Quantitative Raman microscopy to describe structural organisation in hollow microcrystals built from silicon catecholate and amines.

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.

Raman microscopy tracks maturity of melanin intermediates in Botrytis cinerea, a plant pathogen.

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.

Diazines on graphene: adsorption, structural variances and electronic states.

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.

Cu(Proline)2 Complex: A Model of Bio-Copper Structural Ambivalence.

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.

Ethanol electro-oxidation reaction on the Pd(111) surface in alkaline media: insights from quantum and molecular mechanics.

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.

Anchoring of a hydrophobic heptapeptide (AFILPTG) on silica facilitates peptide unfolding at the abiotic-biotic interface.

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.

Mapping blood biochemistry by Raman spectroscopy at the cellular level.

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.

Polariton condensation and surface enhanced Raman in spherical ZnO microcrystals.

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.

Distributions of Silica and Biopolymer Structural Components in the Spore Elater of Equisetum arvense, an Ancient Silicifying Plant.

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.

From phage display to structure: an interplay of enthalpy and entropy in the binding of the LDHSLHS polypeptide to silica.

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.

The structural and electronic properties of 3,3'-azothiophene photo-switching systems.

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.

Correspondence between light-absorption spectrum and nonequilibrium work distribution as a mean to access free energy differences between electronic states.

The problem of recovering the free energy difference between two electronic states has been investigated by Frezzato [Chem. Phys. Lett. 533, 106 (2012)], exploring the equivalence between light-absorption spectra and work distribution, hence opening to the application of a spectroscopic version of the Jarzynski equality (JE) [Phys. Rev. Lett. 78, 2690 (1997)]. Here, assuming the validity of the time-dependent perturbation theory, we demonstrate that such equivalence does not lead to the known form of the JE. This is ascribed to the fact that light-absorption processes cannot be described as stochastic processes. To emphasize such an aspect, we devise a stochastic model for the UV-vis (ultraviolet and visible) absorption, suitable for determining the free energy difference between two generic quantum manifolds in a JE-like fashion. However, the model would require explicit knowledge of the transition dipole moments, which are in general not available. Nonetheless, we derive a spectroscopic version of the JE that allows us to recover the free energy difference between the ground and an excited electronic state when the latter state is the only one observed in the spectrum.

Do Material Discontinuities in Silica Affect Vibration Modes?

Structural properties of bioinorganic composites are of current interest in the areas of drug delivery, bone repair, and biomimetics. In such composite systems, structural analysis is enhanced when we combine methods of spectroscopy and simulation. Depending on size and shape, structural discontinuities of inorganic matter may modulate the optical response of a bound molecule. Using density functional theory, we explore the effects of a local field next to the surface of a silica cluster on frequencies of methyl stretching modes of associated methanols. Computation results predict that the electrostatic potential modulated by structural discontinuities of silica should not contribute to any systematic frequency shifts for normal modes of a guest molecule. Regardless of position, the methyl stretching modes of methanol demonstrate sensitivity only to the local chemistry of bonding with silanols, which may lead either to a low or high frequency shift for vibrations. In support, experimental studies of deuterated methanol at impurity levels in water show uniform broadening of resonances of carbon-deuterium stretching modes in the presence of both crystalline and amorphous silica nanoparticles. The significance of these findings is that the spectral responses of guest molecules on such surfaces should not be subject to bias introduced by edge effects.

Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation.

In the companion article (Giovannelli et al., 10.1021/acs.jctc.7b00594), we presented an alchemical approach, based on nonequilibrium molecular dynamics simulations, to compute absolute binding free energies of a generic host-guest system. Two alternative computational routes, called binded-domain and single-point alchemical-path schemes, have been proposed. This study is addressed to furnish numerical validation and illustrative examples of the above-mentioned alchemical schemes. Validation is provided by comparing binding free-energy data relative to two poses of a Zn(II)·anion complex with those recovered from an alternative approach, based on steered molecular dynamics simulations. We illustrate important technical and theoretical aspects for a good practice in applying both alchemical schemes, not only through the calculations on the Zn(II)·anion complex, but also estimating absolute binding free energies of 1:1 complexes of ß-cyclodextrin with aromatic compounds (benzene and naphthalene). Comparison with experimental data and previous molecular dynamics simulation studies further confirms the validity of the present nonequilibrium-alchemical methodology.

Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework.

The fast-switching decoupling method is a powerful nonequilibrium technique to compute absolute binding free energies of ligand-receptor complexes (Sandberg et al., J. Chem. Theory Comput. 2014, 11, 423-435). Inspired by the theory of noncovalent binding association of Gilson and co-workers (Biophys. J. 1997, 72, 1047-1069), we develop two approaches, termed binded-domain and single-point alchemical-path schemes (BiD-AP and SiP-AP), based on the possibility of performing alchemical trajectories during which the ligand is constrained to fixed positions relative to the receptor. The BiD-AP scheme exploits a recent generalization of nonequilibrium work theorems to estimate the free energy difference between the coupled and uncoupled states of the ligand-receptor complex. With respect to the fast-switching decoupling method without constraints, BiD-AP prevents the ligand from leaving the binding site, but still requires an estimate of the positional binding-site volume, which may not be a simple task. On the other side, the SiP-AP scheme allows avoidance of the calculation of the binding-site volume by introducing an additional equilibrium simulation of ligand and receptor in the bound state. In the companion article (DOI: 10.1021/acs.jctc.7b00595), we show that the extra computational effort required by SiP-AP leads to a significant improvement of accuracy in the free energy estimates.

Modeling of Infrared-Visible Sum Frequency Generation Microscopy Images of a Giant Liposome.

The article explores the theory of infrared-visible sum frequency generation microscopy of phospholipid envelopes with dimensions larger than the wavelength of the nonlinear emission. The main part of the study concerns derivation and accounting for the contributions of effective nonlinear responses specific to sites on the surfaces of a bilayer envelope and their dependence on polarization condition and experimental geometry. The nonlinear responses of sites are mapped onto the image plane according to their emission directions and the numerical aperture of a sampling microscope objective. According to the simulation results, we discuss possible approaches to characterize the shape of the envelope, to extract molecular hyperpolarizabilities, and to anticipate possible heterogeneity in envelope composition and anisotropy of the environment proximal to the envelope. The modeling approach offers a promising analytic facility to assist connecting microscopy observations in engineered liposomes, cellular envelopes, and subcellular organelles of relatively large dimensions to molecular properties, and hence to chemistry and structure down to available spatial resolution.

Tip-induced deformation of a phospholipid bilayer: theoretical perspective of sum frequency generation imaging.

The paper addresses theory of Sum Frequency Generation imaging of an atomic force microscopy tip-induced deformation of a bilayer phospholipid membrane deposited over a pore: known as a nano-drum system. Image modeling employed nonlinearities of the normal modes specific to hydrocarbon terminal methyls, which are distributed about the deformed surfaces of inner and outer leaflets. The deformed profiles are according to the solutions of shape equation for Canham-Helfrich Hamiltonian accounting properties of four membranes, which differ in elasticity and adhesion. The results indicate that in continuous deformed surfaces, the difference in the curvature of the outer and inner leaflets dominates in the imaged nonlinearity. This is different comparing to the results for a perfect bilayer spherical cap system (the subject of previous study), where nonlinear image response is dominated by the mismatch of the inner and outer leaflets' surface areas (as projected to the image plane) at the edge of perfectly spherical structure. The results of theoretical studies, here, demonstrate that Sum Frequency Generation imaging in continuous and deformed bilayer surfaces are helpful to address curvature locally and anticipate mechanical properties of membrane. The articles discuss applicability and practical limitations of the approach. Combination of Atomic Force Microscopy and Sum Frequency Generation imaging under controlled tip-induced deformation provides a good opportunity to probe and test membranes physical properties with rigor of adopted theory.

Sum-frequency generation echo and grating from interface.

The work addresses spectroscopy of fourth-order Sum Frequency Generation Echo and Grating responses as an experimental tool to study structure and dynamics at interfaces. First, it addresses experimental geometry to extract background-free fourth-order Echo and Grating responses. Further, the article provides the analytical expressions of the response functions for these nonlinearities. The derived expressions are used to model the χ((4)) two-dimensional spectral responses of a hydrated methyl acetate, which resembles a hydrated carbonyl moiety at the polar outer side of a phospholipid membrane. Orientation, transition dipole moments, and Raman tensors are obtained from the results of classical and quantum calculations, respectively. The numerical studies for the nonlinear responses under different polarization schemes and timings suggest the possibility of securely factoring of spectral contributions of χ(YYYZX) and χ(YYYZY) macroscopic susceptibilities. As such, the nonlinearities provide an experimental perspective on orientation of a generic (low-symmetry) molecular system at interfaces. Besides, the spectral properties of the tensors may reflect correlations of the in-plane and out-of-plane field components specific to the interface. For the case of a phospholipid membrane, the experiment would address in-plane and out-of-plane anisotropy of hydrogen bonding and related dynamics.

Sum frequency generation image reconstruction: aliphatic membrane under spherical cap geometry.

The article explores an opportunity to approach structural properties of phospholipid membranes using Sum Frequency Generation microscopy. To establish the principles of sum frequency generation image reconstruction in such systems, at first approach, we may adopt an idealistic spherical cap uniform assembly of hydrocarbon molecules. Quantum mechanical studies for decanoic acid (used here as a representative molecular system) provide necessary information on transition dipole moments and Raman tensors of the normal modes specific to methyl terminal - a typical moiety in aliphatic (and phospholipid) membranes. Relative degree of localization and frequencies of the normal modes of methyl terminals make nonlinearities of this moiety to be promising in structural analysis using Sum Frequency Generation imaging. Accordingly, the article describes derivations of relevant macroscopic nonlinearities and suggests a mapping procedure to translate amplitudes of the nonlinearities onto microscopy image plane according to geometry of spherical assembly, local molecular orientation, and optical geometry. Reconstructed images indicate a possibility to extract local curvature of bilayer envelopes of spherical character. This may have practical implications for structural extractions in membrane systems of practical relevance.