---
_id: '13361'
abstract:
- lang: eng
  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."
article_processing_charge: No
article_type: original
author:
- first_name: Angela B.
  full_name: Grommet, Angela B.
  last_name: Grommet
- first_name: Lucia M.
  full_name: Lee, Lucia M.
  last_name: Lee
- first_name: Rafal
  full_name: Klajn, Rafal
  id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
  last_name: Klajn
citation:
  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>
  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>
  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>.
  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.
  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.
date_created: 2023-08-01T09:35:50Z
date_published: 2020-11-17T00:00:00Z
date_updated: 2023-08-07T10:06:46Z
day: '17'
doi: 10.1021/acs.accounts.0c00434
extern: '1'
external_id:
  pmid:
  - '32969638'
intvolume: '        53'
issue: '11'
keyword:
- General Medicine
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1021/acs.accounts.0c00434
month: '11'
oa: 1
oa_version: Published Version
page: 2600-2610
pmid: 1
publication: Accounts of Chemical Research
publication_identifier:
  eissn:
  - 1520-4898
  issn:
  - 0001-4842
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular photoswitching in confined spaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2020'
...
---
_id: '9675'
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.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: Ryan-Rhys
  full_name: Griffiths, Ryan-Rhys
  last_name: Griffiths
- first_name: Simon
  full_name: Wengert, Simon
  last_name: Wengert
- first_name: Christian
  full_name: Kunkel, Christian
  last_name: Kunkel
- first_name: Tamas
  full_name: Stenczel, Tamas
  last_name: Stenczel
- first_name: Bonan
  full_name: Zhu, Bonan
  last_name: Zhu
- first_name: Volker L.
  full_name: Deringer, Volker L.
  last_name: Deringer
- first_name: Noam
  full_name: Bernstein, Noam
  last_name: Bernstein
- first_name: Johannes T.
  full_name: Margraf, Johannes T.
  last_name: Margraf
- first_name: Karsten
  full_name: Reuter, Karsten
  last_name: Reuter
- first_name: Gabor
  full_name: Csanyi, Gabor
  last_name: Csanyi
citation:
  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>
  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>
  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>.
  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.
  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.
  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>.
  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.
date_created: 2021-07-16T06:25:53Z
date_published: 2020-08-14T00:00:00Z
date_updated: 2021-11-24T15:54:41Z
day: '14'
doi: 10.1021/acs.accounts.0c00403
extern: '1'
external_id:
  pmid:
  - '32794697'
intvolume: '        53'
issue: '9'
language:
- iso: eng
month: '08'
oa_version: None
page: 1981-1991
pmid: 1
publication: Accounts of Chemical Research
publication_identifier:
  eissn:
  - 1520-4898
  issn:
  - 0001-4842
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mapping materials and molecules
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 53
year: '2020'
...