Charge Transfer and Energy Transfer: Methods Development and Applications in Bio-molecular Systems

Abstract

System-environment interactions are essential in determining charge-transfer (CT) rates and mechanisms. We developed a computationally accessiblemethod, suitable to simulate CT in flexible molecules (i.e., DNA) with hundreds ofsites, where the system-environment interactions are explicitly treated with numericalnoise modeling of time-dependent site energies and couplings. The properties of thenoise are tunable, providing us a flexible tool to investigate the detailed effects ofcorrelated thermal fluctuations on CT mechanisms. The noise is parameterizable bymolecular simulation and quantum calculation results of specific molecular systems,giving us better molecular resolution in simulating the system-environment interactions than sampling fluctuations from generic spectral density functions. The spatially correlated thermal fluctuations among different sites are naturally built-in in our method but are hard to be incorporated by approximate spectral densities. Our method has quantitative accuracy in systems with small redox potential differences ($With the method of incorporating spatially and temporally correlated thermal fluctuations into charge transfer process, we study and engineercoherence in guanine-rich DNA sequences.Electronic delocalization in redox-active polymers may be disrupted by the heterogeneity of the environment that surrounds each monomer. When the differences in monomer redox-potential induced by the environment are small (as compared with the monomer-monomer electronic interactions), delocalization persists. Here we show that guanine (G) runs in double-stranded DNA support delocalization over 4-5 guanine bases. The weak interaction between delocalized G blocks on opposite DNA strands is known to support partially coherent long-range charge transport. The molecular-resolution model developed here finds that the coherence among these G blocks follows an even-odd orbital-symmetry rule and predicts that weakening the interaction between G blocks exaggerates the resistance oscillations. These findings indicate how sequence can be exploited to change the balance between coherent and incoherent transport. The predictions are tested and confirmed using break-junction experiments. Thus, tailored orbital symmetry and structural fluctuations may be used to produce coherent transport with a length scale of multiple nanometers in soft-matter assemblies, a length scale comparable to that of small proteins.We extend our charge transport studies from linear molecules to branched molecules.Self-assembling circuitry on the molecular scale demands building blocks with three or more terminals, the sine qua non for circuit elements like current splitters or combiners\cite{Molen2013,RN2,Tao2006}. A promising material for such building blocks is DNA, wherein multiple strands can self-assemble into multi-ended junctions and nucleobase stacks can transport charge over long distances\cite{Genereux2010,Cohen2005,RN6,RN7,RN8,RN9}. However, nucleobase stacking is often disrupted at the junction point, hindering electric charge transport between different terminals of the junction\cite{RN10,RN11}. Thus, the challenge of designing a multi-ended DNA circuit element remains open. Here, we address the challenge by using a guanine-quadruplex (G4) motif as the connector element of a multi-ended DNA junction, and designing the terminal groups of the motif to ensure efficient current splitting in the DNA junction with minimal carrier transport attenuation. We describe the design, assembly, and charge transport measurement\cite{RN46} of a 3-way G4 junction structure, in which charge can enter the structure from one terminal at one end of the G4, and exit from one of two terminals at the other end of the G4. We find that the charge transport characteristics are the same along the two pathways, and are also similar to those of the corresponding linear DNA duplexes. Thus, the G4-based junction indeed enables effective three-way transport, which is a necessary step towards building of DNA-based electrical networks. We optimize G4-based junction structures and interpret the charge-transport measurements with molecular dynamics and quantum chemistry simulations.Energy transfer with an associated spin change of the donor and acceptor, Dexter energy transfer, is critically important in solar energy harvesting assemblies, damage protection schemes of photobiology, and organometallic opto-electronic materials. Dexter transfer between chemically linked donors and acceptors is bridge mediated, presenting an enticing analogy with bridge-mediated electron and hole transfer. However, Dexter coupling pathways must convey both an electron and a hole from donor to acceptor, and this adds considerable richness to the mediation process. We dissect the bridge-mediated Dexter coupling mechanisms and formulate a theory for triplet energy transfer coupling pathways. Virtual donor-acceptor charge-transfer exciton intermediates dominate at shorter distances or higher tunneling energy gaps, whereas virtual intermediates with an electron and a hole both on the bridge (virtual bridge excitons) dominate for longer distances or lower energy gaps. The effects of virtual bridge excitons were neglected in earlier treatments. The two-particle pathway framework developed here shows how Dexter energy-transfer rates depend on donor, bridge, and acceptor energetics, as well as on orbital symmetry and quantum interference among pathways.