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2,3,4,5-Tetrahydro-1,3,3-trimethyldipyrrin (1) is a crucial building block in the rational synthesis of chlorins and oxochlorins. The prior five-step synthesis of 1 from pyrrole-2-carboxaldehyde (2) employed relatively simple and well-known reactions yet suffered from several drawbacks, including limited scale (≤0.5 g of 1 per run). A streamlined preparation of 1 has been developed that entails four steps:  (i) nitro-aldol condensation of 2 and nitromethane under neat conditions to give 2-(2-nitrovinyl)pyrrole (3), (ii) reduction of 3 with NaBH4 to give 2-(2-nitroethyl)pyrrole (4), (iii) Michael addition of 4 with mesityl oxide under neat conditions or at high concentration to give γ-nitrohexanone-pyrrole 5, and (iv) reductive cyclization of 5 with zinc/ammonium formate to give 1. Several multistep transformations have been established, including the direct conversion of 2 → 1. The advantages of the new procedures include (1) fewer steps, (2) avoidance of several problematic reagents, (3) diminished consumption of solvents and reagents, (4) lessened reliance on chromatography, and (5) scalability. The new procedures facilitate the preparation of 1 at the multigram scale.

Thermal treatment of ethynyl porphyrin monomers on a surface has been found to yield robust porphyrin films. The scope of this in situ polymerization has been surveyed by the synthesis and characterization of a collection of 20 zinc porphyrins bearing diverse patterns of 1−4 ethyne (or protected ethyne) groups and a variety of nonlinking substituents. Films have been prepared on Si(100), SiO2, Au(111), and glass. The films prepared on Si(100) have been examined by electrochemical methods, which indicate that surface coverages 50-fold greater than those of saturation-coverage monolayers are achievable, although the coverage varies appreciably (10-fold) among the survey group of molecules under a controlled set of film-forming conditions. Variation in these conditions affords control over the number of layers in the film (from a few to tens or more). The electrochemical characteristics of the multilayer films further indicate that the redox thermodynamics are of comparable homogeneity to those of monolayers. Examination of the films by FTIR and resonance Raman spectroscopy indicates the absence of an ethynyl or ethenyl linkage between the porphyrins. SEM analysis indicates the porphyrin polymer films range in thickness from tens to hundreds of nanometers. The in situ polymerization technique not only enables control over the thickness of the porphyrin polymer film but also sidesteps solubility problems that typically result upon solution polymerization. The ability to access the porphyrins in the films electrochemically to form porphyrin cation radicals affords increased surface charge density versus that with a monolayer, suggesting the application of the porphyrin films as materials for electrically addressable, molecular-based information storage.

A one-flask synthesis of meso-substituted dipyrromethanes has been refined. The procedure entails reaction of an aldehyde in 100 equiv of pyrrole as the solvent containing a mild Lewis acid (e.g., InCl3) at room temperature. Following removal and recovery of excess pyrrole, the dipyrromethane is obtained by crystallization. The procedure generates minimal waste and does not require aqueous/organic extraction, chromatography, or distillation. The procedure has been scaled linearly to obtain >100 g of 5-phenyldipyrromethane. The utility of various analytical methods for characterizing dipyrromethanes has been investigated.

The redox kinetics for a variety of porphyrin-containing self-assembled monolayers (SAMs) on Au are reported. The measurements probe both the rate of electron-transfer (k⁰) for oxidation (in the presence of applied potential) and the rate of charge dissipation after the applied potential is disconnected (characterized by a charge-retention half-life (t1/2)). The porphyrins include (1) monomeric Zn complexes that contain phenylmethylene linkers wherein the number of methylene spacers varies from 0 to 3, (2) monomeric Zn complexes that contain different ethynylphenyl-derived linkers, and (3) a triple-decker lanthanide sandwich complex with a phenylethynylphenyl linker. The k⁰ values for all the porphyrin SAMs are in the range of 10⁴−10⁵ s^-1. The k⁰ values for the monomeric ethynylphenyl-linked porphyrin SAMs are generally faster than those for the monomeric phenylmethylene-linked SAMs. The rates for the latter SAMs decrease as the number of methylene spacers increases. The rates for the triple-decker SAM are generally slower than those for the monomers. The trends observed in the k⁰ values are paralleled in the t1/2 values, that is, porphyrin SAMs that exhibit relatively faster electron-transfer rates also exhibit faster charge-dissipation rates (shorter t1/2 values). However, the charge-dissipation rates (no applied potential) are approximately 6 orders of magnitude slower than the electron-transfer rates (applied potential). Both the k⁰ and t1/2 values for the porphyrin SAMs are sensitive to the surface coverage of the molecules. The rates for both processes decrease as the monolayers become more densely packed. This behavior is attributed to exclusion of solvent/counterions and space-charge effects. The effect of surface coverage on rates can overshadow differences that result from differences in linker type/length. Collectively, the studies help to delineate the molecular design features that could be manipulated to control the redox processes in porphyrin SAMs. The understanding of these processes is essential for the successful implementation of molecules as the active media in information-storage elements.

Self-assembled monolayers (SAMs) of thiol-derivatized alkyl ferrocenes and Zn tetraarylporphyrins on a gold surface have been characterized under open circuit conditions using fluorescence imaging microscopy and a variety of electrochemical methods. The fluorescence of the neutral form of the Zn tetraarylporphyrin SAM and the electrode cell potential are monitored simultaneously after oxidation of the SAM and subsequent establishment of an open circuit condition. These experiments capitalize on the fact that the neutral Zn tetraarylporphyrin SAM is fluorescent whereas emission from the oxidized Zn tetraarylporphyrin SAM is quenched. Accordingly, the fluorescence recovery after disconnection from an oxidizing potential provides an independent measure of the change in oxidation state of the porphyrin SAM as a function of time after the cell is open-circuited. This measurement demonstrates that the porphyrin SAM remains oxidized for an extended period (hundreds of seconds) even though the electrochemical cell potential decays rapidly to the open circuit potential (OCP). Cyclic voltammetry was used to confirm the electrochemical properties of the redox SAMs and to determine the surface coverage of the redox-active molecules. A new method, designated open circuit potential amperometry, was used to read the charge of the oxidized SAM at the OCP after charging currents have decayed away. Additionally, open circuit potential voltammetry yields a sigmoidal response with a characteristic half-wave potential identical to that observed with cyclic voltammetry, indicative of a Nernstian process. Collectively, these studies show that the electrochemical cell discharges to the OCP quickly, that the SAM remains oxidized under these conditions, and that these methods can be used to quantitatively determine the amount of stored charge in the SAM.

A highly efficient functional mimic of a photosynthetic antenna−reaction center complex has been designed, synthesized, and studied spectroscopically. The antenna, consisting of four covalently linked zinc tetraarylporphyrins, (PZP)3−PZC, has been coupled to a free-base porphyrin−fullerene artificial photosynthetic reaction center, P−C60, to form a (PZP)3−PZC−P−C60 hexad. As revealed by time-resolved absorption and emission studies in 2-methyltetrahydrofuran solution at ambient temperature, excitation of a peripheral zinc porphyrin moiety is followed by singlet−singlet energy transfer to the central zinc porphyrin to give (PZP)3−¹PZC−P−C60 with a time constant of 50 ps. The excitation is passed on to the free-base porphyrin in 32 ps to produce (PZP)3−PZC−¹P−C60, which decays by electron transfer to the fullerene with a time constant of 25 ps. The resulting (PZP)3−PZC−P^•+−C60^•- charge-separated state is generated with a quantum yield of 0.98 based on light absorbed by the porphyrin antenna. Direct excitation of the free-base porphyrin moiety or the fullerene also generates this state with a yield near unity. Thermodynamically favorable migration of positive charge into the zinc porphyrin array transforms the initial state into a long-lived ((PZP)3−PZC)^•+−P−C60^•- charge-separated state with a time constant of 380 ps. The final charge-separated state, formed in high yield (~0.90), decays to the ground state with a lifetime of 240 ns. In benzonitrile, the lifetime is 25 μs. A previous hexad, which differs from the current hexad solely in the nature of the free-base porphyrin, gave a charge-separated state with a lower yield (0.69) and a shorter lifetime (1.3 ns). The difference in performance is attributed to differences in electronic composition (a2u versus a1u HOMO), conformation, and oxidation potential (1.05 versus 0.84 V) between the meso-tetraarylporphyrin and the β-octaalkylporphyrin of the current and former hexads, respectively. These results can be explained on the basis of an understanding of factors that affect through-bond energy-transfer and electron-transfer processes. The results demonstrate that it is possible to design and prepare synthetic, porphyrin-based antenna−reaction center complexes that mimic the basic photochemical functions of natural photosynthetic light-harvesting antennas and reaction centers in simple, structurally well-defined constructs.

Understanding electronic communication among the constituents in multicomponent macromolecular architectures is essential for the rational design of molecular devices for photonic, electronic, or optoelectronic applications. This Account describes studies aimed at understanding the mechanisms of electronic communication in porphyrin-based architectures that undergo excited-state energy migration and ground-state hole/electron hopping. Porphyrins are ideal building blocks for such constructs owing to their attractive and versatile physical properties and amenability to synthetic control. These properties have permitted the creation of covalently linked multiporphyrin arrays wherein the rates of excited-state energy migration and ground-state hole/electron hopping can be tuned over a wide range.

The photophysical properties of two perylene−porphyrin dyads have been examined in detail with the aim of expanding the functional utility of these constructs for molecular optoelectronics applications. The dyads consist of a perylene-bis(imide) dye (PDI) connected to either a magnesium porphyrin (Mg) or a free base porphyrin (Fb) via a diphenylethyne (pep) linker. The photophysical behavior of these two dyads show both similarities and differences to one another and to the dyad containing a zinc porphyrin (Zn) that was examined in the previous paper in this series. In the case of both PDI−pep−Fb and PDI−pep−Mg in toluene, the excited perylene unit (PDI*) decays rapidly (Fb = 2.9 ps; Mg = 2.5 ps) by energy transfer to the porphyrin forming PDI−pep−Por* in relatively high yield (Fb ~ 85%; Mg ~ 50%) and hole transfer to the porphyrin forming PDI^-−pep−Por⁺ (Fb ~ 15%; Mg ~ 50%). This behavior parallels that observed for PDI−pep−Zn, for which rapid (2.5 ps) decay of PDI* affords PDI−pep−Zn* and PDI^-−pep−Por⁺ with yields of 80% and 20%, respectively. The subsequent behavior of the Fb-containing dyad is distinctly different in two ways from that of the Zn or Mg porphyrin-containing dyads. (1) Charge recombination within PDI^-−pep−Fb⁺ primarily forms PDI−pep−Fb*, thereby complementing the formation of the latter species from PDI*−pep−Fb. (2) PDI−pep−Fb* subsequently decays to the ground state via fluorescence emission with a rate and yield that are nearly identical to those of an isolated Fb porphyrin. In contrast, for both PDI−pep−Mg and PDI−pep−Zn, the predominant decay process for PDI−pep−Por* is electron-transfer yielding PDI^-−pep−Por⁺ (Zn ~ 80%; Mg >99%). The rapid electron-transfer quenching of PDI−pep−Por* and the nonemissive character of PDI^-−pep−Por⁺ leads to negligible fluorescence from the two metalloporphyrin-containing dyads after photoexcitation. The PDI^-−pep−Por⁺ charge-separated product with Por = Mg or Zn is very long-lived (>10 ns) in toluene but decays much more rapidly (<0.5 ns) in acetonitrile. The differences in the rates of the various charge-transfer and charge-recombination processes of all of the dyads are consistent with a rate versus free-energy-gap profile (based on the relative redox potentials of the porphyrin constituents) that is in qualitative accord with electron-transfer theory. Collectively, the studies reported in this and the previous paper indicate that PDI−pep−Fb has the greatest potential utility in photonics applications wherein light harvesting by an accessory pigment, energy transport to an output chromophore, and emission (or energy transfer to another chromophore) are desired. On the other hand, PDI−pep−Mg (like PDI−pep−Zn) would be most useful as an all-optical gating element in which excited-state energy in an appended chromophore chain can be quenched by the charge-separated state of the perylene-porphyrin dyad, thereby shunting the light output or flow of energy.

The photophysical properties of a perylene−porphyrin dyad have been examined with the aim of using this construct for molecular photonics applications. The dyad consists of a perylene-bis(imide) dye (PDI) connected to a zinc porphyrin (Zn) via a diphenylethyne linker (pep). In both polar and nonpolar solvents, the photoexcited perylene unit (PDI*) decays very rapidly (lifetimes of 2.5 (toluene) and 2.4 ps (acetonitrile)) by energy transfer to the porphyrin, forming PDI−pep−Zn* in high yield (80%, toluene; 70% acetonitrile), and hole transfer to the porphyrin, forming PDI^-−pep−Zn⁺ in lesser yield (20%, toluene; 30% acetonitrile). In both toluene and acetonitrile, the Zn* excited state subsequently decays with a lifetime of 0.4 ns primarily (80%) by electron transfer to the perylene (forming PDI^-−pep−Zn⁺). In the nonpolar solvent (toluene), the PDI^-−pep−Zn⁺ charge-transfer product has a lifetime of >10 ns and decays by charge recombination primarily to the ground state but also by thermal repopulation of the Zn* excited state. The occurrence of the latter process provides a direct experimental measure of the energy of the charge-separated state. In the polar solvent (acetonitrile), the PDI^-−pep−Zn⁺ charge-separated state decays much more rapidly (<0.5 ns) and exclusively to the ground state. In general, the complementary perylene and porphyrin absorption properties together with very fast and efficient PDI*−pep−Zn → PDI−pep−Zn* energy transfer suggest that perylenes have significant potential as accessory pigments in porphyrin-based arrays for light-harvesting and energy-transport applications. Furthermore, the finding of fast energy transfer initiated in PDI*, charge-transfer reactions that can be elicited either in PDI* or Zn*, and a charge-separated state (PDI^-−pep−Zn⁺) that can be long- or short-lived depending on solvent polarity, indicates the versatility of the perylene−porphyrin motif for a variety of applications in molecular photonics.

We have investigated electrochemical switching of excited-state electronic energy migration in two optoelectronic gates with different architectures. Each gate consists of diarylethyne-linked subunits:  a boron-dipyrrin (BDPY) input unit, a Zn-porphyrin transmission unit, a free-base-porphyrin (Fb-porphyrin) output unit, and a Mg-porphyrin redox-switched site connected either to the Fb porphyrin (linear gate) or to the Zn porphyrin (branched, T gate). Both the linear and branched architectures show Fb-porphyrin emission when the Mg porphyrin is neutral and nearly complete quenching when the Mg porphyrin is oxidized to the π-cation radical. To determine the mechanism of gating, we undertook a systematic photophysical study of the gates and their dyad and triad components in neutral and oxidized forms, using static and time-resolved optical spectroscopy. Two types of photoinduced energy-transfer (and/or charge-transfer) processes are involved in gate operation:  transfer between adjacent subunits and transfer between nonadjacent subunits. All of the individual energy-transfer steps that funnel input light energy to the fluorescent output element in the neutral systems are highly efficient, occurring primarily by a through-bond mechanism. Similarly efficient energy-transfer processes occur between the BDPY and the Zn and Fb porphyrins in the oxidized systems, but are followed by rapid and efficient energy/charge transfer to the redox-switched site and consequent nonradiative deactivation. Energy/charge transfer between nonadjacent porphyrins, which occurs principally by superexchange, is crucial to the operation of the T gate. Collectively, our studies elucidate the photophysics of gating and afford great flexibility and control in the design of more elaborate arrays for molecular photonics applications.

Two porphyrin-based optoelectronic gates and several prototypical redox-switching components of gates have been synthesized for studies in molecular photonics. Linear and T-shaped molecular optoelectronic gates contain a boron-dipyrrin (BDPY) dye as the input unit, a zinc (Zn) porphyrin as the transmission unit, a free base (Fb) porphyrin as the output unit, and a magnesium (Mg) porphyrin as the redox-switching unit. The linear gate and T gate were synthesized using a molecular building block approach. In the linear gate synthesis, a BDPY−Zn porphyrin dyad was coupled with a Fb porphyrin−Mg porphyrin dimer. The synthesis of the T gate utilized a Zn porphyrin bearing four different meso substituents:  mesityl, 4-iodophenyl, 4-[2-(trimethylsilyl)ethynyl]phenyl, and 4-[2-triisopropyl)ethynyl]phenyl. Attachment of the three different groups to the Zn porphyrin was accomplished using successive Pd-mediated coupling reactions in the following sequence:  Fb porphyrin (output unit), BDPY dye (input unit), and Mg porphyrin (redox-switching unit). Both the linear gate and T gate syntheses introduce the Mg porphyrin at the final step to minimize demetalation of the Mg porphyrin. Refinements to various components of these gates were investigated through the preparation of a ferrocene−porphyrin, a ferrocene−phthalocyanine, and a ferrocene−porphyrin−phthalocyanine. A dyad motif for studies of optically based redox switching was prepared that contains a derivative of Ru(bpy)3X2 coupled to a porphyrin. From these and related studies have emerged a number of design considerations for the development of refined optoelectronic gates.

A shape-persistent cyclic array of six zinc porphyrins provides an effective host for a dipyridyl-substituted free base porphyrin, yielding a self-assembled structure for studies of light harvesting. Energy transfer occurs essentially quantitatively from uncoordinated to pyridyl-coordinated zinc porphyrins in the cyclic array. Energy transfer from the coordinated zinc porphyrin to the guest free base porphyrin is less efficient (Φtrans ~40%) and is attributed to a Förster through-space process.

Diverse Lewis acids and Brønsted acids were examined in the two-step, one-flask synthesis of meso-tetraphenylporphyrin, N-confused tetraphenylporphyrin, and tetraphenylsapphyrin. The scope of acid catalysis was found to be very broad, with 35 of 45 acids providing TPP in yields ranging from 5% to 58%. NC-TPP was also widely observed in yields of 1−40%, and TPS was infrequently observed in yields of <1%. Additionally, conditions were found for direct preparation of magnesium TPP and copper TPP.

N-Confused meso-substituted porphyrin is a porphyrin isomer previously available from one-flask porphyrin syntheses as a low-yield byproduct (<7.5%). We have found that methanesulfonic acid catalyzed condensation of pyrrole and benzaldehyde followed by DDQ oxidation provides N-confused tetraphenylporphyrin (NC-TPP) in up to 39% yield in analytical scale experiments. Preparative synthesis provided an isolated yield of 35% (800 mg). This represents a >5-fold yield improvement and makes significant quantities of NC-TPP readily available.

The synthesis of diarylethyne-linked multiporphyrin arrays requires Pd-mediated coupling conditions that are performed in dilute solution in the absence of copper and that give reaction mixtures that are easily purified. We previously developed copper-free Pd-mediated coupling conditions (Pd2(dba)3 and AsPh3 in toluene/triethylamine (5:1) at 35 °C) but extensive chromatography was required to remove unidentified porphyrinic byproducts. We have used laser-desorption mass spectrometry (LD-MS) and analytical size-exclusion chromatography (SEC) to assay the products from the coupling reaction of a zinc(II) iodophenylporphyrin (ZnI) and a zinc(II) ethynylphenylporphyrin (ZnU‘). Analysis of the crude reaction mixture revealed the diphenylethyne-linked dimer (Zn2U) as the major product, byproducts plausibly derived from phenyl−aryl exchange processes (a phenylated derivative of ZnU‘, a Ph2As-substituted derivative of ZnI), byproducts believed to originate from direct phenylation processes (a phenylated derivative of ZnI, the phenylated dimer Ph-Zn2U), and higher molecular weight material (HMWM) comprised of undefined porphyrin oligomers. The HMWM is readily removed but the phenylated dimer causes severe purification problems. Our observations concerning the phenylation processes are as follows:  (1) The phenylated dimer was observed in significant quantity (~7:1 ratio of Zn2U/Ph-Zn2U by LD-MS). (2) Control experiments showed that direct phenylation of free base (Fb) porphyrins or zinc porphyrins occurred with Pd2(dba)3 and AsPh3 in the absence of iodo- or ethynylporphyrins. (3) Phenylation occurred at the earliest stage of the reaction (3 min time point). (4) The inclusion of CuI (with Pd2(dba)3 and PPh3) accelerated formation of Zn2U but did not reduce the amount of phenylation. (5) The use of P(o-tol)3 in conjunction with Pd2(dba)3 caused slower reaction, a slight increase in HMWM, and significantly diminished arylation (Zn2U/Ar-Zn2U ratio ~65:1). (6) Replacement of Pd2(dba)3 with Pd(OAc)2 gave the same arylation ratio (65:1) but slightly lower yield. Application of the refined conditions (Pd2(dba)3 and P(o-tol)3 in toluene/triethylamine (5:1) at 35 °C) to the stepwise synthesis of porphyrin trimers having metalation states of Zn and Fb (ZnZnFbU) or Mg, Zn, and Fb (MgZnFbU) afforded coupling efficiencies of 45−55% and a substantially simpler chromatographic purification process.

Prior manual work has shown that the condensation of mesitaldehyde and pyrrole leading to tetramesitylporphyrin depends sensitively on concentration and requires cocatalysis involving BF3·O(Et)2 and ethanol or other protic species. We have applied an automated microscale chemistry workstation capable of parallel or adaptive experimentation to systematically investigate these cocatalysis conditions. Examination of experimental grids spanning a 1000-fold range of the concentrations of BF3·O(Et)2 and ethanol identified the best cocatalysis conditions for various mesitaldehyde and pyrrole concentrations. As the reaction concentration increased from 10 to 200 mM, the optimal yields were achieved with a parallel increase in BF3·O(Et)2 concentration (from 3.3 to 56 mM), but the amount of ethanol remained relatively constant. Catalysis conditions were identified that afforded ~30% yields for reactants in the range of 10−73 mM, thereby enabling the reaction to be performed at increased concentration without loss in yield. Application of a catalyst searching protocol identified ethylene glycol, 2-methoxyethanol, and methanol as effective cocatalysts from a set of 12 candidates. Collectively, these results show the utility of an automated chemistry workstation in acquiring a comprehensive set of data concerning the scope of cocatalysis in the reaction of mesitaldehyde and pyrrole.

The ground- and excited-state properties of a series of p-phenylene-linked porphyrin dimers have been examined using a variety of static and time-resolved spectroscopic techniques. The dimers consist of a zinc porphyrin and a free base (Fb) porphyrin (ZnFbΦ), two zinc porphyrins (Zn2Φ), or two Fb porphyrins (Fb2Φ). In each array, the porphyrins are joined by the p-phenylene linker at one meso position, with the nonlinking meso positions bearing mesityl groups. Three analogous dimers in which the mesityl groups are replaced with pentafluorophenyl groups (F30ZnFbΦ, F30Zn2Φ, and F30Fb2Φ) were also synthesized and characterized. The excited-state energy-transfer rate from the photoexcited Zn porphyrin to the Fb porphyrin is (3.5 ps)^-1 for ZnFbΦ and (10 ps)^-1 for F30ZnFbΦ. The quantum yields of excited-state energy transfer are ≥99% for both complexes. The energy-transfer rates in the p-phenylene-linked dimers are considerably faster than those observed for the analogous dimers containing a diphenylethyne linker ((24 ps)^-1, ZnFbU; (240 ps)^-1, F30ZnFbU). At these distances, both through bond and through space contributions to the electronic coupling are important. The faster energy-transfer rates in the p-phenylene- versus diarylethyne-linked dimers are attributed to enhanced electronic coupling between the porphyrins in the former dimers arising primarily from the shorter inter-porphyrin separation. The electronic coupling in the p-phenylene-linked dimers is sufficient to support ultrafast energy transfer in both ZnFbΦ and F30ZnFbΦ, but is not so large as to significantly perturb the redox or inherent lowest excited-state photophysical properties of the porphyrin constituents. Electronic perturbations resulting from fluorination have little effect on the energy-transfer rates in the p-phenylene-linked dimers, but the rates of room-temperature ground-state hole/electron hopping processes in the corresponding monocation radicals of the bis-Zn analogues of the p-phenylene-linked dimers (≥(0.05 μs)^-1, [Zn2Φ]⁺; ≤(2.5 μs)^-1, [F30Zn2Φ]⁺) are significantly influenced by the fluorination-induced changes in the electronic structure. Collectively, these characteristics make these constructs attractive candidates for incorporation into extended multi-porphyrin arrays for a variety of molecular photonics applications.

Excited-state energy migration among a collection of pigments forms the basis for natural light-harvesting processes and synthetic molecular photonic devices. The rational design of efficient energy-transfer devices requires the ability to analyze the expected performance characteristics of target molecular architectures comprised of various pigments. Toward that goal, we present a general tool for modeling the kinetics of energy migration in weakly coupled multipigment arrays. A matrix-formulated eigenvalue/eigenvector approach has been implemented, using empirical data from a small set of prototypical molecules, to predict the quantum efficiency (QE) of energy migration in a variety of arrays as a function of rate, competitive processes, and architecture. Trends in the results point to useful design strategies including the following:  (1) The QE for energy transfer to a terminal acceptor upon random excitation within a linear array of isoenergetic pigments decreases rapidly as the length of the array is increased. (2) Increasing the rate of transfer and/or the lifetime of the competitive deactivation processes significantly improves QE. (3) Qualitatively similar results are obtained in simulations of linear molecular photonic wires in which excitation and trapping occur at opposite ends of the array. (4) Branched and cyclic array architectures exhibit higher QEs than linear architectures with equal numbers of pigments. (5) Dramatic improvements in QE are achieved when energy transfer is directed by a progressive downward cascade in excited-state energy. (6) The most effective light-harvesting architectures are those where isolated pools of donors each have independent paths directly to the terminal acceptor. Collectively, these results provide valuable insight into the types of molecular designs that are expected to exhibit high efficiency in overall energy transfer.

The Pem gene encodes an atypical homeodomain protein, distantly related to Prd/Pax family members, that we demonstrate is regulated in a complex transcriptional and post-transcriptional manner. We show that the rat Pem genomic structure includes three 5'-untranslated (5'-UT) exons and four coding exons, three of which encode the homeodomain. Several alternatively spliced transcripts were identified, including one that skips an internal coding exon, enabling this mRNA to express a novel form of the Pem protein. Other alternatively spliced mRNAs were characterized that possess different 5'-UT regions, including a muscle-specific transcript. The different 5'-UT termini present in Pem transcripts conferred different levels of translatability in vitro. Two promoters containing multiple transcription initiation sites were identified: a distal promoter (Pd) in the first 5'-UT exon and a proximal promoter (Pp) located in the "intron" upstream of the first coding exon. The Pd was active in placenta, ovary, tumor cell lines, and to a lesser extent in skeletal muscle. In contrast, transcripts from the Pp were only detectable in testis and epididymis and were only expressed in epididymis in the presence of testosterone. To our knowledge no transcription factors have previously been identified that exhibit androgen-dependent expression in the epididymis.