells is considered to be a major bottleneck in the way of hydrogen production by electro-synthesis, mainly due to a sluggish kinetics that characterizes the OER steps. Layered transition metal dichalcogenides, such as WSe2, are emerging as promising non-precious electrocatalysts for water splitting due to their excellent activity and stability. This paper aims to shed light on the (100) WSe2-aqueous interface in catalyzing the slow kinetics of the OER in the context of water splitting electro-catalysis. We employ state-of-the-art DFT-metadynamics to explore reaction mechanisms, activation free energies, and catalytic sites. This study reveals an energetically preferred water-assisted OER mechanism, where proton transfer is facilitated by the surrounding aqueous environment. Our findings not only provide insights into the OER process but also offer a design strategy for optimizing WSe2-based catalysts and a modeling protocol for future DFT-based OER investigations.
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Affiliation(s)
- Fabrizio Creazzo
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Kevin Sivula
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Station 6, 1015 Lausanne, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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3
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Molina-Taborda A, Cossio P, Lopez-Acevedo O, Gabrié M. Active Learning of Boltzmann Samplers and Potential Energies with Quantum Mechanical Accuracy. J Chem Theory Comput 2024; 20:8833-8843. [PMID: 39370622 DOI: 10.1021/acs.jctc.4c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Extracting consistent statistics between relevant free energy minima of a molecular system is essential for physics, chemistry, and biology. Molecular dynamics (MD) simulations can aid in this task but are computationally expensive, especially for systems that require quantum accuracy. To overcome this challenge, we developed an approach combining enhanced sampling with deep generative models and active learning of a machine learning potential (MLP). We introduce an adaptive Markov chain Monte Carlo framework that enables the training of one normalizing flow (NF) and one MLP per state, achieving rapid convergence toward the Boltzmann distribution. Leveraging the trained NF and MLP models, we compute thermodynamic observables such as free energy differences and optical spectra. We apply this method to study the isomerization of an ultrasmall silver nanocluster belonging to a set of systems with diverse applications in the fields of medicine and catalysis.
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Affiliation(s)
- Ana Molina-Taborda
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia
- Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, 050010 Medellin, Colombia
- Center for Computational Biology, Flatiron Institute, 10010 New York, New York, United States
| | - Pilar Cossio
- Center for Computational Biology, Flatiron Institute, 10010 New York, New York, United States
- Center for Computational Mathematics, Flatiron Institute, 10010 New York, New York, United States
| | - Olga Lopez-Acevedo
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia
- Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, 050010 Medellin, Colombia
| | - Marylou Gabrié
- CMAP, CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
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4
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Calvani D, Louwersheimer R, Buda F. Effect of Anchoring Dynamics on Proton-Coupled Electron Transfer in the Ru(bda) Coordination Oligomer on a Graphitic Surface. Chempluschem 2024; 89:e202400082. [PMID: 38625893 DOI: 10.1002/cplu.202400082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/18/2024]
Abstract
The oligomeric ruthenium-based water oxidation catalyst, Ru(bda), is known to be experimentally anchored on graphitic surfaces through CH-π stacking interactions between the auxiliary bda ([2,2'-bipyridine]-6,6'-dicarboxylate) ligand bonded to ruthenium and the hexagonal rings of the surface. This anchoring provides control over their molecular coverage and enables efficient catalysis of water oxidation to dioxygen. The oligomeric nature of the molecule offers multiple anchoring sites at the surface, greatly enhancing the overall stability of the hybrid catalyst-graphitic surface anode through dynamic bonding. However, the impact of this dynamic anchoring on the overall catalytic mechanism is still a topic of debate. In this study, a crucial proton-coupled electron transfer event in the catalytic cycle is investigated using DFT-based molecular dynamics simulations plus metadynamics. The CH-π stacking anchoring plays a critical role not only in stabilizing this hybrid system but also in facilitating the proton-coupled electron transfer event with possible vibronic couplings between the anchoring bonds motion and charge fluctuations at the catalyst - graphitic surface interface. Furthermore, this computational investigation displays the presence of a quartet spin state intermediate that can lead to the experimentally observed and thermodynamically more stable doublet spin state.
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Affiliation(s)
- Dario Calvani
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Rick Louwersheimer
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, The Netherlands
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5
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Ruffman C, Steenbergen KG, Garden AL, Gaston N. Dynamic sampling of liquid metal structures for theoretical studies on catalysis. Chem Sci 2023; 15:185-194. [PMID: 38131068 PMCID: PMC10732005 DOI: 10.1039/d3sc04416e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
Liquid metals have recently emerged as promising catalysts that can outcompete their solid counterparts for many reactions. Although theoretical modelling is extensively used to improve solid-state catalysts, there is currently no way to capture the interactions of adsorbates with a dynamic liquid metal. We propose a new approach based on ab initio molecular dynamics sampling of an adsorbate on a liquid catalyst. Using this approach, we describe time-resolved structures for formate adsorbed on liquid Ga-In, and for all intermediates in the methanol oxidation pathway on Ga-Pt. This yields a range of accessible adsorption energies that take into account the at-temperature motion of the liquid metal. We find that a previously proposed pathway for methanol oxidation on Ga-Pt results in unstable intermediates on a dynamic liquid surface, and propose that H desorption must occur during the path. The results showcase a more accurate way to treat liquid metal catalysts in this emerging field.
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Affiliation(s)
- Charlie Ruffman
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, University of Auckland Private Bag 92019 Auckland New Zealand
| | - Krista G Steenbergen
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, School of Chemical and Physical Sciences, Victoria University of Wellington PO Box 600 Wellington 6140 New Zealand
| | - Anna L Garden
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Chemistry, University of Otago P.O. Box 56 Dunedin 9054 New Zealand
| | - Nicola Gaston
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, University of Auckland Private Bag 92019 Auckland New Zealand
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6
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Gorantla KR, Mallik BS. Copper Complex Catalyzed Two-Electron and Proton Shuttle Mechanism of O-O Bond Formation from DFT-Based Metadynamics Simulations. J Phys Chem A 2023; 127:3788-3795. [PMID: 37094099 DOI: 10.1021/acs.jpca.3c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We performed first-principles metadynamics simulations to explore the mechanistic pathway of oxygen-oxygen bond formation catalyzed by cis-bis(hydroxo) and cis-(hydroxo)oxo copper complexes. The ligands of considered complexes involve modified bipyridine ligands with oxo and hydroxo groups on 6, 6' positions. The study focuses on the kinetics and thermodynamics of the oxygen-oxygen bond formation. The individual migration of the proton to the hydroxyl group and hydroxide to the oxo and hydroxo moieties of the complexes was examined. The proton transfer requires more kinetic barrier than the hydroxide migration. The nature of the electronic density was analyzed with the help of spin population analysis. The molecular orbitals and natural orbital analysis were carried out to examine the nature of the orbitals involved in the oxygen-oxygen bond formation. The σ*(dx2-y2-px) molecular orbital of the Cu-O or Cu-OH bond overlaps with the pz orbital of the hydroxide ion in forming the oxygen-oxygen bond. The two-electron two-centered (2e--2C) bond is observed in the oxygen-oxygen bond formation. In the oxidation process, these ligands stabilize the electron density from the water or hydroxide ion. These redox-active ligands also help stabilize the formed hydrogen peroxide or peroxide complexes.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangaredddy, Telangana 502285, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangaredddy, Telangana 502285, India
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7
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Zhang J, Zhang H, Qin Z, Kang Y, Hong X, Hou T. Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. J Chem Inf Model 2023; 63:1133-1142. [PMID: 36791039 DOI: 10.1021/acs.jcim.2c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Direct trajectory calculations have become increasingly popular in recent computational chemistry investigations. However, the exorbitant computational cost of ab initio trajectory calculations usually limits its application in mechanistic explorations. Recently, machine learning-based potential energy surface (ML-PES) provides a powerful strategy to circumvent the heavy computational cost and meanwhile maintain the required accuracy. Despite the appealing potential, constructing a robust ML-PES is still challenging since the training set of the PES should cover a broad enough configuration space. In this work, we demonstrate that when the concerned properties could be collected by the localized sampling of the configuration space, quasiclassical trajectory (QCT) calculations can be invoked to efficiently obtain locally accurate ML-PESs. We prove our concept with two model reactions: methyl migration of i-pentane cation and dimerization of cyclopentadiene. We found that the locally accurate ML-PESs are sufficiently robust for reproducing the static and dynamic features of the reactions, including the time-resolved free energy and entropy changes, and time gaps.
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Affiliation(s)
- Jintu Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Haotian Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zhixin Qin
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, Zhejiang, China.,Beijing National Laboratory for Molecular Sciences, North First Street No. 2, Zhongguancun, Beijing 100190, China.,Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Laboratory of Computer-aided Design & Computer Graphics, Zhejiang University, Hangzhou 310058, Zhejiang, China
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8
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Fan Y, Xia W, Ma C, Huang Y, Li S, Wang X, Qian C, Chen K, Liu D. Recent advances of computational studies on bioethanol to light olefin reactions using zeolite and metal oxide catalysts. Chem Eng Sci 2023. [DOI: 10.1016/j.ces.2023.118532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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9
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Gorantla KR, Mallik BS. Three-Electron Two-Centered Bond and Single-Electron Transfer Mechanism of Water Splitting via a Copper-Bipyridine Complex. J Phys Chem A 2023; 127:160-168. [PMID: 36594604 DOI: 10.1021/acs.jpca.2c07630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report the atomistic and electronic details of the mechanistic pathway of the oxygen-oxygen bond formation catalyzed by a copper-2,2'-bipyridine complex. Density functional theory-based molecular dynamics simulations and enhanced sampling methods were employed for this study. The thermodynamics and electronic structure of the oxygen-oxygen bond formation are presented in this study by considering the cis-bishydroxo, [CuIII(bpy)(OH)2]+, and cis-(hydroxo)oxo, [CuIV(bpy)(OH)(═O)]+, complexes as active catalysts. In the cis-bishydroxo complex, the hydroxide transfer requires a higher kinetic barrier than the proton transfer process. In the case of [CuIV(bpy)(OH)(═O)]+, the proton transfer requires a higher free energy than the hydroxide one. The peroxide bond formation is thermodynamically favorable for the [CuIV(bpy)(OH)(═O)]+ complex compared with the other. The hydroxide ion is transferred to one of the Cu-OH moieties, and the proton is transferred to the solvent. The free energy barrier for this migration is higher than that for the former transfer. From the analysis of molecular orbitals, it is found that the electron density is primarily present on the water molecules near the active sites in the highest occupied molecular orbital (HOMO) state and lowest unoccupied molecular orbital (LUMO) of the ligands. Natural bond orbital (NBO) analysis reveals the electron transfer process during the oxygen-oxygen bond formation. The σ*Cu(dxz)-O(p) orbitals are involved in the oxygen-oxygen bond formation. During the bond formation, three-electron two-centered (3e--2C) bonds are observed in [CuIII(bpy)(OH)2]+ during the transfer of the hydroxide before the formation of the oxygen-oxygen bond.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy502284, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy502284, Telangana, India
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10
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Gorantla KR, Mallik BS. Non-heme oxoiron complexes as active intermediates in the water oxidation process with hydrogen/oxygen atom transfer reactions. Dalton Trans 2022; 51:11899-11908. [PMID: 35876181 DOI: 10.1039/d2dt01295b] [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
In this study, we explore the water oxidation process with the help of density functional theory. The formation of an oxygen-oxygen bond is crucial in the water oxidation process. Here, we report the formation of the oxygen-oxygen bond by the N5-coordinate oxoiron species with a higher oxidation state of FeIV and FeV. This bond formation is studied through the nucleophilic addition of water molecules and the transfer of the oxygen atom from meta-chloroperbenzoic acid (mCPBA). Our study reveals that the oxygen-oxygen bond formation by reacting mCPBA with FeVO requires less activation barrier (13.7 kcal mol-1) than the other three pathways. This bond formation by the oxygen atom transfer (OAT) pathway is more favorable than that achieved by the hydrogen atom transfer (HAT) pathway. In both cases, the oxygen-oxygen bond formation occurs by interacting the σ*dz2-2pz molecular orbital of the iron-oxo intermediate with the 2px orbital of the oxygen atom. From this study, we understand that the oxygen-oxygen bond formation by FeIVO with the OAT process is also feasible (16 kcal mol-1), suggesting that FeVO may not always be required for the water oxidation process by non-heme N5-oxoiron. After the oxygen-oxygen bond formation, the release of the dioxygen molecule occurs with the addition of the water molecule. The release of dioxygen requires a barrier of 7.0 kcal mol-1. The oxygen-oxygen bond formation is found to be the rate-determining step.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy-502285, Telangana, India.
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy-502285, Telangana, India.
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11
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Gorantla KR, Mallik BS. Mechanistic Insights into Cobalt-Based Water Oxidation Catalysis by DFT-Based Molecular Dynamics Simulations. J Phys Chem A 2022; 126:3301-3310. [PMID: 35593706 DOI: 10.1021/acs.jpca.2c01043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the mechanistic details of the water oxidation process by the complex, [CoII(bpbH2)Cl2], where bpbH2 = N, N'-bis(2'-pyridinecarboxamide)-1,2-benzene. An experimental study reported the complex as the efficient catalyst for the water oxidation process. We performed density functional theory calculations at the M06-L level and first-principles molecular dynamics simulations to study the catalytic nature of the complex. We investigated the energetics of the total catalytic cycle, which combines the oxygen-oxygen bond formation, proton-coupled electron transfer (PCET) steps, and release of oxygen molecule. The formed peroxide and superoxide intermediates in the catalytic cycle were characterized with the help of the Mulliken spin density parameters. Mulliken spin densities of the metal-oxo bond reveal that the triplet state of CoV═O has a double-bond nature, but the quintet state of the complex has a radical nature (CoIV-O•-). In an alternative way, the deprotonation of the amide groups of the ligand is also considered. The deprotonation and formation of higher oxidation metal-oxo intermediates are also possible. In addition to this, we have considered the effect of phosphate buffer on water nucleophilic addition. The oxygen-oxygen bond formation is favorable by the catalyst with the deprotonated form of the ligand, with the addition of water as the nucleophile. In the oxidation process, the C═O bonds of the ligand transfer the electron density to nitrogen atoms, stabilizing the higher order oxo, peroxide, and superoxide bonds. The oxygen-oxygen bond formation is the rate-determining step in the overall water oxidation process. This bond was further investigated using first-principles molecular dynamics at the PBE-D2 level. The dynamics of proton, hydroxide ion, and the nature of the ligand structure on the oxygen-oxygen bond were examined. We find that the oxygen molecule is released from the superoxide complex with the addition of water molecules.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, India
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12
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Ketkaew R, Creazzo F, Luber S. Machine Learning-Assisted Discovery of Hidden States in Expanded Free Energy Space. J Phys Chem Lett 2022; 13:1797-1805. [PMID: 35171614 DOI: 10.1021/acs.jpclett.1c04004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Collective variables (CVs) are crucial parameters in enhanced sampling calculations and strongly impact the quality of the obtained free energy surface. However, many existing CVs are unique to and dependent on the system they are constructed with, making the developed CV non-transferable to other systems. Herein, we develop a non-instructor-led deep autoencoder neural network (DAENN) for discovering general-purpose CVs. The DAENN is used to train a model by learning molecular representations upon unbiased trajectories that contain only the reactant conformers. The prior knowledge of nonconstraint reactants coupled with the here-introduced topology variable and loss-like penalty function are only required to make the biasing method able to expand its configurational (phase) space to unexplored energy basins. Our developed autoencoder is efficient and relatively inexpensive to use in terms of a priori knowledge, enabling one to automatically search for hidden CVs of the reaction of interest.
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Affiliation(s)
- Rangsiman Ketkaew
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabrizio Creazzo
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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13
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Brémond É, Savarese M, Rega N, Ciofini I, Adamo C. Free Energy Profiles of Proton Transfer Reactions: Density Functional Benchmark from Biased Ab Initio Dynamics. J Chem Theory Comput 2022; 18:1501-1511. [PMID: 35129987 DOI: 10.1021/acs.jctc.1c01002] [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
By coupling an enhanced sampling algorithm with an orbital-localized variant of Car-Parrinello molecular dynamics, the so-called atomic centered density matrix propagation model, we reconstruct the free energy profiles along reaction pathways using different density functional approximations (DFAs) ranging from locals to hybrids. In particular, we compare the computed free energy barrier height of proton transfer (PT) reactions to those obtained by a more traditional static approach, based on the intrinsic reaction coordinate (IRC), for two case systems, namely malonaldehyde and formic acid dimer. The obtained results show that both the IRC profiles and the potentials of mean force, derived from biased dynamic trajectories, are very sensitive to the density functional approximation applied. More precisely, we observe that, with the notable exception of M06-L, local density functionals always strongly underestimate the reaction barrier heights. More generally, we find that also the shape of the free energy profile is very sensitive to the density functional choice, thus highlighting the effect, often neglected, that the choice of DFA has also in the case of dynamics simulations.
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Affiliation(s)
- Éric Brémond
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Marika Savarese
- Chimie ParisTech-PSL, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
| | - Nadia Rega
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, via Cintia, I-80126 Napoli, Italy.,Scuola Superiore Meridionale, Largo S. Marcellino 10, I-80138 Napoli, Italy.,Centro Interdipartimentale di Ricerca sui Biomateriali (CRIB), Piazzale Tecchio 80, I-80125, Napoli, Italy
| | - Ilaria Ciofini
- Chimie ParisTech-PSL, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
| | - Carlo Adamo
- Chimie ParisTech-PSL, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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14
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Creazzo F, Luber S. Water-Assisted Chemical Route Towards the Oxygen Evolution Reaction at the Hydrated (110) Ruthenium Oxide Surface: Heterogeneous Catalysis via DFT-MD and Metadynamics Simulations. Chemistry 2021; 27:17024-17037. [PMID: 34486184 PMCID: PMC9293344 DOI: 10.1002/chem.202102356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 11/15/2022]
Abstract
Notwithstanding that RuO2 is a promising catalyst for the oxygen evolution reaction (OER), a plethora of fundamental details on its catalytic properties are still elusive, severely limiting its large-scale deployment. It is also established experimentally that corrosion and wettability of metal oxides can, in fact, enhance the catalytic activity for OER owing to the formation of a hydrated surface layer. However, the mechanistic interplay between surface wettability, interfacial water dynamics and OER across RuO2 , and what degree these processes are correlated are still debated. Herein, spin-polarized Density Functional Theory Molecular Dynamics (DFT-MD) simulations, coupled with advanced enhanced sampling methods in the well-tempered metadynamics framework, are applied to gain a global understanding of RuO2 aqueous interface (explicit water solvent) in catalyzing the OER, and hence possibly help in the design of novel catalysts in the context of photochemical water oxidation. The present study quantitatively assesses the free-energy barriers behind the OER at the (110)-RuO2 catalyst surface revealing plausible pathways composing the reaction network of the O2 evolution. In particular, OER is investigated at room temperature when such a surface is exposed to both gas-phase and liquid-phase water. Albeit a unique efficient pathway has been identified in the gas-phase OER, a surprisingly lowest-free-energy-requiring reaction route is possible when (110)-RuO2 is in contact with explicit liquid water. By estimating the free-energy surfaces associated to these processes, we reveal a noticeable water-assisted OER mechanism which involves a crucial proton-transfer-step assisted by the local water environment. These findings pave the way toward the systematic usage of DFT-MD coupled with metadynamics techniques for the fine assessment of the activity of catalysts, considering finite-temperature and explicit-solvent effects.
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Affiliation(s)
| | - Sandra Luber
- Department of ChemistryUniversity of ZurichZurichSwitzerland
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15
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Ketkaew R, Creazzo F, Luber S. Closer Look at Inverse Electron Demand Diels–Alder and Nucleophilic Addition Reactions on s-Tetrazines Using Enhanced Sampling Methods. Top Catal 2021; 65:1-17. [PMID: 35153451 PMCID: PMC8816378 DOI: 10.1007/s11244-021-01516-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2021] [Indexed: 12/30/2022]
Abstract
Inverse electron demand [4+2] Diels–Alder (iEDDA) reactions as well as unprecedented nucleophilic (azaphilic) additions of R-substituted silyl-enol ethers (where R is Phenyl, Methyl, and Hydrogen) to 1,2,4,5-tetrazine (s-tetrazine) catalyzed by \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {BF}_{3}$$\end{document}BF3 have recently been discovered (Simon et al. in Org Lett 23(7):2426–2430, 2021), where static calculations were employed for calculation of activation energies. In order to have a more realistic dynamic description of these reactions in explicit solution at ambient conditions, in this work we use a semiempirical tight-binding method combined with enhanced sampling techniques to calculate free energy surfaces (FESs) of the iEDDA and azaphilic addition reactions. Relevant products of not only s-tetrazine but also its derivatives such as \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {BF}_{3}$$\end{document}BF3-mediated s-tetrazine adducts are investigated. We reconstruct the FESs of the iEDDA and azaphilic addition reactions using metadynamics and blue moon ensemble, and compare the ability of different collective variables (CVs) including bond distances, Social PeRmutation INvarianT (SPRINT) coordinates, and path-CV to describe the reaction pathway. We find that when a bulky Phenyl is used as a substituent at the dienophile the azaphilic addition is preferred over the iEDDA reaction. In addition, we also investigate the effect of \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {BF}_{3}$$\end{document}BF3 in the diene and steric hindrance in the dienophile on the competition between the iEDDA and azaphilic addition reactions, providing chemical insight for reaction design.
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Affiliation(s)
- Rangsiman Ketkaew
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Fabrizio Creazzo
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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16
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Li Y, Meijer EJ, Liao R. Elucidating the Role of Aqueous Solvent in an Iron‐Based Water Oxidation System by DFT‐based Molecular Simulation. ChemCatChem 2021. [DOI: 10.1002/cctc.202100616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ying‐Ying Li
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical Engineering Huazhong University of Science and Technology Luoyu Road 1037 Wuhan 430074 P. R. China
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam (The Netherlands
| | - Evert Jan Meijer
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam (The Netherlands
| | - Rong‐Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical Engineering Huazhong University of Science and Technology Luoyu Road 1037 Wuhan 430074 P. R. China
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17
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Menzel JP, Kloppenburg M, Belić J, de Groot HJM, Visscher L, Buda F. Efficient workflow for the investigation of the catalytic cycle of water oxidation catalysts: Combining GFN-xTB and density functional theory. J Comput Chem 2021; 42:1885-1894. [PMID: 34278594 PMCID: PMC8456855 DOI: 10.1002/jcc.26721] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/26/2022]
Abstract
Photocatalytic water oxidation remains the bottleneck in many artificial photosynthesis devices. The efficiency of this challenging process is inherently linked to the thermodynamic and electronic properties of the chromophore and the water oxidation catalyst (WOC). Computational investigations can facilitate the search for favorable chromophore‐catalyst combinations. However, this remains a demanding task due to the requirements on the computational method that should be able to correctly describe different spin and oxidation states of the transition metal, the influence of solvation and the different rates of the charge transfer and water oxidation processes. To determine a suitable method with favorable cost/accuracy ratios, the full catalytic cycle of a molecular ruthenium based WOC is investigated using different computational methods, including density functional theory (DFT) with different functionals (GGA, Hybrid, Double Hybrid) as well as the semi‐empirical tight binding approach GFN‐xTB. A workflow with low computational cost is proposed that combines GFN‐xTB and DFT and provides reliable results. GFN‐xTB geometries and frequencies combined with single‐point DFT energies give free energy changes along the catalytic cycle that closely follow the full DFT results and show satisfactory agreement with experiment, while significantly decreasing the computational cost. This workflow allows for cost efficient determination of energetic, thermodynamic and dynamic properties of WOCs.
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Affiliation(s)
- Jan Paul Menzel
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Jelena Belić
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Lucas Visscher
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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18
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Shao Y, de Groot HJM, Buda F. Two-Channel Model for Electron Transfer in a Dye-Catalyst-Dye Supramolecular Complex for Photocatalytic Water Splitting. CHEMSUSCHEM 2021; 14:3155-3162. [PMID: 34097820 PMCID: PMC8453919 DOI: 10.1002/cssc.202100846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/24/2021] [Indexed: 05/04/2023]
Abstract
To improve the performance of dye-sensitized photoelectrochemical cell (DS-PEC) devices for splitting water, the tailoring of the photocatalytic four-photon water oxidation half-reaction represents a principle challenge of fundamental significance. In this study, a Ru-based water oxidation catalyst (WOC) covalently bound to two 2,6-diethoxy-1,4,5,8-diimide-naphthalene (NDI) dye functionalities provides comparable driving forces and channels for electron transfer. Constrained ab initio molecular dynamics simulations are performed to investigate the photocatalytic cycle of this two-channel model for photocatalytic water splitting. The introduction of a second light-harvesting dye in the Ru-based dye-WOC-dye supramolecular complex enables two separate parallel electron-transfer channels, leading to a five-step catalytic cycle with three intermediates and two doubly oxidized states. The total spin S=1 is conserved during the catalytic process and the system with opposite spin on the oxidized NDI proceeds from the Ru=O intermediate to the final Ru-O2 intermediate with a triplet molecular 3 O2 ligand that is eventually released into the environment. The in-depth insight into the proposed photocatalytic cycle of the two-channel model provides a strategy for the development of novel high-efficiency supramolecular complexes for DS-PEC devices with buildup and conservation of spin multiplicity along the reaction coordinate as a design principle.
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Affiliation(s)
- Yang Shao
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
| | - Huub J. M. de Groot
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
| | - Francesco Buda
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeidenThe Netherlands
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19
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Gorantla KR, Mallik BS. Mechanistic Insight into the O 2 Evolution Catalyzed by Copper Complexes with Tetra- and Pentadentate Ligands. J Phys Chem A 2021; 125:6461-6473. [PMID: 34282907 DOI: 10.1021/acs.jpca.1c06008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mononuclear complexes ([(bztpen)Cu] (BF4)2 (bztpen = N-benzyl-N,N',N'-tris (pyridin-2-yl methyl ethylenediamine))) and ([(dbzbpen)Cu(OH2)] (BF4)2 (dbzbpen = N,N'-dibenzyl-N,N'-bis(pyridin-2-ylmethyl) ethylenediamine)) have been reported as water oxidation catalysts in basic medium (pH = 11.5). We explore the O2 evolution process catalyzed by these copper catalysts with various ligands (L) by applying the first-principles molecular dynamics simulations. First, the oxidation of catalysts to the metal-oxo intermediates [LCu(O)]2+ occurs through the proton-coupled electron transfer (PCET) process. These intermediates are involved in the oxygen-oxygen bond formation through the water-nucleophilic addition process. Here, we have considered two types of oxygen-oxygen bond formation. The first one is the transfer of the hydroxide of the water molecule to the Cu═O moiety; the proton transfer to the solvent leads to the formation of the peroxide complex ([LCu(OOH)]+). The other is the formation of the hydrogen peroxide complex ([LCu(HOOH)]2+) by the transfer of proton and hydroxide of the water molecule to the metal-oxo intermediate. The formation of the peroxide complex requires less activation free energy than hydrogen peroxide formation for both catalysts. We found two transition states in the well-tempered metadynamics simulations: one for proton transfer and another for hydroxide transfer. In both cases, the proton transfer requires higher free energy. Following the formation of the oxygen-oxygen bond, we study the release of the dioxygen molecule. The formed peroxide and hydrogen peroxide complexes are converted into the superoxide complex ([LCu(OO)]2+) through the transfer of proton, electron, and PCET processes. The superoxide complex releases an oxygen molecule upon the addition of a water molecule. The free energy of activation for the release of the dioxygen molecule is lesser than that of the oxygen-oxygen bond formation. When we observe the entire water oxidation process, the oxygen-oxygen bond formation is the rate-determining step. We calculated the rates of reaction by using the Eyring equation and found them to be close to the experimental values.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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20
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Gorantla KR, Mallik BS. Mechanism and Dynamics of Formation of Bisoxo Intermediates and O-O Bond in the Catalytic Water Oxidation Process. J Phys Chem A 2021; 125:279-290. [PMID: 33370125 DOI: 10.1021/acs.jpca.0c09943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work elucidates the reactivity of water molecules toward the tridentate nitrogen-containing iron complex in the water oxidation process. Here, we consider the FeV-bisoxo complex {[FeV(Me3tacn)(OH2)(═O)2]+} to be responsible for the oxygen-oxygen bond formation. This O-O bond formation happens through the addition of water as a nucleophile. The transition state was determined by the synchronous transit-guided quasi-Newton method using reactants and products and verified by intrinsic reaction coordinates (IRCs). From the IRC calculations, we observe that the FeV═O moiety is attacked by water and assisted by the H-bonded interaction with the oxygen atom of the bisoxo complex. The hydrogen atom is transferred to the oxygen atom of the bisoxo complex through the transition state, and subsequently, the hydroxide is transferred to another oxygen of the bisoxo complex, resulting in the formation of the oxygen-oxygen bond. This work also explains the effect of explicit water molecules on the oxygen-oxygen bond formation. Our results also show how the formation of superoxide plays an essential role in O2 evolution. We used the potential energy scan method to compute the transition state in the oxygen evolution step. In the present work, we study the effect of chlorine on the formation of the oxygen-oxygen bond formation. In this study, the changes in the oxidation state, spin density, and spin multiplicity of the complexes are investigated for each successive step. Apart from these static theoretical calculations, we also studied the oxygen-oxygen bond formation through first-principles molecular dynamics with the aid of the well-tempered metadynamics sampling technique. From the observation of the free energy surfaces from metadynamics simulations, it is evident that the hydroxide transfer has a lesser free energetic reaction as compared to the proton transfer. This complete mechanistic study may give an idea to design a suitable water oxidation catalyst.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285 Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285 Telangana, India
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21
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Yang, de Groot HJM, Buda F. Tuning the Proton-Coupled Electron-Transfer Rate by Ligand Modification in Catalyst-Dye Supramolecular Complexes for Photocatalytic Water Splitting. CHEMSUSCHEM 2021; 14:479-486. [PMID: 32871047 PMCID: PMC7821158 DOI: 10.1002/cssc.202001863] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/31/2020] [Indexed: 05/21/2023]
Abstract
In view of the considerably high activation energy barrier of the O-O bond formation photocatalytic step in water oxidation, it is essential to understand if and how nonadiabatic factors can accelerate the proton-coupled electron transfer (PCET) rate in this process to find rational design strategies facilitating this step. Herein, constrained ab initio molecular dynamics simulations are performed to investigate this rate-limiting step in a series of catalyst-dye supramolecular complexes functionalized with different alkyl groups on the catalyst component. These structural modifications lead to tunable thermodynamic driving forces, PCET rates, and vibronic coupling with specific resonant torsional modes. These results reveal that such resonant coupling between electronic and nuclear motions contributes to crossing catalytic barriers in PCET reactions by enabling semiclassical coherent conversion of a reactant into a product. Our results provide insight on how to engineer efficient catalyst-dye supramolecular complexes by functionalization with steric substituents for high-performance dye-sensitized photoelectrochemical cells.
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Affiliation(s)
- Yang
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeiden (TheNetherlands
| | - Huub J. M. de Groot
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeiden (TheNetherlands
| | - Francesco Buda
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552300 RALeiden (TheNetherlands
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22
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Collinge G, Yuk SF, Nguyen MT, Lee MS, Glezakou VA, Rousseau R. Effect of Collective Dynamics and Anharmonicity on Entropy in Heterogenous Catalysis: Building the Case for Advanced Molecular Simulations. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01501] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Greg Collinge
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Simuck F. Yuk
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Manh-Thuong Nguyen
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mal-Soon Lee
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vassiliki-Alexandra Glezakou
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Roger Rousseau
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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23
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Schilling M, Cunha RA, Luber S. Enhanced Ab Initio Molecular Dynamics Exploration Unveils the Complex Role of Different Intramolecular Bases on the Water Nucleophilic Attack Mechanism. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mauro Schilling
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Richard A. Cunha
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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