Extended Data Fig. 2: Characterization of the stacked DTBT or BBT and enhanced multi-ring vibration mode following the DTBT-DTBT stacking. | Nature Biotechnology

Extended Data Fig. 2: Characterization of the stacked DTBT or BBT and enhanced multi-ring vibration mode following the DTBT-DTBT stacking.

From: Self-stacked small molecules for ultrasensitive, substrate-free Raman imaging in vivo

Extended Data Fig. 2: Characterization of the stacked DTBT or BBT and enhanced multi-ring vibration mode following the DTBT-DTBT stacking.

a, XRD analysis of BBT or DTBT powder on the SiO2/Si substrate. The diffraction peak of 10.5° demonstrated an in-plane d-spacing distance of 8.5 Å of the two adjacent BBT backbones. The π-π stacking between the BBT backbones in the direction of π-orbitals of the conjugated rings, with the diffraction peaks at 18.4°, 19.6°, 20.6°, 21.6°, 23.7° and 26.5° corresponding to the d-spacing distances of 4.8 Å, 4.5 Å, 4.3 Å, 4.2 Å, 3.7 Å and 3.3 Å, respectively (inset, blue curves). The lamellar stacking separated the multi-ring backbones by side chains in the direction perpendicular to the π-π stacking, with the diffraction peak at around 5.3° (d-spacing distance = 16.6 Å). Comparatively, DTBT displayed the backbone-to-backbone repeat construction and π-π stacking, verified by the diffraction peak of 10.5° (d-spacing distances = 8.6 Å) and peaks between 20.6° and 25.6° (d-spacing distances = 4.3-3.5 Å), but lack of the lamellar stacking (red curves). b, Size distribution of DTBT in the water/THF mixture with a water fraction of 95% analyzed by dynamic light scattering. c-e, Raman spectra of DTBT (10 μM) measured in the mixture of H2O and THF (95%: 5%) with 532-nm (c), 785-nm (d) and 830-nm (e) laser excitation, respectively. Raman measurement was carried out with a 5 × objective, acquisition time of 1 s, one time accumulation, and laser powers of 15.8 mW for 532-nm laser, 84.5 mW for 785-nm laser or 62.6 mW for 830-nm laser. f, BFDH theoretical crystal morphology of DTBT simulated by Mercury 3.8 based on the single-crystal structure from the Cambridge Crystallographic Data Centre (CCDC, code: 1308377). The whole view of the packing pattern in the crystal. g, The amplitude and direction of atomic vibration of the two DTBT molecules packed in the in-plane direction at 894 cm−1 and 1264 cm−1 by Gaussian 09/B3LYP/6-31 G(d), respectively (Supplementary Videos 7 and 9). h, The amplitude and direction of atomic vibration of the two DTBT molecules packed in the out-of-plane direction at 894 cm−1 and 1264 cm−1 by Gaussian 09/B3LYP/6-31 G(d), respectively (Supplementary Videos 8 and 10). Red arrows, the amplitude and direction of the atomic vibration.

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