Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge

In the context of the SAMPL6 challenges, series of blinded predictions of standard binding free energies were made with the SOMD software for a dataset of 27 host–guest systems featuring two octa-acids hosts (OA and TEMOA) and a cucurbituril ring (CB8) host. Three different models were used, ModelA computes the free energy of binding based on a double annihilation technique; ModelB additionally takes into account long-range dispersion and standard state corrections; ModelC additionally introduces an empirical correction term derived from a regression analysis of SAMPL5 predictions previously made with SOMD. The performance of each model was evaluated with two different setups; buffer explicitly matches the ionic strength from the binding assays, whereas no-buffer merely neutralizes the host–guest net charge with counter-ions. ModelC/no-buffer shows the lowest mean-unsigned error for the overall dataset (MUE 1.29?<?1.39?<?1.50 kcal mol^?1, 95% CI), while explicit modelling of the buffer improves significantly results for the CB8 host only. Correlation with experimental data ranges from excellent for the host TEMOA (R² 0.91?<?0.94?<?0.96), to poor for CB8 (R² 0.04?<?0.12?<?0.23). Further investigations indicate a pronounced dependence of the binding free energies on the modelled ionic strength, and variable reproducibility of the binding free energies between different simulation packages.     

Hydroxymethylfurfural: an enemy or a friendly xenobiotic? A bioanalytical approach

Hydroxymethylfurfural (HMF), a well-known heterocyclic Maillard reaction product, has often been studied for its potential toxic, mutagenic, and carcinogenic effects. Recent clinical studies, however, have strongly suggested that HMF might have exciting antitumor potential. We report on the development and validation of a bioanalytical assay for HMF that could be suitable as a basis for pharmacokinetic models in cancer patients. Two strategies were tested, i.e., direct and indirect methodologies. A direct isocratic LC determination at 283 nm was designed. Two indirect attempts involved derivatization coupled to HPLC-UV. It was possible to resolve the stereoisomers of the HMF derivative, and factors influencing their equilibrium ratio are discussed. HMF was extracted from the biomatrix by solid-phase extraction using different cartridges. A comparative study was made of the implemented methods as well as the extraction protocols. Both indirect assays proved to be more sensitive and were used to assess HMF quantitatively in human plasma. However, the newly introduced derivatization conditions led to the highest sensitivity with a LOD (S/N ratio = 3) of at least 2 pmol analyte on column. The assay selectivity was satisfactory in pre- and post-dose real samples. The mean recoveries of the assays were 79% and 89%, with acceptable accuracies and reproducibilities. Figure Schematic representation of hydroxymethylfurfural (HMF) in human plasma     

MALDI TOF/TOF tandem mass spectrometry as a new tool for amino acid analysis

This is the first report of an application of collisionally induced fragmentation of amino acids (AA) and their derivatives by MALDI TOF/TOF tandem mass spectrometry (MS). In this work, we collected the data on high-energy fragmentation reactions of a large group of protonated amino acids and their derivatives with the goal of determining which product ions are analyte specific and if yields of these fragment could be used for quantitative analysis. From 34 different amino acids (20 alpha-amino acids, beta-amino acids, homocysteine, GABA, and modified AA Met sulfone and sulfoxide, hydroxyproline, etc.) we observed that high yields of the target specific immonium ions and fragmentation patterns are most similar to EI or FAB CID on sector instruments. The major exceptions were two highly basic amino acids, Arg and Orn. It is noted that neither beta-, gamma-, nor delta-amino acids produce immonium ions. As might be predicted from high-energy CID work on peptides from the sectors and TOF/TOF, the presence of specific indicator ions in MALDI tandem MS allows distinguishing isomeric and isobaric amino acids. These indicator ions, in combination with careful control of data acquisition, ensure quantitative analysis of amino acids. We believe our data provide strong basis for the application of MALDI TOF/TOF MS/MS in qualitative and quantitative analysis of amino and organic acids, including application in clinical medicine.     

Warfarin Sodium Stability in Oral Formulations

Warfarin sodium is a low-dose pharmaceutical blood thinner that exists in two forms: the clathrate form and the amorphous form. In commercially available warfarin sodium oral suspension, the active pharmaceutical ingredient (API) is added in the amorphous state. This study investigates the apparent instability of the commercially available warfarin liquid oral formulation using Raman and IR spectroscopy, X-ray diffraction, differential scanning calorimetry, UV spectroscopy, and optical microscopy. Warfarin, not its sodium salt, was identified as the undissolved solid existing in the suspension. This was found to be due to the dissociation of sodium salt and the protonation of the warfarin ion in the liquid phase, which triggered the crystallization of the sparingly soluble unsalted form. The coexistence of protonated and unprotonated warfarin ions in the supernatant, as detected by Raman and UV spectroscopy, confirmed this assumption. Study of the dissolution of warfarin sodium amorphous salt and crystalline sodium clathrate in the placebo and pure water verified the results. The effect of pH and temperature on warfarin precipitation was also explored.     

Polypropylene,modified with some oligoesters

Miscibility of polypropylene with some oligoesters was evaluated by optical wedge interference microscopy. Mechanical, thermal, rheological and relaxation properties were studied. Compatibility between the polymers and modifying agents was shown to have a marked effect on stress-strain properties as well as on the structure and melting characteristics of the modified polymers.     

The layered structure of poly­[[di‐μ‐chloro‐bis­[chloro(2‐ethyl­tetrazole‐κN4)copper(II)]]‐di‐μ‐2‐ethyl­tetrazole‐κ2N1:N4]

In the polymeric title complex, [CuCl₂(C₃H₆N₄)₂]_n, there are two ligands in the asymmetric unit. The Cu atom adopts an elongated octahedral geometry, with two 2‐ethyl­tetrazole ligands [Cu—N = 2.0037 (16) and 2.0136 (16) Å] and two Cl atoms [Cu—Cl = 2.2595 (6) and 2.2796 (6) Å] in equatorial positions. A Cl atom and a symmetry‐related 2‐ethyl­tetrazole mol­ecule [Cu—Cl = 2.8845 (8) Å and Cu—N = 2.851 (2) Å] lie in the axial positions of the octahedron. One of the two 2‐­ethyltetrazole ligands of the asymmetric unit exhibits bidentate binding to two Cu atoms through two N atoms of the tetrazole ring, whereas the other ligand is coordinated in a monodentate fashion via one tetrazole N atom. The Cu‐atom octahedra form dimer entities by sharing edges with equatorial and axial Cl atoms. The dimers are linked together through the 2‐ethyl­tetrazole ligands to form one‐dimensional polymeric zigzag chains extending along the b axis. The chains are connected into infinite layers parallel to the (10) plane via the 2‐ethyl­tetrazole ligands.     

[3+2]- Versus [4+2]-cycloaddition reactions of 3-methylsulfanyl-2-arylazo-3-(pyrrolidin-1-yl)acrylonitriles with N-substituted maleimides involving pyrrolidine-derived azomethine ylides

3-Methylsulfanyl-2-arylazo-3-(pyrrolidin-1-yl)acrylonitriles do not enter into [4+2]-cycloaddition reactions with maleimides to form the expected pyrrolo-pyridazines. Instead the formation of novel pyrrolo-pyridazines of type 4 takes place via a formal [3+2]-cycloaddition of initially formed pyrrolidine-derived azomethine ylides 7. The mechanism leading to the final product is discussed.     

Studying the energy dependence of intrinsic conversion efficiency of single crystal scintillators under X-ray excitation

Single crystal scintilators are used in various radiation detectors applications. The efficiency of the crystal can be determined by the Detector Optical Gain (DOG) defined as the ratio of the emitted optical photon flux over the incident radiation photons flux. A parameter affecting DOG is the intrinsic conversion efficiency (n _C ) giving the percentage of the X-ray photon power converted to optical photon power. n _C is considered a constant value for X-ray energies in the order of keV although a non-proportional behavior has been reported. In this work an analytical model, has been utilized to single crystals scintillators GSO:Ce, LSO:Ce and LYSO:Ce to examine whether the intrinsic conversion efficiency shows non proportional behavior under X-ray excitation. DOG was theoretically calculated as a function of the incident X-ray spectrum, the X-ray absorption efficiency, the energy of the produced optical photons and the light transmission efficiency. The theoretical DOG values were compared with experimental data obtained by irradiating the crystals with X-rays at tube voltages from 50 to 140 kV and by measuring the light energy flux emitted from the irradiated screen. An initial value for n _C (calculated from literature data) was assumed for the X-ray tube voltage of 50 kV. For higher X-ray tube voltages the optical photon propagation phenomena was assumed constant and any deviations between experimental and theoretical data were associated with changes in the intrinsic conversion efficiency. The experimental errors were below 7% for each experimental setup. The behavior of n _C values for LSO:Ce and LYSO:Ce were found very similar, i.e., ranging with values from 0.089 at 50 kV to 0.015 at 140 kV, while for GSO:Ce, n _C demonstrated a peak at 80 kV.