Oligomeric phthalonitriles and tetrakis(phenylethynyl)benzene blends with improved processing and thermal properties

Blended resins were prepared from the resorcinol-based PEEK-like oligomeric phthalonitrile resin (RES) and tetrakis(phenylethynyl)benzene (TPEB), a high char yield arylacetylene resin. Initial probing of curing properties using differential scanning calorimetry, indicated that TPEB and RES co-cure when heated. Characterization of thermal properties using thermogravimetric analysis indicated that a 1:1 TPEB-RES blend (by weight) exhibited a char yield of 80% which was 6% larger compared to pure RES (74%). According to FTIR characterization, the enhanced thermal properties of TPEB-RES were the result of increased crosslinking density. Rheological studies of TPEB, RES, and TPEB-RES blends indicated that blended systems exhibit similar processing characteristics as RES resin. For example, resins display ideal viscosities and relatively large processing windows when cured at 175 °C. Alternatively, pure TPEB resin exhibits low viscosities when melted, which are not suitable for preparing composite materials. This study indicates that preparing TPEB-RES blends is an effect strategy for improving thermal performance of potential RES composites while still maintaining the required processability for fabrication of dense polymer composites. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018 , 56, 2630–2640     

Protein–ligand docking using FFT based sampling: D3R case study

Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein–peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein–ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein–ligand interaction landscape, which will be explored in further applications.     

SAMPL6 challenge results from $$pK_a$$ predictions based on a general Gaussian process model

A variety of fields would benefit from accurate \(pK_a\) predictions, especially drug design due to the effect a change in ionization state can have on a molecule’s physiochemical properties. Participants in the recent SAMPL6 blind challenge were asked to submit predictions for microscopic and macroscopic \(pK_a\)s of 24 drug like small molecules. We recently built a general model for predicting \(pK_a\)s using a Gaussian process regression trained using physical and chemical features of each ionizable group. Our pipeline takes a molecular graph and uses the OpenEye Toolkits to calculate features describing the removal of a proton. These features are fed into a Scikit-learn Gaussian process to predict microscopic \(pK_a\)s which are then used to analytically determine macroscopic \(pK_a\)s. Our Gaussian process is trained on a set of 2700 macroscopic \(pK_a\)s from monoprotic and select diprotic molecules. Here, we share our results for microscopic and macroscopic predictions in the SAMPL6 challenge. Overall, we ranked in the middle of the pack compared to other participants, but our fairly good agreement with experiment is still promising considering the challenge molecules are chemically diverse and often polyprotic while our training set is predominately monoprotic. Of particular importance to us when building this model was to include an uncertainty estimate based on the chemistry of the molecule that would reflect the likely accuracy of our prediction. Our model reports large uncertainties for the molecules that appear to have chemistry outside our domain of applicability, along with good agreement in quantile–quantile plots, indicating it can predict its own accuracy. The challenge highlighted a variety of means to improve our model, including adding more polyprotic molecules to our training set and more carefully considering what functional groups we do or do not identify as ionizable.     

Isonitrile Formation by a Non‐Heme Iron(II)‐Dependent Oxidase/Decarboxylase

The electron‐rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We herein provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non‐heme iron(II)‐dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)‐3‐((carboxymethyl)amino)butanoic acid to (R)‐3‐isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, of which several members are critical for the virulence of pathogenic mycobacteria.     

Terminal Hydride Species in [FeFe]‐Hydrogenases Are Vibrationally Coupled to the Active Site Environment

A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe?H/D bending modes in CrHydA1 [FeFe]‐hydrogenase Cys‐to‐Ser variant C169S. Mutagenesis of cysteine to serine at position 169 changes the functional group adjacent to the H‐cluster from a ‐SH to ‐OH, thus altering the proton transfer pathway. The catalytic activity of C169S is significantly reduced compared to that of native CrHydA1, presumably owing to less efficient proton transfer to the H‐cluster. This mutation enabled effective capture of a hydride/deuteride intermediate and facilitated direct detection of the Fe?H/D normal modes. We observed a significant shift to higher frequency in an Fe?H bending mode of the C169S variant, as compared to previous findings with reconstituted native and oxadithiolate (ODT)‐substituted CrHydA1. On the basis of DFT calculations, we propose that this shift is caused by the stronger interaction of the ‐OH group of C169S with the bridgehead ‐NH‐ moiety of the active site, as compared to that of the ‐SH group of C169 in the native enzyme.     

Ruthenium‐Containing Linear Helicates and Mesocates with Tuneable p53‐Selective Cytotoxicity in Colorectal Cancer Cells

The ligands L¹ and L² both form separable dinuclear double‐stranded helicate and mesocate complexes with Ru^II. In contrast to clinically approved platinates, the helicate isomer of [Ru₂( L¹ )₂]⁴⁺ was preferentially cytotoxic to isogenic cells (HCT116 p53^?/?), which lack the critical tumour suppressor gene. The mesocate isomer shows the reverse selectivity, with the achiral isomer being preferentially cytotoxic towards HCT116 p53^+/+. Other structurally similar Ru^II‐containing dinuclear complexes showed very little cytotoxic activity. This study demonstrates that alterations in ligand or isomer can have profound effects on cytotoxicity towards cancer cells of different p53 status and suggests that selectivity can be “tuned” to either genotype. In the search for compounds that can target difficult‐to‐treat tumours that lack the p53 tumour suppressor gene, [Ru₂( L¹ )₂]⁴⁺ is a promising compound for further development.     

A Traveling Wave Ion Mobility Spectrometry (TWIMS) Study of the Robo1-Heparan Sulfate Interaction

Roundabout 1 (Robo1) interacts with its receptor Slit to regulate axon guidance, axon branching, and dendritic development in the nervous system and to regulate morphogenesis and many cell functions in the nonneuronal tissues. This interaction is known to be critically regulated by heparan sulfate (HS). Previous studies suggest that HS is required to promote the binding of Robo1 to Slit to form the minimal signaling complex, but the molecular details and the structural requirements of HS for this interaction are still unclear. Here, we describe the application of traveling wave ion mobility spectrometry (TWIMS) to study the conformational details of the Robo1-HS interaction. The results suggest that Robo1 exists in two conformations that differ by their compactness and capability to interact with HS. The results also suggest that the highly flexible interdomain hinge region connecting the Ig1 and Ig2 domains of Robo1 plays an important functional role in promoting the Robo1-Slit interaction. Moreover, variations in the sulfation pattern and size of HS were found to affect its binding affinity and selectivity to interact with different conformations of Robo1. Both MS measurements and CIU experiments show that the Robo1-HS interaction requires the presence of a specific size and pattern of modification of HS. Furthermore, the effect of N-glycosylation on the conformation of Robo1 and its binding modes with HS is reported.

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Spectroscopic and time-dependent density functional investigation of the role of structure on the acid-base effects of citrinin detection

A time-dependent density functional theory (TD-DFT) study was carried out on tautomers of the mycotoxin citrinin in the neutral, anionic, and cationic forms to gain insight into the role of chemical structure on detection. Steady-state fluorescence studies of citrinin in micellar aqueous solutions produced unusual results for ionic surfactants and the neutral Triton X-100 enhanced fluorescence emission. Ground-state and time-dependent density functional studies were carried out on five tautomers of citrinin using the B3LYP density functional and the 6-311+G(2df,2p) basis set. The investigation revealed that deprotonation is a major factor governing the shifts in fluorescence excitation and emission maxima. Moreover, the position of the lowest unoccupied molecular orbitals is removed from the fluorophore moiety of citrinin in the dianionic state which is consistent with the diminished fluorescence of the toxin in basic solutions. The ionic characteristics of certain chemosensors can influence the structure and intrinsic spectroscopic properties of citrinin.