Effects of Iron Addition on the Collision of Polycyclic Aromatic Hydrocarbon Clusters: A Molecular Dynamics Study.

In this work, soot particle size distributions in iron-doped premixed ethylene flames are examined using scanning mobility particle sizer measurements. It is found that iron addition promotes the growth in soot particle size, and the enhanced particle coagulation is inferred to be an important reason. To support that, the influence of iron addition on the coagulation of polycyclic aromatic hydrocarbon (PAH) clusters, the analogue of incipient soot particles, is further investigated using molecular dynamics simulations. Based on the results of hundreds of binary head-on collision simulations, the collision between two coronene-Fe-coronene dimers is found to have a significantly higher coagulation efficiency than that between two coronene dimers. However, this enhancement effect weakens as the size of the PAH monomer increases. Although the coagulation efficiency can be increased by iron addition, the collision frequency is almost unaffected, as revealed from the binary off-central collision simulations. Moreover, the simulation results of coronene cluster growth via coagulation show that iron addition promotes coronene cluster growth, leading to larger cluster size, which may explain the larger soot particle size observed in iron-doped flames.

Theoretical studies on Lennard-Jones parameters of benzene and polycyclic aromatic hydrocarbons.

Lennard-Jones (L-J) parameters, i.e. collision diameter and well depth, of benzene and polycyclic aromatic hydrocarbons (PAHs) interacting with bath gases helium and nitrogen are studied theoretically in this work. The results of three different computing methods, called SA, σ-ε, η-ξ methods respectively, are compared with literature data. The SA method determines effective L-J parameters from the spherically averaged intermolecular potentials; the σ-ε method averages L-J parameters obtained from different relative orientations of interacting partners; and the η-ξ method uses an orientation-averaging rule on the basis of two characteristic variables η and ξ representing repulsive and attractive energy scales respectively. The σ-ε and η-ξ methods require much less computational time than the SA method due to the use of an iterative search algorithm. For validation of the L-J parameters, binary diffusion coefficients computed using L-J parameters by these three methods and those by empirical estimations are compared with experimental data from literature. Results show that while the SA method is reliable and the σ-ε method is efficient, the η-ξ method is both reliable and efficient for computing L-J parameters for benzene and PAHs, and captures the anisotropic effects of molecular structure on L-J parameters better than empirical methods.

Prediction Model of Photodegradation for PBAT/PLA Mulch Films: Strategy to Fast Evaluate Service Life.

Eco-friendly biodegradable PBAT/PLA mulch films are attracting increasing interest in sustainable agricultural production. However, currently, little is known about the service life for the PBAT/PLA mulch films. Herein, PBAT/PLA mulch films are subjected to indoor UV-accelerated degradation (UAD) experiments and field cultivation environment degradation (CED) experiments to systematically investigate the relationship between UAD and CED processes. Results demonstrate that 10 days of indoor UAD treatment corresponds to around 120 days aging under outdoor CED conditions. Using eight PBAT/PLA evaluation indicators (haze, elongation at break, tensile strength, gel content, light transmittance, polydispersity index, Mn, Mw), we established a service life prediction model for PBAT/PLA mulch films based on short-term indoor UAD experiments, which could accurately estimate the long-term service life of the mulch films in the field. In particular, using the haze value, near-perfect correlation (R2 = 0.995 for eq. 1 and R2 = 0.993 for eq. 2) was found between CED days and UAD days. The establishment of these reliable predictive models for the service lifetime of PBAT/PLA mulch films will avoid the undesirable premature breakdown during crop growth, thus fostering end-user confidence in eco-friendly biodegradable mulch films.

On the determination of Lennard-Jones parameters for polyatomic molecules.

Characterizing the key length and energy scales of intermolecular interactions, Lennard-Jones parameters, i.e., collision diameter and well depth, are prerequisites for predicting transport properties and rate constants of chemical species in dilute gases. Due to anisotropy in molecular structures, Lennard-Jones parameters of many polyatomic molecules are only empirically estimated or even undetermined. This study focuses on determining the effective Lennard-Jones parameters between a polyatomic molecule and a bath gas molecule from interatomic interactions. An iterative search algorithm is developed to find orientation-dependent collision diameters and well depths on intermolecular potential energy surfaces. An orientation-averaging rule based on characteristic variables is proposed to derive the effective parameters. Cross-interaction parameters for twelve hydrocarbons with varying molecular shapes, including long-chain and planar ones, interacting with four bath gases He, Ar, N2, and O2 are predicted and reported. Three-dimensional parametric surfaces are constructed to quantitatively depict molecular anisotropy. Algorithmic complexity analysis and numerical experiments demonstrate that the iterative search algorithm is robust and efficient. By using the latest experimental diffusion data, it is found that the proposed orientation-averaging rule improves the prediction of cross-interaction Lennard-Jones parameters for polyatomic molecules, including for long-chain molecules that challenge the consistency of previous methods. By introducing characteristic variables, the present study shows a new route to determining effective Lennard-Jones parameters for polyatomic molecules.

Molecular Dynamics Study on the Condensation of PAH Molecules on Quasi Soot Surfaces.

In this paper, the condensation efficiency of polycyclic aromatic hydrocarbon (PAH) molecules up to coronene, from 500 to 2000 K, is calculated based on hundreds of collisions between a PAH molecule and the quasi soot surface, which is composed of stacked coronene molecules with periodic boundary conditions, using molecular dynamics simulations. The results show that the condensation efficiency increases with the PAH molecular mass but decreases as the temperature increases, following a Gaussian function. Meanwhile, when the presence of aliphatic chains on soot particle surfaces is considered, the condensation efficiency can be lowered by up to 40%, being affected more significantly at higher temperatures. A condensation efficiency model is thus proposed from the molecular trajectories. Finally, when this newly proposed PAH condensation efficiency model is adopted, better agreement with the experiments is achieved in predicting soot volume fractions of an ethylene/oxygen/nitrogen mixture in a tandem jet-stirred reactor and a plug-flow reactor.

NUDT21 knockdown inhibits proliferation and promotes apoptosis of pancreatic ductal adenocarcinoma through EIF2 signaling.

The NUDT family is thought to play an important role in cancer growth and progression. However, the clinicopathologic significance and potential role of nucleotide diphosphate-linked X-component motif 21, NM_007006 (NUDT21) in pancreatic ductal adenocarcinoma (PDAC) remains largely unknown. In this study, we observed that NUDT21 was frequently up-expressed in PDAC. Clinical data revealed that its level positively correlated with poor survival of patients with PDAC. We found that knockdown of NUDT21 significantly inhibited cell proliferation and promoted apoptosis both in vitro and in vivo. Screening by microarray analysis and verifying by Western blot, we found that the EIF2 signaling pathway represented the main molecular mechanism underlying the effects of NUDT21 knockdown in PANC-1 cells, and PKR, HSPA5, EIF4E and DDIT3 may be its target genes. Thus, our results revealed for the first time that NUDT21, a valuable marker of PDAC prognosis, promotes tumor proliferation, inhibits cells apoptosis and might represent a potential target for gene-based therapy.

Peroxide-mediated site-specific C-H methylation of imidazo[1,2-a]pyridines and quinoxalin-2(1H)-ones under metal-free conditions.

An effective approach to realize the direct methylation of imidazo[1,2-a]pyridines and quinoxalin-2(1H)-ones with peroxides under metal-free conditions is described. In this protocol, peroxides serve as both the radical initiator and methyl source. Methylated imidazopyridines and quinoxalin-2(1H)-ones were smoothly synthesized in moderate to good yields. A free radical reaction mechanism was proposed to describe the methylation process.

Promoting SO2 Resistance of a CeO2(5)-WO3(9)/TiO2 Catalyst for Hg0 Oxidation via Adjusting the Basicity and Acidity Sites Using a CuO Doping Method.

The competition between SO2 and elemental mercury (Hg0) for active sites was an important factor for suppressing the Hg0 oxidation properties of catalysts. There were obvious differences in properties of basicity and acidity between SO2 and Hg0. Raising the SO2 resistance via adjusting the basicity and acidity sites of catalysts was promising for reducing the competition between SO2 and Hg0. This study aimed to form multiple active sites with different basicities via Cu, Fe, Mn, and Sn doping. The results indicated that Cu doping had the best modification performance. Five percent CuO doping could significantly improve the SO2 resistance of CuO(5)-CeO2(5)-WO3(9)/TiO2 and increase the mercury oxidation efficiency (MOE) from 54.7 to 85.5% in the condition (6% O2, 100 ppm NO, 100 ppm NH3, and 100 ppm SO2). CO2 temperature-programmed desorption analysis showed that CuO(5)-CeO2(5)-WO3(9)/TiO2 exhibited weak basic sites (CeO2), medium-strong basic sites (Cu-O-Ce), and strong basic sites (CuO). Therefore, the CuO in the Ce-O-Cu structure was prioritized for the reaction with acid gas SO2 and protected CeO2 from SO2 poisoning. This study prepared a highly SO2-resistant catalyst for Hg0 oxidation. This research and development will be conducive for use in Hg0 oxidation in actual coal-fired flue gases.

Reaction kinetics of hydrogen addition reactions to methyl butenoate.

To investigate the kinetics of hydrogen addition reactions of unsaturated methyl esters, we selected two representative molecules that are isomers with C[double bond, length as m-dash]C double bonds at different locations, i.e. methyl 2-butenoate and methyl 3-butenoate for study. An appropriate quantum chemical method was determined to compute the potential energy surfaces. The high-pressure limit rate constants were computed by applying multi-structural canonical variational transition state theory including tunneling by the multi-dimensional small-curvature tunneling approximation. The master equation analysis was followed to study the pressure-dependence of the rate constants of H addition and the subsequent dissociation reactions. The results show that it is easier for the H atom to add to the C[double bond, length as m-dash]C than to the C[double bond, length as m-dash]O bond because of the lower barrier heights, and the hydrogen addition reactions are faster for both methyl 2-butenoate and methyl 3-butenoate, except that the hydrogen abstraction is dominant at above 1700 K for methyl 2-butenoate. Using our computed rate constants, the prediction for methyl propanoate mole fraction agreed better with experimental data of methyl 2-butenoate combustion.

Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum).

BACKGROUND: Leaf mold, one of the major diseases of tomato caused by Cladosporium fulvum (C. fulvum), can dramatically reduce the yield and cause multimillion dollar losses annually worldwide. Mapping the resistance genes (R genes) of C. fulvum and devising MAS based strategies for breeding new cultivars is an effective approach to improve the resistance in tomato. Up to now, many C. fulvum genes or QTLs have been mapped using different genetic materials, but few studies focused on Cf-10 gene positioning. RESULTS: In this study, we investigated the genetic rules for Cf-10 and used a novel combinatorial strategy to rapidly map the Cf-10 gene. Initially, the performance of F1, F2 and BC1F1 individuals after infection, demonstrated that the resistance against C. fulvum was controlled by a single dominant gene. Two pools of resistant and susceptible individuals from F2 population were investigated, using mapping by sequencing approach and Cf-10 was found to be localized to 3.35 Mb and 3.74 Mb on chromosome 1, employing SNP/InDel index methods, respectively. After accounting for overlapping regions, these two algorithms yielded a total length of 3.29 Mb, narrowing down the target region. We further developed five serviceable KASP markers for this region based on sequencing data and conducted local QTL mapping using individuals from the F2 population, except for mapping by sequencing as mentioned above. Finally Cf-10 gene was mapped spanning a region of 790 kb, where only one gene (Solyc01g007130.3) was annotated as probable receptor protein kinase TMK1 with a LRR motif, a common R gene characteristic. The RT-qPCR analysis further confirmed the localization and the relative expression of Solyc01g007130.3 in Ontario 792 and was found to be significantly higher than that in Moneymaker at 9 dpi and 12 dpi, respectively. CONCLUSION: This study proposed a novel combinatorial strategy by combining SNP-index, InDel-index analyses and local QTL mapping using KASP genotyping approach to rapidly map genes responsible for specific traits and provided a robust base for cloning the Cf-10 gene. Furthermore, these analyses suggest that Solyc01g007130.3 is a potential candidate to be regarded as Cf-10 gene.

Effect of hindered internal rotation treatments on predicting the thermodynamic properties of alkanes.

When considering hindered internal rotation, we usually have several options, including (i) single structure harmonic oscillator (SS-HO) approximation that considers the lowest-energy conformer only and approximates all molecular vibrations as harmonic oscillations, (ii) one-dimensional (1-D) internal rotation treatment that replaces the corresponding vibrational mode with one-dimensional torsion, and (iii) the multistructural method with torsional anharmonicity (MS-T) that considers the multiple-structure and torsional anharmonicity. These methods differ greatly in computational cost and accuracy. To evaluate the effect of different treatments on predicting thermodynamic properties, we calculated enthalpy, entropy, and heat capacity for a series of normal and branched alkanes using six different methods, including the SS-HO treatment, three 1-D methods, the MS-T method, and the group additivity (GA) method. The comparison of the computational results with experimental data shows that GA and two 1-D methods proposed in this study are more suitable for reliable and rapid predictions of thermodynamic properties for large hydrocarbons with many carbon-carbon single bonds.

On the Prediction of Standard Enthalpy of Formation of C2-C4 Oxygenated Species.

In this study, to determine an efficient and accurate method for predicting standard enthalpy of formation (ΔfHo) of oxygenated species, we calculated ΔfHo for several typical C2-C4 oxygenated species using atomization and isodesmic reactions in combination with various quantum chemical methods, including six density functional theory methods, three compound methods, and CCSD(T)/CBS. Compared with experimental values, at the same quantum chemical level, ΔfHo values predicted by using isodesmic reactions are more accurate than those using atomization reactions. Comparing various quantum chemical methods when isodesmic reactions are used, the performance of G4 is the best with a mean unsigned deviation (MUE) of 0.3 kcal/mol and a standard deviation (SD) of 0.3 kcal/mol, while M06-2X can predict ΔfHo efficiently and accurately with an MUE of 0.6 kcal/mol and SD of 0.5 kcal/mol. Using the best methods we have found, we calculated the enthalpies of formation and other thermodynamic properties for dimethyl carbonate (DMC) and its associated species and then applied them in a DMC combustion model for predicting ignition delay times. Better agreement with the experiments is achieved when the newly computed thermodynamic properties are adopted.

Kinetics of Hydrogen Abstraction Reactions of Methyl Palmitate and Octadecane by Hydrogen Atoms.

Hydrogen abstractions play a crucial role in the consumption of fuel molecules during fuel pyrolysis and combustion processes. In this study, a generalized energy-based fragmentation approach was used to obtain CCSD(T)-F12a/cc-pVTZ energy barriers of hydrogen abstraction reactions by hydrogen atoms from methyl palmitate (C15H31COOCH3), a key component of biodiesel. The accuracy of M06-2X/6-311++G(d,p) for obtaining the energy barriers was evaluated against the CCSD(T) results. Based on the quantum chemical results, the high-pressure-limit rate constants for C15H31COOCH3 + H were calculated and compared with those of octadecane ( n-C18H38) reacting with H. The treatment of hindered internal rotations for such long-chain molecules was discussed and the rate rules for different abstraction sites were summarized. The results show that in the C15H31COOCH3 + H system, the α hydrogen abstraction no longer plays a dominant role as in small methyl esters, and the hydrogen atoms of CH2 groups far away from the ester group are more easily abstracted than those near the ester group.

Energy transfer in intermolecular collisions of polycyclic aromatic hydrocarbons with bath gases He and Ar.

Classical trajectory simulations of intermolecular collisions were performed for a series of polycyclic aromatic hydrocarbons interacting with the bath gases helium and argon for bath gas temperature from 300 to 2500 K. The phase-space average energy transferred per deactivating collision, ⟨∆Edown⟩, was obtained. The Buckingham pairwise intermolecular potentials were validated against high-level quantum chemistry calculations and used in the simulations. The reactive force-field was used to describe intramolecular potentials. The dependence of ⟨∆Edown⟩ on initial vibrational energy is discussed. A canonical sampling method was compared with a microcanonical sampling method for selecting initial vibrational energy at high bath gas temperatures. Uncertainties introduced by the initial angular momentum distribution were identified. The dependence of the collisional energy transfer parameters on the type of bath gas and the molecular structure of polycyclic aromatic hydrocarbons was examined.

Physiological and RNA-seq analyses provide insights into the response mechanism of the Cf-10-mediated resistance to Cladosporium fulvum infection in tomato.

KEY MESSAGE: Based on the physiological and RNA-seq analysis, some progress has been made in elucidating the Cf-10-mediated resistance responses to C. fulvum infection in tomato. GO and KEGG enrichment analysis revealed that the DEGs were significantly associated with defense-signaling pathways like oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Leaf mold, caused by the fungus Cladosporium fulvum, is one of the most common diseases affecting tomatoes worldwide. Cf series genes including Cf-2, Cf-4, Cf-5, Cf-9 and Cf-10 play very important roles in resisting tomato leaf mold. Understanding the molecular mechanism of Cf gene-mediated resistance is thus the key to facilitating genetic engineering of resistance to C. fulvum infection. Progress has been made in elucidating two Cf genes, Cf -19 and Cf -12, and how they mediate resistance responses to C. fulvum infection in tomato. However, the mechanism of the Cf-10- mediated resistance response is still unclear. In the present study, RNA-seq was used to analyze changes in the transcriptome at different stages of C. fulvum infection. A total of 2,242 differentially expressed genes (DEGs) responsive to C. fulvum between 0 and 16 days post infection (dpi) were identified, including 1,501 upregulated and 741 downregulated genes. The majority of DEGs were associated with defense-signaling pathways including oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Four DEGs associated with plant-pathogen interaction were uniquely activated in Cf-10 tomato and validated by qRT-PCR. In addition, physiological indicators including reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were measured at 0-21 dpi, and hormone expression [Jasmonic acid (JA) and salicylic acid (SA)] was estimated at 0 and 16 dpi to elucidate the mechanism of the Cf-10-mediated resistance response. C. fulvum infection induced the activities of POD, CAT and SOD, and decreased ROS levels. JA was determined to participate in the resistance response to C. fulvum during the initial infection period. The results of this study provide accountable evidence for the physiological and transcriptional regulation of the Cf-10-mediated resistance response to C. fulvum infection, facilitating further understanding of the molecular mechanism of Cf-10-mediated resistance to C. fulvum infection.

Dimerization of Polycyclic Aromatic Hydrocarbon Molecules and Radicals under Flame Conditions.

This work presents a dynamic and kinetic study on the dimerization of polycyclic aromatic hydrocarbon (PAH) molecules and radicals under flame conditions using reactive force field (ReaxFF) molecular dynamics (MD) simulations. The accuracy of the ReaxFF force field is evaluated through comparing with quantum chemistry (QC) calculations of the barrier heights and species concentrations of PAHs reacting with H and OH radicals. A series of homobinary collisions between PAH molecules/radicals are performed to reveal the influence of temperature, molecular size, PAH composition, and the number of radical sites on the dynamics and kinetics of PAH dimerization. Instead of directly forming the strong covalent bonds, the majority of the binary collisions between PAH radicals are bound with weak intermolecular interactions. Effects of oxygen on PAH radical dimerization are also investigated, which indicates that the oxygenated PAH radicals are less likely to contribute to soot nucleation. In addition, the temperature, PAH characteristic, and radical site dependent collision efficiency for PAH radical-radical combinations is extracted from this study.

Reaction kinetics of hydrogen abstraction from polycyclic aromatic hydrocarbons by H atoms.

Hydrogen abstraction reactions of polycyclic aromatic hydrocarbons (PAH) by H atoms play a very important role in both PAH and soot formation processes. However, large discrepancies up to a few orders of magnitude exist among the literature rate constant values. To increase the reliability of the computed rate constants, it is critical to obtain highly accurate potential energy surfaces. For this purpose, we have investigated the energetics of hydrogen abstraction from benzene and naphthalene using both high level-of-theory quantum chemistry methods and a series of density functional theory (DFT) methods, among which M06-2X/6-311g(d,p) has the best performance with a mean unsigned deviation from the CCSD(T)/CBS calculations of 1.0 kcal mol-1 for barrier heights and reaction energies. Thus, M06-2X/6-311g(d,p) has then been applied to compute the potential energy surfaces of the hydrogen abstraction reactions of a series of larger PAH. Based on the quantum chemistry calculations, rate constants are computed using the canonical transition state theory. The effects of the PAH size, structure, and reaction site on the energetics and rate constants are examined systematically. Finally, the hydrogen abstraction rate constants for application in PAH and soot surface chemistry models are recommended.

Kinetics and branching fractions of the hydrogen abstraction reaction from methyl butenoates by H atoms.

In order to explore the hydrogen abstraction reaction kinetics of unsaturated methyl esters by hydrogen atoms, we selected two molecules for study, in particular methyl 3-butenoate and methyl 2-butenoate, whose C[double bond, length as m-dash]C double bonds are at different locations. We first determined an accurate and efficient electronic structure method for the investigation by considering eight hydrogen abstraction reactions and comparing their barrier heights and reaction energies computed using several exchange-correlation density functionals to those obtained from CCSD(T)-F12a/jun-cc-pVTZ coupled cluster calculations. In this way, we found the M06-2X/ma-TZVP method to have the best performance with a mean unsigned deviation from the CCSD(T) calculations of 0.51 kcal mol-1. Based on quantum-chemical calculations by using the M06-2X/ma-TZVP method, we then computed rate constants for 298-2500 K by direct dynamics calculations using multi-structural canonical variational transition state theory including tunneling by the multi-dimensional small-curvature tunneling approximation (MS-CVT/SCT). The computed transmission coefficients were compared with those obtained using the zero-curvature tunneling (ZCT) and one-dimensional Eckart tunneling (ET) approximations. We employed the multi-structural torsional method (MS-T) to include the multiple-structure and torsional potential anharmonic effects. The results show that the variational recrossing transmission coefficients range from 0.6 to 1.0, and the multi-structural torsional anharmonicity introduces a factor of 0.5-2.5 into the rate constant, while the tunneling transmission coefficients obtained by SCT can be as large as 17.4 and differ considerably from those determined by the less accurate ZCT and ET approximations. In addition, independent of the location of the C[double bond, length as m-dash]C double bond, the dominant hydrogen abstraction reactions occur at the allylic sites.

Obtaining effective rate coefficients to describe the decomposition kinetics of the corannulene oxyradical at high temperatures.

Unimolecular reactions play an important role in combustion kinetics. An important task of reaction kinetic analysis is to obtain the phenomenological rate coefficients for unimolecular reactions based on the master equation approach. In most cases, the eigenvalues of the transition matrix describing collisional internal energy relaxation are of much larger magnitude than and well separated from the chemically significant eigenvalues, so that phenomenological rate coefficients may be unequivocally derived for incorporation in combustion mechanisms. However, when dealing with unimolecular reactions for a large molecule, especially at high temperatures, the large densities of states of the reactant cause the majority of the population distribution to lie at very high energy levels where the microcanonical reaction rate constants are large and the relaxation and chemical eigenvalues overlap, so that well-defined phenomenological rate coefficients cannot be determined. This work attempts to analyze the effect of overlapping eigenvalues on the high-temperature kinetics of a large oxyradical, based on microcanonical reaction rates and population distributions as well as the eigenvalue spectrum of the transition matrix from the master equation. The aim is to provide a pragmatic method for obtaining the most effective rate coefficients for competing elimination, dissociation, and bimolecular reactions for incorporation in combustion mechanisms. Our approach is demonstrated with a representative example, thermal decomposition and H addition reactions of the corannulene oxyradical.