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Zhou C, Ieritano C, Hopkins WS. Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility. Front Chem 2019; 7:519. [PMID: 31440497 PMCID: PMC6693329 DOI: 10.3389/fchem.2019.00519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022] Open
Abstract
Evolutionary algorithms such as the basin-hopping (BH) algorithm have proven to be useful for difficult non-linear optimization problems with multiple modalities and variables. Applications of these algorithms range from characterization of molecular states in statistical physics and molecular biology to geometric packing problems. A key feature of BH is the fact that one can generate a coarse-grained mapping of a potential energy surface (PES) in terms of local minima. These results can then be utilized to gain insights into molecular dynamics and thermodynamic properties. Here we describe how one can employ concepts from unsupervised machine learning to augment BH PES searches to more efficiently identify local minima and the transition states connecting them. Specifically, we introduce the concepts of similarity indices, hierarchical clustering, and multidimensional scaling to the BH methodology. These same machine learning techniques can be used as tools for interpreting and rationalizing experimental results from spectroscopic and ion mobility investigations (e.g., spectral assignment, dynamic collision cross sections). We exemplify this in two case studies: (1) assigning the infrared multiple photon dissociation spectrum of the protonated serine dimer and (2) determining the temperature-dependent collision cross-section of protonated alanine tripeptide.
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Affiliation(s)
- Ce Zhou
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
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Abstract
The low-energy region of the potential energy surface (PES) of the protonated phenylalanine/serine dimer is mapped using the basin-hoping search algorithm, and 37 isomers are identified within 180 kJ·mol-1 of the global-minimum structure. Cluster structures are grouped using hierarchical clustering to partition the PES in terms of nuclear configuration. Calculated IR spectra for the various isomers are then compared with the isomer-specific IR spectra by means of the cosine distance metric to facilitate spectral assignment and identify which regions of the PES are populated in the electrospray ionization process.
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Affiliation(s)
- Weiqiang Fu
- Department of Chemistry, University of Waterloo , Waterloo, ON N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo , Waterloo, ON N2L 3G1, Canada
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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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Tamp S, Danilas K, Kreen M, Vares L, Kiirend E, Vija S, Pehk T, Parve O, Metsala A. A total conformational analysis of diastereomeric esters and calculation of their conformational shielding models. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2007.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Massen CP, Doye JPK. Preferential attachment during the evolution of a potential energy landscape. J Chem Phys 2007; 127:114306. [PMID: 17887836 DOI: 10.1063/1.2773721] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has previously been shown that the network of connected minima on a potential energy landscape is scale-free, and that this reflects a power-law distribution for the areas of the basins of attraction surrounding the minima. Here, the aim is to understand more about the physical origins of these puzzling properties by examining how the potential energy landscape of a 13-atom cluster evolves with the range of the potential. In particular, on decreasing the range of the potential the number of stationary points increases and thus the landscape becomes rougher and the network gets larger. Thus, the evolution of the potential energy landscape can be followed from one with just a single minimum to a complex landscape with many minima and a scale-free pattern of connections. It is found that during this growth process, new edges in the network of connected minima preferentially attach to more highly connected minima, thus leading to the scale-free character. Furthermore, minima that appear when the range of the potential is shorter and the network is larger have smaller basins of attraction. As there are many of these smaller basins because the network grows exponentially, the observed growth process thus also gives rise to a power-law distribution for the hyperareas of the basins.
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Affiliation(s)
- Claire P Massen
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Call ST, Zubarev DY, Boldyrev AI. Global minimum structure searches via particle swarm optimization. J Comput Chem 2007; 28:1177-86. [PMID: 17299774 DOI: 10.1002/jcc.20621] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Novel implementation of the evolutionary approach known as particle swarm optimization (PSO) capable of finding the global minimum of the potential energy surface of atomic assemblies is reported. This is the first time the PSO technique has been used to perform global optimization of minimum structure search for chemical systems. Significant improvements have been introduced to the original PSO algorithm to increase its efficiency and reliability and adapt it to chemical systems. The developed software has successfully found the lowest-energy structures of the LJ(26) Lennard-Jones cluster, anionic silicon hydride Si(2)H(5) (-), and triply hydrated hydroxide ion OH(-) (H(2)O)(3). It requires relatively small population sizes and demonstrates fast convergence. Efficiency of PSO has been compared with simulated annealing, and the gradient embedded genetic algorithm.
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Affiliation(s)
- Seth T Call
- Department of Computer Science, Utah State University, Logan, Utah 84322-0300, USA
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Affiliation(s)
- Susan E. Hill
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8-91, P.O. Box 999, Richland, Washington 99352
| | - David Feller
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MS K8-91, P.O. Box 999, Richland, Washington 99352
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Faken DB, Voter AF, Freeman DL, Doll JD. Dimensional Strategies and the Minimization Problem: Barrier-Avoiding Algorithms. J Phys Chem A 1999. [DOI: 10.1021/jp9920949] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel B. Faken
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, Theoretical Division, Los Alamos National Laboratory, Mail Stop B268 Los Alamos, NM 87545, and Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
| | - A. F. Voter
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, Theoretical Division, Los Alamos National Laboratory, Mail Stop B268 Los Alamos, NM 87545, and Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
| | - David L. Freeman
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, Theoretical Division, Los Alamos National Laboratory, Mail Stop B268 Los Alamos, NM 87545, and Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
| | - J. D. Doll
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, Theoretical Division, Los Alamos National Laboratory, Mail Stop B268 Los Alamos, NM 87545, and Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
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Li Z, Laidig KE, Daggett V. Conformational search using a molecular dynamics-minimization procedure: Applications to clusters of coulombic charges, Lennard-Jones particles, and waters. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(19980115)19:1<60::aid-jcc5>3.0.co;2-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Pillardy J, Piela L. Smoothing techniques of global optimization: Distance scaling method in searches for most stable Lennard-Jones atomic clusters. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(199712)18:16<2040::aid-jcc8>3.0.co;2-l] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Wales DJ, Doye JPK. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms. J Phys Chem A 1997. [DOI: 10.1021/jp970984n] [Citation(s) in RCA: 2261] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jonathan P. K. Doye
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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Shamovsky IL, Ross GM, Riopelle RJ, Weaver DF. Theoretical Studies on the Bioactive Conformation of Nerve Growth Factor Using VBMCA Novel Variable Basis Monte Carlo Simulated Annealing Algorithm for Peptides. J Am Chem Soc 1996. [DOI: 10.1021/ja9611194] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Igor L. Shamovsky
- Contribution from the Departments of Chemistry and Medicine, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Gregory M. Ross
- Contribution from the Departments of Chemistry and Medicine, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Richard J. Riopelle
- Contribution from the Departments of Chemistry and Medicine, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Donald F. Weaver
- Contribution from the Departments of Chemistry and Medicine, Queen's University, Kingston, Ontario, Canada K7L 3N6
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