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Wiggins KM, Brantley JN, Bielawski CW. Methods for activating and characterizing mechanically responsive polymers. Chem Soc Rev 2013; 42:7130-47. [PMID: 23389104 DOI: 10.1039/c3cs35493h] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mechanically responsive polymers harness mechanical energy to facilitate unique chemical transformations and bestow materials with force sensing (e.g., mechanochromism) or self-healing capabilities. A variety of solution- and solid-state techniques, covering a spectrum of forces and strain rates, can be used to activate mechanically responsive polymers. Moreover, many of these methods have been combined with optical spectroscopy or chemical labeling techniques to characterize the products formed via mechanical activation of appropriate precursors in situ. In this tutorial review, we discuss the methods and techniques that have been used to supply mechanical force to macromolecular systems, and highlight the advantages and challenges associated with each.
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Affiliation(s)
- Kelly M Wiggins
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
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52
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Michalet X, Colyer RA, Scalia G, Ingargiola A, Lin R, Millaud JE, Weiss S, Siegmund OHW, Tremsin AS, Vallerga JV, Cheng A, Levi M, Aharoni D, Arisaka K, Villa F, Guerrieri F, Panzeri F, Rech I, Gulinatti A, Zappa F, Ghioni M, Cova S. Development of new photon-counting detectors for single-molecule fluorescence microscopy. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120035. [PMID: 23267185 PMCID: PMC3538434 DOI: 10.1098/rstb.2012.0035] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level.
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Affiliation(s)
- X Michalet
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1547, USA.
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53
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Zheng YB, Pathem BK, Hohman JN, Thomas JC, Kim M, Weiss PS. Photoresponsive molecules in well-defined nanoscale environments. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:302-312. [PMID: 22933316 DOI: 10.1002/adma.201201532] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/01/2012] [Indexed: 06/01/2023]
Abstract
Stimuli-responsive molecules are key building blocks of functional molecular materials and devices. These molecules can operate in a range of environments. A molecule's local environment will dictate its conformation, reactivity, and function; by controlling the local environment we can ultimately develop interfaces of individual molecules with the macroscopic environment. By isolating molecules in well-defined environments, we are able to obtain both accurate measurements and precise control. We exploit defect sites in self-assembled monolayers (SAMs) to direct the functional molecules into precise locations, providing a basis for the measurements and engineering of functional molecular systems. The structure and functional moieties of the SAM can be tuned to control not only the intermolecular interactions but also molecule-substrate interactions, resulting in extraction or control of desired molecular functions. Herein, we report our progress toward the assembly and measurements of photoresponsive molecules and their precise assemblies in SAM matrices.
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Affiliation(s)
- Yue Bing Zheng
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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54
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Kim T, Jeon KS, Heo K, Kim HM, Park J, Suh YD, Hong S. Multilayered nano-prism vertex tips for tip-enhanced Raman spectroscopy and imaging. Analyst 2013; 138:5588-93. [DOI: 10.1039/c3an00808h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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55
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Wang Q, Moerner WE. Lifetime and Spectrally Resolved Characterization of the Photodynamics of Single Fluorophores in Solution Using the Anti-Brownian Electrokinetic Trap. J Phys Chem B 2012. [DOI: 10.1021/jp308949d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quan Wang
- Department
of Chemistry and ‡Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry and ‡Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
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56
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Zheng YB, Kiraly B, Weiss PS, Huang TJ. Molecular plasmonics for biology and nanomedicine. Nanomedicine (Lond) 2012; 7:751-70. [PMID: 22630155 DOI: 10.2217/nnm.12.30] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The optical excitation of surface plasmons in metal nanoparticles leads to nanoscale spatial confinement of electromagnetic fields. The confined electromagnetic fields can generate intense, localized thermal energy and large near-field optical forces. The interaction between these effects and nearby molecules has led to the emerging field known as molecular plasmonics. Recent advances in molecular plasmonics have enabled novel optical materials and devices with applications in biology and nanomedicine. In this article, we categorize three main types of interactions between molecules and surface plasmons: optical, thermal and mechanical. Within the scope of each type of interaction, we will review applications of molecular plasmonics in biology and nanomedicine. We include a wide range of applications that involve sensing, spectral analysis, imaging, delivery, manipulation and heating of molecules, biomolecules or cells using plasmonic effects. We also briefly describe the physical principles of molecular plasmonics and progress in the nanofabrication, surface functionalization and bioconjugation of metal nanoparticles.
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Affiliation(s)
- Yue Bing Zheng
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
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58
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Pelaz B, Jaber S, de Aberasturi DJ, Wulf V, Aida T, de la Fuente JM, Feldmann J, Gaub HE, Josephson L, Kagan CR, Kotov NA, Liz-Marzán LM, Mattoussi H, Mulvaney P, Murray CB, Rogach AL, Weiss PS, Willner I, Parak WJ. The state of nanoparticle-based nanoscience and biotechnology: progress, promises, and challenges. ACS NANO 2012; 6:8468-83. [PMID: 23016700 DOI: 10.1021/nn303929a] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Colloidal nanoparticles (NPs) have become versatile building blocks in a wide variety of fields. Here, we discuss the state-of-the-art, current hot topics, and future directions based on the following aspects: narrow size-distribution NPs can exhibit protein-like properties; monodispersity of NPs is not always required; assembled NPs can exhibit collective behavior; NPs can be assembled one by one; there is more to be connected with NPs; NPs can be designed to be smart; surface-modified NPs can directly reach the cytosols of living cells.
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Affiliation(s)
- Beatriz Pelaz
- Fachbereich Physik and WZMW, Philipps Universität Marburg, 35037 Marburg, Germany
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59
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Zheng YB, Payton JL, Song TB, Pathem BK, Zhao Y, Ma H, Yang Y, Jensen L, Jen AKY, Weiss PS. Surface-enhanced Raman spectroscopy to probe photoreaction pathways and kinetics of isolated reactants on surfaces: flat versus curved substrates. NANO LETTERS 2012; 12:5362-5368. [PMID: 22978482 DOI: 10.1021/nl302750d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We identify and control the photoreaction paths of self-assembled monolayers (SAMs) of thiolate-linked anthracene phenylethynyl molecules on Au substrate surfaces, and study the effects of nanoscale morphology of substrates on regioselective photoreactions. Two types of morphologies, atomically flat and curved, are produced on Au surfaces by controlling substrate structure and metal deposition. We employ surface-enhanced Raman spectroscopy (SERS), combined with Raman mode analyses using density functional theory, to identify the different photoreaction paths and to track the photoreaction kinetics and efficiencies of molecules in monolayers. The SAMs on curved surfaces exhibit dramatically lower regioselective photoreaction kinetics and efficiencies than those on atomically flat surfaces. This result is attributed to the increased intermolecular distances and variable orientations on the curved surfaces. Better understanding of the morphological effects of substrates will enable control of nanoparticle functionalization in ligand exchange in targeted delivery of therapeutics and theranostics and in catalysis.
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Affiliation(s)
- Yue Bing Zheng
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
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60
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Ribas-Arino J, Marx D. Covalent mechanochemistry: theoretical concepts and computational tools with applications to molecular nanomechanics. Chem Rev 2012; 112:5412-87. [PMID: 22909336 DOI: 10.1021/cr200399q] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jordi Ribas-Arino
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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61
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Cheng CL, Zhao GJ. Steered molecular dynamics simulation study on dynamic self-assembly of single-stranded DNA with double-walled carbon nanotube and graphene. NANOSCALE 2012; 4:2301-2305. [PMID: 22392473 DOI: 10.1039/c2nr12112c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In the present work, we explored the diameter selectivity of dynamic self-assembly for the single-strand DNA (ssDNA) encapsulation in double-walled nanotubes (DWNTs) via molecular dynamics simulation method. Moreover, the pulling out process was carried out by steered molecular dynamics simulations. Considering π-π stacking and solvent accessibility together, base-CNT binding should be strongest on a graphene sheet and weakest on the inner CNT surface. When pulling the ssDNA out of the single-walled carbon nanotube (SWNT), the force exhibits characteristic fluctuations around a plateau about 300 pN. Each fluctuation force pulse to pull ssDNA corresponds to the exit of one base. In addition, the solvents used for the system are also of significant interest. Water does play an important role in encapsulation process but doesn't in the pulling out process.
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Affiliation(s)
- Chang-Li Cheng
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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62
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Ménard A, Huang Y, Karam P, Cosa G, Auclair K. Site-specific fluorescent labeling and oriented immobilization of a triple mutant of CYP3A4 via C64. Bioconjug Chem 2012; 23:826-36. [PMID: 22433037 DOI: 10.1021/bc200672s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The generation of site-specific bioconjugates of proteins is highly desired for a number of biophysical and nanotechnological applications. To this end, many strategies have been developed that allow the specific modification of certain canonical amino acids and, more recently, noncanonical functional groups. P450 enzymes are heme-dependent monooxygenases involved in xenobiotic metabolism and in the biosynthesis of a variety of secondary metabolites. We became interested in the site-specific modification of these enzymes, CYP3A4 in particular, through our studies of their in vitro biocatalytic properties and our desire to exploit their remarkable ability to oxidize unactivated C-H bonds in a regio- and stereospecific manner. Obtained via a partial cysteine-depletion approach, a functional triple mutant of CYP3A4 (C98S/C239S/C468G) is reported here which is singly modified at C64 by maleimide-containing groups. While cysteine-labeling of the wild-type enzyme abolished >90% of its enzymatic activity, this mutant retained ≥75% of the activity of the unmodified wild-type enzyme with 9 of the 18 maleimides that were tested. These included both fluorescent and solid-supported maleimides. The loss of activity observed after labeling with some maleimides is attributed to direct enzyme inhibition rather than to steric effects. We also demonstrate the functional immobilization of this mutant on maleimide-functionalized agarose resin and silica microspheres.
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Affiliation(s)
- Amélie Ménard
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 0B8
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63
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64
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Della Pia EA, Elliott M, Jones DD, Macdonald JE. Orientation-dependent electron transport in a single redox protein. ACS NANO 2012; 6:355-361. [PMID: 22088136 DOI: 10.1021/nn2036818] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The redox-active protein cytochrome b(562) has been engineered to introduce pairs of thiol groups in the form of cysteine residues at specified sites. Successful STM imaging of the molecules adsorbed on a gold surface indicated that one thiol group controls the orientation of the molecule and that the protein maintains its native form under the experimental conditions. Stable protein-gold STM tip electrical contact was directly observed to form via the second free thiol group in current-voltage and current-distance measurements. Proteins with thiol contacts positioned across the protein's short axis displayed a conductance of (3.48 ± 0.05) × 10(-5)G(0). However proteins with thiol groups placed along the long axis reproducibly yielded two distinct values of (1.95 ± 0.03) × 10(-5)G(0) and (3.57 ± 0.11) × 10(-5)G(0), suggesting that the placement of the asymmetrically located haem within the protein influences electron transfer. In contrast, the unengineered wild-type cytochrome b(562) had conductance values at least 1 order of magnitude less. Here we show that an electron transfer protein engineered to bind gold surfaces can be controllably oriented and electrically contacted to metallic electrodes, a prerequisite for potential integration into electronic circuits.
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65
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Choi Y, Moody IS, Sims PC, Hunt SR, Corso BL, Perez I, Weiss GA, Collins PG. Single-molecule lysozyme dynamics monitored by an electronic circuit. Science 2012; 335:319-24. [PMID: 22267809 PMCID: PMC3914775 DOI: 10.1126/science.1214824] [Citation(s) in RCA: 191] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Tethering a single lysozyme molecule to a carbon nanotube field-effect transistor produced a stable, high-bandwidth transducer for protein motion. Electronic monitoring during 10-minute periods extended well beyond the limitations of fluorescence techniques to uncover dynamic disorder within a single molecule and establish lysozyme as a processive enzyme. On average, 100 chemical bonds are processively hydrolyzed, at 15-hertz rates, before lysozyme returns to its nonproductive, 330-hertz hinge motion. Statistical analysis differentiated single-step hinge closure from enzyme opening, which requires two steps. Seven independent time scales governing lysozyme's activity were observed. The pH dependence of lysozyme activity arises not from changes to its processive kinetics but rather from increasing time spent in either nonproductive rapid motions or an inactive, closed conformation.
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Affiliation(s)
- Yongki Choi
- Institute for Surface and Interface Science, University of California Irvine, Irvine, CA 92697-2375
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697-4576
| | - Issa S. Moody
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697-4292
| | - Patrick C. Sims
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697-4576
| | - Steven R. Hunt
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697-4576
| | - Brad L. Corso
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697-4576
| | - Israel Perez
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697-4576
| | - Gregory A. Weiss
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697-4292
- Department of Chemistry, University of California Irvine, Irvine, CA 92697-2025
| | - Philip G. Collins
- Institute for Surface and Interface Science, University of California Irvine, Irvine, CA 92697-2375
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697-4576
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66
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Harriman OLJ, Leake MC. Single molecule experimentation in biological physics: exploring the living component of soft condensed matter one molecule at a time. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:503101. [PMID: 22067659 DOI: 10.1088/0953-8984/23/50/503101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The soft matter of biological systems consists of mesoscopic length scale building blocks, composed of a variety of different types of biological molecules. Most single biological molecules are so small that 1 billion would fit on the full-stop at the end of this sentence, but collectively they carry out the vital activities in living cells whose length scale is at least three orders of magnitude greater. Typically, the number of molecules involved in any given cellular process at any one time is relatively small, and so real physiological events may often be dominated by stochastics and fluctuation behaviour at levels comparable to thermal noise, and are generally heterogeneous in nature. This challenging combination of heterogeneity and stochasticity is best investigated experimentally at the level of single molecules, as opposed to more conventional bulk ensemble-average techniques. In recent years, the use of such molecular experimental approaches has become significantly more widespread in research laboratories around the world. In this review we discuss recent experimental approaches in biological physics which can be applied to investigate the living component of soft condensed matter to a precision of a single molecule.
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Affiliation(s)
- O L J Harriman
- Clarendon Laboratory, Department of Physics, Oxford University, Parks Road, Oxford OX1 3PU, UK
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67
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Sriram S, Bhaskaran M, Chen S, Jayawardhana S, Stoddart PR, Liu JZ, Medhekar NV, Kalantar-Zadeh K, Mitchell A. Influence of Electric Field on SERS: Frequency Effects, Intensity Changes, and Susceptible Bonds. J Am Chem Soc 2011; 134:4646-53. [DOI: 10.1021/ja208893q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sharath Sriram
- Microplatforms Research Group, School of Electrical and Computer Engineering, RMIT University, Melbourne, Australia
| | - Madhu Bhaskaran
- Microplatforms Research Group, School of Electrical and Computer Engineering, RMIT University, Melbourne, Australia
| | | | - Sasani Jayawardhana
- Faculty of Engineering and Industrial Science, Swinburne University of Technology, Hawthorn, Australia
| | - Paul R. Stoddart
- Faculty of Engineering and Industrial Science, Swinburne University of Technology, Hawthorn, Australia
| | | | | | - Kourosh Kalantar-Zadeh
- Microplatforms Research Group, School of Electrical and Computer Engineering, RMIT University, Melbourne, Australia
| | - Arnan Mitchell
- Microplatforms Research Group, School of Electrical and Computer Engineering, RMIT University, Melbourne, Australia
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Zheng YB, Payton JL, Chung CH, Liu R, Cheunkar S, Pathem BK, Yang Y, Jensen L, Weiss PS. Surface-enhanced Raman spectroscopy to probe reversibly photoswitchable azobenzene in controlled nanoscale environments. NANO LETTERS 2011; 11:3447-3452. [PMID: 21749070 DOI: 10.1021/nl2019195] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We apply in situ surface-enhanced Raman spectroscopy (SERS) to probe the reversible photoswitching of azobenzene-functionalized molecules inserted in self-assembled monolayers that serve as controlled nanoscale environments. Nanohole arrays are fabricated in Au thin films to enable SERS measurements associated with excitation of surface plasmons. A series of SERS spectra are recorded for azobenzene upon cycling exposure to UV (365 nm) and blue (450 nm) light. Experimental spectra match theoretical calculations. On the basis of both the simulations and the experimental data analysis, SERS provides quantitative information on the reversible photoswitching of azobenzene in controlled nanoscale environments.
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Affiliation(s)
- Yue Bing Zheng
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
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