Automated exploitation of the big configuration space of large adsorbates on transition metals reveals chemistry feasibility

Gu, Geun Ho; Lee, Miriam; Jung, Yousung; Vlachos, Dionisios G.

doi:10.1038/s41467-022-29705-7

Automated exploitation of the big configuration space of large adsorbates on transition metals reveals chemistry feasibility

Journal Article · Tue Apr 26 00:00:00 UTC 2022 · Nature Communications

DOI:https://doi.org/10.1038/s41467-022-29705-7· OSTI ID:1904561

^[1]; Lee, Miriam ^[2]; ^[3]; ^[2]

Korea Institute of Energy Technology, Naju (Korea, Republic of); Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of); Korean Institute of Energy Technology (KIST), Naju (Korea, Republic of)
University of Delaware, Newark, DE (United States)
Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of)

Mechanistic understanding of large molecule conversion and the discovery of suitable heterogeneous catalysts have been lagging due to the combinatorial inventory of intermediates and the inability of humans to enumerate all structures. Here, we introduce an automated framework to predict stable configurations on transition metal surfaces and demonstrate its validity for adsorbates with up to 6 carbon and oxygen atoms on 11 metals, enabling the exploration of ~10⁸ potential configurations. It combines a graph enumeration platform, force field, multi-fidelity DFT calculations, and first-principles trained machine learning. Clusters in the data reveal groups of catalysts stabilizing different structures and expose selective catalysts for showcase transformations, such as the ethylene epoxidation on Ag and Cu and the lack of C-C scission chemistry on Au. Deviations from the commonly assumed atom valency rule of small adsorbates are also manifested. This library can be leveraged to identify catalysts for converting large molecules computationally.

View Accepted Manuscript (DOE)

Research Organization:: University of Delaware, Newark, DE (United States)

Sponsoring Organization:: Ministry of Science and ICT; National Research Foundation of Korea; USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0001004

OSTI ID:: 1904561

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 13; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (59)

The Optimally Performing Fischer-Tropsch Catalyst Filot, Ivo A. W.; van Santen, Rutger A.; Hensen, Emiel J. M. Angewandte Chemie International Edition, Vol. 53, Issue 47 https://doi.org/10.1002/anie.201406521	journal	August 2014
Universality in Oxygen Evolution Electrocatalysis on Oxide Surfaces Man, Isabela C.; Su, Hai‐Yan; Calle‐Vallejo, Federico ChemCatChem, Vol. 3, Issue 7 https://doi.org/10.1002/cctc.201000397	journal	March 2011
The relationship between adsorption energies of methyl on metals and the metallic electronic properties: A first-principles DFT study Wang, Gui-Chang; Li, Jun; Xu, Xiu-Fang Journal of Computational Chemistry, Vol. 26, Issue 9 https://doi.org/10.1002/jcc.20225	journal	January 2005
Some Understanding of Fischer–Tropsch Synthesis from Density Functional Theory Calculations Cheng, Jun; Hu, P.; Ellis, Peter Topics in Catalysis, Vol. 53, Issue 5-6 https://doi.org/10.1007/s11244-010-9450-7	journal	February 2010
Global Optimization of Adsorbate–Surface Structures While Preserving Molecular Identity Peterson, Andrew A. Topics in Catalysis, Vol. 57, Issue 1-4 https://doi.org/10.1007/s11244-013-0161-8	journal	October 2013
Methyl on Cu(111)––structural determination including influence of co-adsorbed iodine Pascal, M.; Lamont, C. L. A.; Kittel, M. Surface Science, Vol. 512, Issue 3 https://doi.org/10.1016/S0039-6028(02)01724-7	journal	July 2002
Rhenium promotion of Ag and Cu–Ag bimetallic catalysts for ethylene epoxidation Dellamorte, J. C.; Lauterbach, J.; Barteau, M. A. Catalysis Today, Vol. 120, Issue 2 https://doi.org/10.1016/j.cattod.2006.07.051	journal	February 2007
Building large microkinetic models with first-principles׳ accuracy at reduced computational cost Sutton, Jonathan E.; Vlachos, Dionisios G. Chemical Engineering Science, Vol. 121 https://doi.org/10.1016/j.ces.2014.09.011	journal	January 2015
AFLOW: An automatic framework for high-throughput materials discovery Curtarolo, Stefano; Setyawan, Wahyu; Hart, Gus L. W. Computational Materials Science, Vol. 58 https://doi.org/10.1016/j.commatsci.2012.02.005	journal	June 2012
Electrolysis of water on oxide surfaces Rossmeisl, J.; Qu, Z. -W.; Zhu, H. Journal of Electroanalytical Chemistry, Vol. 607, Issue 1-2 https://doi.org/10.1016/j.jelechem.2006.11.008	journal	September 2007
Intermediates in the hydrogenation of benzene to cyclohexene on Pt(111) and Pd(111): A comparison from DFT calculations Morin, C.; Simon, D.; Sautet, P. Surface Science, Vol. 600, Issue 6 https://doi.org/10.1016/j.susc.2006.01.033	journal	March 2006
Gold-Catalyzed Synthesis of Small Rings Mato, Mauro; Franchino, Allegra; Garcı́a-Morales, Cristina Chemical Reviews, Vol. 121, Issue 14 https://doi.org/10.1021/acs.chemrev.0c00697	journal	November 2020
Understanding Catalytic Activity Trends in the Oxygen Reduction Reaction Kulkarni, Ambarish; Siahrostami, Samira; Patel, Anjli Chemical Reviews, Vol. 118, Issue 5 https://doi.org/10.1021/acs.chemrev.7b00488	journal	December 2017
NWPEsSe: An Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems Zhang, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger Journal of Chemical Theory and Computation, Vol. 16, Issue 6 https://doi.org/10.1021/acs.jctc.9b01107	journal	May 2020
Graph Theory Approach to High-Throughput Surface Adsorption Structure Generation Boes, Jacob R.; Mamun, Osman; Winther, Kirsten The Journal of Physical Chemistry A, Vol. 123, Issue 11 https://doi.org/10.1021/acs.jpca.9b00311	journal	February 2019
Application of Density Functional Tight Binding and Machine Learning to Evaluate the Stability of Biomass Intermediates on the Rh(111) Surface Chang, Chaoyi; Medford, Andrew J. The Journal of Physical Chemistry C, Vol. 125, Issue 33 https://doi.org/10.1021/acs.jpcc.1c05715	journal	August 2021
Group Additivity and Modified Linear Scaling Relations for Estimating Surface Thermochemistry on Transition Metal Surfaces: Application to Furanics Vorotnikov, Vassili; Vlachos, Dionisios G. The Journal of Physical Chemistry C, Vol. 119, Issue 19 https://doi.org/10.1021/acs.jpcc.5b01696	journal	April 2015
Heterogeneous Catalytic Transfer Hydrogenation as an Effective Pathway in Biomass Upgrading Gilkey, Matthew J.; Xu, Bingjun ACS Catalysis, Vol. 6, Issue 3 https://doi.org/10.1021/acscatal.5b02171	journal	January 2016
Mechanism of Dehydration of Phenols on Noble Metals via First-Principles Microkinetic Modeling Gu, Geun Ho; Mullen, Charles A.; Boateng, Akwasi A. ACS Catalysis, Vol. 6, Issue 5 https://doi.org/10.1021/acscatal.6b00776	journal	April 2016
Selectivity of Synthesis Gas Conversion to C ₂₊ Oxygenates on fcc(111) Transition-Metal Surfaces Schumann, Julia; Medford, Andrew J.; Yoo, Jong Suk ACS Catalysis, Vol. 8, Issue 4 https://doi.org/10.1021/acscatal.8b00201	journal	March 2018
Overview of Selective Oxidation of Ethylene to Ethylene Oxide by Ag Catalysts Pu, Tiancheng; Tian, Huijie; Ford, Michael E. ACS Catalysis, Vol. 9, Issue 12 https://doi.org/10.1021/acscatal.9b03443	journal	October 2019
Accurate Multiobjective Design in a Space of Millions of Transition Metal Complexes with Neural-Network-Driven Efficient Global Optimization Janet, Jon Paul; Ramesh, Sahasrajit; Duan, Chenru ACS Central Science, Vol. 6, Issue 4 https://doi.org/10.1021/acscentsci.0c00026	journal	March 2020
Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17 Ruddigkeit, Lars; van Deursen, Ruud; Blum, Lorenz C. Journal of Chemical Information and Modeling, Vol. 52, Issue 11 https://doi.org/10.1021/ci300415d	journal	November 2012
DFT Study of Furfural Conversion to Furan, Furfuryl Alcohol, and 2-Methylfuran on Pd(111) Vorotnikov, Vassili; Mpourmpakis, Giannis; Vlachos, Dionisios G. ACS Catalysis, Vol. 2, Issue 12 https://doi.org/10.1021/cs300395a	journal	October 2012
Catalyst Evaluation for Catalytic Biomass Pyrolysis Samolada, M. C.; Papafotica, A.; Vasalos, I. A. Energy & Fuels, Vol. 14, Issue 6 https://doi.org/10.1021/ef000026b	journal	November 2000
Synthesis of γ-Valerolactone by Hydrogenation of Biomass-derived Levulinic Acid over Ru/C Catalyst Yan, Zhi-pei; Lin, Lu; Liu, Shijie Energy & Fuels, Vol. 23, Issue 8 https://doi.org/10.1021/ef900259h	journal	August 2009
Microkinetic Modeling and Reduced Rate Expressions of Ethylene Hydrogenation and Ethane Hydrogenolysis on Platinum Salciccioli, M.; Chen, Y.; Vlachos, D. G. Industrial & Engineering Chemistry Research, Vol. 50, Issue 1 https://doi.org/10.1021/ie100364a	journal	January 2011
UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations Rappe, A. K.; Casewit, C. J.; Colwell, K. S. Journal of the American Chemical Society, Vol. 114, Issue 25, p. 10024-10035 https://doi.org/10.1021/ja00051a040	journal	December 1992
Catalyst Design by Interpolation in the Periodic Table: Bimetallic Ammonia Synthesis Catalysts Jacobsen, Claus J. H.; Dahl, Søren; Clausen, Bjerne S. Journal of the American Chemical Society, Vol. 123, Issue 34 https://doi.org/10.1021/ja010963d	journal	August 2001
Origin of the Overpotential for Oxygen Reduction at a Fuel-Cell Cathode Nørskov, J. K.; Rossmeisl, J.; Logadottir, A. The Journal of Physical Chemistry B, Vol. 108, Issue 46 https://doi.org/10.1021/jp047349j	journal	November 2004
Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt Sutton, Jonathan E.; Panagiotopoulou, Paraskevi; Verykios, Xenophon E. The Journal of Physical Chemistry C, Vol. 117, Issue 9 https://doi.org/10.1021/jp312593u	journal	February 2013
Probing the Coverage Dependence of Site and Adsorbate Configurational Correlations on (111) Surfaces of Late Transition Metals Xu, Zhongnan; Kitchin, John R. The Journal of Physical Chemistry C, Vol. 118, Issue 44 https://doi.org/10.1021/jp508805h	journal	October 2014
Hydrogen from catalytic reforming of biomass-derived hydrocarbons in liquid water Cortright, R. D.; Davda, R. R.; Dumesic, J. A. Nature, Vol. 418, Issue 6901 https://doi.org/10.1038/nature01009	journal	August 2002
Towards the computational design of solid catalysts Nørskov, J.; Bligaard, T.; Rossmeisl, J. Nature Chemistry, Vol. 1, Issue 1, p. 37-46 https://doi.org/10.1038/nchem.121	journal	April 2009
Effects of correlated parameters and uncertainty in electronic-structure-based chemical kinetic modelling Sutton, Jonathan E.; Guo, Wei; Katsoulakis, Markos A. Nature Chemistry, Vol. 8, Issue 4 https://doi.org/10.1038/nchem.2454	journal	February 2016
Alloys of platinum and early transition metals as oxygen reduction electrocatalysts Greeley, J.; Stephens, I. E. L.; Bondarenko, A. S. Nature Chemistry, Vol. 1, Issue 7, p. 552-556 https://doi.org/10.1038/nchem.367	journal	September 2009
Computational high-throughput screening of electrocatalytic materials for hydrogen evolution Greeley, Jeff; Jaramillo, Thomas F.; Bonde, Jacob Nature Materials, Vol. 5, Issue 11, p. 909-913 https://doi.org/10.1038/nmat1752	journal	October 2006
Understanding trends in C–H bond activation in heterogeneous catalysis Latimer, Allegra A.; Kulkarni, Ambarish R.; Aljama, Hassan Nature Materials, Vol. 16, Issue 2 https://doi.org/10.1038/nmat4760	journal	October 2016
The Open Quantum Materials Database (OQMD): assessing the accuracy of DFT formation energies Kirklin, Scott; Saal, James E.; Meredig, Bryce npj Computational Materials, Vol. 1, Issue 1 https://doi.org/10.1038/npjcompumats.2015.10	journal	December 2015
Statistical learning goes beyond the d-band model providing the thermochemistry of adsorbates on transition metals García-Muelas, Rodrigo; López, Núria Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12709-1	journal	October 2019
Graph theory approach to determine configurations of multidentate and high coverage adsorbates for heterogeneous catalysis Deshpande, Siddharth; Maxson, Tristan; Greeley, Jeffrey npj Computational Materials, Vol. 6, Issue 1 https://doi.org/10.1038/s41524-020-0345-2	journal	June 2020
Catalysis-Hub.org, an open electronic structure database for surface reactions Winther, Kirsten T.; Hoffmann, Max J.; Boes, Jacob R. Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0081-y	journal	May 2019
A theoretical evaluation of possible transition metal electro-catalysts for N ₂ reduction Skúlason, Egill; Bligaard, Thomas; Gudmundsdóttir, Sigrídur Phys. Chem. Chem. Phys., Vol. 14, Issue 3 https://doi.org/10.1039/C1CP22271F	journal	January 2012
Thermochemistry of gas-phase and surface species via LASSO-assisted subgraph selection Gu, Geun Ho; Plechac, Petr; Vlachos, Dionisios G. Reaction Chemistry & Engineering, Vol. 3, Issue 4 https://doi.org/10.1039/C7RE00210F	journal	January 2018
Supported gold nanoparticles as catalysts for organic reactions Corma, Avelino; Garcia, Hermenegildo Chemical Society Reviews, Vol. 37, Issue 9 https://doi.org/10.1039/b707314n	journal	January 2008
The selective hydrogenation of biomass-derived 5-hydroxymethylfurfural using heterogeneous catalysts Alamillo, Ricardo; Tucker, Mark; Chia, Mei Green Chemistry, Vol. 14, Issue 5, p. 1413-1419 https://doi.org/10.1039/c2gc35039d	journal	January 2012
Aqueous-phase hydrogenation and hydrodeoxygenation of biomass-derived oxygenates with bimetallic catalysts Lee, Jechan; Kim, Yong Tae; Huber, George W. Green Chemistry, Vol. 16, Issue 2 https://doi.org/10.1039/c3gc41071d	journal	January 2014
Noble-metal catalyzed hydrodeoxygenation of biomass-derived lignin to aromatic hydrocarbons Laskar, Dhrubojyoti D.; Tucker, Melvin P.; Chen, Xiaowen Green Chemistry, Vol. 16, Issue 2 https://doi.org/10.1039/c3gc42041h	journal	January 2014
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu Grimme, Stefan; Antony, Jens; Ehrlich, Stephan The Journal of Chemical Physics, Vol. 132, Issue 15 https://doi.org/10.1063/1.3382344	journal	April 2010
The structure and chemistry of CH ₃ and CH radicals adsorbed on Ni(111) Yang, Q. Y.; Maynard, K. J.; Johnson, A. D. The Journal of Chemical Physics, Vol. 102, Issue 19 https://doi.org/10.1063/1.469026	journal	May 1995
Commentary: The Materials Project: A materials genome approach to accelerating materials innovation Jain, Anubhav; Ong, Shyue Ping; Hautier, Geoffroy APL Materials, Vol. 1, Issue 1 https://doi.org/10.1063/1.4812323	journal	July 2013
Special points for Brillouin-zone integrations Monkhorst, Hendrik J.; Pack, James D. Physical Review B, Vol. 13, Issue 12, p. 5188-5192 https://doi.org/10.1103/PhysRevB.13.5188	journal	June 1976
High-precision sampling for Brillouin-zone integration in metals Methfessel, M.; Paxton, A. T. Physical Review B, Vol. 40, Issue 6 https://doi.org/10.1103/PhysRevB.40.3616	journal	August 1989
Improved tetrahedron method for Brillouin-zone integrations Blöchl, Peter E.; Jepsen, O.; Andersen, O. K. Physical Review B, Vol. 49, Issue 23 https://doi.org/10.1103/PhysRevB.49.16223	journal	June 1994
Projector augmented-wave method Blöchl, P. E. Physical Review B, Vol. 50, Issue 24, p. 17953-17979 https://doi.org/10.1103/PhysRevB.50.17953	journal	December 1994
Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set Kresse, G.; Furthmüller, J. Physical Review B, Vol. 54, Issue 16, p. 11169-11186 https://doi.org/10.1103/PhysRevB.54.11169	journal	October 1996
Efficient Global Structure Optimization with a Machine-Learned Surrogate Model Bisbo, Malthe K.; Hammer, Bjørk Physical Review Letters, Vol. 124, Issue 8 https://doi.org/10.1103/PhysRevLett.124.086102	journal	February 2020
Generalized Gradient Approximation Made Simple Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868 https://doi.org/10.1103/PhysRevLett.77.3865	journal	October 1996
Trends in the Exchange Current for Hydrogen Evolution Nørskov, J. K.; Bligaard, T.; Logadottir, A. Journal of The Electrochemical Society, Vol. 152, Issue 3 https://doi.org/10.1149/1.1856988	journal	January 2005

Similar Records

A Perturbative Solution for Nonlinear Stratified Upwelling over a Frictional Slope

Journal Article · Sun Oct 01 04:00:00 UTC 2023 · Journal of Physical Oceanography · OSTI ID:2580152

Extensions of the full optimized reaction space model for molecular electronic wavefunctions

Thesis/Dissertation · Sun Jan 01 04:00:00 UTC 1984 · OSTI ID:5363067

Extensions of the full optimized reaction space model for molecular electronic wavefunctions

Technical Report · Sat Dec 01 04:00:00 UTC 1984 · OSTI ID:6275786

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
applied mathematics
bioenergy
computer science
heterogeneous catalysis
method development

Automated exploitation of the big configuration space of large adsorbates on transition metals reveals chemistry feasibility

Citation Formats

References (59)

Similar Records

Related Subjects