SciCombinator

For most applications, zirconia (ZrO2) is doped with yttria. Doping leads to the stabilization of the tetragonal or cubic phase and increased oxygen ion conductivity. Most previous surface studies of yttria-doped zirconia were plagued by impurities, however. We have studied doping of pure, 5-monolayer ZrO2 films on Rh(111) by x-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and low-energy electron diffraction (LEED). STM and LEED show that the tetragonal phase is stabilized by unexpectedly low dopant concentrations, 0.5 mol % Y2O3, even when the films are essentially fully oxidized (as evidenced by XPS core level shifts). XPS also shows Y segregation to the surface with an estimated segregation enthalpy of -23 ± 4 kJ/mol.

Zero-electron-kinetic-energy (ZEKE) spectra are presented for m-chlorotoluene (mClT), employing different low-lying torsional and vibration-torsional (“vibtor”) levels of the S1 state as intermediates. The adiabatic ionization energy is determined to be 71 319 cm-1 ± 5 cm-1 (8.8424 ± 0.0006 eV). It is found that the activity in the ZEKE spectra varies greatly for different levels and is consistent with the assignments of the S1 levels of m-fluorotoluene (mFT) deduced in the recent fluorescence study of Stewart et al. [J. Chem. Phys. 150, 174303 (2019)] and the ZEKE study from Kemp et al. [J. Chem. Phys. 151, 084311 (2019)]. As with mFT, the intensities in the ZEKE spectra of mClT are consistent with a phase change in the torsional potential upon ionization, allowing a large number of torsions and vibtor levels to be observed for the cation. Vibration-induced modifications of the torsional potential are discussed. Calculated vibrational wavenumbers for the S0, S1, and D0+ states are also presented.

Many fundamental chemical reactions are triggered by electronic excitations. Here, we propose and benchmark a novel approximate first-principles molecular dynamics simulation idea for increasing the computational efficiency of density functional theory-based calculations of the excited states. We focus on obtaining proton transfer energy at the S1 excited state through actual density functional theory calculations at the T1 state with additional optimized effective potentials. The potentials are optimized as such to reproduce the excited-state energy surface obtained using time-dependent density functional theory, but can be generalized to other more accurate quantum chemical methods. We believe that the presented method is not only suitable for studies on excited-state proton transfer and ion mobility in general systems but can also be extended to investigate more involved processes, such as photo-induced isomerization.

We develop several configuration interaction approaches for characterizing the electronic structure of an adsorbate on a metal surface (at least in model form). When one can separate the adsorbate from the substrate, these methods can achieve a reasonable description of adsorbate on-site electron-electron correlation in the presence of a continuum of states. While the present paper is restricted to the Anderson impurity model, there is hope that these methods can be extended to ab initio Hamiltonians and provide insight into the structure and dynamics of molecule-metal surface interactions.

We investigate the effect of hydrodynamic interactions (HIs) on the crystal nucleation of hard-sphere colloids for varying supersaturations. We use molecular dynamics and stochastic rotation dynamics techniques to account for the HIs. For high supersaturation values, we perform brute force simulations and compute the nucleation rate, obtaining good agreement with previous studies where HIs were neglected. In order to access low supersaturation values, we use a seeding approach method and perform simulations with and without HIs. We compute the nucleation rates for the two cases and surprisingly find good agreement between them. The nucleation rate in both cases follows the trend of the previous numerical results, thereby corroborating the discrepancy between experiments and simulations. Furthermore, we investigate the amount of fivefold symmetric clusters (FSCs) in a supersaturated fluid under different physical conditions, following the idea that FSCs compete against nucleation. To this end, we explore the role of the softness of the pair interactions, different solvent viscosities, and different sedimentation rates in simulations that include HIs. We do not find significant variations in the amount of FSCs, which might reflect the irrelevance of these three features on the nucleation process.

The rotational constants and quartic centrifugal distortion coefficients of hexafluoro-o-xylene were precisely derived from the 8 GHz to 18 GHz gas phase microwave spectrum. In addition, the rotational constants of all singly substituted 13C isotopologues were determined. Instead of the intuitively expected symmetry of C2v, as in o-xylene, calculations with a variety of methods (B3LYP, CAM-B3LYP, ωB97XD, MP2, and coupled-cluster singles, doubles, and perturbative triples) predict a C2 symmetry structure in which the two CF3 groups rotate in opposite directions by about 16°. While the experimental results in this study are not capable of proving this unusual symmetry, they can support future microwave, gas phase electron diffraction or nuclear magnetic resonance studies. From the presented data, a preliminary r0 structure was determined, reproducing the experimental rotational constants with deviations of no more than 15 kHz. Analysis of the interactions between the two CF3 groups using an effective fragment potential approach identifies two major contributions to their interaction, due to exchange-repulsion and electrostatic repulsion, with electrostatic repulsion responsible for the barrier at the C2v geometry.

Using experimentally determined structures of ubiquitin at 1 and 3000 bar, we generate sufficiently large ensembles of model structures in the native and pressure-induced (denatured) states by means of molecular dynamics simulations with explicit water. We calculate the values of a free-energy function (FEF), which comprises the hydration free energy (HFE) and the intramolecular (conformational) energy and entropy, for the two states at 1 and 3000 bar. The HFE and the conformational entropy, respectively, are calculated using our statistical-mechanical method, which has recently been shown to be accurate, and the Boltzmann-quasi-harmonic method. The HFE is decomposed into a variety of physically insightful components. We show that the FEF of the native state is lower than that of the denatured state at 1 bar, whereas the opposite is true at 3000 bar, thus being successful in reproducing the pressure denaturation. We argue that the following two quantities of hydration play essential roles in the denaturation: the WASA-dependent term in the water-entropy loss upon cavity creation for accommodating the protein (WASA is the water-accessible surface area of the cavity) and the protein-water Lennard-Jones interaction energy. At a high pressure, the mitigation of the serious water crowding in the system is the most important, and the WASA needs to be sufficiently enlarged with the increase in the excluded-volume being kept as small as possible. The denatured structure thus induced is characterized by the water penetration into the protein interior. The pressure denaturation is accompanied by a significantly large gain of water entropy.

We investigate the interaction of polyfluorene and fluorene/carbazole copolymers bearing various functional groups and side chains with small to large diameter-from 1.7 nm to 9 nm-carbon nanotubes (CNTs) in vacuo. We use variable-charge molecular dynamics simulations based on the reactive force field ReaxFF. We show that non-covalent functionalization of nanotubes, driven by π - π interactions, is effective for all the polymers studied, thanks to their conjugated backbone and regardless of the presence of specific functional groups. The geometry at equilibrium of these polymer/CNT hybrids is analyzed in detail at the scale of each fluorene or carbazole unit. The role of both the functional groups and the alkyl chain length is analyzed in detail. Adsorption of the polymers on the nanotube sidewalls is shown to be either complete-with the whole chain physisorbed-or partial-due to intrachain coiling or interchain repulsion-depending on the initial geometry, number of polymers, and nanotube diameter. Energetic arguments supplement the described geometric features. Both energetic and geometric adsorption features are derived here for the first time for large diameter carbon nanotubes (up to 9 nm) and fluorene/carbazole copolymers having up to 30 monomers and bearing different functional groups. The force field ReaxFF and its available parameterization used for the simulations are validated, thanks to a benchmark and review on higher-level quantum calculations-for simple π - π interacting compounds made up of polycyclic aromatic molecules adsorbed on a graphene sheet or bilayer graphene. Although it is shown that the influence of the nanotube chirality on the adsorption pattern and binding strength cannot be discussed with our method, we highlight that an available force field such as ReaxFF and its parameterization can be transferable to simulate new systems without specific re-parameterization, provided that this model is validated against reference methods or data. This methodology proves to be a valuable tool for optimal polymer design for nanotube functionalization at no re-parameterization cost and could be adapted to simulate and assist the design of other types of molecular systems.

In an effort to elucidate the origin of avian magnetoreception, it was postulated that a radical-pair formed in a cryptochrome upon light activation provided the basis for the mechanism that enables an inclination compass sensitive to the geomagnetic field. Photoreduction in this case involves formation of a flavin adenine dinucleotide (FAD)-tryptophan (TRP) radical-pair, following electron transfer within a conserved TRP triad in the cryptochrome. Recently, an animal-like cryptochrome from Chlamydomonas reinhardtii (CraCRY) was analyzed, demonstrating the role of a fourth aromatic residue, which serves as a terminal electron donor in the photoreduction pathway, resulting in the creation of a more distal radical-pair and exhibiting fast electron transfer. In this work, we investigated the electron transfer in CraCRY with a combination of free energy molecular dynamics (MD) simulations, frozen density functional theory, and QM/MM MD simulations, supporting the suggestion of a proton coupled electron transfer mechanism. Spin dynamics simulations discerned details on the dependence of the singlet yield on the direction of the external magnetic field for the [FAD•- TYRH•+] and [FAD•- TYR•] radical-pairs in CraCRY, in comparison with the previously modeled [FAD•- TRPH•+] radical-pair.

Model studies on the adsorption of simple amino acids on single-crystalline substrates provide the basis for understanding the interactions of more complex biomolecules with inorganic materials. In this study, the adsorption and thermal stability of cysteine on Pt(111) and on monolayer FeO(111)/Pt(111) and thick Fe3O4(111)/Pt(111) films have been investigated in ultrahigh vacuum by means of x-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, and temperature-programmed desorption. At low adsorption temperature (160 K), cysteine stays intact on all studied surfaces. However, the thermal stability differs dramatically. Decomposition via dehydrogenation, decarbonylation/decarboxylation, and deamination starts already below room temperature on Pt(111). By contrast, adsorbed cysteine is stable up to 500 K on Fe3O4(111) and then gets oxidized in a redox reaction involving the Fe3O4 substrate. FeO(111)/Pt(111) is a special case, where decarbonylation of cysteine occurs below room temperature, which is most likely initiated by a structural modification and concomitant charge transfer at the Pt-FeO interface induced by the carboxyl group of the adsorbed cysteine. The experimental results suggest that cysteine binds to the surfaces with the carboxyl group on the iron oxides and with the carboxyl and amino groups on Pt(111).