Boosting Activity and Selectivity of UiO-66 through Acidity/Alkalinity Functionalization in Dimethyl Carbonate Catalysis.

The acid-base properties of supports have an enormous impact on catalytic reactions to regulate the selectivity and activity of supported catalysts. Herein, a train of Pd-X-UiO-66 (X = NO2 , NH2 , and CH3 ) catalysts with different acidity/alkalinity functional groups and encapsulated Pd(II) species is first developed, whose activities in dimethyl carbonate (DMC) catalysis are then investigated in details. Thereinto, the Pd-NO2 -UiO-66 catalyst with acidity functionalization exhibits the best catalytic behavior: the DMC selectivity stemmed from methyl nitrite (MN) is up to 68%, the conversion of CO is 73.4%. The obtained experimental results demonstrate that the NO2 group not only affected the interaction between X-UiO-66 and Pd(II) active sites but also play an indispensable role in the adsorption and activation of MN and CO, which remarkably promote the formation of the COOCH3 * intermediate and DMC product.

Enhanced logical chaotic resonance.

It was demonstrated recently that logical chaotic resonance (LCR) can be observed in a bistable system. In other words, the system can operate robustly as a specific logic gate in an optimal window of chaotic signal intensity. Here, we report that the size of the optimal window of chaotic signal intensity can be remarkably extended by exploiting the constructive interaction of chaotic signal and periodic force, as well as coupling, in a coupled bistable system. In addition, medium-frequency periodic force and an increasing system size can also lead to an improvement in the response speed of logic devices. The results are corroborated by circuit experiments. Taken together, a reliable and rapid-response logic operation can be realized based on periodic force- and array-enhanced LCR.

milRNApredictor: Genome-free prediction of fungi milRNAs by incorporating k-mer scheme and distance-dependent pair potential.

MicroRNA-like small RNAs (milRNAs) with length of 21-22 nucleotides are a type of small non-coding RNAs that are firstly found in Neurospora crassa in 2010. Identifying milRNAs of species without genomic information is a difficult problem. Here, knowledge-based energy features are developed to identify milRNAs by tactfully incorporating k-mer scheme and distance-dependent pair potential. Compared with k-mer scheme, features developed here can alleviate the inherent curse of dimensionality in k-scheme once k becomes large. In addition, milRNApredictor built on novel features performs comparably to k-mer scheme, and achieves sensitivity of 74.21%, and specificity of 75.72% based on 10-fold cross-validation. Furthermore, for novel miRNA prediction, there exists high overlap of results from milRNApredictor and state-of-the-art mirnovo. However, milRNApredictor is simpler to use with reduced requirements of input data and dependencies. Taken together, milRNApredictor can be used to de novo identify fungi milRNAs and other very short small RNAs of non-model organisms.

Periodic and aperiodic force-induced logical stochastic resonance in a bistable system.

It was demonstrated recently that there are optimal windows of noise intensity or frequency and amplitude of the periodic driving force, which let a bistable system operate reliably as logic gates. These phenomena are called logical stochastic resonance (LSR). Given that the driving force is not always perfect regular, there may be phase disturbance in driving force; therefore, the Wiener process is used here to model phase disturbance of driving force, and then the effects of phase disturbance on reliability and agility of logic gates are explored in detail. Comparing with the periodic force, the aperiodic force with appropriate intensity phase disturbance can drive a bistable system to yield phenomena similar to LSR in a wider reliable region and can reduce mean switching time to obtain a faster response of logic devices to the input signal. On the other hand, depending on the amplitude and average angular frequency, moderate-intensity phase disturbance may also reduce success probability and increase mean switching time and thus lead to the instability and the slower response of logic devices.

Set-reset latch logic operation in a bistable system under suprathreshold and subthreshold signals.

A set-reset latch is a basic building block of computers and can be used to store state information. Here, by testing the influence of the two logical input signals on the reliable set-reset latch logic operation in the bistable system, we found that there are two types of input signals, namely, suprathreshold and subthreshold signals. For the suprathreshold signals, reliable set-reset logic operation can be achieved without any driving forces and exhibits certain anti-interference ability; for the subthreshold signals, a single harmonic could induce correct set-reset latch logic operation but with a narrow optimal parameter region. The introduction of biharmonic-induced set-reset latch logic operation (logical vibrational resonance) could greatly expand the parameter region. Explanations for the above results were provided by taking the logical inputs as the dynamic bias to analyze the dynamic changes in the system. Finally, the results were further verified by circuit simulation and actual hardware circuit.

ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment.

BACKGROUND: The knowledge-based statistical potential has been widely used in protein structure modeling and model quality assessment. They are commonly evaluated based on their abilities of native recognition as well as decoy discrimination. However, these two aspects are found to be mutually exclusive in many statistical potentials. RESULTS: We developed an atomic ANgle- and DIStance-dependent (ANDIS) statistical potential for protein structure quality assessment with distance cutoff being a tunable parameter. When distance cutoff is ≤9.0 Å, "effective atomic interaction" is employed to enhance the ability of native recognition. For a distance cutoff of ≥10 Å, the distance-dependent atom-pair potential with random-walk reference state is combined to strengthen the ability of decoy discrimination. Benchmark tests on 632 structural decoy sets from diverse sources demonstrate that ANDIS outperforms other state-of-the-art potentials in both native recognition and decoy discrimination. CONCLUSIONS: Distance cutoff is a crucial parameter for distance-dependent statistical potentials. A lower distance cutoff is better for native recognition, while a higher one is favorable for decoy discrimination. The ANDIS potential is freely available as a standalone application at http://qbp.hzau.edu.cn/ANDIS/ .

Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction.

BACKGROUND: As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model refinement, and model assessment. During the last two decades, great efforts have been made to improve the reference state of the potential, while other factors that also strongly affect the performance of the potential have been relatively less investigated. RESULTS: Based on different distance cutoffs (from 5 to 22 Å) and residue intervals (from 0 to 15) as well as six different reference states, we constructed a series of distance-dependent atom-pair potentials and tested them on several groups of structural decoy sets collected from diverse sources. A comprehensive investigation has been performed to clarify the effects of distance cutoff and residue interval on the potential's performance. Our results provide a new perspective as well as a practical guidance for optimizing distance-dependent statistical potentials. CONCLUSIONS: The optimal distance cutoff and residue interval are highly related with the reference state that the potential is based on, the measurements of the potential's performance, and the decoy sets that the potential is applied to. The performance of distance-dependent statistical potential can be significantly improved when the best statistical parameters for the specific application environment are adopted.

Carbon monoxide oxidation catalysed by defective palladium chloride: DFT calculations, EXAFS, and in situ DRIRS measurements.

We examined the potential catalytic role of the palladium chloride catalyst in CO oxidation using density functional theory and experimental investigations. The active plane of the palladium chloride catalyst is identified as (140). We found that the defective PdCl2(140) surface is able to facilitate the activation of O2 and subsequently promote the oxidation of CO. The most significant reaction channel, the Eley-Rideal mechanism (MER1), proceeds first by a peroxo-type (OOCO) intermediate formation, second by O adsorption with the first CO2 release, then by the second CO attraction and the second CO2 formation, and finally by the second CO2 desorption and restoration of the defective PdCl2(140) surface. The rate-determining step is the formation of the second CO2 in the whole catalytic cycle. Compared to the previously reported catalytic systems, the reaction activation barrier (0.54 eV) of CO oxidation in the PdCl2 catalyst is low, indicating PdCl2 as a potential high-performance catalyst for CO oxidation. The present results enrich our understanding of CO oxidation of Pd-based catalysts and provide a basis for fabricating Pd-based catalysts with high activity.

Insights into the reaction mechanism of CO oxidative coupling to dimethyl oxalate over palladium: a combined DFT and IR study.

Oxidative coupling of toxic pollutant CO to form the platform raw chemical material dimethyl oxalate (DMO) has been industrialized however the catalytic mechanism has been unknown so far. The reaction mechanism of CO oxidative coupling to form DMO on a Pd(111) surface has been investigated using density functional theory (DFT) and in situ diffuse reflectance infrared (DRIR) spectroscopy. DFT calculations and in situ DRIRS measurements indicate that two co-adsorbed intermediates COOMe and OCCO, initiate the reaction. C-C coupling occurs earlier due to a low coupling barrier and small steric hindrance. The results also suggest that Pd(111) is selective towards DMO over DMC, and that CO pre-adsorption and CO in excess effectively enhance the yield of DMO. The microscopic elucidation of this important reaction suggests improvements in coal-to-EG (CTEG) production which can be applied in practice to effectively enhance the yield and reduce the cost. The results may help with further fine-tuning and designing of high-efficient noble metal catalysts.

Systematic characterization of small RNAome during zebrafish early developmental stages.

BACKGROUND: During early vertebrate development, various small non-coding RNAs (sRNAs) such as MicroRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) are dynamically expressed for orchestrating the maternal-to-zygotic transition (MZT). Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. RESULTS: We first determined the expression profiles of sRNAs during eight distinct stages of early zebrafish development by sRNA-seq technology. Integrative analyses with a new computational platform of CSZ (characterization of small RNAome for zebrafish) demonstrated an sRNA class transition from piRNAs to miRNAs as development proceeds. We observed that both the abundance and diversity of miRNAs are gradually increased, while the abundance is enhanced more dramatically than the diversity during development. However, although both the abundance and diversity of piRNAs are gradually decreased, the diversity was firstly increased then rapidly decreased. To evaluate the computational accuracy, the expression levels of four known miRNAs were experimentally validated. We also predicted 25 potentially novel miRNAs, whereas two candidates were verified by Northern blots. CONCLUSIONS: Taken together, our analyses revealed the piRNA to miRNA transition as a conserved mechanism in zebrafish, although two different types of sRNAs exhibit distinct expression dynamics in abundance and diversity, respectively. Our study not only generated a better understanding for sRNA regulations in early zebrafish development, but also provided a useful platform for analyzing sRNA-seq data. The CSZ was implemented in Perl and freely downloadable at: http://csz.biocuckoo.org.

Emerging catalysts for the ambient synthesis of ethylene glycol from CO2 and its derivatives.

Ethylene glycol (EG), a useful chemical raw material, has been widely applied in many aspects of modern society. The conventional preparation of ethylene glycol mainly uses the petroleum route at high temperatures and pressure. More and more approaches have been developed to synthesize EG from CO2 and its derivatives under mild conditions. In this review, the ambient synthesis of EG from thermocatalysis, photocatalysis, and electrocatalysis is highlighted. The coal-to-ethylene glycol technology, one of the typical thermal catalysis routes for EG preparation, is relatively mature. However, it still faces some problems to be solved in industrialization. The recent progress in the development of coal-to-ethylene glycol technology is introduced. The main focus is on how to realize the preparation of EG under mild conditions. The strategies include doping promoters, modification of supports, design of catalysts with special structures, etc. Furthermore, the emerging technological progress of photocatalytic and electrocatalytic ethylene glycol synthesis under ambient conditions is introduced. Compared with the thermal catalytic reaction, the reaction conditions are milder. However, there are still many problems in large-scale production. Finally, we propose future development issues and related prospects for the ambient synthesis of EG using different catalytic routes.

Ambient-pressure synthesis of ethylene glycol catalyzed by C60-buffered Cu/SiO2.

Bulk chemicals such as ethylene glycol (EG) can be industrially synthesized from either ethylene or syngas, but the latter undergoes a bottleneck reaction and requires high hydrogen pressures. We show that fullerene (exemplified by C60) can act as an electron buffer for a copper-silica catalyst (Cu/SiO2). Hydrogenation of dimethyl oxalate over a C60-Cu/SiO2 catalyst at ambient pressure and temperatures of 180° to 190°C had an EG yield of up to 98 ± 1%. In a kilogram-scale reaction, no deactivation of the catalyst was seen after 1000 hours. This mild route for the final step toward EG can be combined with the already-industrialized ambient reaction from syngas to the intermediate of dimethyl oxalate.

PlantMirP2: An Accurate, Fast and Easy-To-Use Program for Plant Pre-miRNA and miRNA Prediction.

MicroRNAs (miRNAs) are a kind of short non-coding ribonucleic acid molecules that can regulate gene expression. The computational identification of plant miRNAs is of great significance to understanding biological functions. In our previous studies, we have put firstly forward and further developed a set of knowledge-based energy features to construct two plant pre-miRNA prediction tools (plantMirP and riceMirP). However, these two tools cannot be used for miRNA prediction from NGS (Next-Generation Sequencing) data. In addition, for further improving the prediction performance and accessibility, plantMirP2 has been developed. Based on the latest dataset, plantMirP2 achieves a promising performance: 0.9968 (Area Under Curve, AUC), 0.9754 (accuracy), 0.9675 (sensitivity) and 0.9876 (specificity). Additionally, the comparisons with other plant pre-miRNA tools show that plantMirP2 performs better. Finally, the webserver and stand-alone version of plantMirP2 are available.

Boron Modified Bifunctional Cu/SiO2 Catalysts with Enhanced Metal Dispersion and Surface Acid Sites for Selective Hydrogenation of Dimethyl Oxalate to Ethylene Glycol and Ethanol.

Boron (B) promoter modified Cu/SiO2 bifunctional catalysts were synthesized by sol-gel method and used to produce ethylene glycol (EG) and ethanol (EtOH) through efficient hydrogenation of dimethyl oxalate (DMO). Experimental results showed that boron promoter could significantly improve the catalytic performance by improving the structural characteristics of the Cu/SiO2 catalysts. The optimized 2B-Cu/SiO2 catalyst exhibited excellent low temperature catalytic activity and long-term stability, maintaining the average EG selectivity (Sel.EG) of 95% at 190 °C, and maintaining the average EtOH selectivity (Sel.EtOH) of 88% at 260 °C, with no decrease even after reaction of 150 h, respectively. Characterization results revealed that doping with boron promoter could significantly increase the copper dispersion, enhance the metal-support interaction, maintain suitable Cu+/(Cu+ + Cu0) ratio, and diminish metallic copper particles during the hydrogenation of DMO. Thus, this work introduced a bifunctional boron promoter, which could not only improve the copper dispersion, reduce the formation of bulk copper oxide, but also properly enhance the acidity of the sample surface, so that the Cu/SiO2 sample could exhibit superior EG selectivity at low temperature, as well as improving the EtOH selectivity at high temperature.

Multifunctional homochiral lanthanide camphorates with mixed achiral terephthalate ligands.

Seven homochiral lanthanide camphorates with mixed achiral terephthalate ligands, namely, {Ln(2)(cam)(2)(bdc)(H(2)O)(2)}·DMF [Ln = Sm (1), Eu (2), Gd (3), Tb (4), Dy (5), Ho (6), Er (7); d-H(2)cam = d-(+)-camphoric acid; H(2)bdc = 1,4-benzenedicarboxylic acid; DMF = N,N'-dimethylformamide], have been solvothermally synthesized. Single-crystal X-ray diffraction analyses reveal that compounds 1-7 are isostructural and crystallize in orthorhombic, chiral space group P2(1)2(1)2(1). These structures feature three-dimensional open frameworks based on rodlike [Ln(2)(OCO)(6)(H(2)O)(2)](n) secondary building units, with the guest DMF molecules occupying the void space of the host {Ln(2)(cam)(3)(bdc)(H(2)O)(2)} framework. The photophysical and magnetic properties of some of these complexes have been investigated. Notably, the terbium compound 4 is highly emissive with a quantum yield of 63.68%. Additionally, thermogravimetric analyses, variable-temperature IR spectroscopy, and powder X-ray diffraction of 2 as a representative were performed to determine its thermal stability, which indicates that the framework still remains intact until 300 °C.

PlantMirP-Rice: An Efficient Program for Rice Pre-miRNA Prediction.

Rice microRNAs (miRNAs) are important post-transcriptional regulation factors and play vital roles in many biological processes, such as growth, development, and stress resistance. Identification of these molecules is the basis of dissecting their regulatory functions. Various machine learning techniques have been developed to identify precursor miRNAs (pre-miRNAs). However, no tool is implemented specifically for rice pre-miRNAs. This study aims at improving prediction performance of rice pre-miRNAs by constructing novel features with high discriminatory power and developing a training model with species-specific data. PlantMirP-rice, a stand-alone random forest-based miRNA prediction tool, achieves a promising accuracy of 93.48% based on independent (unseen) rice data. Comparisons with other competitive pre-miRNA prediction methods demonstrate that plantMirP-rice performs better than existing tools for rice and other plant pre-miRNA classification.

Breaking the mirror: pH-controlled chirality generation from a meso ligand to a racemic ligand.

To study the conversion from a meso form to a racemic form of tetrahydrofurantetracarboxylic acid (H(4)L), seven novel coordination polymers were synthesized by the hydrothermal reaction of Zn(NO(3))(2)6 H(2)O with (2S,3S,4R,5R)-H(4)L in the presence of 1,10-phenanthroline (phen), 2,2'-bipyridine (2,2'-bpy), or 4,4'-bipyridine (4,4'-bpy): [Zn(2){(2S,3S,4R,5R)-L}(phen)(2)(H(2)O)]2 H(2)O (1), [Zn(4){(2S,3R,4R,5R)-L}{(2S,3S,4S,5R)-L}(phen)(2)(H(2)O)(2)] (2), [Zn(2){(2S,3S,4R,5R)-L}(H(2)O)(2)]H(2)O (3), [Zn(4){(2S,3R,4R,5R)-L}{(2S,3S,4S,5R)-L} (2,2'-bpy)(2)(H(2)O)(2)]2 H(2)O (4), [Zn(2) {(2S,3S,4R,5R)-L}(2,2'-bpy)(H(2)O)] (5), [Zn(4){(2S,3R,4R,5R)-L}{(2S,3S,4S,5R)-L} (4,4'-bpy)(2)(H(2)O)(2)] (6), and [Zn(2) {(2S,3S,4R,5R)-L}(4,4'-bpy)(H(2)O)] 2 H(2)O (7). These complexes were obtained by control of the pH values of reaction mixtures, with an initial of pH 2.0 for 1, 2.5 for 2, 4, and 6, and 4.5 for 3, 5, and 7, respectively. The expected configuration conversion has been successfully realized during the formation of 2, 4, and 6, and the enantiomers of L, (2S,3R,4R,5R)-L and (2S,3S,4S,5R)-L, are trapped in them, whereas L ligands in the other four complexes retain the original meso form, which indicates that such a conversion is possibly pH controlled. Acid-catalyzed enol-keto tautomerism has been introduced to explain the mechanism of this conversion. Complex 1 features a simple 1D metal-L chain that is extended into a 3D supramolecular structure by pi-pi packing interactions between phen ligands and hydrogen bonds. Complex 2 has 2D racemic layers that consist of centrosymmetric bimetallic units, and a final 3D supramolecular framework is formed by the interlinking of these layers through pi-pi packing interactions of phen. Complex 3 is a 3D metal-organic framework (MOF) involving meso-L ligands, which can be regarded as (4,6)-connected nets with vertex symbol (4(5).6)(4(7).6(8)). Complexes 4 and 5 contain 2D racemic layers and (6,3)-honeycomb layers, respectively, both of which are combined into 3D supramolecular structures through pi-pi packing interactions of 2,2'-bpy. The structure of complex 6 is a 2D network formed by 4,4'-bpy bridging 1D tubes, which consist of metal atoms and enantiomers of L. These layers are connected through hydrogen bonds to give the final 3D porous supramolecular framework of 6. Complex 7 is a 3D MOF with novel (3,4,5)-connected (6(3))(4(2).6(4))(4(2).6(6).8(2)) topology. The thermal stability of these compounds was also investigated.

Ag(I)-mediated in situ dehydrogenative coupling of 3-amino-1,2,4-triazole into 3,3'-azobis(1,2,4-triazole) in Cd(II) coordination polymers.

Ag(I)-mediated in situ generation of 3,3'-azobis(1,2,4-triazole) (AzTAZ) from 3-amino-1,2,4-triazole (AmTAZ) through dehydrogenative coupling has been realized during the crystallization process of two Cd(II) coordination polymers with novel topological architectures: a (3, 4, 5)-connected (4 x 6(2))(2)(4 x 6(7) x 8(2))(2)(6(5) x 10) net for [Cd(2)(AmTAZ)(2)(AzTAZ)](n) (1) and a 4-connected (6(2) x 8(4))(6(4) x 8(2))(6(5) x 8)(2) net for [Cd(AzTAZ)(2)(H(2)O)](n) (2), whereas AmTAZ retains its original form in a heterometallic complex, [Ag(2)Cd(AmTAZ)(4)](n) (3).

Temperature-controlled syntheses of substituted 1,2,4-triazolelead(II) complexes: active lone pair and N-H...X (X = Cl, Br, I) hydrogen bonds.

Three isomorphous lead(II) complexes with a new {N(3)SX}-coordinated (X = Cl, Br, I) mode have been synthesized and characterized by X-ray diffraction. The structural analyses reveal that the coordination environment around the center metal is distinctly influenced by the stereochemical 6s(2) lone pair and N-H...X hydrogen bonds. Additionally, doubly deprotonated trzS(2-) (HtrzSH = 1,2,4-triazole-3-thiol) generated in situ via deamination and dehydrazination of ahtrzS(-) (ahtrzSH = 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole) was first observed in a semiconducting three-dimensional coordination network at higher reaction temperature.

Synthesis, structure, and luminescent properties of hybrid inorganic-organic framework materials formed by lead aromatic carboxylates: inorganic connectivity variation from 0D to 3D.

The hydro(solvo)thermal reactions of Pb(OAc)(2).3H(2)O with the aromatic carboxylic ligands 1,3,5-benzenetricarboxylic and 1,4-, 1,2-, and 1,3-benzenedicarboxylic acids (1,3,5-H(3)BTC; 1,4-, 1,2-, and 1,3-H(2)BDC) have yielded a family of inorganic-organic framework materials: [Pb(2)(1,3,5-BTC)(mu(3)-OH)(H(2)O)](n) (Iota), [NaPb(1,3,5-BTC)(H(2)O)](n) (IotaIota), [Pb(1,4-BDC)](n) (IotaIotaIota), [Pb(5)(1,2-BDC)(4)(OAc)(2)](n) (IV), and {[Pb(5)(1,3-BDC)(5)(H(2)O)(2)](2).H(2)O}(n) (V). These complexes have been characterized by means of single-crystal X-ray diffraction, X-ray powder diffraction, thermogravimetric analysis-mass spectrometry, and photoluminescence spectra. They are all three-dimensional structures except for two-dimensional IV. Topology analysis reveals that complexes I an V represent rare (4,8)-connected flu and (3,4)-connected zeolite-like nets, respectively. The five complexes exhibit diverse inorganic connectivity, including a 0D Pb(4)O(16) cluster for I, a 1D Pb-O-Pb chain for II, a 2D Pb-O-Pb network for III and IV, and an unprecedented 3D Pb-O-Pb framework for V. And the diversity in inorganic arrays leads to differences in luminescent properties of these complexes.