1
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Chaquin P, Fuster F, Markovits A. How the addition of atomic hydrogen to a multiple bond can be catalyzed by water molecules. J Comput Chem 2024; 45:2325-2332. [PMID: 38887140 DOI: 10.1002/jcc.27447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/15/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024]
Abstract
Observational data show complex organic molecules in the interstellar medium (ISM). Hydrogenation of small unsaturated carbon double bond could be one way for molecular complexification. It is important to understand how such reactivity occurs in the very cold and low-pressure ISM. Yet, there is water ice in the ISM, either as grain or as mantle around grains. Therefore, the addition of atomic hydrogen on double-bonded carbon in a series of seven molecules have been studied and it was found that water catalyzes this reaction. The origin of the catalysis is a weak charge transfer between the π MO of the unsaturated molecule and H atom, allowing a stabilizing interaction with H2O. This mechanism is rationalized using the non-covalent interaction and the quantum theory of atoms in molecules approaches.
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Affiliation(s)
- Patrick Chaquin
- Laboratoire de Chimie Théorique, Sorbonne Université, Paris, France
| | - Franck Fuster
- Laboratoire de Chimie Théorique, Sorbonne Université, Paris, France
| | - Alexis Markovits
- Laboratoire de Chimie Théorique, Sorbonne Université, Paris, France
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2
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Villavicencio N, Groves MN. Tuning Reinforcement Learning Parameters for Cluster Selection to Enhance Evolutionary Algorithms. ACS ENGINEERING AU 2024; 4:381-393. [PMID: 39185391 PMCID: PMC11342372 DOI: 10.1021/acsengineeringau.3c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 08/27/2024]
Abstract
The ability to find optimal molecular structures with desired properties is a popular challenge, with applications in areas such as drug discovery. Genetic algorithms are a common approach to global minima molecular searches due to their ability to search large regions of the energy landscape and decrease computational time via parallelization. In order to decrease the amount of unstable intermediate structures being produced and increase the overall efficiency of an evolutionary algorithm, clustering was introduced in multiple instances. However, there is little literature detailing the effects of differentiating the selection frequencies between clusters. In order to find a balance between exploration and exploitation in our genetic algorithm, we propose a system of clustering the starting population and choosing clusters for an evolutionary algorithm run via a dynamic probability that is dependent on the fitness of molecules generated by each cluster. We define four parameters, MFavOvrAll-A, MFavClus-B, NoNewFavClus-C, and Select-D, that correspond to a reward for producing the best structure overall, a reward for producing the best structure in its own cluster, a penalty for not producing the best structure, and a penalty based on the selection ratio of the cluster, respectively. A reward increases the probability of a cluster's future selection, while a penalty decreases it. In order to optimize these four parameters, we used a Gaussian distribution to approximate the evolutionary algorithm performance of each cluster and performed a grid search for different parameter combinations. Results show parameter MFavOvrAll-A (rewarding clusters for producing the best structure overall) and parameter Select-D (appearance penalty) have a significantly larger effect than parameters MFavClus-B and NoNewFavClus-C. In order to produce the most successful models, a balance between MFavOvrAll-A and Select-D must be made that reflects the exploitation vs exploration trade-off often seen in reinforcement learning algorithms. Results show that our reinforcement-learning-based method for selecting clusters outperforms an unclustered evolutionary algorithm for quinoline-like structure searches.
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Affiliation(s)
- Nathan Villavicencio
- Department
of Mathematics, California State University
Fullerton, Fullerton, California 92834, United States
| | - Michael N. Groves
- Department
of Chemistry and Biochemistry, California
State University Fullerton, Fullerton, California 92834, United States
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3
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Rojas-González FE, Castillo-Quevedo C, Rodríguez-Kessler PL, Jimenez-Halla JOC, Vásquez-Espinal A, Eithiraj RD, Cortez-Valadez M, Cabellos JL. Exploration of Free Energy Surface of the Au 10 Nanocluster at Finite Temperature. Molecules 2024; 29:3374. [PMID: 39064952 PMCID: PMC11279810 DOI: 10.3390/molecules29143374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The first step in comprehending the properties of Au10 clusters is understanding the lowest energy structure at low and high temperatures. Functional materials operate at finite temperatures; however, energy computations employing density functional theory (DFT) methodology are typically carried out at zero temperature, leaving many properties unexplored. This study explored the potential and free energy surface of the neutral Au10 nanocluster at a finite temperature, employing a genetic algorithm coupled with DFT and nanothermodynamics. Furthermore, we computed the thermal population and infrared Boltzmann spectrum at a finite temperature and compared it with the validated experimental data. Moreover, we performed the chemical bonding analysis using the quantum theory of atoms in molecules (QTAIM) approach and the adaptive natural density partitioning method (AdNDP) to shed light on the bonding of Au atoms in the low-energy structures. In the calculations, we take into consideration the relativistic effects through the zero-order regular approximation (ZORA), the dispersion through Grimme's dispersion with Becke-Johnson damping (D3BJ), and we employed nanothermodynamics to consider temperature contributions. Small Au clusters prefer the planar shape, and the transition from 2D to 3D could take place at atomic clusters consisting of ten atoms, which could be affected by temperature, relativistic effects, and dispersion. We analyzed the energetic ordering of structures calculated using DFT with ZORA and single-point energy calculation employing the DLPNO-CCSD(T) methodology. Our findings indicate that the planar lowest energy structure computed with DFT is not the lowest energy structure computed at the DLPN0-CCSD(T) level of theory. The computed thermal population indicates that the 2D elongated hexagon configuration strongly dominates at a temperature range of 50-800 K. Based on the thermal population, at a temperature of 100 K, the computed IR Boltzmann spectrum agrees with the experimental IR spectrum. The chemical bonding analysis on the lowest energy structure indicates that the cluster bond is due only to the electrons of the 6 s orbital, and the Au d orbitals do not participate in the bonding of this system.
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Affiliation(s)
| | - César Castillo-Quevedo
- Departamento de Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, Carretera Federal No. 23, km. 191, Colotlán 46200, Jalisco, Mexico;
| | | | - José Oscar Carlos Jimenez-Halla
- Departamento de Química, División de Ciencias Exactas y Naturales, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Guanajuato, Mexico;
| | - Alejandro Vásquez-Espinal
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat. Casilla 121, Iquique 1100000, Chile;
| | | | - Manuel Cortez-Valadez
- CONAHCYT-Departamento de Investigación en Física, Universidad de Sonora, Apdo. Postal 5-88, Hermosillo 83190, Sonora, Mexico;
| | - José Luis Cabellos
- Coordinación de Investigación y Desarrollo Tecnológico, Universidad Politécnica de Tapachula, Carretera Tapachula a Puerto Madero km. 24, Tapachula 30830, Chiapas, Mexico
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4
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Long H, Larson C, Coms F, Pivovar B, Dahlke G, Yandrasits M. Role of H 3O· Radical in the Degradation of Fuel Cell Proton-Exchange Membranes. ACS PHYSICAL CHEMISTRY AU 2022; 2:527-534. [PMID: 36855605 PMCID: PMC9955370 DOI: 10.1021/acsphyschemau.2c00037] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Membrane durability in proton-exchange membrane fuel cells (PEMFCs) is one of the major obstacles limiting its applications, especially in heavy-duty vehicles. Membrane degradation reactions are thought to be attacks by radicals such as hydroxyl (HO•) or hydrogen atom (H•) generated during fuel cell operation. For the H• case, computational modeling results have suggested that the reaction between H• and the sulfonic group should be the dominant degradation pathway. However, experimental work implies that the tertiary fluorine (t-F) attack is the dominant H• reaction pathway, apparently contradicting the theoretical prediction. Based on previous experimental evidence on isotopic substitution, we postulate that the hydronium radical (H3O•) might be present in PEMFCs. Our ab initio modeling indicates that this radical can be stabilized by the sulfonic anion on the polymer side chain. With the assistance of explicit water, the polymer side chain can undergo a conformational change, leading to a greatly reduced barrier for the t-F degradation reaction. Thus, our H3O• hypothesis is able to explain not only the previous isotopic substitution experiment but also why the t-F degradation reaction is a highly plausible H• degradation mechanism for proton-exchange membranes. To our knowledge, this is the first suggestion that H3O• radicals could be present in electrochemical devices with both experimental and theoretical support.
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Affiliation(s)
- Hai Long
- Computational
Science Center, National Renewable Energy
Laboratory, 15013 Denver West Parkway, Golden, Colorado80401, United
States,
| | - Clara Larson
- Computational
Science Center, National Renewable Energy
Laboratory, 15013 Denver West Parkway, Golden, Colorado80401, United
States
| | - Frank Coms
- Global
Fuel Cell Business, General Motors Company, 850 N Glenwood Avenue, Pontiac, Michigan48340, United States
| | - Bryan Pivovar
- Chemical
and Materials Science Center, National Renewable
Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado80401, United
States
| | - Gregg Dahlke
- 3M
Advanced Materials Division Laboratory, 3M Center, Saint Paul, Minnesota55144-1000, United States
| | - Michael Yandrasits
- 3M
Corporate Research Materials Laboratory, 3M Center, Saint Paul, Minnesota55144-1000, United States
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5
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Barlow JM, Clarke LE, Zhang Z, Bím D, Ripley KM, Zito A, Brushett FR, Alexandrova AN, Yang JY. Molecular design of redox carriers for electrochemical CO 2 capture and concentration. Chem Soc Rev 2022; 51:8415-8433. [PMID: 36128984 DOI: 10.1039/d2cs00367h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Developing improved methods for CO2 capture and concentration (CCC) is essential to mitigating the impact of our current emissions and can lead to carbon net negative technologies. Electrochemical approaches for CCC can achieve much higher theoretical efficiencies compared to the thermal methods that have been more commonly pursued. The use of redox carriers, or molecular species that can bind and release CO2 depending on their oxidation state, is an increasingly popular approach as carrier properties can be tailored for different applications. The key requirements for stable and efficient redox carriers are discussed in the context of chemical scaling relationships and operational conditions. Computational and experimental approaches towards developing redox carriers with optimal properties are also described.
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Affiliation(s)
- Jeffrey M Barlow
- Department of Chemistry, University of California, Irvine, California 92697, USA.
| | - Lauren E Clarke
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Zisheng Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
| | - Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
| | - Katelyn M Ripley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Alessandra Zito
- Department of Chemistry, University of California, Irvine, California 92697, USA.
| | - Fikile R Brushett
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
| | - Jenny Y Yang
- Department of Chemistry, University of California, Irvine, California 92697, USA.
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6
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Lavroff RH, Morgan HWT, Zhang Z, Poths P, Alexandrova AN. Ensemble representation of catalytic interfaces: soloists, orchestras, and everything in-between. Chem Sci 2022; 13:8003-8016. [PMID: 35919426 PMCID: PMC9278157 DOI: 10.1039/d2sc01367c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022] Open
Abstract
Catalytic systems are complex and dynamic, exploring vast chemical spaces on multiple timescales. In this perspective, we discuss the dynamic behavior of fluxional, heterogeneous thermal and electrocatalysts and the ensembles of many isomers which govern their behavior. We develop a new paradigm in catalysis theory in which highly fluxional systems, namely sub-nano clusters, isomerize on a much shorter timescale than that of the catalyzed reaction, so macroscopic properties arise from the thermal ensemble of isomers, not just the ground state. Accurate chemical predictions can only be reached through a many-structure picture of the catalyst, and we explain the breakdown of conventional methods such as linear scaling relations and size-selected prevention of sintering. We capitalize on the forward-looking discussion of the means of controlling the size of these dynamic ensembles. This control, such that the most effective or selective isomers can dominate the system, is essential for the fluxional catalyst to be practicable, and their targeted synthesis to be possible. It will also provide a fundamental lever of catalyst design. Finally, we discuss computational tools and experimental methods for probing ensembles and the role of specific isomers. We hope that catalyst optimization using chemically informed descriptors of ensemble nature and size will become a new norm in the field of catalysis and have broad impacts in sustainable energy, efficient chemical production, and more.
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Affiliation(s)
- Robert H Lavroff
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles California 90095-1569 USA
| | - Harry W T Morgan
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles California 90095-1569 USA
| | - Zisheng Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles California 90095-1569 USA
| | - Patricia Poths
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles California 90095-1569 USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles California 90095-1569 USA
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7
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Inverse molecular design of alkoxides and phenoxides for aqueous direct air capture of CO 2. Proc Natl Acad Sci U S A 2022; 119:e2123496119. [PMID: 35709322 DOI: 10.1073/pnas.2123496119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aqueous direct air capture (DAC) is a key technology toward a carbon negative infrastructure. Developing sorbent molecules with water and oxygen tolerance and high CO2 binding capacity is therefore highly desired. We analyze the CO2 absorption chemistries on amines, alkoxides, and phenoxides with density functional theory calculations, and perform inverse molecular design of the optimal sorbent. The alkoxides and phenoxides are found to be more suitable for aqueous DAC than amines thanks to their water tolerance (lower pKa prevents protonation by water) and capture stoichiometry of 1:1 (2:1 for amines). All three molecular systems are found to generally obey the same linear scaling relationship (LSR) between [Formula: see text] and [Formula: see text], since both CO2 and proton are bonded to the nucleophilic (alkoxy or amine) binding site through a majorly [Formula: see text] bonding orbital. Several high-performance alkoxides are proposed from the computational screening. Phenoxides have comparatively poorer correlation between [Formula: see text] and [Formula: see text], showing promise for optimization. We apply a genetic algorithm to search the chemical space of substituted phenoxides for the optimal sorbent. Several promising off-LSR candidates are discovered. The most promising one features bulky ortho substituents forcing the CO2 adduct into a perpendicular configuration with respect to the aromatic ring. In this configuration, the phenoxide binds CO2 and a proton using different molecular orbitals, thereby decoupling the [Formula: see text] and [Formula: see text]. The [Formula: see text] trend and off-LSR behaviors are then confirmed by experiments, validating the inverse molecular design framework. This work not only extensively studies the chemistry of the aqueous DAC, but also presents a transferrable computational workflow for understanding and optimization of other functional molecules.
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8
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Shi X, Lin X, Luo R, Wu S, Li L, Zhao ZJ, Gong J. Dynamics of Heterogeneous Catalytic Processes at Operando Conditions. JACS AU 2021; 1:2100-2120. [PMID: 34977883 PMCID: PMC8715484 DOI: 10.1021/jacsau.1c00355] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 05/02/2023]
Abstract
The rational design of high-performance catalysts is hindered by the lack of knowledge of the structures of active sites and the reaction pathways under reaction conditions, which can be ideally addressed by an in situ/operando characterization. Besides the experimental insights, a theoretical investigation that simulates reaction conditions-so-called operando modeling-is necessary for a plausible understanding of a working catalyst system at the atomic scale. However, there is still a huge gap between the current widely used computational model and the concept of operando modeling, which should be achieved through multiscale computational modeling. This Perspective describes various modeling approaches and machine learning techniques that step toward operando modeling, followed by selected experimental examples that present an operando understanding in the thermo- and electrocatalytic processes. At last, the remaining challenges in this area are outlined.
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Affiliation(s)
- Xiangcheng Shi
- Key
Laboratory for Green Chemical Technology of Ministry of Education,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
- Joint
School of National University of Singapore and Tianjin University,
International Campus of Tianjin University, Fuzhou 350207, China
| | - Xiaoyun Lin
- Key
Laboratory for Green Chemical Technology of Ministry of Education,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Ran Luo
- Key
Laboratory for Green Chemical Technology of Ministry of Education,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Shican Wu
- Key
Laboratory for Green Chemical Technology of Ministry of Education,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Lulu Li
- Key
Laboratory for Green Chemical Technology of Ministry of Education,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Zhi-Jian Zhao
- Key
Laboratory for Green Chemical Technology of Ministry of Education,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Jinlong Gong
- Key
Laboratory for Green Chemical Technology of Ministry of Education,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
- Joint
School of National University of Singapore and Tianjin University,
International Campus of Tianjin University, Fuzhou 350207, China
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9
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Lamoureux PS, Choksi TS, Streibel V, Abild-Pedersen F. Combining artificial intelligence and physics-based modeling to directly assess atomic site stabilities: from sub-nanometer clusters to extended surfaces. Phys Chem Chem Phys 2021; 23:22022-22034. [PMID: 34570139 DOI: 10.1039/d1cp02198b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The performance of functional materials is dictated by chemical and structural properties of individual atomic sites. In catalysts, for example, the thermodynamic stability of constituting atomic sites is a key descriptor from which more complex properties, such as molecular adsorption energies and reaction rates, can be derived. In this study, we present a widely applicable machine learning (ML) approach to instantaneously compute the stability of individual atomic sites in structurally and electronically complex nano-materials. Conventionally, we determine such site stabilities using computationally intensive first-principles calculations. With our approach, we predict the stability of atomic sites in sub-nanometer metal clusters of 3-55 atoms with mean absolute errors in the range of 0.11-0.14 eV. To extract physical insights from the ML model, we introduce a genetic algorithm (GA) for feature selection. This algorithm distills the key structural and chemical properties governing the stability of atomic sites in size-selected nanoparticles, allowing for physical interpretability of the models and revealing structure-property relationships. The results of the GA are generally model and materials specific. In the limit of large nanoparticles, the GA identifies features consistent with physics-based models for metal-metal interactions. By combining the ML model with the physics-based model, we predict atomic site stabilities in real time for structures ranging from sub-nanometer metal clusters (3-55 atom) to larger nanoparticles (147 to 309 atoms) to extended surfaces using a physically interpretable framework. Finally, we present a proof of principle showcasing how our approach can determine stable and active nanocatalysts across a generic materials space of structure and composition.
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Affiliation(s)
- Philomena Schlexer Lamoureux
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA.,SLAC National Accelerator Laboratory, SUNCAT Center for Interface Science and Catalysis, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
| | - Tej S Choksi
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA.,SLAC National Accelerator Laboratory, SUNCAT Center for Interface Science and Catalysis, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
| | - Verena Streibel
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, USA.,SLAC National Accelerator Laboratory, SUNCAT Center for Interface Science and Catalysis, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
| | - Frank Abild-Pedersen
- SLAC National Accelerator Laboratory, SUNCAT Center for Interface Science and Catalysis, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
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10
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Jesus WS, Prudente FV, Marques JMC, Pereira FB. Modeling microsolvation clusters with electronic-structure calculations guided by analytical potentials and predictive machine learning techniques. Phys Chem Chem Phys 2021; 23:1738-1749. [PMID: 33427847 DOI: 10.1039/d0cp05200k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We propose a new methodology to study, at the density functional theory (DFT) level, the clusters resulting from the microsolvation of alkali-metal ions with rare-gas atoms. The workflow begins with a global optimization search to generate a pool of low-energy minimum structures for different cluster sizes. This is achieved by employing an analytical potential energy surface (PES) and an evolutionary algorithm (EA). The next main stage of the methodology is devoted to establish an adequate DFT approach to treat the microsolvation system, through a systematic benchmark study involving several combinations of functionals and basis sets, in order to characterize the global minimum structures of the smaller clusters. In the next stage, we apply machine learning (ML) classification algorithms to predict how the low-energy minima of the analytical PES map to the DFT ones. An early and accurate detection of likely DFT local minima is extremely important to guide the choice of the most promising low-energy minima of large clusters to be re-optimized at the DFT level of theory. In this work, the methodology was applied to the Li+Krn (n = 2-14 and 16) microsolvation clusters for which the most competitive DFT approach was found to be the B3LYP-D3/aug-pcseg-1. Additionally, the ML classifier was able to accurately predict most of the solutions to be re-optimized at the DFT level of theory, thereby greatly enhancing the efficiency of the process and allowing its applicability to larger clusters.
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Affiliation(s)
- W S Jesus
- Instituto de Física, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil.
| | - F V Prudente
- Instituto de Física, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil.
| | - J M C Marques
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
| | - F B Pereira
- Coimbra Polytechnic - ISEC, Coimbra, Portugal and Centro de Informática e Sistemas da Universidade de Coimbra (CISUC), Coimbra, Portugal.
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11
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Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be 6B 11- Flux-Ional Cluster. MATERIALS 2020; 14:ma14010112. [PMID: 33383889 PMCID: PMC7796227 DOI: 10.3390/ma14010112] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 02/06/2023]
Abstract
The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11− clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11− clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations’ temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer’s infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.
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12
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Zhang Z, Zandkarimi B, Alexandrova AN. Ensembles of Metastable States Govern Heterogeneous Catalysis on Dynamic Interfaces. Acc Chem Res 2020; 53:447-458. [PMID: 31977181 DOI: 10.1021/acs.accounts.9b00531] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Heterogeneous catalysis is at the heart of the chemical industry. Being able to tune and design efficient catalysts for processes of interest is of the utmost importance, and for this, a molecular-level understanding of heterogeneous catalysts is the first step and indeed a prime focus of modern catalysis research. For a long time, the single most thermodynamically stable structure of the catalytic interface attained under the reaction conditions had been envisioned as the reactive phase. However, some catalytic interfaces continue to undergo structural dynamics in the steady state, triggered by high temperatures and pressures and binding and changing reagents. Among particularly dynamic interfaces are such widely used catalysts as crystalline and amorphous surfaced supporting (sub)nanometallic clusters. Recently, it became clear that this dynamic fluxionality causes the supported clusters to populate many distinct structural and stoichiometric states under catalytic conditions. Hence, the catalytic interface should be viewed as an evolving statistical ensemble of many structures (rather than one structure). Every member in the ensemble contributes to the properties of the catalyst differently, in proportion to its probability of being populated. This new notion flips the established paradigm and calls for a new theory, new modeling approaches, operando measurements, and updated design strategies. The statistical ensemble nature of surface-supported subnanocluster catalysts can be exemplified by oxide-supported and adsorbate-covered Pt, Pd, Cu, and CuPd clusters, which are catalytic toward oxidative and nonoxidative dehydrogenation. They have access to a variety of 3D and quasi-2D shapes. The compositions of their thermal ensembles are dependent on the cluster size, leading to size-specific catalytic activities and the famous "every atom counts" phenomenon. The support and adsorbates affect catalyst structures, and the state of the reacting species causes the ensemble to change in every reaction intermediate. The most stable member of the ensemble dominates the thermodynamic properties of the corresponding intermediate, whereas the kinetics can be determined by more active but less populated metastable catalyst states, and that suggests that many earlier studies might have overlooked the actual active sites. Both effects depend on the relative time scales of catalyst restructuring and reaction dynamics. The catalyst may routinely operate off-equilibrium. Ensemble phenomena lead to surprising exceptions from established rules of catalysis, such as scaling relations and Arrhenius behavior. Catalyst deactivation is also an ensemble property, and its extent of mitigation can be predicted through the new paradigm. These findings were enabled by advances in theory, such as global optimization and subsequent utilization of multiple local minima and pathways sampling as well as operando catalyst characterization. The fact that the per-site and per-species resolution is needed for the description and prediction of catalyst properties gives theory the central role in catalysis research, as most experiments provide ensemble-average information and cannot detect the crucial minority species that may be responsible for the catalytic activity.
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Affiliation(s)
- Zisheng Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Borna Zandkarimi
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
- California NanoSystems Institute, 570 Westwood Plaza, Los Angeles, California 90095, United States
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13
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Zhai H, Sautet P, Alexandrova AN. Global Optimization of Adsorbate Covered Supported Cluster Catalysts: The Case of Pt
7
H
10
CH
3
on α‐Al
2
O
3. ChemCatChem 2019. [DOI: 10.1002/cctc.201901830] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Huanchen Zhai
- Department of Chemistry and BiochemistryUniversity of California Los Angeles CA-90095 USA
| | - Philippe Sautet
- Department of Chemistry and BiochemistryUniversity of California Los Angeles CA-90095 USA
- Department of Chemical and Biomolecular EngineeringUniversity of California Los Angeles CA-90095 USA
- California NanoSystems Institute Los Angeles CA 90095 USA
| | - Anastassia N. Alexandrova
- Department of Chemistry and BiochemistryUniversity of California Los Angeles CA-90095 USA
- California NanoSystems Institute Los Angeles CA 90095 USA
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14
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Zandkarimi B, Alexandrova AN. Surface‐supported cluster catalysis: Ensembles of metastable states run the show. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1420] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Borna Zandkarimi
- Department of Chemistry and Biochemistry University of California, Los Angeles Los Angeles California
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry University of California, Los Angeles Los Angeles California
- California NanoSystems Institute University of California, Los Angeles Los Angeles California
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15
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Yañez O, Garcia V, Garza J, Orellana W, Vásquez‐Espinal A, Tiznado W. (Li
6
Si
5
)
2–5
: The Smallest Cluster‐Assembled Materials Based on Aromatic Si
5
6−
Rings. Chemistry 2019; 25:2467-2471. [DOI: 10.1002/chem.201805677] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Osvaldo Yañez
- Departamento de Ciencias QuímicasFacultad de Ciencias ExactasComputational and Theoretical Chemistry GroupUniversidad Andres Bello Av. República 275 8370146 Santiago Chile
| | - Victor Garcia
- Doctorado en Fisicoquímica MolecularFacultad de Ciencias ExactasUniversidad Andres Bello Av. República 275 8370146 Santiago Chile
| | - Jorge Garza
- Departamento de QuímicaDivisión de Ciencias Básicas e IngenieríasUniversidad Autónoma Metropolitana-Iztapalapa San Rafael Atlixco 186, Col Vicentina, Iztapalapa 09340 Mexico City Mexico
| | - Walter Orellana
- Departamento de Ciencias FísicasFacultad de Ciencias ExactasUniversidad Andres Bello Av. Sazié 2212 8370146 Santiago Chile
| | - Alejandro Vásquez‐Espinal
- Departamento de Ciencias QuímicasFacultad de Ciencias ExactasComputational and Theoretical Chemistry GroupUniversidad Andres Bello Av. República 275 8370146 Santiago Chile
| | - William Tiznado
- Departamento de Ciencias QuímicasFacultad de Ciencias ExactasComputational and Theoretical Chemistry GroupUniversidad Andres Bello Av. República 275 8370146 Santiago Chile
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16
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Yañez O, Vásquez-Espinal A, Báez-Grez R, Rabanal-León WA, Osorio E, Ruiz L, Tiznado W. Carbon rings decorated with group 14 elements: new aromatic clusters containing planar tetracoordinate carbon. NEW J CHEM 2019. [DOI: 10.1039/c9nj01022j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and chemically intuitive approach is used to design ptC-containing E–C clusters (E = Si–Pb).
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Affiliation(s)
- Osvaldo Yañez
- Doctorado en Fisicoquímica Molecular
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Alejandro Vásquez-Espinal
- Computational and Theoretical Chemistry Group
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
| | - Rodrigo Báez-Grez
- Doctorado en Fisicoquímica Molecular
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Walter A. Rabanal-León
- Laboratorio de Química Inorgánica y Organometálica
- Departamento de Química Analítica e Inorgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Casilla 160-C
| | - Edison Osorio
- Facultad de Ciencias Naturales y Matemáticas
- Universidad de Ibagué
- Ibagué
- Colombia
| | - Lina Ruiz
- Instituto de Ciencias Biomédicas
- Facultad Ciencias de la Salud
- Universidad Autónoma de Chile
- Santiago
- Chile
| | - William Tiznado
- Doctorado en Fisicoquímica Molecular
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
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17
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Yañez O, Báez-Grez R, Inostroza D, Rabanal-León WA, Pino-Rios R, Garza J, Tiznado W. AUTOMATON: A Program That Combines a Probabilistic Cellular Automata and a Genetic Algorithm for Global Minimum Search of Clusters and Molecules. J Chem Theory Comput 2018; 15:1463-1475. [DOI: 10.1021/acs.jctc.8b00772] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Osvaldo Yañez
- Doctorado en Fisicoquı́mica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, República 275 (2do piso), Santiago, 8370146, Chile
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Computacional and Theoretical Chemistry Group, Universidad Andres Bello, República 275 (3er piso), Santiago, 8370146, Chile
| | - Rodrigo Báez-Grez
- Doctorado en Fisicoquı́mica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, República 275 (2do piso), Santiago, 8370146, Chile
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Computacional and Theoretical Chemistry Group, Universidad Andres Bello, República 275 (3er piso), Santiago, 8370146, Chile
| | - Diego Inostroza
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Computacional and Theoretical Chemistry Group, Universidad Andres Bello, República 275 (3er piso), Santiago, 8370146, Chile
| | - Walter A. Rabanal-León
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Computacional and Theoretical Chemistry Group, Universidad Andres Bello, República 275 (3er piso), Santiago, 8370146, Chile
| | - Ricardo Pino-Rios
- Laboratorio de Química Teórica, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Avenida Bernardo O’Higgins 3363, Santiago, 9170022, Chile
| | - Jorge Garza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C.P. 09340 Mexico City, Mexico
| | - W. Tiznado
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Computacional and Theoretical Chemistry Group, Universidad Andres Bello, República 275 (3er piso), Santiago, 8370146, Chile
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18
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Vásquez‐Espinal A, Palacio‐Rodríguez K, Ravell E, Orozco‐Ic M, Barroso J, Pan S, Tiznado W, Merino G. E
5
M
7
+
(E=C–Pb, M=Li–Cs): A Source of Viable Star‐Shaped Clusters. Chem Asian J 2018; 13:1751-1755. [DOI: 10.1002/asia.201800654] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/16/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Alejandro Vásquez‐Espinal
- Departamento de Física AplicadaCentro de Investigación y de Estudios Avanzados, Unidad Mérida Km 6 Antigua carretera a Progreso, Apdo. Postal 73, Cordemex 97310 Mérida Yuc. México
| | - Karen Palacio‐Rodríguez
- Química de Recursos Energéticos y Medio AmbienteInstituto de Química, Facultad de Ciencias Exactas y NaturalesUniversidad de Antioquia Calle 70 No. 52-21 Medellín Colombia
| | - Estefanía Ravell
- Departamento de Física AplicadaCentro de Investigación y de Estudios Avanzados, Unidad Mérida Km 6 Antigua carretera a Progreso, Apdo. Postal 73, Cordemex 97310 Mérida Yuc. México
| | - Mesías Orozco‐Ic
- Departamento de Física AplicadaCentro de Investigación y de Estudios Avanzados, Unidad Mérida Km 6 Antigua carretera a Progreso, Apdo. Postal 73, Cordemex 97310 Mérida Yuc. México
| | - Jorge Barroso
- Departamento de Física AplicadaCentro de Investigación y de Estudios Avanzados, Unidad Mérida Km 6 Antigua carretera a Progreso, Apdo. Postal 73, Cordemex 97310 Mérida Yuc. México
| | - Sudip Pan
- Institute of Advanced SynthesisSchool of Chemistry and Molecular EngineeringJiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Nanjing 211816 China
| | - William Tiznado
- Departamento de Ciencias Químicas, Facultad de Ciencias ExactasUniversidad Andres Bello República 275 Santiago Chile
| | - Gabriel Merino
- Departamento de Física AplicadaCentro de Investigación y de Estudios Avanzados, Unidad Mérida Km 6 Antigua carretera a Progreso, Apdo. Postal 73, Cordemex 97310 Mérida Yuc. México
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19
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Affiliation(s)
- Elisa Jimenez-Izal
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), 20080 Donostia, Euskadi, Spain
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- California NanoSystems Institute, Los Angeles, California 90095, USA
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20
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Sun G, Sautet P. Metastable Structures in Cluster Catalysis from First-Principles: Structural Ensemble in Reaction Conditions and Metastability Triggered Reactivity. J Am Chem Soc 2018; 140:2812-2820. [PMID: 29424224 DOI: 10.1021/jacs.7b11239] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Reactivity studies on catalytic transition metal clusters are usually performed on a single global minimum structure. With the example of a Pt13 cluster under a pressure of hydrogen, we show from first-principle calculations that low energy metastable structures of the cluster can play a major role for catalytic reactivity and that hence consideration of the global minimum structure alone can severely underestimate the activity. The catalyst is fluxional with an ensemble of metastable structures energetically accessible at reaction conditions. A modified genetic algorithm is proposed to comprehensively search for the low energy metastable ensemble (LEME) structures instead of merely the global minimum structure. In order to reduce the computational cost of density functional calculations, a high dimensional neural network potential is employed to accelerate the exploration. The presence and influence of LEME structures during catalysis is discussed by the example of H covered Pt13 clusters for two reactions of major importance: hydrogen evolution reaction and methane activation. The results demonstrate that although the number of accessible metastable structures is reduced under reaction condition for Pt13 clusters, these metastable structures can exhibit high activity and dominate the observed activity due to their unique electronic or structural properties. This underlines the necessity of thoroughly exploring the LEME structures in catalysis simulations. The approach enables one to systematically address the impact of isomers in catalysis studies, taking into account the high adsorbate coverage induced by reaction conditions.
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Affiliation(s)
- Geng Sun
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Philippe Sautet
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
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21
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Rabanal-León WA, Tiznado W, Osorio E, Ferraro F. Exploring the potential energy surface of small lead clusters using the gradient embedded genetic algorithm and an adequate treatment of relativistic effects. RSC Adv 2018. [DOI: 10.1039/c7ra11449d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Theoretical inclusion of relativistic effects (scalar and spin–orbit) play a crucial role to assure an adequate structural assignment on lead clusters.
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Affiliation(s)
- Walter A. Rabanal-León
- Departamento de Ciencias Químicas
- Facultad Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - William Tiznado
- Departamento de Ciencias Químicas
- Facultad Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Edison Osorio
- Departamento de Ciencias Básicas
- Universidad Católica Luis Amigó
- Medellín
- Colombia
| | - Franklin Ferraro
- Departamento de Ciencias Básicas
- Universidad Católica Luis Amigó
- Medellín
- Colombia
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22
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Yañez O, Vásquez-Espinal A, Inostroza D, Ruiz L, Pino-Rios R, Tiznado W. A Fukui function-guided genetic algorithm. Assessment on structural prediction of Sin(n = 12-20) clusters. J Comput Chem 2017; 38:1668-1677. [DOI: 10.1002/jcc.24810] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Osvaldo Yañez
- Doctorado en Fisicoquímica Molecular; Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
| | - Alejandro Vásquez-Espinal
- Doctorado en Fisicoquímica Molecular; Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
| | - Diego Inostroza
- Centro de Bioinformatica y Simulación Molecular; Facultad de Ingeniería, Universidad de Talca; 2 Norte 685, Casilla 721 Talca Chile
| | - Lina Ruiz
- Centro de Investigación Biomédica, Universidad Autónoma de Chile; Santiago Chile
| | - Ricardo Pino-Rios
- Doctorado en Fisicoquímica Molecular; Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
| | - William Tiznado
- Doctorado en Fisicoquímica Molecular; Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
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23
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Zhai H, Alexandrova AN. Fluxionality of Catalytic Clusters: When It Matters and How to Address It. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03243] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Huanchen Zhai
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- California NanoSystems Institute, Los Angeles, California 90095, United States
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24
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Giraldo C, Ferraro F, Hadad CZ, Riuz L, Tiznado W, Osorio E. Theoretical design of stable hydride clusters: isoelectronic transformation in the EnAl4−nH7+n− series. RSC Adv 2017. [DOI: 10.1039/c7ra01422h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Design of stable hydrogen-rich metallic hydrides through substitutions of one aluminum atom by one E–H unit in the Al4H7− cluster (E = Be, Mg, Ca, Sr and Ba atoms).
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Affiliation(s)
- Carolina Giraldo
- Departamento de Ciencias Básicas
- Universidad Católica Luis Amigó
- SISCO
- Medellín
- Colombia
| | - Franklin Ferraro
- Departamento de Ciencias Básicas
- Universidad Católica Luis Amigó
- SISCO
- Medellín
- Colombia
| | - C. Z. Hadad
- Grupo de Química-Física Teórica
- Instituto de Química
- Universidad de Antioquia
- Medellín
- Colombia
| | - Lina Riuz
- Centro de Investigación Biomédica
- Universidad Autónoma de Chile
- Santiago
- Chile
| | - William Tiznado
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Edison Osorio
- Departamento de Ciencias Básicas
- Universidad Católica Luis Amigó
- SISCO
- Medellín
- Colombia
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25
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Zhai H, Alexandrova AN. Ensemble-Average Representation of Pt Clusters in Conditions of Catalysis Accessed through GPU Accelerated Deep Neural Network Fitting Global Optimization. J Chem Theory Comput 2016; 12:6213-6226. [DOI: 10.1021/acs.jctc.6b00994] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huanchen Zhai
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- California NanoSystems
Institute, Los Angeles, California 90095, United States
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26
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Zhao J, Shi R, Sai L, Huang X, Su Y. Comprehensive genetic algorithm forab initioglobal optimisation of clusters. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2015.1121386] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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28
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Fuenzalida-Valdivia I, Beltran MJ, Ferraro F, Vasquez-Espinal A, Tiznado W, Osorio E. Isoelectronic substitution from Si52− to Al5H52−: Exploration of the series Si5−(AlH)2− (n= 0–5). Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.01.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Vásquez-Espinal A, Torres-Vega JJ, Alvarez-Thon L, Fuentealba P, Islas R, Tiznado W. Boron avoids cycloalkane-like structures in the LinBnH2n series. NEW J CHEM 2016. [DOI: 10.1039/c5nj02051d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The stability of cycloalkane-like structures in the series LinBnH2n is analyzed using ab initio calculations. Neither of these cyclic species is energetically favored, contrary to what happens with aromatic lithium boron hydride rings.
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Affiliation(s)
- Alejandro Vásquez-Espinal
- Doctorado en Fisicoquímica Molecular
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Juan J. Torres-Vega
- Facultad de Ciencias Físicas
- Universidad Nacional Mayor de San Marcos
- Lima
- Peru
| | - Luis Alvarez-Thon
- Departamento de Ciencias Físicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Patricio Fuentealba
- Departamento de Física
- Universidad de Chile
- Santiago
- Chile
- Centro para el Desarrollo de la Nanociencia y Nanotecnologia
| | - Rafael Islas
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - William Tiznado
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
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30
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Hernández FJ, Capello MC, Naito A, Manita S, Tsukada K, Miyazaki M, Fujii M, Broquier M, Gregoire G, Dedonder-Lardeux C, Jouvet C, Pino GA. Trapped Hydronium Radical Produced by Ultraviolet Excitation of Substituted Aromatic Molecule. J Phys Chem A 2015; 119:12730-5. [PMID: 26637013 DOI: 10.1021/acs.jpca.5b10142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The gas phase structure and excited state dynamics of o-aminophenol-H2O complex have been investigated using REMPI, IR-UV hole-burning spectroscopy, and pump-probe experiments with picoseconds laser pulses. The IR-UV spectroscopy indicates that the isomer responsible for the excitation spectrum corresponds to an orientation of the OH bond away from the NH2 group. The water molecule acts as H-bond acceptor of the OH group of the chromophore. The complexation of o-aminophenol with one water molecule induced an enhancement in the excited state lifetime on the band origin. The variation of the excited state lifetime of the complex with the excess energy from 1.4 ± 0.1 ns for the 0-0 band to 0.24 ± 0.3 ns for the band at 0-0 + 120 cm(-1) is very similar to the variation observed in the phenol-NH3 system. This experimental result suggests that the excited state hydrogen transfer reaction is the dominant channel for the non radiative pathway. Indeed, excited state ab initio calculations demonstrate that H transfer leading to the formation of the H3O(•) radical within the complex is the main reactive pathway.
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Affiliation(s)
- Federico J Hernández
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC) CONICET - UNC. Dpto. de Fisicoquímica - Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Marcela C Capello
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC) CONICET - UNC. Dpto. de Fisicoquímica - Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Ayumi Naito
- Chemical Resources Laboratory and Integrated Research Institute, Tokyo Institute of Technology , 4259 Nagatsuta , Midori-ku,Yokohama 226-8503, Japan
| | - Shun Manita
- Chemical Resources Laboratory and Integrated Research Institute, Tokyo Institute of Technology , 4259 Nagatsuta , Midori-ku,Yokohama 226-8503, Japan
| | - Kohei Tsukada
- Chemical Resources Laboratory and Integrated Research Institute, Tokyo Institute of Technology , 4259 Nagatsuta , Midori-ku,Yokohama 226-8503, Japan
| | - Mitsuhiko Miyazaki
- Chemical Resources Laboratory and Integrated Research Institute, Tokyo Institute of Technology , 4259 Nagatsuta , Midori-ku,Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Chemical Resources Laboratory and Integrated Research Institute, Tokyo Institute of Technology , 4259 Nagatsuta , Midori-ku,Yokohama 226-8503, Japan
| | - Michel Broquier
- Centre Laser de l'Université Paris Sud (CLUPS/LUMAT), Université Paris-Sud, CNRS, Institut d'Optique Graduate School, Université Paris-Saclay , F-91405 Orsay, France.,Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay, France
| | - Gilles Gregoire
- Centre Laser de l'Université Paris Sud (CLUPS/LUMAT), Université Paris-Sud, CNRS, Institut d'Optique Graduate School, Université Paris-Saclay , F-91405 Orsay, France.,Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay, France
| | | | - Christophe Jouvet
- Aix Marseille Université, CNRS , PIIM UMR 7345, 13397, Marseille, France
| | - Gustavo A Pino
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC) CONICET - UNC. Dpto. de Fisicoquímica - Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
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31
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Hanson-Heine MW, Besley NA. Spectroscopic and structural analysis of mixed carbon dioxide and fluorinated methane clusters. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Valiev M, Deng SHM, Wang XB. How Anion Chaotrope Changes the Local Structure of Water: Insights from Photoelectron Spectroscopy and Theoretical Modeling of SCN(-) Water Clusters. J Phys Chem B 2015; 120:1518-25. [PMID: 26352899 DOI: 10.1021/acs.jpcb.5b07257] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The behavior of charged solute molecules in aqueous solutions is often classified using the concept of kosmotropes ("structure makers") and chaotropes ("structure breakers"). There is a growing consensus that the key to kosmotropic/chaotropic behaviors lies in the local solvent region, but the exact microscopic basis for such differentiation is not well-understood. This issue is examined in this work by analyzing size selective solvation of a well-known chaotrope, a negatively charged SCN(-) molecule. Combining experimental photoelectron spectroscopy measurements with theoretical modeling, we examine evolution of solvation structure up to eight waters. We observe that SCN(-) indeed fits the description of weakly hydrated ion, and its solvation is heavily driven by stabilization of water-water interaction network. However, the impact on water structure is more subtle than that associated with "structure breaker". In particular, we observe that the solvation structure of SCN(-) preserves the "packing" structure of the water network but changes local directionality of hydrogen bonds in the local solvent region. The resulting effect is closer to that of "structure weakener", where solute can be readily accommodated into the native water network, at the cost of compromising its stability due to constraints on hydrogen bonding directionality.
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Affiliation(s)
- Marat Valiev
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
| | - Shihu H M Deng
- Physical Sciences Division, Pacific Northwest National Laboratory , 902 Battelle Boulevard, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory , 902 Battelle Boulevard, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
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33
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Dadras J, Jimenez-Izal E, Alexandrova AN. Alloying Pt Sub-nano-clusters with Boron: Sintering Preventative and Coke Antagonist? ACS Catal 2015. [DOI: 10.1021/acscatal.5b01513] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonny Dadras
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Elisa Jimenez-Izal
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- California Nano-Systems Institute, Los Angeles, California 90095, United States
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34
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Zhang Q, Cheng L. Structural Determination of (Al2O3)(n) (n = 1-15) Clusters Based on Graphic Processing Unit. J Chem Inf Model 2015; 55:1012-20. [PMID: 25928795 DOI: 10.1021/acs.jcim.5b00069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Global optimization algorithms have been widely used in the field of chemistry to search the global minimum structures of molecular and atomic clusters, which is a nondeterministic polynomial problem with the increasing sizes of clusters. Considering that the computational ability of a graphic processing unit (GPU) is much better than that of a central processing unit (CPU), we developed a GPU-based genetic algorithm for structural prediction of clusters and achieved a high acceleration ratio compared to a CPU. On the one-dimensional (1D) operation of a GPU, taking (Al2O3)n clusters as test cases, the peak acceleration ratio in the GPU is about 220 times that in a CPU in single precision and the value is 103 for double precision in calculation of the analytical interatomic potential. The peak acceleration ratio is about 240 and 107 on the block operation, and it is about 77 and 35 on the 2D operation compared to a CPU in single precision and double precision, respectively. And the peak acceleration ratio of the whole genetic algorithm program is about 35 compared to CPU at double precision. Structures of (Al2O3)n clusters at n = 1-10 reported in previous works are successfully located, and their low-lying structures at n = 11-15 are predicted.
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Affiliation(s)
- Qiyao Zhang
- Department of Chemistry, Anhui University, Hefei, Anhui 230039, People's Republic of China
| | - Longjiu Cheng
- Department of Chemistry, Anhui University, Hefei, Anhui 230039, People's Republic of China
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35
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Hybrid genetic–particle swarm algorithm: An efficient method for fast optimization of atomic clusters. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Zhai H, Ha MA, Alexandrova AN. AFFCK: Adaptive Force-Field-Assisted ab Initio Coalescence Kick Method for Global Minimum Search. J Chem Theory Comput 2015; 11:2385-93. [DOI: 10.1021/acs.jctc.5b00065] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huanchen Zhai
- School
of Physics, Shandong University, Jinan 250100, P. R. China
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37
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Torres-Vega JJ, Vásquez-Espinal A, Beltran MJ, Ruiz L, Islas R, Tiznado W. Li7(BH)5+: a new thermodynamically favored star-shaped molecule. Phys Chem Chem Phys 2015; 17:19602-6. [DOI: 10.1039/c5cp02006a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The feasibility of stabilizing a new star-shaped molecule, the Li7(BH)5+, is demonstrated by anin silicoinvestigation, combining DFT andAb initiomethods.
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Affiliation(s)
- Juan J. Torres-Vega
- Doctorado en Fisicoquímica Molecular
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Alejandro Vásquez-Espinal
- Doctorado en Fisicoquímica Molecular
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Maria J. Beltran
- Doctorado en Fisicoquímica Molecular
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Lina Ruiz
- Centro de Investigación Biomédica
- Universidad Autónoma de Chile
- Santiago
- Chile
| | - Rafael Islas
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - William Tiznado
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
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38
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Shayeghi A, Götz D, Davis JBA, Schäfer R, Johnston RL. Pool-BCGA: a parallelised generation-free genetic algorithm for the ab initio global optimisation of nanoalloy clusters. Phys Chem Chem Phys 2014; 17:2104-12. [PMID: 25482360 DOI: 10.1039/c4cp04323e] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Birmingham cluster genetic algorithm is a package that performs global optimisations for homo- and bimetallic clusters based on either first principles methods or empirical potentials. Here, we present a new parallel implementation of the code which employs a pool strategy in order to eliminate sequential steps and significantly improve performance. The new approach meets all requirements of an evolutionary algorithm and contains the main features of the previous implementation. The performance of the pool genetic algorithm is tested using the Gupta potential for the global optimisation of the Au10Pd10 cluster, which demonstrates the high efficiency of the method. The new implementation is also used for the global optimisation of the Au10 and Au20 clusters directly at the density functional theory level.
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Affiliation(s)
- A Shayeghi
- Eduard-Zintl-Institut, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany.
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39
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Kanters RPF, Donald KJ. cluster: Searching for Unique Low Energy Minima of Structures Using a Novel Implementation of a Genetic Algorithm. J Chem Theory Comput 2014; 10:5729-37. [DOI: 10.1021/ct500744k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- René P. F. Kanters
- Department of Chemistry,
Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
| | - Kelling J. Donald
- Department of Chemistry,
Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
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40
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Zhang X, Liu G, Ganteför G, Bowen KH, Alexandrova AN. PtZnH5(-), A σ-Aromatic Cluster. J Phys Chem Lett 2014; 5:1596-1601. [PMID: 26270102 DOI: 10.1021/jz500322n] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a joint photoelectron spectroscopic and theoretical study of the PtZnH5(-) cluster anion. This cluster exhibited an unprecedented planar pentagonal coordination for Pt and an unusual stability and high intensity in the mass spectrum. Both are due to the σ-aromaticity found in the H5-cycle supported by the 5d orbitals on the Pt atom. σ-Aromaticity in all-H systems has been predicted in the past but never found in experimentally observed species. Besides fundamental importance, mixed transition-metal hydrides can be found as intermediates in catalytic processes, and thus, the unexpected stability facilitated by σ-aromaticity can be appreciated also in practical applications.
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Affiliation(s)
- Xinxing Zhang
- †Department of Chemistry and Materials Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gaoxiang Liu
- †Department of Chemistry and Materials Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gerd Ganteför
- †Department of Chemistry and Materials Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kit H Bowen
- †Department of Chemistry and Materials Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Anastassia N Alexandrova
- ‡Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
- §California NanoSystems Institute, 570 Westwood Plaza, Building 114, Los Angeles, California 90095, United States
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41
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Liu YR, Wen H, Huang T, Lin XX, Gai YB, Hu CJ, Zhang WJ, Huang W. Structural Exploration of Water, Nitrate/Water, and Oxalate/Water Clusters with Basin-Hopping Method Using a Compressed Sampling Technique. J Phys Chem A 2014; 118:508-16. [DOI: 10.1021/jp4109128] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi-Rong Liu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Hui Wen
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Teng Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Xiao-Xiao Lin
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Yan-Bo Gai
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Chang-Jin Hu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Wei-Jun Zhang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Wei Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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42
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Shen L, Dadras J, Alexandrova AN. Pure and Zn-doped Pt clusters go flat and upright on MgO(100). Phys Chem Chem Phys 2014; 16:26436-42. [DOI: 10.1039/c4cp01877j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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43
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Pomogaeva A, Chipman DM. Hydrogen atom in water from ambient to high temperatures. J Phys Chem B 2013; 117:16530-41. [PMID: 24298910 DOI: 10.1021/jp4106844] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The aqueous hydrogen atom is studied with molecular dynamics simulations from ambient temperature to near the critical point. The radial distribution functions find a hydrogen atom coordination number of about 13 water molecules at 300 K to about 4 water molecules at 646 K. The radial and angular distribution functions indicate that first-shell water molecules tend to orient to maximize hydrogen bonding interactions with other water molecules. These orientational tendencies diminish with temperature. The calculated diffusion coefficient agrees very well with experimental results known near ambient temperatures. It fits a simple activation model to about 575 K, above which the diffusion becomes much faster than predicted by the fit. To temperatures of at least 500 K there is evidence for caging on a time scale of about 1 ps, but the evidence disappears at very high temperatures. Values of the aqueous hydrogen hyperfine coupling constant are obtained by averaging the results of density functional calculations on clusters extracted from the simulations. The hyperfine coupling calculations do not agree well with experiment for reasons that are not understood now, pointing to the need for further research on this problem.
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Affiliation(s)
- Anna Pomogaeva
- Radiation Laboratory, University of Notre Dame , Notre Dame, Indiana 46556-5674, United States
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44
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Oña OB, Alcoba DR, Torre A, Lain L, Torres-Vega JJ, Tiznado W. Orbital Localization Criterion as a Complementary Tool in the Bonding Analysis by Means of Electron Localization Function: Study of the Sin(BH)5-n2- (n = 0–5) Clusters. J Phys Chem A 2013; 117:12953-8. [DOI: 10.1021/jp4081228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ofelia B. Oña
- Instituto de Investigaciones
Fisicoquímicas Teóricas y Aplicadas, Universidad Nacional de La Plata, CCT La Plata, Consejo
Nacional de Investigaciones Científicas y Técnicas, Diag. 113 y 64 (s/n), Sucursal 4, CC 16, 1900 La Plata, Argentina
| | - Diego R. Alcoba
- Departamento de Física, Facultad
de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
- Instituto de Física de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Alicia Torre
- Departamento de Química Física, Facultad
de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644, E-48080 Bilbao, Spain
| | - Luis Lain
- Departamento de Química Física, Facultad
de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644, E-48080 Bilbao, Spain
| | - Juan J. Torres-Vega
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 275, Santiago de Chile, Chile
| | - William Tiznado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 275, Santiago de Chile, Chile
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45
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46
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Pang R, Yu LJ, Wu DY, Mao BW, Tian ZQ. Surface electron–hydronium ion-pair bound to silver and gold cathodes: A density functional theoretical study of photocatalytic hydrogen evolution reaction. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.03.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Osorio E, Vasquez A, Florez E, Mondragon F, Donald KJ, Tiznado W. Theoretical design of stable small aluminium–magnesium binary clusters. Phys Chem Chem Phys 2013; 15:2222-9. [DOI: 10.1039/c2cp42015e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Alexandrova AN, Nayhouse MJ, Huynh MT, Kuo JL, Melkonian AV, Chavez G, Hernando NM, Kowal MD, Liu CP. Selected AB4(2-/-) (A = C, Si, Ge; B = Al, Ga, In) ions: a battle between covalency and aromaticity, and prediction of square planar Si in SiIn4(2-/-). Phys Chem Chem Phys 2012; 14:14815-21. [PMID: 22868353 PMCID: PMC3478443 DOI: 10.1039/c2cp41821e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CAl(4)(2-/-) (D(4h), (1)A(1g)) is a cluster ion that has been established to be planar, aromatic, and contain a tetracoordinate planar C atom. Valence isoelectronic substitution of C with Si and Ge in this cluster leads to a radical change of structure toward distorted pentagonal species. We find that this structural change goes together with the cluster acquiring partial covalency of bonding between Si/Ge and Al(4), facilitated by hybridization of the atomic orbitals (AOs). Counter intuitively, for the AAl(4)(2-/-) (A = C, Si, Ge) clusters, hybridization in the dopant atom is strengthened from C, to Si, and to Ge, even though typically AOs are more likely to hybridize if they are closer in energy (i.e. in earlier elements in the Periodic Table). The trend is explained by the better overlap of the hybrids of the heavier dopants with the orbitals of Al(4). From the thus understood trend, it is inferred that covalency in such clusters can be switched off, by varying the relative sizes of the AOs of the main element and the dopant. Using this mechanism, we then successfully killed covalency in Si, and predicted a new aromatic cluster ion containing a tetracoordinate square planar Si, SiIn(4)(2-/-).
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Affiliation(s)
- Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
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49
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Do H, Besley NA. Structural optimization of molecular clusters with density functional theory combined with basin hopping. J Chem Phys 2012; 137:134106. [DOI: 10.1063/1.4755994] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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50
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Abstract
The potential energy surface of the hypothetical NaMgAlSiPSCl system (heavy periodane) is exhaustively analyzed via the gradient embedded genetic algorithm (GEGA) in combination with density functional theory (DFT) computations. The electronegativity differences among the elements in both the second and third rows of the periodic table indicate that low-energy heavy periodane structures are obtained when highly electronegative and electropositive elements are bound together, but the global minimum of the heavy periodane system is completely different to its second-row analog (LiBeBCNOF).
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