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 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.Comment: accepted by J. Chem. Phy

Electronic structure of copper phthalocyanine:An experimental and theoretical study of occupied and unoccupied levels

An experimental and theoretical study of the electronic structure of copper phthalocyanine (CuPc) molecule is presented. We performed x-ray photoemission spectroscopy (XPS) and photoabsorption [x-ray absorption near-edge structure (XANES)] gas phase experiments and we compared the results with self-consistent field, density functional theory (DFT), and static-exchange theoretical calculations. In addition, ultraviolet photoelectron spectra (UPS) allowed disentangling several outer molecular orbitals. A detailed study of the two highest occupied orbitals (having a(1u) and b(1g) symmetries) is presented: the high energy resolution available for UPS measurements allowed resolving an extra feature assigned to vibrational stretching in the pyrrole rings. This observation, together with the computed DFT electron density distributions of the outer valence orbitals, suggests that the a(1u) orbital (the highest occupied molecular orbital) is mainly localized on the carbon atoms of pyrrole rings and it is doubly occupied, while the b(1g) orbital, singly occupied, is mainly localized on the Cu atom. Ab initio calculations of XPS and XANES spectra at carbon K-edge of CuPc are also presented. The comparison between experiment and theory revealed that, in spite of being formally not equivalent, carbon atoms of the benzene rings experience a similar electronic environment. Carbon K-edge absorption spectra were interpreted in terms of different contributions coming from chemically shifted C 1s orbitals of the nonequivalent carbon atoms on the inner ring of the molecule formed by the sequence of CN bonds and on the benzene rings, respectively, and also in terms of different electronic distributions of the excited lowest unoccupied molecular orbital (LUMO) and LUMO+1. In particular, the degenerate LUMO appears to be mostly localized on the inner pyrrole ring

Electronic structure of copper phthalocyanine:An experimental and theoretical study of occupied and unoccupied levels

An experimental and theoretical study of the electronic structure of copper phthalocyanine (CuPc) molecule is presented. We performed x-ray photoemission spectroscopy (XPS) and photoabsorption [x-ray absorption near-edge structure (XANES)] gas phase experiments and we compared the results with self-consistent field, density functional theory (DFT), and static-exchange theoretical calculations. In addition, ultraviolet photoelectron spectra (UPS) allowed disentangling several outer molecular orbitals. A detailed study of the two highest occupied orbitals (having a(1u) and b(1g) symmetries) is presented: the high energy resolution available for UPS measurements allowed resolving an extra feature assigned to vibrational stretching in the pyrrole rings. This observation, together with the computed DFT electron density distributions of the outer valence orbitals, suggests that the a(1u) orbital (the highest occupied molecular orbital) is mainly localized on the carbon atoms of pyrrole rings and it is doubly occupied, while the b(1g) orbital, singly occupied, is mainly localized on the Cu atom. Ab initio calculations of XPS and XANES spectra at carbon K-edge of CuPc are also presented. The comparison between experiment and theory revealed that, in spite of being formally not equivalent, carbon atoms of the benzene rings experience a similar electronic environment. Carbon K-edge absorption spectra were interpreted in terms of different contributions coming from chemically shifted C 1s orbitals of the nonequivalent carbon atoms on the inner ring of the molecule formed by the sequence of CN bonds and on the benzene rings, respectively, and also in terms of different electronic distributions of the excited lowest unoccupied molecular orbital (LUMO) and LUMO+1. In particular, the degenerate LUMO appears to be mostly localized on the inner pyrrole ring

Atomistic Modelling of Si Nanoparticles Synthesis

Silicon remains the most important material for electronic technology. Presently, some efforts are focused on the use of Si nanoparticles—not only for saving material, but also for improving the efficiency of optical and electronic devices, for instance, in the case of solar cells coated with a film of Si nanoparticles. The synthesis by a bottom-up approach based on condensation from low temperature plasma is a promising technique for the massive production of such nanoparticles, but the knowledge of the basic processes occurring at the atomistic level is still very limited. In this perspective, numerical simulations can provide fundamental information of the nucleation and growth mechanisms ruling the bottom-up formation of Si nanoclusters. We propose to model the low temperature plasma by classical molecular dynamics by using the reactive force field (ReaxFF) proposed by van Duin, which can properly describe bond forming and breaking. In our approach, first-principles quantum calculations are used on a set of small Si clusters in order to collect all the necessary energetic and structural information to optimize the parameters of the reactive force-field for the present application. We describe in detail the procedure used for the determination of the force field and the following molecular dynamics simulations of model systems of Si gas at temperatures in the range 2000–3000 K. The results of the dynamics provide valuable information on nucleation rate, nanoparticle size distribution, and growth rate that are the basic quantities for developing a following mesoscale model

Dynamics and Self-Assembly of Bio-functionalized Gold Nanoparticles (AuNPs) in Solution: Reactive MD Simulations

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Dynamics and Self-Assembly of Bio-functionalized Gold Nanoparticles (AuNPs) in Solution: Reactive MD Simulations

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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. The reaction barriers are estimated through the nudged elastic band approach and checked by QC calculations. Surface reconstructions, induced by the strong adsorption of the molecule, are identified, and their role, as further adsorbate stabilizers, is properly disclosed. The satisfactory agreement with QC data and experiments confirm the reliability of the simulations and the unique opportunity they provide to follow locally molecule adsorption on selected materials

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. The reaction barriers are estimated through the nudged elastic band approach and checked by QC calculations. Surface reconstructions, induced by the strong adsorption of the molecule, are identified, and their role, as further adsorbate stabilizers, is properly disclosed. The satisfactory agreement with QC data and experiments confirm the reliability of the simulations and the unique opportunity they provide to follow locally molecule adsorption on selected materials

Reactive Dynamics Simulation of Monolayer and Multilayer Adsorption of Glycine on Cu(110)

The process of mono- and multilayer adsorption of glycine on copper surface Cu(110) and the preferred binding modes of the molecule were studied theoretically by means of classical reactive (ReaxFF) molecular dynamics simulations. Starting from glycines in gas phase in the neutral nonzwitterionic form, the most stably adsorbed structures are found to be the molecules which release their carboxyl protons (anionic form) to molecules in the second layer and place both the carboxyl oxygens and the nitrogen atom on top of copper sites, at an average distance of about 2 Å. The surface binding mechanism consists of different phases during which major conformational rearrangements and several intermediate adsorption configurations are observed. The overall stability of the glycine adlayers is essentially due to the combination of different intermolecular forces, namely chemical bonds with the copper top layer and intermolecular hydrogen bonds within the adsorbed molecular units. At low coverage the molecules are prevalently attached to the substrate in a bidentate fashion, i.e., through the nitrogen atom and one oxygen atom of the carboxyl group, whereas at higher coverage the molecules tend to diffuse on the surface and pack in long-range ordered heterochiral domains where tridentate geometries are most likely observed. The picture that emerges from the present reactive dynamics simulations satisfactorily agrees with the experimental data and theoretical results, based on geometry optimization, reported to date

Ethanol in Aqueous Solution Studied by Microjet Photoelectron Spectroscopy and Theory

ConspectusBy 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 CH3to 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