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Célerse F, Wodrich MD, Vela S, Gallarati S, Fabregat R, Juraskova V, Corminboeuf C. From Organic Fragments to Photoswitchable Catalysts: The OFF-ON Structural Repository for Transferable Kernel-Based Potentials. J Chem Inf Model 2024; 64:1201-1212. [PMID: 38319296 PMCID: PMC10900300 DOI: 10.1021/acs.jcim.3c01953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
Structurally and conformationally diverse databases are needed to train accurate neural networks or kernel-based potentials capable of exploring the complex free energy landscape of flexible functional organic molecules. Curating such databases for species beyond "simple" drug-like compounds or molecules composed of well-defined building blocks (e.g., peptides) is challenging as it requires thorough chemical space mapping and evaluation of both chemical and conformational diversities. Here, we introduce the OFF-ON (organic fragments from organocatalysts that are non-modular) database, a repository of 7869 equilibrium and 67,457 nonequilibrium geometries of organic compounds and dimers aimed at describing conformationally flexible functional organic molecules, with an emphasis on photoswitchable organocatalysts. The relevance of this database is then demonstrated by training a local kernel regression model on a low-cost semiempirical baseline and comparing it with a PBE0-D3 reference for several known catalysts, notably the free energy surfaces of exemplary photoswitchable organocatalysts. Our results demonstrate that the OFF-ON data set offers reliable predictions for simulating the conformational behavior of virtually any (photoswitchable) organocatalyst or organic compound composed of H, C, N, O, F, and S atoms, thereby opening a computationally feasible route to explore complex free energy surfaces in order to rationalize and predict catalytic behavior.
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Affiliation(s)
- Frédéric Célerse
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Matthew D. Wodrich
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
- National
Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Sergi Vela
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Simone Gallarati
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Raimon Fabregat
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Veronika Juraskova
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Clémence Corminboeuf
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
- National
Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- National
Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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Briling K, Calvino Alonso Y, Fabrizio A, Corminboeuf C. SPA HM(a,b): Encoding the Density Information from Guess Hamiltonian in Quantum Machine Learning Representations. J Chem Theory Comput 2024; 20:1108-1117. [PMID: 38227222 PMCID: PMC10867806 DOI: 10.1021/acs.jctc.3c01040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/17/2024]
Abstract
Recently, we introduced a class of molecular representations for kernel-based regression methods─the spectrum of approximated Hamiltonian matrices (SPAHM)─that takes advantage of lightweight one-electron Hamiltonians traditionally used as a self-consistent field initial guess. The original SPAHM variant is built from occupied-orbital energies (i.e., eigenvalues) and naturally contains all of the information about nuclear charges, atomic positions, and symmetry requirements. Its advantages were demonstrated on data sets featuring a wide variation of charge and spin, for which traditional structure-based representations commonly fail. SPAHM(a,b), as introduced here, expand the eigenvalue SPAHM into local and transferable representations. They rely upon one-electron density matrices to build fingerprints from atomic and bond density overlap contributions inspired from preceding state-of-the-art representations. The performance and efficiency of SPAHM(a,b) is assessed on the predictions for data sets of prototypical organic molecules (QM7) of different charges and azoheteroarene dyes in an excited state. Overall, both SPAHM(a) and SPAHM(b) outperform state-of-the-art representations on difficult prediction tasks such as the atomic properties of charged open-shell species and of π-conjugated systems.
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Affiliation(s)
- Ksenia
R. Briling
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yannick Calvino Alonso
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alberto Fabrizio
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
- National
Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
- National
Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
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Abstract
The ab initio determination of electronic excited state (ES) properties is the cornerstone of theoretical photochemistry. Yet, traditional ES methods become impractical when applied to fairly large molecules, or when used on thousands of systems. Machine learning (ML) techniques have demonstrated their accuracy at retrieving ES properties of large molecular databases at a reduced computational cost. For these applications, nonlinear algorithms tend to be specialized in targeting individual properties. Learning fundamental quantum objects potentially represents a more efficient, yet complex, alternative as a variety of molecular properties could be extracted through postprocessing. Herein, we report a general framework able to learn three fundamental objects: the hole and particle densities, as well as the transition density. We demonstrate the advantages of targeting those outputs and apply our predictions to obtain properties, including the state character and the exciton topological descriptors, for the two bands (nπ* and ππ*) of 3427 azoheteroarene photoswitches.
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Affiliation(s)
- Sergi Vela
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Computational Molecular Design, Lausanne, CH-1015, Switzerland
| | - Alberto Fabrizio
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Computational Molecular Design, Lausanne, CH-1015, Switzerland
| | - Ksenia R Briling
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Computational Molecular Design, Lausanne, CH-1015, Switzerland
| | - Clémence Corminboeuf
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Computational Molecular Design, Lausanne, CH-1015, Switzerland
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Vela S, Scheidegger A, Fabregat R, Corminboeuf C. Tuning the Thermal Stability and Photoisomerization of Azoheteroarenes through Macrocycle Strain*. Chemistry 2021; 27:419-426. [PMID: 32991023 PMCID: PMC7839710 DOI: 10.1002/chem.202003926] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/27/2020] [Indexed: 11/24/2022]
Abstract
Azobenzene and its derivatives are one of the most widespread molecular scaffolds used in a range of modern applications, as well as in fundamental research. After photoexcitation, azo-based photoswitches revert back to the most stable isomer on a timescale ( t 1 / 2 ) that determines the range of potential applications. Attempts to bring t 1 / 2 to extreme values prompted the development of azobenzene and azoheteroarene derivatives that either rebalance the E- and Z-isomer stabilities, or exploit unconventional thermal isomerization mechanisms. In the former case, one successful strategy has been the creation of macrocycle strain, which tends to impact the E/Z stability asymmetrically, and thus significantly modifyt 1 / 2 . On the bright side, bridged derivatives have shown an improved optical switching owing to the higher quantum yields and absence of degradation. However, in most (if not all) cases, bridged derivatives display a reversed thermal stability (more stable Z-isomer), and smaller t 1 / 2 than the acyclic counterparts, which restricts their potential interest to applications requiring a fast forward and backwards switch. In this paper, the impact of alkyl bridges on the thermal stability of phenyl-azoheteroarenes is investigated by using computational methods, and it is revealed that it is indeed possible to combine such improved photoswitching characteristics while preserving the regular thermal stability (more stable E-isomer), and increased t 1 / 2 values under the appropriate connectivity and bridge length.
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Affiliation(s)
- Sergi Vela
- Institute of Chemical Sciences and EngineeringLaboratory for Computational Molecular DesignÉcole Polytechnique Fédérale de Lausanne (EPFL)1015LausanneSwitzerland
| | - Alan Scheidegger
- Institute of Chemical Sciences and EngineeringLaboratory for Computational Molecular DesignÉcole Polytechnique Fédérale de Lausanne (EPFL)1015LausanneSwitzerland
| | - Raimon Fabregat
- Institute of Chemical Sciences and EngineeringLaboratory for Computational Molecular DesignÉcole Polytechnique Fédérale de Lausanne (EPFL)1015LausanneSwitzerland
| | - Clémence Corminboeuf
- Institute of Chemical Sciences and EngineeringLaboratory for Computational Molecular DesignÉcole Polytechnique Fédérale de Lausanne (EPFL)1015LausanneSwitzerland
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Vela S, Corminboeuf C. The Photoisomerization Pathway(s) of Push-Pull Phenylazoheteroarenes*. Chemistry 2020; 26:14724-14729. [PMID: 32692427 PMCID: PMC7756763 DOI: 10.1002/chem.202002321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/17/2020] [Indexed: 12/31/2022]
Abstract
Azoheteroarenes are the most recent derivatives targeted to further improve the properties of azo-based photoswitches. Their light-induced mechanism for trans-cis isomerization is assumed to be very similar to that of the parent azobenzene. As such, they inherited the controversy about the dominant isomerization pathway (rotation vs. inversion) depending on the excited state (nπ* vs. ππ*). Although the controversy seems settled in azobenzene, the extent to which the same conclusions apply to the more structurally diverse family of azoheteroarenes is unclear. Here, by means of non-adiabatic molecular dynamics, the photoisomerization mechanism of three prototypical phenyl-azoheteroarenes with increasing push-pull character is unraveled. The evolution of the rotational and inversion conical intersection energies, the preferred pathway, and the associated kinetics upon both nπ* and ππ* excitations can be linked directly with the push-pull substitution effects. Overall, the working conditions of this family of azo-dyes is clarified and a possibility to exploit push-pull substituents to tune their photoisomerization mechanism is identified, with potential impact on their quantum yield.
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Affiliation(s)
- Sergi Vela
- Institute of Chemical Sciences and EngineeringLaboratory for Computational Molecular DesignÉcole Polytechnique Fédérale de Lausanne (EPFL)1015LausanneSwitzerland
| | - Clémence Corminboeuf
- Institute of Chemical Sciences and EngineeringLaboratory for Computational Molecular DesignÉcole Polytechnique Fédérale de Lausanne (EPFL)1015LausanneSwitzerland
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