Investigation and Control of Single Molecular Structures of meso-meso

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Investigation and Control of Single Molecular Structures of meso-meso Linked Long Porphyrin Arrays Sang Hyeon Lee, Sujin Ham, Seungsoo Nam, Naoki Aratani, Atsuhiro Osuka, Eunji Sim, and Dongho Kim J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.8b00213 • Publication Date (Web): 26 Apr 2018 Downloaded from http://pubs.acs.org on April 27, 2018

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The Journal of Physical Chemistry

Investigation and Control of Single Molecular Structures of meso-meso Linked Long Porphyrin Arrays Sang Hyeon Lee†, Sujin Ham†, Seungsoo Nam‡, Naoki Aratani§, Atsuhiro Osuka*,§, Eunji Sim*,‡, and Dongho Kim*,† †

Spectroscopy Laboratory for Functional π-electronic Systems and Department of Chemistry,

Yonsei University, Seoul 03722, Republic of Korea ‡Department of Chemistry and Institute of Nano-Bio Molecular Assemblies, Yonsei University, Seoul 03722, Republic of Korea §

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto

606-8502, Japan

ACS Paragon Plus Environment

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ABSTRACT

We have investigated conformational structures of meso-meso linked porphyrin arrays (Zn) by single molecule fluorescence spectroscopy. Modulation depths (M values) were measured by excitation polarization fluorescence spectroscopy. The M values decrease from 0.85 to 0.46 as the number of porphyrin units increases from 3 to 128, indicating that longer arrays exhibit coiled structures. Such conformational changes depending on the length have been confirmed by coarse-grained simulation. The histograms of M values and traces of centroid position of emitting sites by localization microscopy showed that the structures of longer arrays changed to more stretched after solvent vapor annealing with THF.

INTRODUCTION There has been a continuous research interest in strongly coupled multichromophoric systems for the development of single-molecule photonic and electronic devices.1–16 Owing to rigid and stable planar structure, intense electronic absorption, and small HOMO–LUMO energy gap, porphyrins have been recognized as an attractive molecular entity among many chromophores. In this regard, meso-meso directly-linked zinc(II) porphyrin arrays are appealing due to the expected simple linear rod-like molecular shape and repeated regular arrangement of porphyrin moieties with large electronic interactions.17–21 These properties are quite attractive in view of their potential applications as molecular photonic and electronic wires. In the past, we investigated the excitonic coupling strength of meso-meso linked Zn(II) porphyrin arrays. The excitonic coherence length of these porphyrin arrays was measured to be


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about 4.5 porphyrins at both ensemble and single-molecule level.18,20,22 The coherence length is an important factor determining the efficiency of energy transfer, since it represents a collective behavior of the transition dipole moments of multichromophores. Despite the close distance between the constituent porphyrin units, meso-meso porphyrin arrays exhibit relatively short coherence length, reflecting that porphyrin arrays largely behave as a summation of individual chromophores. Furthermore, broad Soret band and nonexponential fluorescence decays observed in longer porphyrin arrays have been interpreted in terms of nonlinear distorted structures.22 These features are regarded to arise from heterogeneity of long meso-meso linked porphyrin arrays. In this sense, we also investigated the conformational heterogeneity of these arrays by changing the number of porphyrin units. In meso-meso linked porphyrin arrays bearing an energy acceptor at the end, the energy-transfer efficiency decreased in longer porphyrin arrays.23 In addition, by using single molecule spectroscopy, we measured fluorescence intensity trajectories (FITs) and revealed complex photobleaching behaviors of longer arrays.24 We have concluded that nonradiative deactivation channels due to the conformational heterogeneity of longer arrays play an important role in their energy relaxation processes. But, these studies on the structural heterogeneity of long porphyrin arrays are based on indirect methods. Therefore, to understand the structural heterogeneity, it is necessary to unveil the conformational structures of meso-meso linked porphyrin arrays more directly at the single molecule level. Further, it is highly desirable to reduce the structural heterogeneity and align the porphyrin arrays in an extended form for potential applications of these arrays as single molecular photonic and electronic wires. In this study, we have investigated the conformational structures of meso-meso linked Zn(II) porphyrin arrays from short trimer Z3 to long array Z128 (Chart 1) by using single molecule fluorescence spectroscopy (SMFS). By using SMFS, we can investigate individual molecular


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conformation by monitoring fluorescence coming from single molecules without ensemble averaging. Herein, the conformations of porphyrin arrays depending on the array length have been investigated by excitation polarization fluorescence spectroscopy. Coarse-grained simulation on the conformational dynamics of Zn arrays was performed for comparison with the experimental results. Further, we have controlled the conformation of porphyrin arrays by changing their environments by solvent vapor annealing (SVA) technique. The traces of central positions of emitting sites by localization microscopy supported the conformational change after SVA. Conclusively, we have demonstrated that directly-linked porphyrin arrays exhibit various conformations depending on the array length and environment.

Ar

Ar N N

N Zn N

N

N

Ar

Zn N Ar N

N Zn N

N N Ar

Ar

n-2 Ar = 3,5-dioctyloxyphenyl

Zn (n=3, 4, 5, , 96, 128)

Chart 1. Molecular structures of meso-meso directly-linked zinc(II) porphyrin arrays

RESULTS & DISCUSSION To explore the conformational structures of the porphyrin arrays, we utilized excitation polarization fluorescence spectroscopy (ExPFS), which provides information on the


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conformations of single molecules from the orientation of absorbing dipoles.25–29 As shown in Figure 1a, fluorescence intensity from the single molecule was recorded as a function of rotating angular orientation, θ, of the linearly polarized excitation light. Then, the modulation depth, M, is determined by fitting the intensity versus θ to the following equation: I(θ)=I0(1+M cos (θ -φ)) where I0 is offset and φ is a reference polarization angle when the emission intensity is maximized. Accordingly, the M value provides structural information. When the conformations of molecular arrays are more randomly oriented, their M values are close to zero. The M values approach 1 when the molecular arrays are linearly aligned. As shown in Figure 1b, the statistical analysis was performed for the M values of porphyrin arrays (Z3 to Z128). The mean values of M decrease as the number of porphyrin units increases (from 0.85 for Z3 to 0.46 for Z128). These results suggest that the porphyrin arrays exhibit bent structures as the porphyrin array becomes longer. Interestingly, the long arrays (Z64 to Z128) show a small portion of high M values, reflecting fewer molecules form linear structures. It is likely that most of longer arrays show bent and coiled structures. Some M values of relatively short arrays show small M values due to our experimental condition of linearly polarized excitation along x–y plane of the sample. In this regard, because the porphyrin arrays embedded in the polymer matrix were projected to the x–y plane, the tilting of porphyrin arrays relative to the x–y plane lowers the M values compared to the true values.


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Figure 1. a) Scheme of the experimental procedure for the measurement of the modulation depth, M by excitation polarization fluorescence spectroscopy b) A series of Modulation depth, M, histograms of single porphyrin arrays. The histograms consist of 238, 303, 326, 328, 547, 412, 478, 417, 511, 519, 486, and 505 M values from single molecules, respectively (red). Blue bars indicate the histograms of Mcal values from simulation. c) The representative simulated molecular structures of Z3, Z12, Z48, and Z128. To analyze the structural properties of porphyrin arrays, we modeled the Zn arrays with coarse-grained beads by employing dissipative particle dynamics simulations and local structure library sampling method.30 We replaced the porphyrin monomer by a 3x3 array of coarse-grained


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beads and simulated the structures of porphyrin arrays. In our ExPFS experiment, because we used an excitation source at 488 nm, which corresponds to the split Soret band region of Zn, we mainly excited linearly coupled long-axis dipole transitions of porphyrin arrays. In this regard, we selected only linear coarse grained-beads in the middle of the simulated structures (more details are in the Supporting Information). Per given structure, we obtained three twodimensional modulation depth values (Mcal). The Mcal values are calculated from the projected images of the structures to three arbitrarily chosen orthogonal planes as the following: Mୡୟ୪ = (R ୫ୟ୶ − R ୫୧୬ )/(R ୫ୟ୶ + R ୫୧୬ ) where Rmax (Rmin) is the maximum (minimum) radius of gyration obtained from the plane projected image. Histograms for the Mcal values of Z3 to Z128 are shown in Figure 1b (blue bars). The histograms of the Mcal values show similar tendencies to the experimental results. Some Mcal values show smaller values than the experimental M values due to different conditions. In the simulation, because the peripheral substituents of porphyrins were omitted to reduce the computational cost, the Mcal values of intermediate arrays (Z12 to Z48) are smaller than the experimental M values. The simulated porphyrin arrays were set to have randomly oriented 3-dimensional directions and were projected to three arbitrarily chosen orthogonal planes as shown in Figure S3. The randomly projected porphyrin arrays could show lower Mcal values than the experimental M values. To control the bent/kink structures of longer porphyrin arrays, we employed solvent vapor annealing (SVA) technique for longer porphyrin arrays (Z64, Z96, and Z128). Through SVA method, we may change the conformations of Zn arrays in polymer blend films. SVA has been recognized as an important post-processing technique without thermal damage. During SVA, solvent vapor makes host polymer swell, making guest molecules move rather freely.26,31–34 We


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put the PMMA embedded samples to a chamber with nitrogen gas saturated by THF for 5 min. After annealing process, we dried samples with pure nitrogen gas. During SVA process, PMMA film was kept to be liquid-like phase, allowing for single porphyrin arrays to move rather freely. As shown in Figures 2a–c, longer porphyrin arrays exhibit higher M values after SVA (from 0.51 to 0.65 for Z64, from 0.45 to 0.59 for Z96, and from 0.46 to 0.60 for Z128), corroborating that the conformational structures of porphyrin arrays are changed to largely extended structures. These features indicate that porphyrin arrays can change their conformation to more extended during SVA. c)

b)

a) Occurrence

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ഥ =0.51) Z64 (‫ۻ‬

ഥ =0.45) Z96 (‫ۻ‬

ഥ =0.46) Z128 (‫ۻ‬

Z64 after SVA ഥ =0.65) (‫ۻ‬

Z96 after SVA ഥ =0.59) (‫ۻ‬

Z128 after SVA ഥ =0.60) (‫ۻ‬

0 0.2 0.4 0.6 0.8 1.0 1.2 0 0.2 0.4 0.6 0.8 1.0 1.2 0 0.2 0.4 0.6 0.8 1.0 1.2

Modulation depth (M)

Figure 2. a–c) Modulation depth, M, histograms of Z64, Z96, and Z128 without and with solvent vapor annealing by THF vapor for 5 min. The histograms consist of 519, 486, and 505 single molecules for Z64, Z96, and Z128 before SVA and 479, 337, and 442 after SVA, respectively. To support our interpretation, we performed the localization microscopy measurements. Localization microscopy has previously been used to precisely identify the centroid position of emission from single molecules by 2D-Gaussian fitting.35–39 By tracing the centroid positions of molecules, we traced the changes of emitting sites, caused by partial photobleaching behaviors or quenching to surrounding environments. From the distribution of emitting sites, we could expect the molecular conformations. The FITs of Z96 molecules in Figures 3a and d show the intensity


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jumps, indicating the changes of emitting sites. The colors of dots in FITs indicate the progress of time, corresponding to the changes of the centroid positions of the emitting sites as shown in Figures 3b and e. Before SVA, the emitting sites of Z96 molecule are localized in a relatively narrow region, showing the observed longest distance between the centroid positions to be about 28 nm. After SVA, the emitting sites were distributed in an extended area, making the longest distance between the centroid positions longer, ca. 53 nm (More data are in the Supporting Information). Because the emission of the porphyrin array does not come from the entire molecule but from the localized regions, we could not determine the overall shapes of porphyrin arrays directly. However, by using the distributions of emitting sites, we could estimate the conformations of porphyrin arrays. The emitting sites of Z96 molecule show more elongated distribution after SVA than before. Thus, it was concluded that the SVA process unfolded Z96 molecule to more stretched structure.


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Figure 3. FITs of single Z96 molecules a) before and d) after SVA. b, e) Centroid positions correlated with FITs by localization microscopy. The small dots indicate frame-by-frame centroid localization of the molecules, measured by 1 s. The colors of dots display the progress of time (red, green, and blue order). The histograms of x positions and y positions are shown at top and right side of plot respectively. c, f) The molecular structures of Z96 which show similar structures to the distribution of the centroid positions.

CONCLUSIONS In this study, we have investigated the conformational structures of Zn by single-molecule spectroscopy. The experimentally determined M histograms showed that longer porphyrin arrays have coiled structures which was stretched by SVA with THF. From localization microscopy


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method, we identified emitting sites more precisely and assured that longer arrays changed their conformations to extended ones by SVA with THF. The present study provides detailed information on not only size-dependent conformational heterogeneity of porphyrin arrays but also the possibility of suppression of the conformational heterogeneity.

ASSOCIATED CONTENT Supporting Information. The following files are available free of charge. Experimental procedures, Computational details, Supporting figures (PDF)

AUTHOR INFORMATION Corresponding Author *E-mail: [email protected] (D.K.), [email protected] (E.S.), [email protected] (A.O.). Notes The authors declare no competing financial interests. ACKNOWLEDGMENT We thank Prof. John Lupton at University of Regensburg for helpful discussions about excitation polarization fluorescence spectroscopy. We also thank Prof. Laura Kaufman and Dr. Jaesung Yang at Columbia University and Prof. Heungman Park at Texas A&M University - Commerce for providing the software of localization microscopy. D.K. acknowledges the support from


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Global Research Laboratory (2013K1A1A2A02050183) through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT (Information and Communication Technologies) and Future Planning. E.S. acknowledges the support from the National Research Foundation of Korea(NRF) grant funded by the Korea government(MEST) (2017R1A2B2003552).

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TOC Graphic


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Ar

Ar N N

N Zn N

N

N

Ar

Zn N Ar N

N Zn N

N N Ar

Ar

n-2 Ar = 3,5-dioctyloxyphenyl

Zn (n=3, 4, 5, …, 96, 128)

Chart 1. Molecular structures of meso-meso directly-linked zinc(II) porphyrin arrays



a)

Imax

Imax - Imin Imax + Imin

M=

9000

θ

z

6000

Imin Absorption Ellipsoid

b) Z3

Intensity (a.u.)

Z24

3000

0

60

0 120 180

Angle (θ)

c) Z3

Occurrence

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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Z4

Z32

Z5

Z48

Z6

Z64

Z12

Z48 Z8

Z96

Z12

Z128

Z128

0 0.2 0.4 0.6 0.8 1.0 1.2 0 0.2 0.4 0.6 0.8 1.0 1.2


Figure 1. a) Scheme of the experimental procedure for the measurement of the modulation depth, M by excitation polarization fluorescence spectroscopy b) A series of Modulation depth, M, histograms of single porphyrin arrays. The histograms consist of 238, 303, 326, 328, 547, 412, 478, 417, 511, 519, 486, and 505 M values from single molecules, respectively (red). Blue bars indicate the histograms of Mcal values from simulation. c) The representative simulated molecular structures of Z3, Z12, Z48, and Z128.


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c)

b)

a) Occurrence

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Z64 ( =0.51)

Z96 ( =0.45)

Z128 ( =0.46)

Z64 after SVA ( =0.65)

Z96 after SVA ( =0.59)

Z128 after SVA ( =0.60)

0 0.2 0.4 0.6 0.8 1.0 1.2 0 0.2 0.4 0.6 0.8 1.0 1.2 0 0.2 0.4 0.6 0.8 1.0 1.2


Figure 2. a–c) Modulation depth, M, histograms of Z64, Z96, and Z128 without and with solvent vapor annealing by THF vapor for 5 min. The histograms consist of 519, 486, and 505 single molecules for Z64, Z96, and Z128 before SVA and 479, 337, and 442 after SVA, respectively.



a) Z96

b)

c) 20

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d) Z96 after SVA

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Figure 3. FITs of single Z96 molecules a) before and d) after SVA. b, e) Centroid positions correlated with FITs by localization microscopy. The small dots indicate frame-by-frame centroid localization of the molecules, measured by 1 s. The colors of dots display the progress of time (red, green, and blue order). The histograms of x positions and y positions are shown at top and right side of plot respectively. c, f) The molecular structures of Z96 which show similar structures to the distribution of the centroid positions.


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0

0.4 0.8 1.2 M

0

0.4 0.8 1.2 M

0

0.4 0.8 1.2 M

Coiled Linear Structure

TOC Graphic


Investigation and Control of Single Molecular Structures of meso-meso

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