1
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Haro Mares NB, Döller SC, Wissel T, Hoffmann M, Vogel M, Buntkowsky G. Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry. Molecules 2024; 29:1669. [PMID: 38611950 PMCID: PMC11013127 DOI: 10.3390/molecules29071669] [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: 02/29/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores.
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Affiliation(s)
- Nadia B. Haro Mares
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Sonja C. Döller
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Till Wissel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Markus Hoffmann
- Department of Chemistry and Biochemistry, State University of New York at Brockport, Brockport, NY 14420, USA
| | - Michael Vogel
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, D-64289 Darmstadt, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
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2
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Frömbgen T, Drysch K, Zaby P, Dölz J, Ingenmey J, Kirchner B. Quantum Cluster Equilibrium Theory for Multicomponent Liquids. J Chem Theory Comput 2024; 20:1838-1846. [PMID: 38372002 DOI: 10.1021/acs.jctc.3c00799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
In this work, we present a new theory to treat multicomponent liquids based on quantum-chemically calculated clusters. The starting point is the binary quantum cluster equilibrium theory, which is able to treat binary systems. The theory provides one equation with two unknowns. In order to obtain another linearly independent equation, the conservation of mass is used. However, increasing the number of components leads to more unknowns, and this requires linearly independent equations. We address this challenge by introducing a generalization of the conservation of arbitrary quantities accompanied by a comprehensive mathematical proof. Furthermore, a case study for the application of the new theory to ternary mixtures of chloroform, methanol, and water is presented. Calculated enthalpies of vaporization for the whole composition range are given, and the populations or weights of the different clusters are visualized.
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Affiliation(s)
- Tom Frömbgen
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4 + 6, Bonn D-53115, Germany
- Max-Planck-Institut Für Chemische Energiekonversion, Stiftstrasse 34-36, Mülheim an der Ruhr D-45470, Germany
| | - Katrin Drysch
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4 + 6, Bonn D-53115, Germany
| | - Paul Zaby
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4 + 6, Bonn D-53115, Germany
| | - Jürgen Dölz
- Institute for Numerical Simulation, University of Bonn, Friedrich-Hirzebruch-Allee 7, Bonn D-53115, Germany
| | - Johannes Ingenmey
- CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, Sorbonne Université, Paris F-75005, France
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4 + 6, Bonn D-53115, Germany
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3
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Chu ZQ, Zhu RY, Su J. Dynamic dissolution of Cm 3+ ions incorporated at the calcite-water interface: an ab initio molecular dynamics simulation study. Phys Chem Chem Phys 2024; 26:7545-7553. [PMID: 38357997 DOI: 10.1039/d3cp05611b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The stability of actinide-mineral solid solution in a water environment is critical for assessing the safety of nuclear-waste geological repositories and studying actinide migration in natural systems. However, the dissolution behavior of actinide ions incorporated at the mineral-water interface is still unclear at the atomic level. Herein, we present metadynamics simulations of the reaction pathways, thermodynamics and kinetics of trivalent curium ions (Cm3+) dissolving from calcite surfaces. Cm3+ ions incorporated in different calcite surfaces (i.e., terrace and stepped surfaces) with distinct coordination environments have different reaction pathways, free energy barriers and free energy changes. We found that Cm dissolution from a stepped surface is more favorable than that from a terrace surface, both thermodynamically and kinetically. In addition, water molecules seem to promote the detachment of curium ions from the surface by exerting a pulling force via water coordination with Cm3+ and a pushing force via proton migration to the surface layer and water diffusion in the vacant Cm site. Thus, the findings from this work prove to be a milestone in revealing the dynamic dissolution mechanism of trivalent actinides from minerals and would also help predict the dissolution behaviors of other metal ions at the solid-water interface in chemical and environmental sciences.
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Affiliation(s)
- Zhao-Qin Chu
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Ru-Yu Zhu
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Jing Su
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
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4
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Alizadeh Sahraei A, Azizi D, Mokarizadeh AH, Boffito DC, Larachi F. Emerging Trends of Computational Chemistry and Molecular Modeling in Froth Flotation: A Review. ACS ENGINEERING AU 2023; 3:128-164. [PMID: 37362006 PMCID: PMC10288516 DOI: 10.1021/acsengineeringau.2c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 06/28/2023]
Abstract
Froth flotation is the most versatile process in mineral beneficiation, extensively used to concentrate a wide range of minerals. This process comprises mixtures of more or less liberated minerals, water, air, and various chemical reagents, involving a series of intermingled multiphase physical and chemical phenomena in the aqueous environment. Today's main challenge facing the froth flotation process is to gain atomic-level insights into the properties of its inherent phenomena governing the process performance. While it is often challenging to determine these phenomena via trial-and-error experimentations, molecular modeling approaches not only elicit a deeper understanding of froth flotation but can also assist experimental studies in saving time and budget. Thanks to the rapid development of computer science and advances in high-performance computing (HPC) infrastructures, theoretical/computational chemistry has now matured enough to successfully and gainfully apply to tackle the challenges of complex systems. In mineral processing, however, advanced applications of computational chemistry are increasingly gaining ground and demonstrating merit in addressing these challenges. Accordingly, this contribution aims to encourage mineral scientists, especially those interested in rational reagent design, to become familiarized with the necessary concepts of molecular modeling and to apply similar strategies when studying and tailoring properties at the molecular level. This review also strives to deliver the state-of-the-art integration and application of molecular modeling in froth flotation studies to assist either active researchers in this field to disclose new directions for future research or newcomers to the field to initiate innovative works.
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Affiliation(s)
- Abolfazl Alizadeh Sahraei
- Department
of Chemical Engineering, Université
Laval, 1065 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
| | - Dariush Azizi
- Department
of Chemical Engineering, École Polytechnique
de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal H3T 1J4, Canada
| | - Abdol Hadi Mokarizadeh
- School
of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325, United States
| | - Daria Camilla Boffito
- Department
of Chemical Engineering, École Polytechnique
de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal H3T 1J4, Canada
| | - Faïçal Larachi
- Department
of Chemical Engineering, Université
Laval, 1065 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
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5
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Medvedev N, Voronkov R, Volkov AE. Metallic water: Transient state under ultrafast electronic excitation. J Chem Phys 2023; 158:074501. [PMID: 36813717 DOI: 10.1063/5.0139802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The modern means of controlled irradiation by femtosecond lasers or swift heavy ion beams can transiently produce such energy densities in samples that reach collective electronic excitation levels of the warm dense matter state, where the potential energy of interaction of the particles is comparable to their kinetic energies (temperatures of a few eV). Such massive electronic excitation severely alters the interatomic potentials, producing unusual nonequilibrium states of matter and different chemistry. We employ density functional theory and tight binding molecular dynamics formalisms to study the response of bulk water to ultrafast excitation of its electrons. After a certain threshold electronic temperature, the water becomes electronically conducting via the collapse of its bandgap. At high doses, it is accompanied by nonthermal acceleration of ions to a temperature of a few thousand Kelvins within sub-100 fs timescales. We identify the interplay of this nonthermal mechanism with the electron-ion coupling, enhancing the electron-to-ions energy transfer. Various chemically active fragments are formed from the disintegrating water molecules, depending on the deposited dose.
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Affiliation(s)
- Nikita Medvedev
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Prague 8, Czech Republic
| | - Roman Voronkov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Leninskij pr., 53, 119991 Moscow, Russia
| | - Alexander E Volkov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Leninskij pr., 53, 119991 Moscow, Russia
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6
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Kraka E, Quintano M, La Force HW, Antonio JJ, Freindorf M. The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena. J Phys Chem A 2022; 126:8781-8798. [DOI: 10.1021/acs.jpca.2c05962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Hunter W. La Force
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Juliana J. Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
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7
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Gijón A, Hernández ER. Quantum simulations of neutral water clusters and singly-charged water cluster anions. Phys Chem Chem Phys 2022; 24:14440-14451. [PMID: 35662295 DOI: 10.1039/d2cp01088g] [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 report a computational study of the structural and energetic properties of water clusters and singly-charged water cluster anions containing from 20 to 573 water molecules. We have used both a classical and a quantum description of the molecular degrees of freedom. Water intra and inter-molecular interactions have been modelled through the SPC/F model, while the water-excess electron interaction has been described via the well-known Turi-Borgis potential. We find that in general the quantum effects of the water degrees of freedom are small, but they do influence the cluster-size at which the excess electron stabilises inside the cluster, which occurs at smaller cluster sizes when quantum effects are taken into consideration.
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Affiliation(s)
- A Gijón
- Instituto de Ciencia de Materiales de Madrid (ICMM-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| | - E R Hernández
- Instituto de Ciencia de Materiales de Madrid (ICMM-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
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8
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Yang Y, Peltier CR, Zeng R, Schimmenti R, Li Q, Huang X, Yan Z, Potsi G, Selhorst R, Lu X, Xu W, Tader M, Soudackov AV, Zhang H, Krumov M, Murray E, Xu P, Hitt J, Xu L, Ko HY, Ernst BG, Bundschu C, Luo A, Markovich D, Hu M, He C, Wang H, Fang J, DiStasio RA, Kourkoutis LF, Singer A, Noonan KJT, Xiao L, Zhuang L, Pivovar BS, Zelenay P, Herrero E, Feliu JM, Suntivich J, Giannelis EP, Hammes-Schiffer S, Arias T, Mavrikakis M, Mallouk TE, Brock JD, Muller DA, DiSalvo FJ, Coates GW, Abruña HD. Electrocatalysis in Alkaline Media and Alkaline Membrane-Based Energy Technologies. Chem Rev 2022; 122:6117-6321. [PMID: 35133808 DOI: 10.1021/acs.chemrev.1c00331] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen energy-based electrochemical energy conversion technologies offer the promise of enabling a transition of the global energy landscape from fossil fuels to renewable energy. Here, we present a comprehensive review of the fundamentals of electrocatalysis in alkaline media and applications in alkaline-based energy technologies, particularly alkaline fuel cells and water electrolyzers. Anion exchange (alkaline) membrane fuel cells (AEMFCs) enable the use of nonprecious electrocatalysts for the sluggish oxygen reduction reaction (ORR), relative to proton exchange membrane fuel cells (PEMFCs), which require Pt-based electrocatalysts. However, the hydrogen oxidation reaction (HOR) kinetics is significantly slower in alkaline media than in acidic media. Understanding these phenomena requires applying theoretical and experimental methods to unravel molecular-level thermodynamics and kinetics of hydrogen and oxygen electrocatalysis and, particularly, the proton-coupled electron transfer (PCET) process that takes place in a proton-deficient alkaline media. Extensive electrochemical and spectroscopic studies, on single-crystal Pt and metal oxides, have contributed to the development of activity descriptors, as well as the identification of the nature of active sites, and the rate-determining steps of the HOR and ORR. Among these, the structure and reactivity of interfacial water serve as key potential and pH-dependent kinetic factors that are helping elucidate the origins of the HOR and ORR activity differences in acids and bases. Additionally, deliberately modulating and controlling catalyst-support interactions have provided valuable insights for enhancing catalyst accessibility and durability during operation. The design and synthesis of highly conductive and durable alkaline membranes/ionomers have enabled AEMFCs to reach initial performance metrics equal to or higher than those of PEMFCs. We emphasize the importance of using membrane electrode assemblies (MEAs) to integrate the often separately pursued/optimized electrocatalyst/support and membranes/ionomer components. Operando/in situ methods, at multiscales, and ab initio simulations provide a mechanistic understanding of electron, ion, and mass transport at catalyst/ionomer/membrane interfaces and the necessary guidance to achieve fuel cell operation in air over thousands of hours. We hope that this Review will serve as a roadmap for advancing the scientific understanding of the fundamental factors governing electrochemical energy conversion in alkaline media with the ultimate goal of achieving ultralow Pt or precious-metal-free high-performance and durable alkaline fuel cells and related technologies.
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Affiliation(s)
- Yao Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Cheyenne R Peltier
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Rui Zeng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Roberto Schimmenti
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Qihao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xin Huang
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Zhifei Yan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Georgia Potsi
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Ryan Selhorst
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xinyao Lu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Weixuan Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Mariel Tader
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Alexander V Soudackov
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Hanguang Zhang
- Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Mihail Krumov
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ellen Murray
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Pengtao Xu
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy Hitt
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Linxi Xu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Hsin-Yu Ko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Colin Bundschu
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Aileen Luo
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Danielle Markovich
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Meixue Hu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Cheng He
- Chemical and Materials Science Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Hongsen Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jiye Fang
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Lena F Kourkoutis
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Andrej Singer
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Kevin J T Noonan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Li Xiao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Lin Zhuang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Bryan S Pivovar
- Chemical and Materials Science Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Piotr Zelenay
- Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Enrique Herrero
- Instituto de Electroquímica, Universidad de Alicante, Alicante E-03080, Spain
| | - Juan M Feliu
- Instituto de Electroquímica, Universidad de Alicante, Alicante E-03080, Spain
| | - Jin Suntivich
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Emmanuel P Giannelis
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | | | - Tomás Arias
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Manos Mavrikakis
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas E Mallouk
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Joel D Brock
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - David A Muller
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Francis J DiSalvo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Geoffrey W Coates
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Héctor D Abruña
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Center for Alkaline Based Energy Solutions (CABES), Cornell University, Ithaca, New York 14853, United States
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9
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Zhao X, Liu B, Li J, Nan J. Ab initio molecular dynamics simulations on the adsorption of 1-hydroxyethane-1,1-diphosphonic acid on the iron (100) surface. NEW J CHEM 2022. [DOI: 10.1039/d2nj00668e] [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
Through IRI, Bader charges and ELF analysis, an electrostatic interaction network exists between HEDP and the iron (100) surface, which is responsible for the stability of the adsorption state.
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Affiliation(s)
- Xiaoyang Zhao
- School of Geomatic and Environmental Engineering, Henan Polytechnic Institute, Nanyang 473000, P. R. China
| | - Bin Liu
- School of Electronic and Information Engineering, Henan Polytechnic Institute, Nanyang 473000, P. R. China
| | - Jianhua Li
- School of Geomatic and Environmental Engineering, Henan Polytechnic Institute, Nanyang 473000, P. R. China
| | - Junmin Nan
- School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China
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10
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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: 1] [Impact Index Per Article: 0.3] [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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11
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Abstract
Given the importance of catalysts in the chemical industry, they have been extensively investigated by experimental and numerical methods. With the development of computational algorithms and computer hardware, large-scale simulations have enabled influential studies with more atomic details reflecting microscopic mechanisms. This review provides a comprehensive summary of recent developments in molecular dynamics, including ab initio molecular dynamics and reaction force-field molecular dynamics. Recent research on both approaches to catalyst calculations is reviewed, including growth, dehydrogenation, hydrogenation, oxidation reactions, bias, and recombination of carbon materials that can guide catalyst calculations. Machine learning has attracted increasing interest in recent years, and its combination with the field of catalysts has inspired promising development approaches. Its applications in machine learning potential, catalyst design, performance prediction, structure optimization, and classification have been summarized in detail. This review hopes to shed light and perspective on ML approaches in catalysts.
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Zheng D, Wang F. Performing Molecular Dynamics Simulations and Computing Hydration Free Energies on the B3LYP-D3(BJ) Potential Energy Surface with Adaptive Force Matching: A Benchmark Study with Seven Alcohols and One Amine. ACS PHYSICAL CHEMISTRY AU 2021; 1:14-24. [PMID: 34939071 PMCID: PMC8679650 DOI: 10.1021/acsphyschemau.1c00006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Indexed: 12/13/2022]
Abstract
The potential energy surfaces at the B3LYP-D3(BJ) level for eight solutes in dilute aqueous solutions were mapped into simple pairwise additive force field expressions using the adaptive force matching (AFM) method. The quality of the fits was validated by computing the hydration free energy (HFE), enthalpy of hydration, and diffusion constant for each solute. By force matching B3LYP-D3(BJ), the predictions from the models agree with the closest experimental HFE and enthalpy of hydration within chemical accuracy. The diffusion constants from the models are also in good agreement with experimental references. The good agreement provides confidence on the quality of B3LYP-D3(BJ) in producing potential energy surfaces for thermodynamic property calculations through AFM for the molecules studied. Accurate computational predictions could potentially provide validations to experimental measurements in cases where experimental measurements from different sources do not agree.
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Fedorov DA, Otten MJ, Gray SK, Alexeev Y. Ab initio molecular dynamics on quantum computers. J Chem Phys 2021; 154:164103. [PMID: 33940828 DOI: 10.1063/5.0046930] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, we present an approach to running AIMD simulations on noisy intermediate-scale quantum (NISQ)-era quantum computers. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. Algorithms for computation of analytical gradients entirely on a quantum computer require quantum fault-tolerant hardware, which is beyond NISQ-era. Therefore, we compute the energy gradients numerically using finite differences, the Hellmann-Feynman theorem, and a correlated sampling technique. This method only requires additional classical calculations of electron integrals for each degree of freedom without any additional computations on a quantum computer beyond the initial VQE run. As a proof of concept, AIMD simulations are demonstrated for the H2 molecule on IBM quantum devices. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular systems.
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Affiliation(s)
- Dmitry A Fedorov
- Oak Ridge Associated Universities, 100 Orau Way, Oak Ridge, Tennessee 37830, USA
| | - Matthew J Otten
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Stephen K Gray
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Yuri Alexeev
- Computational Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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Mazurek AH, Szeleszczuk Ł, Pisklak DM. A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations. Int J Mol Sci 2021; 22:4378. [PMID: 33922192 PMCID: PMC8122754 DOI: 10.3390/ijms22094378] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/17/2021] [Accepted: 04/20/2021] [Indexed: 01/19/2023] Open
Abstract
This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.
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Affiliation(s)
- Anna Helena Mazurek
- Department of Physical Chemistry, Chair and Department of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Doctoral School, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland;
| | - Łukasz Szeleszczuk
- Department of Physical Chemistry, Chair and Department of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland;
| | - Dariusz Maciej Pisklak
- Department of Physical Chemistry, Chair and Department of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland;
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15
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Jindal A, Vasudevan S. Molecular Conformation and Hydrogen Bond Formation in Liquid Ethylene Glycol. J Phys Chem B 2020; 124:9136-9143. [PMID: 32945675 DOI: 10.1021/acs.jpcb.0c06324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ethylene glycol (EG) molecule, HOCH2CH2OH, adopts a conformation where the central OCCO dihedral is exclusively gauche in the gaseous and crystalline states, but in the liquid state, for close to 20% of the molecules, the central OCCO adopts the energetically unfavorable trans conformation. Here we report calculations, based on ab initio molecular dynamics simulations, on the thermodynamics associated with hydrogen bond formation in the liquid state of EG between donor-acceptor pairs with different molecular conformations. We establish an operational, geometric definition of hydrogen bonds in liquid EG from an analysis of the proton NMR data and show that the key feature, irrespective of the conformation, is marked directionality with almost linear ∠HO···O angles. The free energy for hydrogen bond formation estimated as the potential of mean force for the reversible work associated with the passage from a hypothetical state where hydrogen bonding is absent and donor-acceptor pairs are randomly oriented to the hydrogen-bonded state where the pairs are oriented showed comparable magnitudes irrespective of the molecular conformation of either the donor or acceptor. The results suggest that the presence of the trans conformer in liquid EG would require an understanding of its role in the extended hydrogen-bonded network of the liquid.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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Cheeseman S, Christofferson AJ, Kariuki R, Cozzolino D, Daeneke T, Crawford RJ, Truong VK, Chapman J, Elbourne A. Antimicrobial Metal Nanomaterials: From Passive to Stimuli-Activated Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902913. [PMID: 32440470 PMCID: PMC7237851 DOI: 10.1002/advs.201902913] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/23/2020] [Accepted: 02/22/2020] [Indexed: 05/20/2023]
Abstract
The development of antimicrobial drug resistance among pathogenic bacteria and fungi is one of the most significant health issues of the 21st century. Recently, advances in nanotechnology have led to the development of nanomaterials, particularly metals that exhibit antimicrobial properties. These metal nanomaterials have emerged as promising alternatives to traditional antimicrobial therapies. In this review, a broad overview of metal nanomaterials, their synthesis, properties, and interactions with pathogenic micro-organisms is first provided. Secondly, the range of nanomaterials that demonstrate passive antimicrobial properties are outlined and in-depth analysis and comparison of stimuli-responsive antimicrobial nanomaterials are provided, which represent the next generation of microbiocidal nanomaterials. The stimulus applied to activate such nanomaterials includes light (including photocatalytic and photothermal) and magnetic fields, which can induce magnetic hyperthermia and kinetically driven magnetic activation. Broadly, this review aims to summarize the currently available research and provide future scope for the development of metal nanomaterial-based antimicrobial technologies, particularly those that can be activated through externally applied stimuli.
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Affiliation(s)
- Samuel Cheeseman
- School of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
- Nanobiotechnology LaboratorySchool of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
| | - Andrew J. Christofferson
- School of EngineeringRMIT UniversityMelbourneVIC3001Australia
- Food Science and TechnologyBundoora CampusSchool of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3086Australia
| | - Rashad Kariuki
- School of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
- Nanobiotechnology LaboratorySchool of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
| | - Daniel Cozzolino
- School of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
- Food Science and TechnologyBundoora CampusSchool of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3086Australia
| | - Torben Daeneke
- School of EngineeringRMIT UniversityMelbourneVIC3001Australia
| | - Russell J. Crawford
- School of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
- Nanobiotechnology LaboratorySchool of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
| | - Vi Khanh Truong
- School of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
- Nanobiotechnology LaboratorySchool of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
| | - James Chapman
- School of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
- Nanobiotechnology LaboratorySchool of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
| | - Aaron Elbourne
- School of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
- Nanobiotechnology LaboratorySchool of ScienceCollege of ScienceEngineering and HealthRMIT UniversityMelbourneVIC3001Australia
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Onawole AT, Hussein IA, Ahmed ME, Saad MA, Aparicio S. Ab Initio molecular dynamics of the dissolution of oilfield pyrite scale using borax. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112500] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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