Schoepfer, A., Weinreich, J., Laplaza, R., Waser, J., & Corminboeuf, C. (2024). Cost-Informed Bayesian Reaction Optimization. American Chemical Society (ACS); \urlhttp://dx.doi.org/10.26434/chemrxiv-2024-44ft2. http://dx.doi.org/10.26434/chemrxiv-2024-44ft2
@unpublished{Schoepfer2024_cibo,
title = {Cost-Informed Bayesian Reaction Optimization},
url = {http://dx.doi.org/10.26434/chemrxiv-2024-44ft2},
note = {\url{http://dx.doi.org/10.26434/chemrxiv-2024-44ft2}},
doi = {10.26434/chemrxiv-2024-44ft2},
publisher = {American Chemical Society (ACS)},
author = {Schoepfer, Alexandre and Weinreich, Jan and Laplaza, Rubén and Waser, Jerome and Corminboeuf, Clemence},
year = {2024},
month = apr
}
Refereed journal articles
Laplaza, R., Wodrich, M. D., & Corminboeuf, C. (2024). Overcoming the Pitfalls of Computing Reaction Selectivity from Ensembles of Transition States. J. Phys. Chem. Lett., 15(29), 7363–7370. http://dx.doi.org/10.1021/acs.jpclett.4c01657
@article{Laplaza2024_jpcl,
title = {Overcoming the Pitfalls of Computing Reaction Selectivity from Ensembles of Transition States},
volume = {15},
issn = {1948-7185},
url = {http://dx.doi.org/10.1021/acs.jpclett.4c01657},
doi = {10.1021/acs.jpclett.4c01657},
number = {29},
journal = {J. Phys. Chem. Lett.},
publisher = {American Chemical Society (ACS)},
author = {Laplaza, Rubén and Wodrich, Matthew D. and Corminboeuf, Clemence},
year = {2024},
month = jul,
pages = {7363–7370}
}
van Gerwen, P., Briling, K. R., Bunne, C., Somnath, V. R., Laplaza, R., Krause, A., & Corminboeuf, C. (2024). 3DReact: Geometric Deep Learning for Chemical Reactions. J. Chem. Inf. Model. http://dx.doi.org/10.1021/acs.jcim.4c00104
@article{vanGerwen2024,
title = {3DReact: Geometric Deep Learning for Chemical Reactions},
issn = {1549-960X},
url = {http://dx.doi.org/10.1021/acs.jcim.4c00104},
doi = {10.1021/acs.jcim.4c00104},
journal = {J. Chem. Inf. Model.},
publisher = {American Chemical Society (ACS)},
author = {van Gerwen, Puck and Briling, Ksenia R. and Bunne, Charlotte and Somnath, Vignesh Ram and Laplaza, Rubén and Krause, Andreas and Corminboeuf, Clemence},
year = {2024},
month = jul
}
Worakul, T., Laplaza, R., Das, S., Wodrich, M. D., & Corminboeuf, C. (2024). Microkinetic Molecular Volcano Plots for Enhanced Catalyst Selectivity and Activity Predictions. ACS Catal., 9829–9839. http://dx.doi.org/10.1021/acscatal.4c01175
@article{Worakul2024,
title = {Microkinetic Molecular Volcano Plots for Enhanced Catalyst Selectivity and Activity Predictions},
issn = {2155-5435},
url = {http://dx.doi.org/10.1021/acscatal.4c01175},
doi = {10.1021/acscatal.4c01175},
journal = {ACS Catal.},
publisher = {American Chemical Society (ACS)},
author = {Worakul, Thanapat and Laplaza, Rubén and Das, Shubhajit and Wodrich, Matthew D. and Corminboeuf, Clemence},
year = {2024},
month = jun,
pages = {9829–9839}
}
Schoepfer, A. A., Laplaza, R., Wodrich, M. D., Waser, J., & Corminboeuf, C. (2024). Reaction-Agnostic Featurization of Bidentate Ligands for Bayesian Ridge Regression of Enantioselectivity. ACS Catal., 9302–9312. http://dx.doi.org/10.1021/acscatal.4c02452
@article{Schoepfer2024,
title = {Reaction-Agnostic Featurization of Bidentate Ligands for Bayesian Ridge Regression of Enantioselectivity},
issn = {2155-5435},
url = {http://dx.doi.org/10.1021/acscatal.4c02452},
doi = {10.1021/acscatal.4c02452},
journal = {ACS Catal.},
publisher = {American Chemical Society (ACS)},
author = {Schoepfer, Alexandre A. and Laplaza, Rubén and Wodrich, Matthew D. and Waser, Jerome and Corminboeuf, Clemence},
year = {2024},
month = jun,
pages = {9302–9312}
}
Das, S., Laplaza, R., Blaskovits, J. T., & Corminboeuf, C. (2024). Engineering Frustrated Lewis Pair Active Sites in Porous Organic Scaffolds for Catalytic CO2 Hydrogenation. J. Am. Chem. Soc., 146(23), 15806–15814. http://dx.doi.org/10.1021/jacs.4c01890
@article{Das2024,
title = {Engineering Frustrated Lewis Pair Active Sites in Porous Organic Scaffolds for Catalytic CO2 Hydrogenation},
volume = {146},
issn = {1520-5126},
url = {http://dx.doi.org/10.1021/jacs.4c01890},
doi = {10.1021/jacs.4c01890},
number = {23},
journal = {J. Am. Chem. Soc.},
publisher = {American Chemical Society (ACS)},
author = {Das, Shubhajit and Laplaza, Rubén and Blaskovits, J. Terence and Corminboeuf, Clémence},
year = {2024},
month = may,
pages = {15806–15814}
}
Cho, Y., Laplaza, R., Vela, S., & Corminboeuf, C. (2024). Automated prediction of ground state spin for transition metal complexes. Digital Discovery, 3(8), 1638–1647. http://dx.doi.org/10.1039/D4DD00093E
@article{Cho2024,
title = {Automated prediction of ground state spin for transition metal complexes},
volume = {3},
issn = {2635-098X},
url = {http://dx.doi.org/10.1039/D4DD00093E},
doi = {10.1039/d4dd00093e},
number = {8},
journal = {Digital Discovery},
publisher = {Royal Society of Chemistry (RSC)},
author = {Cho, Yuri and Laplaza, Rubén and Vela, Sergi and Corminboeuf, Clémence},
year = {2024},
pages = {1638–1647}
}
Gallarati, S., van Gerwen, P., Laplaza, R., Brey, L., Makaveev, A., & Corminboeuf, C. (2024). A genetic optimization strategy with generality in asymmetric organocatalysis as a primary target. Chem. Sci., 15(10), 3640–3660. http://dx.doi.org/10.1039/D3SC06208B
@article{Gallarati2024,
title = {A genetic optimization strategy with generality in asymmetric organocatalysis as a primary target},
volume = {15},
issn = {2041-6539},
url = {http://dx.doi.org/10.1039/D3SC06208B},
doi = {10.1039/d3sc06208b},
number = {10},
journal = {Chem. Sci.},
publisher = {Royal Society of Chemistry (RSC)},
author = {Gallarati, Simone and van Gerwen, Puck and Laplaza, Rubén and Brey, Lucien and Makaveev, Alexander and Corminboeuf, Clemence},
year = {2024},
pages = {3640–3660}
}
Blaskovits, J. T., Laplaza, R., Vela, S., & Corminboeuf, C. (2023). Data‐Driven Discovery of Organic Electronic Materials Enabled by Hybrid Top‐Down/Bottom‐Up Design. Adv. Mater., 36(2), 2305602. http://dx.doi.org/10.1002/adma.202305602
@article{Blaskovits2023,
title = {Data‐Driven Discovery of Organic Electronic Materials Enabled by Hybrid Top‐Down/Bottom‐Up Design},
volume = {36},
pages = {2305602},
url = {http://dx.doi.org/10.1002/adma.202305602},
doi = {10.1002/adma.202305602},
number = {2},
journal = {Adv. Mater.},
publisher = {Wiley},
author = {Blaskovits, J. Terence and Laplaza, Rub{\'{e}}n and Vela, Sergi and Corminboeuf, Clémence},
year = {2023},
month = nov
}
van Gerwen, P., Wodrich, M. D., Laplaza, R., & Corminboeuf, C. (2023). Reply to Comment on ‘Physics-based representations for machine learning properties of chemical reactions.’ Mach. Learn.: Sci. Technol., 4(4), 048002. http://dx.doi.org/10.1088/2632-2153/acee43
@article{vanGerwen2023_mlst,
title = {Reply to Comment on ‘Physics-based representations for machine learning properties of chemical reactions’},
volume = {4},
issn = {2632-2153},
url = {http://dx.doi.org/10.1088/2632-2153/acee43},
doi = {10.1088/2632-2153/acee43},
number = {4},
journal = {Mach. Learn.: Sci. Technol.},
publisher = {IOP Publishing},
author = {van Gerwen, Puck and Wodrich, Matthew D and Laplaza, Rubén and Corminboeuf, Clemence},
year = {2023},
month = oct,
pages = {048002}
}
Novoa, T., Laplaza, R., Peccati, F., Fuster, F., & Contreras-Garcı́a Julia. (2023). The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems. J. Chem. Inf. Model., 63(15), 4483–4489. https://doi.org/10.1021/acs.jcim.3c00271
@article{Novoa2023_jcim,
doi = {10.1021/acs.jcim.3c00271},
url = {https://doi.org/10.1021/acs.jcim.3c00271},
year = {2023},
month = aug,
publisher = {American Chemical Society ({ACS})},
volume = {63},
number = {15},
pages = {4483--4489},
author = {Novoa, Trinidad and Laplaza, Rub{\'{e}}n and Peccati, Francesca and Fuster, Franck and Contreras-Garc{\'{\i}}a, Julia},
title = {The {NCIWEB} Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems},
journal = {J. Chem. Inf. Model.}
}
Wodrich, M. D., Laplaza, R., Cramer, N., Reiher, M., & Corminboeuf, C. (2023). Toward in silico Catalyst Optimization. CHIMIA, 77(3), 139. https://doi.org/10.2533/chimia.2023.139
@article{Wodrich2023_chimia,
doi = {10.2533/chimia.2023.139},
url = {https://doi.org/10.2533/chimia.2023.139},
year = {2023},
month = mar,
publisher = {Swiss Chemical Society},
volume = {77},
number = {3},
pages = {139},
author = {Wodrich, Matthew D. and Laplaza, Rubén and Cramer, Nicolai and Reiher, Markus and Corminboeuf, Clemence},
title = {Toward in silico Catalyst Optimization},
journal = {{CHIMIA}}
}
Gallarati, S., Gerwen, P. V., Schoepfer, A. A., Laplaza, R., & Corminboeuf, C. (2023). Genetic Algorithms for the Discovery of Homogeneous Catalysts. CHIMIA, 77(1/2), 39. https://doi.org/10.2533/chimia.2023.39
@article{Gallarati2023_chimia,
doi = {10.2533/chimia.2023.39},
url = {https://doi.org/10.2533/chimia.2023.39},
year = {2023},
month = feb,
publisher = {Swiss Chemical Society},
volume = {77},
number = {1/2},
pages = {39},
author = {Gallarati, Simone and Gerwen, Puck Van and Schoepfer, Alexandre A. and Laplaza, Rubén and Corminboeuf, Clemence},
title = {Genetic Algorithms for the Discovery of Homogeneous Catalysts},
journal = {{CHIMIA}}
}
Wieduwilt, E. K., Boto, R. A., Macetti, G., Laplaza, R., Contreras-Garcı́a Julia, & Genoni, A. (2023). Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses. J. Chem. Theory Comput., 19(3), 1063–1079. https://doi.org/10.1021/acs.jctc.2c01092
@article{Wieduwilt2023_jctc,
doi = {10.1021/acs.jctc.2c01092},
url = {https://doi.org/10.1021/acs.jctc.2c01092},
year = {2023},
month = jan,
publisher = {American Chemical Society ({ACS})},
volume = {19},
number = {3},
pages = {1063--1079},
author = {Wieduwilt, Erna K. and Boto, Roberto A. and Macetti, Giovanni and Laplaza, Rubén and Contreras-Garc{\'{\i}}a, Julia and Genoni, Alessandro},
title = {Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses},
journal = {J. Chem. Theory Comput.}
}
Vela, S., Laplaza, R., Cho, Y., & Corminboeuf, C. (2022). cell2mol: Encoding chemistry to interpret crystallographic data. Npj Comput. Mater., 8(1), 188. https://doi.org/10.1038/s41524-022-00874-9
@article{Vela2022,
author = {Vela, Sergi and Laplaza, Rubén and Cho, Yuri and Corminboeuf, Cl\'emence},
title = {cell2mol: {Encoding} chemistry to interpret crystallographic data},
journal = {npj Comput. Mater.},
year = {2022},
month = aug,
day = {31},
volume = {8},
number = {1},
pages = {188},
issn = {2057-3960},
doi = {10.1038/s41524-022-00874-9},
url = {https://doi.org/10.1038/s41524-022-00874-9},
source = {Crossref},
publisher = {Springer Science and Business Media LLC}
}
The creation and maintenance of crystallographic data repositories is one of the greatest data-related achievements in chemistry. Platforms such as the Cambridge Structural Database host what is likely the most diverse collection of synthesizable molecules. If properly mined, they could be the basis for the large-scale exploration of new regions of the chemical space using quantum chemistry (QC). Yet, it is currently challenging to retrieve all the necessary information for QC codes based exclusively on the available structural data, especially for transition metal complexes. To overcome this limitation, we present cell2mol, a software that interprets crystallographic data and retrieves the connectivity and total charge of molecules, including the oxidation state (OS) of metal atoms. We demonstrate that cell2mol outperforms other popular methods at assigning the metal OS, while offering a comprehensive interpretation of the unit cell. The code is made available, as well as reliable QC-ready databases totaling 31k transition metal complexes and 13k ligands that contain incomparable chemical diversity.
Laplaza, R., Das, S., Wodrich, M. D., & Corminboeuf, C. (2022). Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes. Nat. Protoc., 17(11), 2550–2569. https://doi.org/10.1038/s41596-022-00726-2
@article{Laplaza2022_natprot,
author = {Laplaza, Rubén and Das, Shubhajit and Wodrich, Matthew D. and Corminboeuf, Cl\'emence},
title = {Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes},
journal = {Nat. Protoc.},
year = {2022},
month = aug,
day = {17},
issn = {1754-2189, 1750-2799},
doi = {10.1038/s41596-022-00726-2},
url = {https://doi.org/10.1038/s41596-022-00726-2},
number = {11},
source = {Crossref},
volume = {17},
publisher = {Springer Science and Business Media LLC},
pages = {2550--2569}
}
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 has been demonstrated in several areas of catalysis, with recent applications to homogeneous catalysts having been pioneered by our research group. Both volcano plots and activity maps are built from linear free energy scaling relationships that connect the value of a descriptor variable(s) with the relative energies of other catalytic cycle intermediates/transition states. These relationships must be both constructed and postprocessed appropriately to obtain the resulting plots/maps; this process requires careful execution to obtain meaningful results. In this protocol, we provide a step-by-step guide to building volcano plots and activity maps using curated reaction profile data. The reaction profile data are obtained using density functional theory computations to model the catalytic cycle. In addition, we provide volcanic, a Python code that automates the steps of the process following data acquisition. Unlike the computation of individual reaction energy profiles, our tools lead to a holistic view of homogeneous catalyst performance that can be broadly applied for both explanatory and screening purposes.
Das, S., Laplaza, R., Blaskovits, J. T., & Corminboeuf, C. (2022). Mapping Active Site Geometry to Activity in Immobilized Frustrated Lewis Pair Catalysts. Angew. Chem. Int. Ed., 134(32). https://doi.org/10.1002/ange.202202727
@article{Das2022,
author = {Das, Shubhajit and Laplaza, Rub\'en and Blaskovits, J. Terence and Corminboeuf, Cl\'emence},
url = {https://doi.org/10.1002/ange.202202727},
year = {2022},
month = may,
publisher = {Wiley},
volume = {134},
number = {32},
title = {Mapping Active Site Geometry to Activity in Immobilized Frustrated {Lewis} Pair Catalysts},
journal = {Angew. Chem. Int. Ed.},
source = {Crossref},
issn = {0044-8249, 1521-3757}
}
Jurásková, V., Célerse, F., Laplaza, R., & Corminboeuf, C. (2022). Assessing the persistence of chalcogen bonds in solution with neural network potentials. J. Chem. Phys., 156(15), 154112. https://doi.org/10.1063/5.0085153
@article{Juraskova2022,
author = {Jur\'askov\'a, Veronika and C\'elerse, Frederic and Laplaza, Rubén and Corminboeuf, Clemence},
url = {https://doi.org/10.1063/5.0085153},
year = {2022},
month = apr,
publisher = {AIP Publishing},
title = {Assessing the persistence of chalcogen bonds in solution with neural network potentials},
journal = {J. Chem. Phys.},
doi = {10.1063/5.0085153},
number = {15},
source = {Crossref},
volume = {156},
issn = {0021-9606, 1089-7690},
pages = {154112}
}
Laplaza, R., Gallarati, S., & Corminboeuf, C. (2022). Genetic Optimization of Homogeneous Catalysts. Chemistry–Methods, 2(6), e202100107. https://doi.org/10.1002/cmtd.202100107
@article{Laplaza2022_chemm,
author = {Laplaza, Rubén and Gallarati, Simone and Corminboeuf, Clemence},
doi = {10.1002/cmtd.202100107},
url = {https://doi.org/10.1002/cmtd.202100107},
year = {2022},
month = mar,
publisher = {Wiley},
volume = {2},
number = {6},
pages = {e202100107},
title = {Genetic Optimization of Homogeneous Catalysts},
journal = {Chemistry{\textendash}Methods},
source = {Crossref},
issn = {2628-9725, 2628-9725}
}
Schwaller, P., Vaucher, A. C., Laplaza, R., Bunne, C., Krause, A., Corminboeuf, C., & Laino, T. (2022). Machine intelligence for chemical reaction space. WIREs Comput. Mol. Sci., 12(5). https://doi.org/10.1002/wcms.1604
@article{Schwaller2022,
author = {Schwaller, Philippe and Vaucher, Alain C. and Laplaza, Rubén and Bunne, Charlotte and Krause, Andreas and Corminboeuf, Clemence and Laino, Teodoro},
url = {https://doi.org/10.1002/wcms.1604},
year = {2022},
month = mar,
publisher = {Wiley},
title = {Machine intelligence for chemical reaction space},
journal = {WIREs Comput. Mol. Sci.},
number = {5},
source = {Crossref},
volume = {12},
issn = {1759-0876, 1759-0884}
}
Laplaza, R., Contreras-Garcia, J., Fuster, F., Volatron, F., & Chaquin, P. (2022). Dependence of hydrocarbon sigma CC bond strength on bond angles: The concepts of “inverted”, “direct” and “superdirect” bonds. Comput. Theor. Chem., 1207, 113505. https://doi.org/10.1016/j.comptc.2021.113505
@article{Laplaza2022_CTC,
author = {Laplaza, Rubén and Contreras-Garcia, Julia and Fuster, Franck and Volatron, Fran\c{c}ois and Chaquin, Patrick},
url = {https://doi.org/10.1016/j.comptc.2021.113505},
year = {2022},
month = jan,
publisher = {Elsevier BV},
volume = {1207},
pages = {113505},
title = {Dependence of hydrocarbon sigma {CC} bond strength on bond angles: {The} concepts of “inverted”, “direct” and “superdirect” bonds},
journal = {Comput. Theor. Chem.},
source = {Crossref},
issn = {2210-271X},
doi = {10.1016/j.comptc.2021.113505}
}
Gallarati, S., van Gerwen, P., Laplaza, R., Vela, S., Fabrizio, A., & Corminboeuf, C. (2022). OSCAR: An Extensive Repository of Chemically and Functionally Diverse Organocatalysts. Chem. Sci., 13(46), 13782–13794.
@article{Gallarati2022_chemsci,
author = {Gallarati, Simone and van Gerwen, Puck and Laplaza, Rubén and Vela, Sergi and Fabrizio, Alberto and Corminboeuf, Clemence},
doi = {10.1039/d2sc04251g},
year = {2022},
publisher = {Royal Society of Chemistry (RSC)},
volume = {13},
number = {46},
pages = {13782--13794},
title = {{OSCAR:} {An} Extensive Repository of Chemically and Functionally Diverse Organocatalysts},
journal = {Chem. Sci.},
source = {Crossref},
issn = {2041-6520, 2041-6539}
}
Garner, M. H., Laplaza, R., & Corminboeuf, C. (2022). Helical versus linear Jahn–Teller distortions in allene and spiropentadiene radical cations. Phys. Chem. Chem. Phys., 24(42), 26134–26143. https://doi.org/10.1039/d2cp03544h
@article{Garner2022,
author = {Garner, Marc H. and Laplaza, Rubén and Corminboeuf, Clemence},
url = {https://doi.org/10.1039/d2cp03544h},
doi = {10.1039/d2cp03544h},
year = {2022},
publisher = {Royal Society of Chemistry (RSC)},
title = {Helical versus linear {Jahn–Teller} distortions in allene and spiropentadiene radical cations},
journal = {Phys. Chem. Chem. Phys.},
number = {42},
source = {Crossref},
volume = {24},
issn = {1463-9076, 1463-9084},
pages = {26134--26143}
}
Landeros-Rivera, B., Gallegos, M., Munarriz, J., Laplaza, R., & Contreras-Garcia, J. (2022). New venues in electron density analysis. Phys. Chem. Chem. Phys., 24(36), 21538–21548. https://doi.org/10.1039/d2cp01517j
@article{LanderosRivera2022,
author = {Landeros-Rivera, Bruno and Gallegos, Miguel and Munarriz, Julen and Laplaza, Rubén and Contreras-Garcia, Julia},
doi = {10.1039/d2cp01517j},
url = {https://doi.org/10.1039/d2cp01517j},
year = {2022},
publisher = {Royal Society of Chemistry (RSC)},
volume = {24},
number = {36},
pages = {21538--21548},
title = {New venues in electron density analysis},
journal = {Phys. Chem. Chem. Phys.},
source = {Crossref},
issn = {1463-9076, 1463-9084}
}
Laplaza, R., Sobez, J.-G., Wodrich, M. D., Reiher, M., & Corminboeuf, C. (2022). The (not so) simple prediction of enantioselectivity – a pipeline for high-fidelity computations. Chem. Sci., 13(23), 6858–6864. https://doi.org/10.1039/d2sc01714h
@article{Laplaza2022_chemsci,
author = {Laplaza, Rubén and Sobez, Jan-Grimo and Wodrich, Matthew D. and Reiher, Markus and Corminboeuf, Cl\'emence},
doi = {10.1039/d2sc01714h},
url = {https://doi.org/10.1039/d2sc01714h},
year = {2022},
publisher = {Royal Society of Chemistry (RSC)},
volume = {13},
number = {23},
pages = {6858--6864},
title = {The (not so) simple prediction of enantioselectivity – a pipeline for high-fidelity computations},
journal = {Chem. Sci.},
source = {Crossref},
issn = {2041-6520, 2041-6539}
}
Gallarati, S., Laplaza, R., & Corminboeuf, C. (2022). Harvesting the fragment-based nature of bifunctional organocatalysts to enhance their activity. Org. Chem. Front., 9(15), 4041–4051. https://doi.org/10.1039/d2qo00550f
@article{D2QO00550F,
author = {Gallarati, Simone and Laplaza, Rubén and Corminboeuf, Clemence},
title = {Harvesting the fragment-based nature of bifunctional organocatalysts to enhance their activity},
journal = {Org. Chem. Front.},
year = {2022},
volume = {9},
issue = {15},
pages = {4041--4051},
publisher = {Royal Society of Chemistry (RSC)},
doi = {10.1039/d2qo00550f},
url = {https://doi.org/10.1039/d2qo00550f},
number = {15},
source = {Crossref},
issn = {2052-4129}
}
Bifunctional hydrogen-bond donors/amines are commonly encountered organocatalysts in asymmetric synthesis. Existing computational tools do not take full advantage of their modularity to suggest tailored designs because they generally rely on evaluating the organocatalyst’s structure as a whole. Herein, we introduce a fragment-based approach, coupled with volcano plots and activity maps, to evaluate hundreds of building block combinations and extract mechanistic insight. This bottom-up protocol gives feedback on the choice of improved molecular fragments and makes activity-based screening faster and more transferable.
Romero-Tamayo, S., Laplaza, R., Velazquez-Campoy, A., Villanueva, R., Medina, M., & Ferreira, P. (2021). W196 and the β-Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor. Oxid. Med. Cell. Longev., 2021, 1–19. https://doi.org/10.1155/2021/6673661
@article{RomeroTamayo2021,
author = {Romero-Tamayo, Silvia and Laplaza, Rubén and Velazquez-Campoy, Adrian and Villanueva, Raquel and Medina, Milagros and Ferreira, Patricia},
doi = {10.1155/2021/6673661},
year = {2021},
month = jan,
publisher = {Hindawi Limited},
volume = {2021},
pages = {1--19},
title = {W196 and the β-Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor},
journal = {Oxid. Med. Cell. Longev.},
source = {Crossref},
issn = {1942-0994, 1942-0900},
url = {https://doi.org/10.1155/2021/6673661}
}
Gallarati, S., Fabregat, R., Laplaza, R., Bhattacharjee, S., Wodrich, M. D., & Corminboeuf, C. (2021). Reaction-based machine learning representations for predicting the enantioselectivity of organocatalysts. Chem. Sci., 12(20), 6879–6889. https://doi.org/10.1039/d1sc00482d
@article{Gallarati2021,
author = {Gallarati, Simone and Fabregat, Raimon and Laplaza, Rubén and Bhattacharjee, Sinjini and Wodrich, Matthew D. and Corminboeuf, Clemence},
doi = {10.1039/d1sc00482d},
year = {2021},
publisher = {Royal Society of Chemistry (RSC)},
volume = {12},
number = {20},
pages = {6879--6889},
title = {Reaction-based machine learning representations for predicting the enantioselectivity of organocatalysts},
journal = {Chem. Sci.},
source = {Crossref},
issn = {2041-6520, 2041-6539},
url = {https://doi.org/10.1039/d1sc00482d}
}
Laplaza, R., Cárdenas, C., Chaquin, P., Contreras-Garcı́a Julia, & Ayers, P. W. (2020). Orbital energies and nuclear forces in DFT : Interpretation and validation. J. Comput. Chem., 42(5), 334–343. https://doi.org/10.1002/jcc.26459
@article{jcc_dof,
author = {Laplaza, Rubén and C\'ardenas, Carlos and Chaquin, Patrick and Contreras-Garc{\'\i}a, Julia and Ayers, Paul W.},
title = {Orbital energies and nuclear forces in {DFT} : {Interpretation} and validation},
journal = {J. Comput. Chem.},
volume = {42},
number = {5},
pages = {334--343},
keywords = {conceptual density functional theory, density functional theory, dynamic orbital forces, nuclear forces, nuclear Fukui function},
doi = {10.1002/jcc.26459},
year = {2020},
source = {Crossref},
publisher = {Wiley},
issn = {0192-8651, 1096-987X},
month = dec,
url = {https://doi.org/10.1002/jcc.26459}
}
Abstract The bonding and antibonding character of individual molecular orbitals has been previously shown to be related to their orbital energy derivatives with respect to nuclear coordinates, known as dynamical orbital forces. Albeit usually derived from Koopmans’ theorem, in this work we show a more general derivation from conceptual DFT, which justifies application in a broader context. The consistency of the approach is validated numerically for valence orbitals in Kohn–Sham DFT. Then, we illustrate its usefulness by showcasing applications in aromatic and antiaromatic systems and in excited state chemistry. Overall, dynamical orbital forces can be used to interpret the results of routine ab initio calculations, be it wavefunction or density based, in terms of forces and occupations.
Laplaza, R., Peccati, F., A. Boto, R., Quan, C., Carbone, A., Piquemal, J.-P., Maday, Y., & Contreras-Garcı́a Julia. (2020). NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient. WIREs Comput. Mol. Sci., 11(2).
@article{Laplaza2020,
author = {Laplaza, Rub\'en and Peccati, Francesca and A. Boto, Roberto and Quan, Chaoyu and Carbone, Alessandra and Piquemal, Jean-Philip and Maday, Yvon and Contreras-Garc{\'\i}a, Julia},
year = {2020},
month = aug,
publisher = {Wiley},
volume = {11},
number = {2},
title = {{NCIPLOT} and the analysis of noncovalent interactions using the reduced density gradient},
journal = {WIREs Comput. Mol. Sci.},
source = {Crossref},
issn = {1759-0876, 1759-0884}
}
Boto, R. A., Peccati, F., Laplaza, R., Quan, C., Carbone, A., Piquemal, J.-P., Maday, Y., & Contreras-Garcı́a Julia. (2020). NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions. J. Chem. Theory Comput., 16(7), 4150–4158. https://doi.org/10.1021/acs.jctc.0c00063
@article{doi:10.1021/acs.jctc.0c00063,
author = {Boto, Roberto A. and Peccati, Francesca and Laplaza, Rub\'en and Quan, Chaoyu and Carbone, Alessandra and Piquemal, Jean-Philip and Maday, Yvon and Contreras-Garc{\i}́a, Julia},
title = {{NCIPLOT4:} {Fast,} Robust, and Quantitative Analysis of Noncovalent Interactions},
journal = {J. Chem. Theory Comput.},
volume = {16},
number = {7},
pages = {4150--4158},
year = {2020},
doi = {10.1021/acs.jctc.0c00063},
source = {Crossref},
publisher = {American Chemical Society (ACS)},
issn = {1549-9618, 1549-9626},
month = may,
url = {https://doi.org/10.1021/acs.jctc.0c00063}
}
Laplaza, R., Contreras-Garcia, J., Fuster, F., Volatron, F., & Chaquin, P. (2020). The “Inverted Bonds” Revisited: Analysis of “In Silico” Models and of [1.1.1]Propellane by Using Orbital Forces. Chem. Eur. J. , 26(30), 6839–6845. https://doi.org/10.1002/chem.201904910
@article{doi:10.1002/chem.201904910,
author = {Laplaza, Rub\'en and Contreras-Garcia, Julia and Fuster, Franck and Volatron, Fran\c{c}ois and Chaquin, Patrick},
title = {The {“Inverted} Bonds” Revisited: {Analysis} of {“In} Silico” Models and of {[1.1.1]Propellane} by Using Orbital Forces},
journal = {Chem. Eur. J. },
volume = {26},
number = {30},
pages = {6839--6845},
keywords = {1.1.1propellane, bond energies, inverted bonds, orbital forces},
doi = {10.1002/chem.201904910},
year = {2020},
source = {Crossref},
publisher = {Wiley},
issn = {0947-6539, 1521-3765},
month = feb,
url = {https://doi.org/10.1002/chem.201904910}
}
Abstract This article dwells on the nature of “inverted bonds”, which refer to the \ensuremathσ interaction between two sp hybrids by their smaller lobes, and their presence in [1.1.1]propellane. Firstly, we study H3C\ensuremath-C models of C\ensuremath-C bonds with frozen H-C-C angles reproducing the constraints of various degrees of “inversion”. Secondly, the molecular orbital (MO) properties of [1.1.1]propellane and [1.1.1]bicyclopentane are analyzed with the help of orbital forces as a criterion of bonding/antibonding character and as a basis to evaluate bond energies. Triplet and cationic states of [1.1.1]propellane species are also considered to confirm the bonding/antibonding character of MOs in the parent molecule. These approaches show an essentially non-bonding character of the \ensuremathσ central C\ensuremath-C interaction in propellane. Within the MO theory, this bonding is thus only due to \ensuremath\pi-type MOs (also called “banana” MOs or “bridge” MOs) and its total energy is evaluated to approximately 50 kcal mol\ensuremath-1. In bicyclopentane, despite a strong \ensuremathσ-type repulsion, a weak bonding (15–20 kcal mol\ensuremath-1) exists between both central C\ensuremath-C bonds, also due to \ensuremath\pi-type interactions, though no bond is present in the Lewis structure. Overall, the so-called “inverted” bond, as resulting from a \ensuremathσ overlap of the two sp hybrids by their smaller lobes, appears highly questionable.
Laplaza, R., Boto, R. A., Contreras-Garcı́a Julia, & Montero-Campillo, M. M. (2020). Steric clash in real space: Biphenyl revisited. Phys. Chem. Chem. Phys., 22(37), 21251–21256. https://doi.org/10.1039/d0cp03359f
@article{D0CP03359F,
author = {Laplaza, Rub\'en and Boto, Roberto A. and Contreras-Garc{\'\i}a, Julia and Montero-Campillo, M. Merced},
title = {Steric clash in real space: {Biphenyl} revisited},
journal = {Phys. Chem. Chem. Phys.},
year = {2020},
volume = {22},
issue = {37},
pages = {21251--21256},
publisher = {Royal Society of Chemistry (RSC)},
doi = {10.1039/d0cp03359f},
number = {37},
source = {Crossref},
issn = {1463-9076, 1463-9084},
url = {https://doi.org/10.1039/d0cp03359f}
}
A textbook case of twisted structure due to hydrogen–hydrogen steric clash, the biphenyl molecule, has been studied in real space from a new perspective. Long-term discrepancies regarding the origin of the steric repulsion are now reconciled under the NCI (Non Covalent Interaction) method, which reflects in 3D the balance between attractive and repulsive interactions taking place in the region between the phenyl rings. The NCI method confirms that the steric repulsion does not merely come from the H–H interaction itself, but from the many-atom interactions arising from the Cortho–H region, therefore providing rigorous physical grounds for the steric clash. This method allows a continuous scan of all the subtle changes on the electron density on going from the planar to the perpendicular biphenyl structure. The NCI results agree with other topological approaches (IQA, ELF) and are in line with previous findings in the literature regarding controversial H–H interactions in steric clash situations: H–H interactions are attractive, but repulsion appears between (Cortho–H)\ensuremath⋯(Cortho–H), raising the intraatomic energy of the ortho H. ELF is also used to support these conclusions. Indeed, deformations are observed in compressed basins that allow to visualize the intraatomic effect of steric repulsion. These results can be easily extrapolated to systems with similar topological features in which steric clash is claimed to be the reason for instability.
Laplaza, R., Polo, V., & Contreras-Garcı́a Julia. (2019). A Bond Charge Model Ansatz for Intrinsic Bond Energies: Application to C–C Bonds. J. Phys. Chem. A, 124(1), 176–184. https://doi.org/10.1021/acs.jpca.9b10251
@article{doi:10.1021/acs.jpca.9b10251,
author = {Laplaza, Rub\'en and Polo, Victor and Contreras-Garc{\'\i}a, Julia},
title = {A Bond Charge Model Ansatz for Intrinsic Bond Energies: {Application} to {C–C} Bonds},
journal = {J. Phys. Chem. A},
volume = {124},
number = {1},
pages = {176--184},
year = {2019},
doi = {10.1021/acs.jpca.9b10251},
source = {Crossref},
publisher = {American Chemical Society (ACS)},
issn = {1089-5639, 1520-5215},
month = dec,
url = {https://doi.org/10.1021/acs.jpca.9b10251}
}
Villanueva, R., Romero-Tamayo, S., Laplaza, R., Martı́nez-Olivan Juan, Velázquez-Campoy, A., Sancho, J., Ferreira, P., & Medina, M. (2019). Redox- and Ligand Binding-Dependent Conformational Ensembles in the Human Apoptosis-Inducing Factor Regulate Its Pro-Life and Cell Death Functions. Antioxid. Redox Signal., 30(18), 2013–2029. https://doi.org/10.1089/ars.2018.7658
@article{doi:10.1089/ars.2018.7658,
author = {Villanueva, Raquel and Romero-Tamayo, Silvia and Laplaza, Rubén and Mart{\'\i}nez-Olivan, Juan and Vel\'azquez-Campoy, Adri\'an and Sancho, Javier and Ferreira, Patricia and Medina, Milagros},
title = {Redox- and Ligand Binding-Dependent Conformational Ensembles in the Human Apoptosis-Inducing Factor Regulate Its Pro-Life and Cell Death Functions},
journal = {Antioxid. Redox Signal.},
volume = {30},
number = {18},
pages = {2013--2029},
year = {2019},
doi = {10.1089/ars.2018.7658},
source = {Crossref},
publisher = {Mary Ann Liebert Inc},
issn = {1523-0864, 1557-7716},
month = jun,
url = {https://doi.org/10.1089/ars.2018.7658}
}
Peccati, F., Laplaza, R., & Contreras-Garcı́a Julia. (2019). Overcoming Distrust in Solid State Simulations: Adding Error Bars to Computational Data. J. Phys. Chem. C, 123(8), 4767–4772. https://doi.org/10.1021/acs.jpcc.8b10510
@article{doi:10.1021/acs.jpcc.8b10510,
author = {Peccati, Francesca and Laplaza, Rub\'en and Contreras-Garc{\'\i}a, Julia},
title = {Overcoming Distrust in Solid State Simulations: {Adding} Error Bars to Computational Data},
journal = {J. Phys. Chem. C},
volume = {123},
number = {8},
pages = {4767--4772},
year = {2019},
doi = {10.1021/acs.jpcc.8b10510},
source = {Crossref},
publisher = {American Chemical Society (ACS)},
issn = {1932-7447, 1932-7455},
month = jan,
url = {https://doi.org/10.1021/acs.jpcc.8b10510}
}
Munárriz, J., Laplaza, R., Martı́n Pendás A., & Contreras-Garcı́a Julia. (2019). A first step towards quantum energy potentials of electron pairs. Phys. Chem. Chem. Phys., 21(8), 4215–4223. https://doi.org/10.1039/c8cp07509c
@article{C8CP07509C,
author = {Mun\'arriz, Julen and Laplaza, Rub\'en and Mart{\'\i}n Pend\'as, A. and Contreras-Garc{\'\i}a, Julia},
title = {A first step towards quantum energy potentials of electron pairs},
journal = {Phys. Chem. Chem. Phys.},
year = {2019},
volume = {21},
issue = {8},
pages = {4215--4223},
publisher = {Royal Society of Chemistry (RSC)},
doi = {10.1039/c8cp07509c},
number = {8},
source = {Crossref},
issn = {1463-9076, 1463-9084},
url = {https://doi.org/10.1039/c8cp07509c}
}
A first step towards the construction of a quantum force field for electron pairs in direct space is taken. Making use of topological tools (Interacting Quantum Atoms and the Electron Localisation Function), we have analysed the dependency of electron pairs electrostatic, kinetic and exchange–correlation energies upon bond stretching. Simple correlations were found, and can be explained with elementary models such as the homogeneous electron gas. The resulting energy model is applicable to various bonding regimes: from homopolar to highly polarized and even to non-conventional bonds. Overall, this is a fresh approach for developing real space-based force fields including an exchange–correlation term. It provides the relative weight of each of the contributions, showing that, in common Lewis structures, the exchange correlation contribution between electron pairs is negligible. However, our results reveal that classical approximations progressively fail for delocalised electrons, including lone pairs. This theoretical framework justifies the success of the classic Bond Charge Model (BCM) approach in solid state systems and sets the basis of its limits. Finally, this approach opens the door towards the development of quantitative rigorous energy models based on the ELF topology.
Laplaza, R., Polo, V., & Contreras-Garcı́a Julia. (2019). Localizing electron density errors in density functional theory. Phys. Chem. Chem. Phys., 21(37), 20927–20938. https://doi.org/10.1039/c9cp02806d
@article{C9CP02806D,
author = {Laplaza, Rub\'en and Polo, Victor and Contreras-Garc{\'\i}a, Julia},
title = {Localizing electron density errors in density functional theory},
journal = {Phys. Chem. Chem. Phys.},
year = {2019},
volume = {21},
issue = {37},
pages = {20927--20938},
publisher = {Royal Society of Chemistry (RSC)},
doi = {10.1039/c9cp02806d},
number = {37},
source = {Crossref},
issn = {1463-9076, 1463-9084},
url = {https://doi.org/10.1039/c9cp02806d}
}
The accuracy of different density functional approximations is assessed through the use of quantum chemical topology on molecular electron densities. In particular, three simple yet ever-important systems are studied: N2, CO and ethane. Our results exemplify how real-space descriptors can help understand the sources of errors in density functional theory, avoiding unwanted error compensation present in simplified statistical metrics. Errors in “well-built” functionals are shown to be concentrated in chemically meaningful regions of space, and hence they are predictable. Conversely, strongly parametrized functionals show isotropic errors that cannot be traced back to chemically transferable units. Moreover, we will show that energetic corrections are mapped back into improvements in the density in chemically meaningful regions. These results point at the relevance of real-space perspectives when parametrizing or relating energy and density errors.
Munárriz, J., Laplaza, R., & Polo Vı́ctor. (2018). A bonding evolution theory study on the catalytic Noyori hydrogenation reaction. Mol. Phys., 117(9-12), 1315–1324. https://doi.org/10.1080/00268976.2018.1542168
@article{doi:10.1080/00268976.2018.1542168,
author = {Mun\'arriz, Julen and Laplaza, Rubén and Polo, V{\'\i}ctor},
title = {A bonding evolution theory study on the catalytic Noyori hydrogenation reaction},
journal = {Mol. Phys.},
volume = {117},
number = {9-12},
pages = {1315--1324},
year = {2018},
publisher = {Informa UK Limited},
doi = {10.1080/00268976.2018.1542168},
source = {Crossref},
issn = {0026-8976, 1362-3028},
month = nov,
url = {https://doi.org/10.1080/00268976.2018.1542168}
}
Quero, J., Cabello, S., Fuertes, T., Mármol, I., Laplaza, R., Polo, V., Gimeno, M. C., Rodriguez-Yoldi, M. J., & Cerrada, E. (2018). Proteasome versus Thioredoxin Reductase Competition as Possible Biological Targets in Antitumor Mixed Thiolate-Dithiocarbamate Gold(III) Complexes. Inorg. Chem., 57(17), 10832–10845. https://doi.org/10.1021/acs.inorgchem.8b01464
@article{doi:10.1021/acs.inorgchem.8b01464,
author = {Quero, Javier and Cabello, Silvia and Fuertes, Teresa and M\'armol, In\'es and Laplaza, Rubén and Polo, Victor and Gimeno, M. Concepci\'on and Rodriguez-Yoldi, M. Jes\'us and Cerrada, Elena},
title = {Proteasome versus Thioredoxin Reductase Competition as Possible Biological Targets in Antitumor Mixed Thiolate-Dithiocarbamate {Gold(III)} Complexes},
journal = {Inorg. Chem.},
volume = {57},
number = {17},
pages = {10832--10845},
year = {2018},
doi = {10.1021/acs.inorgchem.8b01464},
source = {Crossref},
publisher = {American Chemical Society (ACS)},
issn = {0020-1669, 1520-510X},
month = aug,
url = {https://doi.org/10.1021/acs.inorgchem.8b01464}
}
Martı́nez-Júlvez Marta, Goñi, G., Pérez-Amigot, D., Laplaza, R., Ionescu, I., Petrocelli, S., Tondo Marı́a, Sancho, J., Orellano, E., & Medina, M. (2017). Identification of Inhibitors Targeting Ferredoxin-NADP+ Reductase from the Xanthomonas citri subsp. citri Phytopathogenic Bacteria. Molecules, 23(1), 29. https://doi.org/10.3390/molecules23010029
@article{MartnezJlvez2017,
author = {Mart{\'\i}nez-J\'ulvez, Marta and Go\~ni, Guillermina and P\'erez-Amigot, Daniel and Laplaza, Rubén and Ionescu, Irina and Petrocelli, Silvana and Tondo, Mar{\'\i}a and Sancho, Javier and Orellano, Elena and Medina, Milagros},
doi = {10.3390/molecules23010029},
year = {2017},
month = dec,
publisher = {MDPI AG},
volume = {23},
number = {1},
pages = {29},
title = {Identification of Inhibitors Targeting Ferredoxin-{NADP+} Reductase from the Xanthomonas citri subsp. citri Phytopathogenic Bacteria},
journal = {Molecules},
source = {Crossref},
issn = {1420-3049},
url = {https://doi.org/10.3390/molecules23010029}
}
Refereed book chapters
Laplaza, R., Munárriz, J., & Contreras-García, J. (2022). Chemical Information. In Conceptual Density Functional Theory: Towards a New Chemical Reactivity Theory (pp. 349–374). Wiley. https://doi.org/10.1002/9783527829941.ch18
@inbook{Laplaza2022,
author = {Laplaza, Rub\'en and Mun\'arriz, Julen and Contreras-Garc\'ia, Julia},
doi = {10.1002/9783527829941.ch18},
url = {https://doi.org/10.1002/9783527829941.ch18},
year = {2022},
month = apr,
publisher = {Wiley},
pages = {349--374},
title = {Chemical Information},
booktitle = {Conceptual Density Functional Theory: Towards a New Chemical Reactivity Theory}
}
Laplaza, R., Peccati, F., Arias-Olivares, D., & Contreras-Garcı́a Julia. (2021). 14 Visualizing non-covalent interactions with NCIPLOT. In Complementary Bonding Analysis (pp. 353–378). De Gruyter. https://doi.org/10.1515/9783110660074-014
@inbook{Laplaza2021,
author = {Laplaza, Rub\'en and Peccati, Francesca and Arias-Olivares, David and Contreras-Garc{\'\i}a, Julia},
doi = {10.1515/9783110660074-014},
url = {https://doi.org/10.1515/9783110660074-014},
year = {2021},
month = apr,
publisher = {De Gruyter},
pages = {353--378},
title = {14 Visualizing non-covalent interactions with {NCIPLOT}},
booktitle = {Complementary Bonding Analysis},
source = {Crossref},
isbn = {9783110660074}
}