The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck–Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI and Schrödinger FEP+ are shown that should encourage others to explore the value of TI in routine Structure-based Drug Design.     

Electrocatalysis of oxygen reduction on multi-walled carbon nanotube supported copper and manganese phthalocyanines in alkaline media

Manganese phthalocyanine (MnPc) and copper phthalocyanine (CuPc)-modified electrodes were prepared using multi-walled carbon nanotubes (MWCNTs) as a support material. The catalyst materials were heat treated at four different temperatures to investigate the effect of pyrolysis on the oxygen reduction reaction (ORR) activity of these electrocatalysts. The MWCNT to metal phthalocyanine ratio was varied. Scanning electron microscopy (SEM) was employed to visualise the surface morphology of the electrodes and the x-ray photoelectron spectroscopic (XPS) study was carried out to analyse the surface composition of the most active catalyst materials. The ORR was studied in 0.1 M KOH solution employing the rotating disk electrode (RDE) method. Glassy carbon (GC) electrodes were modified with carbon nanotube-supported metal phthalocyanine catalysts using Tokuyama AS-4 ionomer. The RDE results revealed that the highest electrocatalytic activity for ORR was achieved upon heat treatment at 800 °C. CuPc-derived catalyst demonstrated lower catalytic activity as compared to the MnPc-derived counterpart, which is in good agreement with previous literature, whereas the activity of MnPc-based catalyst was higher than that reported earlier.     

Comparison of standard addition and conventional isotope dilution mass spectrometry for the quantification of endogenous progesterone in milk

In this study, a standard addition–isotope dilution mass spectrometry (SA-IDMS) method for quantification of endogenous progesterone in milk has been described. The method validation results, linearity, limits of detection and quantification, recovery and uncertainty were fit for the purpose of assigning reference mass fractions to proficiency testing schemes. The developed technique was compared to the isotope dilution mass spectrometry (IDMS) method already existing in the laboratory. Analytical results of two milk samples were (1.377 ± 0.048) μg/kg and (4.457 ± 0.155) μg/kg by SA-ID-LC/MS method, while the results were (1.355 ± 0.019) μg/kg and (4.359 ± 0.059) μg/kg by ID-LC/MS, respectively. Since SA-IDMS was an effective quantitative method that overcame matrix effect, similar quantitative results from IDMS and SA-IDMS indicated that the quantification of progesterone in milk was barely influenced by matrix. Both IDMS and SA-IDMS could be used to assign reference mass fractions to progesterone in milk inter-laboratory proficiency testing schemes.     

Destruction Kinetics of 2,4 Dichlorophenol Aqueous Solutions in an Atmospheric Pressure Dielectric Barrier Discharge in Oxygen

The processes of degradation of 2,4-dichlorophenol (2,4-DCP) aqueous solutions under the action of atmospheric pressure of DBD in oxygen were studied. The degradation of 2,4-DCP proceeds efficiently, the degree of decomposition reaching 100%. The degradation kinetics of 2,4-DCP obeys a formal first-order kinetic law on concentration of 2,4-DCP. The effective rate constants depend weakly on the experimental conditions and are equal to ~ 2 s^?1. Based on experimental data, the energy efficiency of 2,4-DCP decomposition was determined to be in the range of 0.039–0.173 molecules per 100 eV depending on the experimental conditions. The composition of the products was studied by gas chromatography, chromatography-mass spectrometry, UV/visible spectroscopy, fluorescent methods and some chemical methods. The main decomposition products present in the solution were found to be carboxylic acids, aldehydes and chloride ions, whereas carbon dioxide and molecular chlorine appear in the gas. The results obtained are compared with similar data from other advanced oxidation processes (AOP’s) methods.     

Perylene Bisimide In-chain Polyethylene with Unique Self-assembly Nanostructure through Acyclic Diene Metathesis (ADMET) Polymerization

A novel perylene tetracarboxylic acid bisimide(PTCBI) in-chain polyethylene(PE) was first prepared via acyclic diene metathesis(ADMET) polymerization of PTCBI-functionalized α,ω-diene monomer. The polymers could spontaneously self-assemble into hollow cylindrical structures in which the π-π interaction between adjacent PTCBI moieties was enhanced and the electron mobility was possibly promoted. The hydrogenation of as-obtained polymer was readily accomplished, affording the desired precision PTCBI in-chain PE with a saturated backbone, which showed high glass transition temperature(Tg = 63 °C), relatively wide range of light absorption(λ = 200-575 nm), and higher LUMO level(-3.62 e V). It can therefore serve as a superior model for facile construction of functional polyolefin and soluble PTCBI polymer with ordered architecture.     

Spectral stability of periodic waves in the generalized reduced Ostrovsky equation

We consider stability of periodic travelling waves in the generalized reduced Ostrovsky equation with respect to co-periodic perturbations. Compared to the recent literature, we give a simple argument that proves spectral stability of all smooth periodic travelling waves independent of the nonlinearity power. The argument is based on the energy convexity and does not use coordinate transformations of the reduced Ostrovsky equations to the semi-linear equations of the Klein–Gordon type.