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. One starting point for studying the surface of aerosols is to investigate the surface of aqueous solutions. We review here studies of the surface composition of aqueous solutions using liquid-jet photoelectron spectroscopy in combination with theoretical simulations. Our focus is on model systems containing two functional groups, the carboxylic group and the amine group, which are both common in atmospheric organics. For alkanoic carboxylic acids and alkyl amines, we find that the surface propensity of such amphiphiles can be considered to be a balance between the hydrophilic interactions of the functional group and the hydrophobic interactions of the alkyl chain. For the same chain length, the neutral alkyl amine has a lower surface propensity than the neutral alkanoic carboxylic acid, whereas the surface propensity of the corresponding alkyl ammonium ion is higher than that of the alkanoic carboxylate ion. This different propensity leads to a pH-dependent surface composition which differs from the bulk, with the neutral forms having a much higher surface propensity than the charged ones. In aerosols, alkanoic carboxylic acids and alkyl amines are often found together. For such mixed systems, we find that the oppositely charged molecular ions form ion pairs at the surface. This cooperative behavior leads to a more organic-rich and hydrophobic surface than would be expected in a wide, environmentally relevant pH range. Amino acids contain a carboxylic and an amine group, and amino acids of biological origin are found in aerosols. Depending on the side group, we observe surface propensity ranging from surface-depleted to enriched by a factor of 10. Cysteine contains one more titratable group, which makes it exhibit more complex behavior, with some protonation states found only at the surface and not in the bulk. Moreover, the presence of molecular ions at the surface is seen to affect the distribution of inorganic ions. As the charge of the molecular ions changes with protonation, the effects on the inorganic ions also exhibit a pH dependence. Our results show that for these systems the surface composition differs from the bulk and changes with pH and that the results obtained for single-component solutions may be modified by ion-ion interactions in the case of mixed solutions.

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. The water mixtures of the two simplest alcohols, methanol and ethanol, have generated particular attention due to their delicate hydrogen bonding networks that underlie their structural and thermodynamic properties. Macroscopically ethanol-water seems to mix very well, however microscopically this is not true. The aberrant thermodynamics of water-alcohol mixtures have been suggested to be caused by energy differences of hydrogen bonding between water-water, alcohol-alcohol and alcohol-water molecules. These networks may perturb the local character of the interaction between X-rays and matter, calling for analysis that go beyond the normally applied local selection and building block rules and that can combine the effects of light-matter, intra- and intermolecular interactions. However, despite decades of ongoing research there are still controversies of the precise nature of hydrogen bonding networks that underlie the mixing of these simple molecules. Our combined analysis indicates that at low concentration ethanol molecules form a film at the surface since ethanol at the surface can expose its hydrophobic part to the vacuum retaining its two (or three) possible hydrogen bonds, while water at the surface cannot retain all its four possible hydrogen bonds. Thus, ethanol at the surface becomes energetically favorable. Ethanol molecules show a tilting angle variation of the C-C axis with respect to the surface normal as large as 60° at very low concentration. In bulk, around ca. ten %, the ethanol oxygen atoms tend to make a third acceptor hydrogen bond to water molecules. At ca. 20 %, there is a U-shaped change in the CH3 to CH2OH binding energy (BE) shift indicating the presence of ring-like agglomerates called clathrate structures. At the surface, between 5 and 25%, ethanol forms a closely packed layer with the smallest C-C tilting angle variation down to ∼20°. Above 25% and below the azeotrope at the surface, ethanol shows an increase in the tilting angle variation, while at very high ethanol concentrations water tends to move to the surface so giving a microscopic explanation of the azeotrope effect. This migration is connected to the presence of longer (shorter) ethanol chains in the bulk (surface). A brief comparison with discussions and predictions from other spectroscopic techniques is also given. We emphasize the execution of an integrated approach that combines molecular structural dynamics with quantum predictions of the core electronic chemical shift, so establishing a protocol with considerable interpretative as well as predictive power for cMJ-PES measurements. We believe that this protocol can valorize cMJ-PES for studies of properties of other alcohol mixtures as well as of binary solutions in general.

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 CeO2(111)/Cu(111) and Ce2O3(111)/Cu(111) films by photoelectron and soft X-ray absorption spectroscopies and supported by ab initio 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 via the carboxylate oxygen atoms bound to cerium cations. A third bonding point through the amino group was observed for the glycine adlayers on CeO2. In the course of stepwise annealing of the molecular adlayers on CeO2 and Ce2O3, the surface chemistry and decomposition products were analyzed and found to relate to different reactivities of glycinate on Ce4+ and Ce3+ cations, observed as two dissociation channels via C-N and C-C bond scission, respectively. The oxidation state of cerium cations in the oxide was shown to be an important factor, which defines the properties, electronic structure, and thermal stability of the molecular adlayer.

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 via 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. Large model systems have been employed to simulate, by molecular dynamics, slabs of the aqueous solutions and obtain an atomistic description of both bulk and surface regions. We show how the azeotropic behaviour results from an unexpected concentration-dependence of the surface composition. While ethanol strongly dominates the surface and water is almost completely depleted from the surface for most mixing ratios, the different intermolecular bonding patterns of the two components cause water to penetrate to the surface region at high ethanol concentrations. The addition of surface water increases its relative vapour pressure, giving rise to the azeotropic behaviour.

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 et al., Phys. Chem. Chem. Phys., 2021, 23, 11568-11578, DOI: 10.1039/D0CP06387H.

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 0.1 leads to a steep increase of the surface density of the ethanol molecules, and an increased ordering of the ethanol molecules at the surface. When the ethanol concentration is further increased, the surface density of ethanol remains more or less constant, while the orientation of the ethanol molecules becomes increasingly disordered. The used techniques of PES and VSFG provide complementary information on the density and orientation of ethanol molecules at the surface of water, thus providing new information on the molecular-scale properties of the surface of water-alcohol mixtures over a wide range of compositions. This information is invaluable in understanding the chemical and physical properties of water-alcohol mixtures.

Breaking inversion symmetry by protonation: experimental and theoretical NEXAFS study of the diazynium ion, N2H.

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 N2H+. 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 0.23 eV, only slightly exceeding the difference in the corresponding dark (symmetry forbidden) and bright (symmetry allowed) core excitations of neutral N2. By DFT and calculations and vibrational analysis, the complex π* excitation band of N2H+ is understood as due to the superposition of the significantly different vibrational progressions of excitations from terminal and central nitrogen atoms, both leading to bent final state geometries. We also show computationally that the electronic structure of the charge transfer excitation smoothly depends on the nitrogen-proton distance and that there is a clear extension of the spectra going from infinity to close nitrogen-proton distance where fine structures show some, although not fully detailed, similarities. An interesting feature of partial localization of the nitrogen core orbitals, with a strong, non-monotonous, variation with nitrogen-proton distance could be highlighted. Specific effects could be unraveled when comparing molecular cation NEXAFS spectra, as represented by recently recorded spectra of N2+ and CO+, and spectra of protonated molecules as represented here by the N2H+ ion. Both types containing rich physical effects not represented in NEXAFS of neutral molecules because of the positive charge, whereas protonation also breaks the symmetry. The effect of the protonation on dinitrogen can be separated in charge, which extends the high-energy part of the spectrum, and symmetry-breaking, which is most clearly seen in the low-energy π* transition.

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. These parts, none of which has correspondence in NEXAFS spectra of neutral molecules, are dictated by the localization of the singly occupied 5σ orbital, adding a dimension of chemistry to the ionic NEXAFS technique.

Experimental and theoretical elucidation of catalytic pathways in TiO2-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. First, classical reactive molecular dynamics (MD) simulations based on the ReaxFF approach were used to reproduce the adsorption of the experimental glycine solution droplets sprayed onto an oxide support and to identify the most probable arrangement of the molecules that triggered the polymerization mechanisms. Then, quantum chemistry density functional tight binding (DF-TB) MDs and static density functional theory (DFT) calculations were carried out to further explore favorable configurations and to evaluate the energy barriers of the most promising reaction pathways for the peptide bond-formation reactions. The results confirmed the fundamental role played by the substrate to thermodynamically and kinetically favor the process and disclosed its main function as an immobilizing agent: the molecules accommodated in the surface channels close to each other were the ones starting the key events of the dimerization process and the most favorable mechanism was the one where a water molecule acted as a proton exchange mediator in the condensation process.

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. The outcomes of the molecular dynamics simulations suggest that the trend of the nanoparticulate sintering/coalescence time vs. temperature could provide a valid tool to determine the melting points of nanoparticles theoretically/experimentally.

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. It is demonstrated that all these events are connected with the specific orientation and location of cystine on the substrate. Simulations in pure water reveal that the disulfide bridge is stable, whereas dissociation is observed on gold. This is favored at low coverage, whereas at high coverage both intact and dissociated forms can be observed depending on local arrangements. The computed photoemission spectra at different K-edges for the predicted adsorbate structures satisfactorily agree with the experimental measurements extracted from literature.

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). To facilitate the NEXAFS feature assignments, X-ray Photoelectron Spectroscopy (XPS) measurements for NMA and FNMA have been carried out with the aim of obtaining the 1s electron ionization potentials, which are compared with the values predicted by our Hartree-Fock (ΔHF) and Multi Configuration Self Consistent Field (ΔMCSCF) calculations. We also demonstrate an approach to compensate for screening effects that are neglected in the STEX method. Ion yield measurements of FNMA associated with the excitation of several C, N, O, and F K-shell pre-edge resonances have revealed site-specific fragmentation in some cases which we interpret with the aid of our theoretical calculations.

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. Largely different photoabsorption cross-section patterns are experimentally observed in core excitations from the investigated quantum shells (n = 1, 2). This finding is confirmed by the oscillator strength distributions calculated at different absorption edges; in the case of the n = 2 shell the bands below the threshold are extremely weak and most of the absorption intensity is due to excitations in the continuum.

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. It is shown that the interaction of cysteine with the TiO2(110) surface has multipoint character involving the carboxylic group as well as the amino and sulfur groups. The proton-transfer reactivity of cysteine is enhanced by the presence of the surface, and different forms of cysteines are confirmed to be present in the adsorbate. A general conclusion is that reactive force field dynamics combined with selected spectroscopy provides a viable path to understanding bioinorganic surfaces with ramifications for the design of such surfaces for future technological applications.

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. New diglycine-copper bonding is predicted, and the results of the chemical shift analysis are, in all cases, fully compatible with structural information obtained through experimental measurements. Moreover, we have found that the process of proton transfer, which is fundamental in the dynamics of amino acids and peptides, occurs mainly by intermolecular interaction between the first and second layer of the adsorbate.

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. The contribution to the core electronic binding energy from all interactions within and between the two (DFT and MM) parts is accounted for, except charge transfer and dispersion. While the obtained results were found to be in qualitative agreement with experiment, their precision must be qualified with respect to the problem of counter ions, charge transfer and optimal division of QM and MM parts of the system. Results are compared to those of a recent study [Ottoson et al., J. Am. Chem. Soc., 2011, 133, 3120].

Photoemission and photoabsorption spectroscopy of glycyl-glycine in the gas phase.

The high-resolution outer and inner valence band (VB) spectra, as well as core level X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectra at the carbon, nitrogen, and oxygen K-edges of glycyl-glycine in the gas phase have been measured, and the results interpreted by means of ab initio calculations. By comparison with our previous glycine spectra, the features characteristic of the peptide bond in the carbon, nitrogen, and oxygen XPS and NEXAFS spectra of glycyl-glycine have been identified and assigned. The K-edge NEXAFS spectra at all edges were found to be in reasonable agreement with published electron energy loss spectra, but showed more prominent structure due to the higher resolution. Effects on the nitrogen K-edge NEXAFS spectrum of glycyl-glycine due to intramolecular hydrogen bonding were observed. The N(NH(2)) 1s --> pi*(CN) resonance shifts to 0.6 eV lower energy, due to internal hydrogen bonding between the NH(2) and NH groups.

Oxidation states of graphene: insights from computational spectroscopy.

When it is oxidized, graphite can be easily exfoliated forming graphene oxide (GO). GO is a critical intermediate for massive production of graphene, and it is also an important material with various application potentials. With many different oxidation species randomly distributed on the basal plane, GO has a complicated nonstoichiometric atomic structure that is still not well understood in spite of intensive studies involving many experimental techniques. Controversies often exist in experimental data interpretation. We report here a first principles study on binding energy of carbon 1s orbital in GO. The calculated results can be well used to interpret experimental x-ray photoelectron spectroscopy (XPS) data and provide a unified spectral assignment. Based on the first principles understanding of XPS, a GO structure model containing new oxidation species epoxy pair and epoxy-hydroxy pair is proposed. Our results demonstrate that first principles computational spectroscopy provides a powerful means to investigate GO structure.

Electronic structure of [121]tetramantane-6-thiol on gold and silver surfaces.

The mechanism for electron photoemission of [121]tetramantane and its functionalized compound [121]tetramantane-6-thiol adsorbed on different noble metal surfaces has been investigated by density functional theory calculations. It is found that good chemical bonding between molecules and metal surfaces is a helpful but not a necessary condition for electron photoemission. A lower work function and weaker hybridization between the molecule and the metal could lead to much more efficient electron photoemission. It is observed that, neglecting final state effect, a simple ground state picture cannot result in negative electron affinity for the systems under investigation. Calculations have shown that by exciting an electron in the lowest unoccupied molecular orbital, the highest singly occupied molecular orbital of the molecule can be shifted above the vacuum level, resulting in negative electron affinity and emission of the accumulated electrons.

Electronic structure of aromatic amino acids studied by soft x-ray spectroscopy.

The electronic structure of phenylalanine, tyrosine, tryptophan, and 3-methylindole in the gas phase was investigated by x-ray photoemission spectroscopy (XPS) and near edge x-ray absorption fine structure (NEXAFS) spectroscopy at the C, N, and O K-edges. The XPS spectra have been calculated for the four principal conformers of each amino acid, and the spectra weighted by the Boltzmann population ratios calculated from published free energies. Instead of the single peaks expected from the stoichiometry of the compounds, the N 1s core level spectra of phenylalanine and tryptophan show features indicating that more than one conformer is present. The calculations reproduce the experimental features. The C and O 1s spectra do not show evident effects due to conformational isomerism. The calculations predict that such effects are small for carbon, and for oxygen it appears that only broadening occurs. The carbon K-edge NEXAFS spectra of these aromatic amino acids are similar to the published data of the corresponding molecules in the solid state, but show more structure due to the higher resolution in the present study. The N K-edge spectra of tryptophan and 3-methylindole differ from phenylalanine and tyrosine, as the first two both contain a nitrogen atom located in a pyrrole ring. The nitrogen K-edge NEXAFS spectra of aromatic amino acids do not show any measurable effects due to conformational isomerism, in contrast to the photoemission results. Calculations support this result and show that variations of the vertical excitation energies of different conformers are small, and cannot be resolved in the present experiment. The O NEXAFS spectra of these three aromatic compounds are very similar to other, simpler amino acids, which have been studied previously.