Theoretical Kinetics studies of isoprene peroxy radical chemistry: The fate of Z-δ-(4-OH, 1-OO)-ISOPOO radical.

The OH radical recycling mechanism in isoprene oxidation is one of the most exciting topics in atmospheric chemistry, and the corresponding studies expand our understanding of oxidation mechanisms of volatile organic compounds in the troposphere and provide reliable evidence to improve and develop conventional atmospheric models. In this work, we performed a detailed theoretical kinetics study on the Z-δ-(4-OH, 1-OO)-ISOPOO radical chemistry, which is proposed as the heart of OH recycling in isoprene oxidation. With the full consideration of its accumulation and consumption channels, we studied and discussed the fate of Z-δ-(4-OH, 1-OO)-ISOPOO radical by solving the energy-resolved master equation over a broad range of conditions, including not only room temperatures but also high temperatures of a forest fire or low temperatures and pressures of the upper troposphere. We found non-negligible pressure dependence of its fate at combustion temperatures (up to two orders of magnitude) and demonstrated the significance of both the multi-structural torsional anharmonicity and tunneling for accurately calculating kinetics of the studied system. More interestingly, the tunneling effect on the phenomenological rate constants of the H-shift reaction channel is also found to be pressure-dependent due to the competition with the O2 loss reaction. In addition, our time evolution calculations revealed a two-stage behavior of critical species in this reaction system and estimated the shortest half-lives for the Z-δ-(4-OH, 1-OO)-ISOPOO radical at various temperatures, pressures and altitudes. This detailed kinetics study of Z-δ-(4-OH, 1-OO)-ISOPOO radical chemistry offers a typical example to deeply understand the core mechanism of OH recycling pathways in isoprene oxidation, and provides valuable insights for promoting the development of relevant atmospheric models.

Comprehensive Theoretical Study on Four Typical Intramolecular Hydrogen Shift Reactions of Peroxy Radicals: Multireference Character, Recommended Model Chemistry, and Kinetics.

Intramolecular hydrogen shift reactions in peroxy radicals (RO2• → •QOOH) play key roles in the low-temperature combustion and in the atmospheric chemistry. In the present study, we found that a mild-to-moderate multireference character of a potential energy surface (PES) is widely present in four typical hydrogen shift reactions of peroxy radicals (RO2•, R = ethyl, vinyl, formyl methyl, and acetyl) by a systematic assessment based on the T1 diagnostic, %TAE diagnostic, M diagnostic, and contribution of the dominant configuration of the reference CASSCF wavefunction (C02). To assess the effects of these inherent multireference characters on electronic structure calculations, we compared the PESs of the four reactions calculated by the multireference method CASPT2 in the complete basis set (CBS) limit, single-reference method CCSD(T)-F12, and single-reference-based composite method WMS. The results showed that ignoring the multireference character will introduce a mean unsigned deviation (MUD) of 0.46-1.72 kcal/mol from CASPT2/CBS results by using the CCSD(T)-F12 method or a MUD of 0.49-1.37 kcal/mol by WMS for three RO2• reactions (R = vinyl, formyl methyl, and acetyl) with a stronger multireference character. Further tests by single-reference Kohn-Sham (KS) density functional theory methods showed even larger deviations. Therefore, we specifically developed a new hybrid meta-generalized gradient approximation (GGA) functional M06-HS for the four typical H-shift reactions of peroxy radicals based on the WMS results for the ethyl peroxy radical reaction and on the CASPT2/CBS results for the others. The M06-HS method has an averaged MUD of 0.34 kcal/mol over five tested basis sets against the benchmark PESs, performing best in the tested 38 KS functionals. Last, in a temperature range of 200-3000 K, with the new functional, we calculated the high-pressure-limit rate coefficients of these H-shift reactions by the multi-structural variational transition-state theory with the small-curvature tunneling approximation (MS-CVT/SCT) and the thermochemical properties of all of the involved key radicals by the multi-structural torsional (MS-T) anharmonicity approximation method.

Master equation study of hydrogen abstraction from HCHO by OH via a chemically activated intermediate.

The abstraction reaction of hydrogen from formaldehyde by OH radical plays an important role in formaldehyde oxidation. The reaction involves a bimolecular association to form a chemically activated hydrogen-bonded reaction complex followed by a unimolecular reaction of the complex to generate the products. The reaction rate is usually considered to be pressure-independent by assuming equilibrium between the reactants and the complex. However, our nonequilibrium calculations based on the chemically significant eigenmode of the master equation, carried out with our recently developed TUMME program, indicate that the reaction complex makes the rate constant dependent on pressure at low temperatures (T < 200 K). The calculations include anharmonicity, variational effects, and multi-dimensional tunneling. We find that the reaction rate constant reaches a low-pressure limit at pressures below 10 Torr over the whole investigated temperature range (20-1800 K), which explains why the available low-temperature experiments, which are for pressures below 2 Torr, did not observe the pressure dependence. A new extension of the TUMME master-equation program is used to explore the time evolutions of the concentrations of the OH radical and the complex under pseudo-first-order conditions. The time-dependent evolution of the concentrations of the complex at a low temperature provide direct evidence for the stabilization of the reaction complex at high pressures, and it shows the negligible role of the stabilized reaction complex at low pressures. The picture that emerges is qualitatively consistent with our previous study of the reaction of methanol with OH in that the tunneling in the unimolecular step from the complex to the products affects the phenomenological reaction rate constants differently at high and low pressures and leads to a significant pressure effect.

Observing Intramolecular Vibrational Energy Redistribution via the Short-Time Fourier Transform.

Intramolecular vibrational energy relaxation (IVR) is important in many problems in chemical physics. Here, we apply the short-time Fourier transform method for analyzing IVR with classical dynamics. Calculating time-dependent Fourier transforms to perform such an analysis requires extending the usual Fourier transform method, and we do that here. The guiding concept behind the generalization is that if there is a shift of vibrational energy from one frequency range to another, we see a difference between the spectrum before the shift and the spectrum after the shift. We use time-window functions to transform the power spectrum of a trajectory into a time-dependent density spectrum of the average kinetic energy. The time-dependent average kinetic energy for each interval of the spectrum becomes an indicator to monitor the extent and nature of the energy transfer into and out of the corresponding modes. We illustrate this method for the H2O molecule. By analyzing cases with different initial conditions, we show that the short-time Fourier transform method can distinguish trends in IVR that depend on the initial distribution of energy and not just on the total energy.

Evaluation of digestibility differences for apple polyphenolics using in vitro elderly and adult digestion models.

We evaluated the in vitro digestibility of apple polyphenols mimicking elderly and adult digestion models (dynamic and static systems). The digestibility of total apple polyphenols in small intestine was much higher in the adult dynamic system (62 µg/100 g fresh apple) compared to the static system (20 µg/100 g fresh apple) and elderly dynamic digestion conditions (33 µg/100 g fresh apple). Elderly in vitro static digestion showed better antioxidant activity than the adult system (OH and ABTS+ methods). Thus, the in vitro dynamic digestion system can more truly reflect the digestion of apple polyphenols than static digestion system. Moreover, elderly digestion conditions negatively influenced the digestibility of apple polyphenols including chlorogenic acid, epicatechin, phlorizin, rutin, phloretin, hyperoside, proanthocyanidin B2, and quercetin. Hence, appropriate selection of in vitro digestion models for elderly is a prerequisite to exploring the digestibility of phytochemicals for the development of functional food products for elderly.

Purification, structural characterization, and anticoagulant activity evaluation of chondroitin sulfate from codfish (Gadus macrocephalus) bones.

Chondroitin sulfate (CCS) was purified from discarded codfish (Gadus macrocephalus) bones, and its chemical structure and anticoagulant activity were assessed. CCS was obtained via enzymatic lysis and ion-exchange column chromatography, with a yield of approximately 0.15%. High-performance gel performance chromatography revealed CCS to be a largely homogeneous polysaccharide with a relatively low molecular weight of 12.3 kDa. FT-IR spectroscopy, NMR spectroscopy, and SAX-HPLC indicated that CCS was composed of monosulfated disaccharides (ΔDi4S 73.85% and ΔDi6S 19.06%) and nonsulfated disaccharides (ΔDi0S 7.09%). In vitro anticoagulation analyses revealed that CCS was able to significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT) (p < 0.05). At a CCS concentration of 5 µg/mL and 25 µg/mL, APTT and TT were approximately 1.08 and 1.12 times higher, respectively, compared to the negative control group. The results indicated that CCS might offer value as a dietary fiber supplement with the potential to prevent the incidence of coagulation-related thrombosis.

Pressure-dependent kinetics of the o-xylene reaction with OH radicals.

OH-initiated oxidation reactions of o-xylene are widely concerned both in combustion and atmospheric chemistry. In this work, the kinetics of the o-xylene reaction with OH radicals has been studied systematically in a wide temperature range of 220-3000 K for the high-pressure limit and several selected pressures from 1 torr to 500 atm using multi-structural variational transition state theory with the small-curvature tunneling approximation (MS-CVT/SCT) and the system-specific quantum Rice-Ramsperger-Kassel (SS-QRRK) method. The calculations fully considered various factors which could affect the accuracy of the calculated rate constants including anharmonicity of both low- and high-frequency modes and multiple low-energy conformers, variational effect, and tunneling. The results are in good agreement with the available experimental data. The obtained overall rate constants exhibit a nonmonotonic temperature dependence due to the competition between the hydrogen abstraction and addition reactions. At low temperatures, the addition channels are dominant reactions, but the abstraction reactions are also non-ignorable with a ∼12% contribution to the overall rate constants at 298 K and 1 atm. Above 800 K, the abstraction reactions become dominant under all the pressure conditions. In addition, we observed a more significant pressure dependence of o-xylene plus OH reaction as compared to the similar toluene plus OH reaction, which is the effect of the additional methyl group. At T = 500-1000 K, the pressure can influence the total rate constants of the o-xylene reaction by a factor of up to 2.5. These kinetics data provide us with a comprehensive understanding of the mechanism and pressure-dependence of kinetics for the o-xylene + OH reaction, which is also beneficial for the study of other similar aromatic hydrocarbon reactions.

Mechanisms underlying operational energy consumption of buildings for low carbon city construction: A review.

With rapid urbanization, the increasing building stock, building operation energy consumption and the corresponding carbon emissions have become the important factors restricting the sustainable development of cities. To reduce energy consuming, it is necessary to explore the mechanisms underlying building's operational energy consumption and carbon emission. Although previous studies have analyzed the influencing factors and driving mechanism of urban building carbon emission from different perspectives, a systematical review of the relevant studies which could provide comprehensive guidance for building energy conservation and consumption reduction is fairly scarce. Following the Social-Economic-Natural Complex Ecosystem theory, we comprehensively discussed the driving mechanisms of the building's operational energy consumption and carbon emission. We further analyzed the various single-source driving mechanisms from the perspective of socio-economic, building feature, regional climate and microclimate conditions. Finally, we tackled the weaknesses of current researches and addressed the prospect for future development. The driving mechanism summarized in this work would contribute to the development of related research and support low carbon city construction.

Energy Dependence of Ensemble-Averaged Energy Transfer Moments and Its Effect on Competing Decomposition Reactions.

We carried out a direct dynamics study on the internal-energy dependence of the ensemble-averaged energy transfer moments of the isobutyl radical in collisions with N2 bath gas. We find a linear dependence of the downward moment ⟨ΔEd⟩ and the root-mean-square moment ⟨ΔE2⟩ on the initial internal energy, but the upward moment ⟨ΔEu⟩ is found to be independent of the molecule's internal energy. We improved the exponential-down relaxation model by including a linear dependence of ⟨ΔEd⟩ on the initial energy, and we used the improved treatment in the 1D master equation for isobutyl radical decomposition reactions and for a model of competitive reactions with a larger difference in barrier heights. We calculated phenomenological rate constants and branching ratios from chemically significant eigenmodes of the master equation and showed that the energy dependence of ⟨ΔEd⟩ has a greater influence on channels with higher barriers in competitive reactions. Rate constants and branching ratios from master equation calculations indicate that for a given temperature and pressure, there is a constant ⟨ΔEd⟩ that can reproduce results obtained with an E-dependent ⟨ΔEd⟩. But a constant ⟨ΔEd⟩ cannot do this for all temperatures and pressures, with larger differences when the barriers for the competing channels differ more. We conclude that when the branching ratio of competitive reactions is sensitive to pressure, including the energy dependence of ⟨ΔEd⟩ in master equation simulations can make a significant difference in the results.

Phonon lasing with an atomic thin membrane resonator at room temperature.

Graphene has been considered as one of the best materials to implement mechanical resonators due to their excellent properties such as low mass, high quality factors and tunable resonant frequencies. Here we report the observation of phonon lasing induced by the photonthermal pressure in a few-layer graphene resonator at room temperature, where the graphene resonator and the silicon substrate form an optical cavity. A marked threshold in the oscillation amplitude and a narrowing linewidth of the vibration mode are observed, which confirms a phonon lasing process in the graphene resonator. Our findings will stimulate the studies on phononic phenomena, help to establish new functional devices based on graphene mechanical resonators, and might find potential applications in classical and quantum sensing fields, as well as in information processing.

Low-Pressure Limit of Competitive Unimolecular Reactions.

Barker and Ortiz found unusual falloff effects in the flux coefficients of the competitive unimolecular reactions of 2-methylhexyl radicals, and they concluded that this might have important effects on the rate constants of reactions with higher thresholds. To study this effect, we carried out master equation calculations of the same reaction system to learn whether this effect shows up in measurable rate constants, and the answer is yes. We also studied specially designed mechanisms to reveal that the various reactive pathways connecting the reagents can have a large effect on the rate constants, causing them to be quite different than if the reactions proceeded independently, and that reactions with significantly higher barriers may nevertheless have larger rate constants. This provides a new perspective for interpreting and predicting the kinetics of competitive unimolecular reactions.

Computational kinetics of the hydrogen abstraction reactions of n-propanol and iso-propanol by OH radical.

Propanol (n-propanol or iso-propanol (i-propanol)) is a promising clean-burning oxygenated fuel component and fuel additive. Understanding its reactions with OH radical is of great significance in both combustion and atmospheric chemistry. In this work, we calculate the rate constants and branching ratios of the hydrogen abstraction reactions of n-propanol and i-propanol by OH radical in a broad temperature range of 63-2000 K using the competitive canonical unified statistical (CCUS) model. For both n-propanol and i-propanol, in both the high-pressure and low-pressure limits, the total reaction rate constants show a significant negative dependence on temperature in the low temperature regime and approach the capture rate for the formation of the pre-reactive complex when temperature is down to the ultracold regime. Several factors, tunneling, remarkable anharmonicity of high-frequency modes of transition states, and the presence of reaction channels with a negative free energy barrier, contribute to this phenomenon. We observe pressure-dependent branching fractions at T < ∼400 K for n-propanol or T < 200 K for i-propanol, and at higher temperatures, the branching fractions are independent of the pressure. The alpha-hydrogen (Hα) abstraction with a lower barrier is not always dominant as traditionally expected. The H-abstraction from the terminal carbon (Ht) of i-propanol, with a higher barrier, is dominant above 1000 K because of the remarkably larger effect of multi-structural and torsional (MS-T) anharmonicity. In the pressure-dependent ultra-low temperature regime and high-pressure limit, the beta-hydrogen (Hß) abstraction and the hydrogen abstraction from the hydroxyl group (HO) become dominant for n-propanol and i-propanol, respectively, mainly due to the tunneling effect.

Kinetics of the Toluene Reaction with OH Radical.

We calculated the kinetics of chemical activation reactions of toluene with hydroxyl radical in the temperature range from 213 K to 2500 K and the pressure range from 10 Torr to the high-pressure limit by using multistructural variational transition state theory with the small-curvature tunneling approximation (MS-CVT/SCT) and using the system-specific quantum Rice-Ramsperger-Kassel method. The reactions of OH with toluene are important elementary steps in both combustion and atmospheric chemistry, and thus it is valuable to understand the rate constants both in the high-pressure, high-temperature regime and in the low-pressure, low-temperature regime. Under the experimental pressure conditions, the theoretically calculated total reaction rate constants agree well with the limited experimental data, including the negative temperature dependence at low temperature. We find that the effect of multistructural anharmonicity on the partition functions usually increases with temperature, and it can change the calculated reaction rates by factors as small as 0.2 and as large as 4.2. We also find a large effect of anharmonicity on the zero-point energies of the transition states for the abstraction reactions. We report that abstraction of H from methyl should not be neglected in atmospheric chemistry, even though the low-temperature results are dominated by addition. We calculated the product distribution, which is usually not accessible to experiments, as a function of temperature and pressure.

Quantum Effects on H2 Diffusion in Zeolite RHO: Inverse Kinetic Isotope Effect for Sieving.

We use canonical variational theory (CVT) with small-curvature tunneling (SCT) contributions to investigate quantum effects on the H2 diffusion process in the pure-silica zeolite RHO. At low temperature we find an inverse kinetic isotopic sieving effect in that the heavier isotopic species diffuses faster than the lighter one. Three quantum effects contribute to this kinetic isotope effect (KIE). The first one is quantum mechanical tunneling; this-on its own-would lead to a normal kinetic isotopic sieving effect, in which lighter diprotium diffuses faster than dideuterium. The second factor, which we find to dominate in the present case, is zero-point energy (ZPE). Deuterium has a lower ZPE, which leads to a smaller effective barrier for tunneling because the transition state has a larger ZPE than the precursor stable state; this results in an inverse KIE. The third factor, the thermal vibrational energy (computed from the quantized vibrational partition function), also favors a normal KIE, but it is outweighed by the ZPE effect. The vibrations of the zeolite host framework are found to play an important role at low temperatures, and our calculations consider up to 7296 degrees of freedom at the equilibrium structure and the saddle point and up to 221 degrees of freedom along the reaction path. The importance of quantum considerations on the dynamics is elucidated by comparison to a purely classical treatment.

The Wnt/ß-catenin signaling pathway mechanism for pancreatic cancer chemoresistance in a three-dimensional cancer microenvironment.

ß-catenin is a key protein that is encoded by the CTNNB1 gene in the Wnt signaling pathway. This study investigated the associations between ß-catenin expression and implications for the efficacy of gemcitabine on pancreatic cancer cells in a three-dimensional (3-D) cancer microenvironment. For low ß-catenin expression pancreatic carcinoma cells, the inhibition rates (IRs) for low, middle, and high doses of gemcitabine were 0.615 ± 0.079, 0.691 ± 0.093, and 0.765 ± 0.061, respectively. For the high ß-catenin expression pancreatic carcinoma cells, the IRs for the same doses were 0.325 ± 0.072, 0.453 ± 0.075, and 0.537 ± 0.056, respectively. Additionally, the evaluation of ß-catenin immunoreactivity in 31 pancreatic cancer patients revealed that the low ß-catenin protein expression group had significantly longer overall survival (OS) and disease free survival (DFS) than the high ß-catenin protein group (P < 0.05). Overall, ß-catenin protein expression levels were significantly correlated to gemcitabine sensitivity in seven pancreatic carcinoma cell lines in the 3-D cancer microenvironment. These data suggest that large-scale clinical studies are warranted to assess the role of the Wnt/ß-catenin signaling pathway on ß-catenin protein expression and chemosensitivity to gemcitabine in pancreatic cancer.

miR-410-3p suppresses breast cancer progression by targeting Snail.

miR-410-3p acts as an oncogene or tumor-suppressor gene in various types of cancer. However, its role in breast cancer remains unknown. In the present study, expression of miR-410-3p in 30 breast cancer and paired adjacent normal tissues was detected by RT-qPCR. The expression of miR-410-3p was downregulated in 76.7% of the breast cancer samples. To further validate the expression of miR-410-3p in breast cancer, we analyzed miR-410-3p expression profiling data set from The Cancer Genome Atlas (TCGA) including 683 breast cancer and 87 normal breast tissues. We observed that the expression of miR-410-3p was downregulated in breast cancer tissues. Next, we investigated the influence of miR-410-3p on cell proliferation by transiently transfecting the miR-410-3p mimic or inhibitor, as well as their corresponding controls in the MDA-MB-231 and MCF7 cell lines. miR-410-3p overexpression reduced cell growth, colony formation and the number of EdU-positive cells in the MDA-MB-231 cells. In contrast, inhibition of miR-410-3p in the MCF7 cells resulted in a higher proliferation rate as assessed by MTT assay, plate colony formation and EdU assays. Furthermore, miR-410-3p inhibited epithelial-mesenchymal transition. In addition, Snail was found to be a direct target of miR-410-3p based on a luciferase assay. Overexpression of Snail was able to rescue the effect of miR-410-3p in breast cancer cells. Moreover, miR­410-3p was inversely expressed with Snail in breast cancer samples. Our data provide new knowledge regarding the role of miR-410-3p in breast cancer progression.

Invasion Genetics of Woolly Apple Aphid (Hemiptera: Aphididae) in China.

In China, the woolly apple aphid, Eriosoma lanigerum (Hausmann), was first detected as an invasive species during the 1910s to 1930s, restricted to Shandong, Liaoning, and Yunnan Provinces. However, since the 1990s, the pest has spread into many other areas of China. To determine the possible spread routes of the recently established populations, the genetic diversity and genetic structure of 24 populations in 10 provinces were analyzed using eight microsatellite loci. Analyses using STRUCTURE software identified two genetic clusters overall. Three populations from Yunnan and Xinjiang consisted of individuals originating from a single cluster. Nineteen populations from eight northern provinces consisted only of individuals from another cluster, which formed a single large and panmictic population, resembling a distinct "supercolony" in Northern China. The other two populations from Yunnan consisted of individuals from both clusters. The possible routes of spread of the recently established populations of E. lanigerum in China were revealed as follows: 1) the populations in Northern China (including these from Henan, Hebei, Shanxi, Shannxi, Jiangsu, and Gansu) may have been introduced from Shandong or Liaoning Provinces; 2) the populations in Yunnan consisted of an early-established population and a population introduced secondarily from Shandong or neighboring areas, indicating that the population in Yunnan has at least two sources; and 3) the recently established populations of E. lanigerum in Xinjiang might not have been introduced from the "supercolony" in Northern China. Knowledge of these routes of spread is useful for avoiding further dissemination and/or additional introductions.