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Ryo Kudo, Hiroki Hanayama, [Balaraman Vedhanarayanan](https://orcid.org/0000-0002-7785-136X), [Hitoshi Tamiaki](https://orcid.org/0000-0003-4797-0349), Nobuyuki Hara, [Sarah E. Rogers](https://orcid.org/0000-0003-2418-6965), [Martin J. Hollamby](https://orcid.org/0000-0002-6775-3539), [Biplab Manna](https://orcid.org/0000-0002-7619-7765), [Koji Harano](https://orcid.org/0000-0001-6800-8023), [Shiki Yagai](https://orcid.org/0000-0002-4786-8603)

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[Dendron-mediated control over self-assembly of chlorophyll rosettes into columnar <i>vs.</i> discrete aggregates](https://mdr.nims.go.jp/datasets/700c1e0c-442a-4f0b-8cf9-88af19161426)

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Dendron-mediated control over self-assembly of chlorophyll rosettes into columnar vs. discrete aggregatesORGANIC  CHEMISTRYF R O N T I E R SVolume 11 | Number 22 | 21 November 2024rsc.li/frontiers-organicAs featured in:See Shiki Yagai  et al. ,  Org. Chem. Front. , 2024,  11 , 6304.Registered charity number: 207890 Showcasing research from Professor Shiki Yagai’s laboratory, Division of Advanced Science and Engineering, Graduate School of Engineering, Chiba University, Chiba, Japan.   Dendron-mediated control over self-assembly of chlorophyll rosettes into columnar  vs.  discrete aggregates   By controlling the π–π stacking of chlorophyll supramolecular rosettes through steric hindrance of alkyl dendrons, it becomes possible to create chlorophyll tubes and discrete rings that resemble natural chlorophyll assemblies. rsc.li/frontiers-organicORGANIC CHEMISTRYFRONTIERSRESEARCH ARTICLECite this: Org. Chem. Front., 2024,11, 6304Received 3rd September 2024,Accepted 5th October 2024DOI: 10.1039/d4qo01629grsc.li/frontiers-organicDendron-mediated control over self-assembly ofchlorophyll rosettes into columnar vs. discreteaggregates†Ryo Kudo,a Hiroki Hanayama,b Balaraman Vedhanarayanan, c Hitoshi Tamiaki, dNobuyuki Hara,d,e Sarah E. Rogers, f Martin J. Hollamby, g Biplab Manna, hKoji Harano h,i and Shiki Yagai *b,jPhotosynthetic bacteria have evolved highly efficient light-harvesting systems by organizing chlorophyll(Chl) pigments into circular and tubular supramolecular arrays. To construct these surapmoelcular Chlarrays from the same molecular design, we synthesized two hydrogen-bonding chlorins using naturalChl-a as the starting material: free-base chlorin functionalized with hydrogen-bonding barbituric acid andsecond- or third-generation alkyl dendrons (G2 and G3, respectively). The barbituric acid moiety pro-motes the formation of a hydrogen-bonded cyclic hexamer known as rosette. In chloroform, both thesynthetic Chl-a derivatives formed rosettes; however, in methylcyclohexane as a low-polarity solvent, theG2-dendron chlorin formed columnar structures by stacking rosettes, while the G3-dendron chlorinformed disc-shaped particles. AFM revealed the formation of extended helical fibers for the former andhomogeneous nanoparticles, possibly single rosettes, for the latter. These results suggest that the third-generation of the dendron can inhibit the stacking of rosettes, leading to the formation of two distincttypes of chlorin aggregates: circular and tubular.IntroductionLight-harvesting (LH) antenna systems used in bacterial photo-synthesis are characterized by highly organized arrays ofchlorophyll (Chl) pigments. In purple photosynthetic bacteria,circular organization of Chl pigments is achieved throughsupercomplexation with intrinsic membrane proteins.1–18 Ingreen photosynthetic bacteria, on the other hand, the self-assembly of specifically evolved self-aggregative Chls(“chlorosomal” Chls) enables the construction of tubularmesoscale structures without the need for protein scaffoldingin extramembranous LH apparatuses.19–25 The self-assembly isdriven by the concerted action of a variety of noncovalent inter-actions. Mimicking these highly organized arrays of naturally-occurring pigments through synthetic supramolecular dyechemistry not only provides insights into structure–propertycorrelations but also paves the way for using these naturally-abundant π-conjugated molecules as active materials in opto-electronic devices.25–27In synthetic systems, self-assembly of metallochlorinsdesigned based on the structures of chlorosomal Chls hasbeen investigated in both organic solvents and aqueoussolutions.28–41 These chlorins formed nanotubes through theconcerted action of hydrogen bonds, coordination bonds, π–πstacking and van der Waals interactions. Although nanotubesare formed through non-hierarchical processes, from a topolo-†Electronic supplementary information (ESI) available: General information,synthesis, structural characterization data, photophysical, morphological, small-angle X-ray and neutron scattering studies and their model fittings. See DOI:https://doi.org/10.1039/d4qo01629gaDivision of Advanced Science and Engineering, Graduate School of Engineering,Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, JapanbDepartment of Applied Chemistry and Biotechnology, Graduate School ofEngineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan.E-mail: yagai@faculty.chiba-u.jpcDepartment of Chemistry, Faculty of Engineering and Technology, SRM Institute ofScience and Technology, Kattankulathur, Chengalpattu 603 203, Tamil Nadu, IndiadGraduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577,JapaneDepartment of Chemistry, College of Humanities & Sciences, Nihon University,Setagaya-ku, Tokyo 156-8550, JapanfISIS Pulsed Neutron Source, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UKgDepartment of Chemistry, School of Chemical and Physical Sciences, KeeleUniversity, Keele, Staffordshire ST55BG, UKhCenter for Basic Research on Materials, National Institute for Materials Science, 1-1Namiki, Tsukuba, Ibaraki 305-0044, JapaniResearch Center for Autonomous Systems Materialogy (ASMat), Institute ofIntegrated Research, Institute of Science Tokyo, 4259 Nagatsuda-cho, Midori-ku,Yokohama, Kanagawa 226-8501, JapanjInstitute for Advanced Academic Research (IAAR), Chiba University, 1-33 Yayoi-cho,Inage-ku, Chiba 263-8522, Japan6304 | Org. Chem. Front., 2024, 11, 6304–6310 This journal is © the Partner Organisations 2024Open Access Article. Published on 08 October 2024. Downloaded on 11/5/2024 8:25:37 PM.  This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.View Article OnlineView Journal  | View Issuehttp://rsc.li/frontiers-organichttp://orcid.org/0000-0002-7785-136Xhttp://orcid.org/0000-0003-4797-0349http://orcid.org/0000-0003-2418-6965http://orcid.org/0000-0002-6775-3539http://orcid.org/0000-0002-7619-7765http://orcid.org/0000-0001-6800-8023http://orcid.org/0000-0002-4786-8603https://doi.org/10.1039/d4qo01629ghttps://doi.org/10.1039/d4qo01629ghttp://crossmark.crossref.org/dialog/?doi=10.1039/d4qo01629g&domain=pdf&date_stamp=2024-10-31http://creativecommons.org/licenses/by/3.0/http://creativecommons.org/licenses/by/3.0/https://doi.org/10.1039/d4qo01629ghttps://pubs.rsc.org/en/journals/journal/QOhttps://pubs.rsc.org/en/journals/journal/QO?issueid=QO011022gical perspective, slicing these nanotubes yields ring struc-tures.42 Conversely, from the viewpoint of hierarchical self-assembly, stacking rings results in the formation of nanotubes.Therefore, by designing circular supramolecular assembly andcontrolling their hierarchical stacking, both ring and tubestructures can be created.We herein report the construction of circular and tubularassemblies of synthetic Chl-a derivatives by hierarchicalassembly control of the similar supramolecular motif. We havepreviously demonstrated that by modifying π-conjugated mole-cules with barbituric acid and a tri(dodecyloxy)phenyl (mini-dendron) units,43 supramolecular polymers can be constructedthrough the formation of hydrogen-bonded cyclic hexamers(rosettes) and their hierarchical stacking.44–49 In order toobtain discrete and stackable rosettes of Chl-a derivatives, wesynthesized a series of barbituric-acid-functionalized chlorinsChG2 and ChG3, modified with Percec-type dendrons43 ofdifferent bulkiness: second- (G2) and third-generation (G3)dendrons (Fig. 1). ChG2 formed supramolecular nanofibers ofstacked rosettes, while ChG3 only assembled to rosette level.Results and discussionFree base chlorins ChG2 and ChG3 were synthesized followingScheme S1 (in the ESI†). These compounds were characterizedby 1H and 13C NMR spectroscopies and ESI mass spectrometry.To study the rosette formation, we measured concentration-dependent 1H NMR spectra of ChG2 and ChG3 (Fig. S1†). Atsubmillimolar concentrations (e.g., 0.1 mM), two sharp signalscorresponding to the N–H protons (Hsyn and Hanti) of the barbi-turic acid unit appeared around 8.1 ppm for both the mole-cules. As the concentration increased to 20 mM, these two N–H signals gradually shifted downfield, indicating hydrogen-bonding. The difference in downfield shifts, Δ(δsyn − δanti),between Hsyn and Hanti reached 0.29 ppm for ChG2 and0.27 ppm for ChG3 at 20 mM, respectively (Fig. S2†). Thisresult is characteristic of rosette formation where the two N–Hprotons experience different deshielding environments.49Next, we studied self-assembly of ChG2 and ChG3 inmethylcyclohexane (MCH), a nonpolar solvent, by using vari-able-temperature (VT) UV/Vis and circular dichroism (CD)spectroscopies (Fig. 2). The UV/Vis spectrum of ChG2 (c =10 μM) at 100 °C showed Soret and Qy absorption maxima at386 and 713 nm, respectively (Fig. 2a, upper). Upon cooling to20 °C at a rate of 1 °C min−1, these peaks shifted hypsochromi-cally to 362 and 698 nm. The spectral change indicates thatthe chlorin chromophore stacks in a face-to-face (H-type)arrangement. Plotting the UV/Vis absorption change at386 nm against temperature revealed a non-sigmoidal aggrega-tion curve (Fig. S3a,† blue line). Upon heating at a rate of 1 °Cmin−1, the plot showed significant thermal hysteresis,suggesting that the cooling process is not under thermo-dynamic control. This was further supported by retardation ofnucleation upon increasing cooling rate (Fig. S4†).50 Theseresults indicated that ChG2 exhibits cooperative supramolecu-lar polymerization involving nucleation followed by elongationprocesses.51 In the VT-CD measurements, the growth of astrong Cotton effect was observed in the Soret region uponcooling, while the Qy band showed a weak Cotton effect(Fig. 2a, lower). These CD signals are in good agreement withthe face-to-face stacking of the entire chlorin chromophores,which is different from aggregation of chlorosomal Chls alongto their Qy axes. In sharp contrast, UV/Vis and CD spectra ofChG3 displayed only marginal changes upon cooling even at amuch higher concentration of 150 μM (Fig. 2b). Temperature-dependence of the absorption spectra are unlikely thoserecorded for aggregation and dissociation, and no significantthermal hysteresis was observed upon heating at a rate of 1 °CFig. 1 (a) Molecular structures of ChG2 and ChG3. (b) Schematic repre-sentation showing the self-assembly of ChG2 and ChG3 into columnarand discrete aggregates.Fig. 2 UV/Vis (upper) and CD absorption spectra (lower) of ChG2 (a)and ChG3 (b) in MCH at 100 °C (red lines) and 20 °C (blue lines).(Concentration: ChG2 = 10 μM, ChG3 = 150 μM.)Organic Chemistry Frontiers Research ArticleThis journal is © the Partner Organisations 2024 Org. Chem. Front., 2024, 11, 6304–6310 | 6305Open Access Article. Published on 08 October 2024. Downloaded on 11/5/2024 8:25:37 PM.  This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.View Article Onlinehttp://creativecommons.org/licenses/by/3.0/http://creativecommons.org/licenses/by/3.0/https://doi.org/10.1039/d4qo01629gmin−1 (Fig. S3b†). The entirely different temperature-depen-dence of ChG2 and ChG3 implies their distinct self-organiz-ation behaviors.The formation of extended fibrous structures by ChG2 andsmall species by ChG3 was demonstrated by small-angle X-rayand neutron scattering (SAXS/SANS) experiments in MCH-d14(Fig. 3). Analysis of the combined datasets for each solution,using a model representing a core–shell cylinder with globallyconstrained assembly dimensions, was performed usingSasView,52 as detailed in the ESI.† The SAXS/SANS data for asolution of ChG2 is indicative of elongated fibers, with length,L ≥ 100 nm, aromatic core radius, Rcore = 2.6 ± 0.1 nm andn-alkyl shell thickness, δshell = 1.2 ± 0.1 nm (Fig. 3a and c).This gives a fiber diameter of 7.6 ± 0.2 nm, in line with the dia-meter of the ChG2 rosette estimated by molecular modellingcalculations (Fig. S5†). There is good agreement betweenSAXS/SANS data and the model for much of the Q-range.However, maximum at Q ∼ 0.28 Å−1 is visible in the SAXS thatis not apparent in the SANS and unaccounted for in the ana-lysis. While we are presently unable to definitively explain thisphenomenon, its possible origin is suggested in the ESI.† TheSAXS/SANS data for a solution of ChG3 is quite different tothat for ChG2 (Fig. 3b and d). The SANS data exhibits a flatI(Q) ∼ Q° region at low Q on the log–log plot and thereforeindicates far less elongated assembly structures in solution.Combined SAXS/SANS analysis gave Rcore = 3.1 ± 0.1 nm, δshell= 1.1 ± 0.1 nm and L = 2.1 ± 0.1 nm. This supports the exist-ence of rosettes of ChG3 in solution but suggests that, unlikeChG2, they do not extensively stack—in line with the UV/Visand CD findings. The upturn in I(Q) at low Q in the SAXS datafor ChG3 may suggest some localised aggregation or limitedstacking of a small number of rosettes, which may explain theslight differences before and after cooling noted in Fig. 2b.Highly extended nanofibers were imaged for self-assembledChG2 by atomic force microscopy (AFM) and transmission electron microscopy (TEM) (Fig. 4). In the AFM imagesacquired for spin-coated samples, right-handed helical struc-tures with a helical pitch of 9.5 nm are observed (Fig. 4a, band S6†). The right-handed helicity indicates clockwiserotation of the ChG2 rosette upon stacking. On the otherhand, TEM imaging of drop-cast samples visualized both iso-lated individual nanofibers and also dense arrays of bundlednanofibers (Fig. 4c, e and S7†). This finding could be attribu-ted to a concentration gradient during a slow drying process ofsolvent after drop casting, which was confirmed by concen-tration-dependent AFM images (Fig. S8†). For the isolatednanofibers, the visible width was measured to be approxi-mately 5.1 nm (Fig. 4c and d). This value is very similar to thediameter of the π-conjugated core (2Rcore = 5.2 nm) indicatedby SAXS/SANS analysis. For the bundled nanofibers, their long-range ordering with a periodicity of 6.8 nm was observed(Fig. 4e and f). This value is smaller than the diameter of sol-vated nanofibers (7.6 nm) shown by SAXS/SANS analysis,suggesting that the alkyl chains are tightly packed or interdigi-tated between nanofibers on the substrate.In stark contrast, uniform small particles with heights of2–3 nm and widths of 7–8 nm were imaged for ChG3 by AFMFig. 3 (a and b) SANS (red circles) and SAXS (blue triangles) data ofChG2 (a) and ChG3 (b) in MCH-d14 (c = 300 μM). Black solid lines rep-resent fits of the data. The scattered intensity, I(Q), is plotted as a func-tion of the scattering vector, Q. (c and d) Schematic illustrations ofassemblies of ChG2 (c) and ChG3 (d).Fig. 4 (a) AFM image of aggregates spin-coated immediately aftercooling an MCH solution of ChG2 (10 μM) from 100 °C to 20 °C at a rateof 1 °C min−1. The inset image is magnified view. (b) AFM height analysisof a fiber formed by ChG2 (along the yellow line in a). (c and e) TEMimages of ChG2 (30 μM) drop-casted on an amorphous carbon film. (c)TEM image of an individual and bundled fibers. (d) Intensity profile ofthe selected area in c (yellow box). The horizontal line (red) correspondsto gray value of the image background. (e) TEM image of aligned fibers.Yellow dotted lines indicate fiber orientation and spacing. (f ) Fast Fouriertransform pattern corresponding to (e), showing the signal assignable tothe interfiber spacing of 6.8 nm.Research Article Organic Chemistry Frontiers6306 | Org. Chem. Front., 2024, 11, 6304–6310 This journal is © the Partner Organisations 2024Open Access Article. Published on 08 October 2024. Downloaded on 11/5/2024 8:25:37 PM.  This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.View Article Onlinehttp://creativecommons.org/licenses/by/3.0/http://creativecommons.org/licenses/by/3.0/https://doi.org/10.1039/d4qo01629g(Fig. 5 and S9†), corresponding to the dimension of the height(2.1 nm) and diameter (8.4 nm) of the rosette indicated bySAXS/SANS analysis. Additionally, TEM imaging of the spin-coated samples revealed particles with a smallest width ofapproximately 6 nm (Fig. 5e and f), corresponding to the dia-meter of the π-conjugated core (2Rcore = 6.2 nm) as indicatedby SAXS/SANS. This dimension closely matches that of a singleChG3 rosette in TEM simulation (Fig. S10†). These analysescorroborate that ChG3 rosette indeed exists as discrete species,likely due to the bulky G3 dendrons inhibiting the stacking ofchlorin moieties.ConclusionsWhile Chl nanotubes have been the subject of numerousstudies, there has been limited exploration into the cross-sec-tional counterpart, i.e., circular assemblies that can hierarchi-cally assemble into nanotubes. Our present research focusedon engineering circular assemblies of Chl pigments using thehydrogen-bonding capability of barbituric acid. These circularassemblies tend to stack into tubular structures; however, byaltering the bulkiness of surrounding alkyl side chains, wehave effectively distinguished between the formation of circu-lar and tubular assemblies. This approach enables precisecontrol over the hierarchical organization of molecular assem-blies with similar motifs, allowing for an unbiased comparisonof their structural and functional properties. Investigating theoptical characteristics of these ring and tube structures mayprovide crucial insights into the evolutionary importance ofChl’s light-harvesting mechanism in photosynthesis, and pavethe way for future applications.Author contributionsConceptualization, R. K., S. Y.; resources, H. T., N. H.; investi-gation, data curation, formal analysis except for SAXS/SANSand TEM, R. K.; investigation of SANS, S. R.; investigation ofSANS, data curation and formal analysis of SAXS/SANS, M. H.,H. H.; investigation, data curation, formal analysis of TEM,B. M., K. H.; all authors prepared and edited the overall manu-script including figures; funding acquisition, H. T., S. Y.;supervision, S. Y. All authors have read and agreed to the finalversion of the manuscript.Data availabilityThe data that support the findings of this work have beenincluded in the main text and ESI.†Conflicts of interestAuthors declare no conflicts of interest.AcknowledgementsThis work was supported by the Japan Society for thePromotion for Science (JSPS) KAKENHI grant no. JP22H00331,JP22H02203, JP23H04874 and JP23H04873 in a Grant-in-AidFig. 5 (a and b) AFM images of aggregates spin-coated immediatelyafter cooling an MCH solution of ChG3 (150 μM) from 100 °C to 20 °C ata rate of 1 °C min−1. (c and d) AFM cross-sectional analysis of particlesformed by ChG3 along the yellow line in (a) and the blue line in (b),respectively. (e) TEM images of ChG3 particles on an amorphous carbonfilm. (f ) High-magnification TEM image showing individual ChG3particles.Organic Chemistry Frontiers Research ArticleThis journal is © the Partner Organisations 2024 Org. Chem. Front., 2024, 11, 6304–6310 | 6307Open Access Article. Published on 08 October 2024. Downloaded on 11/5/2024 8:25:37 PM.  This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.View Article Onlinehttp://creativecommons.org/licenses/by/3.0/http://creativecommons.org/licenses/by/3.0/https://doi.org/10.1039/d4qo01629gfor Transformative Research Areas “Materials Science of Meso-Hierarchy”. B. V. thanks the JSPS for research fellowshipP1934. This work was performed under the approval of thePhoton Factory Program Advisory Committee (Proposal No.2022G537). The authors are grateful to Dr Nobutaka Shimizu,Dr Hideaki Takagi, and Dr Rie Haruki for the measurementsof SAXS. This work benefited from the use of the SasViewapplication, originally developed under NSF awardDMR-0520547. 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