The novel secretome ST266 activates Akt and protects against oxidative stress-mediated injury in human RPE and Müller cells.

Oxidative stress-mediated retinal pigment epithelial (RPE) cell damage is associated with age-related macular degeneration (AMD). ST266 is the biological secretome produced by a novel population of amnion-derived multipotent progenitor cells. Herein, we investigated the effect of ST266 on RPE cell injury induced by hydroquinone (HQ), a cigarette smoke related oxidant, hydrogen peroxide (HO) and all-trans retinal (atRal), a pro-oxidant component of the retinoid cycle.

Direct measurement of single-molecule dynamics and reaction kinetics in confinement using time-resolved transmission electron microscopy.

We report experimental methodologies utilising transmission electron microscopy (TEM) as an imaging tool for reaction kinetics at the single molecule level, in direct space and with spatiotemporal continuity. Using reactions of perchlorocoronene (PCC) in nanotubes of different diameters and at different temperatures, we found a period of molecular movement to precede the intermolecular addition of PCC, with a stronger dependence of the reaction rate on the nanotube diameter, controlling the local environments around molecules, than on the reaction temperature (-175, 23 or 400 °C). Once initiated, polymerisation of PCC follows zero-order reaction kinetics with the observed reaction cross section of 1.

Quantum Chemical Characterization and Design of Quantum Dots for Sensing Applications.

The ability to tune the optoelectronic properties of quantum dots (QDs) makes them ideally suited for the use as fluorescence sensing probes. The vast structural diversity in terms of the composition and size of QDs can make designing a QD for a specific sensing application a challenging process. Quantum chemical calculations have the potential to aid this process through the characterization of the properties of QDs, leading to their design.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods.

Density Functional Theory Calculations of Core-Electron Binding Energies at the K-Edge of Heavier Elements.

The capability to determine core-electron binding energies (CEBEs) is vital in the analysis of X-ray photoelectron spectroscopy, and the continued development of light sources has made inner shell spectroscopy of heavier elements increasingly accessible. Density functional theory is widely used to determine CEBEs of lighter elements (boron-fluorine). It is shown that good performance of exchange-correlation functionals for these elements does not necessarily translate to the calculation of CEBEs for the heavier elements from the next row of the periodic table, and in general, larger errors are observed.

Risuteganib Protects against Hydroquinone-induced Injury in Human RPE Cells.

Purpose: Cigarette smoking has been implicated in the pathogenesis of AMD. Integrin dysfunctions have been associated with AMD. Herein, we investigate the effect of risuteganib (RSG), an integrin regulator, on RPE cell injury induced by hydroquinone (HQ), an important oxidant in cigarette smoke.

Observation of Double Excitations in the Resonant Inelastic X-ray Scattering of Nitric Oxide.

The nitrogen K-edge resonant inelastic X-ray scattering (RIXS) map of nitric oxide (NO) has been measured and simulated to provide a detailed analysis of the observed features. High-resolution experimental RIXS maps were collected using an gas flow cell and a high-transmission soft X-ray spectrometer. Accurate descriptions of the ground, excited, and core-excited states are based upon restricted active space self-consistent-field calculations using second order multiconfigurational perturbation theory.

Density Functional Theory Based Methods for the Calculation of X-ray Spectroscopy.

The availability of new light sources combined with the realization of the unique capabilities of spectroscopy in the X-ray region has driven tremendous advances in the field of X-ray spectroscopy. Currently, these techniques are emerging as powerful analytical tools for the study of a wide range of problems encompassing liquids, materials, and biological systems. Time-resolved measurements add a further dimension to X-ray spectroscopy, opening up the potential to resolve ultrafast chemical processes at an atomic level.

Resveratrol Protects Against Hydroquinone-Induced Oxidative Threat in Retinal Pigment Epithelial Cells.

Purpose: Oxidative stress in retinal pigment epithelial (RPE) cells is associated with age-related macular degeneration (AMD). Resveratrol exerts a range of protective biologic effects, but its mechanism(s) are not well understood. The aim of this study was to investigate how resveratrol could affect biologic pathways in oxidatively stressed RPE cells.

Influence of molecular design on radical spin multiplicity: characterisation of BODIPY dyad and triad radical anions.

A strategy to create organic molecules with high degrees of radical spin multiplicity is reported in which molecular design is correlated with the behaviour of radical anions in a series of BODIPY dyads. Upon reduction of each BODIPY moiety radical anions are formed which are shown to have different spin multiplicities by electron paramagnetic resonance (EPR) spectroscopy and distinct profiles in their cyclic voltammograms and UV-visible spectra. The relationship between structure and multiplicity is demonstrated showing that the balance between singlet, biradical or triplet states in the dyads depends on relative orientation and connectivity of the BODIPY groups.

Improving the predictive quality of time-dependent density functional theory calculations of the X-ray emission spectroscopy of organic molecules.

The simulation of X-ray emission spectra of organic molecules using time-dependent density functional theory (TDDFT) is explored. TDDFT calculations using standard hybrid exchange-correlation functionals in conjunction with large basis sets can predict accurate X-ray emission spectra provided an energy shift is applied to align the spectra with experiment. The relaxation of the orbitals in the intermediate state is an important factor, and neglect of this relaxation leads to considerably poorer predicted spectra.

Probing the electronic structure of ether functionalised ionic liquids using X-ray photoelectron spectroscopy.

The charge distribution associated with individual components in functionalised ionic liquids (ILs) can be tuned by careful manipulation of the substituent groups incorporated into the ions. Here we use X-ray photoelectron spectroscopy to investigate the impact of substituent atoms on the electronic structure of similar imidazolium-based systems each paired with a common anion, [TfN]. The experimental measurements revealed an unexpected variation in the charge density distribution within the IL cation when the oxygen atom in a poly-ether containing side chain is moved by just one atomic position.

Infrared spectroscopy of a small ion solvated by helium: OH stretching region of He-HOCO.

Messenger spectroscopy is a well-established method for recording infrared (IR) spectra of molecular ions. It relies upon the tagging of weakly bound atoms or molecules, known as the "messenger," to the ion of interest. The ideal tag species is helium since it has the weakest possible interaction with any molecular ion and is consequently the least likely to alter the structure and function.

Zinc 1s Valence-to-Core X-ray Emission Spectroscopy of Halozincate Complexes.

The Zn 1s valence-to-core (VtC) X-ray emission spectra of seven ionic liquids have been measured experimentally and simulated on the basis of time-dependent density-functional theory (TDDFT) calculations. Six of the ionic liquids were made by mixing [CCIm]X and Zn(II)X at three different ZnX mole fractions (0.33, 0.

AIRBED: A Simplified Density Functional Theory Model for Physisorption on Surfaces.

Dispersion interactions are commonly included in density functional theory (DFT) calculations through the addition of an empirical correction. In this study, a modification is made to the damping function in DFT-D2 calculations to describe repulsion at small internuclear distances. The resulting Atomic Interactions Represented By Empirical Dispersion (AIRBED) approach is used to model the physisorption of molecules on surfaces such as graphene and hexagonal boron nitride, where the constituent atoms of the surface are no longer required to be included explicitly in the density functional theory calculation but are represented by a point charge to capture electrostatic effects.

A scaled CIS(D) based method for the calculation of valence and core electron ionization energies.

The calculation of electron ionization energies is a key component for the simulation of photoelectron spectroscopy. CIS(D) is a perturbative doubles correction for the single excitation configuration interaction (CIS) method which provides a new approach for computing excitation energies. It is shown that by introducing a virtual orbital subspace that consists of a single "ghost" orbital, valence electron ionization energies can be computed using a scaled CIS(D) approach with an accuracy comparable with considerably more computationally intensive methods, such as ionization-potential equation of motion coupled cluster theory, and simulated spectra show a significant improvement relative to spectra based upon Koopmans' theorem.

Monitoring the Formation and Reactivity of Organometallic Alkane and Fluoroalkane Complexes with Silanes and Xe Using Time-Resolved X-ray Absorption Fine Structure Spectroscopy.

Complexes with weakly coordinating ligands are often formed in chemical reactions and can play key roles in determining the reactivity, particularly in catalytic reactions. Using time-resolved X-ray absorption fine structure (XAFS) spectroscopy in combination with time-resolved IR (TRIR) spectroscopy and tungsten hexacarbonyl, W(CO), we are able to structurally characterize the formation of an organometallic alkane complex, determine the W-C distances, and monitor the reactivity with silane to form an organometallic silane complex. Experiments in perfluorosolvents doped with xenon afford initially the corresponding solvated complex, which is sufficiently reactive in the presence of Xe that we can then observe the coordination of Xe to the metal center, providing a unique insight into the metal-xenon bonding.

Synthesis and characterisation of rylene diimide dimers using molecular handcuffs.

A strategy for positioning, and loosely connecting, molecules in close proximity using mechanically interlocked handcuffs is described. The strategy is demonstrated using rylene diimides, creating dimeric structures in which two components are linked through pillar[5]arene/imidazolium rotaxanes. Investigation of the resulting molecules demonstrates intriguing and new properties that arise from placing these redox active dye molecules together, allowing interactions, whilst allowing the molecules to separate as required.

Probing Elusive Cations: Infrared Spectroscopy of Protonated Acetic Acid.

Protonated carboxylic acids, (RCOOH)H, are the initial intermediates in acid-catalyzed (Fischer) esterification reactions. However, the identity of the isomeric form has been debated. Surprisingly, no optical spectra have been reported for any isomer of the protonated carboxylic acid monomer, despite it being a fundamental organic cation.

Dimers of acetic acid in helium nanodroplets.

The structural arrangement of small carboxylic acid molecules in the liquid phase remains a controversial topic. Some studies indicate a dominance of the cyclic dimer that prevails in the gas phase, whilst other studies favor short fragments of the infinite catemer chains that are found in the crystalline phase. Furthermore, difficulties in preparing and probing size-selected catemer segments have resulted in a lack of benchmark data upon which theoretical models of the condensed phases can be built.

Simulation of the Raman spectroscopy of multi-layered carbon nanomaterials.

Multi-layered carbon nanomaterials can have an important role in modern nanotechnology. Raman spectroscopy is a widely used analytical technique that is used to characterise the structure of these materials. In this work, an approach based upon an empirical potential for the simulation of the Raman spectroscopy of carbon nanomaterials [P.

Photoionization of the iodine 3d, 4s, and 4p orbitals in methyl iodide.

Ionization of the I 3d, 4s, and 4p orbitals in methyl iodide (CHI) has been studied by using synchrotron radiation to measure the total ion yield and by recording photoelectron spectra with linearly polarized radiation in two polarization orientations. The complete photoelectron spectrum of CHI has been recorded at several photon energies, and bands due to the C 1s, I 3d, 4s, 4p, and 4d atomic-like orbitals, as well as the molecular orbitals, have been observed and assigned. In the vicinity of the I 3d and 3d ionization thresholds at 626.

The growth and fluorescence of phthalocyanine monolayers, thin films and multilayers on hexagonal boron nitride.

Free-base phthalocyanine forms distinct interfacial phases and thin films on hexagonal boron nitride including a monolayer arrangement as determined using high resolution atomic force microscopy. The phases reveal significant differences in photoluminescence with an intense peak for monolayer coverages of flat-lying molecules which is red-shifted in agreement with theoretical models.

Reactivity of the O·(HO) and NO·(HO) cluster ions in the D-region of the ionosphere.

The protonated water clusters present in the D-region of the ionosphere have been postulated to be formed from cluster ions such as O2+·(H2O)n and NO+·(H2O)n, although the detailed mechanism of the underlying reactions is not understood. Second order Møller-Plesset perturbation theory based Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations of the reactions of the O2+·(H2O)n and NO+·(H2O)n cluster ions to form protonated water clusters reveal different mechanisms for the O2+ and NO+ based ions. AIMD simulations of O2+·(H2O)n=2-5 with initial velocities of the atoms sampled from the Maxwell-Boltzmann distribution at 220 K show that following charge transfer, a reaction to form a protonated water cluster and OH occurs rapidly where the neutral O2 molecule is just a spectator.

The impact of sulfur functionalisation on nitrogen-based ionic liquid cations.

It has been demonstrated that bonding and interactions within ionic liquids (ILs) can be elegantly tuned by manipulation of structure and the introduction of functional groups. Here we use XPS to investigate the impact of sulfur containing substituents on the electronic structure of a series of N-based cations, all with a common anion, [NTf2]-. The experiments reveal complexity and perturbation of delocalised systems which cannot be easily interpreted by NMR and XPS alone, DFT provides critical insight into bonding and underpins the assignment of spectra and development of deconstruction models for each system studied.