Angela Violi

Kinetic Modeling of Methyl Butanoate in Shock Tube

An increased necessity for energy independence and heightened concern about the effects of rising carbon dioxide levels have intensified the search for renewable fuels that could reduce our current consumption of petrol and diesel. One such fuel is biodiesel, which consists of the methyl esters of fatty acids. Methyl butanoate (MB) contains the essential chemical structure of the long-chain fatty acids and a shorter, but similar, alkyl chain. This paper reports on a detailed kinetic mechanism for MB that is assembled using theoretical approaches. Thirteen pathways that include fuel decomposition, isomerization, and propagation steps were computed using ab initio calculations [J. Org. Chem. 2008, 73, 94]. Rate constants from first principles for important reactions in CO(2) formation, namely CH(3)OCO=CH(3) + CO(2) (R1) and CH(3)OCO=CH(3)O + CO (R2) reactions, are computed at high levels of theory and implemented in the mechanism. Using the G3B3 potential energy surface together with the B3LYP/6-31G(d) gradient, Hessian and geometries, the rate constants for reactions R1 and R2 are calculated using the Rice-Ramsperger-Kassel-Marcus theory with corrections from treatments for tunneling, hindered rotation, and variational effects. The calculated rate constants of reaction R1 differ from the data present in the literature by at most 20%, while those of reaction R2 are about a factor of 4 lower than the available values. The new kinetic model derived from ab initio simulations is combined with the kinetic mechanism presented by Fisher et al. [Proc. Combust. Inst. 2000, 28, 1579] together with the addition of the newly found six-centered unimolecular elimination reaction that yields ethylene and methyl acetate, MB = C(2)H(4) + CH(3)COOCH(3). This latter pathway requires the inclusion of the CH(3)COOCH(3) decomposition model suggested by Westbrook et al. [Proc. Combust. Inst. 2008, accepted]. The newly composed kinetic mechanism for MB is used to study the CO(2) formation during the pyrolysis of MB as well as to investigate the autoignition of MB in a shock tube reactor at different temperatures and pressures. The computed results agree very well with experimental data present in the literature. Sensitivity and flux (rate-of-production) analyses are carried out for the CO(2) formation with the new MB mechanism, together with available reaction mechanisms, to assess the importance of various kinetic pathways for each regime. With the new mechanism, the flux analyses for the formation of C(2)H species, one of the most important species for ignition delay time, are also presented at different conditions. In addition to giving a better chemical insight of the pyrolysis/oxidation of MB, the results suggest ways to improve the mechanisms capability to predict CO(2) formation and ignition delay times in pyrolysis and oxidation conditions.

Simulation of Nanoparticle Permeation through a Lipid Membrane

A metric of nanoparticle toxicity is the passive permeability rate through cellular membranes. To assess the influence of nanoparticle morphology on this process, the permeability of buckyball-sized molecules through a representative lipid bilayer was investigated by molecular-dynamics simulation. When C(60) was compared with a prototypical opened C(60) molecule and a representative combustion-generated particle, C(68)H(29), the calculated free-energy profiles along the permeation coordinate revealed a sizable variation in form and depth. The orientation of the anisotropic molecules was determined by monitoring the principal axis corresponding to the largest moment of inertia, and free rotation was shown to be hindered in the bilayer interior. Diffusion constant values of the permeant molecules were calculated from a statistical average of seven to 10 trajectories at five locations along the permeation coordinate. A relatively minor variation of the values was observed in the bilayer interior; however, local resistance values spanned up to 24 orders of magnitude from the water layer to the bilayer center, due primarily to its exponential dependence on free energy. The permeability coefficient values calculated for the three similarly sized but structurally distinct nanoparticles showed a significant variance. The use of C(60) to represent similarly sized carbonaceous nanoparticles for assessments of toxicity is questioned.

KINETIC MONTE CARLO–MOLECULAR DYNAMICS APPROACH TO MODEL SOOT INCEPTION

The processes involved in soot precursor formation exhibit a wide range of timescales, spanning pico- or nanoseconds for intramolecular processes that can occur on a particle surface to milliseconds for the formation of the first soot precursors. To accurately describe the soot formation process, it is important to model the reactions happening at different timescales. The use of atomistic models allows this. The code, named KMC/MD, combines the strengths of Kinetic Monte Carlo for long-time sampling, and Molecular Dynamics for relaxation processes. It enables the investigation of physical as well as chemical properties of the carbonaceous nanoparticles formed, such as particle morphology and concentration of free radicals.

Molecular Dynamics Simulation Study of a Pulmonary Surfactant Film Interacting with a Carbonaceous Nanoparticle

This article reports an all-atom molecular dynamics simulation to study a model pulmonary surfactant film interacting with a carbonaceous nanoparticle. The pulmonary surfactant is modeled as a dipalmitoylphosphatidylcholine monolayer with a peptide consisting of the first 25 residues from surfactant protein B. The nanoparticle model with a chemical formula C188H53 was generated using a computational code for combustion conditions. The nanoparticle has a carbon cage structure reminiscent of the buckyballs with open ends. A series of molecular-scale structural and dynamical properties of the surfactant film in the absence and presence of nanoparticle are analyzed, including radial distribution functions, mean-square displacements of lipids and nanoparticle, chain tilt angle, and the surfactant protein B peptide helix tilt angle. The results show that the nanoparticle affects the structure and packing of the lipids and peptide in the film, and it appears that the nanoparticle and peptide repel each other. The ability of the nanoparticle to translocate the surfactant film is one of the most important predictions of this study. The potential of mean force for dragging the particle through the film provides such information. The reported potential of mean force suggests that the nanoparticle can easily penetrate the monolayer but further translocation to the water phase is energetically prohibitive. The implication is that nanoparticles can interact with the lung surfactant, as supported by recent experimental data by Bakshi et al.

A Coarse-Grained Molecular Dynamics Study of Carbon Nanoparticle Aggregation

A multiscale coarse-graining procedure is used to study carbonaceous nanoparticle assembly. The computational methodology is applied to an ensemble of 10 000 nanoparticles (or effectively 2 million total carbon atoms) to simulate the agglomeration of carbonaceous nanoparticles using coarse-grained atomistic-scale information. In particular, with the coarse-graining approach, we are able to assess the influence of nanoparticle morphology and temperature on the agglomeration process. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to data obtained from trajectories and forces from all-atom molecular dynamics simulation. The coarse-grained molecular dynamics results show rich and varied clustering behaviors for different particle morphologies. They are shown to reproduce accurately the structural properties of the nanoparticles systems studied, while allowing for molecular dynamics simulations of much larger self-assembled nanoparticles systems.

Pyrolytic Hydrocarbon Growth from Cyclopentadiene

Aromatic hydrocarbon growth from cyclopentadiene (CPD) was studied using a laminar flow reactor operating in the temperature range 550-950 °C without oxygen. Benzene, indene, and naphthalene were the major products, which is in agreement with the previous computational studies on the reaction pathways from CPD. A crossover of indene and naphthalene yields around 775 °C was also observed, which further supports the results of the computational studies. Although the specific intermediates in the proposed pathways from CPD were not detected, the high selectivity of products and the observation of other methylindene and dihydronaphthalene intermediates suggest that the recombination of two CPDs via radical-molecule and/or radical-radical pathways to form indene and naphthalene is the dominant formation pathway. In addition to the products from the CPD-CPD reactions, the products from the reactions of CPD with indene, naphthalene, and acenaphthylene were also observed, which demonstrate the importance of CPD in carbon growth.

Order-disorder phase transformation of triacylglycerols: effect of the structure of the aliphatic chains.

Plant oils have been used as environmentally benign lubricants since they present high viscosity index and flash points and low evaporation loss. Triacylglycerols (TAG) are the major components of naturally occurring oils and fats and are able to produce high strength lubricant films. One of the main concerns that hinders the usage of triacylglycerols as lubricants, however, is the thermal stability of these molecules. In this paper, we report on the effect of chain structure on density, viscosity, and thermal stability of triacylglycerols using molecular dynamics simulations. The selected triacylglycerols are trilauroylglycerol (LLL-TAG), tristearoylglycerol (SSS-TAG), trans-trioleoylglycerol (trans-OOO-TAG), and trans-trilinolenoylglycerol (trans-LeLeLe-TAG). The first two TAGs are saturated molecules with a different number of carbons in the chain, and the second two TAGs are monounsaturated and polyunsaturated molecules, respectively. The computed results demonstrate that the length of the aliphatic chain influences the physical properties of triacylglycerols. TAGs with short chain (LLL-TAG) show higher density than TAGs with longer chains. Viscosity is determined by the degree of recoil of the aliphatic chains and by the number and location of unsaturated bonds. Thermal stability, as represented by the ability of triacylglycerols to stay in a disordered phase during the cooling process, is related to the order-disorder phase transition temperature. Since the phase transition temperature can be correlated to the thermal stability during the cooling process, LeLeLe-TAG shows the highest thermal stability among the systems considered. These results can aid in the design of molecules with specific lubrication properties.

Modeling aerosol formation in opposed-flow diffusion flames

The microstructures of atmospheric pressure, counter-flow, sooting, flat, laminar ethylene diffusion flames have been studied numerically by using a new kinetic model developed for hydrocarbon oxidation and pyrolysis. Modeling results are in reasonable agreement with experimental data in terms of concentration profiles of stable species and gas-phase aromatic compounds. Modeling results are used to analyze the controlling steps of aromatic formation and soot growth in counter-flow configurations. The formation of high molecular mass aromatics in diffusion controlled conditions is restricted to a narrow area close to the flame front where these species reach a molecular weight of about 1000 u. Depending on the flame configuration, soot formation is controlled by the coagulation of nanoparticles or by the addition of PAH to soot nuclei.

Reaction pathways for the thermal decomposition of methyl butanoate.

In recent years, biodiesel fuels, consisting of long-chain alkyl (methyl, ethyl, propyl) esters, have emerged as viable alternatives to petroleum-based fuels. From a combustion chemistry standpoint, there is great interest in developing accurate reaction models for these new molecules that can be used to predict their behaviors in various regimes. In this paper, we report a detailed study of the unimolecular decomposition pathways of methyl butanoate (MB), a short-chain ester that contains the basic chemical structure of biodiesel fuels. Using ab initio/DFT methods, we identified five homolytic fissions of C-C and C-O bonds and five hydrogen transfer reactions. Rate constants were determined using the G3B3 theory coupled with both variational transition state theory and Rice-Ramsperger-Kassel-Marcus/master equation simulations with hindered rotation corrections. Branching ratios in the temperature range 1500-2200 K indicate that the main pathway for thermal decomposition of MB is the reaction CH3CH2CH2C(═O)OCH3 → C2H5 + CH2C(═O)OCH3. The results, in terms of reaction pathways and rate constants, can be used for future development of mechanisms for long alkyl-chain esters.

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.