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Jaiswal AK, Saha P, Jiang J, Suzuki K, Jasny A, Schmidt BM, Maeda S, Hecht S, Huang CYD. Accessing a Diverse Set of Functional Red-Light Photoswitches by Selective Copper-Catalyzed Indigo N-Arylation. J Am Chem Soc 2024; 146:21367-21376. [PMID: 39058407 DOI: 10.1021/jacs.4c03543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
The ability to correlate the structure of a molecule with its properties is the key to the rational and accelerated design of new functional compounds and materials. Taking photoswitches as an example, the thermal stability of the metastable state is a crucial property that dictates their application in molecular systems. Indigos have recently emerged as an attractive motif for designing photoswitchable molecules due to their red-light addressability, which can be advantageous in biomedical and material applications. The lack of synthetic techniques to derivatize the abundant parent dye and a thorough understanding of the impact of structural factors on the photochemical and thermal properties hinder broad applications of this emerging photoswitch class. Herein, we report an efficient copper-catalyzed indigo N-arylation that enables the installation of a wide variety of aryl moieties carrying useful functional groups. The exclusive selectivity for monoarylation likely originates from a bimetallic cooperative mechanism through a binuclear copper-indigo intermediate. Functional N-aryl-N'-alkylindigos were prepared and shown to photoisomerize efficiently under red light. Moreover, this design allows for the modulation of thermal half-lives through N-aryl substituents, while the N'-alkyl groups enable the independent attachment of functional moieties without affecting the photochromic properties. A strong correlation between the structure of the N-aryl moiety and the thermal stability of the photogenerated Z-isomers was achieved by multivariate linear regression models obtained through a data-science workflow. This work thus builds an avenue leading to versatile red-light photoswitches and a general method for structure-property correlation that is expected to be broadly applicable to the design of photoresponsive molecules.
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Affiliation(s)
- Amit K Jaiswal
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Priya Saha
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Julong Jiang
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-8628, Japan
| | - Kimichi Suzuki
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Anna Jasny
- DWI-Leibniz Institute for Interactive Materials, Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen 52074, Germany
| | - Bernd M Schmidt
- Institute for Organic Chemistry and Macromolecular Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-8628, Japan
| | - Stefan Hecht
- Department of Chemistry, IRIS Adlershof and Center for the Science of Materials Berlin, Humboldt-Universität zu Berlin, Berlin 12489, Germany
| | - Chung-Yang Dennis Huang
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
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2
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Dang T, Zhang ZY, Li T. Visible-Light-Activated Heteroaryl Azoswitches: Toward a More Colorful Future. J Am Chem Soc 2024; 146:19609-19620. [PMID: 38991225 DOI: 10.1021/jacs.4c03135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Azobenzenes (Ph-N═N-Ph) are known as the most widely studied molecular photoswitches, and the recent rise of azoheteroarenes (Het-N═N-Ph or Het-N═N-Het) offers great opportunities to advance this already mature field. A common limitation is that azo-switches generally require harmful UV light for activation, which hinders their application across various fields. Despite great efforts in developing visible-light azobenzenes over the past few decades, the potential of visible-light heteroaryl azoswitches remains largely unexplored. This Perspective summarizes the state-of-the-art advancements in visible-light heteroaryl azoswitches, covering molecular design strategies, the structure-property relationship, and potential applications. We highlight the distinctive advantages of azoheteroarenes over azobenzenes in the research and development of visible-light switches. Furthermore, we discuss the opportunities and challenges in this emerging field and propose potential solutions to address crucial issues such as spectral red-shift and thermal half-life. Through this Perspective paper, we aim to provide inspiration for further exploration in this field, in anticipation of the growing prosperity and bright future of visible-light azoheteroarene photoswitches.
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Affiliation(s)
- Tongtong Dang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Key Laboratory of Thin Film and Microfabrication (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Yang Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Key Laboratory of Thin Film and Microfabrication (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Key Laboratory of Thin Film and Microfabrication (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
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3
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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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4
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Hillers-Bendtsen AE, Elholm JL, Obel OB, Hölzel H, Moth-Poulsen K, Mikkelsen KV. Searching the Chemical Space of Bicyclic Dienes for Molecular Solar Thermal Energy Storage Candidates. Angew Chem Int Ed Engl 2023; 62:e202309543. [PMID: 37489860 DOI: 10.1002/anie.202309543] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 07/26/2023]
Abstract
Photoswitches are molecular systems that are chemically transformed subsequent to interaction with light and they find potential application in many new technologies. The design and discovery of photoswitch candidates require intricate molecular engineering of a range of properties to optimize a candidate to a specific applications, a task which can be tackled efficiently using quantum chemical screening procedures. In this paper, we perform a large scale screening of approximately half a million bicyclic diene photoswitches in the context of molecular solar thermal energy storage using ab initio quantum chemical methods. We further device an efficient strategy for scoring the systems based on their predicted solar energy conversion efficiency and elucidate potential pitfalls of this approach. Our search through the chemical space of bicyclic dienes reveals systems with unprecedented solar energy conversion efficiencies and storage densities that show promising design guidelines for next generation molecular solar thermal energy storage systems.
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Affiliation(s)
| | - Jacob Lynge Elholm
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
- The Institute of Materials Science of Barcelona, ICMAB-CSIC, 08193, Bellaterra, Barcelona, Spain
| | - Oscar Berlin Obel
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Helen Hölzel
- Department of Chemical Engineering, Universitat Politècnica de Catalunya, EEBE, Eduard Maristany 10-14, 08019, Barcelona, Spain
| | - Kasper Moth-Poulsen
- Department of Chemical Engineering, Universitat Politècnica de Catalunya, EEBE, Eduard Maristany 10-14, 08019, Barcelona, Spain
- The Institute of Materials Science of Barcelona, ICMAB-CSIC, 08193, Bellaterra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
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5
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Axelrod S, Shakhnovich E, Gómez-Bombarelli R. Mapping the Space of Photoswitchable Ligands and Photodruggable Proteins with Computational Modeling. J Chem Inf Model 2023; 63:5794-5802. [PMID: 37671878 DOI: 10.1021/acs.jcim.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Light-activated drugs are a promising way to localize biological activity and minimize side effects. However, their development is complicated by the numerous photophysical and biological properties that must be simultaneously optimized. To accelerate the design of photoactive drugs, we describe a procedure that combines ligand-protein docking with chemical property prediction based on machine learning (ML). We apply this procedure to 58 proteins and 9000 photo-drug candidates based on azobenzene cis-trans isomerism. We find that most proteins display a preference for trans isomers over cis and that the binding affinities of nominally active/inactive pairs are in fact highly correlated. These findings have significant value for photopharmacology research, and reinforce the need for virtual screening to identify compounds with rare desirable properties. Further, we combine our procedure with quantum chemical validation to identify promising candidates for the photoactive inhibition of PARP1, an enzyme that is over-expressed in cancer cells. The top compounds are predicted to have long-lived active forms, differential bioactivity, and absorption in the near-infrared therapeutic window.
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Affiliation(s)
- Simon Axelrod
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Rafael Gómez-Bombarelli
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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6
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Jablonka K, Rosen AS, Krishnapriyan AS, Smit B. An Ecosystem for Digital Reticular Chemistry. ACS CENTRAL SCIENCE 2023; 9:563-581. [PMID: 37122448 PMCID: PMC10141625 DOI: 10.1021/acscentsci.2c01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The vastness of the materials design space makes it impractical to explore using traditional brute-force methods, particularly in reticular chemistry. However, machine learning has shown promise in expediting and guiding materials design. Despite numerous successful applications of machine learning to reticular materials, progress in the field has stagnated, possibly because digital chemistry is more an art than a science and its limited accessibility to inexperienced researchers. To address this issue, we present mofdscribe, a software ecosystem tailored to novice and seasoned digital chemists that streamlines the ideation, modeling, and publication process. Though optimized for reticular chemistry, our tools are versatile and can be used in nonreticular materials research. We believe that mofdscribe will enable a more reliable, efficient, and comparable field of digital chemistry.
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Affiliation(s)
- Kevin
Maik Jablonka
- Laboratory of molecular simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Rue de l’Industrie 17, CH-1951 Sion, Switzerland
| | - Andrew S. Rosen
- Department of Materials
Science and Engineering, University of California, Berkeley, California 94720, United States
- Miller Institute for Basic Research in Science, University of California, Berkeley, California 94720, United States
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aditi S. Krishnapriyan
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Electrical Engineering and
Computer Science, University of California, Berkeley, California 94720, United States
- Computational
Research Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Berend Smit
- Laboratory of molecular simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Rue de l’Industrie 17, CH-1951 Sion, Switzerland
- E-mail:
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7
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Axelrod S, Shakhnovich E, Gómez-Bombarelli R. Thermal Half-Lives of Azobenzene Derivatives: Virtual Screening Based on Intersystem Crossing Using a Machine Learning Potential. ACS CENTRAL SCIENCE 2023; 9:166-176. [PMID: 36844486 PMCID: PMC9951306 DOI: 10.1021/acscentsci.2c00897] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Indexed: 05/27/2023]
Abstract
Molecular photoswitches are the foundation of light-activated drugs. A key photoswitch is azobenzene, which exhibits trans-cis isomerism in response to light. The thermal half-life of the cis isomer is of crucial importance, since it controls the duration of the light-induced biological effect. Here we introduce a computational tool for predicting the thermal half-lives of azobenzene derivatives. Our automated approach uses a fast and accurate machine learning potential trained on quantum chemistry data. Building on well-established earlier evidence, we argue that thermal isomerization proceeds through rotation mediated by intersystem crossing, and incorporate this mechanism into our automated workflow. We use our approach to predict the thermal half-lives of 19,000 azobenzene derivatives. We explore trends and trade-offs between barriers and absorption wavelengths, and open-source our data and software to accelerate research in photopharmacology.
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Affiliation(s)
- Simon Axelrod
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts02138, United States
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Eugene Shakhnovich
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts02138, United States
| | - Rafael Gómez-Bombarelli
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts02139, United States
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