MechaSuite: An Integrated Software for Chemical Reaction Mechanism Analysis and Microkinetic Modeling

Vista sencilla de ítem
dc.contributor.affiliationInstituto Universitario Mixto de Tecnología Química
dc.contributor.authorMillán-Cabrera, Reisel
dc.contributor.authorMiguel
dc.contributor.authorMisturini, Alechaniaes_ES
dc.contributor.funderEuropean Social Fundes_ES
dc.contributor.funderAgencia Estatal de Investigaciónes_ES
dc.date.accessioned2026-05-18T09:32:28Z
dc.date.available2026-05-18T09:32:28Z
dc.date.issued2026-05es_ES
dc.description.abstract[EN] We present MechaSuite, an open-source modular software suite designed to streamline the analysis of quantum-chemical reaction mechanisms. MechaSuite combines an intuitive data manager (MechaData), a molecular geometry editor (MechaEdit), and a microkinetic modeling engine (MechaKinetics). It facilitates the calculation of thermodynamic and kinetic parameters from quantum chemical outputs, the visualization and editing of molecular structures, and the simulation of complex reaction networks. This integration enables chemists to transition seamlessly from ab initio calculations to kinetic predictions in a user-friendly and efficient manner. MechaSuite is primarily implemented in Python with its high-performance 3D visualization engine written in C++ for optimal rendering and interactivity.es_ES
dc.description.accrualMethodSes_ES
dc.description.bibliographicCitationMillán-Cabrera, Reisel;Miguel;Misturini, A. (2026). MechaSuite: An Integrated Software for Chemical Reaction Mechanism Analysis and Microkinetic Modeling. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.6c00861es_ES
dc.description.referencesEyring, H. (1935). The Activated Complex in Chemical Reactions. The Journal of Chemical Physics, 3(2), 107-115. https://doi.org/10.1063/1.1749604es_ES
dc.description.referencesBecke, A. D. (2014). Perspective: Fifty years of density-functional theory in chemical physics. The Journal of Chemical Physics, 140(18). https://doi.org/10.1063/1.4869598es_ES
dc.description.referencesRiley, K. E., Op’t Holt, B. T., & Merz, K. M. (2007). Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties. Journal of Chemical Theory and Computation, 3(2), 407-433. https://doi.org/10.1021/ct600185aes_ES
dc.description.referencesNeese, F. (2011). The ORCA program system. WIREs Computational Molecular Science, 2(1), 73-78. Portico. https://doi.org/10.1002/wcms.81es_ES
dc.description.referencesShao, Y., Gan, Z., Epifanovsky, E., Gilbert, A. T. B., Wormit, M., Kussmann, J., Lange, A. W., Behn, A., Deng, J., Feng, X., Ghosh, D., Goldey, M., Horn, P. R., Jacobson, L. D., Kaliman, I., Khaliullin, R. Z., Kuś, T., Landau, A., Liu, J., et al. (2014). Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Molecular Physics, 113(2), 184-215. https://doi.org/10.1080/00268976.2014.952696es_ES
dc.description.referencesKresse, G., & Furthmüller, J. (1996). Efficient iterative schemes for<i>ab initio</i>total-energy calculations using a plane-wave basis set. Physical Review B, 54(16), 11169-11186. https://doi.org/10.1103/physrevb.54.11169es_ES
dc.description.referencesLuchini, G., Alegre-Requena, J. V., Funes-Ardoiz, I., & Paton, R. S. (2020). GoodVibes: automated thermochemistry for heterogeneous computational chemistry data. F1000Research, 9, 291. https://doi.org/10.12688/f1000research.22758.1es_ES
dc.description.referencesBhoorasingh, P. L., Slakman, B. L., Seyedzadeh Khanshan, F., Cain, J. Y., & West, R. H. (2017). Automated Transition State Theory Calculations for High-Throughput Kinetics. The Journal of Physical Chemistry A, 121(37), 6896-6904. https://doi.org/10.1021/acs.jpca.7b07361es_ES
dc.description.referencesGao, C. W., Allen, J. W., Green, W. H., & West, R. H. (2016). Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms. Computer Physics Communications, 203, 212-225. https://doi.org/10.1016/j.cpc.2016.02.013es_ES
dc.description.referencesLiu, 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. (2021). Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation. Journal of Chemical Information and Modeling, 61(6), 2686-2696. https://doi.org/10.1021/acs.jcim.0c01480es_ES
dc.description.referencesJohnson, M. S., Dong, X., Grinberg Dana, A., Chung, Y., Farina, D., 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. (2022). RMG Database for Chemical Property Prediction. Journal of Chemical Information and Modeling, 62(20), 4906-4915. https://doi.org/10.1021/acs.jcim.2c00965es_ES
dc.description.referencesSchneider, F. S. S., & Caramori, G. F. (2022). Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions. Journal of Computational Chemistry, 44(3), 209-217. Portico. https://doi.org/10.1002/jcc.26861es_ES
dc.description.referencesGEEM lab. Overreact . https://github.com/geem-lab/overreact (accessed 2026–03–18).es_ES
dc.description.referencesHjorth Larsen, A., Jørgen Mortensen, J., Blomqvist, J., Castelli, I. E., Christensen, R., Dułak, M., Friis, J., Groves, M. N., Hammer, B., Hargus, C., Hermes, E. D., Jennings, P. C., Bjerre Jensen, P., Kermode, J., Kitchin, J. R., Leonhard Kolsbjerg, E., Kubal, J., Kaasbjerg, K., Lysgaard, S., et al. (2017). The atomic simulation environment—a Python library for working with atoms. Journal of Physics: Condensed Matter, 29(27), 273002. https://doi.org/10.1088/1361-648x/aa680ees_ES
dc.description.referencesKrep, L., Roy, I. S., Kopp, W., Schmalz, F., Huang, C., & Leonhard, K. (2022). Efficient Reaction Space Exploration with ChemTraYzer-TAD. Journal of Chemical Information and Modeling, 62(4), 890-902. https://doi.org/10.1021/acs.jcim.1c01197es_ES
dc.description.referencesVan de Vijver, R., & Zádor, J. (2020). KinBot: Automated stationary point search on potential energy surfaces. Computer Physics Communications, 248, 106947. https://doi.org/10.1016/j.cpc.2019.106947es_ES
dc.description.referencesGoodwin, D. G.; Moffat, H. K.; Schoegl, I.; Speth, R. L.; Weber, B. W. Cantera: An Object-oriented Software Toolkit for Chemical Kinetics, Thermodynamics, and Transport Processes; Cantera Developers, 2025. https://www.cantera.org.es_ES
dc.description.referencesZhang, Y., Xu, C., & Lan, Z. (2023). Automated Exploration of Reaction Networks and Mechanisms Based on Metadynamics Nanoreactor Simulations. Journal of Chemical Theory and Computation, 19(23), 8718-8731. https://doi.org/10.1021/acs.jctc.3c00752es_ES
dc.description.referencesMedford, A. J., Shi, C., Hoffmann, M. J., Lausche, A. C., Fitzgibbon, S. R., Bligaard, T., & Nørskov, J. K. (2015). CatMAP: A Software Package for Descriptor-Based Microkinetic Mapping of Catalytic Trends. Catalysis Letters, 145(3), 794-807. https://doi.org/10.1007/s10562-015-1495-6es_ES
dc.description.referencesMedasani, B., Kasiraju, S., & Vlachos, D. G. (2023). OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions. Journal of Chemical Information and Modeling, 63(11), 3377-3391. https://doi.org/10.1021/acs.jcim.3c00088es_ES
dc.description.referencesFilot, I. A. W., van Santen, R. A., & Hensen, E. J. M. (2014). The Optimally Performing Fischer–Tropsch Catalyst. Angewandte Chemie International Edition, 53(47), 12746-12750. Portico. https://doi.org/10.1002/anie.201406521es_ES
dc.description.referencesSCM. AMS GUI 2025.1 ; Software for Chemistry and Materials (SCM): Amsterdam, The Netherlands, 2025. http://www.scm.com (accessed 2026–03–18).es_ES
dc.description.referencesRiverbank Computing Ltd. PyQt5 ; 2025. https://pypi.org/project/PyQt5 (accessed 2025–12–13).es_ES
dc.description.referencesHarris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N. J., Kern, R., Picus, M., Hoyer, S., van Kerkwijk, M. H., Brett, M., Haldane, A., del Río, J. F., Wiebe, M., Peterson, P., et al. (2020). Array programming with NumPy. Nature, 585(7825), 357-362. https://doi.org/10.1038/s41586-020-2649-2es_ES
dc.description.referencesHunter, J. D. (2007). Matplotlib: A 2D Graphics Environment. Computing in Science &amp; Engineering, 9(3), 90-95. https://doi.org/10.1109/mcse.2007.55es_ES
dc.description.referencesVirtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., van der Walt, S. J., Brett, M., Wilson, J., Millman, K. J., Mayorov, N., Nelson, A. R. J., Jones, E., Kern, R., Larson, E., et al. (2020). SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods, 17(3), 261-272. https://doi.org/10.1038/s41592-019-0686-2es_ES
dc.description.referencesQt Group. Qt | Tools for Each Stage of Software Development Lifecycle ; 2025. https://www.qt.io (accessed 2025–10–12).es_ES
dc.description.referencesMillan Cabrera, R. Computational study of heterogeneous catalytic systems. Kinetic and structural insights from Density Functional Theory (, ed.) [Universitat Politecnica de Valencia]. https://doi.org/10.4995/thesis/10251/161934es_ES
dc.description.referencesLisboa, F. M., & Pliego, J. R. (2022). SN2 versus E2 reactions in a complex microsolvated environment: theoretical analysis of the equilibrium and activation steps of a nucleophilic fluorination. Journal of Molecular Modeling, 28(6). https://doi.org/10.1007/s00894-022-05160-5es_ES
dc.description.referencesJørgensen, M., & Grönbeck, H. (2018). MonteCoffee: A programmable kinetic Monte Carlo framework. The Journal of Chemical Physics, 149(11). https://doi.org/10.1063/1.5046635es_ES
dc.description.referencesPrats, H., Illas, F., & Sayós, R. (2017). General concepts, assumptions, drawbacks, and misuses in kinetic <scp>M</scp>onte <scp>C</scp>arlo and microkinetic modeling simulations applied to computational heterogeneous catalysis. International Journal of Quantum Chemistry, 118(9). Portico. https://doi.org/10.1002/qua.25518es_ES
dc.description.referencesLorquet, J. C., & Leyh-Nihant, B. (1988). Nonadiabatic unimolecular reactions. 1. A statistical formulation for the rate constants. The Journal of Physical Chemistry, 92(16), 4778-4783. https://doi.org/10.1021/j100327a043es_ES
dc.description.sponsorshipWe thankfully acknowledge Red Espanola de Supercomputacion (RES) for computational resources and technical support, and the computer resources and technical support provided by BSC. M.R. thanks the Spanish Ministry of Science and Innovation for support given through MCIN/AEI/10.13039/501100011033 and also the FSE+ for the scholarship PRE2022-101971.es_ES
dc.identifier.doi10.1021/acs.jcim.6c00861es_ES
dc.identifier.issn1549-9596es_ES
dc.identifier.pmid42087460es_ES
dc.identifier.urihttps://riunet.upv.es/handle/10251/235193
dc.languageIngléses_ES
dc.publisherAmerican Chemical Societyes_ES
dc.relation.ispartofJournal of Chemical Information and Modelinges_ES
dc.relation.pasarelaS\583409es_ES
dc.relation.projectIDinfo:eu-repo/grantAgreement/AEI//PRE2022-101971/es_ES
dc.relation.publisherversionhttps://doi.org/10.1021/acs.jcim.6c00861es_ES
dc.rightsReconocimiento (by)es_ES
dc.rights.accessRightsAbiertoes_ES
dc.subjectReaction mechanism analysises_ES
dc.subjectQuantum chemistry softwarees_ES
dc.subjectMicrokinetic modelinges_ES
dc.subjectKinetic simulationses_ES
dc.subjectOpen-source softwarees_ES
dc.subjectComputational chemistryes_ES
dc.titleMechaSuite: An Integrated Software for Chemical Reaction Mechanism Analysis and Microkinetic Modelinges_ES
dc.typeArtículoes_ES
dc.type.versioninfo:eu-repo/semantics/publishedVersiones_ES
dspace.entity.typePublication
person.identifier689714
person.identifier640810
person.identifier.orcid0000-0002-4489-5411
relation.isAuthorOfPublication73457236-fe1c-4a71-ba8e-7ba710aaf4f7
relation.isAuthorOfPublication355f6d5c-4968-4ed8-b97d-fdedd88b18bb
relation.isAuthorOfPublication.latestForDiscovery73457236-fe1c-4a71-ba8e-7ba710aaf4f7
relation.isOrgUnitOfPublicationb97c2806-5147-442a-a1a8-a2c75cc2a941
relation.isOrgUnitOfPublication.latestForDiscoveryb97c2806-5147-442a-a1a8-a2c75cc2a941
upv.uuidf3fa733f-9dc1-48bd-9870-41e85f577d99es_ES

Archivos

Bloque original

Mostrando 1 - 1 de 1
Miniatura
Nombre:
Millan-CabreraRodenasMisturini - MechaSuite An Integrated Software for Chemical Reaction Mechanis....pdf
Tamaño:
2.1 MB
Formato:
Adobe Portable Document Format
Descripción:
Versión editorial
[object Object] Descargar

Colecciones

Artículos, conferencias, monografías