Paolo Elvati

Effect of molecular configuration on binary diffusion coefficients of linear alkanes.

Mass diffusion coefficients are critically related to the predictive capability of computational combustion modeling. To date, the most common approach used to determine the molecular transport of gases is the Boltzmann transport equation of the gas kinetic theory. The Chapman-Enskog (CE) solution of this transport equation, combined with Lennard-Jones potential parameters, suggests a simple analytical expression for computing self and mutual diffusion coefficients. This approach has been applied over a wide range of flame modeling conditions due to its minimal computational requirement, despite the fact that the theory was developed only for molecules that have a spherical structure. In this study, we computed the binary diffusion coefficients of linear alkanes using all-atom molecular dynamics simulations over the temperature range 500-1000 K. The effect of molecular configurations on diffusion coefficients was determined relating the radii of gyration of the molecules to their corresponding collision diameters. The comparison between diffusion coefficients determined with molecular dynamics and the values obtained from the CE theory shows significant discrepancies, especially for nonspherical molecules. This study reveals the inability of CE theory with spherical potentials to account for the effect of molecular shapes on diffusion coefficients.

Size-and phase-dependent structure of copper(II) oxide nanoparticles

Copper(II) oxide (CuO) nanoparticles (NPs) have found numerous applications in electronics, optics, catalysis, energy storage, health, and water purification. Controlled synthesis of CuO NPs requires information on their nanoscale structure, which is expected to vary depending on the size, shape, phase, and most importantly, on the surface morphology. In this work, we report a detailed analysis of the structure of solid and melted CuO nanoparticles as functions of size and temperature at global and local scales, using molecular dynamics simulations. Comparisons of simulated X-ray diffraction profiles, mean bond lengths, average coordination numbers, and melting points with available experimental data support the modeling results. Melting points of CuO NPs vary linearly with the reciprocal of the diameters of NPs. The long-range order seen in solid nanoparticles with diameters greater than 6 nm gradually vanishes as size decreases, indicating the loss of translational symmetry of the lattice structure and the emergence of amorphous-like structure even below the melting point. Melted nanoparticles show liquid-like characteristics with only a short-range order. Mean bond lengths and average Cu–O coordination numbers of both solid and melted NPs indicate weakening of the structural stabilization for smaller NPs that leads to an increased deformation in the local atomic arrangement because of the lack of long-range interactions. For the cases studied, most of the structural features are independent of temperature, with the notable exception of the number of oxygen atoms coordinated to Cu. This latter quantity is indeed indicative of melting phase transition and can be used to compute the melting point accurately. Atoms on the surface of solid NPs show amorphous-like behavior even at temperatures well below the melting point of the NPs due to the limited coordination environment. This study represents a useful step towards the establishment of a structure–property relationship for CuO nanoparticles.

Critical Assessment of Photoionization Efficiency Measurements for Characterization of Soot-Precursor Species

We present a critical evaluation of photoionization efficiency (PIE) measurements coupled with aerosol mass spectrometry for the identification of condensed soot-precursor species extracted from a premixed atmospheric-pressure ethylene/oxygen/nitrogen flame. Definitive identification of isomers by any means is complicated by the large number of potential isomers at masses likely to comprise particles at flame temperatures. This problem is compounded using PIE measurements by the similarity in ionization energies and PIE-curve shapes among many of these isomers. Nevertheless, PIE analysis can provide important chemical information. For example, our PIE curves show that neither pyrene nor fluoranthene alone can describe the signal from C16H10 isomers and that coronene alone cannot describe the PIE signal from C24H12 species. A linear combination of the reference PIE curves for pyrene and fluoranthene yields good agreement with flame-PIE curves measured at 202 u, which is consistent with pyrene and fluoranthene being the two major C16H10 isomers in the flame samples, but does not provide definite proof. The suggested ratio between fluoranthene and pyrene depends on the sampling conditions. We calculated the values of the adiabatic-ionization energy (AIE) of 24 C16H10 isomers. Despite the small number of isomers considered, the calculations show that the differences in AIEs between several of the isomers can be smaller than the average thermal energy at room temperature. The calculations also show that PIE analysis can sometimes be used to separate hydrocarbon species into those that contain mainly aromatic rings and those that contain significant aliphatic content for species sizes investigated in this study. Our calculations suggest an inverse relationship between AIE and the number of aromatic rings. We have demonstrated that further characterization of precursors can be facilitated by measurements that test species volatility.

Free energy calculation of permeant-membrane interactions using molecular dynamics simulations

Nanotoxicology, the science concerned with the safe use of nanotechnology and nanostructure design for biological applications, is a field of research that has recently received great attention, as a result of the rapid growth in nanotechnology. Many nanostructures are of a scale and chemical composition similar to many biomolecular environments, and recent papers have reported evident toxicity of selected nanoparticles. Molecular simulations can help develop a mechanistic understanding of how structural properties affect bioactivity. In this chapter, we describe how to compute the free energy of interactions between cellular membranes and benzene, the main constituent of some toxic carbonaceous particles, with well-tempered metadynamics. This algorithm reconstructs the free energy surface and accelerates rare events in a coarse-grained representation of the system.

Graphene quantum dots: effect of size, composition and curvature on their assembly

Graphene Quantum Dots (GQDs) are a relatively new class of molecules that have ignited tremendous research interest due to their extraordinary and tunable optical, electrical, chemical and structural properties. In this work, we report a molecular-level elucidation of the key mechanisms and physical–chemical factors controlling the assembly and stability of nanostructures formed by GQDs in an aqueous environment, using molecular dynamics simulations. We observe the general tendency to form small aggregates and three recurring configurations, one of them with a single layer of water separating two GQDs. The type and characteristics of the structure are mostly determined by the hydrophobicity of the GQDs as well as the steric hindrance of the dangling groups. The composition of the terminal groups plays a key role in determining the configuration of the GQDs, which is also markedly affected by the formation of clusters. Notably, the aggregated GQDs assume strongly correlated shapes and, in some cases, display a radically different conformation distribution compared to single molecules. This cooperative effect prolongs the lifetime of the GQD configurations and can explain the observed persistence of chiral conformations that are only marginally more stable than their specular images.

Photoionization Efficiencies of Five Polycyclic Aromatic Hydrocarbons

We have measured photoionization-efficiency curves for pyrene, fluoranthene, chrysene, perylene, and coronene in the photon energy range of 7.5-10.2 eV and derived their photoionization cross-section curves in this energy range. All measurements were performed using tunable vacuum ultraviolet (VUV) radiation generated at the Advanced Light Source synchrotron at Lawrence Berkeley National Laboratory. The VUV radiation was used for photoionization, and detection was performed using a time-of-flight mass spectrometer. We measured the photoionization efficiency of 2,5-dimethylfuran simultaneously with those of pyrene, fluoranthene, chrysene, perylene, and coronene to obtain references of the photon flux during each measurement from the known photoionization cross-section curve of 2,5-dimethylfuran.

Twisting graphene quantum dots to impart chirality

Light-responsive chiral nanomaterials are attractive for their applications as metamaterials, in hyperbolic geometry, as highsensitivity bioanalysis agents, and as catalysts for asymmetric reactions. Nanocarbons belong to the family of light-responsive materials that includes fullerenes (spheres), carbon nanotubes (pillars), and graphene (sheets). Several studies have sought to introduce chirality to these materials, or to produce separate chiral configurations. Compared with some semiconductor inorganic nanoparticles (e.g., cadmium telluride), these materials are expected to be less toxic and thus may be considered as strong candidates for bioapplications. The synthetic methods for imparting chirality, however, are not transferable from one structure to another, and for the past decade, the goal of achieving chiral nanocarbons based on graphene has proved elusive. For example, methods that are suitable for the synthesis of chiral fullerenes cannot be extended to the preparation of enantiopure carbon nanotubes (those that have only one chiral geometry) because the growth of the graphene network requires a temperature in the range of several hundred degrees celsius, at which traditional asymmetric catalysts cannot survive. Another problem lies in the inherent geometry of the flat graphene sheet. In contrast with some fullerenes and nanotubes, with potential asymmetric arrangement of carbon atoms, flat graphene does not have defect-free, surface-configurational chiral symmetry (see Figure 1). In our work, we have thus focused on exploiting conformational flexibility as the key element to introduce chiral geometry into a nanocarbon structure. In our technique, we cut a nano-sized graphene quantum dot (GQD) from a flat sheet of graphene. This allows us to tune the wavelength of light that interacts with the material by quantum confinement of electrons or holes. With this size-control of the graphene sheet, we make the Figure 1. Nanocarbons considered for bioapplications, include chiral fullerene (left), chiral carbon nanotube (center), and flat graphene (right).