PUBLICATIONS

2024

• Johnson, M. S., Mueller, J. N., Daniels, C., Najm, H. N., Zádor, J.: Diffusion limited kinetics in reactive systems. J. Phys. Chem. A, 2024

• 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