Tuning SERS Signal via Substrate Structuring: Valves of Different Diatom Species with Ultrathin Gold Coating.

The discovered light modulation capabilities of diatom silicious valves make them an excellent toolkit for photonic devices and applications. In this work, a reproducible surface-enhanced Raman scattering (SERS) enhancement was achieved with hybrid substrates employing diatom silica valves coated with an ultrathin uniform gold film. Three structurally different hybrid substrates, based on the valves of three dissimilar diatom species, have been compared to elucidate the structural contribution to SERS enhancement. The comparative analysis of obtained results showed that substrates containing cylindrical Aulacoseira sp. valves achieved the highest enhancement, up to 14-fold. Numerical analysis based on the frequency domain finite element method was carried out to supplement the experimental results. Our results demonstrate that diatom valves of different shapes can enhance the SERS signal, offering a toolbox for SERS-based sensors, where the magnitude of the enhancement depends on valve geometry and ultrastructure.

Numerical Analysis of the Light Modulation by the Frustule of Gomphonema parvulum: The Role of Integrated Optical Components.

Siliceous diatom frustules present a huge variety of shapes and nanometric pore patterns. A better understanding of the light modulation by these frustules is required to determine whether or not they might have photobiological roles besides their possible utilization as building blocks in photonic applications. In this study, we propose a novel approach for analyzing the near-field light modulation by small pennate diatom frustules, utilizing the frustule of Gomphonema parvulum as a model. Numerical analysis was carried out for the wave propagation across selected 2D cross-sections in a statistically representative 3D model for the valve based on the finite element frequency domain method. The influences of light wavelength (vacuum wavelengths from 300 to 800 nm) and refractive index changes, as well as structural parameters, on the light modulation were investigated and compared to theoretical predictions when possible. The results showed complex interference patterns resulting from the overlay of different optical phenomena, which can be explained by the presence of a few integrated optical components in the valve. Moreover, studies on the complete frustule in an aqueous medium allow the discussion of its possible photobiological relevance. Furthermore, our results may enable the simple screening of unstudied pennate frustules for photonic applications.

Potential modulations in flatland: near-infrared sensitization of MoS2 phototransistors by a solvatochromic dye directly tethered to sulfur vacancies.

Near-infrared sensitization of monolayer MoS2 is here achieved via the covalent attachment of a novel heteroleptic nickel bis-dithiolene complex into sulfur vacancies in the MoS2 structure. Photocurrent action spectroscopy of the sensitized films reveals a discreet contribution from the sensitizer dye centred around 1300 nm (0.95 eV), well below the bandgap of MoS2 (2.1 eV), corresponding to the excitation of the monoanionic dithiolene complex. A mechanism of conductivity enhancement is proposed based on a photo-induced flattening of the corrugated energy landscape present at sulfur vacancy defect sites within the MoS2 due to a dipole change within the dye molecule upon photoexcitation. This method of sensitization might be readily extended to other functional molecules that can impart a change to the dielectric environment at the MoS2 surface under stimulation, thereby extending the breadth of detector applications for MoS2 and other transition metal dichalcogenides.

Rate-determining process in MISIM photocells for optoelectronic conversion using photo-induced pure polarization current without carrier transfer across interfaces.

Recently, we proposed a [metal|insulator|semiconductor|insulator|metal] (MISIM) photocell, as a novel architecture for high-speed organic photodetectors. The electric polarization in the S layer, induced by modulated light illumination, propagates into the outside circuit as a polarization current through the I layers, without any carrier transfer across the interfaces. In the present work, we examined the MISIM photocells consisting of zinc-phthalocyanine(ZnPc)-C60 bilayers for the S layer and Parylene C for the two I layers, to understand the fundamental aspects of the MISIM photocells, such as current polarity and modulation-frequency dependence. It was found that, in such devices, the current polarity was primarily determined by the polarization in the S layer, which was induced by the donor-acceptor charge-transfer upon illumination. Furthermore, the ON and OFF current, which appeared in the periods of illumination-on and -off, respectively, exhibited significantly different dependence on the modulation frequency. This was well-explained by an imbalance between a quick polarization in the S layer during illumination and its slow relaxation in the dark.

Towards high-bandwidth organic photodetection based on pure active layer polarization.

Organic photodetectors offer distinct advantages over their inorganic analogues, most notably through optical transparency and flexibility, yet their figures-of-merit still lag behind those of inorganic devices, and optimization strategies generally encounter a trade-off between device responsivity and bandwidth. Here we propose a novel photodetector architecture in which an organic photoactive semiconductor layer (S) is sandwiched between two thick insulating layers (I) that separate the semiconductor from the metallic contacts (M). In this architecture a differential photocurrent response is generated purely from the polarization of the active layer under illumination. Especially for an asymmetric MISIM design, where one insulating layer is a high-k ionic liquid IIL and the other a low-k polymer dielectric Ip, the responsivity/bandwidth trade-off is broken, since the role of the IIL in efficient charge separation is maintained, while the total device capacitance is reduced according to Ip. Thus the benefits of single insulating layer differential photodetectors (MISM) using either IIL or Ip are combined in a single device. Further improvements in device performance are also demonstrated by decreasing the series resistance of the photoactive layer through semiconductor:metal blending and by operation under strong background light.

Molecular and thin film properties of cobalt half-sandwich compounds for optoelectronic application.

The structure and electronic properties of a novel cobalt half sandwich complex of cyclopentadiene (Cp) and diaminonaphthalene (DAnap) [CpCo(DAnap)] are described and compared to the previously reported diaminobenzene derivative [CpCo(DAbnz)] in view of their potential for (opto)electronic device application. Both complexes show stable redox processes, tunable through the diaminoacene ligand, and show strong absorption in the visible region, with additional transitions stretching into the near infrared (NIR). CpCo(DAnap) crystallises with a particularly large unit cell (9301 Å3), comprising 32 molecules, with a gradual rotation over 8 molecules along the long c-axis. In the solid state the balance of the optical transitions in both complexes is reversed, with a suppression of the visible band and an enhancement of the NIR band, attributed to extensive intermolecular electronic interaction. In the case of CpCo(DAnap), highly crystalline thin films could be formed under physical vapor deposition, which show a photocurrent response stretching into the NIR, and p-type semiconductor behavior in field effect transistors with mobility values of the order 1 × 10-4 cm2 V-1 s-1. The device performance is understood through investigation of the morphology of the grown films.

Structural and functional roles of the N- and C-terminal extended modules in channelrhodopsin-1.

Channelrhodopsins have become a focus of interest because of their ability to control neural activity by light, used in a technology called optogenetics. The channelrhodopsin in the eukaryote Chlamydomonas reinhardtii (CrChR-1) is a light-gated cation channel responsible for motility changes upon photo-illumination and a member of the membrane-embedded retinal protein family. Recent crystal structure analysis revealed that CrChR-1 has unique extended modules both at its N- and C-termini compared to other microbial retinal proteins. This study reports the first successful expression of a ChR-1 variant in Escherichia coli as a holoprotein: the ChR-1 variant lacking both the N- and C-termini (CrChR-1_82-308). However, compared to ChR-1 having the extended modules (CrChR-1_1-357), truncation of the termini greatly altered the absorption maximum and photochemical properties, including the pKa values of its charged residues around the chromophore, the reaction rates in the photocycle and the photo-induced ion channeling activity. The results of some experiments regarding ion transport activity suggest that CrChR-1_82-308 has a proton channeling activity even in the dark. On the basis of these results, we discuss the structural and functional roles of the N- and C-terminal extended modules in CrChR-1.

Factors affecting the stability and performance of ionic liquid-based planar transient photodetectors.

A novel planar architecture has been developed for the study of photodetectors utilizing the transient photocurrent response induced by a metal/insulator/semiconductor/metal (MISM) structured device, where the insulator is an ionic liquid (IL-MISM). Using vanadyl 2,3-naphthalocyanine, which absorbs in the communications-relevant near-infrared wavelength region (λ(max,film) ≈ 850 nm), in conjunction with C60 as a bulk heterojunction, the high capacitance of the formed electric double layers at the ionic liquid interfaces yields high charge separation efficiency within the semiconductor layer, and the minimal potential drop in the bulk ionic liquid allows the electrodes to be offset by distances of over 7 mm. Furthermore, the decrease in operational speed with increased electrode separation is beneficial for a clear modeling of the waveform of the photocurrent signal, free from the influence of measurement circuitry. Despite the use of a molecular semiconductor as the active layer in conjunction with a liquid insulating layer, devices with a stability of several days could be achieved, and the operational stability of such devices was shown to be dependent solely on the solubility of the active layer in the ionic liquid, even under atmospheric conditions. Furthermore, the greatly simplified device construction process, which does not rely on transparent electrode materials or direct electrode deposition, provides a highly reproducible platform for the study of the electronic processes within IL-MISM detectors that is largely free from architectural constraints.

A blue-shifted light-driven proton pump for neural silencing.

Ion-transporting rhodopsins are widely utilized as optogenetic tools both for light-induced neural activation and silencing. The most studied representative is Bacteriorhodopsin (BR), which absorbs green/red light (∼570 nm) and functions as a proton pump. Upon photoexcitation, BR induces a hyperpolarization across the membrane, which, if incorporated into a nerve cell, results in its neural silencing. In this study, we show that several residues around the retinal chromophore, which are completely conserved among BR homologs from the archaea, are involved in the spectral tuning in a BR homolog (HwBR) and that the combination mutation causes a large spectral blue shift (λmax = 498 nm) while preserving the robust pumping activity. Quantum mechanics/molecular mechanics calculations revealed that, compared with the wild type, the ß-ionone ring of the chromophore in the mutant is rotated ∼130° because of the lack of steric hindrance between the methyl groups of the retinal and the mutated residues, resulting in the breakage of the π conjugation system on the polyene chain of the retinal. By the same mutations, similar spectral blue shifts are also observed in another BR homolog, archearhodopsin-3 (also called Arch). The color variant of archearhodopsin-3 could be successfully expressed in the neural cells of Caenorhabditis elegans, and illumination with blue light (500 nm) led to the effective locomotory paralysis of the worms. Thus, we successfully produced a blue-shifted proton pump for neural silencing.

Large spectral change due to amide modes of a ß-sheet upon the formation of an early photointermediate of middle rhodopsin.

Rhodopsin contains retinal as the chromophore within seven transmembrane helices. Recently, we found a unique rhodopsin (middle rhodopsin, MR), which is evolutionarily located between the well-studied bacteriorhodopsin and sensory rhodopsin II, and which accommodates three retinal isomers in its ground state (the all-trans, the 13-cis, and, uniquely, the 11-cis isomers). In this study, we investigated structural changes of both the protein moiety and the retinal chromophore during photocycles of MR by time-resolved Fourier-transform infrared spectroscopy. Three photointermediates with decay time constants of 95 µs, 0.9 ms, and >~10 ms were identified by the global exponential fitting analysis. The first and third intermediates were attributed to the all-trans photocycle, in accordance with recently published results, whereas the second intermediate was likely one that was spectroscopically silent in the visible region and that was formed between the first and third states or resulted from the activation of the 13-cis isomer. By comparing light-induced difference spectra with various isotope labels in either the retinal or the protein moiety, we concluded that a ß-sheet structure in the hydrophilic part was significantly altered during the all-trans photocycle of MR, which may involve an active state of the protein. This feature is characteristic of MR among microbial (type-1) rhodopsins.

Influence of halide binding on the hydrogen bonding network in the active site of Salinibacter sensory rhodopsin I.

In nature, organisms are subjected to a variety of environmental stimuli to which they respond and adapt. They can show avoidance or attractive behaviors away from or toward such stimuli in order to survive in the various environments in which they live. One such stimuli is light, to which, for example, the receptor sensory rhodopsin I (SRI) has been found to respond by regulating both negative and positive phototaxis in, e.g., the archaeon Halobacterium salinarum. Interestingly, to date, all organisms having SRI-like proteins live in highly halophilic environments, suggesting that salt significantly influences the properties of SRIs. Taking advantage of the discovery of the highly stable SRI homologue from Salinibacter ruber (SrSRI), which maintains its color even in the absence of salt, the importance of the chloride ion for the color tuning and for the slow M-decay, which is thought to be essential for the phototaxis function of SRIs, has been reported previously [Suzuki, D., et al. (2009) J. Mol. Biol.392, 48-62]. Here the effects of the anion binding on the structure and structural changes of SRI during its photocycle are investigated by means of Fourier transform infrared (FTIR) spectroscopy and electrochemical experiments. Our results reveal that, among other things, the structural change and proton movement of a characteristic amino acid residue, Asp102 in SrSRI, is suppressed by the binding of an anion in its vicinity, both in the K- and M-intermediate. The presence of this anion also effects the extent of chromophore distrotion, and tentative results indicate an influence on the number and/or properties of internal water molecules. In addition, a photoinduced proton transfer could only be observed in the absence of the bound anion. Possible proton movement pathways, including the residues Asp102 and the putative Cl binding site His131, are discussed. In conclusion, the results show that the anion binding to SRI is not only important for the color tuning, and for controlling the photocycle kinetics, but also induces some structural changes which facilitate the observed properties.

Absorption spectra and photochemical reactions in a unique photoactive protein, middle rhodopsin MR.

Photoactive proteins with cognate chromophores are widespread in organisms, and function as light-energy converters or receptors for light-signal transduction. Rhodopsins, which have retinal (vitamin A aldehyde) as their chromophore within their seven transmembrane α-helices, are classified into two groups, microbial (type-1) and animal (type-2) rhodopsins. In general, light absorption by type-1 or type-2 rhodopsins triggers a trans-cis or cis-trans isomerization of the retinal, respectively, initiating their photochemical reactions. Recently, we found a new microbial rhodopsin (middle rhodopsin, MR), binding three types of retinal isomers in its original state: all-trans, 13-cis, and 11-cis. Here, we identified the absolute absorption spectra of MR by a combination of high performance liquid chromatography (HPLC) and UV-vis spectroscopy under varying light conditions. The absorption maxima of MR with all-trans, 13-cis, or 11-cis retinal are located at 485, 479, and 495 nm, respectively. Their photocycles were analyzed by time-resolved laser spectroscopy using various laser wavelengths. In conclusion, we propose that the photocycles of MR are MR(trans) → MR(K):lifetime = 93 µs → MR(M):lifetime = 12 ms → MR, MR(13-cis) → MR(O-like):lifetime = 5.1 ms → MR, and MR(11-cis) → MR(K-like):lifetime = 8.2 µs → MR, respectively. Thus, we demonstrate that a single photoactive protein drives three independent photochemical reactions.

Structural characteristics around the ß-ionone ring of the retinal chromophore in Salinibacter sensory rhodopsin I.

Organisms sense and respond to environmental stimuli through membrane-embedded receptors and transducers. Sensory rhodopsin I (SRI) and sensory rhodopsin II (SRII) are the photoreceptors for the positive and negative phototaxis in microorganisms, respectively. They form signaling complexes in the membrane with their cognate transducer proteins, HtrI and HtrII, and these SRI-HtrI and SRII-HtrII complexes transmit a light signal through their cytoplasmic sensory signaling system, inducing opposite effects (i.e., the inactivation or activation of the kinase CheA). Here we found, by using Fourier transformed infrared spectroscopy, that a conserved residue, Asp102 in Salinibacter SRI (SrSRI), which is located close to the ß-ionone ring of the retinal chromophore, is deprotonated upon formation of the active M-intermediate. Furthermore, the D102E mutant of SrSRI affects the structure and/or structural changes of Cys130. This mutant shows a large spectral shift and is comparably unstable, especially in the absence of Cl(-). These phenomena have not been observed in the wild-type, or the N105Q and N105D mutants of Natronomonas pharaonis SRII (NpSRII), indicating differences in the structure and structural changes between SrSRI and NpSRII around the ß-ionone ring. These differences could also be supported by the measurements of the reactivity with the water-soluble reagent azide. On the basis of these results, we discuss the structure and structural changes around the retinal chromophore in SrSRI.

Three-dimensional structure and growth of myelins.

After contact with water, surfactant lamellar phases (L(α)) can show spectacular interface instabilities: multibilayer tubules, so-called myelins, grow from the L(α)/water interface into the water. We have studied the shape, size, and growth of myelins in aqueous solutions of the nonionic surfactant C(12)E(3) (triethylene glycol monododecyl ether) during dissolution. We used a combination of different imaging techniques: optical microscopy providing 2-D projections of the sample and confocal microscopy offering a complete 3-D reconstruction. These techniques provide quantitative information on the shape and growth of myelins, such as their width, length, and depth profile as a function of time. The growth rate of myelins, characterized by a swelling or diffusion coefficient, was found to increase with surfactant mass fraction and, seemingly, with sample thickness. We demonstrate that myelin creaming due to buoyancy can explain the apparent dependence on sample thickness. Our experiments furthermore suggest that myelin growth is controlled by an interplay between the water mobility in the lamellar phase and the osmotic pressure difference between the lamellar phase and the contacting water.