Polymorphism of Two-Dimensional Cyanine Dye J-Aggregates and Its

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Polymorphism of Two-Dimensional Cyanine Dye J-Aggregates and Its Genesis: Fluorescence Microscopy and Atomic Force Microscopy Study Valery V. Prokhorov, Olga M. Perelygina, Sergey I. Pozin, Eugeny I. Mal’tsev, and Anatoly V. Vannikov J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.5b07821 • Publication Date (Web): 21 Oct 2015 Downloaded from http://pubs.acs.org on November 3, 2015

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The Journal of Physical Chemistry

Polymorphism of Two-dimensional Cyanine Dye JAggregates and Its Genesis: Fluorescence Microscopy and Atomic Force Microscopy Study Valery V. Prokhorov *, Olga M. Perelygina, Sergey I. Pozin, Eugene I. Mal’tsev, Anatoly V. Vannikov A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russia E-mail: [email protected]

________________________________________

•

To whom correspondence should be addressed

ACS Paragon Plus Environment

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ABSTRACT

Polymorphic J-aggregates of monomethine cyanine dye 3,3'-di(γ-sulfopropyl)-5,5'dichlorotiamonomethinecyanine (TC) have been studied by fluorescence optical microscopy (FOM) and by atomic force microscopy (AFM). The in situ FOM observations in a solution drop distinguish two J-aggregate morphology classes: flexible strips and rigid rods. The AFM imaging of dried samples reveals a strong J-aggregate structural rearrangement under adsorption on a mica surface with the strips self-folding and the rods squashing into rectangular bilayers and much deeper destruction. In the present work, the following structural conclusions have been drawn on the base of careful consideration of strip crystal habits and various structural features of squashed/destructed rods: (1) the tubular morphology of TC rods is directly proved by FOM measurements in the solution bulk; (2) the staircase model of molecular arrangement in strips is proposed explaining the characteristic ~44° skew angle in strip vertices; (3) a model of tube formation by a close-packed helical winding of flexible monolayer strips is proposed and justified which explains the observed J-aggregate polymorphism and strip-to-rod polymorphic transformations in a wide spatio-temporal scale; (4) at a nanoscale, an unexpectedly complex quasi-one-dimensional organization in J-aggregate two-dimensional monolayers is observed by high-resolution AFM imaging of constituent nanostrips separated by a characteristic distance in the range of 6-10 nm. The obtained results indicate that the underlying monolayer structure is the same for all J-aggregate polymorphs.


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INTRODUCTION Cyanine dyes have a large conjugated π-system promoting self-assembly into supramolecular structures, called J-aggregates, with a narrow intense absorption band shifted toward longer wavelengths compared with the spectrum of monomers.1,2 The particular optical properties of Jaggregates, i.e., the strong narrow absorption and intensive luminescence, result from the excitation of delocalized Frenkel excitons.1-4 The remarkable optical and transport properties of molecular aggregates have led to a variety of optoelectronic applications.5 The J-aggregates were used as wavelength-selective sensitizers in color photography,6 single-mode optical waveguides,7 materials in nonlinear optics,8 components of hybrid nanostructures consisting of dye molecules and semiconducting nanocrystals,9 light-emitting dopants to electron–hole conducting polymer layers in polymer OLEDs,10 and in biosensing.11 In live nature, J-type aggregation in stacked porphyrin-based molecules has a primary importance in transferring sunlight energy in the tubular antennae of light-harvesting reaction centers.12-14 At the molecular level, the red shift and the narrowness of the absorption band is achieved in the so-called staircase, ladder and brickwork models of the molecular arrangement in which the adjacent stacked dye molecules are notably shifted laterally, forming the so called slip angle between the molecular transition dipoles and the translation vector connecting adjacent stacked molecules.1,2 Although molecular aggregates have been known for more than 70 years, their structural organization is still insufficiently characterized and needs further attention. In recent years, different morphological types of J-aggregates have been revealed by fluorescence optical microscopy (FOM),15 cryogenic transmission electron microscopy (cryo-TEM) 16-18 and atomic force microscopy (AFM).2,4,15,18-21


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The advantage of AFM is the capability to characterize the three-dimensional structure in a wide spatial range of nano- and micrometer scales. The wide morphological variety of J-aggregates can be subdivided into subclasses of quasi-one-dimensional fibrillar and tubular structures with a transverse size in the nanometer range

2,4,16,18,21

and essentially two-dimensional structures

(monolayer sheets of various shapes and giant tubes). 15,19,20 Polymorphism, i.e., the coexistence of several morphological types, is a characteristic feature of J-aggregates, but the factors governing the formation, coexistence and interconversion of different polymorphic J-aggregate structures have not yet been clarified. For 3,3’-di(γsulfopropyl)-4,4’,5,5’-dibenzo-9-ethylthiacarbocyanine betaine pyridinium, the J-aggregate polymorphism and also the characteristic crystallographic features and monolayer thickness of polymorphic structures have been explained by two plausible molecular packing arrangements at the nanoscale,19 i.e., by the staircase and ladder molecular arrangements.1,2 In another case, two polymorphs of 3,3'-di(γ-sulfopropyl)-5,5'-dichlorotiamonomethinecyanine (thiacyanine, TC) were observed in a solution by FOM imaging, i.e., flexible strings and rigid rods.15 It was also found that the strings slowly convert to rods in the solution with a large characteristic time measured by several days. Based on indirect information, i.e., AFM imaging of the rod edges, a tubular structure of the rods in solution was assumed with tube diameters in the micron range.15 The TC tubes with a smaller diameter, ~100–200 nm, were observed in a longitudinal cross section by cryo-TEM.17 In the present work polymorphic TC J-aggregate structures, their crystal habits and origin of polymorphism have been thoroughly studied by combined FOM and AFM measurements both in situ in a solution drop and in a dried state. The polymorphism of TC J-aggregates was explained by a morphological interconversion of flexible monolayer strips to giant tubes due to close-


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packed helical winding. The strips asymmetric shape with a fixed skew angle in the vertices was shown to indicate unambiguously the staircase molecular arrangement in strips. The highresolution AFM imaging reveals complex linear substructure of strips at a nanoscale. EXPERIMENTAL SECTION Figure 1a shows the chemical structure and dimensions of the TC molecule. The molecular dimensions shown were obtained based on the Chem Draw modeling of the TC molecule with mostly extended sulfopropyl chains (see Figure 1 supplementary materials). The inner dark grey rectangle in Figure 1a has dimensions 1.5*1.0 nm2 corresponding to the distances between most distant outside atoms (Cl-Cl in the horizontal direction and H-O in the vertical direction respectively). The outer light grey rectangle includes additionally van-der-Waals radii of outer Cl, O and H atoms. Figure 1b shows the geometry of the TC J-dimer at the maximal overlapping of heterocycles. Absorption spectra of a TC solution with and without J-aggregates (Figure 1c) were

recorded with a PC 2000 Ocean Optics spectrophotometer by use of a cuvette with the optical path length 1 mm. The FOM measurements were performed on Meiji MT6000 epi-fluorescence laboratory microscope (Japan) with the blue excitation filter at 470 nm (40 nm spectral width) and emission filter at 515 nm. J-aggregation was stimulated by diluting of aqueous TC stock solution [Sigma-Aldrich] heated to ~80OC to reach a monomeric state in an appropriate amount of a salt solution (sodium bicarbonate NaHCO3, ammonium acetate CH3COONH4 or europium chloride EuCl3). The time delay between the dilution and J-aggregate observation by FOM or AFM is specified in captions for figures. The FOM measurements were performed on Meiji MT6000 epi-fluorescence laboratory microscope (Japan) with a blue excitation filter. For in-situ optical measurements, a 1 µL drop of TC J-aggregates was placed directly under the microscope objective at magnifications of ×20, ×40, and ×60, and single images or video were captured. For


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the AFM measurements, the TC J-aggregate solution was applied on a freshly cleaved mica surface for ~ 1 min, the solution excess was then removed by blotting, and the sample was dried in a nitrogen gas flow. The AFM measurements were performed on Ntegra Prima (NT-MDT, Zelenograd, Russia). Ultra sharp AFM probes (carbon nanowhiskers with a curvature radius of several nanometers grown at the tips of common silicon cantilevers 22) with a spring constant of ~5 N/m were used. The scanning was performed with small cantilever oscillation amplitudes within 3–10 nm. For consistency, the heights of J-aggregate monolayers were measured in both the attraction and the repulsion regimes of probe–surface interaction.23 The repulsion regime was used for the acquisition of the highest possible AFM resolution in the operation with the ultrasharp cantilevers; the operational protocol is described in more detail in ref 24. The AFM images

were

subsequently

analyzed

using

the

Femtoscan

Online

software

(http://www.nanoscopy.net/en/Femtoscan_V.shtm). RESULTS AND DISCUSSION The advantage of TC over other cyanine dyes is the high fluorescence yield and the large size (in the range of tens and hundreds microns) of J-aggregates. This allows both real-time optical measurements in the solution bulk and AFM imaging of J-aggregates adsorbed on a surface. The polymorphism of TC J-aggregates: in-situ FOM measurements Figure 2 shows FOM images of two structurally different coexisting types of TC J-aggregates with the morphologies of curved strips (called strings in ref 15) (Figure 2a) and of straight rods (Figure 2b). The images were obtained in a solution drop under the microscope objective. The width of strips and rods is in the micron range, and their length varies in a wide range from several microns to several hundred microns in dependence on concentrations of TC and salt (compare Figures 2 a and b).

Real-time monitoring of the J-aggregate shapes reveals


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characteristic differences in the rigidity of the strips and rods: strips are flexible entities constantly changing shape because of the thermal motion and local solution flow gradients in the micro droplet, while the rods are rigid straight objects that can only change their orientation. Moreover, the arrow in the lower left corner in Figure 2a indicates a strip that is evidently twisted along its long axis, thus indicating the longitudinal flexibility. Figure 2b shows four successive time-lapse images of short rods in a solution flow (the capture time is shown in the upper-right corner). In the real-time observations, the long rods such as those shown in Figure 2a and most of the short rods in Figure 2b are oriented approximately parallel to the substrate and have the same linear morphology as previously reported.15 Some short rods, such as indicated by a white arrow in Figure 2b, gradually change their angular orientation with respect to the observation direction, as shown in the four zoom images at the bottom of Figure 2b. At one instant, these rods have a ring shape, which provides direct evidence of their tubular structure. The rods are consequently called tubes in what follows. A comparison of optical images shows that the tubes have different diameters in the range of 0.5–10 µm. Moreover, the cross section of the envelope of the tubes with the largest diameter can change shape from the circular to an elliptic, which also demonstrates the tube wall flexibility. It was also noted that the widest tubes are typically short, with their diameter and length being about the same. It is noteworthy that J-aggregates can form both in the solution bulk and on the substrate surface. Figure 3 shows FOM images of dried J-aggregates that were preliminarily adsorbed from the solution bulk (Figure 3a) or grown directly on the mica (Figure 3b). Under adsorption from the solution bulk (Figure 3a), the flexible curved strips (S) straighten with parallel sides and an oblique (skew) angle close to 45°, while the tubes (T) acquire rectangular or close to rectangular shapes. Some J-aggregates, such as the two shown in the upper part of Figure 3a, can


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overlap during adsorption. At low dye concentrations (no J-aggregates in the solution bulk), the mica surface can initiate the rapid formation of surface-induced J-aggregate strips from the dye monomeric fraction constantly present in the solution. The rate of surface-induced aggregation increases as the solution ionic strength increases; the growth is additionally highly stimulated by multivalent cations such as Mg2+ and Eu3+ (Figure 3b). No overlaps are observed for surfaceinduced J-aggregates, and the growth of J-aggregates frequently proceeds from a single nucleation center, which yields characteristic flowerlike structures as shown in Figure 3b. The molecular model of TC strips A characteristic crystal habit of TC strips grown both in the solution bulk (Figure 3a) and on the mica surface (Figure 3b) is their asymmetric shapes with the oblique ends fixed in the vertices with a single skew angle (β). The histogram in Figure 3c with a maximum at β=44° was obtained by analyzing 310 FOM images of TC strips. For the angular analysis, the optical images of strips (Figure 3) are preferable to the AFM images (see Figures 5 and 8 below) because the FOM images lack the image distortion intrinsic to AFM. The J-aggregate slip angle α (Figure 4 a) is determined from the geometry of stacking adjacent dye molecules; in a particular TC case, α is ~27° for the stacking distance D=0.35 nm and completely overlapped heterocycles (selected by light blue in Figure 1) acquired at the slippage distance S1=0.7 nm. The elementary unit cell is shown by the blue parallelograms in Figures 4a and 4b; the [100] direction is chosen parallel to the translation vector connecting adjacent stacked molecules (which is the staircase direction), while the [010] direction is parallel to the molecular long axes. The longer dimension of the unit cell S2 equal the molecular van-der-Waals length ~ 1.85 nm (Figure 1a) at the tight contact of adjacent staircases. The experimentally measured vertex angle β=44° is significantly larger than the slip angle α. This means that the simple structural model of molecular arrangement at the


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vertex (Figure 4a) in which the vertex sides are formed by the [100] and [010] crystallographic directions of the oblique unit cell (previously proposed by us for the leaf morphology of the carbocyanine dye 19) is inapplicable to the TC strips. With the designation of the crystallographic axes in Figure 4a, the 45° angle is formed by the [100] and the (diagonal) [1-10] directions of the unit cell (Figure 4b). The only two crystallographic models satisfying the oblique geometry of TC strips with the 45° interfacial angle and the significantly smaller slip angle of ~27° are shown in Figure 4 (c,d). Both models imply the staircase molecular arrangement with the staircases directed along the long side (c) and short oblique side (d) of the TC strips. The exact formula taking into account the geometric parameters shown in Figure 4 a is β = arctan(D/S1) + arctan(D/(S2-S1)). This purely geometric analysis does not allow choosing between the two structural models of strips in Figure 4 c and d. Of these two possible configurations, the model in Figure 4c seems preferable based on general crystallographic arguments about the growth rate.20,24 For onedimensional structures formed by side-by-side packing of rod like molecules (such as dye molecules20 and oligopeptides

24

), the fastest growth proceeds along the long axes of the

structures. From this standpoint, the staircases are expected to be oriented along the strips, as shown in Figure 4c. An unambiguous choice in favor of the arrangement in Figure 4c could be provided by polarization fluorescence measurements (currently being conducted). AFM measurements of dried samples Additional information on the structure of the strips and tubes was obtained from AFM measurements of dried samples. The AFM reveals that the adsorption from a solution on a mica surface results in strong structural rearrangements in J-aggregates as a result of the action of


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adhesive surface forces. The character of the shape rearrangement differs for the strips (Figure 5a) and tubes (Figure 6). Overlapped and self-folded strips AFM topography image in Figure 5a shows that the flexible strips have multiple overlaps and self-folding (the axes of self-folding are shown by the dashed white lines). This indicates that the strips originally formed in the solution bulk and the overlapping and folding occurred during adsorption. The multiple overlapping in several layers allows measuring the monolayer thickness accurately (see the profile in the panel 5a1): it is about 1.3 nm, i.e. larger than the TC molecule vertical dimension ~ 1 nm (Figure 1a). As argued in ref 19, the height ~1.35 nm indicates a symmetric monolayer (in the top-bottom direction) with the dye monomers in an all-trans conformation and the sulfopropyl chains occupying both sides of the monolayer plane. Interestingly, the AFM height measurements reveal a smaller monolayer height of ~1.0 nm for the TC strips grown directly on the mica surface (such as shown in Figure 3b). The height of ~1.0 nm is equal to the TC molecular dimension in the direction of extended sulfopropyl chains (see Figure 1a). Therefore, in contrast to J-aggregates formed in the solution, the TC strips grown on the mica surface are asymmetric monolayers (in the top-bottom direction) with the sulfopropyl chains occupying single side of the monolayer plane. The unidirectional molecular alignment (in the direction normal to the surface) is evidently stimulated by interaction with the mica. The fine linear substructure of J-aggregate monolayers at a nanoscale High-resolution AFM imaging of TC stripes reveals the unexpected structural complexity at a nanoscale of two-dimensional J-aggregate monolayers. The seemingly smooth (at the large scale) monolayer surface has a fine linear substructure formed by close packed parallel nanostrips


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(Figures 5 b,c,d). The topography images reveal a notable surface corrugation; particularly the height variation in a profile in Figure 5c1 drawn across nanostrips is about 0.5 nm, i.e. large in comparison with monolayer thickness ~ 1.4 nm. The substructure seems to be not quite periodical, so that adjacent parallel nanostrips are separated by a distance in the range of 6-10 nm. Moreover, the nanostrips are not homogeneous and consist of segments with the length of several tens of nanometers. The origin of this substructure and the internal structure of constituent nanostrips are unclear at present. The expected width of nanostrips is small (≤ 6 nm), still it is several times larger than the width of a single staircase (~ 1 nm). Thus, the nanostrips could be considered as lateral aggregates of several “elementary” staircases; but the physical reasons providing the approximately fixed small aggregation number are not clear. Very similar substructure has been observed by AFM for J-aggregates of another cyanine dye20 and by electron microscopy for H-aggregates of a carbocyanine dye.25 As a whole, these observations indicate the quasi-one-dimensional organization of dye molecules in J-aggregate twodimensional monolayers at its complexity at the nanometer scale.

Moreover, the quasi-one-

dimensional nanostrips and their longitudinal inhomogeneity can sufficiently affect the exciton transport in J-aggregate monolayers. Flattened tubes and the model of tube formation In contrast to strips, which exhibit self-folding during adsorption on the mica, tubes flatten as a result of the action of adhesion forces and finally become almost rectangular bilayer rods (Figure 3a) or even exhibit much deeper destruction (Figures 6 a and c). Figure 6 shows AFM topography images of some typical morphological transformations of TC tubes destroyed during adsorption on the mica surface: (a) partial tube unwinding to the level of the monolayer strip with the formation of characteristic zigzags (Figure 6a), (b) rough sides and rough ends (Figure


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6b) and (c) partial peeling of the upper monolayer piece from the bilayer with the formation of tilted segments (Figure 6c). The squashed bilayer rods frequently have characteristic ragged ends (Figure 6b). The AFM observation of such ragged ends was interpreted in ref 15 as an indirect proof that the rods had a tubular structure before adsorption. A more careful analysis of the tube images in Figure 6 reveals various tilted patterns. The white solid lines in Figures 6 a and c are inclined with respect to the normal (dotted lines) to the long tube axes. The corresponding inclination angle φ was measured in the range of 12–20°. Altogether, these observations allow concluding that the tubes formed in solution as a result of close-packed helical winding of flexible monolayer strips. The proposed tube model (already flattened on a surface) is shown in Figure 7. The strictly bilayer thickness of squashed tubes observed by AFM (see the height histograms in Figures 6a2, 6b2, 6c1 and the height profile 6c2) implies winding in a single continuous layer and limits the maximum width W of the constituent strips forming the tube: W =2Ds tanφ (see Figure 7),. where W is the strip width, φ is the inclination angle and Ds is the squashed tube width (for the squashed tube, Ds=πDv/2 where Dv is the tube diameter in the solution bulk). For angles φ < 15°, we have W < Ds/2. For tube diameters in the range of 1–10 µm, the strip width is expected in the micron and submicron range. Another support for the tube model in Figure 7 was obtained by observing in a real-time of the temperature-induced decomposition of tubes into shorter cylindrical fragments, which remained bound to each other by narrow flexible strips in a heated solution (data not published). Noteworthy, the proposed mechanism of tube formation due to helical winding of flexible strips has a general nature. Similar polymorphic transitions from helical ribbons to closed nanotubes are observed at different length scales in various systems such as amphiphilic organic molecules26 and oligo- and polypeptides forming fibrillar amyloid structures.27 The notable


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difference is that the self-assembled structures in refs 26, 27 are chiral due to intrinsic molecular chirality while dye molecules forming J-aggregate monolayers are achiral. Despite the dye achirality, the tubes (and monolayer strips) are chiral as it is expected from their structural models. AFM measurements of the early aggregation stages and the general scheme of Jaggregate polymorphic transformations The proposed models of TC strip and tube polymorphic structures explain both the observed polymorphism and the mechanism for the strip-to-tube morphological interconversion. It is noteworthy that the reported characteristic time of the observed by FOM morphological transformations from string to rods is large, i.e. of the order of several days.15 We have studied earliest aggregation stages by the AFM measurements of TC J-aggregates formed at a much shorter time scale measured by several minutes and hours after adding the salt (Figure 8). These measurements support the model of the tube formation in Figure 7 and extend it in a number of important particular details. Several conclusions have been drawn. First, narrow strips with a width < 100 nm form at characteristic times in the second or minute range depending on the salt concentration (Figure 8a). In accordance with the spectroscopic data for several carbocyanines, the production of J-aggregates proceeds (i.e. the absorbance in J-band saturates) within the range of tens to hundreds of seconds and the rate of formation of J-aggregates increases as the dye and salt concentrations increase (and depends on the charge of the metal ion).28 The wider strips with the width ~ 1 µm were also observed at the early stage and the narrow strips seem to be the “building units” for forming these wider strips (Figure 8a). The narrow strips were not observed at later growth times of ~15 min (Figure 8c). Second, contrary to giant tubes formed for several days,15 the tubes with a small diameter ~ 0.1-0.2 µm were found in our specimens even at


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earliest time (~1 min). Figure 8b shows a narrow ribbon with a width 120 nm, which is helicoidally twisted in a central part, forming a loosely packed solenoid with a diameter ~ 150 nm. The solenoid is evidently the tube predecessor. Interestingly, the outgoing narrow strip at the right solenoid end has the same inclination angle of ~70° observed for the wide tubes shown in Figure 6. The characteristic 45° oblique ends were observed in Figures 8 a–c for both wide and narrow strips, indicating same strip internal structure described by the staircase model in Figure 4c. As a conclusion, the general scheme of J-aggregate polymorphic transformations is shown in Figure 9. It implies that kinetics of strip-to-rode transformation essentially depends on the strip width (and on the dye and salt concentrations as well). The narrow J-aggregate strips with a width < 100 nm quickly form at the earliest aggregation stage in the second or minute range. They originate from some narrowest precursors which are probably the isolated staircases composed of a single molecular row. The narrow strips grow in a width or merge in the wider strips as close-packed “building units”. In parallel, some narrow strips roll and form tubes with a small diameter. The twisting flexibility of wide strips is highly reduced and for this reason the characteristic time of the strip-to-tube interconversion (and the tube diameter) is much larger for wide strips. The narrowest tube can form quickly for the time of several minutes, while the formation of giant tubes needs a long time measured by hours or days, as noticed in Figures 2,3,6 and reported in refs 15,17. As a general feature, the proposed strip-to-tube interconversion mechanism implies that the underlying monolayer structure at the nanoscale is the same for all TC J-aggregate polymorphs. CONCLUSIONS


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The polymorphism of TC J-aggregates was extensively studied by in-situ FOM measurements in solution drops and by AFM measurements of dried samples. The tubular morphology of TC rods was directly proved by FOM measurements in the solution bulk.

The structural

rearrangement observed by AFM on dry samples of strips and (squashed) tubes was analyzed in detail, which led to the model of tube formation by helical winding of flexible monolayer strips. In a universal way, the proposed model explains the observed polymorphism of TC J-aggregates and the strip-to-tube morphological interconversion.

The crystallographic analysis of the

asymmetric oblique shapes of the strips yielded unambiguous support for the staircase molecular arrangement in TC monolayers. At the nanoscale, high-resolution AFM imaging of reveals the unexpected fine linear substructure of J-aggregate monolayers with close packed parallel constituent nanostrips separated by a typical distance of 6-10 nm. AUTHOR INFORMATION Corresponding Author *E-mail: [email protected] Notes The authors declare no competing financial interest.

REFERENCES (1) Kuhn, H.; Kuhn, C. Chromophore Coupling Effects; in J-Aggregates; Kobayashi, T., Ed.; World Scientific: Singapore, 1996, p. 1-40. (2) Würthner, F.; Kaiser, T. E.; Saha-Möller, C. R. J-Aggregates: From Serendipitous Discovery to Supramolecular Engineering of Functional Dye Materials. Angew. Chem. Int. Ed. 2011, 50, 3376-3410.


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(3) Spano, F. The Spectral Electroluminescence in Polymer Composites Based on Organic Nanocrystals. Appl. Phys. Lett. 2002, 81, 3088-3090. (4) Tian, Y.; Stepanenko, V.; Kaiser, T. E.; Würthner, F.; Scheblykin, I. G. Reorganization of Perylene Bisimide J-Aggregates: from Delocalized Collective to Localized Individual Excitations. Nanoscale 2012, 4, 218-223. (5) Saikin, S. K.; Eisfeld, A.; Valleau, S.; Aspuru-Guzik, A. Photonics Meets Excitonics: Natural and Artificial Molecular Aggregates. Nanophotonics 2013, 2, 21–38. (6) Tani, T. J-Aggregates in Spectral Sensitization of Photographic Materials; in J-Aggregates; Kobayashi, T., Ed.; World Scientific: Singapore, 1996, p. 209. (7) Takazawa, K. Waveguiding Properties of Fiber-Shaped Aggregates Self-Assembled from Thiacyanine Dye Molecules. J. Phys. Chem. C 2007, 111, 8671-8676. (8) Innocenzi, P.; Lebeau, B. Organic–Inorganic Hybrid Materials for Non-linear Optic. Journal of Materials Chemistry 2005, 15, 3821–3831. (9) Walker, B. J.; Dorn, A.; Bulovic, V.; Bawendi, M. G. Color-Selective Photocurrent Enhancement in Coupled J-Aggregate/Nanowires Formed in Solution. Nano Lett. 2011, 11, 2655-2659. (10) Mal’tsev, E. I.; Lypenko, D. A.; Bobinkin, V. V.; Tameev, A. R.; Kirillov, S. V.; Shapiro, B. I.; Schoo, H. F. M.; Vannikov, A. V. Near-Infrared Electroluminescence in Polymer Composites Based on Organic Nanocrystals. Appl. Phys. Lett. 2002, 81, 3088-3090.


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(11) Jones, R. M.; Lu, L.; Helgeson, R.; Bergstedt, T. S.; McBranch, D. W.; Whitten, D. G. Building Highly Sensitive Dye Assemblies for Biosensing from Molecular Building Blocks. PNAS 2001, 98, 14769–14772. (12) Prokhorenko, V. I.; Steensgaard, D. B.; Holzwarth, A. R. Exciton Theory for Supramolecular Chlorosomal Aggregates: 1. Aggregate Size Dependence of the Linear Spectra. Biophys. J. 2003, 85, 3173-3186. (13) Ganapathy, S.; Oostergetel, G. T.; Wawrzyniak, P. K.; Reus, M.; Chew, A. G. M.; Buda, F.; Boekema, E. J.; Bryant, D. A.; Holzwarth, A. R.; de Groot, H. J. M. Alternating Syn-anti Bacteriochlorophylls Form Concentric Helical Nanotubes in Chlorosomes. PNAS 2009, 106, 8525–8530. (14) Valleau, S.; Saikin, S. K.; Ansari-Oghol-Beig, D.; Rostami, M.; Mossallaei, H.; AspuruGuzik A. Electromagnetic Study of the Chlorosome Antenna Complex of Chlorobium tepidum. ACS Nano 2014, 8, 3884-3894. (15) Yao, H. Morphology Transformations in Solutions: Dynamic Supramolecular Aggregates. Ann. Rep. Prog. Chem., Sec. C 2004, 100, 99-148. (16) von Berlepsch, H.; Böttcher, C.; Dähne, L. Structure of J-Aggregates of Pseudoisocyanine Dye in Aqueous Solution. J. Phys. Chem. B 2000 104, 8792-8799. (17) von Berlepsch, H.; Brandenburg, E.; Koksch, B.; Böttcher, C. Peptide Adsorption to Cyanine Dye Aggregates Revealed by Cryo-Transmission Electron Microscopy.

Langmuir

2010, 26, 11452-11460.


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Proteins Fibrils from a Polymer Physics Perspective.

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Table of Contents Graphic


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Figure 1. (a) A schematic drawing of a single TC molecule (front view). The dimensions of the outer light grey rectangle correspond to van-der-Waals size of the TC molecule with the mostly extended sulfopropyl chains. (b) The scheme of the TC J-dimer with the slip angle 27° (top view); the heterocycles are denoted by light blue. (c) Absorption spectra of the TC solution c=0.14 mM in 5 mM ammonium acetate at a temperature 70°C (black curve) and 20°C (red curve). 75x116mm (300 x 300 DPI)



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Figure 2. In situ FOM images of polymorphic TC J-aggregates in a solution drop: (a) flexible strips (S) with two long rigid rod like tubes (T), scan size 150 µm, (b) four successive images of short tubes in a solution flow. The arrows show the tubular J-aggregate oriented approximately along the observation direction; zoom images of it are insets at the bottom. Preparation conditions: (a) c=0.035 mM in 5 mM NaHCO3, t=5 min, (b) c=0.14 mM in 5 mM NaHCO3, t=1 day. 162x80mm (300 x 300 DPI)


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Figure 3. (a,b) FOM images of dried samples of TC J-aggregates on a mica surface. (a) wide strips (S) and tubes (T) adsorbed from a solution, (b) strips grown on the mica surface. The image size of (a) is 75 µm and of (b) 280 µm. Preparation conditions: (a) c=0.035 mM in 5 mM NaHCO3, t=5 h, (b) c=0.02 mM in 0.03 mM EuCl3, t=1 min. (c) The histogram of the skew angle distribution for 310 strips. 152x54mm (300 x 300 DPI)



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Figure. 4. (a) The designations of crystallographic axes in the unit cell (denoted by blue) with the slip angle α=25°. (b) The scheme explaining the interfacial angle β=44° in strip vertices formed by [100] and [110] directions. (c) and (d) Two staircase models of the molecular arrangement in TC strips with the staircases (denoted by dark gray) directed along (c) the strip long side and (d) the inclined short side. 114x55mm (300 x 300 DPI)


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Figure 5. (a) The AFM topography image of overlapped and self-folded strips adsorbed on the mica surface: the dashed white lines show the self-folding axes. The panel a1 shows the height profile along the solid white line a1 in the overlapped area. (b,c,d) High-resolution AFM imaging (b,c - height, d - phase) of a fine linear substructure of a TC strip. Images (c) and (d) correspond to the rectangular area b2 in image (b). Panels (b1) and (c1) show the height profiles along the white lines b1 and c1 in the images (b) and (c) respectively. The height histogram (b2) corresponds to image (b). Preparation conditions: (a) c=1.4 mM in water, t=5 min, (b) c=0.14 mM in 5 mM ammonium acetate, t=5 days. 161x88mm (300 x 300 DPI)



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Figure 6. The AFM topography images of TC tubes destructed during adsorption on the mica surface: (a) partial unwinding, (b) rough sides, (c) monolayer peeling with transverse tilted cracks; image (b) is a zoom of the area selected by the black square in image (a). Images (a1) and (b1) are zooms of rectangular areas a1 in image (a) and b1 in image (b) respectively. The height histograms (a2), (b2), (c1) correspond to the areas a1, b, c1 respectively. The height profile (c2) is drawn along the line c2 in image (c). Preparation conditions: c=0.14 mM in 5 mM NaHCO3, t=10 day. 177x75mm (300 x 300 DPI)


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Figure 7. A model of (flattened on a surface) tubular J-aggregates formed by helical winding of a monolayer strip of width W, φ is the winding angle. 70x33mm (300 x 300 DPI)



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Figure 8. AFM topography images of J-aggregates formed in early stages of aggregation: (a and b) 1 min and (c) 15 min after dissolving TC (c=0.14 mM) in 5 mM ammonium acetate: the arrows in (b) show the sites where narrow strips attach to the wide strip. The height histogram in the inset in image (c) corresponds to the area selected by the white rectangle. 176x64mm (300 x 300 DPI)


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Figure 9. The scheme of morphological transformations in TC J-aggregates. 76x75mm (300 x 300 DPI)


Polymorphism of Two-Dimensional Cyanine Dye J-Aggregates and Its

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