---
_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. Accounts
of Chemical Research. 2020;53(11):2600-2610. doi:10.1021/acs.accounts.0c00434
apa: Grommet, A. B., Lee, L. M., & Klajn, R. (2020). Molecular photoswitching
in confined spaces. Accounts of Chemical Research. American Chemical Society.
https://doi.org/10.1021/acs.accounts.0c00434
chicago: Grommet, Angela B., Lucia M. Lee, and Rafal Klajn. “Molecular Photoswitching
in Confined Spaces.” Accounts of Chemical Research. American Chemical Society,
2020. https://doi.org/10.1021/acs.accounts.0c00434.
ieee: A. B. Grommet, L. M. Lee, and R. Klajn, “Molecular photoswitching in confined
spaces,” Accounts of Chemical Research, 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.” Accounts
of Chemical Research, vol. 53, no. 11, American Chemical Society, 2020, pp.
2600–10, doi:10.1021/acs.accounts.0c00434.
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: 2024-10-14T12:12:31Z
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.
Accounts of Chemical Research. 2020;53(9):1981-1991. doi:10.1021/acs.accounts.0c00403
apa: Cheng, B., Griffiths, R.-R., Wengert, S., Kunkel, C., Stenczel, T., Zhu, B.,
… Csanyi, G. (2020). Mapping materials and molecules. Accounts of Chemical
Research. American Chemical Society. https://doi.org/10.1021/acs.accounts.0c00403
chicago: Cheng, Bingqing, Ryan-Rhys Griffiths, Simon Wengert, Christian Kunkel,
Tamas Stenczel, Bonan Zhu, Volker L. Deringer, et al. “Mapping Materials and Molecules.”
Accounts of Chemical Research. American Chemical Society, 2020. https://doi.org/10.1021/acs.accounts.0c00403.
ieee: B. Cheng et al., “Mapping materials and molecules,” Accounts of
Chemical Research, 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.” Accounts of Chemical
Research, vol. 53, no. 9, American Chemical Society, 2020, pp. 1981–91, doi:10.1021/acs.accounts.0c00403.
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'
...
---
OA_type: closed access
_id: '17943'
abstract:
- lang: eng
text: "This Account provides an overview of our recent efforts to uncover the fundamental
charge transport properties of Si–Si and Ge–Ge single bonds and introduce useful
functions into group 14 molecular wires. We utilize the tools of chemical synthesis
and a scanning tunneling microscopy-based break-junction technique to study the
mechanism of charge transport in these molecular systems. We evaluated the fundamental
ability of silicon, germanium, and carbon molecular wires to transport charge
by comparing conductances within families of well-defined structures, the members
of which differ only in the number of Si (or Ge or C) atoms in the wire. For each
family, this procedure yielded a length-dependent conductance decay parameter,
β. Comparison of the different β values demonstrates that Si–Si and Ge–Ge σ bonds
are more conductive than the analogous C–C σ bonds. These molecular trends mirror
what is seen in the bulk.\r\n\r\nThe conductance decay of Si and Ge-based wires
is similar in magnitude to those from π-based molecular wires such as paraphenylenes
However, the chemistry of the linkers that attach the molecular wires to the electrodes
has a large influence on the resulting β value. For example, Si- and Ge-based
wires of many different lengths connected with a methyl–thiomethyl linker give
β values of 0.36–0.39 Å–1, whereas Si- and Ge-based wires connected with aryl–thiomethyl
groups give drastically different β values for short and long wires. This observation
inspired us to study molecular wires that are composed of both π- and σ-orbitals.
The sequence and composition of group 14 atoms in the σ chain modulates the electronic
coupling between the π end-groups and dictates the molecular conductance. The
conductance behavior originates from the coupling between the subunits, which
can be understood by considering periodic trends such as bond length, polarizability,
and bond polarity.\r\n\r\nWe found that the same periodic trends determine the
electric field-induced breakdown properties of individual Si–Si, Ge–Ge, Si–O,
Si–C, and C–C bonds. Building from these studies, we have prepared a system that
has two different, alternative conductance pathways. In this wire, we can intentionally
break a labile, strained silicon–silicon bond and thereby shunt the current through
the secondary conduction pathway. This type of in situ bond-rupture provides a
new tool to study single molecule reactions that are induced by electric fields.
Moreover, these studies provide guidance for designing dielectric materials as
well as molecular devices that require stability under high voltage bias.\r\n\r\nThe
fundamental studies on the structure/function relationships of the molecular wires
have guided the design of new functional systems based on the Si- and Ge-based
wires. For example, we exploited the principle of strain-induced Lewis acidity
from reaction chemistry to design a single molecule switch that can be controllably
switched between two conductive states by varying the distance between the tip
and substrate electrodes. We found that the strain intrinsic to the disilaacenaphthene
scaffold also creates two state conductance switching. Finally, we demonstrate
the first example of a stereoelectronic conductance switch, and we demonstrate
that the switching relies crucially on the electronic delocalization in Si–Si
and Ge–Ge wire backbones. These studies illustrate the untapped potential in using
Si- and Ge-based wires to design and control charge transport at the nanoscale
and to allow quantum mechanics to be used as a tool to design ultraminiaturized
switches."
article_processing_charge: No
article_type: original
author:
- first_name: Timothy A.
full_name: Su, Timothy A.
last_name: Su
- first_name: Haixing
full_name: Li, Haixing
last_name: Li
- first_name: Rebekka S.
full_name: Klausen, Rebekka S.
last_name: Klausen
- first_name: Nathaniel T.
full_name: Kim, Nathaniel T.
last_name: Kim
- first_name: Madhav
full_name: Neupane, Madhav
last_name: Neupane
- first_name: James L.
full_name: Leighton, James L.
last_name: Leighton
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
- first_name: Colin
full_name: Nuckolls, Colin
last_name: Nuckolls
citation:
ama: Su TA, Li H, Klausen RS, et al. Silane and Germane molecular electronics. Accounts
of Chemical Research. 2017;50(4):1088-1095. doi:10.1021/acs.accounts.7b00059
apa: Su, T. A., Li, H., Klausen, R. S., Kim, N. T., Neupane, M., Leighton, J. L.,
… Nuckolls, C. (2017). Silane and Germane molecular electronics. Accounts of
Chemical Research. American Chemical Society. https://doi.org/10.1021/acs.accounts.7b00059
chicago: Su, Timothy A., Haixing Li, Rebekka S. Klausen, Nathaniel T. Kim, Madhav
Neupane, James L. Leighton, Michael L. Steigerwald, Latha Venkataraman, and Colin
Nuckolls. “Silane and Germane Molecular Electronics.” Accounts of Chemical
Research. American Chemical Society, 2017. https://doi.org/10.1021/acs.accounts.7b00059.
ieee: T. A. Su et al., “Silane and Germane molecular electronics,” Accounts
of Chemical Research, vol. 50, no. 4. American Chemical Society, pp. 1088–1095,
2017.
ista: Su TA, Li H, Klausen RS, Kim NT, Neupane M, Leighton JL, Steigerwald ML, Venkataraman
L, Nuckolls C. 2017. Silane and Germane molecular electronics. Accounts of Chemical
Research. 50(4), 1088–1095.
mla: Su, Timothy A., et al. “Silane and Germane Molecular Electronics.” Accounts
of Chemical Research, vol. 50, no. 4, American Chemical Society, 2017, pp.
1088–95, doi:10.1021/acs.accounts.7b00059.
short: T.A. Su, H. Li, R.S. Klausen, N.T. Kim, M. Neupane, J.L. Leighton, M.L. Steigerwald,
L. Venkataraman, C. Nuckolls, Accounts of Chemical Research 50 (2017) 1088–1095.
date_created: 2024-09-09T08:51:18Z
date_published: 2017-03-27T00:00:00Z
date_updated: 2024-12-18T07:41:16Z
day: '27'
doi: 10.1021/acs.accounts.7b00059
extern: '1'
external_id:
pmid:
- '28345881'
intvolume: ' 50'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 1088-1095
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: Silane and Germane molecular electronics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2017'
...
---
OA_type: closed access
_id: '17960'
abstract:
- lang: eng
text: "Over the past 10 years, there has been tremendous progress in the measurement,
modeling and understanding of structure–function relationships in single molecule
junctions. Numerous research groups have addressed significant scientific questions,
directed both to conductance phenomena at the single molecule level and to the
fundamental chemistry that controls junction functionality. Many different functionalities
have been demonstrated, including single-molecule diodes, optically and mechanically
activated switches, and, significantly, physical phenomena with no classical analogues,
such as those based on quantum interference effects. Experimental techniques for
reliable and reproducible single molecule junction formation and characterization
have led to this progress. In particular, the scanning tunneling microscope based
break-junction (STM-BJ) technique has enabled rapid, sequential measurement of
large numbers of nanoscale junctions allowing a statistical analysis to readily
distinguish reproducible characteristics. Harnessing fundamental link chemistry
has provided the necessary chemical control over junction formation, enabling
measurements that revealed clear relationships between molecular structure and
conductance characteristics. Such link groups (amines, methylsuflides, pyridines,
etc.) maintain a stable lone pair configuration that selectively bonds to specific,
undercoordinated transition metal atoms available following rupture of a metal
point contact in the STM-BJ experiments. This basic chemical principle rationalizes
the observation of highly reproducible conductance signatures. Subsequently, the
method has been extended to probe a variety of physical phenomena ranging from
basic I–V characteristics to more complex properties such as thermopower and electrochemical
response. By adapting the technique to a conducting cantilever atomic force microscope
(AFM-BJ), simultaneous measurement of the mechanical characteristics of nanoscale
junctions as they are pulled apart has given complementary information such as
the stiffness and rupture force of the molecule-metal link bond. Overall, while
the BJ technique does not produce a single molecule circuit for practical applications,
it has proved remarkably versatile for fundamental studies. Measured data and
analysis have been combined with atomic-scale theory and calculations, typically
performed for representative junction structures, to provide fundamental physical
understanding of structure–function relationships.\r\n\r\nThis Account integrates
across an extensive series of our specific nanoscale junction studies which were
carried out with the STM- and AFM-BJ techniques and supported by theoretical analysis
and density functional theory based calculations, with emphasis on the physical
characteristics of the measurement process and the rich data sets that emerge.
Several examples illustrate the impact of measured trends based on the most probable
values for key characteristics (obtained from ensembles of order 1000–10 000 individual
junctions) to build a solid picture of conductance phenomena as well as attributes
of the link bond chemistry. The key forward-looking question posed here is the
extent to which the full data sets represented by the individual trajectories
can be analyzed to address structure–function questions at the level of individual
junctions. Initial progress toward physical modeling of conductance of individual
junctions indicates trends consistent with physical junction structures. Analysis
of junction mechanics reveals a scaling procedure that collapses existing data
onto a universal force–extension curve. This research directed to understanding
the distribution of structures and physical characteristics addresses fundamental
questions concerning the interplay between chemical control and stochastically
driven diversity."
article_processing_charge: No
article_type: original
author:
- first_name: Mark S.
full_name: Hybertsen, Mark S.
last_name: Hybertsen
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: 'Hybertsen MS, Venkataraman L. Structure–property relationships in atomic-scale
junctions: Histograms and beyond. Accounts of Chemical Research. 2016;49(3):452-460.
doi:10.1021/acs.accounts.6b00004'
apa: 'Hybertsen, M. S., & Venkataraman, L. (2016). Structure–property relationships
in atomic-scale junctions: Histograms and beyond. Accounts of Chemical Research.
American Chemical Society. https://doi.org/10.1021/acs.accounts.6b00004'
chicago: 'Hybertsen, Mark S., and Latha Venkataraman. “Structure–Property Relationships
in Atomic-Scale Junctions: Histograms and Beyond.” Accounts of Chemical Research.
American Chemical Society, 2016. https://doi.org/10.1021/acs.accounts.6b00004.'
ieee: 'M. S. Hybertsen and L. Venkataraman, “Structure–property relationships in
atomic-scale junctions: Histograms and beyond,” Accounts of Chemical Research,
vol. 49, no. 3. American Chemical Society, pp. 452–460, 2016.'
ista: 'Hybertsen MS, Venkataraman L. 2016. Structure–property relationships in atomic-scale
junctions: Histograms and beyond. Accounts of Chemical Research. 49(3), 452–460.'
mla: 'Hybertsen, Mark S., and Latha Venkataraman. “Structure–Property Relationships
in Atomic-Scale Junctions: Histograms and Beyond.” Accounts of Chemical Research,
vol. 49, no. 3, American Chemical Society, 2016, pp. 452–60, doi:10.1021/acs.accounts.6b00004.'
short: M.S. Hybertsen, L. Venkataraman, Accounts of Chemical Research 49 (2016)
452–460.
date_created: 2024-09-09T09:31:45Z
date_published: 2016-03-03T00:00:00Z
date_updated: 2024-12-18T09:18:36Z
day: '03'
doi: 10.1021/acs.accounts.6b00004
extern: '1'
external_id:
pmid:
- '26938931'
intvolume: ' 49'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 452-460
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: 'Structure–property relationships in atomic-scale junctions: Histograms and
beyond'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2016'
...