Mechanisms of Formaldehyde and C₂ Formation from Methylene Reacting with CO₂ Adsorbed on Ni(110)

Methylene (CH₂) is thought to play a significant role as a reaction intermediate in the catalysis of methane dry reforming as well as in converting synthesis gas to light olefins via Fischer–Tropsch synthesis. Here, we report high quality Born–Oppenheimer molecular dynamics (BOMD) simulations of the reaction mechanisms associated with CH₂ impinging on a Ni(110) surface with CO₂ adsorbed at 0.33 ML coverage. The results show the formation of formaldehyde, carbon monoxide, C₂ species such as H₂C–CO₂, and others. Furthermore, we provide real-time demonstration of both Eley–Rideal (ER) and hot atom (HA) reaction mechanisms. The ER mechanism mostly happens when CH₂ directly collides with an oxygen of CO₂, while CH₂ attacks the carbon of CO₂, dominantly following the HA mechanism. If CH₂ reaches the Ni surface, it can easily break one C–H bond to form CH and H on the surface. The mechanistic details of H₂CO, H/CO, C₂, and H/CH formation are illuminated through the study of bond breaking/formation, charge transfer, and spin density of the reactants and catalytic surface. This illuminates the key contribution of geometry and electronic structure of catalytic surface to the reaction selectivity. Moreover, we find that ³CH₂ switches to surfaces of ¹CH₂ character as soon as the methylene and nickel/CO₂ orbitals show significant interaction, and as a result the reactivity is dominated by low barrier mechanisms. Overall, the BOMD simulations provide dynamical information that allows us to monitor details of the reaction mechanisms, confirming and extending current understanding of CH₂ radical chemistry in the dry reforming of methane and Fischer–Tropsch synthesis

Systematic Study of Structural and Thermodynamic Properties of HCl(H₂O)_<i>n</i> Clusters from Semiempirical Replica Exchange Simulations

The structural and thermodynamic properties of HCl­(H₂O)_<i>n</i> clusters with <i>n</i> = 4–10 are studied using Born–Oppenheimer replica exchange molecular dynamics simulations with the PM3-MAIS semiempirical Hamiltonian. Independently of the cluster size, the simulations predict that HCl exists in the dissociated form in all low-energy isomers. Different local structures are identified within the clusters due to the presence of the dissociated proton, including Zundel, Eigen, Eigen-like, H₇O₃⁺, and intermediate Zundel–Eigen configurations. As the cluster size increases, several groups of isomers are identified, whose relative stabilities vary as a function of temperature. A detailed analysis of the heat capacity indicates that the melting behavior of HCl­(H₂O)_<i>n</i> clusters is strongly size-dependent. In particular, melting is observed in clusters with <i>n</i> = 7–10 in the temperature range <i>T</i> = 100–150 K. By contrast, melting is not observed in clusters with <i>n</i> = 4–6. Minimum energy structures for HCl­(H₂O)_<i>n</i> clusters with <i>n</i> = 11–15 and <i>n</i> = 21 are also characterized

Mechanisms of Formaldehyde and C₂ Formation from Methylene Reacting with CO₂ Adsorbed on Ni(110)

Methylene (CH₂) is thought to play a significant role as a reaction intermediate in the catalysis of methane dry reforming as well as in converting synthesis gas to light olefins via Fischer–Tropsch synthesis. Here, we report high quality Born–Oppenheimer molecular dynamics (BOMD) simulations of the reaction mechanisms associated with CH₂ impinging on a Ni(110) surface with CO₂ adsorbed at 0.33 ML coverage. The results show the formation of formaldehyde, carbon monoxide, C₂ species such as H₂C–CO₂, and others. Furthermore, we provide real-time demonstration of both Eley–Rideal (ER) and hot atom (HA) reaction mechanisms. The ER mechanism mostly happens when CH₂ directly collides with an oxygen of CO₂, while CH₂ attacks the carbon of CO₂, dominantly following the HA mechanism. If CH₂ reaches the Ni surface, it can easily break one C–H bond to form CH and H on the surface. The mechanistic details of H₂CO, H/CO, C₂, and H/CH formation are illuminated through the study of bond breaking/formation, charge transfer, and spin density of the reactants and catalytic surface. This illuminates the key contribution of geometry and electronic structure of catalytic surface to the reaction selectivity. Moreover, we find that ³CH₂ switches to surfaces of ¹CH₂ character as soon as the methylene and nickel/CO₂ orbitals show significant interaction, and as a result the reactivity is dominated by low barrier mechanisms. Overall, the BOMD simulations provide dynamical information that allows us to monitor details of the reaction mechanisms, confirming and extending current understanding of CH₂ radical chemistry in the dry reforming of methane and Fischer–Tropsch synthesis

Mechanisms of Formaldehyde and C₂ Formation from Methylene Reacting with CO₂ Adsorbed on Ni(110)

Methylene (CH₂) is thought to play a significant role as a reaction intermediate in the catalysis of methane dry reforming as well as in converting synthesis gas to light olefins via Fischer–Tropsch synthesis. Here, we report high quality Born–Oppenheimer molecular dynamics (BOMD) simulations of the reaction mechanisms associated with CH₂ impinging on a Ni(110) surface with CO₂ adsorbed at 0.33 ML coverage. The results show the formation of formaldehyde, carbon monoxide, C₂ species such as H₂C–CO₂, and others. Furthermore, we provide real-time demonstration of both Eley–Rideal (ER) and hot atom (HA) reaction mechanisms. The ER mechanism mostly happens when CH₂ directly collides with an oxygen of CO₂, while CH₂ attacks the carbon of CO₂, dominantly following the HA mechanism. If CH₂ reaches the Ni surface, it can easily break one C–H bond to form CH and H on the surface. The mechanistic details of H₂CO, H/CO, C₂, and H/CH formation are illuminated through the study of bond breaking/formation, charge transfer, and spin density of the reactants and catalytic surface. This illuminates the key contribution of geometry and electronic structure of catalytic surface to the reaction selectivity. Moreover, we find that ³CH₂ switches to surfaces of ¹CH₂ character as soon as the methylene and nickel/CO₂ orbitals show significant interaction, and as a result the reactivity is dominated by low barrier mechanisms. Overall, the BOMD simulations provide dynamical information that allows us to monitor details of the reaction mechanisms, confirming and extending current understanding of CH₂ radical chemistry in the dry reforming of methane and Fischer–Tropsch synthesis

Large Covariance Estimation for Compositional Data Via Composition-Adjusted Thresholding

<p>High-dimensional compositional data arise naturally in many applications such as metagenomic data analysis. The observed data lie in a high-dimensional simplex, and conventional statistical methods often fail to produce sensible results due to the unit-sum constraint. In this article, we address the problem of covariance estimation for high-dimensional compositional data and introduce a composition-adjusted thresholding (COAT) method under the assumption that the basis covariance matrix is sparse. Our method is based on a decomposition relating the compositional covariance to the basis covariance, which is approximately identifiable as the dimensionality tends to infinity. The resulting procedure can be viewed as thresholding the sample centered log-ratio covariance matrix and hence is scalable for large covariance matrices. We rigorously characterize the identifiability of the covariance parameters, derive rates of convergence under the spectral norm, and provide theoretical guarantees on support recovery. Simulation studies demonstrate that the COAT estimator outperforms some existing optimization-based estimators. We apply the proposed method to the analysis of a microbiome dataset to understand the dependence structure among bacterial taxa in the human gut.</p

Table_1_The effect of emotion regulation on happiness and resilience of university students: The chain mediating role of learning motivation and target positioning.DOCX

ObjectiveTo investigate the effect andmechanism among emotion regulation, relationship,happiness, learning motivation, target positioning, and resilience of university students.MethodA total of 904 university students in China were included in this cross-sectional survey from April to May this year. The self-administered questionnaires, including the adapted Mental Health Scale with a Healthy Personality Orientation for College Students, were used to construct structural equations to test the chain mediating effects of learning motivation and target positioning based on a multi-stage whole group sample of university students.ResultEmotion regulation indirectly affected happiness through the mediating effect of interpersonal relationship (Med = −0.387, p = 0.001). Learning motivation and target positioning play the chain mediating role in the effect of emotion regulation on happiness (Med = −0.307, p = 0.001) and resilience (Med = −0.275, p = 0.001).ConclusionEmotion regulation indirectly affected happiness and resilience through the chain mediating effect of learning motivation and target positioning.</p

Fast and Slow Proton Transfer in Ice: The Role of the Quasi-Liquid Layer and Hydrogen-Bond Network

The proton mobility in ice is studied through molecular dynamics simulations carried out with a newly developed ab initio-based reactive force field, <i>a</i>MS-EVB3/ice. The analysis of both structural and dynamical properties of protonated ice as a function of temperature indicates that the mobility of excess protons at the surface is largely suppressed, with protons becoming essentially immobile at temperatures below 200 K. In contrast, fast proton transfer/transport can exist in bulk ice I_h at low temperature through connected regions of the proton-disordered hydrogen-bond network. Based on the simulation results, it is shown that the mechanisms associated with proton transfer/transport in both bulk and interfacial regions of ice are largely dependent on the local hydrogen-bond structure surrounding the charge defect. A molecular-level picture of the mechanisms responsible for proton transfer/transport in ice is then developed and used to interpret the available experimental data

Supplemental Material for Brand, Lin, and Johnson, 2018

Supplemental Figure 1 Phylogenetic tree of the pectinase gene family. All phasmatodea pectinases cluster within the gammaproteobacteria and form a highly supported monophyletic clade, supporting a single horizontal gene transfer event in the ancestor of the three insect lineages analyzed. Pectinases detected in the B. germanica genome cluster within bacteria as well, but do not form a monophyletic clade. It is likely that the pectinases identified are due to bacterial contamination of the genome assembly (see main text). Known chrysomelid beetle pectinases cluster within fungi, representing independent horizontal gene transfer events of pectinases from fungi to insects (Pauchet et al. 2010) Orange: M. extradentata, Blue: C. hookeri, Purple: D. australis, Red: B. germanica. Bootstrap support of 100 replicates is indicated for each branch. Gene models of the four newly annotated species with insect or bacterial genes in the 20kb flanking regions are indicated.<br> <br>Supplemental Figure 2 Phylogenetic tree of the cellulase gene family. All identified cellulase genes cluster within other known bacterial cellulase genes. Orange: M. extradentata, Blue: C. hookeri, Purple: D. australis, Red: B. germanica, Brown: Z. nevadensis, Pink: T. cristinae. Bootstrap support of 100 replicates is indicated for each branch

A comprehensive overview and evaluation of circular RNA detection tools - Fig 3

<p>Coverage between circRNA detection methods on <b>(a)</b> HeLa and <b>(b)</b> Hs68 RNase R–treated data. For a pair of methods (i, j), the number of candidates detected by each method and the common candidates between them are calculated, then the proportion of common candidates for each method can be further computed and depicted. Cells within the same column reflect proportions of candidates detected by a specific method (column name) covered by other methods (row names) while cells within the same row show the proportions of candidates detected by other methods (column names) covered by a specific method (row name). CE, CIRCexplorer; CF, circRNA_finder; circRNA, circular RNA; FC, find_circ; MS, MapSplice; SG, Segemehl; NCLS, NCLScan; PF, PTESFinder; RNase R, exonuclease that digests linear RNAs but preserves circRNAs; UB, UROBORUS.</p

Visualization of Peroxynitrite-Induced Changes of Labile Zn²⁺ in the Endoplasmic Reticulum with Benzoresorufin-Based Fluorescent Probes

Zn²⁺ plays essential roles in biology, and the homeostasis of Zn²⁺ is tightly regulated in all cells. Subcellular distribution and trafficking of labile Zn²⁺, and its inter-relation with reactive nitrogen species, are poorly understood due to the scarcity of appropriate imaging tools. We report a new family of red-emitting fluorescent sensors for labile Zn²⁺, ZBR1–3, based on a benzo­resorufin platform functionalized with dipicolyl­amine or picolyl­amine-derived metal binding groups. In combination, the pendant amines and fluorophore afford an [N₃O] binding motif that resembles that of previously reported fluorescein-based sensors of the Zinpyr family, reproducing well their binding capabilities and yielding comparable <i>K</i>_d values in the sub-nanomolar and picomolar ranges. The ZBR sensors display up to 8.4-fold emission fluorescence enhancement upon Zn²⁺ binding in the cuvette, with similar responses obtained in live cells using standard wide-field fluorescence microscopy imaging. The new sensors localize spontaneously in the endoplasmic reticulum (ER) of various tested cell lines, allowing for organelle-specific monitoring of zinc levels in live cells. Study of ER zinc levels in neural stem cells treated with a peroxy­nitrite generator, Sin-1, revealed an immediate decrease in labile Zn²⁺ thus providing evidence for a direct connection between ER stress and ER Zn²⁺ homeostasis