Understanding the electronic properties and energy relaxation pathways of semiconductors, is essential for developing next-generation materials for applications in areas as diverse as medicine, flat panel-displays and sensing. In this contribution we apply two-dimensional excitation-emission spectroscopy to interpret energy relaxation pathways in pure and biohybrid zinc oxide (ZnO) micro- and nanostructures of differing morphologies and evaluate the effects of chemical processing and plasmonic doping. In pure ZnO microcrystals with low surface-to-volume ratio, ultraviolet near-band-edge exciton emission dominates relaxation. In contrast, ZnO nanorods, with high surface-to-volume ratio exhibit strong red and near-infrared emission we ascribe to zinc interstitials, oxygen vacancies, and oxygen interstitial defects. Hybrid ZnO structures display a redistribution of energy flow to yield a distinctly different set of red and green emissions stimulated from lower energy states we assign to extended zinc interstitials, oxygen vacancies, and zinc vacancies. Post-synthetic modification preferentially attenuates lower-energy donor states, thereby enhancing higher-energy emission channels. For treatment with polyvinyl alcohol we discuss the role of hydroxyl groups in the restructuring of surface interstitial defects and passivation of negative zinc vacancies, while borohydride treatment can stimulate reduction-driven compensation of positively charged defects and hydrogen ion diffusion. Application of two-dimensional spectral analysis is critically important to avoid ambiguity in evaluation of electronic properties of semiconductors such as zinc oxide and materials with complex networks of energy relaxation pathways.

Ambystoma mexicanum is often used in regeneration studies because it reaches sexual maturity as aquatic larvae within 360 hours, and it can regenerate its appendages. In developing a spectroscopic approach for regeneration studies, in this contribution, we show that Raman confocal microscopy can be used as a diagnostic tool to describe the chemical composition of axolotl embryonal tissues at different stages of development. Experimental observations, supported by quantum chemistry studies on molecules reported or considered to be present in the tissues of the living organism, show that in the early stages of development (Harrison stage 11), there is only limited spatial differentiation of phospholipid, carotenoids and proteins, though, in the later stages of development (Harrison stage 33), differentiation of chemical species is possible and can be related to the development of tissues and organs. In particular, we were able to assess the oxidation state of proteins, their packing and the role of pigments in protection of cellular tissues. We believe the results presented here will be helpful for those involved in planning experiments to combine biochemistry, emission and Raman microscopy to research axolotl tissue regeneration mechanisms.

We develop a quantitative Raman microscopy approach to study erythrocyte biochemistry at the sub-cellular level. To model Raman microscopy images, we review theory of Raman tensors and derive expressions for Raman responses suitable to compute Raman micro-images accounting effects of radial and vertical deformations of cellular envelopes. In application to membrane components, we extend the approach to a "counted per rotation" fast imaging protocol: once having Raman tensors for a molecule, precomputed expressions of molecular distributions can be used to construct Raman images of the modelled membrane envelope and its Raman spectra under any polarisation setting instantly. Using the theory, we review sub-cellular distributions of oxy-, deoxy- and methaemoglobins, as measured in experiment, considering their role in oxygen transport and oxidative stress mechanisms in the cytosol and when next to a membrane. We discuss possible applications of the approach in membrane specific studies, and its potential for combination with phase-sensitive and confocal fluorescence microscopy for advancing health care diagnostics.

We explore the structural and electronic properties of representative insulin-mimetic oxovanadium and zinc complexes as computed in vacuum, in water clusters and upon binding to PTEN and PTP1B phosphatases. Albeit diverse, the enzymes’ active sites represent evolutionary variant choices of the same type of biochemistry. Though different in respect to covalency and the orbital nature of bonding, theory predicts comparable ionic radii, bond lengths and square pyramidal coordination for the considered vanadyl and zinc systems when in an aqueous environment. Employing docking, DFT and quantum mechanics/molecular mechanics methods, we address possible polar interactions in the protein environments and compute infrared/Raman modes and optical electronic properties, which may be suitable for the structural analysis of the specific chemical moieties in binding studies. Accounting for how protein embedding may alter the electronic states of metal centres, we discuss artificial intelligence-assisted protein field engineering to assist biomedical and quantum information applications.

Confocal microscopy using silicaphilic molecular probes is a promising approach to identify the ionic character of silica interfaces. Using ab initio and density functional theory we model structural and electronic properties of the (2-(4-pyridyl)-5(4-(2-dimethyl-aminoethyl-aminocarbamoyl)-methoxy)phenyl)-oxazole (PDMPO) chromophore at different protonation states, in vacuum, and when next to silica of different ionicity. For protonated chromophores next to anionic silica sites, theory suggests strong emission in the visible spectral range from higher excited states and the probability of weaker near infrared fluorescence from a lower energy manifold. Using theory insights, we conduct single- and two-color confocal microscopy in the visible and in the near infrared, respectively, to study open and closed stomata of Equisetum arvense, a heavily silicified primitive plant. Three-dimensional ionic tomography resolves sub-micron neighbouring regions of high and low ionic charges of exo/endo-skeletal silica components according to whether they are open or closed. Considering the variance of methane and carbon dioxide levels prior to, during and after the Silurian, we discuss the observed high ionic contrast of stomatal apertures upon opening as a signature of bioinorganic machinery able to moderate methane and carbon dioxide transport for optimal growth under a range of atmospheric conditions.

Macroscopic scale hollow microcrystals are a promising group of materials for gas and liquid uptake as well as sensing. In this contribution we describe the structure of hollow hexagonal cross-section crystals formulated as salts of a silicon catecholate anion and a tetramethylenediamine (TEMED) cation. Using a combination of X-ray single crystal diffraction, Raman spectroscopy and quantum chemistry we explore the structural properties of the hollow microcrystals. With the X-ray structural data as a starting point and assisted with quantum chemistry we compute Raman tensors to fit polarisation sensitive spectral responses and predict the orientation and packing of unit cells in respect to the long and short axis of the synthesised microcrystals. Using these newly developed methods for predicting molecular Raman responses in space with dependence on local orientation, we present the quantitative analysis of experimental Raman images of both hexagonal and tetragonal cross section hollow microcrystals formed from silicon catecholate anions using different amines as counterions. We describe the distributions of chemical components at the surfaces and edges of microcrystals, address the effect of catcholate hydrophobicity on water uptake and discuss possible strategies in chemical and post-assembly modifications to widen the functional properties of this group of environmentally friendly silicon organic framework (SOF) materials.

A new approach to analyze band‐gap and defect states within semiconductors is reported. Solid state excitation‐emission matrices are used to deconvolve spectral signatures that will be superimposed in 1D spectral space; for example, the 570 nm emission peak in ZnO whose emissive state is of a different physical nature depending on the excitation wavelength used. The broad applicability of the technique is shown for a library of widely studied inorganic semiconductors CdS, CdSe, ZnS, ZnSe, ZnO (analytical standard and nanorods), and TiO 2 . Anthracene is included as a representative example of an organic semiconductor. The developed approach can identify spectral features from the band gap, defects, and trace impurities and provide information on the relative contributions of the different emission pathways. The technique, based on using a plate‐reader conventionally used for the study of biological samples in solution has applicability in both academic and industrial settings for semiconductor studies and quality control applications.

We use Raman microscopy to describe the structure and chemical composition of both conidiophore and hyphae of Botrytis cinerea, a common plant pathogen. To interpret experimental data, we use density functional theory (DFT) to compute Raman tensors specific to an important fungal glycopeptide, a segment of α-chitin, and several naphthalene-based precursors of increasing complexity, which we propose play a role in the melanin synthesis pathway. Using spectral interpretations based on quantum chemical validation, we review microscopy images reconstructed for specific Raman activities and describe differences in distributions of structural components, photo-protective secondary naphthalene-based pigments, and proteins in both spores and hyphal filaments. Comparison of our results with literature data on other fungi suggests an example of convergent evolution expressed at the level of secondary metabolites specific to plant pathogenic fungi. Our results indicate that pre-resonant Raman monitoring of melanin precursors may help assessment of local Botrytis population biology to aid agricultural production.

Complexes of Cu2+(d9) with proline may be considered a simple model to address the structural flexibility and electronic properties of copper metalloproteins. To discuss optical electronic spectra and infrared spectral responses, we use quantum chemistry applied to model systems prepared under different geometries and degree of hydration. A comparison of experimental data with calculations indicates that first explicit neighbor water clustering next to the Cu2+(d9) complex is critical for a correct description of the electronic properties of this system. We deduce that the moderately hydrated trans conformer is the main structural form of the complex in water. Further, we suggest that the antisymmetric stretching mode of the carbonyl moieties of the conformer is dominant in the spectrally broadened infrared resonance at 1605 cm−1, where inhomogeneity of the transition at the blue side can be ascribed to a continuum of less optimal interactions with the solvent. Extracted structural properties and hydration features provide information on the structural flexibility/plasticity specific to Cu2+(d9) systems in correlation with the electronic behavior upon photoexcitation. We discuss the role and the nature of the axial ligand in bio-copper structural ambivalence and reactivity.

The ethanol electro-oxidation catalyzed by Pd in an alkaline environment involves several intermediate reaction steps promoted by the hydroxyl radical, OH. In this work, we report on the dynamical paths of the first step of this oxidation reaction, namely the hydrogen atom abstraction CH3CH2OH + OH → CH3CHOH + H2O, occurring at the Pd(111) surface and address the thermodynamic stability of the adsorbed reactants by means of quantum and molecular mechanics calculations, with special focus on the effect of the solvent. We have found that the impact of the solvent is significant for both ethanol and OH, contributing to a decrease in their adsorption free energies by a few dozen kcal mol-1 with respect to the adsorption energy under vacuum. Furthermore, we observe that hydrogen atom abstraction is enhanced for those simulation paths featuring large surface-reactant distances, namely, when the reactants weakly interact with the catalyst. The picture emerging from our study is therefore that of a catalyst whose coverage in an aqueous environment is largely dominated by OH with respect to ethanol. Nevertheless, only a small amount of them, specifically those weakly bound to the catalyst, is really active in the ethanol electro-oxidation reaction. These results open the idea of a rational design of co-catalysts based on the tuning of surface chemical properties to eventually enhance exchange current density.

We conduct quantum studies of adsorption of diazine heterocycles on graphene to discuss experimental thermodynamics of gas-phase adsorption of pyridazine, pyrimidine and pyrazine on graphitized thermal carbon black, as reported previously. Using Born-Oppenheimer molecular dynamics and density functional studies, we characterize structural and electronic tendencies of the heterocycles on graphene. The theoretical studies predict the adsorption of pyridazine, pyrazine and pyrimidine to cause electronic perturbations of dipole, quadrupole and mixed spatial characters, respectively, resulting in a red shift of the electronic components of the heterocycles to modulate graphene electronics upon admixing of diazine orbital components with the πz states of the substrate. Investigating the thermodynamics of adsorption further involves calculating Henry's constant with the expression of the uniform surface limit: using experimental data, we estimate binding energies and force derivatives with respect to the surface normal. The extracted association energies agree with the results of Lennard-Jones potential calculations. Together, the reported pyridazine anomalous retention required the association force constant to be lower compared with values for the other diazines. Exploring energies of intermolecular relations, we ascribe the pyridazine anomalous retention to possibility of the formation of pyridazine dimers: when on the surface, only for pyridazine, the computed benefit of pairing is larger than the energy of molecular association with graphene.

Protein-mediated doping of ZnO with plasmonic nanoparticles offers control over surfaces, electronic states, carrier dynamics, and spectral fingerprints. Here, we report on ZnO-nano-Au bioinorganic heterostructures prepared using a chimeric polypeptide that combines most of the ZnO-binding sequence GLHVMHKVAPPR and the gold-binding AYSSGAPPMPPF sequence. The one-pot peptide-mediated synthesis was performed in the presence and absence of HAuCl4 to determine the impact of the peptide and metallic component on the structural and electronic properties of the ZnO assembly. Electron microscopy confirms that the chimera polypeptide promotes the synthesis of both spherical and nonspherical gold nanoparticles, which are properly embedded in ZnO. The optical absorption spectra describe a complex palette of plasmon modes, while the luminescence spectra show a dominant subset of near-infrared spectral fingerprints that suggest an increasing role of surfaces in carrier relaxation. Simulations using finite difference time-domain theory describe collective plasmon phenomena specific to gold nanoparticles embedded in ZnO. Furthermore, to confirm experimental data, theory suggests an interinclusion nanogold spacing of 10 nm or less. Flexibility of the primary sequence of the chimera in the synthesis of ZnO-nano-Au composites opens up possibilities for plasmon-modulated ZnO junctions with Ohmic contacts as sought in sensor technologies and for security applications.

A hydrophobic heptapeptide, with sequence AFILPTG, as part of a phage capsid protein binds effectively to silica particles carrying negative charge. Here, we explore the silica binding activity of the sequence as a short polypeptide with polar N and C terminals. To describe the structural changes that occur on binding, we fit experimental infrared, Raman and circular dichroism data for a number of structures simulated in the full configuration space of the hepta-peptide using replica exchange molecular dynamics. Quantum chemistry was used to compute normal modes of infrared and Raman spectra and establish a relationship to structures from MD data. To interpret the circular dichroism data, instead of empirical factoring of optical activity into helical/sheet/random components, we exploit natural transition orbital theory and specify the contributions of backbone amide units, side chain functional groups, water, sodium ions and silica to the observed transitions. Computed optical responses suggest a less folded backbone and importance of the N-terminal when close to silica. We further discuss the thermodynamics of the interplay of charged and hydrophobic moieties of the polypeptide on association with the silica surface. The outcomes of this study may assist in the engineering of novel artificial bio-silica heterostructures.

To advance our understanding of the molecular biochemistry of fungi which impact cultural heritage in libraries, museums and archives we investigated the diagnostic capacity of Raman spectroscopy to identify the composition of colored chromophores of fungi on paper. In this study we explored the diagnostic capacity of resonant Raman to distinguish chromophores in fungal filaments stimulated to grow on paper under high humidity with a focus on characterizing chromophores of Alternaria group species. To facilitate molecular analysis, we conducted quantum chemistry calculations of representative metabolites having optical absorption in the ultraviolet–visible spectral range. Comparing theory and experiment we show that fonsecin, erythroglaucin and aurasperone type chromophores occur in mature hyphal filaments with β-carotene dominant in yeast depositions on paper surfaces. Resonant Raman of mature filaments suggests a further contribution of carotenes longer than β-carotene to the spectral signature. Using microscopic resolution, we distinguish rich sets of Raman signatures that we assign to lignin, flavoglaucin, riboflavin, cycloleucomelon(e) and asperyellone molecular components in the spatial regions where filaments initiate from yeast depositions. In such regions, where filament microstructures stimulate development of a mature three-dimensional scaffold, the diversity of Raman resonances confirms a rich biochemistry of the developing structures. The library of computed optical and spectroscopic responses of characteristic fungal chromophores and metabolites presented here is essential for understanding the effect of fungi on a wide range of objects made from paper including books, prints, drawings, watercolors, engravings and even sculptures as well as designing next generation materials based on fungal hyphal mats.

We report how Raman difference imaging provides insight on cellular biochemistry in vivo as a function of sub-cellular dimensions and the cellular environment. We show that this approach offers a sensitive diagnostic to address blood biochemistry at the cellular level. We examine Raman microscopic images of the distribution of the different hemoglobins in both healthy (discocyte) and unhealthy (echinocyte) blood cells and interpret these images using pre-calculated, accurate pre-resonant Raman tensors for scattering intensities specific to hemoglobins. These tensors are developed from theoretical calculations of models of the oxy, deoxy and met forms of heme benchmarked against the experimental visible spectra of the corresponding hemoglobins. The calculations also enable assignments of the electronic transitions responsible for the colour of blood: these are mainly ligand to metal charge transfer transitions.

Preparation and characterization of polariton Bose–Einstein condensates in micro-cavities of high quality are at the frontier of contemporary solid state physics. Here, we report on three-dimensional polariton condensation and confinement in pseudo-spherical ZnO microcrystals. The boundary of micro-spherical ZnO resembles a stable cavity that enables sufficient coupling of radiation with material response. Exciting under tight focusing at the low frequency side of the bandgap, we detect efficiency and spectral nonlinear dependencies, as well as signatures of spatial delocalization of the excited states which are characteristics of dynamics in polariton droplets. Expansion of the photon component of the condensate boosts the leaky field beyond the boundary of the ZnO microcrystals. Using this, we observe surface polariton field enhanced Raman responses at the interface of ZnO microspheres. The results demonstrate how readily available spherical semiconductor microstructures facilitate engineering of polariton based electronic states and sensing elements for diagnostics at interfaces.

In this study, we explore the molecular mechanisms of the stability of indigo chromophores and pigments. Assisted with density functional theory, we compare visible, infrared and Raman spectral properties of model molecules, chromophores and pigments derived from living organisms. Using indigo carmine as a representative model system, we characterize the structure and dynamics of the chromophore in the first electronic excited state using femtosecond visible pump-infrared probe spectroscopy. Results of experiments and theoretical studies indicate that, while the trans geometry is strongly dominant in the electronic ground state, upon photoexcitation, in the Franck-Condon region, some molecules may experience isomerization and proton transfer dynamics. If this happens, however, the normal modes of the trans geometry of the electronic excited state are reconfirmed within several hundred femtoseconds. Supported by quantum theory, first, we ascribe stabilization of the trans geometry in the Franck-Condon region to the reactive character of the potential energy surface for the indigo chromophore when under the cis geometry in the electronic excited state. Second, we suggest that a conical intersection crossing, due to the high barrier along the isomerization pathway in the ground state, would provide for the effective relaxation and observed dominance of the trans geometry of the chromophore in the ground state. Planarity of the chromophore under the trans geometry assists effective dissipation of energy via a cascade of in-plane C-C, C-O⋯H-N stretchings and C-C-C bending modes delocalized over the molecular mainframe. The described mechanisms help to explain the remarkable photo-stability of indigo chromophores.

A diversity of photo-switching structural elements opens up new opportunities in the engineering of light driven reshaping of matter, in catalysis on-click including photodynamic cancer therapy, in light sensitive transport control and in data storage. With the assistance of quantum calculations we explore the photo-physical properties of novel 3,3'-azothiophene molecular systems, the synthesis of which we reported recently. In the considered azothiophenes, upon exposure to ultraviolet and visible radiation, we observed effective anti(trans) to syn(cis) and syn(cis) to anti(trans) isomerization of the -N[double bond, length as m-dash]N- moiety, respectively. In contrast to azobenzene based photo-switchable molecular systems, the syn(cis) to anti(trans) isomerization in the azothiophenes studied does not take place at 22 °C in the dark. Temperature dependent experiments and theoretical studies suggest a slightly higher barrier for such processes than for azobenzene, which we attribute to the specific structural and electronic properties of the thiophene ring and the nature of the side groups. We discuss the potential of the observed properties in the development of novel molecular photo-switching machinery to promote biocatalytic applications at interfaces.

Polypeptide based biosilica composites show promise as next generation multi-functional nano-platforms for diagnostics and bio-catalytic applications. Following the identification of a strong silica binder (LDHSLHS) by phage display, we conduct structural analysis of the polypeptide at the interface with amorphous silica nanoparticles in an aqueous environment. Our approach relies on modelling infrared and Raman spectral responses using predictions of molecular dynamics simulations and quantum studies of the normal modes for several potential structures. By simultaneously fitting both infrared and Raman responses in the amide spectral region, we show that the main structural conformer has a beta-like central region and helix-twisted terminals. Classical simulations, as conducted previously (Chem. Mater., 2014, 26, 5725), predict that the association of the main structure with the interface is stimulated by electrostatic interactions though surface binding also requires spatially distributed sodium ions to compensate for negatively charged acidic silanol groups. Accordingly, diffusion of sodium ions would contribute to a stochastic character of the peptide association with the surface. Consistent with the described dynamics at the interface, the results obtained from isothermal titration calorimetry (ITC) confirm a significant enhancement of polypeptide binding to silica at higher concentrations of Na+. The results of this study suggest that the tertiary structure of a phage capsid protein plays a significant role in regulating the conformation of peptide LDHSLHS, increasing its binding to silica during the phage display process. The results presented here support design-led engineering of polypeptide-silica nanocomposites for bio-technological applications.

Equisetum species are primitive vascular plants that benefit from the biogenesis of silica bio-organic inclusions in their tissues and participate in the annual biosilica turnover in local eco-systems. As means of Equisetum reproduction and propagation, spores are expected to reflect the evolutionary adaptation of the plants to the climatic conditions at different times of the year. Combining methods of Raman and scanning electron microscopy and assisted with density functional theory, we conducted material spatial-spectral correlations to characterize the distribution of biopolymers and silica based structural elements that contribute to the bio-mineral content of the elater. The elater tip has underlying skeletal-like structural elements where cellulose fibers provide strength and flexibility, both of which are necessary for locomotion. The surface of the elater tips is rich with less ordered pectin like polysaccharide and shows a ridged, folded character. At the surface we observe silica of amorphous, colloidal form in nearly spherical structures where the silica is only a few layers thick. We propose the observed expansion of elater tips upon germination and the form of silica including encapsulated biopolymers are designed for ready dispersion, release of the polysaccharide-arginine rich content and to facilitate silica uptake to the developing plant. This behavior would help to condition local soil chemistry to facilitate competitive rooting potential and stem propagation.