Diffusion Model of Methane Hydrate Formation in “Dry Water”

Russian Journal of Physical Chemistry A - The kinetics of methane hydrate formation in “dry water” is studied using a diffusion model (the well-known modified shrinking core model). An...     

Topological Quantities Determining the Folding/Unfolding Rate of Two-state Folding Proteins

We investigate various topological and energy parameters from the protein native structure and find combinations of some parameters that are well correlated with the rate of folding/unfolding. For folding, the topological quantity that combines the clustering coefficient and the long-range order (or total contact distance/contact order) has a high correlation with the folding rate, expressed as ln k _F , obtained from standard experimental conditions. For unfolding, a combination of the impact of edge removal, obtained from the protein structure, and the stability of the native protein structure, as expressed by the free energy change ΔG, gives a good correlation with unfolding rate, ln k _U .     

Folding of elongated proteins: conventional or anomalous?

The complexity of the mechanisms by which proteins fold has been shown by many studies to be governed by their native-state topologies. This was manifested in the ability of the native topology-based model to capture folding mechanisms and the success of folding rate predictions based on various topological measures, such as the contact order. However, while the finer details of topological complexity have been thoroughly examined and related to folding kinetics, simpler characteristics of the protein, such as its overall shape, have been largely disregarded. In this study, we investigated the folding of proteins with an unusual elongated geometry that differs substantially from the common globular structure. To study the effect of the elongation degree on the folding kinetics, we used repeat proteins, which become more elongated as they include more repeating units. Some of these have apparently anomalous experimental folding kinetics, with rates that are often less than expected on the basis of rates for globular proteins possessing similar topological complexity. Using experimental folding rates and a larger set of rates obtained from simulations, we have shown that as the protein becomes increasingly elongated, its folding kinetics becomes slower and deviates more from the rate expected on the basis of topology measures fitted for globular proteins. The observed slow kinetics is a result of a more complex pathway in which stable intermediates composed of several consecutive repeats can appear. We thus propose a novel measure, an elongation-sensitive contact order, that takes into account both the extent of elongation and the topological complexity of the protein. This new measure resolves the apparent discrimination between the folding of globular and elongated repeat proteins. Our study extends the current capabilities of folding-rate predictions by unifying the kinetics of repeat and globular proteins.     

pH-Controlled Reversible Folding of Copolymers via Formation of β-sheet Secondary Structures

Protein functions are enabled by their perfectly arranged 3D structure, which is the result of a hierarchical intramolecular folding process. Sequence-defined polypeptide chains form locally ordered secondary structures (i.e., α-helix and β-sheet) through hydrogen bonding between the backbone amides, shaping the overall tertiary structure. To generate similarly complex macromolecular architectures based on synthetic materials, a plethora of strategies have been developed to induce and control the folding of synthetic polymers. However, the degree of complexity of the structure-driving ensemble of interactions demonstrated by natural polymers is unreached, as synthesizing long sequence-defined polymers with functional backbones remains a challenge. Herein, we report the synthesis of hybrid peptide-N,N-Dimethylacrylamide copolymers via radical Ring-Opening Polymerization (rROP) of peptide containing macrocycles. The resulting synthetic polymers contain sequence-defined regions of β-sheet encoding amino acid sequences. Exploiting the pH responsiveness of the embedded sequences, protonation or deprotonation in water induces self-assembly of the peptide strands at an intramacromolecular level, driving polymer chain folding via formation of β-sheet secondary structures. We demonstrate that the folding behavior is sequence dependent and reversible.     

Clay Supported Ammonium Nitrate “Clayan” : A Rapid and Convenient Regeneration of Carbonyls in Dry Media

Regeneration of carbonyls from their oximes, phenylhydrazones and tosylhydrazones derivatives using clay supported ammonium nitrate “clayan” under microwave irridiation is described. The inexpensive reagent and solvent free condition makes the procedure simple and economic.     

Microwave Thermolysis VII: Oxidative Coupling of Thiol Acetates and Esters Using “Clayan” in Dry Media

Disulfide bond formation by the oxidative cleavage of thiol acetates and thiol esters using “Clayan”s under microwave irradiation is described. The non-metallic and inexpensive nature of the reagent are the important features of the procedure.     

Real-Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy

The kinase inhibitory domain of the cell cycle regulatory protein p27^Kip1 (p27) was nuclear spin hyperpolarized using dissolution dynamic nuclear polarization (D-DNP). While intrinsically disordered in isolation, p27 adopts secondary structural motifs, including an α-helical structure, upon binding to cyclin-dependent kinase 2 (Cdk2)/cyclin A. The sensitivity gains obtained with hyperpolarization enable the real-time observation of ¹³C NMR signals during p27 folding upon binding to Cdk2/cyclin A on a time scale of several seconds. Time-dependent intensity changes are dependent on the extent of folding and binding, as manifested in differential spin relaxation. The analysis of signal decay rates suggests the existence of a partially folded p27 intermediate during the timescale of the D-DNP NMR experiment.     

Application of Catalytic Wet Air Oxidation to Treatment of Landfill Leachate on Co／Bi Catalyst

Catalytic wet air oxidation(CWAO) was employed to reduce the organic compounds in landfill leachate and the effects of temperature, oxygen pressure, catalyst dosage, and concentration of the organic compounds on the TOC and CODcr removal rates were studied. The degradation kinetics of landfill leachate was also investigated and an exponential experiential model consisting of four influential factors was established to describe the reduction of the organic compounds in the landfill leachate. Meanwhile, the GC-MS technique was used to detect the components of the organic intermediates for the inference of the decomposition mechanisms of the organic compounds in landfill leachate. The results reveal that the reaction temperature and the catalyst dosage are the most important factors affecting the degradation reaction of the organic compounds and that the principal intermediates confirmed by GC-MS are organic acids at a percentage of more than 88% with no aldehydes or alcohols detected. The decomposition mechanisms of the organic compounds in landfill leachate were inferred based on the GC-MS information as follows;the activated gas phase O2 captured the hydrogen of the organic pollutants to produce free radicals, which then initiated the catalytic reaction. So most of the organic compounds were oxidized into CO2 and H2O ultimately. In general, catalytic wet air oxidation over catalyst Co3O4/Bi2O3 was a very promising technique for the treatment of landfill leachate.     

Hollow Versus Hydrogen-Occupied Icosahedral Cages of Coinage–Metal Clusters

It is suggested that the hollow coinage–metal icosahedral cage of the [Ag₄₄(SR)₃₀]^4? tetraanion (1a) may be occupied by two hydrogen atoms, giving rise to a dihydridic cluster [H₂Ag₄₄(SR)₃₀]^4? tetraanion (2b). As a consequence, two series of clusters, with different electron counts, can be formed by chemical means: the 18-electron series [H _x Ag₄₄(SR)₃₀]^(4?x)? via stepwise protonation of 1a and the 20-electron series [H _x Ag₄₄(SR)₃₀]^(6?x)? via stepwise deprotonation of 2b (here x = 0, 1, 2). Both series are closed-shell Jelliumatic clusters and expected to be stable. The corresponding members of these two series (for a given x value) are related by a two-electron reduction. These pairs raise the possibility of the hollow icosahedral metal cages in housing a number of hydrogen atoms, either via stepwise protonations or by absorption of hydrogen molecules.     

Evaluation of Biogas Production Potential by Dry Anaerobic Digestion of Switchgrass–Animal Manure Mixtures

Anaerobic digestion is a biological method used to convert organic wastes into a stable product for land application with reduced environmental impacts. The biogas produced can be used as an alternative renewable energy source. Dry anaerobic digestion [>15% total solid (TS)] has an advantage over wet digestion (<10% TS) because it allows for the use of a smaller volume of reactor and because it reduces wastewater production. In addition, it produces a fertilizer that is easier to transport. Performance of anaerobic digestion of animal manure–switchgrass mixture was evaluated under dry (15% TS) and thermophilic conditions (55 °C). Three different mixtures of animal manure (swine, poultry, and dairy) and switchgrass were digested using batch-operated 1-L reactors. The swine manure test units showed 52.9% volatile solids (VS) removal during the 62-day trial, while dairy and poultry manure test units showed 9.3% and 20.2%, respectively. Over the 62 day digestion, the swine manure test units yielded the highest amount of methane 0.337 L CH₄ /g VS, while the dairy and poultry manure test units showed very poor methane yield 0.028 L CH₄/g VS and 0.002 L CH₄/g VS, respectively. Although dairy and poultry manure performed poorly, they may still have high potential as biomass for dry anaerobic digestion if appropriate designs are developed to prevent significant volatile fatty acid (VFA) accumulation and pH drop.     

Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study

The conformational preferences of oligopeptides of an ϵ-amino acid (2-((1R,3S)-3-(aminomethyl)cyclopentyl)acetic acid, Amc₅a) with a cyclopentane substituent in the C^β−C^γ−C^δ sequence of the backbone were investigated using DFT methods in chloroform and water. The most preferred conformation of Amc₅a oligomers (dimer to hexamer) was the H₁₆ helical structure both in chloroform and water. Four residues were found to be sufficient to induce a substantial H₁₆ helix population in solution. The Amc₅a hexamer adopted a stable left-handed (M)-2.3₁₆ helical conformation with a rise of 4.8 Å per turn. The hexamer of Ampa (an analogue of Amc₅a with replacing cyclopentane by pyrrolidine) adopted the right-handed mixed (P)-2.9_18/16 helical conformation in chloroform and the (M)-2.4₁₆ helical conformation in water. Therefore, hexamers of ϵ-amino acid residues exhibited different preferences of helical structures depending on the substituents in peptide backbone and the solvent polarity as well as the chain length.     

Cyclopropanation Versus Deoxygenation in the Reactions of Halocarbenes with pre-Aromatic Ketones

Cyclopropanesareveryusefillintermediatesinorganicsynthesis'.OurpreviousstUdiesshowedthatthereactionsof2,4,6-triphenyIcycIoheptatrienonewithhaIcoarbenesgavealmostnocyclopropaneproduct'.Ontheotherhand.whenanotherpre-aromaticketoneIwasusedassubstrate,theonlyisolatedproductwasfoundtocontaincyclopropane(eq.I).Furthermore,whenthesubstratewastetraphenylcyclone(TPCP,2),bothcyclopropanationanddeoxygenationproductswereobtained(eq.2).Nowwewishtoreporttheserecentfindingsandelucidatethepossiblefactorsw…     

CuZnAl Mixed Oxide Catalyst Prepared from Hydrotalcite-like Precursor for Catalytic Wet Oxidation of Phenol

Theefficiencyofseveralnoblemetalsforcatalyt icwetoxidation (CWO )ofvarious pollutantshasbeendemonstrated[1,2 ] .However ,thenoblemetalsareexpensive ,affectinggreatlytheeconomicsofthecorrespondingprocess .Asanalternative ,theuseoftransition metaloxideshasbeenconsidered[3～ 5] ,buttheyhaveamainproblemofleachinginthecorrosivereactionmixtures .Alejandreetal[6,7] reportedthattheleachingcanbemuchreducedwhenCuAlorCu NiAlmixedoxide preparedfromhydrotalcite likecompound (HTLC) precursorsisusedasth…     

Highly Efficient Synthesis of 3,5-Diaryl-1,2,4-thiadiazoles in Water–Wet Paste Conditions

1,3-Dibromo-5,5-diphenylimidazolidine-2,4-dione (N,N’-dibromo phenytoin) was efficiently used for the rapid conversion of thiobenzamides to the corresponding 3,5-diaryl-1,2,4-thiadiazoles in water–wet paste conditions.

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Dry etching characteristics of III–V semiconductors in microwave BCl3 discharges

Electron cyclotron resonance (ECR) BCl₃ discharges with additional rf biasing of the sample position have been used to etch a variety of III–V semiconductors. GaAs and Al_xGa_1–xAs (x = 0–1) etch at equal rates in BCl₃ or BCl₃/Ar discharges, whereas SF₆ addition produces high selectivities for etching GaAs over AlGaAs. These selectivities are in excess of 600 for dc biases of –150 V, and fall to 6 for biases of –300 V. If the dc biases are kept to – 100 V, there is no measurable degradation of the optical properties of the GaAs and AlGaAs. The AlF₃ formed on the AlGaAs surface during exposure to BCl₃/SF₆ plasmas can be removed by sequential rinsing in dilute NH₄OH and water. In-based materials (InP, InAs, InSb, InGaAs) etch at slow rates with relatively rough morphologies in BCl₃ plasmas.     

Condensation of Meldrum Acids with Carbonyl Compounds in Dry Media under Microwave Irradiation

以冰醋酸－六氢吡啶为催化剂，硅胶或氧化铝为载体，Ｍｅｌｄｒｕｍ酸与一系列醛酮在微波辐射下发生缩合反应，产率为２２～９７％。     

Folding of a β-cyclodextrin monosubstituted at its secondary face,revealed by NMR studies of local structural variations

The ¹H NMR study of a CD mono-functionalized at its secondary face is presented. It is shown that mono-(3-Tyr-3-deoxy-altro)-β-CD undergoes a solvent-dependent conformational change. Passing from organic medium to water, a stable self-inclusion complex is formed. Such a folding is accompanied by a local structural modification of the substituted altrose ring, which can be easily detected from the important variation of its H1–H2 coupling constant.     

Formation of Dioxolane on the Surface of Silica–Sulphuric Acid in Dry Media—Chemoselective Protection of Aryl Aldehydes

Chemoselective protection of aryl aldehydes can be accomplished through the formation of dioxolane on the surface of silica–sulphuric acid under solvent‐free conditions where aliphatic aldehydes, dialkyl ketones, aryl alkyl ketones, and diaryl ketones remain intact.