Objective. Biomimetic protein-based artificial retinas offer a new paradigm for restoring vision for patients blinded by retinal degeneration. Artificial retinas, comprised of an ion-permeable membrane and alternating layers of bacteriorhodopsin (BR) and a polycation binder, are assembled using layer-by-layer electrostatic adsorption. Upon light absorption, the oriented BR layers generate a unidirectional proton gradient. The main objective of this investigation is to demonstrate the ability of the ion-mediated subretinal artificial retina to activate retinal ganglion cells (RGCs) of degenerated retinal tissue. Approach. Ex vivo extracellular recording experiments with P23H line 1 rats are used to measure the response of RGCs following selective stimulation of our artificial retina using a pulsed light source. Single-unit recording is used to evaluate the efficiency and latency of activation, while a multielectrode array (MEA) is used to assess the spatial sensitivity of the artificial retina films. Main results. The activation efficiency of the artificial retina increases with increased incident light intensity and demonstrates an activation latency of ∼150 ms. The results suggest that the implant is most efficient with 200 BR layers and can stimulate the retina using light intensities comparable to indoor ambient light. Results from using an MEA show that activation is limited to the targeted receptive field. Significance. The results of this study establish potential effectiveness of using an ion-mediated artificial retina to restore vision for those with degenerative retinal diseases, including retinitis pigmentosa.

This chapter gives an overview of the use of biological molecules in optically coupled molecular electronic devices, with an emphasis on the use of the protein bacteriorhodopsin in optical memories and optical computing devices. It describes the use of this protein in selected applications that include holography, spatial light modulators, neural network optical computing, and volumetric and associative optical memories. There are significant advantages inherent in the use of biological molecules, either in their native form or modified via chemical or mutagenic methods, as active components in optoelectronic devices. Optically coupled devices based on bacteriorhodopsin are driven by linear (one-photon) or nonlinear (two-photon) excitation. A majority of these devices operate by switching between two of the intermediates that populate the complex photocycle of the protein. Two-photon three-dimensional optical addressing architectures offer significant promise for the development of a new generation of ultra-high-density random access memories. The chapter illustrates the optical design of a two-photon three-dimensional optical memory.

The inclusion of inorganic nanoparticles in biological environments has led to the creation of hybrid nanosystems that are employed in a variety of applications. One such system includes quantum dots (QDs) coupled with the photoactive protein, bacteriorhodopsin (BR), which has been explored in developing enhanced photovoltaic devices. In this work, we have discovered that the kinetics of the BR photocycle can be manipulated using CdSe/CdS (core/shell) QDs. The photocycle lifetime of protein samples with varying QD amounts were monitored using time-resolved absorption spectroscopy. Concentration-dependent elongations of the bR and M state lifetimes were observed in the kinetic traces, thus suggesting that excitonic coupling occurs between BR and QDs. We propose that the pairing of BR with QDs has the potential to be utilized in protein-based computing applications, specifically for real-time holographic processors, which depend on the temporal dynamics of the bR and M photointermediates.

This chapter examines some proteins that respond to light can be used as the basis of device architectures, such as optical computer memories and holographic recording media. It focuses on bacteriorhodopsin, a photoactive protein with potential in optical and holographic computer memory architectures, and efforts to modify the protein for this specific goal. The chapter discusses the ability to modify bacteriorhodopsin has proven to be paramount to this protein's usefulness to the applied sciences. Bacteriorhodopsin (BR) occupies a unique place in the history of protein-based applications—it is not only one of the more thoroughly examined proteins with respect to structure and function, it has also been evaluated for a number of device architectures. The regions of the cell membrane that contain bacteriorhodopsin have unique properties, and occur as discrete membrane patches consisting of approximately 75% BR and 25% lipid.

We report supramolecular quantum mechanics/molecular mechanics simulations on the peridinin-chlorophyll a protein (PCP) complex from the causative algal species of red tides. These calculations reproduce for the first time quantitatively the distinct peridinin absorptions, identify multichromophoric molecular excitations, and elucidate the mechanisms regulating the strongly allowed S0 (11Ag-) → S2 (11Bu+) absorptions of the bound peridinins that span a 58 nm spectral range in the region of maximal solar irradiance. We discovered that protein binding site-imposed conformations, local electrostatics, and electronic coupling contribute equally to the spectral inhomogeneity. Electronic coupling causes coherent excitations among the densely packed pigments. Complementary pairing of tuning mechanisms is the result of a competition between pigment-pigment and pigment-environment interactions. We found that the aqueous solvent works in concert with the charge distribution of PCP to produce a strong correlation between peridinin spectral bathochromism and the local dielectric environment.

Theoretical studies have predicted the presence of a forbidden 11Bu- state in proximity to the strongly allowed 11Bu+ excited state in polyenes and carotenoids. The 11Bu- state is invariably predicted to have a very low oscillator strength, which precludes direct optical spectroscopic assignment. We report here a direct UV-vis optical spectroscopic feature assigned to the 11Bu- state of S-2-peridinin, a synthetic analogue of the naturally occurring carotenoid, peridinin. The shift of the ground state dipole of S-2-peridinin compared to natural peridinin enhances the oscillator strength of absorption from the ground state to the 11Bu- state by 2 orders of magnitude relative to peridinin. It is postulated that this is due to a quadrupolar electrostatic field generated from the more central location of the lactone ring along the polyene chain in S-2-peridinin. MNDO-PSDCI and EOM-CCSD calculations provide a theoretical basis for this assignment and explain the unique properties of the 11Bu- state and why the transition from the ground state to this state has such a low oscillator strength in most other polyenes and carotenoids.

RhoGC is a rhodopsin (Rho)-guanylyl cyclase (GC) gene fusion molecule that is central to zoospore phototaxis in the aquatic fungus Blastocladiella emersonii. It has generated considerable excitement because of its demonstrated potential as a tool for optogenetic manipulation of cell-signaling pathways involving cyclic nucleotides. However, a reliable method for expressing and purifying RhoGC is currently lacking. We present here an expression and purification system for isolation of the full-length RhoGC protein expressed in HEK293 cells in detergent solution. The protein exhibits robust light-dependent guanylyl cyclase activity, whereas a truncated form lacking the 17- to 20-kDa N-terminal domain is completely inactive under identical conditions. Moreover, we designed several RhoGC mutants to increase the utility of the protein for optogenetic studies. The first class we generated has altered absorption spectra designed for selective activation by different wavelengths of light. Two mutants were created with blue-shifted (E254D, λmax = 390 nm; D380N, λmax = 506 nm) and one with red-shifted (D380E, λmax = 533 nm) absorption maxima relative to the wild-type protein (λmax = 527 nm). We also engineered a double mutant, E497K/C566D, that changes the enzyme to a specific, light-stimulated adenylyl cyclase that catalyzes the formation of cAMP from ATP. We anticipate that this expression/purification system and these RhoGC mutants will facilitate mechanistic and structural exploration of this important enzyme.

Owing to their intense near infrared absorption and emission properties, to the ability to photogenerate singlet oxygen, or to act as photoacoustic imaging agents within the optical window of tissue, bacteriochlorins (2,3,12,13-tetrahydroporphyrins) promise to be of utility in many biomedical and technical applications. The ability to fine-tune the electronic properties of synthetic bacteriochlorins is important for these purposes. In this vein, we report the synthesis, structure determination, optical properties, and theoretical analysis of the electronic structure of a family of expanded bacteriochlorin analogues. The stepwise expansion of both pyrroline moieties in near-planar meso-tetraarylbacteriochlorins to morpholine moieties yields ruffled mono- and bismorpholinobacteriochlorins with broadened and up to 90 nm bathochromically shifted bacteriochlorin-like optical spectra. Intramolecular ring-closure reactions of the morpholine moiety with the flanking meso-aryl groups leads to a sharpened, blue-shifted wavelength λmax band, bucking the general red-shifting trend expected for such linkages. A conformational origin of the optical modulations was previously proposed, but discrepancies between the solid state conformations and the corresponding solution state optical spectra defy simple structure-optical property correlations. Using density functional theory and excited state methods, we derive the molecular origins of the spectral modulations. About half of the modulation is due to ruffling of the bacteriochlorin chromophore. Surprisingly, the other half originates in the localized twisting of the Cβ-Cα-Cα-Cβ dihedral angle within the morpholine moieties. Our calculations suggest a predictable and large spectral shift (2.0 nm/deg twist) for morpholine deformations within these fairly flexible moieties. This morpholine moiety deformation can take place largely independently from the overall macrocycle conformation. The morpholinobacteriochlorins are thus excellent models for localized bacteriochlorin chromophore deformations that are suggested to also be responsible for the optical modulation of naturally occurring bacteriochlorophylls. We propose the use of morpholinobacteriochlorins as mechanochromic dyes in engineering and materials science applications.

Octadecaoctaenal is a psittacofulvin pigment associated with the bright red coloration of parrots. It consists of a linear polyene chain terminated by an aldehyde group and therefore provides an opportunity to examine the fundamental factors controlling the excited state ordering and dynamics of polyenals. Steady-state and ultrafast time-resolved spectroscopy were performed on octadecaoctaenal and a derivative in which the aldehyde group was converted to a methylenehydroxyl group. It was found that for octadecaoctaenal, solvent proticity was more important than polarity in determining its excited state lifetime. Theoretical computations were carried out to reveal the origin of the effect.

Achieving tunable, intense near-infrared absorption in molecular architectures with properties suitable for solar light harvesting and biomedical studies is of fundamental interest. Herein, we report the photophysical, redox, and molecular-orbital characteristics of nine hydroporphyrin dyads and associated benchmark monomers that have been designed and synthesized to attain enhanced light harvesting. Each dyad contains two identical hydroporphyrins (chlorin or bacteriochlorin) connected by a linker (ethynyl or butadiynyl) at the macrocycle β-pyrrole (3- or 13-) or meso (15-) positions. The strong electronic communication between constituent chromophores is indicated by the doubling of prominent absorption features, split redox waves, and paired linear combinations of frontier molecular orbitals. Relative to the benchmarks, the chlorin dyads in toluene show substantial bathochromic shifts of the long-wavelength absorption band (17-31 nm), modestly reduced singlet excited-state lifetimes (τS = 3.6-6.2 ns vs 8.8-12.3 ns), and increased fluorescence quantum yields (Φf = 0.37-0.57 vs 0.34-0.39). The bacteriochlorin dyads in toluene show significant bathochromic shifts (25-57 nm) and modestly reduced τS (1.6-3.4 ns vs 3.5-5.3 ns) and Φf (0.09-0.19 vs 0.17-0.21) values. The τS and Φf values for the bacteriochlorin dyads are reduced substantially (up to ∼20-fold) in benzonitrile. The quenching is due primarily to the increased S1 → S0 internal conversion that is likely induced by increased contribution of charge-resonance configurations to the S1 excited state in the polar medium. The fundamental insights gained into the physicochemical properties of the strongly coupled hydroporphyrin dyads may aid their utilization in solar-energy conversion and photomedicine.

This paper presents a spectroscopic investigation of deoxyperidinin, a synthetic peridinin analogue in which the carbonyl functional group in peridinin was replaced by a nonconjugated methylene group. Steady-state and ultrafast time-resolved absorption and fluorescence spectroscopic experiments are carried out on deoxyperidinin in n-hexane and acetonitrile at room temperature and in 2-methyltetrahydrofuran at 77 K. The spectra of deoxyperidinin have higher vibronic resolution compared to those of peridinin. The higher resolution is due to a substantial reduction in both molecular conformational disorder and inhomogeneous broadening of the spectra of deoxyperidinin compared to peridinin. Features in the steady-state absorption spectrum of deoxyperidinin that are not evident in the spectrum of peridinin are unambiguously assigned to the forbidden S0 (1(1)Ag(-)) → S1 (2(1)Ag(-)) absorption transition. The characteristics of both the steady-state and time-resolved spectra are interpreted using EOM-CCSD, SAC-CI, and MNDO-PSDCI quantum computational formalisms that provided a theoretical framework for understanding the photophysical properties of the molecules.

The paper presents the concept, layout and simulation results for a combined chemical and optical 92×92 pixel array designed as a 3.18×3.18mm 2 ASIC in standard AMS 0.35μm CMOS technology. The optical pixels employ PN junctions as photodiodes, while the chemical pixels use ISFETs that are pH sensitive with the standard passivation layer of the process. Local light intensity and pH level are encoded using pulse frequency modulation (PFM) and conveyed off-chip using the address event representation (AER) protocol. The chip has been conceived specifically to characterize a light sensitive biomolecular thin film that is in turn intended as a retinal implant for the treatment of end-stage retinal degenerative diseases.

The two-photon absorption and excitation spectra in the Q-band region (900-1360 nm) were measured for a number of porphyrinoids, including simple porphyrins (porphin, meso-tetraphenyl-porphyrin), chlorins (meso-tetraphenyl-2,3-dimethoxychlorin), and porphyrin and chlorin-like analogues (meso-tetraphenyl-porpholactone and meso-tetraphenyl-porpholactol, respectively). These molecules were chosen to provide a series of compounds that differed structurally only in single points. Vibronic structure is observed in the two-photon spectra for all porphyrinoids investigated, but their relative intensities show distinct differences from the vibronic development observed in the corresponding one-photon spectra. A Franck-Condon analysis provides insight into the observed differences. The calculations also indicate that the two-photon absorptivities are associated primarily with Type I processes involving multiple intermediate states, and that accurate assignment requires a summation over at least 30 intermediate states. The Q-bands of the meso-tetraphenyl-2,3-dimethoxychlorin exhibit anomalously high two-photon absorptivities, which we have traced to facile conformational distortion of the chlorin chromophore. Calculations indicated that the relative Q-band absorptivities are sensitive to the phase and magnitude of the chlorin ring distortions.