Rate constants, timescales, and free energy barriers

Abstract

Abstract The traditional connection between rate constants and free energy landscapes is extended to define effective free energy landscapes relevant on any chosen timescale. Although the Eyring–Polanyi transition state theory specifies a fixed timescale of τ = h / k B T ${\tau =h/k_{\mathrm {B}}T}$ , we introduce instead the timescale of interest for the system in question, e.g. the observation time. The utility of drawing such landscapes using a variety of timescales is illustrated by the example of Holliday junction resolution. The resulting free energy landscapes are easier to interpret, clearly reveal observation time dependent effects like coalescence of short-lived states, and reveal features of interest for the specific system more clearly.