Defocused Emission Patterns from Chiral Fluorophores: Application to Chiral Axis Orientation Determination

Cyphersmith, Austin Joseph; Hassey-Paradise, Ruthanne; McCarthy, Kevin; Barnes, Michael D.

doi:10.1021/jz2001024

Cited by 15 publications

(16 citation statements)

References 33 publications

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“…Clearly, the polarizer enhances the sensitivity to dipole orientation. In an alternative approach to determining orientation, some single molecule studies have employed a slightly defocused PSF because it inherently ‘mixes in’ the unambiguous azimuthal information clearly present at the BFP (Cyphersmith et al ., 2011; Patra et al ., 2004; Hohlbein & Hübner, 2008; Aguet et al ., 2009; Burghardt, 2011; Pavani et al ., 2009).…”

Section: Emission Through a Dielectric Film‐coated Substratementioning

confidence: 99%

“…One step up in theoretical accuracy is to treat the fluorophore as a classical dipole emitter, either isolated or bathed in the back‐reflection of its own field from an interface. These approaches give information about molecular orientation (Foreman et al ., 2008; Cyphersmith et al ., 2011; Fourkas, 2001; Patra et al ., 2004; Ishitobi et al ., 2010; Holbein & Hübner; 2008). But they do not account for the near field interaction with a (possibly) coated substrate nor the additional information the interaction contains about substrate distance and film thickness and refractive index.…”

Section: Introductionmentioning

confidence: 99%

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Fluorescence excitation and imaging of single molecules near dielectric‐coated and bare surfaces: a theoretical study

Axelrod

2012

Journal of Microscopy

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SummaryMicroscopic fluorescent samples of interest to cell and molecular biology are commonly embedded in an aqueous medium near a solid surface that is coated with a thin film such as a lipid multilayer, collagen, acrylamide, or a cell wall. Both excitation and emission of fluorescent single molecules near film-coated surfaces are strongly affected by the proximity of the coated surface, the film thickness, its refractive index and the fluorophore's orientation. For total internal reflection excitation, multiple reflections in the film can lead to resonance peaks in the evanescent intensity versus incidence angle curve. For emission, multiple reflections arising from the fluorophore's near field emission can create a distinct intensity pattern in both the back focal plane and the image plane of a high aperture objective. This theoretical analysis discusses how these features can be used to report film thickness and refractive index, and fluorophore axial position and orientation.

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Section: Emission Through a Dielectric Film‐coated Substratementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fluorescence excitation and imaging of single molecules near dielectric‐coated and bare surfaces: a theoretical study

Axelrod

2012

Journal of Microscopy

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“…Defocused emission pattern imaging is an optical technique whereby a phase aberration of ∼1–2 optical wavelengths is introduced by translation of a high-numerical aperture objective (>1.3 NA). , This phase-aberration produces an image which can be understood in terms of the distribution of k -vectors (and resulting constructive/destructive interference at the detector plane) in emission from the system. , The measured emission patterns readily distinguish between isotropic emitters (i.e., disordered systems), single (or multiple highly aligned) dipole emitters, ,, or 2D dipole systems whose orientations are defined by the dipole orientation in all three ( x , y , and z ) spatial dimensions. This is a powerful technique that has been used to probe 3D rotation of single molecules in polymer-supported films, , semiconducting polymer nanoparticles, − and quantum dots. ,− We used defocused emission as a means to complement the polarization contrast measurements specifically to assess out-of-plane dipole component, and 2D dipole character.…”

Section: Resultsmentioning

confidence: 99%

Probing the Evolution of Molecular Packing Underlying HJ-Aggregate Transition in Organic Semiconductors Using Solvent Vapor Annealing

et al. 2019

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In this work, we used solvent vapor annealing as a route toward controlled cluster growth of a nitrogen-substituted terrylene molecule (7,8,15,16-tetrazaterrylene or TAT) to probe the underlying molecular packing behind the exciton band curvature (EBC) inversion leading to a so-called HJ aggregates. Using a suite of photoluminescence (PL) imaging tools, we show that the EBCas signaled by PL spectral signaturesare correlated with distinct polarization and defocused emission patterns suggestive of a high degree of chromophore alignment. Selected area electron diffraction showed that the small aggregates adopt nominally the same crystal packing structure as the extended crystals though with a different plane orientation ([010] vs [011]) with respect to the surface normal. These findings demonstrate experimentally that the EBC inversion is not due to a crystal polymorphism but, rather subtle differences in molecular registration that profoundly impacts interchromophore coupling.

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“…27 The cNN based image analysis has been successfully used in recent years in various areas of science and engineering ranging from cancer detection to satellite imaging, 28,29 but has yet to be applied to atomic-resolved and molecular-resolved imaging. 30 The schematics of cNN adopted for the present study is shown in Fig. 2c.…”

Section: P Xjzmentioning

confidence: 99%

Learning surface molecular structures via machine vision

2017

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Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify ('read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function-a centerpiece in analysis of disorderproperty relationship paradigm-as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

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Defocused Emission Patterns from Chiral Fluorophores: Application to Chiral Axis Orientation Determination

Cited by 15 publications

References 33 publications

Fluorescence excitation and imaging of single molecules near dielectric‐coated and bare surfaces: a theoretical study

Fluorescence excitation and imaging of single molecules near dielectric‐coated and bare surfaces: a theoretical study

Probing the Evolution of Molecular Packing Underlying HJ-Aggregate Transition in Organic Semiconductors Using Solvent Vapor Annealing

Learning surface molecular structures via machine vision

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