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1.
Int J Legal Med ; 134(2): 399-409, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31811377

RESUMO

With growing cancer morbidity, forensics cases in which archived tumour tissues can be used as biological samples are increasing, and an effective method to identify the body source of tumour tissues is needed. Single nucleotide polymorphisms (SNPs) may be a promising biomarker to identify the source of tumour tissues because of their low mutation rate and small amplicon size. Next-generation sequencing techniques offers the ability to detect hundreds of SNPs in a single run. The Precision ID Identity Panel (Thermo Fisher Scientific, Waltham, MA, USA) detects 90 autosomal SNPs for individual identification and 34 lineage-informative SNPs on Y chromosome using the Ion PGM system (Thermo Fisher Scientific). In this study, we evaluated performance of the panel for individual identification of tumour tissues. One hundred and fifty pairs of tumour tissues and corresponding normal tissues were analysed. Loss of heterozygosity was detected only in tumour tissues. The identity-by-state (IBS) scoring system was adopted to identify the body source of tumour tissues. The IBS score, as well as the number of loci with 2 alleles (A2), 1 allele (A1) and 0 alleles (A0) shared, were analysed within each tumour-normal pair, unrelated individual pairs, parent-offspring pairs and full-sibling pairs. According to the probability distribution, threshold of A2 in the range of 69 to 89 could achieve accuracy > 99% in identifying the source of tumour tissues. Thus, we developed a new strategy (process and criteria) to identify the source of tumour tissues that could be used in practice.

2.
Phys Chem Chem Phys ; 22(3): 1222-1241, 2020 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-31850421

RESUMO

Through the use of tunable vacuum ultraviolet light generated by the DESIRS VUV synchrotron beamline, a jet-stirred reactor was coupled for the first time to an advanced photoionization mass spectrometer based upon a double imaging PhotoElectron PhotoIon COincidence (i2PEPICO) scheme. This new coupling was used to investigate the low-temperature oxidation of n-pentane, a prototype molecule for gasoline or diesel fuels. Experiments were performed under quasi-atmospheric pressure (1.1 bar) with a residence time of 3 s for two equivalence ratios (1/3 and 0.5) with a fuel initial mole fraction of 0.01. The measured time-of-flight mass spectra are in good agreement with those previously obtained with other photoionization mass spectrometers and, like those previous ones, display several m/z peaks for which the related species assignation is ambiguous. This paper shows how the analysis of the coincident mass-tagged Threshold PhotoElectron Spectra (TPES) together with first principle computations, consisting of the determination of the adiabatic ionization energies and the spectra of some products, may assist products' identification. The results mostly confirm those previously obtained by photoionization mass spectrometry and gas chromatography, but also allow a more accurate estimation of the 1-pentene/2-pentene mole fraction ratio. Our data also indicate a higher formation of acetone and methyl ethyl ketone than what is predicted by current models, as well as the presence of products that were not previously taken into account, such as methoxyacetylene, methyl vinyl ketone or furanone. The formation of three, four and five membered ring cyclic ethers is confirmed along with linear ketones: 2- and 3-pentanone. A significant general trend in indicating higher amounts of ketones than are indicated by gas chromatography is noted. Finally, TPES of alkenylhydroperoxides are also provided for the first time and constrains on the isomers identification are provided.

3.
J Am Chem Soc ; 141(46): 18531-18543, 2019 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-31637914

RESUMO

The OH radical plays an important role in combustion, and isopentanol (3-methylbutan-1-ol) is a promising sustainable fuel additive and second-generation biofuel. The abstractions of H atoms from fuel molecules are key initiation steps for chain branching in combustion chemistry. In comparison with the more frequently studied ethanol, isopentanol has a longer carbon chain that allows a greater number of products, and experimental work is unavailable for the branching fractions to the various products. However, the site-dependent kinetics of isopentanol with OH radicals are usually experimentally unavailable. Alcohol oxidation by OH is also important in the atmosphere, and in the present study we calculate the rate constants and branching fractions of the hydrogen abstraction reaction of isopentanol by OH radical in a broad temperature range of 298-2400 K, covering temperatures important for atmospheric chemistry and those important for combustion. The calculations are done by multipath variational transition state theory (MP-VTST). With a combination of electronic structure calculations, we determine previously missing thermochemical data. With MP-VTST, a multidimensional tunneling approximation, multiple-structure anharmonicity, and torsional potential anharmonicity, we carried out more realistic rate constant calculations than can be computed by conventional single-structure harmonic transition state theory or by the empirical relations that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated, and we show that recrossing, tunneling, and multiple structures are all essential for accurate work. We conclude that the multiple structure anharmonicity is the most important correction to conventional transition state theory for this reaction, although recrossing effects and tunneling are by no means insignificant and the tunneling depends significantly on the path. The thermodynamic and kinetics data determined in this work are indispensable for the gas-phase degradation of alcohols in the atmosphere and for the detailed understanding and prediction of ignition mechanisms of biofuels in combustion.

4.
J Am Chem Soc ; 140(50): 17556-17570, 2018 12 19.
Artigo em Inglês | MEDLINE | ID: mdl-30468384

RESUMO

Hydroperoxyalkylperoxy species (OOQOOH) are important intermediates that are generated during the autoignition of transport fuels. A key reaction of hydroperoxyalkylperoxy radicals is a [1,5] hydrogen shift, for which kinetics data are experimentally unavailable. Here we study two typical OOQOOH reactions and compare their kinetics to one another and to a previous study to learn the effect of structural variations of the alkyl group on the competition between alternative [1,5] hydrogen shifts of hydroperoxyalkylperoxy species. We use electronic structure calculations to determine previously missing thermochemical data, and we use variational transition state theory with multidimensional tunneling, multiple structures, torsional potential anharmonicity, and high-frequency anharmonicity to obtain more accurate rate constants than the ones that can be computed by conventional single-structure harmonic transition state theory and than the empirically estimated rate constants that are currently used in combustion modeling. The calculated temperature range is 298-1500 K. The roles of various factors in determining the rates are elucidated, and we find an especially strong effect of multiple structure anharmonicity due to torsions. Thus, even though there is some cancellation between the anharmonicity of the reactant and the anharmonicity of the transition state, and even though the reactants are very similar in structure, differing only by a methyl group, the effect of multiple structure anharmonicity has a large effect on the relative rates, as large as a factor of 17 at room temperature and as large as a factor of 7 at 1500 K. This has broad implications for the estimation of reaction rates in many subfields of chemistry, including combustion chemistry and atmospheric chemistry, where rates of reaction of complex molecules are usually estimated without explicit consideration of this fundamental entropic effect. In addition, the pressure-dependence of the rate constants is modeled by system-specific quantum Rice-Ramsperger-Kassel theory for a reversible isomerization.

5.
J Hum Genet ; 63(11): 1129-1137, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30131598

RESUMO

Noninvasive prenatal testing (NIPT), which involves analysis of circulating cell-free fetal DNA (cffDNA) from maternal plasma, is highly effective for detecting feto-placental chromosome aneuploidy. However, recent studies suggested that coverage-based shallow-depth NIPT cannot accurately detect smaller single or multi-loci genetic variants. To assess the fetal genotype of any locus using maternal plasma, we developed a novel genotyping algorithm named pseudo tetraploid genotyping (PTG). We performed paired-end captured sequencing of the plasma cell-free DNA (cfDNA), in which case a phenotypically healthy woman is suspected to be carrying a fetus with genetic defect. After a series of independent filtering of 111,407 SNPs, we found one variant in COL1A1 graded with high pathogenic potential which might cause osteogenesis imperfecta (OI). Then, we verified this mutation by Sanger sequencing of fetal and parental blood cells. In addition, we evaluated the accuracy and detection rate of the PTG algorithm through direct sequencing of the genomic DNA from maternal and fetal blood cells. Collectively, our study developed an intuitive and cost-effective method for the noninvasive detection of pathogenic mutations, and successfully identified a de novo variant in COL1A1 (c.2596 G > A, p.Gly866Ser) in the fetus implicated in OI.


Assuntos
Colágeno Tipo I/genética , Feto , Sequenciamento de Nucleotídeos em Larga Escala , Osteogênese Imperfeita/genética , Polimorfismo de Nucleotídeo Único/genética , Diagnóstico Pré-Natal , Feminino , Humanos , Masculino , Osteogênese Imperfeita/embriologia
6.
J Cancer Res Ther ; 14(1): 150-154, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29516978

RESUMO

Objective: To evaluate the expression of programmed death 1 ligand 1 (PD-L1) in the cancer tissues and tumor-adjacent normal tissues of patients with invasive ductal carcinoma of the breast and to analyze the relationship between the expression of PD-L1 and the clinicopathological features of patients. Materials and Methods: This study included 112 cases of patients with invasive ductal carcinoma of breast who received surgical treatment from March 2012 to February 2016 in Xuzhou Cancer Hospital. The clinical materials of included patients were retrospectively analyzed. The immunohistochemical assay and real-time polymerase chain reaction (PCR) assay were applied to examine the expression of mRNA and protein of PD-L1 in breast cancer specimens of 112 cases and paired tumor-adjacent tissue specimens of 57 cases. The relationship between PD-L1 protein expression and clinicopathological features of patients was analyzed. Results: PD-L1 protein was mainly expressed in the cytoplasm. The positive rate of PD-L1 expression in invasive ductal carcinoma was 19.6% (22/112), and the positive rate of PD-L1 expression of tumor-adjacent normal tissues was 3.5% (2/57), indicating that the positive rate of PD-L1 expression of cancerous tissues was significantly higher than that of in tumor-adjacent normal tissues (P < 0.05); the positive expression of PD-L1 was not related with the patients' age, menopause history, family history of breast cancer, tumor size, and location of the tumor (P > 0.05) while it was related with lymph node metastasis, the clinic staging, and histopathological grading (P < 0.05). Real-time PCR was applied to detect the mRNA expression of PD-L1 in breast-invasive ductal carcinoma with the mean ΔCt value of 7.79 ± 2.25. However, the mRNA expression of PD-L1 in normal tumor-adjacent tissues was of low expression with the mean ΔCt value of 12.37 ± 3.33. The difference was statistically significant (P< 0.05). Conclusion: The expression of PD-L1 in breast-invasive ductal carcinoma was significantly increased, and it was related to histological grading, clinical staging, and lymph node metastasis of breast cancer. PD-L1 may be a significant marker for the prognosis of breast cancer patients.


Assuntos
Antígeno B7-H1/genética , Biomarcadores Tumorais , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Expressão Gênica , Adulto , Idoso , Antígeno B7-H1/metabolismo , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/metabolismo , Carcinoma Ductal de Mama/metabolismo , Carcinoma Ductal de Mama/mortalidade , Carcinoma Ductal de Mama/patologia , Feminino , Humanos , Imuno-Histoquímica , Pessoa de Meia-Idade , Gradação de Tumores , Metástase Neoplásica , Estadiamento de Neoplasias , Prognóstico , RNA Mensageiro/genética
7.
Phys Chem Chem Phys ; 20(16): 10806-10814, 2018 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-29411814

RESUMO

We performed a theoretical study on the double hydrogen shift isomerization reaction of a six carbon atom Criegee intermediate (C6-CI), catalyzed by formic acid (HCOOH), to produce vinylhydroperoxide (VHP), C6-CI + HCOOH → VHP + HCOOH. This Criegee intermediate can serve as a surrogate for larger CIs derived from important volatile organic compounds like monoterpenes, whose reactivity is not well understood and which are difficult to handle computationally. The reactant HCOOH exerts a pronounced catalytic effect on the studied reaction by lowering the barrier height, but the kinetic enhancement is hindered by the multistructural anharmonicity. First, the rigid ring-structure adopted by the saddle point to facilitate simultaneous transfer of two atoms does not allow the formation of as many conformers as those formed by the reactant C6-CI. And second, the flexible carbon chain of C6-CI facilitates the formation of stabilizing intramolecular C-HO hydrogen bonds; this stabilizing effect is less pronounced in the saddle point structure due to its tightness and steric effects. Thus, the contribution of the reactant C6-CI conformers to the multistructural partition function is larger than that of the saddle point conformers. The resulting low multistructural anharmonicity factor partially cancels out the catalytic effect of the carboxylic acid, yielding in a moderately large rate coefficient, k(298 K) = 4.9 × 10-13 cm3 molecule-1 s-1. We show that carboxylic acids may promote the conversion of stabilized Criegee intermediates into vinylhydroperoxides in the atmosphere, which generates OH radicals and leads to secondary organic aerosols, thereby affecting the oxidative capacity of the atmosphere and ultimately the climate.

8.
Proc Natl Acad Sci U S A ; 114(50): 13102-13107, 2017 12 12.
Artigo em Inglês | MEDLINE | ID: mdl-29183984

RESUMO

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500-600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound's molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.

9.
J Am Chem Soc ; 139(44): 15821-15835, 2017 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-29022349

RESUMO

Oxygenates with carbonyl and hydroperoxy functional groups are important intermediates that are generated during the autoxidation of organic compounds in the atmosphere and during the autoignition of transport fuels. In the troposphere, the degradation of carbonyl hydroperoxides leads to low-vapor-pressure polyfunctional species that may precipitate in clouds and fog droplets or to the formation of secondary organic aerosols (SOAs). In combustion, the fate of carbonyl hydroperoxides is important for the performance of advanced combustion engines, especially for autoignition. A key fate of the carbonyl hydroperoxides is reaction with OH radicals, for which kinetics data are experimentally unavailable. Here, we study 4-hydroperoxy-2-pentanone (CH3C(═O)CH2CH(OOH)CH3) as a model compound to clarify the kinetics of OH reactions with carbonyl hydroperoxides, in particular H atom abstraction and OH addition reactions. With a combination of electronic structure calculations, we determine previously missing thermochemical data, and with multipath variational transition state theory (MP-VTST), a multidimensional tunneling (MT) approximation, multiple-structure anharmonicity, and torsional potential anharmonicity, we obtained much more accurate rate constants than the ones that can computed by conventional single-structure harmonic transition state theory (TST) and than the empirically estimated rate constants that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated. The pressure-dependent rate constants for the addition reaction are computed using system-specific quantum RRK theory. The calculated temperature range is 298-2400 K, and the pressure range is 0.01-100 atm. The accurate thermodynamic and kinetics data determined in this work are indispensable in the global modeling of SOAs in atmospheric science and in the detailed understanding and prediction of ignition properties of hydrocarbons and alternative fuels.

10.
J Chem Theory Comput ; 13(8): 3537-3560, 2017 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-28636351

RESUMO

Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of various species. However, the application of highly accurate wave function theory methods, such as the "gold standard" coupled cluster approach including single, double, and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-sized molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach. For comparison, eight density functional theory (B3LYP, B3LYP-D3, PBE0, PBE0-D3, M06, M06-2X, ωB97X-D3, and ωB97M-V) and MP2-based (B2PLYP-D3, PWPB95-D3, B2T-PLYP, B2T-PLYP-D, B2GP-PLYP, DSD-PBEP86-D3, SCS-MP2, and OO-SCS-MP2) methods have been tested. The worst performance has been obtained for the standard hybrid DFT functionals, PBE0 (mean unsigned error (MUE)/mean signed error (MSE) = 9.1/6.0 kcal/mol) and B3LYP (MUE/MSE = 13.5/-13.3 kcal/mol). The influence of an empirical dispersion correction term on these functionals' performance is not homogeneous: B3LYP performance is improved (B3LYP-D3 (MUE/MSE = 6.0/0.8 kcal/mol)); meanwhile PBE0 performance is worse (PBE0-D3 (MUE/MSE = 14.1/13.6 kcal/mol)). The Minnesota functionals, M06 (MUE/MSE = 3.8/-2.0 kcal/mol) and M06-2X (MUE/MSE = 3.5/3.0 kcal/mol), and recently developed ωB97X-D3 (MUE/MSE = 3.2/0.2 kcal/mol) and ωB97M-V (MUE/MSE = 2.2/1.3 kcal/mol) methods provided significantly better formation enthalpies. Enthalpies of similar quality can also be obtained from some double hybrid methods (B2PLYP-D3 (MUE/MSE = 4.7/2.0 kcal/mol), PWPB95-D3 (MUE/MSE = 4.3/3.2 kcal/mol), B2T-PLYP (MUE/MSE = 4.1/-3.0 kcal/mol), and B2T-PLYP-D (MUE/MSE = 3.3/1.7 kcal/mol)). The two spin component scaled (SCS) MP2 methods resulted in even smaller errors (SCS-MP2 (MUE/MSE = 1.9/1.2 kcal/mol) and OO-SCS-MP2 (MUE/MSE = 1.6/0.1 kcal/mol)). The best performance was found for the frozen core (FC) DLPNO-CCSD(T) method with a MUE/MSE of 1.6/-1.2 kcal/mol. The performance of the DLPNO-CCSD(T) method can be further improved by running the post-SCF calculations on the B3LYP orbitals: the MUE/MSE for the DLPNO-CCSD(T,B3LYP) approximation is 1.2/-0.4 kcal/mol. We recommend the DLPNO-CCSD(T,B3LYP) method for black box applications in thermodynamics of medium-sized organic molecules when the canonical CCSD(T) calculations with basis sets of reasonable quality are prohibitively expensive.

11.
J Phys Chem A ; 121(9): 1861-1876, 2017 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-28190356

RESUMO

A wide range of hydroperoxides (C1-C3 alkyl hydroperoxides, C3-C7 alkenyl hydroperoxides, C7 ketohydroperoxides, and hydrogen peroxide (H2O2)), as well as ketene and diones, have been quantified during the gas-phase oxidation of n-heptane. Some of these species, as well as C10 alkenyl hydroperoxides and ketohydroperoxides, were also measured during the oxidation of n-decane. These experiments were performed using an atmospheric-pressure jet-stirred reactor at temperatures from 500 to 1100 K and one of three analytical methods, time-of-flight mass spectrometry combined with tunable synchrotron photoionization with a molecular beam sampling: time-of-flight mass spectrometry combined with laser photoionization with a capillary tube sampling, continuous wave cavity ring-down spectroscopy with sonic probe sampling. The experimental temperature at which the maximum mole fraction is observed increases significantly for alkyl hydroperoxides, alkenyl hydroperoxides, and then more so again for hydrogen peroxide, compared to ketohydroperoxides. The influence of the equivalence ratio from 0.25 to 4 on the formation of these peroxides has been studied during n-heptane oxidation. The up-to-date detailed kinetic oxidation models for n-heptane and for n-decane found in the literature have been used to discuss the possible pathways by which these peroxides, ketene, and diones are formed. In general, the model predicts well the reactivity of the two fuels, as well as the formation of major intermediates.

12.
Tumour Biol ; 39(2): 1010428317691413, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-28218040

RESUMO

The carcinogenesis of non-small cell lung carcinoma has been found to associate with activating and resistant mutations in the tyrosine kinase domain of specific oncogenes. Here, we assessed the type, frequency, and abundance of epithelial growth factor receptor, KRAS, BRAF, and ALK mutations in 154 non-small cell lung carcinoma specimens using single-molecule amplification and re-sequencing technology. We found that epithelial growth factor receptor mutations were the most prevalent (44.2%), followed by KRAS (18.8%), ALK (7.8%), and BRAF (5.8%) mutations. The type and abundance of the mutations in tumor specimens appeared to be heterogeneous. Thus, we conclude that identification of clinically significant oncogenic mutations may improve the classification of patients and provide valuable information for determination of the therapeutic strategies.


Assuntos
Carcinoma Pulmonar de Células não Pequenas/genética , Neoplasias Pulmonares/genética , Mutação , Quinase do Linfoma Anaplásico , Biópsia , Carcinoma Pulmonar de Células não Pequenas/enzimologia , Carcinoma Pulmonar de Células não Pequenas/patologia , Análise Mutacional de DNA/métodos , Receptores ErbB/genética , Feminino , Humanos , Neoplasias Pulmonares/enzimologia , Neoplasias Pulmonares/patologia , Masculino , Pessoa de Meia-Idade , Técnicas de Amplificação de Ácido Nucleico/métodos , Proteínas Proto-Oncogênicas B-raf/genética , Proteínas Proto-Oncogênicas p21(ras)/genética , Receptores Proteína Tirosina Quinases/genética , Análise de Sequência de DNA/métodos
13.
J Phys Chem A ; 120(40): 7890-7901, 2016 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-27641828

RESUMO

This work provides new temperature-dependent mole fractions of elusive intermediates relevant to the low-temperature oxidation of dimethyl ether (DME). It extends the previous study of Moshammer et al. [ J. Phys. Chem. A 2015 , 119 , 7361 - 7374 ] in which a combination of a jet-stirred reactor and molecular beam mass spectrometry with single-photon ionization via tunable synchrotron-generated vacuum-ultraviolet radiation was used to identify (but not quantify) several highly oxygenated species. Here, temperature-dependent concentration profiles of 17 components were determined in the range of 450-1000 K and compared to up-to-date kinetic modeling results. Special emphasis is paid toward the validation and application of a theoretical method for predicting photoionization cross sections that are hard to obtain experimentally but essential to turn mass spectral data into mole fraction profiles. The presented approach enabled the quantification of the hydroperoxymethyl formate (HOOCH2OCH2O), which is a key intermediate in the low-temperature oxidation of DME. The quantification of this keto-hydroperoxide together with the temperature-dependent concentration profiles of other intermediates including H2O2, HCOOH, CH3OCHO, and CH3OOH reveals new opportunities for the development of a next-generation DME combustion chemistry mechanism.

14.
J Phys Chem A ; 120(14): 2201-17, 2016 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-26998618

RESUMO

Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model's performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.

15.
J Phys Chem A ; 120(5): 668-82, 2016 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-26757618

RESUMO

The thermal decomposition of cyclopentene was studied in a jet-stirred reactor operated at constant pressure and temperature to provide new experimental information about the formation of the first aromatic rings from cyclic C5 species. Experiments were carried out at a residence time of 1 s, a pressure of 106.7 kPa, temperatures ranging from 773 to 1073 K and under diluted conditions (cyclopentene inlet mole fraction of 0.04). Species were quantified using three analytical methods: gas chromatography, synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS), and single photon laser ionization mass spectrometry (SPI-MS). Several species could be quantified using both methods allowing comparison of experimental data obtained with the three apparatuses. Discrepancies observed in mole fraction profiles of some large aromatics suggest that the direct sampling in the gas phase (with a molecular beam or a capillary tube) provide more reliable results. The main reaction products are 1,3-cyclopentadiene and hydrogen. The formation of many unsaturated C2-C6 olefins, diolefins and alkynes was also observed but in smaller amounts. Benzene, toluene, styrene, indene, and naphthalene were detected from 923 K. SVUV-PIMS data allowed the identification of another C6H6 isomer which is 1,5-hexadien-3-yne rather than fulvene. The quantification of the cyclopentadienyl radical was obtained from SVUV-PIMS and SPI-MS data with some uncertainty induced by the possible contribution to the signal for m/z 65 of a fragment from the decomposition of a larger ion. This is the first time that a radical is quantified in a jet-stirred reactor using non-optical techniques. SPI-MS analyses allowed the detection of species likely being combination products of allyl and cyclopentadienyl radicals. A model was developed for the pyrolysis of cyclopentene. This model includes routes of formation of aromatics from the cyclopentadienyl radical. The comparison of experimental and computed data is overall satisfactory for primary reaction products whereas discrepancies are still observed for aromatics.

16.
J Phys Chem A ; 118(30): 5573-94, 2014 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-25007100

RESUMO

The low-temperature oxidation of the five hexane isomers (n-hexane, 2-methyl-pentane, 3-methyl-pentane, 2,2-dimethylbutane, and 2,3-dimethylbutane) was studied in a jet-stirred reactor (JSR) at atmospheric pressure under stoichiometric conditions between 550 and 1000 K. The evolution of reactant and product mole fraction profiles were recorded as a function of the temperature using two analytical methods: gas chromatography and synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS). Experimental data obtained with both methods were in good agreement for the five fuels. These data were used to compare the reactivity and the nature of the reaction products and their distribution. At low temperature (below 800 K), n-hexane was the most reactive isomer. The two methyl-pentane isomers have about the same reactivity, which was lower than that of n-hexane. 2,2-Dimethylbutane was less reactive than the two methyl-pentane isomers, and 2,3-dimethylbutane was the least reactive isomer. These observations are in good agreement with research octane numbers given in the literature. Cyclic ethers with rings including 3, 4, 5, and 6 atoms have been identified and quantified for the five fuels. While the cyclic ether distribution was notably more detailed than in other literature of JSR studies of branched alkane oxidation, some oxiranes were missing among the cyclic ethers expected from methyl-pentanes. Using SVUV-PIMS, the formation of C2-C3 monocarboxylic acids, ketohydroperoxides, and species with two carbonyl groups have also been observed, supporting their possible formation from branched reactants. This is in line with what was previously experimentally demonstrated from linear fuels. Possible structures and ways of decomposition of the most probable ketohydroperoxides were discussed. Above 800 K, all five isomers have about the same reactivity, with a larger formation from branched alkanes of some unsaturated species, such as allene and propyne, which are known to be soot precursors.

17.
J Phys Chem A ; 118(4): 673-83, 2014 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-24400665

RESUMO

The experimental study of the oxidation of the three linear isomers of hexene was performed in a quartz isothermal jet-stirred reactor (JSR) at temperatures ranging from 500 to 1100 K including the negative temperature coefficient (NTC) zone, at quasi-atmospheric pressure (1.07 bar), at a residence time of 2 s and with dilute stoichiometric mixtures. The fuel and reaction product mole fractions were measured using online gas chromatography. In the case of 1-hexene, the JSR has also been coupled through a molecular-beam sampling system to a reflectron time-of-flight mass spectrometer combined with tunable synchrotron vacuum ultraviolet photoionization. A difference of reactivity between the three fuels, which varies with the temperature range has been observed and is discussed according to the changes in the possible reaction pathways when the double bond is displaced. An enhanced importance of the reactions via the Waddington mechanism and of those of allylic radicals with HO2 radicals can be noted for 2- and 3-hexenes compared to 1-hexene.

18.
J Phys Chem A ; 116(50): 12214-28, 2012 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-23181456

RESUMO

The low-temperature oxidation of propane was investigated using a jet-stirred reactor at atmospheric pressure and two methods of analysis: gas chromatography and synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS) with direct sampling through a molecular jet. The second method allowed the identification of products, such as molecules with hydroperoxy functions, which are not stable enough to be detected by gas chromatography. Mole fractions of the reactants and reaction products were measured as a function of the temperature (530-730 K), with a particular attention to reaction products involved in the low temperature oxidation, such as cyclic ethers, aldehydes, alcohols, ketones, and hydroperoxides. A new model has been obtained from an automatically generated one, which was used as a starting point, with a large number of re-estimated thermochemical and kinetic data. The kinetic data of the most sensitive reactions, i.e., isomerizations of alkylperoxy radicals and the subsequent decompositions, have been calculated at the CBS-QB3 level of theory. The model allows a satisfactory prediction of the experimental data. A flow rate analysis has allowed highlighting the important reaction channels.

19.
Combust Flame ; 159(12): 3455-3471, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23712100

RESUMO

The low-temperature oxidation of n-heptane, one of the reference species for the octane rating of gasoline, was investigated using a jet-stirred reactor and two methods of analysis: gas chromatography and synchrotron vacuum ultra-violet photo-ionization mass spectrometry (SVUV-PIMS) with direct sampling through a molecular jet. The second method allowed the identification of products, such as molecules with hydroperoxy functions, which are not stable enough to be detected using gas chromatography. Mole fractions of the reactants and reaction products were measured as a function of temperature (500-1100K), at a residence time of 2s, at a pressure of 800 torr (1.06 bar) and at stoichiometric conditions. The fuel was diluted in an inert gas (fuel inlet mole fraction of 0.005). Attention was paid to the formation of reaction products involved in the low temperature oxidation of n-heptane, such as olefins, cyclic ethers, aldehydes, ketones, species with two carbonyl groups (diones) and ketohydroperoxides. Diones and ketohydroperoxides are important intermediates in the low temperature oxidation of n-alkanes but their formation have rarely been reported. Significant amounts of organic acids (acetic and propanoic acids) were also observed at low temperature. The comparison of experimental data and profiles computed using an automatically generated detailed kinetic model is overall satisfactory. A route for the formation of acetic and propanoic acids was proposed. Quantum calculations were performed to refine the consumption routes of ketohydroperoxides towards diones.

20.
J Phys Chem A ; 115(5): 602-11, 2011 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-21207985

RESUMO

Alkyl hydroperoxides are found to be important intermediates in the combustion and oxidation processes of hydrocarbons. However, studies of ethyl hydroperoxide (CH(3)CH(2)OOH) are limited. In this work, kinetics and mechanisms for unimolecular decomposition of CH(3)CH(2)OOH have been investigated. The potential energy surface of decomposition reactions have first been predicted at the CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p) level. The results show that the formation of CH(3)CH(2)O + OH via O-O direct bond dissociation is dominant, the branching ratio of which is over 99% in the whole temperature range from 300 to 1000 K, and its rate constant can be expressed as k1 = 9.26 × 10(52)T(-11.91)exp(-26879/T) s(-1) at 1 atm. The rate constants of the reaction CH(3)CH(2)OOH → CH(3)CH(2)O + OH at different temperatures and pressures have been calculated, which can help us to comprehend the reactions of CH(3)CH(2)OOH at experimental conditions.

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