PUBLICATIONS

Preprints

• Johnson, M. S., Bross, D. H., Zádor, J.: Resolving the Coverage Dependence of Surface Reaction Kinetics with Machine Learning and Automated Quantum Chemistry Workflows. https://doi.org/10.26434/chemrxiv-2024-36w9w 

• Johnson, M. S., Pang, H.-W., Doner, A. C., Green, W. H., Zádor, J.: PySIDT: Subgraph Isomorphic Decision Trees for Molecular Property Prediction. https://doi.org/10.26434/chemrxiv-2024-vbh8g 

• Kreitz, B., Gusmão, G. S., Nai, D., Sahoo, S. J., Peterson, A. A., Bross, D. H., Goldsmith, C. F., Medford, A. J.: Unifying thermochemistry concepts in computational heterogeneous catalysis. https://doi.org/10.26434/chemrxiv-2024-fjfmd 

2024

• Eric J. Bylaska, Ajay Panyala, Nicholas P. Bauman, Bo Peng, Himadri Pathak, Daniel Mejia-Rodriguez, Niranjan Govind, David B. Williams-Young, Edoardo Aprà, Abhishek Bagusetty, Erdal Mutlu, Koblar A. Jackson, Tunna Baruah, Yoh Yamamoto, Mark R. Pederson, Kushantha P. K. Withanage, Jesús N. Pedroza-Montero, Jenna A. Bilbrey,Sutanay Choudhury, Jesun Firoz, Kristina M. Herman, Sotiris S. Xantheas, Paul Rigor, Fernando D. Vila, John J. Rehr, Mimi Fung, Adam Grofe, Conrad Johnston, Nathan Baker, Ken Kaneko, Hongbin Liu,  and Karol Kowalski, Electronic structure simulations in the cloud computing environment, J. Chem. Phys., 2024, accepted. https://doi.org/10.1063/5.0226437 

• Mueller, J. N., Sargsyan, K., Daniels, C., Najm., H. N.: Polynomial Chaos Surrogate Construction for Random Fields with Parametric Uncertainty. SIAM/ASA J. Uncertain. Quantif., 2024, accepted, https://arxiv.org/abs/2311.00553 

• Blais, C., Xu, C., West, R. H.: Uncertainty Quantification of Linear Scaling, Machine Learning, and DFT Derived Thermodynamics for the Catalytic Partial Oxidation of Methane on Rhodium. J. Phys. Chem. C, 2024, accepted https://doi.org/10.1021/acs.jpcc.4c05107

• Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization. Nat. Comm., 2024, accepted

• Blöndal, K., Badger, K., Sargsyan, K., Bross, D. H., Ruscic, B., Goldsmith, C. F.: Importance sampling within configuration space integration for adsorbate thermophysical properties: a case study for CH3/Ni(111). Phys. Chem. Chem. Phys., 2024, Advance article, https://doi.org/10.1039/D4CP01197J

• Xu, C., Mazeau, E. J., West, R. H.: Implementing the Blowers Masel Approximation to Scale Activation Energy Based on Reaction Enthalpy in Mean-Field Microkinetic Modeling for Catalytic Methane Partial Oxidation. ACS Catalysis, 2024, 14, 8013–8029 https://doi.org/10.1021/acscatal.3c05436

• Johnson, M. S., Mueller, J. N., Daniels, C., Najm, H. N., Zádor, J.: Diffusion limited kinetics in reactive systems. J. Phys. Chem. A, 2024, 128, 18, 3685–3702 https://doi.org/10.1021/acs.jpca.4c00727 

• Hansen, N. A., Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L., Zádor, J., Kronawitter, C. X.: The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture. J. Chem. Phys., 2024, 160, 124306 https://doi.org/10.1063/5.0197827 

• Diaz-Ibarra, O. H., Kim, K., Safta, C., Najm, H. N.: CSPlib: A Performance Portable Parallel Software Toolkit for Analyzing Complex Kinetic Mechanisms. Comp. Phys. Comm., 2024,  297, 109069 https://doi.org/10.1016/j.cpc.2023.109069 

• Kreitz, B., Blöndal, K., Badger, K., West, R.H, Goldsmith, C. F.: Automatic Mechanism Generation Involving Kinetics of Surface Reactions with Bidentate Adsorbates. Digital Discovery, Advance aticle, https://doi.org/10.1039/D3DD00184A 

2023

• Kreitz, B., Lott, P., Studt, F., Medford, A. J., Deutschmann, O., Goldsmith, C. F..: Automated Generation of Microkinetics for Heterogeneously Catalyzed Reactions Considering Correlated Uncertainties. Angew. Chem. Int. Ed. 2023, 62, e202306514. https://doi.org/10.1002/anie.202306514 (rated as Very Important Paper)

• Mueller, J. N., Sargsyan, K., Najm, H. N.:Polynomial Chaos Surrogate Construction for Stochastic Models with Parametric Uncertainty, 14th International Conference on Applications of Statistics and Probability in Civil Engineering (ICASP14), Dublin, Ireland, 2023. http://www.tara.tcd.ie/handle/2262/103270 

• Johnson, M. S., Gierada, M., Hermes, E. D., Bross, D. H., Sargsyan, K., Najm, H. N., Zádor, J.: Pynta - An automated workflow for calculation of surface and gas-surface kinetics. J. Chem. Inf. Model., 2023, 63, 16, 5153–5168 https://doi.org/10.1021/acs.jcim.3c00948 

• Kreitz, B., Abeywardane, K., Goldsmith, C. F.: Linking Experimental and Ab Initio Thermochemistry of Adsorbates with a Generalized Thermochemical Hierarchy, J. Chem. Theory Comput., 2023, 13, 19–32 https://doi.org/0.1021/acs.jctc.3c00112 

• Bross, D. H., Bacskay, G. B., Peterson, K. A., Ruscic, B.: Active Thermochemical Tables: Enthalpies of Formation of Bromo- and Iodo-Methanes, Ethenes and Ethynes. J. Phys. Chem A, 2023, 127, 704–723 https://doi.org/10.1021/acs.jpca.2c07897

• Song, D., Bauman, N. P., Prawiroatmodjo, G., Peng, B., Granade. C., Rosso, K. M., Low, G. H., Roetteler, M., Kowalski, K., Bylaska, E. J.: Periodic Plane-Wave Electronic Structure Calculations on Quantum Computers. Materials Theory, 2023, 7, 2, https://doi.org/10.1186/s41313-022-00049-5

• Kim, K.,  Díaz-Ibarra, O. H.,  Najm, H. N.,  Zádor, J., Safta, C.: TChem: A performance portable parallel software toolkit for complex kinetic mechanisms. Comp. Phys. Comm. 2023, 285, 108628. https://doi.org/10.1016/j.cpc.2022.108628 

• Thorpe, J. H., Feller, D., Bross, D. H., Ruscic, B., Stanton, J. F.: Sub 20 cm−1 computational prediction of the CH bond energy – A case of systematic error in computational thermochemistry. Phys. Chem. Chem. Phys., Advance Article, 2022, https://doi.org/10.1039/D2CP03964H

• Blöndal, K., Sargsyan, K., Bross, D. H., Ruscic, B., Goldsmith, C. F.: Configuration Space Integration for Adsorbate Partition Functions: The Effect of Anharmonicity on the Thermophysical Properties of CO--Pt(111) and CH3OH--Cu(111). ACS Cat., 2023, 13, 1, 19–32 

2022

• Perdew,  J. P., Shahi, C., Kaplan, A. D., Song, D., Bylaska, E. J.: Symmetry Breaking with the SCAN Density Functional Describes Strong Correlation in the Singlet Carbon Dimer. J. Phys. Chem. A, 2022, 127, 384–389, https://doi.org/10.1021/acs.jpca.2c07590 

• Bylaska, E. J., Tratnyek, P. G., Torralba-Sanchez. T. L., Edwards, K. C., Dixon, D. A., Pignatello, J. J., Xu, W.: Computational Prediction of the Hydrolysis of 2,4,6-Trinitrotoluene (TNT) and 2,4-Dinitroanisole (DNAN). J. Phys. Chem. A, 2022, 136, 9059-9075, https://doi.org/10.1021/acs.jpca.2c06014 

• Johnson, M. S., Dong, X., Dana, A. G., Chung, Y., Farina, D. Jr., Gillis, R. J., Liu, M., Yee, N. W., Blondal, K., Mazeau, E., Grambow, C. A., Payne, A. M., Spiekermann, K. A., Pang, H.-W., Goldsmith, C. F., West, R. H., Green, W. H.: RMG Database for Chemical Property Prediction. J. Chem. Inf. Model., 62, 20, 4906–4915, 2022, https://doi.org/10.1021/acs.jcim.2c00965 

• Hermes, E. D., Sagsyan, K., Najm, H. N., Zádor, J.: Sella, an open-source automation-friendly molecular saddle point optimizer. J Chem. Theory Comp., 18, 11, 6974–6988, 2022, https://doi.org/10.1021/acs.jctc.2c00395 

• Nguyen, T. L., Bross, D. H., Ruscic, B., Ellison, G. B., Stanton, J. F.: Mechanism, thermochemistry, and kinetics of the reversible reactions: C2H3 + H2 ⇌ C2H4 + H ⇌ C2H5, Faraday Discuss. 2022, 238, 405-430, https://doi.org/10.1039/D1FD00124H

• Wehinger, G. D., Kreitz, B., Goldsmith, C. F.: Non-Idealities in Lab-Scale Kinetic Testing: A Theoretical Study of a Modular Temkin Reactor, Catalysts 2022, 12, 349, https://doi.org/10.3390/catal12030349

• Kreitz, B., Lott, P., Bae, J., Blöndal, K., Angeli, S., Ulissi, Z. W., Studt, F., Goldsmith, C. F., Deutschmann, O.: Detailed Microkinetics for the Oxidation of Exhaust Gas Emissions through Automated Mechanism Generation, ACS Catal. 2022, 12, 18, 11137–11151, https://doi.org/10.1021/acscatal.2c03378

• Kreitz, B., Wehinger, G. D., Goldsmith, F. F., Turek, T.: Microkinetic Modeling of the Transient CO2 Methanation with DFT-Based Uncertainties in a Berty Reactor, ChemCatChem 2022, e202200570, https://doi.org/10.1002/cctc.202200570

• Becerra, A.; Diaz-Ibarra, O. H.; Kim, K.; Debusschere, B.; Walker, E. A.: How a quantum computer could accurately solve a hydrogen-air combustion model, Digital Discovery Advance Article. https://pubs.rsc.org/en/content/articlelanding/2022/DD/D2DD00049K 

• Diaz-Ibarra, O. H.; K, Kyungjoo; Safta, C.; Zádor, J.; Najm, H. N.: Using Computational Singular Perturbation as a Diagnostic Tool in ODE and DAE Systems: A Case Study in Heterogeneous Catalysis, Combust. Theory Model. 2021, 26, 201-227, https://doi.org/10.1080/13647830.2021.2002417

2021

• • • Bylaska, E. J.; Song, D.; Ilton, E. S.; O’Leary, S.; Torralba-Sánchez, T. L.; Tratnyek, P. G.: Chapter Five - Building Toward the Future in Chemical and Materials Simulation with Accessible and Intelligently Designed Web Applications. In Annual reports in computational chemistry, Dixon, D. A., Ed. Elsevier: 2021; Vol. 17, pp 163-208. https://doi.org/10.1016/bs.arcc.2021.09.003 

    • Liu, M.; Grinberg Dana, A.; Johnson, M. S.; Goldman, M. J.; Jocher, A.; Payne, A. M.; Grambow, C. A.; Han, K.; Yee, N. W.; Mazeau, E. J.; Blondal, K.; West, R. H.; Goldsmith, C. F.; Green, W. H.: Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation. J. Chem. Inf. Model. 2021, 61, 2686-2696. https://doi.org/10.1021/acs.jcim.0c01480

    • Ruscic, B.; Bross, D. H.: Active Thermochemical Tables: The Thermophysical and Thermochemical Properties of Methyl, CH3, and Methylene, CH2, Corrected for Nonrigid Rotor and Anharmonic Oscillator Effects. Mol. Phys. 2021, e1969046. https://doi.org/10.1080/00268976.2021.1969046

    • Zaleski, D. P.; Sivaramakrishnan, R.; Weller, H. R.; Seifert, N. A.; Bross, D. H.; Ruscic, B.; Moore, K. B.; Elliott, S. N.; Copan, A. V.; Harding, L. B.; Klippenstein, S. J.; Field, R. W.; Prozument, K., Substitution Reactions in the Pyrolysis of Acetone Revealed Through a Modeling, Experiment, Theory Paradigm. J. Am. Chem. Soc. 2021, 143, 3124-3142. https://doi.org/10.1021/jacs.0c11677

    • Mazeau, E. J.; Satpute, P.; Blöndal, K.; Goldsmith, C. F.; West, R. H., Automated mechanism generation using linear scaling relationships and sensitivity analyses applied to catalytic partial oxidation of methane. ACS Catal. 2021, 11, 7114-7125. https://doi.org/10.1021/acscatal.0c04100

    • Blöndal, K.; Sargsyan, K.; Bross, D. H.; Ruscic, B.; Goldsmith, C. F., Adsorbate Partition Functions via Phase Space Integration: Quantifying the Effect of Translational Anharmonicity on Thermodynamic Properties. J. Phys. Chem. C 2021, 125, 20249-20260. https://doi.org/10.1021/acs.jpcc.1c04009

    • Thorpe, J. H.; Kilburn, J. L.; Feller, D.; Changala, P. B.; Bross, D. H.; Ruscic, B.; Stanton, J. F., Elaborated Thermochemical Treatment of HF, CO, N2, and H2O: Insight into HEAT and its Extensions. J. Chem. Phys. 2021, 155, 184109. https://doi.org/10.1063/5.0069322

    • Kreitz, B.; Sargsyan, K.; Blöndal, K.; Mazeau, E. J.; West, R. H.; Wehinger, G. D.; Turek, T.; Goldsmith, C. F., Quantifying the Impact of Parametric Uncertainty on Automatic Mechanism Generation for CO2 Hydrogenation on Ni(111). JACS Au 2021, 1, 1656-1673., https://doi.org/10.1021/jacsau.1c00276

    • Hermes, E. D.; Sargsyan, K.; Najm, H. N.; Zádor, J., Geometry Optimization Speedup through a Geodesic Approach to Internal Coordinates. J. Chem. Phys. 2021, 155, 094105. https://doi.org/10.1063/5.0060146

    • Kreitz, B.; Wehinger, G. D.; Goldsmith, C. F.; Turek, T. Microkinetic Modeling of the CO2 Desorption from Supported Multifaceted Ni Catalysts. J. Phys. Chem. C 2021, 125, 5, 2984–3000. https://doi.org/10.1021/acs.jpcc.0c09985

    • Bylaska, E. J.; Song, D; Bauman, N. P.; Kowalski, K; Claudino, D. Humble, T. S., Quantum Solvers for Plane-Wave Hamiltonians: Abridging Virtual Spaces Through the Optimization of Pairwise Correlations. Front. Chem. 2021, 9, 603019. https://doi.org/10.3389/fchem.2021.603019

2020

• Bylaska, E. J.; Waters, K.; Hermes, E. D.; Zádor, J.; Rosso, K., A Filon-Like Integration Strategy for Calculating Exact Exchange in Periodic Boundary Conditions: A Plane-Wave DFT Implementation. Mater. Theory 2020, 4, 3. https://doi.org/10.1186/s41313-020-00019-9

2019

• Hermes, E. D.; Sargsyan, K.; Najm, H. N.; Zádor, J., Accelerated Saddle Point Refinement through Full Exploitation of Partial Hessian Diagonalization. J. Chem. Theory Comp. 2019, 15, 6536-6549. https://doi.org/10.1021/acs.jctc.9b00869

• Blondal, K.; Jelic, J.; Mazeau, E.; Studt, F.; West, R. H.; Goldsmith, C. F., Computer-Generated Kinetics for Coupled Heterogeneous/Homogeneous Systems: A Case Study in Catalytic Combustion of Methane on Platinum. Ind. Eng. Chem. Res. 2019, 58, 17682-17691. https://doi.org/10.1021/acs.iecr.9b01464

•  Bross, D. H.; Yu, H.-G.; Harding, L. B.; Ruscic, B., Active Thermochemical Tables: The Partition Function of Hydroxymethyl (CH2OH) Revisited. J. Phys. Chem. A 2019, 123, 4212-4231. https://doi.org/10.1021/acs.jpca.9b02295

• Aprà, E.; Bylaska, E. J.; Jong, W. A. d.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Valiev, M.; Dam, H. J. J. v.; Alexeev, Y.; Anchell, J.; Anisimov, V.; Aquino, F. W.; Atta-Fynn, R.; Autschbach, J.; Bauman, N. P.; Becca, J. C.; Bernholdt, D. E.; Bhaskaran-Nair, K.; Bogatko, S.; Borowski, P.; Boschen, J.; Brabec, J.; Bruner, A.; Cauët, E.; Chen, Y.; Chuev, G. N.; Cramer, C. J.; Daily, J.; Deegan, M. J. O.; Dunning Jr., T. H.; Dupuis, M.; Dyall, K. G.; Fann, G. I.; Fischer, S. A.; Fonari, A.; Früchtl, H.; Gagliardi, L.; Garza, J.; Gawande, N.; Ghosh, S.; Glaesemann, K.; Götz, A. W.; Hammond, J.; Helms, V.; Hermes, E. D.; Hirao, K.; Hirata, S.; Jacquelin, M.; Jensen, L.; Johnson, B. G.; Jónsson, H.; Kendall, R. A.; Klemm, M.; Kobayashi, R.; Konkov, V.; Krishnamoorthy, S.; Krishnan, M.; Lin, Z.; Lins, R. D.; Littlefield, R. J.; Logsdail, A. J.; Lopata, K.; Ma, W.; Marenich, A. V.; Campo, J. M. d.; Mejia-Rodriguez, D.; Moore, J. E.; Mullin, J. M.; Nakajima, T.; Nascimento, D. R.; Nichols, J. A.; Nichols, P. J.; Nieplocha, J.; Otero-de-la-Roza, A.; Palmer, B.; Panyala, A.; Pirojsirikul, T.; Peng, B.; Peverati, R.; Pittner, J.; Pollack, L.; Richard, R. M.; Sadayappan, P.; Schatz, G. C.; Shelton, W. A.; Silverstein, D. W.; Smith, D. M. A.; Soares, T. A.; Song, D.; Swart, M.; Taylor, H. L.; Thomas, G. S.; Tipparaju, V.; Truhlar, D. G.; Tsemekhman, K.; Voorhis, T. V.; Vázquez-Mayagoitia, Á.; Verma, P.; Villa, O.; Vishnu, A.; Vogiatzis, K. D.; Wang, D.; Weare, J. H.; Williamson, M. J.; Windus, T. L.; Woliński, K.; Wong, A. T.; Wu, Q.; Yang, C.; Yu, Q.; Zacharias, M.; Zhang, Z.; Zhao, Y.; Harrison, R. J., NWChem: Past, Present, and Future. J. Chem. Phys. 2020, 152, 184102. https://doi.org/10.1063/5.0004997

• Welch, B. K.; Dawes, R.; Bross, D. H.; Ruscic, B., An Automated Thermochemistry Protocol Based on Explicitly Correlated Coupled-Cluster Theory: The Methyl and Ethyl Peroxy Families. J. Phys. Chem. A 2019, 123, 5673-5682. https://doi.org/10.1021/acs.jpca.9b04381

• Bross, D. H.; Jasper, A. W.; Ruscic, B.; Wagner, A. F., Toward Accurate High Temperature Anharmonic Partition Functions. Proc. Combust. Inst. 2019, 37, 315-322. https://doi.org/10.1016/j.proci.2018.05.028

• Ruscic, B.; Bross, D. H., Thermochemistry. In Mathematical Modeling of Complex Reaction Systems: Pyrolysis and Combustion, Faravelli, T.; Manenti, F.; Ranzi, E. M., Eds. Elsevier: New York, NY, 2019; Vol. 45, pp 3-114.

• Feller, D.; Bross, D. H.; Ruscic, B., Enthalpy of Formation of C2H2O4 (Oxalic Acid) from High- Level Calculations and the Active Thermochemical Tables Approach. J. Phys. Chem. A 2019, 123, 3481-3496. https://doi.org/10.1021/acs.jpca.8b12329

• Thorpe, J. H.; Lopez, C. A.; Nguyen, T. L.; Baraban, J. H.; Bross, D. H.; Ruscic, B.; Stanton, J. F., High-Accuracy Extrapolated Ab Initio Thermochemistry. IV. A Modified Recipe for Computational Efficiency. J. Chem. Phys. 2019, 150, 224102. https://doi.org/10.1063/1.5095937

2018

• Nguyen, T. L.; Thorpe, J. H.; Bross, D. H.; Ruscic, B.; Stanton, J. F., Unimolecular Reaction of Methyl Isocyanide to Acetonitrile: A High-Level Theoretical Study. J. Phys. Chem. Lett. 2018, 9, 2532-2538. https://doi.org/10.1021/acs.jpclett.8b01259