Role of the redox state of cerium oxide on glycine adsorption: an experimental and theoretical study.

The role of the oxidation state of cerium cations in a thin oxide film in the adsorption, geometry, and thermal stability of glycine molecules was studied. The experimental study was performed for a submonolayer molecular coverage deposited in vacuum on CeO(111)/Cu(111) and CeO(111)/Cu(111) films by photoelectron and soft X-ray absorption spectroscopies and supported by calculations for prediction of the adsorbate geometries, C 1s and N 1s core binding energies of glycine, and some possible products of the thermal decomposition. The molecules adsorbed on the oxide surfaces at 25 °C in the anionic form the carboxylate oxygen atoms bound to cerium cations.

Superficial Tale of Two Functional Groups: On the Surface Propensity of Aqueous Carboxylic Acids, Alkyl Amines, and Amino Acids.

The gas-liquid interface of water is environmentally relevant due to the abundance of aqueous aerosol particles in the atmosphere. Aqueous aerosols often contain a significant fraction of organics. As aerosol particles are small, surface effects are substantial but not yet well understood.

An atomistic explanation of the ethanol-water azeotrope.

Ethanol and water form an azeotropic mixture at an ethanol molecular percentage of ∼91% (∼96% by volume), which prohibits ethanol from being further purified distillation. Aqueous solutions at different concentrations in ethanol have been studied both experimentally and theoretically. We performed cylindrical micro-jet photoelectron spectroscopy, excited by synchrotron radiation, 70 eV above C1s ionization threshold, providing optimal atomic-scale surface-probing.

Ethanol in Aqueous Solution Studied by Microjet Photoelectron Spectroscopy and Theory.

By combining results and analysis from cylindrical microjet photoelectron spectroscopy (cMJ-PES) and theoretical simulations, we unravel the microscopic properties of ethanol-water solutions with respect to structure and intermolecular bonding patterns following the full concentration scale from 0 to 100% ethanol content. In particular, we highlight the salient differences between bulk and surface. Like for the pure water and alcohol constituents, alcohol-water mixtures have attracted much interest in applications of X-ray spectroscopies owing to their potential of combining electronic and geometric structure probing.

Correction: The molecular structure of the surface of water-ethanol mixtures.

Correction for 'The molecular structure of the surface of water-ethanol mixtures' by Johannes Kirschner , , 2021, , 11568-11578, DOI: 10.1039/D0CP06387H.

Breaking inversion symmetry by protonation: experimental and theoretical NEXAFS study of the diazynium ion, NH.

As an example of symmetry breaking in NEXAFS spectra of protonated species we present a high resolution NEXAFS spectrum of protonated dinitrogen, the diazynium ion NH. By ab initio calculations we show that the spectrum consists of a superposition of two nitrogen 1s absorption spectra, each including a π* band, and a nitrogen 1s to H charge transfer band followed by a weak irregular progression of high energy excitations. Calculations also show that, as an effect of symmetry breaking by protonation, the π* transitions are separated by 0.

The molecular structure of the surface of water-ethanol mixtures.

Mixtures of water and alcohol exhibit an excess surface concentration of alcohol as a result of the amphiphilic nature of the alcohol molecule, which has important consequences for the physico-chemical properties of water-alcohol mixtures. Here we use a combination of intensity vibrational sum-frequency generation (VSFG) spectroscopy, heterodyne-detected VSFG (HD-VSFG), and core-level photoelectron spectroscopy (PES) to investigate the molecular properties of water-ethanol mixtures at the air-liquid interface. We find that increasing the ethanol concentration up to a molar fraction (MF) of 0.

The carbon and oxygen K-edge NEXAFS spectra of CO.

We present and analyze high resolution near edge X-ray absorption fine structure (NEXAFS) spectra of CO+ at the carbon and oxygen K-edges. The spectra show a wealth of features that appear very differently at the two K-edges. The analysis of these features can be divided into three parts; (i) repopulation transition to the open shell orbital - here the C(1s) or O(1s) to 5σ transition, where the normal core hole state is reached from a different initial state and different interaction than in X-ray photoelectron spectroscopy; (ii) spin coupled split valence bands corresponding to C(1s) or O(1s) to π* transitions; (iii) remainder weak and long progressions towards the double ionization potentials containing a manifold of peaks.

pH-dependent X-ray Photoelectron Chemical Shifts and Surface Distribution of Cysteine in Aqueous Solution.

The distribution and protonation states of amino acids in water droplets are of considerable concern in studies on the formation of clouds in the atmosphere as well as in many biological contexts. In the present work we use the amino acid cysteine as a prototypical example and explore the protonation states of this molecule in aqueous solution, which are strongly affected by the acidity of the environment and also can show different distributions between surface and bulk. We use a combination of X-ray photoelectron chemical shift measurements, density functional theory calculations of the shifts, and reactive force field molecular dynamics simulations of the underlying structural dynamics.

Experimental and theoretical elucidation of catalytic pathways in TiO-initiated prebiotic polymerization.

The tendency of glycine to form polymer chains on a rutile(110) surface under wet/dry conditions (dry-wet cycles at high temperature) is studied through a conjunction of surface sensitive experimental techniques and sequential periodic multilevel calculations that mimics the experimental procedures with models of decreasing complexity and increasing accuracy. X-ray photoemission spectroscopy (XPS) and thermal desorption spectroscopy (TDS) experimentally confirmed that the dry-wet cycles lead to Gly polymerization on the oxide support. This was supported by all the theoretical characterizations.

Modeling Nucleation and Growth of ZnO Nanoparticles in a Low Temperature Plasma by Reactive Dynamics.

The very first stages of nucleation and growth of ZnO nanoparticles in a plasma reactor are studied by means of a multiscale computational paradigm where the DFT-GGA approach is used to evaluate structure and electronic energy of small (ZnO) clusters ( N ≤ 24) that are employed as a training set (TS) for the optimization of a Reactive Force Field (ReaxFF). Reactive Molecular Dynamics (RMD) simulations based on this tuned ReaxFF are carried out to reproduce nucleation and growth in a realistic environment. Inside the reaction chamber the temperature is around 1200 K, and the zinc atoms are oxidized in an oxygen-rich atmosphere at high pressure (about 20 atm), whereas in the quenching chamber where the temperature is lower (about 800 K) the ZnO embryo-nanoclusters are grown.

Quantum Effects for a Proton in a Low-Barrier, Double-Well Potential: Core Level Photoemission Spectroscopy of Acetylacetone.

We have performed core level photoemission spectroscopy of gaseous acetylacetone, its fully deuterated form, and two derivatives, benzoylacetone and dibenzoylmethane. These molecules show intramolecular hydrogen bonds, with a proton located in a double-well potential, whose barrier height is different for the three compounds. This has allowed us to examine the effect of the double-well potential on photoemission spectra.

Molecular dynamics simulations of melting and sintering of Si nanoparticles: a comparison of different force fields and computational models.

Melting and sintering of silicon nanoparticles are investigated by means of classical molecular dynamics simulations to disclose the dependence of modelling on the system type, the simulation procedure and interaction potential. The capability of our parametrization of a reactive force field ReaxFF to describe such processes is assessed through a comparison with formally simpler Stillinger-Weber and Tersoff potentials, which are frequently used for simulating silicon-based materials. A substantial dependence of both the predicted melting point and its variation as a function of the nanoparticle size on the simulation model is also highlighted.

Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution.

The adsorption and dynamics of cystine, which is the oxidized dimer of cysteine where the monomers are connected through a disulfide bond, on the Au(110) surface, in water solution, is characterized by means of classical molecular dynamics simulations based on a recently developed reactive force field (ReaxFF). The adopted computational procedure and the force field description are able to give a complete and reliable picture, in line with experiments, of the molecule behavior in solution and in close contact with the metal support. Many different aspects, which have never been explored computationally at this level of theory, are disclosed, namely, physisorption, chemisorption, disulfide bridge breaking/creation, and formation of staples.

Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations.

The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine molecules in water solution is simulated through classical reactive molecular dynamics simulations based on an accurately parametrized force field. The adsorption modes of the molecules are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent experimental and theoretical data and confirm previous findings for a similar system.

Optical Properties of Gold Nanoclusters Functionalized with a Small Organic Compound: Modeling by an Integrated Quantum-Classical Approach.

Motivated by the growing importance of organometallic nanostructured materials and nanoparticles as microscopic devices for diagnostic and sensing applications, and by the recent considerable development in the simulation of such materials, we here choose a prototype system - para-nitroaniline (pNA) on gold nanoparticles - to demonstrate effective strategies for designing metal nanoparticles with organic conjugates from fundamental principles. We investigated the motion, adsorption mode, and physical chemistry properties of gold-pNA particles, increasing in size, through classical molecular dynamics (MD) simulations in connection with quantum chemistry (QC) calculations. We apply the quantum mechanics-capacitance molecular mechanics method [Z.

Simulation of Gold Functionalization with Cysteine by Reactive Molecular Dynamics.

The anchoring mechanism of cysteine to gold in water solution is characterized in detail by means of a combination of quantum chemistry (QC) and reactive classical molecular dynamics (RC-MD) calculations. A possible adsorption-reaction route is proposed, through RC-MD simulations based on a modified version of the protein reactive force field (ReaxFF), in which gold-protein interactions have been included after accurate parametrization at the QC level. The computational results confirm recent experimental findings regarding the mechanism as a two-step binding, namely, a slow physisorption followed by a fast chemisorption.

Experimental and theoretical XPS and NEXAFS studies of N-methylacetamide and N-methyltrifluoroacetamide.

Experimental Near-Edge X-ray Absorption Fine-Structure (NEXAFS) spectra of N-methyltrifluoroacetamide (FNMA), which is a peptide model system, measured at the C, N, O and F K-edges are reported. The features in the spectra have been assigned by Static-Exchange (STEX) calculations. Using the same method, we have also assigned previously measured NEXAFS spectra of another peptide model system, N-methylacetamide (NMA).

Surface-Altered Protonation Studied by Photoelectron Spectroscopy and Reactive Dynamics Simulations.

The extent to which functional groups are protonated at aqueous interfaces as compared to bulk is deemed essential to several areas in chemistry and biology. The origin of such changes has been the source of intense debate. We use X-ray photoelectron spectroscopy and all-atom reactive molecular dynamics simulations as two independent methods to probe, at the molecular scale, both bulk and surface distributions of protonated species of cysteine in an aqueous solution.

NEXAFS and XPS studies of nitrosyl chloride.

The electronic structure of nitrosyl chloride (ClNO) has been investigated in the gas phase by X-ray Photoelectron (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy at the Cl 2p, Cl 2s, N 1s and O 1s edges in a combined experimental and theoretical study. The theoretical calculations at different levels of approximation predict ionization potential values in good agreement with the experimental data and allow us to assign the main features of the absorption spectra. An unexpected failure of the density functional model is, however, observed in the calculation of the Cl 2s binding energy, which is related to a large self-interaction error.

Cysteine on TiO2(110): a theoretical study by reactive dynamics and photoemission spectra simulation.

Owing to the importance of bioinorganic interface properties for the biocompatibility of implants and for biosensing technology, it has become indispensable to gain understanding of their crucial structure-property relations at the atomistic level. Motivated by this fact, we use cysteine amino acid on perfect and defective TiO2(110) surfaces as model systems and study adsorption by means of classical all-atom reactive molecular dynamics and ab initio O 1s, N 1s, and S 2p photoemission spectra (XPS) simulations of the most relevant adsorbate structures. By analysis of the dynamics results and a detailed comparison with spectra recently collected for this adsorbate, we obtain conclusions of both general and particular character.

Theoretical simulations of structure and X-ray photoelectron spectra of glycine and diglycine adsorbed on Cu(110).

The study of adsorption of glycine and glycylglycine (or diglycine) on a copper surface is an important step for the comprehension of mechanisms that determine the stability of biological functionalizers on metal substrates. These two molecules can be considered as prototypes and essential models to investigate, theoretically and experimentally, the adaptability of flexible short peptide chains to a definite interface. In this work, we have improved and updated earlier molecular dynamics simulations by including reactivity of the various species and the comparison of ab initio calculated C, N, and O core photoelectron chemical shifts with the ones found in previous studies.

Hybrid density functional-molecular mechanics calculations for core-electron binding energies of glycine in water solution.

We report hybrid density functional theory-molecular mechanics (DFT/MM) calculations performed for glycine in water solution at different pH values. In this paper, we discuss several aspects of the quantum mechanics-molecular mechanics (QM/MM) simulations where the dynamics and spectral binding energy shifts are computed sequentially, and where the latter are evaluated over a set of configurations generated by molecular or Car-Parrinello dynamics simulations. In the used model, core ionization takes place in glycine as a quantum mechanical (QM) system modeled with DFT, and the solution is described with expedient force fields in a large molecular mechanical (MM) volume of water molecules.