Tetrahelix Conformations and Transformation Pathways in Pt<sub>1</sub>Pd<sub>12</sub> Clusters

Pacheco-Contreras, Rafael; Dessens-Félix, Maribel; Borbón-González, Dora J.; Paz-Borbón, Lauro Oliver; Johnston, Roy L.; Schön, J. Christian; Posada-Amarillas, Álvaro

doi:10.1021/jp3023925

Cited by 14 publications

(17 citation statements)

References 46 publications

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“…Of course, it is far too time consuming to explore the complete PES with all its local minima and all connecting transition states (TS). This can only be done for restricted regions of the PES, very small model systems, [49] or simplified EPs [10] but these so-called disconnectivity graphs, [50][51][52][53] which are a powerful way of representing the PES,…”

Section: Basic Principles Of the Go Of Clusters And Ep-go Applicationsmentioning

confidence: 99%

Global optimization of clusters using electronic structure methods

Heiles

Johnston

2013

Int J of Quantum Chemistry

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191

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Over the past decade, there has been a significant growth in the development and application of methods for performing global optimization (GO) of cluster and nanoparticle structures using first-principles electronic structure methods coupled to sophisticated search algorithms. This has in part been driven by the desire to avoid the use of empirical potentials (EPs), especially in cases where no reliable potentials exist to guide the search toward reasonable regions of configuration space. This has been facilitated by improvements in the reliability of the search algorithms, increased efficiency of the electronic structure methods, and the development of faster, multiprocessor high-performance computing architectures. In this review, we give a brief overview of GO algorithms, though concentrating mainly on genetic algorithm and basin hopping techniques, first in combination with EPs. The major part of the review then deals with details of the implementation and application of these search methods to allow exploration for global minimum cluster structures directly using electronic structure methods and, in particular, density functional theory. Example applications are presented, ranging from isolated monometallic and bimetallic clusters to molecular clusters and ligated and surface supported metal clusters. Finally, some possible future developments are highlighted.

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Section: Basic Principles Of the Go Of Clusters And Ep-go Applicationsmentioning

confidence: 99%

Global optimization of clusters using electronic structure methods

Heiles

Johnston

2013

Int J of Quantum Chemistry

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202

191

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“…33 Such short spiral strands have also appeared in computational models of colloidal clusters involving only isotropic interactions 34,35 and have recently been identified in a bimetallic cluster. 36…”

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confidence: 99%

Designing a Bernal Spiral from Patchy Colloids

Morgan¹,

Chakrabarti

Dorsaz³

et al. 2013

ACS Nano

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A model potential for colloidal building blocks is defined with two different types of attractive surface sites, described as complementary patches and antipatches. A Bernal spiral is identified as the global minimum for clusters with appropriate arrangements of three patch-antipatch pairs. We further derive a minimalist design rule with only one patch and antipatch, which also produces a Bernal spiral. Monte Carlo simulations of these patchy colloidal building blocks in the bulk are generally found to corroborate the global optimization results. KeywordsBernal spiral; patchy colloids; self-assembly; patch-antipatch; anisotropic interactionsThe synthesis of colloidal particles is important in such areas as paints, hygiene products, drug delivery, and nanotechnology. Their diversity makes such particles attractive candidates for the design of self-assembling nanodevices. 1 Much recent synthetic effort has been spent on moving beyond simple spherical colloids to anisotropic particles of various shapes. [2][3][4] Colloidal particles have also been synthesized with "sticky patches" on their surfaces, which interact with patches on other particles. 2,4 This functionality suggests the possibility for self-assembly of complex structures via a bottom-up approach, without the need for the detailed control required in a top-down method. Self-assembly is governed by the interactions between the building blocks, so in principle, rational design of building blocks, tuning their mutual interactions, can lead to systems that self-assemble into specific target structures. 3 Simulation of self-assembling systems is a useful tool in guiding the synthesis of particles, which can suggest interesting synthetic targets. 5 Rational design of building blocks for selfassembly is greatly facilitated if the final structure can be predicted as a function of the building block parameters. The corresponding energy landscape contains all the information necessary for such a prediction, both in terms of the energetically favorable minima, and the pathways between them, which determine the structures that can easily be assembled. [6][7][8] The simplest model of colloidal particles involves hard spheres with a short-range squarewell attraction, 9 but other potentials such as the Lennard-Jones and Morse forms have also been considered. [10][11][12][13] Anisotropic building blocks open up rich avenues for sophisticated self-assembly into a variety of target structures. 3,14 Isotropic models are not sufficient for describing these * To whom correspondence should be addressed dw34@cam.ac.uk. Europe PMC Funders GroupAuthor Manuscript ACS Nano. Author manuscript; available in PMC 2014 January 17. An assembly of particles with a diamond-like crystal structure has been suggested as a synthetic target due to the potentially interesting photonic properties, 18,19 and numerical studies of patchy particles have been carried out to investigate whether they will crystallize to form this lattice. 20 Creating a patchy particle that will assemble into th...

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“…The sixth isomer is a polytetrahedral chain at +0.425 eV, which may be considered as three intertwined chains, forming the basis of a Bernal spiral. This is an exotic motif recently predicted for coinage metal clusters in the subnanometre size range 41. For clusters of twelve atoms and above, the icosahedral motif begins to dominate the low‐lying structures, but for octamers, the structures, whilst similarly compact, are predominantly constructed from smaller building blocks—the tetrahedron, octahedron and pentagonal bipyramid.…”

Section: Resultsmentioning

confidence: 72%

“…In this article, we compare the low‐energy structures of a copper–silver sub‐nanometre cluster in the gas phase for Gupta potential and DFT levels of theory, and map the energy landscape with a range of statistical tools. This work utilises the threshold algorithm,31 which has previously been successfully applied to ionic solids,37–39 molecular clusters40 and noble metal clusters41 and has recently been extended to work in tandem with a plane‐wave DFT code for direct electronic structure energy landscape exploration. The activation energy barrier heights30 are calculated for the low‐energy region of the Gupta potential energy surface in Section 2.1.1 and the corresponding tree graph of connectivity is generated.…”

Section: Introductionmentioning

confidence: 99%

Energy Landscape Exploration of Sub‐Nanometre Copper–Silver Clusters

2015

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The energy landscapes of sub-nanometre bimetallic coinage metal clusters are explored with the Threshold Algorithm coupled with the Birmingham Cluster Genetic Algorithm. Global and energetically low-lying minima along with their permutational isomers are located for the Cu(4)Ag(4) cluster with the Gupta potential and density functional theory (DFT). Statistical tools are employed to map the connectivity of the energy landscape and the growth of structural basins, while the thermodynamics of interconversion are probed, based on probability flows between minima. Asymmetric statistical weights are found for pathways across dividing states between stable geometries, while basin volumes are observed to grow independently of the depth of the minimum. The DFT landscape is found to exhibit significantly more frustration than that of the Gupta potential, including several open, pseudo-planar geometries which are energetically competitive with the global minimum. The differences in local minima and their transition barriers between the two levels of theory indicate the importance of explicit electronic structure for even simple, closed shell clusters.

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Tetrahelix Conformations and Transformation Pathways in Pt₁Pd₁₂ Clusters

Cited by 14 publications

References 46 publications

Global optimization of clusters using electronic structure methods

Global optimization of clusters using electronic structure methods

Designing a Bernal Spiral from Patchy Colloids

Energy Landscape Exploration of Sub‐Nanometre Copper–Silver Clusters

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Tetrahelix Conformations and Transformation Pathways in Pt1Pd12 Clusters

Cited by 14 publications

References 46 publications

Global optimization of clusters using electronic structure methods

Global optimization of clusters using electronic structure methods

Designing a Bernal Spiral from Patchy Colloids

Energy Landscape Exploration of Sub‐Nanometre Copper–Silver Clusters

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Tetrahelix Conformations and Transformation Pathways in Pt₁Pd₁₂ Clusters