Atomic force microscopy (AFM) can get chemists pretty close to actually seeing the atoms and bonds of molecules.
Researchers successfully imaged intermolecular hydrogen bonding between (PTCDA) molecules using an inflexible copper oxide AFM tip.
Article Source for detailed approach:
H. Mönig et al., Nat. Nanotechnol. 2018, DOI: 10.1038/s41565-018-0104-4