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Pracht P, Grimme S, Bannwarth C, Bohle F, Ehlert S, Feldmann G, Gorges J, Müller M, Neudecker T, Plett C, Spicher S, Steinbach P, Wesołowski PA, Zeller F. CREST-A program for the exploration of low-energy molecular chemical space. J Chem Phys 2024; 160:114110. [PMID: 38511658 DOI: 10.1063/5.0197592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Chem. Phys. 22, 7169 (2020)] as an automated driver for calculations at the extended tight-binding level (xTB), it offers a variety of molecular- and metadynamics simulations, geometry optimization, and molecular structure analysis capabilities. Implemented algorithms include automated procedures for conformational sampling, explicit solvation studies, the calculation of absolute molecular entropy, and the identification of molecular protonation and deprotonation sites. Calculations are set up to run concurrently, providing efficient single-node parallelization. CREST is designed to require minimal user input and comes with an implementation of the GFNn-xTB Hamiltonians and the GFN-FF force-field. Furthermore, interfaces to any quantum chemistry and force-field software can easily be created. In this article, we present recent developments in the CREST code and show a selection of applications for the most important features of the program. An important novelty is the refactored calculation backend, which provides significant speed-up for sampling of small or medium-sized drug molecules and allows for more sophisticated setups, for example, quantum mechanics/molecular mechanics and minimum energy crossing point calculations.
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Affiliation(s)
- Philipp Pracht
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Sebastian Ehlert
- AI4Science, Microsoft Research, Evert van de Beekstraat 354, 1118 CZ Schiphol, The Netherlands
| | - Gereon Feldmann
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Johannes Gorges
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Marcel Müller
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Tim Neudecker
- Institute for Physical and Theoretical Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Christoph Plett
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | | | - Pit Steinbach
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Patryk A Wesołowski
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Felix Zeller
- Institute for Physical and Theoretical Chemistry, University of Bremen, 28359 Bremen, Germany
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2
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Sanz Matias A, Roncoroni F, Sundararaman S, Prendergast D. Ca-dimers, solvent layering, and dominant electrochemically active species in Ca(BH 4) 2 in THF. Nat Commun 2024; 15:1397. [PMID: 38360965 DOI: 10.1038/s41467-024-45672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 02/01/2024] [Indexed: 02/17/2024] Open
Abstract
Divalent ions (Mg, Ca, and Zn) are being considered as competitive, safe, and earth-abundant alternatives to Li-ion electrochemistry, but present challenges for stable cycling due to undesirable interfacial phenomena. We explore the formation of electroactive species in the electrolyte Ca(BH4)2∣THF using molecular dynamics coupled with a continuum model of bulk and interfacial speciation. Free-energy analysis and unsupervised learning indicate a majority population of neutral Ca dimers and monomers with diverse molecular conformations and an order of magnitude lower concentration of the primary electroactive charged species - the monocation, CaBH[Formula: see text] - produced via disproportionation of neutral complexes. Dense layering of THF molecules within ~1 nm of the electrode surface strongly modulates local electrolyte species populations. A dramatic increase in monocation population in this interfacial zone is induced at negative bias. We see no evidence for electrochemical activity of fully-solvated Ca2+. The consequences for performance are discussed in light of this molecular-scale insight.
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Affiliation(s)
- Ana Sanz Matias
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Fabrice Roncoroni
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Siddharth Sundararaman
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David Prendergast
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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3
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Vásquez-Pérez JM, Zárate-Hernández LÁ, Gómez-Castro CZ, Nolasco-Hernández UA. A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters. J Chem Inf Model 2023; 63:1157-1165. [PMID: 36749172 DOI: 10.1021/acs.jcim.2c01187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present an improved algorithm to solve the near-congruence problem for rigid molecules and clusters based on the iterative application of assignment and alignment steps with biased Euclidean costs. The algorithm is formulated as a quasi-local optimization procedure with each optimization step involving a linear assignment (LAP) and a singular value decomposition (SVD). The efficiency of the algorithm is increased by up to 5 orders of magnitude with respect to the original unbiased noniterative method and can be applied to systems with hundreds or thousands of atoms, outperforming all state-of-the-art methods published so far in the literature. The Fortran implementation of the algorithm is available as an open source library (https://github.com/qcuaeh/molalignlib) and is suitable to be used in global optimization methods for the identification of local minima or basins.
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4
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Gunde M, Salles N, Hémeryck A, Martin-Samos L. IRA: A Shape Matching Approach for Recognition and Comparison of Generic Atomic Patterns. J Chem Inf Model 2021; 61:5446-5457. [PMID: 34704748 DOI: 10.1021/acs.jcim.1c00567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a versatile, parameter-less approach for solving the shape matching problem, specifically in the context of atomic structures when atomic assignments are not known a priori. The algorithm Iteratively suggests Rotated atom-centered reference frames and Assignments (iterative rotations and assignments (IRA)). The frame for which a permutationally invariant set-set distance, namely, the Hausdorff distance, returns a minimal value is chosen as the solution of the matching problem. IRA is able to find rigid rotations, reflections, translations, and permutations between structures with different numbers of atoms, for any atomic arrangement and pattern, periodic or not. When distortions are present between the structures, optimal rotation and translation are found by further applying a standard singular value decomposition-based method. To compute the atomic assignments under the one-to-one assignment constraint, we develop our own algorithm, constrained shortest distance assignments (CShDA). The overall approach is extensively tested on several structures, including distorted structural fragments. The efficiency of the proposed algorithm is shown as a benchmark comparison against two other shape matching algorithms. We discuss the use of our approach for the identification and comparison of structures and structural fragments through two examples: a replica-exchange trajectory of a cyanine molecule, in which we show how our approach could aid the exploration of relevant collective coordinates for clustering the data, and a SiO2 amorphous model, in which we compute distortion scores, and compare them with a classical strain-based potential. The source code and benchmark data are available at https://github.com/mammasmias/IterativeRotationsAssignments.
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Affiliation(s)
- Miha Gunde
- LAAS-CNRS, Université de Toulouse, CNRS, 7 avenue du Colonel Roche, 31031 Toulouse, France.,CNR-IOM, Democritos National Simulation Center, Istituto Officina dei Materiali, c/o SISSA, via Bonomea 265, IT-34136 Trieste, Italy
| | - Nicolas Salles
- CNR-IOM, Democritos National Simulation Center, Istituto Officina dei Materiali, c/o SISSA, via Bonomea 265, IT-34136 Trieste, Italy
| | - Anne Hémeryck
- LAAS-CNRS, Université de Toulouse, CNRS, 7 avenue du Colonel Roche, 31031 Toulouse, France
| | - Layla Martin-Samos
- CNR-IOM, Democritos National Simulation Center, Istituto Officina dei Materiali, c/o SISSA, via Bonomea 265, IT-34136 Trieste, Italy
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5
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RNA Modeling with the Computational Energy Landscape Framework. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2323:49-66. [PMID: 34086273 DOI: 10.1007/978-1-0716-1499-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The recent advances in computational abilities, such as the enormous speed-ups provided by GPU computing, allow for large scale computational studies of RNA molecules at an atomic level of detail. As RNA molecules are known to adopt multiple conformations with comparable energies, but different two-dimensional structures, all-atom models are necessary to better describe the structural ensembles for RNA molecules. This point is important because different conformations can exhibit different functions, and their regulation or mis-regulation is linked to a number of diseases. Problematically, the energy barriers between different conformational ensembles are high, resulting in long time scales for interensemble transitions. The computational potential energy landscape framework was designed to overcome this problem of broken ergodicity by use of geometry optimization. Here, we describe the algorithms used in the energy landscape explorations with the OPTIM and PATHSAMPLE programs, and how they are used in biomolecular simulations. We present a recent case study of the 5'-hairpin of RNA 7SK to illustrate how the method can be applied to interpret experimental results, and to obtain a detailed description of molecular properties.
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6
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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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7
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Moerman E, Furman D, Wales DJ. Development of ReaxFF Reactive Force Field for Aqueous Iron-Sulfur Clusters with Applications to Stability and Reactivity in Water. J Chem Inf Model 2021; 61:1204-1214. [PMID: 33617718 PMCID: PMC8028049 DOI: 10.1021/acs.jcim.0c01292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-sulfur clusters serve unique roles in biochemistry, geochemistry, and renewable energy technologies. However, a full theoretical understanding of their structures and properties is still lacking. To facilitate large-scale reactive molecular dynamics simulations of iron-sulfur clusters in aqueous environments, a ReaxFF reactive force field is developed, based on an extensive set of quantum chemical calculations. This force field compares favorably with the reference calculations on gas-phase species and significantly improves on a previous ReaxFF parametrization. We employ the new potential to study the stability and reactivity of iron-sulfur clusters in explicit water with constant-temperature reactive molecular dynamics. The aqueous species exhibit a dynamic, temperature-dependent behavior, in good agreement with previous much more costly ab initio simulations.
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Affiliation(s)
- Evgeny Moerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road,Cambridge CB2 1EW, United Kingdom
| | - David Furman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road,Cambridge CB2 1EW, United Kingdom.,Division of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road,Cambridge CB2 1EW, United Kingdom
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8
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Weng J, Yang M, Wang W, Xu X, Tian Z. Revealing Thermodynamics and Kinetics of Lipid Self-Assembly by Markov State Model Analysis. J Am Chem Soc 2020; 142:21344-21352. [PMID: 33314927 DOI: 10.1021/jacs.0c09343] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Self-assembly is ubiquitous in the realm of biology and has become an elegant bottom-up approach to fabricate new materials. Although molecular dynamics (MD) simulations can complement experiments by providing the missing atomic details, it still remains a grand challenge to reveal the thermodynamic and kinetic information on a self-assembly system. In this work, we demonstrate for the first time that the Markov state model analysis can be used to delineate the variation of free energy during the self-assembly process of a typical amphiphilic lipid dipalmitoyl-phosphatidylcholine (DPPC). Free energy profiles against the solvent-accessible surface area and the root-mean-square deviation have been derived from extensive MD results of more than five hundred trajectories, which identified a metastable crossing-cylinder (CC) state and a transition state of the distorted bilayer with a free energy barrier of ∼0.02 kJ mol-1 per DPPC lipid, clarifying a long-standing speculation for 20 years that there exists a free energy barrier during lipid self-assembly. Our simulations also unearth two mesophase structures at the early stage of self-assembly, discovering two assembling pathways to the CC state that have never been reported before. Further thermodynamic analysis derives the contributions from the enthalpy and the entropy terms to the free energy, demonstrating the critical role played by the enthalpy-entropy compensation. Our strategy opens the door to quantitatively understand the self-assembly processes in general and provides new opportunities for identifying common thermodynamic and kinetic patterns in different self-assembly systems and inspiring new ideas for experiments. It may also contribute to the refinement of force field parameters of various self-assembly systems.
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Affiliation(s)
- Jingwei Weng
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Maohua Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Wenning Wang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Zhongqun Tian
- Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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9
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Burke DF, Mantell RG, Pitt CE, Wales DJ. Energy Landscape for the Membrane Fusion Pathway in Influenza A Hemagglutinin From Discrete Path Sampling. Front Chem 2020; 8:575195. [PMID: 33102445 PMCID: PMC7546250 DOI: 10.3389/fchem.2020.575195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/19/2020] [Indexed: 11/22/2022] Open
Abstract
The conformational change associated with membrane fusion for Influenza A Hemagglutinin is investigated with a model based upon pre- and post-fusion structures of the HA2 component. We employ computational methods based on the potential energy landscape framework to obtain an initial path connecting these two end points, which provides the starting point for refinement of a kinetic transition network. Here we employ discrete path sampling, which provides access to the experimental time and length scales via geometry optimization techniques to identify local minima and the transition states that connect them. We then analyse the distinct phases of the predicted pathway in terms of structure and energetics, and compare with available experimental data and previous simulations. Our results provide the foundations for future work, which will address the effect of mutations, changes in pH, and incorporation of additional components, especially the HA1 chain and the fusion peptide.
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Affiliation(s)
- David F. Burke
- EMBL-EBI, Wellcome Genome Campus, Hinxton, United Kingdom
- David F. Burke
| | | | - Catherine E. Pitt
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: David J. Wales
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10
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Röder K, Wales DJ. Improving double-ended transition state searches for soft-matter systems. J Chem Phys 2020; 153:034104. [PMID: 32716181 DOI: 10.1063/5.0011829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Transitions between different stable configurations of biomolecules are important in understanding disease mechanisms, structure-function relations, and novel molecular-scale engineering. The corresponding pathways can be characterized efficiently using geometry optimization schemes based on double-ended transition state searches. An interpolation is first constructed between the known states and then refined, yielding a band that contains transition state candidates. Here, we analyze an example where various interpolation schemes lead to bands with a single step transition, but the correct pathway actually proceeds via an intervening, low-energy minimum. We compare a number of different interpolation schemes for this problem. We systematically alter the number of discrete images in the interpolations and the spring constants used in the optimization and test two schemes for adjusting the spring constants and image distribution, resulting in a total of 2760 different connection attempts. Our results confirm that optimized bands are not necessarily a good description of the transition pathways in themselves, and further refinement to actually converge transition states and establish their connectivity is required. We see an improvement in the optimized bands if we employ the adjustment of spring constants with doubly-nudged elastic band and a smaller improvement from the image redistribution. The example we consider is representative of numerous cases we have encountered in a wide variety of molecular and condensed matter systems.
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Affiliation(s)
- K Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - D J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
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11
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Abstract
We report an embarrassingly parallel method for the evaluation of thermodynamic properties over an energy landscape exhibiting broken ergodicity, nested is the likelihood of the observed data D givenbasin-sampling (NBS). We also introduce the No Galilean U-Turn Sampler (NoGUTS), a new sampling scheme based on the No U-Turn Sampler (NUTS) introduced by Hoffman and Gelman (2014) that works with the Galilean Monte Carlo scheme introduced by Betancourt (2012) to aid the efficient generation of new live points. NoGUTS can be thought of as a form of reflective slice sampling with an automatic stopping criterion. We apply this approach to a benchmark atomic cluster of 31 Lennard-Jones atoms, which exhibits a low temperature solid-solid heat capacity peak. The calculated heat capacity is compared with results generated by parallel tempering (PT), basin-sampling parallel tempering (BSPT), and standard nested sampling (NS) simulations. NBS reproduces the full heat capacity curve predicted by PT and BSPT, while the NS calculation with similar computational cost fails to resolve the low-temperature solid-solid phase transition.
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Affiliation(s)
- Matthew Griffiths
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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12
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Blatov IA, Kitaeva EV, Shevchenko AP, Blatov VA. A universal algorithm for finding the shortest distance between systems of points. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2019; 75:827-832. [PMID: 31692457 DOI: 10.1107/s2053273319011628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/20/2019] [Indexed: 11/10/2022]
Abstract
Three universal algorithms for geometrical comparison of abstract sets of n points in the Euclidean space R3 are proposed. It is proved that at an accuracy ε the efficiency of all the algorithms does not exceed O(n3/ε3/2). The most effective algorithm combines the known Hungarian and Kabsch algorithms, but is free of their deficiencies and fast enough to match hundreds of points. The algorithm is applied to compare both finite (ligands) and periodic (nets) chemical objects.
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Affiliation(s)
- Igor A Blatov
- Volga State University of Telecommunications and Informatics, Moskovskoe sh. 77, Samara, 443010, Russian Federation
| | - Elena V Kitaeva
- Samara Center for Theoretical Material Science (SCTMS), Samara University, Ac. Pavlov Street 1, Samara, 443011, Russian Federation
| | - Alexander P Shevchenko
- Samara Center for Theoretical Material Science (SCTMS), Samara University, Ac. Pavlov Street 1, Samara, 443011, Russian Federation
| | - Vladislav A Blatov
- Samara Center for Theoretical Material Science (SCTMS), Samara University, Ac. Pavlov Street 1, Samara, 443011, Russian Federation
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13
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Sachse T, Martínez TJ, Dietzek B, Presselt M. A program for automatically predicting supramolecular aggregates and its application to urea and porphin. J Comput Chem 2018; 39:763-772. [PMID: 29297589 DOI: 10.1002/jcc.25151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/04/2017] [Accepted: 12/07/2017] [Indexed: 11/08/2022]
Abstract
Not only the molecular structure but also the presence or absence of aggregates determines many properties of organic materials. Theoretical investigation of such aggregates requires the prediction of a suitable set of diverse structures. Here, we present the open-source program EnergyScan for the unbiased prediction of geometrically diverse sets of small aggregates. Its bottom-up approach is complementary to existing ones by performing a detailed scan of an aggregate's potential energy surface, from which diverse local energy minima are selected. We crossvalidate this approach by predicting both literature-known and heretofore unreported geometries of the urea dimer. We also predict a diverse set of dimers of the less intensely studied case of porphin, which we investigate further using quantum chemistry. For several dimers, we find strong deviations from a reference absorption spectrum, which we explain using computed transition densities. This proof of principle clearly shows that EnergyScan successfully predicts aggregates exhibiting large structural and spectral diversity. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Torsten Sachse
- Friedrich Schiller University, Institute of Physical Chemistry, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology Jena (IPHT), Research Department Functional Interfaces, Albert-Einstein-Straße 9, Jena, 07745, Germany
| | - Todd J Martínez
- Stanford University, Department of Chemistry and the PULSE Institute, 333 Campus Drive, Stanford, California 94305.,SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, California, 94025
| | - Benjamin Dietzek
- Friedrich Schiller University, Institute of Physical Chemistry, Helmholtzweg 4, 07743, Jena, Germany.,Center for Energy and Environmental Chemistry Jena, Humboldtstraße 10, Jena, 07743, Germany
| | - Martin Presselt
- Leibniz Institute of Photonic Technology Jena (IPHT), Research Department Functional Interfaces, Albert-Einstein-Straße 9, Jena, 07745, Germany.,SciClus GmbH & Co. KG, Moritz-von-Rohr-Straße 1a, Jena, 07745, Germany
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14
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Zhai H, Alexandrova AN. Local Fluxionality of Surface-Deposited Cluster Catalysts: The Case of Pt 7 on Al 2O 3. J Phys Chem Lett 2018; 9:1696-1702. [PMID: 29551071 DOI: 10.1021/acs.jpclett.8b00379] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Subnano surface-supported catalytic clusters can be generally characterized by many low-energy isomers accessible at elevated temperatures of catalysis. The most stable isomer may not be the most catalytically active. Additionally, isomers may interconvert across barriers, i.e., exhibit fluxionality, during catalysis. To study the big picture of the cluster fluxional behavior, we model such a process as isomerization graph using bipartite matching algorithm, harmonic transition state theory, and paralleled nudged elastic band method. All the minimal energy paths form a minimum spanning tree (MST) of the original graph. Detailed inspection shows that, at temperatures typical for catalysis, the cluster geometry changes frequently within several regions in the MST, while transition across regions is less likely. As a further confirmation, the structural similarity analysis was additionally performed based on molecular dynamics trajectories. This local fluxionality picture provides a new perspective on understanding finite-temperate catalytic processes.
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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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