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Wang B, Hilleke KP, Hajinazar S, Frapper G, Zurek E. Structurally Constrained Evolutionary Algorithm for the Discovery and Design of Metastable Phases. J Chem Theory Comput 2023; 19:7960-7971. [PMID: 37856841 DOI: 10.1021/acs.jctc.3c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Metastable materials are abundant in nature and technology, showcasing remarkable properties that inspire innovative materials design. However, traditional crystal structure prediction methods, which rely solely on energetic factors to determine a structure's fitness, are not suitable for predicting the vast number of potentially synthesizable phases that represent a local minimum corresponding to a state in thermodynamic equilibrium. Here, we present a new approach for the prediction of metastable phases with specific structural features and interface this method with the XtalOpt evolutionary algorithm. Our method relies on structural features that include the local crystalline order (e.g, the coordination number or chemical environment), and symmetry (e.g, Bravais lattice and space group) to filter the breeding pool of an evolutionary crystal structure search. The effectiveness of this approach is benchmarked on three known metastable systems: XeN8, with a two-dimensional polymeric nitrogen sublattice, brookite TiO2, and a high pressure BaH4 phase, which was recently characterized. Additionally, a newly predicted metastable melaminate salt, P1̅ WC3N6, was found to possess an energy that is lower than that of two phases proposed in a recent computational study. The method presented here could help in identifying the structures of compounds that have already been synthesized, and in developing new synthesis targets with desired properties.
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Affiliation(s)
- Busheng Wang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Katerina P Hilleke
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Samad Hajinazar
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Gilles Frapper
- Applied Quantum Chemistry Group, E4 Team, IC2MP UMR 7285, Université de Poitiers, CNRS, Poitiers 86073, France
| | - Eva Zurek
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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Energy landscapes of perfect and defective solids: from structure prediction to ion conduction. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02834-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractThe energy landscape concept is increasingly valuable in understanding and unifying the structural, thermodynamic and dynamic properties of inorganic solids. We present a range of examples which include (i) structure prediction of new bulk phases including carbon nitrides, phosphorus carbides, LiMgF3 and low-density, ultra-flexible polymorphs of B2O3, (ii) prediction of graphene and related forms of ZnO, ZnS and other compounds which crystallise in the bulk with the wurtzite structure, (iii) solid solutions, (iv) understanding grossly non-stoichiometric oxides including the superionic phases of δ-Bi2O3 and BIMEVOX and the consequences for the mechanisms of ion transport in these fast ion conductors. In general, examination of the energy landscapes of disordered materials highlights the importance of local structural environments, rather than sole consideration of the average structure.
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Kirchhoff B, Jónsson EÖ, Dohn AO, Jacob T, Jónsson H. Elastic Collision Based Dynamic Partitioning Scheme for Hybrid Simulations. J Chem Theory Comput 2021; 17:5863-5875. [PMID: 34460258 DOI: 10.1021/acs.jctc.1c00522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In hybrid simulations, such as the QM/MM approach, the system is partitioned into regions that are treated at different levels of theory. The key question then becomes how to evaluate the interactions between particles on opposite sides of the boundary. One approach is to place the boundary in such a way that particles near the boundary on both sides are of the same type, thus simplifying the evaluation of the interactions. If mobile particles are present, such as solvent molecules, and particles are allowed to cross the boundary, the conservation of energy and atomic forces is problematic unless the computational effort is increased significantly. By preventing particles from crossing the boundary but allowing the boundary to be flexible, an accurate estimate of average thermodynamic properties is obtained in principle as illustrated by the flexible inner region ensemble separator (FIRES) method [C. Rowley and B. Roux, J. Chem. Theory Comput. 2012, 8, 3526]. In FIRES, a harmonic restraint is applied to particles near the boundary. Therefore, it can occur that particle cross the boundary to some extent resulting in anomalies in the particle density. Here, a constraint approach is presented where particles instantaneously scatter from the boundary. This scattering-adapted FIRES (SAFIRES) implementation makes use of a variable-time-step propagation algorithm where the time step is scaled automatically to identify the moment a collision should occur. If the length of the time step is kept constant, this propagator reduces to a regular Langevin dynamics algorithm, and to the velocity Verlet algorithm for conservative dynamics if the friction coefficient is set to zero. Correct average ensemble statistics are obtained as demonstrated in simulations where, for testing purposes, the particles in the two regions are treated at the same level of theory, namely, a homogeneous Lennard-Jones (LJ) liquid and liquid water based on the TIP4P potential function. In order to illustrate this approach in solid-liquid interface simulations, a LJ liquid in contact with the surface of a crystal is also simulated. The simulations using SAFIRES are shown to reproduce the unconstrained reference simulations without significant deviations in the particle density and the dynamics are shown to conserve energy when coupling to the heat bath is turned off.
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Affiliation(s)
- Björn Kirchhoff
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Asmus Ougaard Dohn
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland.,Technical University of Denmark, Lyngby, Denmark
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.,Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtz-Straße 16, 89081 Ulm, Germany.,Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
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Banerjee A, Jasrasaria D, Niblett SP, Wales DJ. Crystal Structure Prediction for Benzene Using Basin-Hopping Global Optimization. J Phys Chem A 2021; 125:3776-3784. [PMID: 33881850 PMCID: PMC8279651 DOI: 10.1021/acs.jpca.1c00903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/07/2021] [Indexed: 11/29/2022]
Abstract
Organic molecules can be stable in distinct crystalline forms, known as polymorphs, which have significant consequences for industrial applications. Here, we predict the polymorphs of crystalline benzene computationally for an accurate anisotropic model parametrized to reproduce electronic structure calculations. We adapt the basin-hopping global optimization procedure to the case of crystalline unit cells, simultaneously optimizing the molecular coordinates and unit cell parameters to locate multiple low-energy structures from a variety of crystal space groups. We rapidly locate all the well-established experimental polymorphs of benzene, each of which corresponds to a single local energy minimum of the model. Our results show that basin-hopping can be both an efficient and effective tool for polymorphic crystal structure prediction, requiring no a priori experimental knowledge of cell parameters or symmetry.
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Affiliation(s)
- Atreyee Banerjee
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Max
Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Dipti Jasrasaria
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of California, Berkeley, California 94609, United States
| | - Samuel P. Niblett
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of California, Berkeley, California 94609, United States
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94609, United States
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
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Burnham CJ, English NJ. A New Relatively Simple Approach to Multipole Interactions in Either Spherical Harmonics or Cartesians, Suitable for Implementation into Ewald Sums. Int J Mol Sci 2019; 21:ijms21010277. [PMID: 31906127 PMCID: PMC7017380 DOI: 10.3390/ijms21010277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022] Open
Abstract
We present a novel derivation of the multipole interaction (energies, forces and fields) in spherical harmonics, which results in an expression that is able to exactly reproduce the results of earlier Cartesian formulations. Our method follows the derivations of Smith (W. Smith, CCP5 Newsletter 1998, 46, 18.) and Lin (D. Lin, J. Chem. Phys. 2015, 143, 114115), who evaluate the Ewald sum for multipoles in Cartesian form, and then shows how the resulting expressions can be converted into spherical harmonics, where the conversion is performed by establishing a relation between an inner product on the space of symmetric traceless Cartesian tensors, and an inner product on the space of harmonic polynomials on the unit sphere. We also introduce a diagrammatic method for keeping track of the terms in the multipole interaction expression, such that the total electrostatic energy can be viewed as a 'sum over diagrams', and where the conversion to spherical harmonics is represented by 'braiding' subsets of Cartesian components together. For multipoles of maximum rank n, our algorithm is found to have scaling of n 3.7 vs. n 4.5 for our most optimised Cartesian implementation.
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