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Updated: Aug 6, 2025

Conventional BODIPY Conjugates for Live-Cell Super-Resolution Microscopy and Single-Molecule Tracking
Published on: June 8, 2020
Stereochemical Control of Secondary Benzamide-based BODIPY Emitters
Sara M A Waly1, Andrew C Benniston1, Joshua K G Karlsson1
1Molecular Photonics Laboratory, Bedson Building School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom.
Abstract:
Aromatic amides can be used to construct light-harvesting materials with valuable optical properties. The amide bond is formed using well-known coupling agents in near quantitative yield, as illustrated here through the synthesis of two boron dipyrromethene derivatives bearing an amide linkage. The primary concern with acyl amides is rotation around the C-N bond, leading to cis and trans isomers. Using NMR spectroscopy, quantum chemical calculations and critical comparison to simpler benzamides, the stereochemistry of the target compounds has been addressed. The N-cyclohexyl derivative gave diffraction quality crystals that established a trans geometry for the amide bond. Quantum chemical calculations support the trans geometry as being the lowest-energy structure in solution but indicate that inversion of the aryl ring is an important structural feature. Indeed, rotation around the C(sp2 )-C(aryl) bond has a strong influence on the solution-phase NMR spectra. The amide connection has minimal effect on the photophysical properties.
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