Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Roncoroni, Fabrice; Sanz-Matias, Ana; Sundararaman, Siddharth; Prendergast, David

doi:10.1039/d3cp00525a

Title: Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Journal Article · 02 May 2023 · Physical Chemistry Chemical Physics. PCCP

DOI: https://doi.org/10.1039/d3cp00525a · OSTI ID:2293509

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Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Molecular Foundry

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the right questions of MD data we may miss critical information hidden within it. Here we combine dimensionality reduction (UMAP) and unsupervised hierarchical clustering (HDBSCAN) to quantitatively characterize prevalent coordination environments of chemical species within MD data. By focusing on local coordination, we significantly reduce the amount of data to be analyzed by extracting all distinct molecular formulas within a given coordination sphere. We then efficiently combine UMAP and HDBSCAN with alignment or shape-matching algorithms to partition these formulas into structural isomer families indicating their relative populations. The method was employed to reveal details of cation coordination in electrolytes based on molecular liquids.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2293509

Alternate ID(s):: OSTI ID: 1973145

Journal Information:: Physical Chemistry Chemical Physics. PCCP, Journal Name: Physical Chemistry Chemical Physics. PCCP Journal Issue: 19 Vol. 25; ISSN 1463-9076

Publisher:: Royal Society of ChemistryCopyright Statement

Country of Publication:: United States

Language:: English

References (59)

Concentration-dependent ion correlations impact the electrochemical behavior of calcium battery electrolytes Hahn, Nathan T.; Self, Julian; Driscoll, Darren M. Physical Chemistry Chemical Physics, Vol. 24, Issue 2 https://doi.org/10.1039/D1CP04370F	journal	January 2022
Array programming with NumPy Harris, Charles R.; Millman, K. Jarrod; van der Walt, Stéfan J. Nature, Vol. 585, Issue 7825 https://doi.org/10.1038/s41586-020-2649-2	journal	September 2020
The Hungarian method for the assignment problem Kuhn, H. W. Naval Research Logistics Quarterly, Vol. 2, Issue 1-2, p. 83-97 https://doi.org/10.1002/nav.3800020109	journal	March 1955
Electrolyte Solvation Structure Design for Sodium Ion Batteries Tian, Zhengnan; Zou, Yeguo; Liu, Gang Advanced Science, Vol. 9, Issue 22 https://doi.org/10.1002/advs.202201207	journal	June 2022
IRA: A Shape Matching Approach for Recognition and Comparison of Generic Atomic Patterns Gunde, Miha; Salles, Nicolas; Hémeryck, Anne Journal of Chemical Information and Modeling, Vol. 61, Issue 11 https://doi.org/10.1021/acs.jcim.1c00567	journal	October 2021
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling Torrie, G. M.; Valleau, J. P. Journal of Computational Physics, Vol. 23, Issue 2 https://doi.org/10.1016/0021-9991(77)90121-8	journal	February 1977
Optimal Alignment of Structures for Finite and Periodic Systems Griffiths, Matthew; Niblett, Samuel P.; Wales, David J. Journal of Chemical Theory and Computation, Vol. 13, Issue 10 https://doi.org/10.1021/acs.jctc.7b00543	journal	September 2017
Ion Solvation Engineering: How to Manipulate the Multiplicity of the Coordination Environment of Multivalent Ions Baskin, Artem; Prendergast, David The Journal of Physical Chemistry Letters, Vol. 11, Issue 21 https://doi.org/10.1021/acs.jpclett.0c02682	journal	October 2020
Elucidating Solvation Structures for Rational Design of Multivalent Electrolytes—A Review Rajput, Nav Nidhi; Seguin, Trevor J.; Wood, Brandon M. Topics in Current Chemistry, Vol. 376, Issue 3 https://doi.org/10.1007/s41061-018-0195-2	journal	April 2018
Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields Bedrov, Dmitry; Piquemal, Jean-Philip; Borodin, Oleg Chemical Reviews, Vol. 119, Issue 13 https://doi.org/10.1021/acs.chemrev.8b00763	journal	May 2019
Using collective variables to drive molecular dynamics simulations Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme Molecular Physics, Vol. 111, Issue 22-23 https://doi.org/10.1080/00268976.2013.813594	journal	December 2013
Roles of film-forming additives in diluted and concentrated electrolytes for lithium metal batteries: A density functional theory-based approach Bezabh, Hailemariam Kassa; Tsai, Meng-Che; Hagos, Tesfaye Teka Electrochemistry Communications, Vol. 113 https://doi.org/10.1016/j.elecom.2020.106685	journal	April 2020
The structure of interfacial water on gold electrodes studied by x-ray absorption spectroscopy Velasco-Velez, J. -J.; Wu, C. H.; Pascal, T. A. Science, Vol. 346, Issue 6211 https://doi.org/10.1126/science.1259437	journal	October 2014
Solvation and Dynamics of Sodium and Potassium in Ethylene Carbonate from ab Initio Molecular Dynamics Simulations Pham, Tuan Anh; Kweon, Kyoung E.; Samanta, Amit The Journal of Physical Chemistry C, Vol. 121, Issue 40 https://doi.org/10.1021/acs.jpcc.7b06457	journal	September 2017
Methods of Protein Structure Comparison Kufareva, Irina; Abagyan, Ruben Methods in Molecular Biology https://doi.org/10.1007/978-1-61779-588-6_10	book	January 2011
Nonaqueous Liquid Electrolytes for Lithium-Based Rechargeable Batteries Xu, Kang Chemical Reviews, Vol. 104, Issue 10, p. 4303-4418 https://doi.org/10.1021/cr030203g	journal	October 2004
The solvation structure, transport properties and reduction behavior of carbonate-based electrolytes of lithium-ion batteries Hou, Tingzheng; Fong, Kara D.; Wang, Jingyang Chemical Science, Vol. 12, Issue 44 https://doi.org/10.1039/D1SC04265C	journal	January 2021
Escaping free-energy minima Laio, A.; Parrinello, M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 20 https://doi.org/10.1073/pnas.202427399	journal	September 2002
The critical role of configurational flexibility in facilitating reversible reactive metal deposition from borohydride solutions Hahn, Nathan T.; Self, Julian; Seguin, Trevor J. Journal of Materials Chemistry A, Vol. 8, Issue 15 https://doi.org/10.1039/D0TA02502J	journal	January 2020
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Using metadynamics to explore complex free-energy landscapes Bussi, Giovanni; Laio, Alessandro Nature Reviews Physics, Vol. 2, Issue 4 https://doi.org/10.1038/s42254-020-0153-0	journal	March 2020
hdbscan: Hierarchical density based clustering McInnes, Leland; Healy, John; Astels, Steve The Journal of Open Source Software, Vol. 2, Issue 11 https://doi.org/10.21105/joss.00205	journal	March 2017
Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins Markwick, Phineus R. L.; Cervantes, Carla F.; Abel, Barrett L. Journal of the American Chemical Society, Vol. 132, Issue 4 https://doi.org/10.1021/ja9093692	journal	February 2010
Canonical dynamics: Equilibrium phase-space distributions Hoover, William G. Physical Review A, Vol. 31, Issue 3 https://doi.org/10.1103/PhysRevA.31.1695	journal	March 1985
In-situ/operando X-ray absorption spectroscopic investigation of the electrode/electrolyte interface on the molecular scale Kao, Li Cheng; Feng, Xuefei; Ha, Yang Surface Science, Vol. 702 https://doi.org/10.1016/j.susc.2020.121720	journal	December 2020
Computational Insight into Calcium–Sulfate Ion Pair Formation Byrne, Emily H.; Raiteri, Paolo; Gale, Julian D. The Journal of Physical Chemistry C, Vol. 121, Issue 46 https://doi.org/10.1021/acs.jpcc.7b09820	journal	November 2017
Rationalizing Calcium Electrodeposition Behavior by Quantifying Ethereal Solvation Effects on Ca ²⁺ Coordination in Well-Dissociated Electrolytes Driscoll, Darren M.; Dandu, Naveen K.; Hahn, Nathan T. Journal of The Electrochemical Society, Vol. 167, Issue 16 https://doi.org/10.1149/1945-7111/abc8e3	journal	December 2020
The Solvation Structure of Mg Ions in Dichloro Complex Solutions from First-Principles Molecular Dynamics and Simulated X-ray Absorption Spectra Wan, Liwen F.; Prendergast, David Journal of the American Chemical Society, Vol. 136, Issue 41 https://doi.org/10.1021/ja505967u	journal	October 2014
Molecular Simulation Analysis and X-ray Absorption Measurement of Ca ²⁺ , K ⁺ and Cl ^- Ions in Solution Dang, Liem X.; Schenter, Gregory K.; Glezakou, Vassiliki-Alexandra The Journal of Physical Chemistry B, Vol. 110, Issue 47 https://doi.org/10.1021/jp064661f	journal	November 2006
Reactivity at the Lithium–Metal Anode Surface of Lithium–Sulfur Batteries Camacho-Forero, Luis E.; Smith, Taylor W.; Bertolini, Samuel The Journal of Physical Chemistry C, Vol. 119, Issue 48 https://doi.org/10.1021/acs.jpcc.5b08254	journal	November 2015
A unified formulation of the constant temperature molecular dynamics methods Nosé, Shuichi The Journal of Chemical Physics, Vol. 81, Issue 1 https://doi.org/10.1063/1.447334	journal	July 1984
Structure and dynamics in the lithium solvation shell of nonaqueous electrolytes Han, Sungho Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-42050-y	journal	April 2019
Probing calcium solvation by XAS, MD and DFT calculations Yang, Feipeng; Liu, Yi-Sheng; Feng, Xuefei RSC Advances, Vol. 10, Issue 46 https://doi.org/10.1039/D0RA05905F	journal	January 2020
“Ion Solvation Spectra”: Free Energy Analysis of Solvation Structures of Multivalent Cations in Aprotic Solvents Baskin, Artem; Prendergast, David The Journal of Physical Chemistry Letters, Vol. 10, Issue 17 https://doi.org/10.1021/acs.jpclett.9b01569	journal	July 2019
Unsupervised learning of atomic environments from simple features Reinhart, Wesley F. Computational Materials Science, Vol. 196 https://doi.org/10.1016/j.commatsci.2021.110511	journal	August 2021
In Situ Chemical Imaging of Solid-Electrolyte Interphase Layer Evolution in Li–S Batteries Nandasiri, Manjula I.; Camacho-Forero, Luis E.; Schwarz, Ashleigh M. Chemistry of Materials, Vol. 29, Issue 11 https://doi.org/10.1021/acs.chemmater.7b00374	journal	May 2017
Molecular-Scale Structure of Electrode–Electrolyte Interfaces: The Case of Platinum in Aqueous Sulfuric Acid Wu, Cheng Hao; Pascal, Tod A.; Baskin, Artem Journal of the American Chemical Society, Vol. 140, Issue 47 https://doi.org/10.1021/jacs.8b09743	journal	October 2018
Detecting the First Hydration Shell Structure around Biomolecules at Interfaces Konstantinovsky, Daniel; Perets, Ethan A.; Santiago, Ty ACS Central Science, Vol. 8, Issue 10 https://doi.org/10.1021/acscentsci.2c00702	journal	September 2022
25Mg NMR and computational modeling studies of the solvation structures and molecular dynamics in magnesium based liquid electrolytes Hu, Jian Zhi; Rajput, Nav Nidhi; Wan, Chuan Nano Energy, Vol. 46 https://doi.org/10.1016/j.nanoen.2018.01.051	journal	April 2018
Molecular Dynamics Simulations of Electrolyte Solutions at the (100) Goethite Surface Kerisit, Sebastien; Ilton, Eugene S.; Parker, Stephen C. The Journal of Physical Chemistry B, Vol. 110, Issue 41 https://doi.org/10.1021/jp0636569	journal	October 2006
Insights into Spontaneous Solid Electrolyte Interphase Formation at Magnesium Metal Anode Surface from Ab Initio Molecular Dynamics Simulations Agarwal, Garvit; Howard, Jason D.; Prabhakaran, Venkateshkumar ACS Applied Materials & Interfaces, Vol. 13, Issue 32 https://doi.org/10.1021/acsami.1c07864	journal	August 2021
Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics ^† Raiteri, Paolo; Laio, Alessandro; Gervasio, Francesco Luigi The Journal of Physical Chemistry B, Vol. 110, Issue 8 https://doi.org/10.1021/jp054359r	journal	March 2006
Applying Classical, Ab Initio, and Machine-Learning Molecular Dynamics Simulations to the Liquid Electrolyte for Rechargeable Batteries Yao, Nan; Chen, Xiang; Fu, Zhong-Heng Chemical Reviews, Vol. 122, Issue 12 https://doi.org/10.1021/acs.chemrev.1c00904	journal	May 2022
Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning Rupp, Matthias; Tkatchenko, Alexandre; Müller, Klaus-Robert Physical Review Letters, Vol. 108, Issue 5 https://doi.org/10.1103/PhysRevLett.108.058301	journal	January 2012
Solvation Structure and Dynamics of Mg(TFSI) ₂ Aqueous Electrolyte Yu, Zhou; Juran, Taylor R.; Liu, Xinyi ENERGY & ENVIRONMENTAL MATERIALS https://doi.org/10.1002/eem2.12174	journal	February 2021
Boosting the Optimization of Lithium Metal Batteries by Molecular Dynamics Simulations: A Perspective Sun, Yawen; Yang, Tingzhou; Ji, Haoqing Advanced Energy Materials, Vol. 10, Issue 41 https://doi.org/10.1002/aenm.202002373	journal	September 2020
X-Ray Absorption Spectra of Water from First Principles Calculations Prendergast, David; Galli, Giulia Physical Review Letters, Vol. 96, Issue 21 https://doi.org/10.1103/PhysRevLett.96.215502	journal	May 2006
seaborn: statistical data visualization Waskom, Michael Journal of Open Source Software, Vol. 6, Issue 60 https://doi.org/10.21105/joss.03021	journal	April 2021
A shortest augmenting path algorithm for dense and sparse linear assignment problems Jonker, R.; Volgenant, A. Computing, Vol. 38, Issue 4 https://doi.org/10.1007/BF02278710	journal	December 1987
Preventing Electrolyte Decomposition on a Ca Metal Electrode Interface Using an Artificial Solid‐Electrolyte Interphase Young, Joshua; Smeu, Manuel Advanced Theory and Simulations, Vol. 4, Issue 8 https://doi.org/10.1002/adts.202100018	journal	July 2021
Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids Sambasivarao, Somisetti V.; Acevedo, Orlando Journal of Chemical Theory and Computation, Vol. 5, Issue 4 https://doi.org/10.1021/ct900009a	journal	March 2009
Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan The Journal of Physical Chemistry Letters, Vol. 6, Issue 12 https://doi.org/10.1021/acs.jpclett.5b00831	journal	June 2015
Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J. The Journal of Physical Chemistry C, Vol. 120, Issue 14 https://doi.org/10.1021/acs.jpcc.6b00443	journal	March 2016
LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales Thompson, Aidan P.; Aktulga, H. Metin; Berger, Richard Computer Physics Communications, Vol. 271 https://doi.org/10.1016/j.cpc.2021.108171	journal	February 2022
Stability of Calcium Ion Battery Electrolytes: Predictions from Ab Initio Molecular Dynamics Simulations Yamijala, Sharma S. R. K. C.; Kwon, Hyuna; Guo, Juchen ACS Applied Materials & Interfaces, Vol. 13, Issue 11 https://doi.org/10.1021/acsami.0c21716	journal	March 2021
PACKMOL: A package for building initial configurations for molecular dynamics simulations Martínez, L.; Andrade, R.; Birgin, E. G. Journal of Computational Chemistry, Vol. 30, Issue 13 https://doi.org/10.1002/jcc.21224	journal	October 2009
Algorithms and codes for the assignment problem Carpaneto, Giorgio; Martello, Silvano; Toth, Paolo Annals of Operations Research, Vol. 13, Issue 1 https://doi.org/10.1007/BF02288323	journal	December 1988
Applying machine learning techniques to predict the properties of energetic materials Elton, Daniel C.; Boukouvalas, Zois; Butrico, Mark S. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-27344-x	journal	June 2018
Probing the Hydration Structure of Polarizable Halides: A Multiedge XAFS and Molecular Dynamics Study of the Iodide Anion Fulton, John L.; Schenter, Gregory K.; Baer, Marcel D. The Journal of Physical Chemistry B, Vol. 114, Issue 40 https://doi.org/10.1021/jp106378p	journal	October 2010

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