Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes

Rubén Laplaza, Shubhajit Das, Matthew D. Wodrich, Clémence Corminboeuf

Published: 2022-08-16 DOI: 10.1038/s41596-022-00726-2

homogeneous catalysis

volcano plots

activity maps

descriptor variables

Python code

AI 解读

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

Volcano plots and activity maps are powerful tools for studying homogeneous catalysis. Once constructed, they can be used to estimate and predict the performance of a catalyst from one or more descriptor variables. The relevance and utility of these tools
Introduction
Materials
- Procedure
Procedure
Troubleshooting
Timing
Anticipated results
References
ACKNOWLEDGMENTS

Neese, F., Wennmohs, F., Becker, U. & Riplinger, C. The ORCA quantum chemistry program package. J. Chem. Phys. 152, 224108 (2020).
Smith, D. G. A. et al. Psi4 1.4: open-source software for high-throughput quantum chemistry. J. Chem. Phys. 152, 184108 (2020).
Dennington, R., Keith, T. A. & Millam, J. M. GaussView Version 6. (2019).
Hanwell, M. D. et al. Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. J. Cheminformatics 4, 17 (2012).
Hunter, J. D. Matplotlib: A 2D graphics environment. Comp. Sci. Eng. 9, 90–95 (2007).
Uhe, A., Kozuch, S. & Shaik, S. Automatic analysis of computed catalytic cycles. J. Comp. Chem. 32, 978–985 (2010).
Nørskov, J. K. et al. The nature of the active site in heterogeneous metal catalysis. Chem. Soc. Rev. 37, 2163 (2008).
Kulkarni, A., Siahrostami, S., Patel, A. & Nørskov, J. K. Understanding catalytic activity trends in the oxygen reduction reaction. Chem. Rev. 118, 2302–2312 (2018).
Wodrich, M. D., Sawatlon, B., Busch, M. & Corminboeuf, C. The genesis of molecular volcano plots. Acc. Chem. Res. 54, 1107–1117 (2021).
Sabatier, P. Hydrogénations et déshydrogénations par catalyse. Ber. Dtsch. Chem. Ges. 44, 1984–2001 (1911).
Calle-Vallejo, F., Martı́nez, J. I., Garcı́a-Lastra, J. M., Rossmeisl, J. & Koper, M. T. M. Physical and chemical nature of the scaling relations between adsorption energies of atoms on metal surfaces. Phys. Rev. Lett. 108, 116103 (2012).
Busch, M., Wodrich, M. D. & Corminboeuf, C. Linear scaling relationships and volcano plots in homogeneous catalysis—revisiting the Suzuki reaction. Chem. Sci. 6, 6754–6761 (2015).
Bligaard, T. et al. The Brønsted–Evans–Polanyi relation and the volcano curve in heterogeneous catalysis. J. Catal. 224, 206–217 (2004).
Gerischer, H. Mechanismus der elektrolytischen Wasserstoffabscheidung und Adsorptionsenergie von atomarem Wasserstoff. Bull. Soc. Chim. Belg. 67, 506–527 (2010).
Parsons, R. The rate of electrolytic hydrogen evolution and the heat of adsorption of hydrogen. Trans. Faraday Soc. 54, 1053 (1958).
Nørskov, J. K., Bligaard, T., Rossmeisl, J. & Christensen, C. H. Towards the computational design of solid catalysts. Nat. Chem. 1, 37–46 (2009).
Man, I. C. et al. Universality in oxygen evolution electrocatalysis on oxide surfaces. ChemCatChem 3, 1159–1165 (2011).
Medford, A. J. et al. From the Sabatier principle to a predictive theory of transition-metal heterogeneous catalysis. J. Catal. 328, 36–42 (2015).
Medford, A. J. et al. Activity and selectivity trends in synthesis gas conversion to higher alcohols. Top. Catal. 57, 135–142 (2014).
Andersen, M., Medford, A. J., Nørskov, J. K. & Reuter, K. Analyzing the case for bifunctional catalysis. Angew. Chem. Int. Ed. 55, 5210–5214 (2016).
Busch, M. et al. Beyond the top of the volcano? A unified approach to electrocatalytic oxygen reduction and oxygen evolution. Nano Energy 29, 126–135 (2016).
Exner, K. S. Recent advancements towards closing the gap between electrocatalysis and battery science communities: the computational lithium electrode and activity–stability volcano plots. ChemSusChem 12, 2330–2344 (2019).
Anand, M., Rohr, B., Statt, M. J. & Nørskov, J. K. Scaling relationships and volcano plots in homogeneous catalysis. J. Phys. Chem. Lett. 11, 8518–8526 (2020).
Swiegers, G. Mechanical catalysis: Methods of enzymatic, homogeneous, and heterogeneous catalysis. (John Wiley, 2008).
Sues, P. E., Lough, A. J. & Morris, R. H. Stereoelectronic factors in iron catalysis: synthesis and characterization of aryl-substituted iron(II) carbonyl pnnp complexes and their use in the asymmetric transfer hydrogenation of ketones. Organometallics 30, 4418–4431 (2011).
Meek, S. J., Pitman, C. L. & Miller, A. J. M. Deducing reaction mechanism: a guide for students, researchers, and instructors. J. Chem. Educ. 2, 275–286 (2016).
Fey, N. & Lynam, J. M. Computational mechanistic study in organometallic catalysis: why prediction is still a challenge. WIREs Comput. Mol. Sci. 12, e1590 (2021).
Harvey, J. N., Himo, F., Maseras, F. & Perrin, L. Scope and challenge of computational methods for studying mechanism and reactivity in homogeneous catalysis. ACS Catal. 9, 6803–6813 (2019).
Ryu, H. et al. Pitfalls in computational modeling of chemical reactions and how to avoid them. Organometallics 37, 3228–3239 (2018).
Wodrich, M. D., Sawatlon, B., Busch, M. & Corminboeuf, C. On the generality of molecular volcano plots. ChemCatChem 10, 1586–1591 (2018).
Wodrich, M. D., Busch, M. & Corminboeuf, C. Accessing and predicting the kinetic profiles of homogeneous catalysts from volcano plots. Chem. Sci. 7, 5723–5735 (2016).
Kozuch, S. & Shaik, S. How to conceptualize catalytic cycles? The energetic span model. Acc. Chem. Res. 44, 101–110 (2010).
Wodrich, M. D., Sawatlon, B., Solel, E., Kozuch, S. & Corminboeuf, C. Activity-based screening of homogeneous catalysts through the rapid assessment of theoretically derived turnover frequencies. ACS Catal. 9, 5716–5725 (2019).
Wodrich, M. D., Busch, M. & Corminboeuf, C. Expedited screening of active and regioselective catalysts for the hydroformylation reaction. Helv. Chim. Acta 101, e1800107 (2018).
Sawatlon, B., Wodrich, M. D. & Corminboeuf, C. Probing substrate scope with molecular volcanoes. Org. Lett. 22, 7936–7941 (2020).
Meyer, B., Sawatlon, B., Heinen, S., von Lilienfeld, O. A. & Corminboeuf, C. Machine learning meets volcano plots: computational discovery of cross-coupling catalysts. Chem. Sci. 9, 7069–7077 (2018).
Sawatlon, B., Wodrich, M. D., Meyer, B., Fabrizio, A. & Corminboeuf, C. Data mining the C–C cross-coupling genome. ChemCatChem 11, 4096–4107 (2019).
Wodrich, M. D., Fabrizio, A., Meyer, B. & Corminboeuf, C. Data-powered augmented volcano plots for homogeneous catalysis. Chem. Sci. 11, 12070–12080 (2020).
Busch, M., Wodrich, M. D. & Corminboeuf, C. A generalized picture of CC cross-coupling. ACS Catal. 7, 5643–5653 (2017).
Busch, M., Wodrich, M. D. & Corminboeuf, C. Improving the thermodynamic profiles of prospective Suzuki–Miyaura cross-coupling catalysts by altering the electrophilic coupling component. ChemCatChem 10, 1592–1597 (2018).
Sawatlon, B., Wodrich, M. D. & Corminboeuf, C. Unraveling metal/pincer ligand effects in the catalytic hydrogenation of carbon dioxide to formate. Organometallics 37, 4568–4575 (2018).
Anand, M. & Nørskov, J. K. Scaling relations in homogeneous catalysis: analyzing the Buchwald–Hartwig amination reaction. ACS Catal. 10, 336–345 (2019).
Das, S., Tobel, B. D., Alonso, M. & Corminboeuf, C. Uncovering the activity of alkaline earth metal hydrogenation catalysis through molecular volcano plots. Top. Catal. 65, 289–295 (2021).
Cordova, M., Wodrich, M. D., Meyer, B., Sawatlon, B. & Corminboeuf, C. Data-driven advancement of homogeneous nickel catalyst activity for aryl ether cleavage. ACS Catal. 10, 7021–7031 (2020).
Steinmann, S. N. & Corminboeuf, C. A system-dependent density-based dispersion correction. J. Chem. Theory Comput. 6, 1990–2001 (2010).
Steinmann, S. N. & Corminboeuf, C. A density dependent dispersion correction. CHIMIA 65, 240–244 (2011).
Steinmann, S. N. & Corminboeuf, C. Comprehensive benchmarking of a density-dependent dispersion correction. J. Chem. Theory Comput. 7, 3567–3577 (2011).
Klamt, A. The COSMO and COSMO-RS solvation models. WIREs Comput Mol Sci. 8, (2017).
Martin, R. L., Hay, P. J. & Pratt, L. R. Hydrolysis of ferric ion in water and conformational equilibrium. J. Phys. Chem. A 102, 3565–3573 (1998).
Gallarati, S., Dingwall, P., Fuentes, J. A., Bühl, M. & Clarke, M. L. Understanding catalyst structureselectivity relationships in pd-catalyzed enantioselective methoxycarbonylation of styrene. Organometallics 39, 4544–4556 (2020).
Frisch, M. J. et al. Gaussian16 Revision C.01. (2016).
te Velde, G. et al. Chemistry with ADF. J. Comp. Chem. 22, 931–967 (2001).

Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes

Supplementary information

Supplementary Information

推荐阅读