Conventional and alternative jet fuels, such as petroleum-derived Jet-A, coal-derived IPK, and natural-gas-derived S-8, display significant chemical and physical fuel property differences that influence their ignition characteristics. The current work addresses the need for surrogate mixtures capable of emulating the various properties of these fuels and their select blends, which are often used within compression ignited engines for acceptable ignition behavior. A six-component surrogate palette is proposed with species that are readily available within recent kinetic mechanisms, including n-dodecane, n-decane, iso-cetane, iso-octane, decalin, and toluene. The use of these species allows for a seamless compositional transition between the neat target jet fuels and their blends. The surrogate optimizer, which includes various correlations and models to estimate properties of model mixtures, is used to determine the surrogate composition that best matches target fuel properties. For an accurate ignition quality prediction during the optimization, a non-linear Derived Cetane Number regression equation is generated from Ignition Quality Tester experiments of 76 surrogate component mixtures. The newly formulated surrogates and their blends successfully capture the wide range of properties present within the target fuels, including temperature-dependent physical properties such as density, viscosity, specific heat, and volatility, along with experimental ignition delays obtained from a constant volume spray chamber. Kinetic modeling with a detailed mechanism showed that predicted ignition delay times are in good agreement with shock tube and rapid compression machine ignition delay experiments. A sensitivity analysis with variations in the composition of the Jet-A surrogate showed that its calculated ignition delay times are most sensitive to the composition of n-dodecane among the four Jet-A surrogate constituents over the range of temperatures and pressures examined.

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.

Chiral nanostructures from metals and semiconductors attract wide interest as components for polarization-enabled optoelectronic devices. Similarly to other fields of nanotechnology, graphene-based materials can greatly enrich physical and chemical phenomena associated with optical and electronic properties of chiral nanostructures and facilitate their applications in biology as well as other areas. Here, we report that covalent attachment of l/d-cysteine moieties to the edges of graphene quantum dots (GQDs) leads to their helical buckling due to chiral interactions at the “crowded” edges. Circular dichroism (CD) spectra of the GQDs revealed bands at ca. 210–220 and 250–265 nm that changed their signs for different chirality of the cysteine edge ligands. The high-energy chiroptical peaks at 210–220 nm correspond to the hybridized molecular orbitals involving the chiral center of amino acids and atoms of graphene edges. Diverse experimental and modeling data, including density functional theory calculations of CD spectra with probabilistic distribution of GQD isomers, indicate that the band at 250–265 nm originates from the three-dimensional twisting of the graphene sheet and can be attributed to the chiral excitonic transitions. The positive and negative low-energy CD bands correspond to the left and right helicity of GQDs, respectively. Exposure of liver HepG2 cells to l/d-GQDs reveals their general biocompatibility and a noticeable difference in the toxicity of the stereoisomers. Molecular dynamics simulations demonstrated that d-GQDs have a stronger tendency to accumulate within the cellular membrane than l-GQDs. Emergence of nanoscale chirality in GQDs decorated with biomolecules is expected to be a general stereochemical phenomenon for flexible sheets of nanomaterials.Keywords: biological activity; chiral excitons; chirality; circular dichroism; graphene quantum dots;

Many oxygenated hydrocarbon species formed during combustion, such as furans, are highly toxic and detrimental to human health and the environment. These species may also increase the hygroscopicity of soot and strongly influence the effects of soot on regional and global climate. However, large furans and associated oxygenated species have not previously been observed in flames, and their formation mechanism and interplay with polycyclic aromatic hydrocarbons (PAHs) are poorly understood. We report on a synergistic computational and experimental effort that elucidates the formation of oxygen-embedded compounds, such as furans and other oxygenated hydrocarbons, during the combustion of hydrocarbon fuels. We used ab initio and probabilistic computational techniques to identify low-barrier reaction mechanisms for the formation of large furans and other oxygenated hydrocarbons. We used vacuum-UV photoionization aerosol mass spectrometry and X-ray photoelectron spectroscopy to confirm these predictions. We show that furans are produced in the high-temperature regions of hydrocarbon flames, where they remarkably survive and become the main functional group of oxygenates that incorporate into incipient soot. In controlled flame studies, we discovered ∼100 oxygenated species previously unaccounted for. We found that large alcohols and enols act as precursors to furans, leading to incorporation of oxygen into the carbon skeletons of PAHs. Our results depart dramatically from the crude chemistry of carbon- and oxygen-containing molecules previously considered in hydrocarbon formation and oxidation models and spearhead the emerging understanding of the oxidation chemistry that is critical, for example, to control emissions of toxic and carcinogenic combustion by-products, which also greatly affect global warming.

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.

Nanoparticles formed in gas phase environments, such as combustion, have an important impact on society both as engineering components and hazardous pollutants. A new software package, the Stochastic Nanoparticle Simulator (SNAPS) was developed, applying a stochastic chemical kinetics methodology, to computationally investigate the growth of nanoparticle precursors through trajectories of chemical reactions. SNAPS was applied to characterize the growth of polycyclic aromatic hydrocarbons (PAHs), important precursors of carbonaceous nanoparticles and soot, in a premixed laminar benzene flame, using a concurrently developed PAH growth chemical reaction mechanism, as well as an existing benzene oxidation mechanism. Simulations of PAH ensembles successfully predicted existing experimentally measured data and provided novel insight into chemical composition and reaction pathways. The most commonly observed PAH isomers in simulations showed the importance of 5-membered rings, which contrasts with traditionally assumed compositions involving primarily pericondensed 6-membered rings. In addition, the chemical growth of PAHs involved complex sequences of highly reversible reactions, rather than relatively direct routes of additions and ring closures. Furthermore, the most common reactions involved 5-membered rings, suggesting their importance to PAH growth. The framework developed in this work will facilitate future investigation of particle inception and soot formation and will benefit engineering of novel combustion technologies to mitigate harmful emissions.

Environmental and energy security concerns have motivated an increased focus on developing clean, efficient combustors, which increasingly relies on insight into the combustion chemistry of fuels. In particular, naphthenes (cycloalkanes and alkylcycloalkanes) are important chemical components of distillate fuels, such as diesel and jet fuels. As such, there is a growing interest in describing napthene reactivity with kinetic mechanisms. Use of these mechanisms in predictive combustion models aids in the development of combustors. This study focuses on the pyrolysis of n-butylcyclohexane (n-BCH), an important representative of naphthenes in jet fuels. Seven different unimolecular decomposition pathways of C–C bond fission were explored utilizing ab initio/DFT methods. Accurate reaction energies were computed using the high-level quantum composite G3B3 method. Variational transition state theory, Rice–Ramsperger–Kassel–Marcus/master equation simulations provided temperature- and pressure-dependent rate constants. Implementation of these pathways into an existing chemical kinetic mechanism improved the prediction of experimental OH radical and H2O speciation in shock tube oxidation. Simulations of this combustion showed a change in the expected decomposition chemistry of n-BCH, predicting increased production of cyclic alkyl radicals instead of straight-chain alkenes. The most prominent reaction pathway for the decomposition of n-BCH is n-BCH = C3H7 + C7H13. The results of this study provide insight into the combustion of n-BCH and will aid in the future development of naphthene kinetic mechanisms.

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.

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.

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.

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 CO2 formation, namely CH3OCO═CH3 + CO2 (R1) and CH3OCO═CH3O + 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 = C2H4 + CH3COOCH3. This latter pathway requires the inclusion of the CH3COOCH3 decomposition model suggested by Westbrook et al. [Proc. Combust. Inst. 2008, accepted]. The newly composed kinetic mechanism for MB is used to study the CO2 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 CO2 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 C2H 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 mechanism’s capability to predict CO2 formation and ignition delay times in pyrolysis and oxidation conditions.

A new multiscale coarse-graining procedure is used to study carbonaceous nanoparticle agglomeration in combustion environments. The computational methodology is applied to an ensemble of 10,000 nanoparticles (or effectively 2 million total carbon atoms) to simulate, for the first time, 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 MD simulations. The coarse-grained MD results show rich and varied clustering behaviors for different particle morphology and, in some cases, the formation of primary particles with a diameter around 15 nm are observed for the first time by molecular simulation techniques.

Burgeoning global demand for energy has increased concerns about the fuel security issues and deleterious environmental impacts that result from the ubiquitous use of fossil fuels to meet these needs. This article is a review of completed work towards the goal of creating chemical kinetic mechanisms for biodiesel, which will aid in the development of clean and efficient combustors that utilize alternative fuels. As the composition of biodiesel is too complex to directly model, efforts have instead focused on the development of mechanisms for surrogates, simpler molecules that can produce the primary characteristics of biodiesel combustion. Research initially targeted smaller molecules like methyl butanoate to investigate the role of the characteristic ester group that is present in the fatty acid alkyl esters that comprise biodiesel. The study of isomers and similar unsaturated compounds elucidated the effects of molecular structure on combustion. Subsequent efforts involved the study of larger molecules that are close in scale to biodiesel molecules, such as methyl decanoate, as well as molecules that are present in biodiesel, such as methyl stearate. Applications of kinetic modeling demonstrate its utility in the study of combustion through, for example, revealing the chemistry in the early formation of CO2 in biodiesel and its soot reduction tendencies. The results of this review illustrate key limitations in kinetic modeling, namely a need for high-pressure kinetic methodology and a need for continuous improvement of kinetic mechanisms through theory and experiment. These limitations suggest direction for future research; further experimental and theoretical work will produce accurate mechanisms for appropriate biodiesel surrogates. All of these efforts represent significant advances in kinetic modeling that are important towards the goal of building a predictive capability for biodiesel combustion. Such predictive capability will aid the development of combustion technologies that will help society meet its energy needs in an environmentally conscious manner.

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 C60 was compared with a prototypical opened C60 molecule and a representative combustion-generated particle, C68H29, 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 C60 to represent similarly sized carbonaceous nanoparticles for assessments of toxicity is questioned.

The emission standards of combustion have been steadily reduced in recent years, and a large research effort has been focused on lowering the emissions of hydrocarbons and particulate matter. Addition of oxygenates to fuel reduces these pollutants. In this paper, we report on a detailed investigation of the growth mechanisms for gas-phase species in ethylene/air and ethylene/ethanol/air flames in order to assess the importance of various chemical mechanisms for the molecular growth of soot precursors. We employ a variety of computational techniques that include stochastic and deterministic methods to study the formation of gas-phase species and their growth into soot precursors via chemical and physical mechanisms. We have drawn the following conclusions: 1) the chemistry of oxygenated compounds (specifically the high concentrations of O2 and OH) is critical to reproduce the experiments; 2) using free energy simulations, we found out that the tendency of molecules to form dimers is mainly affected by the molecular shape rather than the mass of the aggregate. Finally we propose a different mechanism for the growth of soot precursors based on radical–radical recombination to form molecules of high molecular masses (>1200 u). These structures are then likely to promote physical aggregation to further the growth mechanism.

Soot particles are a significant pollutant formed as the result of incomplete combustion. Particle nucleation significantly impacts the formation and morphology of soot particles, yet remains a key knowledge gap. To elucidate the process of nucleation, we have investigated the thermodynamic stability of dimers of polycyclic aromatic hydrocarbons (PAHs), towards developing a more comprehensive model for PAH clustering behavior. Using a computational methodology based on molecular dynamics and well-tempered Metadynamics, we quantified the impact of morphological parameters on homo-molecular dimerization, as well as the relative size of monomers on the stability of hetero-molecular dimers. The results illustrated the substantial impact of PAH mass and geometry on the stability of homo-molecular and hetero-molecular dimers at flame temperatures. In particular, dimer stability was found to depend most strongly on monomer mass, followed by solvent-accessible surface area. Additionally, hetero-molecular dimer stability was found to be largely determined by the size of the smallest monomer. Identifying relationships between PAH morphology and thermodynamic stability is a significant step towards a more comprehensive understanding of the physical interactions between PAHs. Altogether, this work presents a framework for elucidating the clustering behavior of arbitrary PAHs and will greatly impact understanding and modeling of particle nucleation and growth.

Soot nucleation bridges the transition from gaseous hydrocarbons to macromolecular building blocks (nanoparticles) that eventually turn into soot. Polycyclic aromatic hydrocarbons (PAH) have often been invoked as important compounds of this process but their role has not been clearly identified. In this paper we report on a detailed analysis of the physical interactions between PAH in the range 200–450 amu using Molecular Dynamics simulations. In particular, we identified a pool of nine aromatics and studied their clustering behaviors in systems composed of thousands of homo-molecular and hetero-molecular molecules to understand the influence of molecular mass, morphology and temperature on the nucleation process. At temperatures higher than 1000 K, small clusters of PAH (2–5 molecules) are detected but they are not stable enough to accommodate the further growth into larger particles. This result raises doubts on the ability of these molecules to become soot nuclei. Molecular morphology is another important parameter for the nucleation process. Aromatics with attached aliphatic chains show considerably faster nucleation rates than the corresponding polycyclic aromatic hydrocarbons of similar mass without any chain. The collision efficiency is not increased by the aliphatic chain attachments, which may indicate that a faster nucleation process for these systems is due to the ability of these molecules to accommodate the collision energy into additional internal vibrational modes of the aliphatic chains. The results of this study provide information on the clustering behavior of PAH and can lead to the development of a more complex model to describe the physical nucleation of PAH that includes molecular masses, morphologies and temperature as main parameters to describe the transition from gas-phase species to macromolecular structures.

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.

Nanoparticles formed in gas phase environments, such as combustion, have an important impact on society both as engineering components and hazardous pollutants. A new software package, the Stochastic Nanoparticle Simulator (SNAPS) was developed, applying a stochastic chemical kinetics methodology, to computationally investigate the growth of nanoparticle precursors through trajectories of chemical reactions. SNAPS was applied to characterize the growth of polycyclic aromatic hydrocarbons (PAHs), important precursors of carbonaceous nanoparticles and soot, in a premixed laminar benzene flame, using a concurrently developed PAH growth chemical reaction mechanism, as well as an existing benzene oxidation mechanism. Simulations of PAH ensembles successfully predicted existing experimentally measured data and provided novel insight into chemical composition and reaction pathways. The most commonly observed PAH isomers in simulations showed the importance of 5-membered rings, which contrasts with traditionally assumed compositions involving primarily pericondensed 6-membered rings. In addition, the chemical growth of PAHs involved complex sequences of highly reversible reactions, rather than relatively direct routes of additions and ring closures. Furthermore, the most common reactions involved 5-membered rings, suggesting their importance to PAH growth. The framework developed in this work will facilitate future investigation of particle inception and soot formation and will benefit engineering of novel combustion technologies to mitigate harmful emissions.