Time and length scales of biochemical reactions

The biological length scales per tinent to SwissFEL applications span the spectrum from individual atomic bonds and small molecules, such as glucose, in the subnanometer range, over individual protein molecules (e.g., hemoglobin) and molecular complexes (e.g., ribosomes) in the 1–10 nm range, over virus par ticles and cell organelles (10–100 nm), to entire cells (1 μm) (see Fig. IV.1). As discussed in Chapter III, with hard radiation from the SwissFEL (λ = 0.1 nm), lensless imaging of nanostructures is feasible at sub-nm resolution. As the sampled objects grow larger and more complex, the realistically achievable resolution degrades, to perhaps several tens of nm for micrometer-sized cells. The vibration period of the two carbon atoms in the ethene molecule against their mutual double bond is 20 fs, and such molecular vibrations also set the time scale for photo-dissociation processes, for example for the photo-detachment of CO from a heme group (i.e., an iron atom surrounded by a porphyrin ring). As biomolecular units increase in size, from methyl groups (0.3 nm) to side-chains (1 nm) to loops (4 nm), to large protein domains (8 nm), collective motions with long periods populate the crowded vibrational density of states. Although electron transfer processes can in principle be very fast, their speed is generally limited by that of molecular reconformation. The same is true for decaging processes – the activation of a biomolecule by the photo-removal of a deactivating cage group.