Facet selectivity in gold binding peptides: exploiting interfacial water structure

Peptide sequences that can discriminate between gold facets under aqueous conditions offer a promising route to control the growth and organisation of biomimetically-synthesised gold nanoparticles. Knowledge of the interplay between sequence, conformations and interfacial properties is essential for predictable manipulation of these biointerfaces, but the structural connections between a given peptide sequence and its binding affinity remain unclear, impeding practical advances in the field. These structural insights, at atomic-scale resolution, are not easily accessed with experimental approaches, but can be delivered via molecular simulation. A current unmet challenge lies in forging links between predicted adsorption free energies derived from enhanced sampling simulations with the conformational ensemble of the peptide and the water structure at the surface. To meet this challenge, here we use an in situ combination of Replica Exchange with Solute Tempering with Metadynamics simulations to predict the adsorption free energy of a gold-binding peptide sequence, AuBP1, at the aqueous Au(111), Au(100)(1 × 1) and Au(100)(5 × 1) interfaces. We find adsorption to the Au(111) surface is stronger than to Au(100), irrespective of the reconstruction status of the latter. Our predicted free energies agree with experiment, and correlate with trends in interfacial water structuring. For gold, surface hydration is predicted as a chief determining factor in peptide–surface recognition. Our findings can be used to suggest how shaped seed-nanocrystals of Au, in partnership with AuBP1, could be used to control AuNP nanoparticle morphology.     

Is a polymer semiconductor having a “perfect” regular structure desirable for organic thin film transistors?

This study utilized high temperature NMR and matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry to reveal that appreciable amounts of structural defects are present in the diketopyrrolopyrrole (DPP)–quaterthiophene copolymers (PDQT) synthesized by the Stille coupling polymerization with Pd(PPh₃)₂Cl₂, Pd₂(dba)₃/P(o-tol)₃, and Pd(PPh₃)₄ catalyst systems. It was proposed that these structural defects were produced via homocoupling side reactions of the C–Br bonds and the organostannane species. Model Stille coupling reactions further substantiated that the amount of structural defects are catalyst-dependent following the order of Pd(PPh₃)₂Cl₂ > Pd₂(dba)₃/P(o-tol)₃ > Pd(PPh₃)₄. To verify the structural assignments, “perfect” structurally regular PDQT polymers were prepared using Yamamoto coupling polymerization. When compared to the structurally regular polymers, the polymers containing defects exhibited notable redshifts in their absorption spectra. Surprisingly, the “perfect” structurally regular polymers showed poor molecular ordering in thin films and very low charge transport performance as channel semiconductors in organic thin film transistors (OTFTs). On the contrary, all the “defected” polymers exhibited much improved molecular ordering and significantly higher charge carrier mobility.     

Extending the biocatalytic scope of regiocomplementary flavin-dependent halogenase enzymes

Flavin-dependent halogenases are potentially valuable biocatalysts for the regioselective halogenation of aromatic compounds. These enzymes, utilising benign inorganic halides, offer potential advantages over traditional non-enzymatic halogenation chemistry that often lacks regiocontrol and requires deleterious reagents. Here we extend the biocatalytic repertoire of the tryptophan halogenases, demonstrating how these enzymes can halogenate a range of alternative aryl substrates. Using structure guided mutagenesis we also show that it is possible to alter the regioselectivity as well as increase the activity of the halogenases with non-native substrates including anthranilic acid; an important intermediate in the synthesis and biosynthesis of pharmaceuticals and other valuable products.     

Oxygen deficient α-Fe2O3 photoelectrodes: a balance between enhanced electrical properties and trap-mediated losses

Intrinsic doping of hematite through the inclusion of oxygen vacancies (V_O) is being increasingly explored as a simple, low temperature route to preparing active water splitting α-Fe₂O_3–x photoelectrodes. Whilst it is widely accepted that the introduction of V_O leads to improved conductivities, little else is verified regarding the actual mechanism of enhancement. Here we employ transient absorption (TA) spectroscopy to build a comprehensive kinetic model for water oxidation on α-Fe₂O_3–x. In contrast to previous suggestions, the primary effect of introducing V_O is to block very slow (ms) surface hole – bulk electron recombination pathways. In light of our mechanistic research we are also able to identify and address a cause of the high photocurrent onset potential, a common issue with this class of electrodes. Atomic layer deposition (ALD) of Al₂O₃ is found to be particularly effective with α-Fe₂O_3–x, leading to the photocurrent onset potential shifting by ca. 200 mV. Significantly TA measurements on these ALD passivated electrodes also provide important insights into the role of passivating layers, that are relevant to the wider development of α-Fe₂O₃ photoelectrodes.     

Cover Picture: Turning Spiroketals Inside Out: A Rearrangement Triggered by an Enol Ether Epoxidation (ChemistryOpen 5/2015)

Invited for this month''s cover picture is the group of Professor Mark Peczuh at the University of Connecticut. The cover picture compares the rearrangement of a small molecule to the process of turning a stuffed animal inside out. The recycled, inside-out stuffed animals are both artistic and philosophically provocative. They capture the essence of the rearrangement reaction because the compounds themselves turn inside out over the course of the reaction, extending the diversity of products that can arise from simple starting materials. Small molecules often have functional groups with latent reactivity; under the appropriate conditions, those groups can react with other compounds (e.g., reagents) and also with other groups in the same molecule in an intramolecular reaction. The research team found that the epoxidation of some highly functionalized spiroketal compounds promoted rearrangements of their structures that turned them inside out. Some of the features of the products led them to use X-ray crystallography or a combination of computer-assisted structure elucidation, computation, and a new version of the 1,1-ADEQUATE NMR experiment to determine their structures. For more details, see the Communication on p. 577 ff.     

Bayesian Model Assessment in Joint Modeling of Longitudinal and Survival Data With Applications to Cancer Clinical Trials

Joint models for longitudinal and survival data are routinely used in clinical trials or other studies to assess a treatment effect while accounting for longitudinal measures such as patient-reported outcomes. In the Bayesian framework, the deviance information criterion (DIC) and the logarithm of the pseudo-marginal likelihood (LPML) are two well-known Bayesian criteria for comparing joint models. However, these criteria do not provide separate assessments of each component of the joint model. In this article, we develop a novel decomposition of DIC and LPML to assess the fit of the longitudinal and survival components of the joint model, separately. Based on this decomposition, we then propose new Bayesian model assessment criteria, namely, ΔDIC and ΔLPML, to determine the importance and contribution of the longitudinal (survival) data to the model fit of the survival (longitudinal) data. Moreover, we develop an efficient Monte Carlo method for computing the conditional predictive ordinate statistics in the joint modeling setting. A simulation study is conducted to examine the empirical performance of the proposed criteria and the proposed methodology is further applied to a case study in mesothelioma. Supplementary materials for this article are available online.     

Evidence for Multiple Binding Modes in the Initial Contact Between SARS-CoV-2 Spike S1 Protein and Cell Surface Glycans**

Infection of host cells by SARS-CoV-2 begins with recognition by the virus S (spike) protein of cell surface heparan sulfate (HS), tethering the virus to the extracellular matrix environment, and causing the subunit S1-RBD to undergo a conformational change into the ‘open’ conformation. These two events promote the binding of S1-RBD to the angiotensin converting enzyme 2 (ACE2) receptor, a preliminary step toward viral-cell membrane fusion. Combining ligand-based NMR spectroscopy with molecular dynamics, oligosaccharide analogues were used to explore the interactions between S1-RBD of SARS CoV-2 and HS, revealing several low-specificity binding modes and previously unidentified potential sites for the binding of extended HS polysaccharide chains. The evidence for multiple binding modes also suggest that highly specific inhibitors will not be optimal against protein S but, rather, diverse HS-based structures, characterized by high affinity and including multi-valent compounds, may be required.     

Outstanding Quadratic to Septic Optical Nonlinearity at Dipolar Alkynylmetal-Porphyrin Hybrids

Porphyrins are important macrocycles with applications in several areas including therapy, catalysis, and sensing. Strong nonlinear optical (NLO) responses are the key to fully exploiting the potential of these biocompatible molecules. We herein report that certain metal-alkynyl donor/nitro acceptor-functionalized porphyrins are attractive candidates for NLO applications. We show that specific examples exhibit record quadratic optical nonlinearity, exceptional two-photon absorption, and outstanding three-photon absorption, and we report the first porphyrins that exhibit four-photon absorption. The two-, three-, and four-photon absorption maxima are found at the corresponding multiples of linear absorption bands that time-dependent density functional theory assigns as admixtures of porphyrin-localized π*←π and donor-porphyrin to porphyrin-acceptor charge-transfer transitions.     

Two-Dimensional Supramolecular Polymerization of a Bis-Urea Macrocycle into a Brick-Like Hydrogen-Bonded Network

We report on a dendronized bis-urea macrocycle 1 self-assembling via a cooperative mechanism into two-dimensional (2D) nanosheets formed solely by alternated urea-urea hydrogen bonding interactions. The pure macrocycle self-assembles in bulk into one-dimensional liquid-crystalline columnar phases. In contrast, its self-assembly mode drastically changes in CHCl₃ or tetrachloroethane, leading to 2D hydrogen-bonded networks. Theoretical calculations, complemented by previously reported crystalline structures, indicate that the 2D assembly is formed by a brick-like hydrogen bonding pattern between bis-urea macrocycles. This assembly is promoted by the swelling of the trisdodecyloxyphenyl groups upon solvation, which frustrates, due to steric effects, the formation of the thermodynamically more stable columnar macrocycle stacks. This work proposes a new design strategy to access 2D supramolecular polymers by means of a single non-covalent interaction motif, which is of great interest for materials development.     

A Covalent Binding Mode of a Pyrazole-Based CD38 Inhibitor

Brain concentrations of nicotinamide adenine dinucleotide (NAD⁺), an important cellular co-factor, tend to decrease with age and in neurodegeneration. As the NADase cluster of differentiation 38 (CD38) significantly contributes to NAD⁺ consumption, we reasoned that CD38 inhibition may be of therapeutic value for CNS disorders. The new pyrazole compound was designed based on a known CD38 inhibitor and showed good inhibitory potency. Several attempts to co-crystallise this pyrazole with CD38 and cyclic adenosine diphosphate ribose (cADPR) culminated in a high-resolution X-ray structure, in which the pyrazolyl group in the new compound formed a covalent bond with one of the ribosyl units of cADPR. This reaction proceeded under retention of configuration and resulted in a neutral ribosyl-pyrazole conjugate that is embedded within the active site of the enzyme. An analysis of this structural complex gave rise to design principles that enabled the preparation of more potent CD38 inhibitors with drug-like properties.