The Area Law of Molecular Entropy: Moving beyond Harmonic Approximation.

This article shows that the gas-phase entropy of molecules is proportional to the area of the molecules, with corrections for the different curvatures of the molecular surface. The ability to estimate gas-phase entropy by the area law also allows us to calculate molecular entropy faster and more accurately than currently popular methods of estimating molecular entropy with harmonic oscillator approximation. The speed and accuracy of our method will open up new possibilities for the explicit inclusion of entropy in various computational biology methods.

Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No).

Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active-while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.

Speciation of toxic metals in metal finishing filter cake by X-ray absorption spectroscopy.

The speciation of Cr, Zn, Cu and Pb in two metal finishing filter cakes (TX and ST) was investigated by X-ray absorption spectroscopy (XAS) complemented by X-ray fluorescence (XRF) and X-ray diffraction (XRD). XRF showed that concentrations of Cr, Zn, Cu and Pb were 1.4%, 0.19%, 0.20% and 0.01%, respectively, in TX, and 12.6%, 3.3%, 1.3% and 0.21% in ST. No crystalline phases were detected in TX by XRD whereas ST was dominated by calcite. Cr and Fe K edge XAS showed Cr to be trivalent and octahedrally coordinated, co-precipitated with Fe as CrxFe1-x-(oxy)hydroxides in both filter cakes. Zn, P and Ca K edge XAS showed that 2ZnCO3∙3Zn(OH)2 and Zn3(PO4)2 were the dominant zinc-containing phases, with combined tetrahedral and octahedral coordination; Zn phases were slightly more crystalline in TX than ST. Pb L3 edge X-ray absorption near edge spectroscopy (XANES) found that Pb was likely adsorbed on amorphous SiO2. Cu, Si and S K edge XAS showed that all Cu was divalent, and the dominant copper phases were found to be Cu2Cl(OH)3, Cu(OH)2 and CuSO4·5H2O for ST, whereas Cu appeared to adsorb to amorphous SiO2 for TX, which contained much less Pb. Cr is thus immobilized in the filter cakes in a phase with low solubility at environmentally feasible pH values, whereas Zn, Cu and Pb could be released when the pH decreases below 8 or above 11. These findings are significant for the development of waste management regulations and/or metal recovery methods (e.g., hydro/pyrometallurgy).

Solvent-Free Depolymerization of Plastic Waste Enabled by Plastic-Catalyst Interfacial Engineering.

Depolymerization of condensation polymers by chemolysis often suffers from the large usage of solvents and homogeneous catalysts such as acids, bases, and metal salts. The catalytic efficiency of heterogeneous catalysts is largely constrained by the poor interfacial contact between solid catalysts and solid plastics below melting points. We report here our discovery of autogenous heterogeneous catalyst layer on polyethylene terephthalate surfaces during the generally believed homogeneous catalytic depolymerization process. Inspired by the "contact mass" concept in industrial chlorosilane production, we further demonstrate that the construction of plastic-catalyst solid-solid interfaces enables solvent-free depolymerization of polyethylene terephthalate by vapor phase methanolysis at relatively low temperatures. Trace amounts of earth-abundant element (zinc) introduced by electrostatic adsorption is sufficient for catalyzing the depolymerization. The concept of plastic-catalyst contact mass interfacial catalysis might inspire new pathways for tackling plastic waste problems.

Speciation of toxic pollutants in Pb/Zn smelter slags by X-ray Absorption Spectroscopy in the context of the literature.

Pb/Zn smelter slag is a hazardous industrial waste from the Imperial Smelting Process (ISP). The speciation of zinc, lead, copper and arsenic in the slag controls their recovery or fate in the environment but has been little investigated. X-ray Absorption Spectroscopy (XAS) was applied to this complex poorly crystalline material for the first time to gain new insights about speciation of elements at low concentration. Zn, Cu, As K-edge and Pb L3-edge XAS was carried out for a Pb/Zn slag from a closed ISP facility in England, supported by Fe, S and P K-edge XAS. Results are presented in the context of a full review of the literature. X-ray fluorescence showed that concentrations of Zn, Pb, Cu and As were 8.4, 1.6, 0.48 and 0.45 wt%, respectively. Wüstite (FeO) was the only crystalline phase identified by X-ray diffraction, but XAS provided a more complete understanding of the matrix. Zn was found to be mainly present in glass, ZnS, and possibly solid solutions with Fe oxides; Pb was mainly present in glass and apatite minerals (e.g., Pb5(PO4)3OH); Cu was mainly speciated as Cu2S, with some metallic Cu and a weathering product, Cu(OH)2; As speciation was likely dominated by arsenic (III) and (V) oxides and sulfides.

Homogeneous versus MOF-supported catalysis: a direct comparison of catalytic hydroboration with Ni tripodal P3E (E = Si, Ge) complexes.

The MOF material NU-1000 was employed to host Ni tripodal complexes prepared from new organometallic precursors [HNi(κ4(E,P,P,P)-E(o-C6H4CH2PPh2)3], E = Si (Ni-1), Ge (Ni-2). The new heterogeneous catalytic materials, Ni-1@NU-1000 and Ni-2@NU-1000, show the advantages of both homogeneous and heterogeneous catalysts. They catalyze the hydroboration of aldehydes and ketones more efficiently than the homogeneous Ni-1 and Ni-2, under aerobic conditions and show recyclability.

A 500 kV, 10 kA, 40 ns coaxial Marx generator pulser for cable fed flash x-ray system.

Flash x-ray (FXR) systems are used for dynamic radiography. Depending on the speed of the object, these systems typically require a very short pulse duration (∼25 ns) for image acquisition without motion blur. The conventional Marx generators with zigzag discharge paths result in higher inductance; hence, they do not meet the requirement of shorter pulse duration (30-40 ns) and low impedance (40-60 Ω) simultaneously. A coaxial Marx generator has been designed and developed, which is capable of generating 500 kV peak voltages and 10 kA peak current within a 40 ns pulse duration. The CST simulation of the coaxial Marx generator has been carried out to validate the design parameters. The FXR electron beam diode is powered by this Marx generator. Experiments were carried out to measure the x-ray parameters like pulse width, source size, x-ray energy spectrum, penetration depth, and cone angle. The maximum measured x-ray dose was 62 mR at 1 m distance from the source window. The x-ray radiograph demonstrates a penetration depth of 32 mm in steel kept at 2.5 m distance from the source for 500 kV diode voltages.

Design, simulation, and development of bipolar pulse forming network based Marx generator for S band backward wave oscillator.

Pulse power systems have a wide range of applications, one of which is microwave generation. Microwave emission is associated with a certain time delay between the application of a high voltage pulse and the generation of the microwave signal. This time delay is known as microwave delay time, and it depends on the time period of the microwave signal being generated. As the time period of the microwave signal increases, the required input electrical pulse duration also goes up. To achieve this, a pulse forming network (PFN) based Marx generator is proposed. The Bipolar Marx generator is preferred over the uni-polar Marx generator to obtain the high voltage high current pulse. This also helps in maintaining the impedance requirement for Backward Wave Oscillator (BWO) devices that generate the microwave pulse. To the best of our knowledge, PFN based Marx generators have been developed up to 400 kV. Here, a bipolar Marx generator has been designed with ratings of 800 kV peak voltage, 10 kA peak current, and 150 ns flattop pulse duration. The design includes analytical calculations and numerical analysis by electromagnetic simulation. The triggering method to get a wide triggering range has also been discussed. The design values have also been experimentally verified, and the resulting parameters were applied to a BWO to simulate the microwave power that it can produce. A peak microwave power of ∼1 GW has been observed in the particle-in-cell simulation.

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets.

The SARS-CoV2 pandemic has highlighted the importance of efficient and effective methods for identification of therapeutic drugs, and in particular has laid bare the need for methods that allow exploration of the full diversity of synthesizable small molecules. While classical high-throughput screening methods may consider up to millions of molecules, virtual screening methods hold the promise of enabling appraisal of billions of candidate molecules, thus expanding the search space while concurrently reducing costs and speeding discovery. Here, we describe a new screening pipeline, called drugsniffer, that is capable of rapidly exploring drug candidates from a library of billions of molecules, and is designed to support distributed computation on cluster and cloud resources. As an example of performance, our pipeline required ∼40,000 total compute hours to screen for potential drugs targeting three SARS-CoV2 proteins among a library of ∼3.7 billion candidate molecules.

CoCrFeNi High-Entropy Alloy as an Enhanced Hydrogen Evolution Catalyst in an Acidic Solution.

High-entropy alloys (HEAs) have intriguing material properties, but their potential as catalysts has not been widely explored. Based on a concise theoretical model, we predict that the surface of a quaternary HEA of base metals, CoCrFeNi, should go from being nearly fully oxidized except for pure Ni sites when exposed to O2 to being partially oxidized in an acidic solution under cathodic bias, and that such a partially oxidized surface should be more active for the electrochemical hydrogen evolution reaction (HER) in acidic solutions than all the component metals. These predictions are confirmed by electrochemical and surface science experiments: the Ni in the HEA is found to be most resistant to oxidation, and when deployed in 0.5 M H2SO4, the HEA exhibits an overpotential of only 60 mV relative to Pt for the HER at a current density of 1 mA/cm2.

A comparative study for phosphate adsorption on amorphous FeOOH and goethite (α-FeOOH): An investigation of relationship between the surface chemistry and structure.

Eutrophication is generally caused by excess nitrogen and phosphorus being released into surface waters by runoff. Developing adsorbents for adsorbing phosphate within soil buffer zones and/or water treatment columns may be effective methods to mitigate this problem. In this study, an amorphous FeOOH (AF) and a well-crystallized α-FeOOH (CF) was formulated to compare phosphate adsorption behavior. The physicochemical properties between these species showed significant differences in morphology, crystallization, zeta potential, and specific surface area. The AF exhibited higher phosphate uptake than CF. X-ray photoelectron spectroscopy (XPS) verified that the hydroxyl groups within AF were 13.28% higher than that in CF. The triply coordinated hydroxyl groups (µ3-OH) associated with AF and CF appeared at different positions as shown in the diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) analyses, confirming that AF contains more adsorption reactive sites (µ3-OH). Mechanisms for monodentate formations and a stable six-member ring structure were proposed. The X-ray absorption near the edge structure (XANES) and XPS results suggested that the iron valence in AF was dominated by Fe (III). XANES also demonstrated that the amorphous structure found in the AF was caused by the disordered tetrahedron and octahedron alignments, leading to a higher phosphate adsorption.

Uniform Mesoporous Amorphous Cobalt-Inherent Silicon Oxide as a Highly Active Heterogeneous Catalyst in the Activation of Peroxymonosulfate for Rapid Oxidation of 2,4-Dichlorophenol: The Important Role of Inherent Cobalt in the Catalytic Mechanism.

Amorphous cobalt-inherent silicon oxide (Co-SiOx) was synthesized for the first time and employed as a highly active catalyst in the activation of peroxymonosulfate (PMS) for the rapid oxidation of 2,4-dichlorophenol (2,4-DCP). The characterization results revealed that the 0.15Co-SiOx possessed a high specific surface area of 607.95 m2/g with a uniform mesoporous structure (24.33 nm). The X-ray diffraction patterns indicate that the substituted cobalt atoms enlarge the unit cell parameter of the original SiO2, and the selected area electron diffraction pattern confirmed the amorphous nature of Co-SiOx. More bulk oxygen vacancies (Ov) existing in the Co-SiOx were identified to be one of the primary contributors to the significantly enhanced catalytic activation of PMS. The cobalt substitution both creates and stabilizes the surficial Ov and forms the adequately active Co(II)-Ov pairs which engine the electron transfer process during the catalytic activities. The active Co(II)-Ov pairs weaken the average electronegativity of Co/Si and Co/O sites, resulting in the prevalent changes in final state energy, which is the main driving cause of the binding energy shifts in the X-ray photoelectron spectroscopy (XPS) spectra of Si and O among all samples. The increase of the relative proportion of Co(III) in the spent Co-SiOx probably causes the binding energy shifts of the Co XPS spectrum compared to that of the Co-SiOx. The amorphous Co-SiOx outperforms stable and quick 2,4-DCP degradation, achieving a much higher kinetic rate of 0.7139 min-1 at pH = 7.02 than others via sulfate radical advanced oxidation processes (AOPs), photo-Fenton AOPs, H2O2 reagent AOPs, and other AOP approaches. The efficient degradation performance makes the amorphous Co-SiOx as a promising catalyst in removing 2,4-DCP or organic-rich pollutants.

Accommodation of In-Register N-Linked Glycans on Prion Protein Amyloid Cores.

Although prion protein fibrils can have either parallel-in-register intermolecular ß-sheet (PIRIBS) or, probably, ß-solenoid architectures, the plausibility of PIRIBS architectures for the usually glycosylated natural prion strains has been questioned based the expectation that such glycans would not fit if stacked in-register on each monomer within a fibril. To directly assess this issue, we have added N-linked glycans to a recently reported cryo-electron microscopy-based human prion protein amyloid model with a PIRIBS architecture and performed in silico molecular dynamics studies to determine if the glycans can fit. Our results show that triantennary glycans can be sterically accommodated in-register on both N-linked glycosylation sites of each monomer. Additional simulations with an artificially mutated ß-solenoid model confirmed that glycans can be accommodated when aligned with ∼4.8 Å spacing on every rung of a fibril. Altogether, we conclude that steric intermolecular clashes between glycans do not, in themselves, preclude PIRIBS architectures for prions.

Magnesium Restores Activity to Peripheral Blood Cells in a Patient With Functionally Impaired Interleukin-2-Inducible T Cell Kinase.

Interleukin-2-inducible T cell kinase (ITK) is critical for T cell signaling and cytotoxicity, and control of Epstein-Barr virus (EBV). We identified a patient with a novel homozygous missense mutation (D540N) in a highly conserved residue in the kinase domain of ITK who presented with EBV-positive lymphomatoid granulomatosis. She was treated with interferon and chemotherapy and her disease went into remission; however, she has persistent elevation of EBV DNA in the blood, low CD4 T cells, low NK cells, and nearly absent iNKT cells. Molecular modeling predicts that the mutation increases the flexibility of the ITK kinase domain impairing phosphorylation of the protein. Stimulation of her T cells resulted in reduced phosphorylation of ITK, PLCγ, and PKC. The CD8 T cells were moderately impaired for cytotoxicity and degranulation. Importantly, addition of magnesium to her CD8 T cells in vitro restored cytotoxicity and degranulation to levels similar to controls. Supplemental magnesium in patients with mutations in another protein important for T cell signaling, MAGT1, was reported to restore EBV-specific cytotoxicity. Our findings highlight the critical role of ITK for T cell activation and suggest the potential for supplemental magnesium to treat patients with ITK deficiency.

Characterisation of ashes from waste biomass power plants and phosphorus recovery.

Biowastes, such as meat and bone meal (MBM), and poultry litter (PL), are used as energy sources for industrial combustion in the UK. However, the biomass ashes remaining after combustion, which contain nutrients such as phosphorus, are landfilled rather than utilised. To promote their utilisation, biomass ashes from industries were characterised in terms of their elemental and mineral compositions, phosphorus extractability, and pH-dependent leachability. These ashes were highly alkaline (pH as high as 13), and rich in calcium and phosphorus. The P bio-availabilities in the ash evaluated by Olsen's extraction were low. Hydroxyapatite and potassium sodium calcium phosphate were identified by X-ray powder diffraction (XRD) as the major phases in the MBM and PL ashes, respectively. The leaching of P, Ca, and many other elements was pH dependent, with considerable increase in leaching below about pH 6. P recovery by acid dissolution (e.g., with H2SO4) seems feasible and promising; the optimized acid consumption for ~90% P recovery could be as low as 3.2-5.3 mol H+/mol P.

A general synthesis approach for supported bimetallic nanoparticles via surface inorganometallic chemistry.

The synthesis of ultrasmall supported bimetallic nanoparticles (between 1 and 3 nanometers in diameter) with well-defined stoichiometry and intimacy between constituent metals remains a substantial challenge. We synthesized 10 different supported bimetallic nanoparticles via surface inorganometallic chemistry by decomposing and reducing surface-adsorbed heterometallic double complex salts, which are readily obtained upon sequential adsorption of target cations and anions on a silica substrate. For example, adsorption of tetraamminepalladium(II) [Pd(NH3)4 2+] followed by adsorption of tetrachloroplatinate [PtCl4 2-] was used to form palladium-platinum (Pd-Pt) nanoparticles. These supported bimetallic nanoparticles show enhanced catalytic performance in acetylene selective hydrogenation, which clearly demonstrates a synergistic effect between constituent metals.

Entropic allostery dominates the phosphorylation-dependent regulation of Syk tyrosine kinase release from immunoreceptor tyrosine-based activation motifs.

Spleen tyrosine kinase (Syk) is an essential player in immune signaling through its ability to couple multiple classes of membrane immunoreceptors to intracellular signaling pathways. Ligand binding leads to the recruitment of Syk to a phosphorylated cytoplasmic region of the receptors called ITAM. Syk binds to ITAM with high-affinity (nanomolar Kd ) via its tandem pair of SH2 domains. The affinity between Syk and ITAM is allosterically regulated by phosphorylation at Y130 in a linker connecting the tandem SH2 domains; when Y130 is phosphorylated, the binding affinity decreases (micromolar Kd ). Previous equilibrium binding studies attribute the increase in the binding free energy to an intra-molecular binding (isomerization) step of the tandem SH2 and ITAM, but a physical basis for the increased free energy is unknown. Here, we provide evidence that Y130 phosphorylation imposes an entropy penalty to isomerization, but surprisingly, has negligible effect on the SH2 binding interactions with ITAM and thus on the binding enthalpy. An analysis of NMR chemical shift differences characterized conformational effects of ITAM binding, and binding thermodynamics were measured from isothermal titration calorimetry. Together the data support a previously unknown mechanism for the basis of regulating protein-protein interactions through protein phosphorylation. The decreased affinity for Syk association with immune receptor ITAMs by Y130 phosphorylation is an allosteric mechanism driven by an increased entropy penalty, likely contributed by conformational disorder in the SH2-SH2 inter-domain structure, while SH2-ITAM binding contacts are not affected, and binding enthalpy is unchanged.