Impacts of annealing on structural and photophysical properties of zinc phthalocyanine adsorbed on graphene
Pith reviewed 2026-05-20 03:48 UTC · model grok-4.3
pith:M5FALSLZ Add to your LaTeX paper
What is a Pith Number?\usepackage{pith}
\pithnumber{M5FALSLZ}
Prints a linked pith:M5FALSLZ badge after your title and writes the identifier into PDF metadata. Compiles on arXiv with no extra files. Learn more
The pith
Annealing reorients zinc phthalocyanine on graphene from planar to shuttlecock geometry.
A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.
Core claim
We report the demonstration and analysis of a 2D phase change in a self-assembled zinc phthalocyanine monolayer adsorbed on graphene using combined scanning-tunneling-microscopy and optical microspectroscopy. By confining molecules within the pores of a self-assembled 2D matrix, a phase change induced by annealing is tracked and discussed as a planar-square to shuttlecock molecular transition. After annealing, the exposition of Zn atoms to reactants in a supernatant solution is improved, for example for metal-ligand formation towards 3D self-assembly.
What carries the argument
The annealing-induced 2D phase change from planar-square to shuttlecock molecular geometry in the confined ZnPc monolayer on graphene.
If this is right
- Improved access of zinc atoms to supernatant reactants enables metal-ligand complexation.
- This paves the way for building 3D self-assembled structures from the 2D layer.
- Photophysical properties of the monolayer are altered by the structural transition.
- The confinement method allows precise tracking of molecular reorientation at the nanoscale.
Where Pith is reading between the lines
- The shuttlecock configuration may enhance catalytic activity of the zinc centers in surface reactions.
- This technique of thermal annealing could be applied to other metal-organic molecules on graphene or similar 2D materials to control orientation.
- Future work might explore if the phase change is reversible under different conditions.
- It suggests a route to hybrid organic-inorganic 3D architectures via sequential self-assembly.
Load-bearing premise
That the changes seen in microscopy and spectroscopy arise specifically from molecules flipping into a shuttlecock shape rather than from other rearrangements or interactions with the graphene.
What would settle it
A measurement showing that zinc atoms remain equally inaccessible to ligands after annealing, or STM images revealing no change in apparent molecular height, would disprove the improved exposure via reorientation.
Figures
read the original abstract
We report the demonstration and analysis by combined scanning-tunneling-microscopy and optical microspectroscopy of a 2D phase change experienced by a self-assembled zinc phthalocyanine (ZnPc) monolayer adsorbed on graphene. To probe the intrinsic properties of individual ZnPc molecules, they are spatially confined within the pores of a self-assembled 2D matrix. This confinement allows us to track a phase change induced by annealing, which we discuss in terms of a planar-square to shuttlecock molecular transition. We show that after annealing of the adsorbed ZnPc, the exposition of Zn atoms to reactants in a supernatant solution is improved, for example, for metal-ligand formation towards 3D self-assembly.
Editorial analysis
A structured set of objections, weighed in public.
Referee Report
Summary. The manuscript reports combined STM and optical microspectroscopy observations of an annealing-induced 2D phase change in a self-assembled ZnPc monolayer on graphene. The authors interpret changes in STM contrast and optical spectra as a transition from planar-square to shuttlecock molecular geometry that improves Zn-atom exposure to supernatant reactants, with potential implications for metal-ligand coordination and 3D assembly.
Significance. If the geometric assignment is confirmed, the result would provide a practical route to reorient metal centers in 2D molecular layers on graphene, relevant to interface design for catalysis and sensing. The dual STM/optical approach is a strength for correlating structure with photophysical response.
major comments (3)
- [STM results] STM results section: the central claim that annealing produces a shuttlecock geometry with improved Zn exposure rests on qualitative contrast changes without reported quantitative apparent-height measurements or line profiles that would directly confirm an out-of-plane Zn displacement relative to the molecular plane.
- [Discussion] Discussion of molecular transition: no DFT-simulated STM images or calculated LDOS for the proposed shuttlecock orientation on graphene are provided to test whether the observed contrast is consistent with that geometry rather than altered packing or electronic effects from the substrate.
- [Methods and results] Experimental controls: the manuscript lacks control experiments (e.g., annealing on different substrates or at varied coverages) that would distinguish the reorientation interpretation from alternatives such as changes in molecular packing density or graphene doping shifts.
minor comments (2)
- [Figure 2] Figure captions should explicitly state the annealing temperature, duration, and ambient conditions used for the post-anneal images.
- [Optical microspectroscopy] Optical spectra: the assignment of specific peak shifts to the shuttlecock geometry would benefit from a brief comparison to literature spectra of known ZnPc orientations.
Simulated Author's Rebuttal
We thank the referee for the positive assessment of our manuscript and for the constructive comments. We address each major comment in turn below, indicating where revisions will be made.
read point-by-point responses
-
Referee: [STM results] STM results section: the central claim that annealing produces a shuttlecock geometry with improved Zn exposure rests on qualitative contrast changes without reported quantitative apparent-height measurements or line profiles that would directly confirm an out-of-plane Zn displacement relative to the molecular plane.
Authors: We agree that quantitative apparent-height data would strengthen the geometric assignment. In the revised manuscript we will add measured apparent heights together with line profiles extracted from the STM images before and after annealing to document the out-of-plane displacement. revision: yes
-
Referee: [Discussion] Discussion of molecular transition: no DFT-simulated STM images or calculated LDOS for the proposed shuttlecock orientation on graphene are provided to test whether the observed contrast is consistent with that geometry rather than altered packing or electronic effects from the substrate.
Authors: We acknowledge that DFT-simulated images and LDOS maps would provide an independent test of the contrast origin. Our interpretation currently rests on the joint STM and optical microspectroscopy evidence, which shows photophysical changes consistent with altered Zn exposure. In revision we will expand the discussion to address alternative explanations (packing-density changes or substrate doping) and will note that comprehensive DFT validation lies beyond the present scope. revision: partial
-
Referee: [Methods and results] Experimental controls: the manuscript lacks control experiments (e.g., annealing on different substrates or at varied coverages) that would distinguish the reorientation interpretation from alternatives such as changes in molecular packing density or graphene doping shifts.
Authors: We accept that additional controls would help exclude alternatives. We will revise the text to show how the optical spectral shifts are inconsistent with simple graphene doping and how the fixed 2D-matrix confinement limits packing-density variations. New annealing runs on other substrates or at different coverages, however, require fresh sample preparation and are not feasible for this revision cycle. revision: partial
- New control experiments on alternative substrates or coverages cannot be performed without additional sample fabrication and measurement time.
Circularity Check
No circularity: purely observational experimental report with no derivations or fitted predictions
full rationale
The manuscript describes STM imaging and optical microspectroscopy measurements of ZnPc monolayers on graphene before and after annealing, reporting observed changes in contrast and spectra that are interpreted as a planar-to-shuttlecock reorientation. No equations, parameter fits, predictions, or derivation chains appear in the provided text. The central claim rests on direct experimental comparison rather than any reduction of a result to its own inputs by construction. Per the enumerated patterns, none of self-definitional, fitted-input-called-prediction, self-citation load-bearing, or related circularities are present; the work is self-contained against external benchmarks as an empirical study.
Axiom & Free-Parameter Ledger
axioms (2)
- domain assumption STM topographic contrast directly reflects molecular orientation (planar vs shuttlecock)
- domain assumption Annealing does not alter the graphene substrate or induce desorption that would mimic the observed change
Reference graph
Works this paper leans on
-
[1]
Gobbi, M.; Orgiu, E.; Samorì, P. Adv. Mater. (Weinheim, Ger.) 2018, 30, 1706103. doi:10.1002/adma.201706103
-
[2]
Berke, K.; Tongay, S.; McCarthy, M. A.; Rinzler, A. G.; Appleton, B. R.; Hebard, A. F. J. Phys.: Condens. Matter 2012, 24, 255802. doi:10.1088/0953 - 8984/24/25/255802
-
[3]
Kim, K.; Lee, T. H.; Santos, E. J. G.; Jo, P. S.; Salleo, A.; Nishi, Y.; Bao, Z. ACS Nano 2015, 9, 5922–5928. doi:10.1021/acsnano.5b00581
-
[4]
Hlaing, H.; Kim, C. -H.; Carta, F.; Nam, C. -Y.; Barton, R. A.; Petrone, N.; Hone, J.; Kymissis, I. Nano Lett. 2015, 15, 69–74. doi:10.1021/nl5029599
-
[5]
Lee, W. H.; Park, J.; Sim, S. H.; Lim, S.; Kim, K. S.; Hong, B. H.; Cho, K. J. Am. Chem. Soc. 2011, 133, 4447–4454. doi:10.1021/ja1097463
-
[6]
Liu, Y.; Zhou, H.; Weiss, N. O.; Huang, Y.; Duan, X. ACS Nano 2015, 9, 11102– 11108. doi:10.1021/acsnano.5b04612
-
[7]
Han, J.; Wang, J.; Yang, M.; Kong, X.; Chen, X.; Huang, Z.; Guo, H.; Gou, J.; Tao, S.; Liu, Z.; Wu, Z.; Jiang, Y.; Wang, X. Adv. Mater. (Weinheim, Ger.) 2018, 30, 1804020. doi:10.1002/adma.201804020
-
[8]
Huisman, E. H.; Shulga, A. G.; Zomer, P. J.; Tombros, N.; Bartesaghi, D.; Bisri, S. Z.; Loi, M. A.; Koster, L. J. A.; Van Wees, B. J. ACS Appl. Mater. Interfaces 2015, 7, 11083–11088. doi:10.1021/acsami.5b00610
-
[9]
Liu, Z.; Li, J.; Yan, F. Adv. Mater. (Weinheim, Ger.) 2013, 25, 4296 –4301. doi:10.1002/adma.201205337
-
[10]
Park, H.; Rowehl, J. A.; Kim, K. K.; Bulovic, V.; Kong, J. Nanotechnology 2010, 21, 505204. doi:10.1088/0957-4484/21/50/505204
-
[11]
Lee, G. -H.; Lee, C. -H.; Van Der Zande, A. M.; Han, M.; Cui, X.; Arefe, G.; Nuckolls, C.; Heinz, T. F.; Hone, J.; Kim, P. APL Materials 2014, 2, 092511. doi:10.1063/1.4894435
-
[12]
Matyba, P.; Yamaguchi, H.; Chhowalla, M.; Robinson, N. D.; Edman, L. ACS Nano 2011, 5, 574–580. doi:10.1021/nn102704h
-
[13]
Kim, C. -H.; Kymissis, I. J. Mater. Chem. C 2017, 5, 4598 –4613. doi:10.1039/C7TC00664K
-
[14]
-H.; Hlaing, H.; Yang, S.; Bonnassieux, Y.; Horowitz, G.; Kymissis, I
Kim, C. -H.; Hlaing, H.; Yang, S.; Bonnassieux, Y.; Horowitz, G.; Kymissis, I. Organic Electronics 2014, 15, 1724–1730. doi:10.1016/j.orgel.2014.04.039 22
-
[15]
Melville, O. A.; Lessard, B. H.; Bender, T. P. ACS Appl. Mater. Interfaces 2015, 7, 13105–13118. doi:10.1021/acsami.5b01718
-
[16]
Gregory, P. J. Porphyrins Phthalocyanines 2000, 4, 432 –437. doi:10.1002/(SICI)1099-1409(200006/07)4:4<432::AID-JPP254>3.3.CO;2-E
-
[17]
De La Torre, G.; Claessens, C. G.; Torres, T. Chem. Commun. 2007, No. 20, 2000–2015. doi:10.1039/B614234F
-
[18]
Feng, S.; Luo, N.; Tang, A.; Chen, W.; Zhang, Y.; Huang, S.; Dou, W. J. Phys. Chem. C 2019, 123, 16614–16620. doi:10.1021/acs.jpcc.8b11757
-
[19]
Assour, J. M. J. Phys. Chem. 1965, 69, 2295–2299. doi:10.1021/j100891a026
-
[20]
Lucia, E. A.; Verderame, F. D. The Journal of Chemical Physics 1968, 48, 2674–
work page 1968
-
[21]
doi:10.1063/1.1669501
-
[22]
Shahiduzzaman, Md.; Horikawa, T.; Hirayama, T.; Nakano, M.; Karakawa, M.; Takahashi, K.; Nunzi, J. -M.; Taima, T. J. Phys. Chem. C 2020, 124, 21338 – 21345. doi:10.1021/acs.jpcc.0c07010
-
[23]
Roy, D.; Chakraborty, M.; Gupta, P. S. Applied Surface Science 2019, 490, 492–
work page 2019
-
[24]
doi:10.1016/j.apsusc.2019.06.094
-
[25]
P.; Naumann, M.; Ziegs, F.; Büchner, B.; Popov, A.; Knupfer, M
Doctor, L. P.; Naumann, M.; Ziegs, F.; Büchner, B.; Popov, A.; Knupfer, M. J. Phys. Chem. C 2021, 125, 12398–12404. doi:10.1021/acs.jpcc.1c02654
-
[26]
Sghaier, T.; Le Liepvre, S.; Fiorini, C.; Douillard, L.; Charra, F. Beilstein J. Nanotechnol. 2016, 7, 862–868. doi:10.3762/bjnano.7.78
-
[27]
Anticipating Activity in Social Media Spikes
Liepvre, S. L.; Gouesmel, A.; Nguyen, K. N.; Bocheux, A.; Charra, F. Molecular Crystals and Liquid Crystals 2017, 655, 5 –15. doi:10.1080/15421406.2017.1362313
work page internal anchor Pith review Pith/arXiv arXiv doi:10.1080/15421406.2017.1362313 2017
-
[28]
-J.; Fiorini - Debuisschert, C.; Douillard, L.; Charra, F
Le Liepvre, S.; Du, P.; Kreher, D.; Mathevet, F.; Attias, A. -J.; Fiorini - Debuisschert, C.; Douillard, L.; Charra, F. ACS Photonics 2016, 3, 2291–2296. doi:10.1021/acsphotonics.6b00793
-
[29]
Brill, A. R.; Kuntumalla, M. K.; De Ruiter, G.; Koren, E. ACS Appl. Mater. Interfaces 2020, 12, 33941–33949. doi:10.1021/acsami.0c09722
-
[30]
Applied Catalysis B: Environmental 2021, 280, 119437
Yu, X.; Lai, S.; Xin, S.; Chen, S.; Zhang, X.; She, X.; Zhan, T.; Zhao, X.; Yang, D. Applied Catalysis B: Environmental 2021, 280, 119437. doi:10.1016/j.apcatb.2020.119437
-
[31]
R.; Ware, B.; Pansegrau, C.; Çakir, D.; Hoffmann, M
Nicholls, D.; Li, R. R.; Ware, B.; Pansegrau, C.; Çakir, D.; Hoffmann, M. R.; Oncel, N. J. Phys. Chem. C 2015, 119, 9845 –9850. doi:10.1021/acs.jpcc.5b00864
-
[32]
Nilson, K.; Åhlund, J.; Shariati, M.-N.; Göthelid, E.; Palmgren, P.; Schiessling, J.; 23 Berner, S.; Mårtensson, N.; Puglia, C. J. Phys. Chem. C 2010, 114, 12166 – 12172. doi:10.1021/jp910180y
-
[33]
Surface Science 2007, 601, 3661 –3667
Åhlund, J.; Schnadt, J.; Nilson, K.; Göthelid, E.; Schiessling, J.; Besenbacher, F.; Mårtensson, N.; Puglia, C. Surface Science 2007, 601, 3661 –3667. doi:10.1016/j.susc.2007.06.008
-
[34]
Olszowski, P.; Zajac, L.; Godlewski, S.; Such, B.; Pawlak, R.; Hinaut, A.; Jöhr, R.; Glatzel, T.; Meyer, E.; Szymonski, M. Beilstein J. Nanotechnol. 2017, 8, 99–
work page 2017
-
[35]
doi:10.3762/bjnano.8.11
-
[36]
Ruggieri, C.; Rangan, S.; Bartynski, R. A.; Galoppini, E. J. Phys. Chem. C 2015, 119, 6101–6110. doi:10.1021/acs.jpcc.5b00217
-
[37]
Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films 2012, 30, 031402
Tskipuri, L.; Shao, Q.; Reutt-Robey, J. Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films 2012, 30, 031402. doi:10.1116/1.4705511
-
[38]
Surface Science 2008, 602, 452 –459
Nilson, K.; Palmgren, P.; Åhlund, J.; Schiessling, J.; Göthelid, E.; Mårtensson, N.; Puglia, C.; Göthelid, M. Surface Science 2008, 602, 452 –459. doi:10.1016/j.susc.2007.10.052
-
[39]
Surface Science 2005, 596, 98–107
Zhang, L.; Peisert, H.; Biswas, I.; Knupfer, M.; Batchelor, D.; Chassé, T. Surface Science 2005, 596, 98–107. doi:10.1016/j.susc.2005.08.022
-
[40]
The Journal of Chemical Physics 2007, 127, 114702
Nilson, K.; Åhlund, J.; Brena, B.; Göthelid, E.; Schiessling, J.; Mårtensson, N.; Puglia, C. The Journal of Chemical Physics 2007, 127, 114702. doi:10.1063/1.2770732
-
[41]
Gonzalez Arellano, D. L.; Burnett, E. K.; Demirci Uzun, S.; Zakashansky, J. A.; Champagne, V. K.; George, M.; Mannsfeld, S. C. B.; Briseno, A. L. J. Am. Chem. Soc. 2018, 140, 8185–8191. doi:10.1021/jacs.8b03078
-
[42]
Arrigoni, C.; Schull, G.; Bléger, D.; Douillard, L.; Fiorini -Debuisschert, C.; Mathevet, F.; Kreher, D.; Attias, A. -J.; Charra, F. J. Phys. Chem. Lett. 2010, 1, 190–194. doi:10.1021/jz900146f
-
[43]
Kalashnyk, N.; Gouesmel, A.; Kim, E.; Attias, A. -J.; Charra, F. 2D Mater. 2019, 6, 045016. doi:10.1088/2053-1583/ab2ba7
-
[44]
Bishop, S. M.; Beeby, A.; Parker, A. W.; Foley, M. S. C.; Phillips, D. Journal of Photochemistry and Photobiology A: Chemistry 1995, 90, 39 –44. doi:10.1016/1010-6030(95)04095-W
-
[45]
Ling, X.; Fang, W.; Lee, Y. -H.; Araujo, P. T.; Zhang, X.; Rodriguez-Nieva, J. F.; Lin, Y.; Zhang, J.; Kong, J.; Dresselhaus, M. S. Nano Lett. 2014, 14, 3033–3040. doi:10.1021/nl404610c
-
[46]
Saini, G. S. S.; Singh, S.; Kaur, S.; Kumar, R.; Sathe, V.; Tripathi, S. K. J. Phys.: Condens. Matter 2009, 21, 225006. doi:10.1088/0953-8984/21/22/225006 24
-
[47]
L.; Dieudonné, P.; Jousselme, B.; Campidelli, S.; Bantignies, J
Alvarez, L.; Almadori, Y.; Mariot, S.; Aznar, R.; Arenal, R.; Michel, T.; Parc, R. L.; Dieudonné, P.; Jousselme, B.; Campidelli, S.; Bantignies, J. -L. Journal of Nanoelectronics and Optoelectronics 2013, 8, 28 –35. doi:10.1166/jno.2013.1426
-
[48]
Kalashnyk, N.; Jaouen, M.; Fiorini -Debuisschert, C.; Douillard, L.; Attias, A. -J.; Charra, F. Chem. Commun. 2018, 54, 9607–9610. doi:10.1039/C8CC05806G
-
[49]
Bellec, A.; Arrigoni, C.; Schull, G.; Douillard, L.; Fiorini -Debuisschert, C.; Mathevet, F.; Kreher, D.; Attias, A. -J.; Charra, F. The Journal of Chemical Physics 2011, 134, 124702. doi:10.1063/1.3569132
-
[50]
Langmuir 2023, 39, 18252 –18262
Fabre, N.; Trojanowicz, R.; Moreaud, L.; Fiorini -Debuisschert, C.; Vassant, S.; Charra, F. Langmuir 2023, 39, 18252 –18262. doi:10.1021/acs.langmuir.3c02038
-
[51]
ACS Photonics 2017, 4, 3130 –3139
Khadir, S.; Bon, P.; Vignaud, D.; Galopin, E.; McEvoy, N.; McCloskey, D.; Monneret, S.; Baffou, G. ACS Photonics 2017, 4, 3130 –3139. doi:10.1021/acsphotonics.7b00845
-
[52]
Ortí, E.; Brédas, J. L.; Clarisse, C. The Journal of Chemical Physics 1990, 92, 1228–1235. doi:10.1063/1.458131
-
[53]
Fernez, Q.; Moradmand, S.; Mattera, M.; Djampa-Tapi, W.; Fiorini-Debuisschert, C.; Charra, F.; Kreher, D.; Mathevet, F.; Arfaoui, I.; Vargas, L. S. J. Mater. Chem. C 2022, 10, 13981–13988. doi:10.1039/D2TC01331B
discussion (0)
Sign in with ORCID, Apple, or X to comment. Anyone can read and Pith papers without signing in.