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The effect of dephasing and relaxation on electron transfer in bridged molecular systems is investigated using a simple molecular model. The interaction between the molecular system and the thermal environment is described on the level of the Redfield theory, modified when needed for the description of steady-state situations. Noting that transient as well as steady-state measurements are possible in such system, we discuss the relationship between the rates obtained from these different types of experiments and, in particular, the conditions under which these rates are the same. Also, a formal relation between the steady-state rate for electron transfer across a molecular bridge and the conductance of this bridge when placed between two metal contacts is established. The effect of dephasing and relaxation on the electron transfer is investigated, and new observations are made with regard to the transition from the superexchange to the thermal (hopping through bridge) regime of the transfer process. In particular, the rate is temperature-independent in the superexchange regime, and its dependence on the bridge length (N) is exponential, exp(-N). The rate behaves like (R 1 + R 2 N) -1 exp(-∆E/k B T) beyond a crossover value of N, where ∆E is the energy gap between the donor/acceptor and the bridge levels, and where R 1 and R 2 are characteristic times for activation onto the bridge and diffusion in the bridge, respectively. We find that, in typical cases, R 1 . R 2 , and therefore, a region of very weak N dependence is expected before the Ohmic behavior, N -1 , is established for large enough N. In addition, a relatively weak exponential dependence, exp(-RN), is expected for long bridges if competing processes capture electrons away from the bridge sites. Finally, we consider ways to distinguish experimentally between the thermal and the tunneling routes.

Temperate phages are common and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses infecting mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity, and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages reveals at least five distinct prophage-expressed viral defense systems that interfere with infection of lytic and temperate phages that are either closely-related (homotypic defense) or unrelated (heterotypic defense). Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defense systems include a single-subunit restriction system, a heterotypic exclusion system, and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival, and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, that acts as a highly effective counter-defense system. Prophage-mediated viral defense offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defense promotes phage co-evolution.

A series of five donor-bridge-acceptor (DBA) molecules in which the donor is tetracene, the acceptor is pyromellitimide, and the bridge molecules are oligo-p-phenylenevinylenes (OPV) of increasing length has been shown to undergo electron transfer (ET) by means of two mechanisms. When the bridge is short, strongly distance dependent superexchange dynamics dominates, whereas when the bridge is longer, bridge-assisted hopping dynamics prevails. The latter mechanism results in relatively soft distance dependence for ET in which the OPV oligomers act effectively as molecular wires. We now report studies on the critical influence that bridge dynamics have on electron transfer through these oligomers. The temperature dependence of the charge separation (CS) rates in all five molecules does not appear to obey the predictions of standard ET theories based upon the Condon approximation. All five molecules show behavior consistent with CS being "gated" by torsional motion between the tetracene donor and the first bridge phenyl ring. This is based on the near equivalence of the CS activation energies measured for all five molecules with the frequency of a known vibrational mode in 5-phenyltetracene. In the molecule containing a trans-stilbene bridge, a competition occurs between the tetracene-phenyl torsional motion and one that occurs between the vinyl group and the phenyls linked to it. This results in complex temperature-dependent CS that exhibits both activated and negatively activated regimes. The charge recombination (CR) reactions within the molecules which have the two shortest bridges, namely phenyl and trans-stilbene, show a weaker dependence on these molecular motions. The three molecules with the longest bridges all display complex temperature dependencies in both their rates of CS and CR, most likely because of the complex torsional motions, which arise from the multiple phenyl-vinyl linkages. The data show that long-distance electron transfer and therefore wire-like behavior within conjugated bridge molecules depend critically on these low-frequency torsional motions. Molecular device designs that utilize such bridges will need to address these issues.

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