In this talk I will discuss how we are confronting a pair of disparate design challenges in biocompatible organic materials design through the common lens of atomistic simulation. The first challenge centers on the design of self-organizing peptide-conducting polymer (p-CP) hybrid gels for bioelectronic actuators. To guide our collaborators' efforts to prepare robust p-CP gels, we simulate the assembly of p-CP hybrid polymers constructed from 3,4-ethylenedioxythiophene (EDOT) attached to short oligopeptides by organic linkers. We examine the relative stabilization energies of parallel and anti-parallel beta sheet conformations through hydrogen bonding interactions. A metadynamics strategy is employed to determine how the free energy barrier to disaggregation of the p-CP hybrid depends on the sequence and hydrogen-bonding interactions of the oligopeptide.
The second challenge concerns the development of singlet-oxygen photosensitizers for use in photodynamic cancer therapy. Here, the involvement of electronic excitation, intersystem crossing, and excitation energy transfer necessitates explicit consideration of electronic degrees of freedom. To overcome the computational bottleneck of excited-state molecular dynamics sampling in this complex chemical environment, we introduce a fast, approximate excited-state electronic structure approach better suited to this purpose. Together, these tools allow us to quantify Jablonski diagrams for candidate photosensitizers and to estimate relative singlet-oxygen quantum yields. A common theme of the strategies presented in this work is the practical value of simple extensions to established atomistic simulation tools for delivering insights at greater time and length scales.