[{"day":"17","doi":"10.1021/acs.accounts.0c00434","abstract":[{"text":"In nature, light is harvested by photoactive proteins to drive a range of biological processes, including photosynthesis, phototaxis, vision, and ultimately life. Bacteriorhodopsin, for example, is a protein embedded within archaeal cell membranes that binds the chromophore retinal within its hydrophobic pocket. Exposure to light triggers regioselective photoisomerization of the confined retinal, which in turn initiates a cascade of conformational changes within the protein, triggering proton flux against the concentration gradient, providing the microorganisms with the energy to live. We are inspired by these functions in nature to harness light energy using synthetic photoswitches under confinement. Like retinal, synthetic photoswitches require some degree of conformational flexibility to isomerize. In nature, the conformational change associated with retinal isomerization is accommodated by the structural flexibility of the opsin host, yet it results in steric communication between the chromophore and the protein. Similarly, we strive to design systems wherein isomerization of confined photoswitches results in steric communication between a photoswitch and its confining environment. To achieve this aim, a balance must be struck between molecular crowding and conformational freedom under confinement: too much crowding prevents switching, whereas too much freedom resembles switching of isolated molecules in solution, preventing communication.\r\n\r\nIn this Account, we discuss five classes of synthetic light-switchable compounds—diarylethenes, anthracenes, azobenzenes, spiropyrans, and donor–acceptor Stenhouse adducts—comparing their behaviors under confinement and in solution. The environments employed to confine these photoswitches are diverse, ranging from planar surfaces to nanosized cavities within coordination cages, nanoporous frameworks, and nanoparticle aggregates. The trends that emerge are primarily dependent on the nature of the photoswitch and not on the material used for confinement. In general, we find that photoswitches requiring less conformational freedom for switching are, as expected, more straightforward to isomerize reversibly under confinement. Because these compounds undergo only small structural changes upon isomerization, however, switching does not propagate into communication with their environment. Conversely, photoswitches that require more conformational freedom are more challenging to switch under confinement but also can influence system-wide behavior.\r\n\r\nAlthough we are primarily interested in the effects of geometric constraints on photoswitching under confinement, additional effects inevitably emerge when a compound is removed from solution and placed within a new, more crowded environment. For instance, we have found that compounds that convert to zwitterionic isomers upon light irradiation often experience stabilization of these forms under confinement. This effect results from the mutual stabilization of zwitterions that are brought into close proximity on surfaces or within cavities. Furthermore, photoswitches can experience preorganization under confinement, influencing the selectivity and efficiency of their photoreactions. Because intermolecular interactions arising from confinement cannot be considered independently from the effects of geometric constraints, we describe all confinement effects concurrently throughout this Account.","lang":"eng"}],"citation":{"ieee":"A. B. Grommet, L. M. Lee, and R. Klajn, “Molecular photoswitching in confined spaces,” <i>Accounts of Chemical Research</i>, vol. 53, no. 11. American Chemical Society, pp. 2600–2610, 2020.","chicago":"Grommet, Angela B., Lucia M. Lee, and Rafal Klajn. “Molecular Photoswitching in Confined Spaces.” <i>Accounts of Chemical Research</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.accounts.0c00434\">https://doi.org/10.1021/acs.accounts.0c00434</a>.","apa":"Grommet, A. B., Lee, L. M., &#38; Klajn, R. (2020). Molecular photoswitching in confined spaces. <i>Accounts of Chemical Research</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.accounts.0c00434\">https://doi.org/10.1021/acs.accounts.0c00434</a>","ama":"Grommet AB, Lee LM, Klajn R. Molecular photoswitching in confined spaces. <i>Accounts of Chemical Research</i>. 2020;53(11):2600-2610. doi:<a href=\"https://doi.org/10.1021/acs.accounts.0c00434\">10.1021/acs.accounts.0c00434</a>","ista":"Grommet AB, Lee LM, Klajn R. 2020. Molecular photoswitching in confined spaces. Accounts of Chemical Research. 53(11), 2600–2610.","mla":"Grommet, Angela B., et al. “Molecular Photoswitching in Confined Spaces.” <i>Accounts of Chemical Research</i>, vol. 53, no. 11, American Chemical Society, 2020, pp. 2600–10, doi:<a href=\"https://doi.org/10.1021/acs.accounts.0c00434\">10.1021/acs.accounts.0c00434</a>.","short":"A.B. Grommet, L.M. Lee, R. Klajn, Accounts of Chemical Research 53 (2020) 2600–2610."},"year":"2020","date_updated":"2023-08-07T10:06:46Z","external_id":{"pmid":["32969638"]},"volume":53,"extern":"1","date_created":"2023-08-01T09:35:50Z","article_processing_charge":"No","publication_status":"published","intvolume":"        53","title":"Molecular photoswitching in confined spaces","scopus_import":"1","pmid":1,"_id":"13361","issue":"11","author":[{"first_name":"Angela B.","last_name":"Grommet","full_name":"Grommet, Angela B."},{"full_name":"Lee, Lucia M.","last_name":"Lee","first_name":"Lucia M."},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"publisher":"American Chemical Society","article_type":"original","quality_controlled":"1","page":"2600-2610","publication_identifier":{"eissn":["1520-4898"],"issn":["0001-4842"]},"oa":1,"type":"journal_article","date_published":"2020-11-17T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.accounts.0c00434"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"11","publication":"Accounts of Chemical Research","keyword":["General Medicine","General Chemistry"],"language":[{"iso":"eng"}]},{"type":"journal_article","date_published":"2020-08-14T00:00:00Z","publication_identifier":{"eissn":["1520-4898"],"issn":["0001-4842"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","publication":"Accounts of Chemical Research","month":"08","oa_version":"None","language":[{"iso":"eng"}],"external_id":{"pmid":["32794697"]},"year":"2020","citation":{"apa":"Cheng, B., Griffiths, R.-R., Wengert, S., Kunkel, C., Stenczel, T., Zhu, B., … Csanyi, G. (2020). Mapping materials and molecules. <i>Accounts of Chemical Research</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.accounts.0c00403\">https://doi.org/10.1021/acs.accounts.0c00403</a>","ama":"Cheng B, Griffiths R-R, Wengert S, et al. Mapping materials and molecules. <i>Accounts of Chemical Research</i>. 2020;53(9):1981-1991. doi:<a href=\"https://doi.org/10.1021/acs.accounts.0c00403\">10.1021/acs.accounts.0c00403</a>","ieee":"B. Cheng <i>et al.</i>, “Mapping materials and molecules,” <i>Accounts of Chemical Research</i>, vol. 53, no. 9. American Chemical Society, pp. 1981–1991, 2020.","chicago":"Cheng, Bingqing, Ryan-Rhys Griffiths, Simon Wengert, Christian Kunkel, Tamas Stenczel, Bonan Zhu, Volker L. Deringer, et al. “Mapping Materials and Molecules.” <i>Accounts of Chemical Research</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.accounts.0c00403\">https://doi.org/10.1021/acs.accounts.0c00403</a>.","short":"B. Cheng, R.-R. Griffiths, S. Wengert, C. Kunkel, T. Stenczel, B. Zhu, V.L. Deringer, N. Bernstein, J.T. Margraf, K. Reuter, G. Csanyi, Accounts of Chemical Research 53 (2020) 1981–1991.","mla":"Cheng, Bingqing, et al. “Mapping Materials and Molecules.” <i>Accounts of Chemical Research</i>, vol. 53, no. 9, American Chemical Society, 2020, pp. 1981–91, doi:<a href=\"https://doi.org/10.1021/acs.accounts.0c00403\">10.1021/acs.accounts.0c00403</a>.","ista":"Cheng B, Griffiths R-R, Wengert S, Kunkel C, Stenczel T, Zhu B, Deringer VL, Bernstein N, Margraf JT, Reuter K, Csanyi G. 2020. Mapping materials and molecules. Accounts of Chemical Research. 53(9), 1981–1991."},"date_updated":"2021-11-24T15:54:41Z","abstract":[{"lang":"eng","text":"The visualization of data is indispensable in scientific research, from the early stages when human insight forms to the final step of communicating results. In computational physics, chemistry and materials science, it can be as simple as making a scatter plot or as straightforward as looking through the snapshots of atomic positions manually. However, as a result of the \"big data\" revolution, these conventional approaches are often inadequate. The widespread adoption of high-throughput computation for materials discovery and the associated community-wide repositories have given rise to data sets that contain an enormous number of compounds and atomic configurations. A typical data set contains thousands to millions of atomic structures, along with a diverse range of properties such as formation energies, band gaps, or bioactivities.It would thus be desirable to have a data-driven and automated framework for visualizing and analyzing such structural data sets. The key idea is to construct a low-dimensional representation of the data, which facilitates navigation, reveals underlying patterns, and helps to identify data points with unusual attributes. Such data-intensive maps, often employing machine learning methods, are appearing more and more frequently in the literature. However, to the wider community, it is not always transparent how these maps are made and how they should be interpreted. Furthermore, while these maps undoubtedly serve a decorative purpose in academic publications, it is not always apparent what extra information can be garnered from reading or making them.This Account attempts to answer such questions. We start with a concise summary of the theory of representing chemical environments, followed by the introduction of a simple yet practical conceptual approach for generating structure maps in a generic and automated manner. Such analysis and mapping is made nearly effortless by employing the newly developed software tool ASAP. To showcase the applicability to a wide variety of systems in chemistry and materials science, we provide several illustrative examples, including crystalline and amorphous materials, interfaces, and organic molecules. In these examples, the maps not only help to sift through large data sets but also reveal hidden patterns that could be easily missed using conventional analyses.The explosion in the amount of computed information in chemistry and materials science has made visualization into a science in itself. Not only have we benefited from exploiting these visualization methods in previous works, we also believe that the automated mapping of data sets will in turn stimulate further creativity and exploration, as well as ultimately feed back into future advances in the respective fields."}],"day":"14","doi":"10.1021/acs.accounts.0c00403","extern":"1","volume":53,"issue":"9","author":[{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Ryan-Rhys","last_name":"Griffiths","full_name":"Griffiths, Ryan-Rhys"},{"first_name":"Simon","last_name":"Wengert","full_name":"Wengert, Simon"},{"full_name":"Kunkel, Christian","first_name":"Christian","last_name":"Kunkel"},{"full_name":"Stenczel, Tamas","first_name":"Tamas","last_name":"Stenczel"},{"first_name":"Bonan","last_name":"Zhu","full_name":"Zhu, Bonan"},{"last_name":"Deringer","first_name":"Volker L.","full_name":"Deringer, Volker L."},{"first_name":"Noam","last_name":"Bernstein","full_name":"Bernstein, Noam"},{"last_name":"Margraf","first_name":"Johannes T.","full_name":"Margraf, Johannes T."},{"full_name":"Reuter, Karsten","first_name":"Karsten","last_name":"Reuter"},{"full_name":"Csanyi, Gabor","first_name":"Gabor","last_name":"Csanyi"}],"scopus_import":"1","_id":"9675","pmid":1,"intvolume":"        53","title":"Mapping materials and molecules","article_processing_charge":"No","date_created":"2021-07-16T06:25:53Z","publication_status":"published","quality_controlled":"1","page":"1981-1991","article_type":"original","publisher":"American Chemical Society"}]