Dissecting Cooperative Communications in a Protein with a High‐Throughput Single‐Molecule Scalpel

Miscued communication often leads to misfolding and aggregation of the proteins involved in many diseases. Owing to the ensemble average property of conventional techniques, detailed communication diagrams are difficult to obtain. Mechanical unfolding affords an unprecedented perspective on cooperative transitions by observing a protein along a trajectory defined by two mutated cysteine residues. Nevertheless, this approach requires tedious sample preparation at the risk of altering native protein conformations. To address these issues, we applied click chemistry to tether a protein to the two dsDNA handles through primary amines in lysine residues as well as at the N terminus. As a proof of concept, we used laser tweezers to mechanically unfold and refold calmodulin along 36 trajectories, maximally allowed by this strategy in a single batch of protein preparation. Without a priori knowledge of the particular residues to which the double‐stranded DNA handles attach, we used hierarchical cluster analysis to identify 20 major trajectories, according to the size and the pattern of unfolding transitions. We dissected the cooperativity into all‐or‐none and partially cooperative events, which represent strong and weak high‐order interactions in proteins, respectively. Although the overall cooperativity is higher within the N or C lobe than that between the lobes, the all‐or‐none cooperativity is anisotropic among different the unfolding trajectories and becomes relatively more predominant when the size of the protein segments increases. The average cooperativity for all‐or‐none transitions falls within the expected range observed by ensemble techniques, which supports the hypothesis that unfolding of a free protein can be reconstituted from individual trajectories.     

Effects of GC temperature and carrier gas flow rate on on‐line oxygen isotope measurement as studied by on‐column CO injection

Although deemed important to δ¹⁸O measurement by on‐line high‐temperature conversion techniques, how the GC conditions affect δ¹⁸O measurement is rarely examined adequately. We therefore directly injected different volumes of CO or CO–N₂ mix onto the GC column by a six‐port valve and examined the CO yield, CO peak shape, CO–N₂ separation, and δ¹⁸O value under different GC temperatures and carrier gas flow rates. The results show the CO peak area decreases when the carrier gas flow rate increases. The GC temperature has no effect on peak area. The peak width increases with the increase of CO injection volume but decreases with the increase of GC temperature and carrier gas flow rate. The peak intensity increases with the increase of GC temperature and CO injection volume but decreases with the increase of carrier gas flow rate. The peak separation time between N₂ and CO decreases with an increase of GC temperature and carrier gas flow rate. δ¹⁸O value decreases with the increase of CO injection volume (when half m/z 28 intensity is <3 V) and GC temperature but is insensitive to carrier gas flow rate. On average, the δ¹⁸O value of the injected CO is about 1‰ higher than that of identical reference CO. The δ¹⁸O distribution pattern of the injected CO is probably a combined result of ion source nonlinearity and preferential loss of C¹⁶O or oxygen isotopic exchange between zeolite and CO. For practical application, a lower carrier gas flow rate is therefore recommended as it has the combined advantages of higher CO yield, better N₂–CO separation, lower He consumption, and insignificant effect on δ¹⁸O value, while a higher‐than‐60 °C GC temperature and a larger‐than‐100 µl CO volume is also recommended. When no N₂ peak is expected, a higher GC temperature is recommended, and vice versa. Copyright © 2015 John Wiley & Sons, Ltd.     

Identification strategies for flame retardants employing time‐of‐flight mass spectrometric detectors along with spectral and spectra‐less databases

In the past, the preferred strategy for the identification of unknown compounds was to search in an appropriate mass spectral database for spectra obtained using either electron ionisation (GC‐MS analyses) or collision‐induced dissociation (LC‐MS/MS analyses). Recently, an increase has been seen in the use of accurate mass instruments and spectra‐less databases, based on monoisotopic accurate mass alone. In this article, we describe a systematic workflow for the screening and identification of new flame retardants. This approach utilises LC‐quadrupole‐time‐of‐flight MS and spectra‐less databases based only on monoisotopic accurate mass for the identification of ‘unknowns’. An in‐house database was built, and the input parameters used in the data analysis process were optimised for flame retardant chemicals, so that it can be easily transferred to other laboratories. The procedure was successfully applied to dust, foam and textiles from car interiors and indoor consumer products. The developed method was demonstrated for the main new flame retardant present in Antiblaze V6 and for the three unreported reaction by‐products/impurities present in the same technical mixture. Copyright © 2015 John Wiley & Sons, Ltd.     

Aerobic Palladium‐Catalyzed Dioxygenation of Alkenes Enabled by Catalytic Nitrite

Catalytic nitrite was found to enable carbon–oxygen bond‐forming reductive elimination from unstable alkyl palladium intermediates, providing dioxygenated products from alkenes. A variety of functional groups were tolerated, and high yields (up to 94 %) were observed with many substrates, also for a multigram‐scale reaction. Nitrogen dioxide, which could form from nitrite under the reaction conditions, was demonstrated to be a potential intermediate in the catalytic cycle. Furthermore, the reductive elimination event was probed with ¹⁸O‐labeling experiments, which demonstrated that both oxygen atoms in the difunctionalized products were derived from one molecule of acetic acid.     

Probing Bis‐FeIV MauG: Experimental Evidence for the Long‐Range Charge‐Resonance Model

The biosynthesis of tryptophan tryptophylquinone, a protein‐derived cofactor, involves a long‐range reaction mediated by a bis‐Fe^IV intermediate of a diheme enzyme, MauG. Recently, a unique charge‐resonance (CR) phenomenon was discovered in this intermediate, and a biological, long‐distance CR model was proposed. This model suggests that the chemical nature of the bis‐Fe^IV species is not as simple as it appears; rather, it is composed of a collection of resonance structures in a dynamic equilibrium. Here, we experimentally evaluated the proposed CR model by introducing small molecules to, and measuring the temperature dependence of, bis‐Fe^IV MauG. Spectroscopic evidence was presented to demonstrate that the selected compounds increase the decay rate of the bis‐Fe^IV species by disrupting the equilibrium of the resonance structures that constitutes the proposed CR model. The results support this new CR model and bring a fresh concept to the classical CR theory.     

Identification of Structure–Activity Relationships from Screening a Structurally Compact DNA‐Encoded Chemical Library

Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA‐encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL‐100K, a DNA‐encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA‐sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate‐specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small‐molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding.     

Ba3P5N10Br:Eu2+: A Natural‐White‐Light Single Emitter with a Zeolite Structure Type

Illumination sources based on phosphor‐converted light emitting diode (pcLED) technology are nowadays of great relevance. In particular, illumination‐grade pcLEDs are attracting increasing attention. Regarding this, the application of a single warm‐white‐emitting phosphor could be of great advantage. Herein, we report the synthesis of a novel nitridophosphate zeolite Ba₃P₅N₁₀Br:Eu²⁺. Upon excitation by near‐UV light, natural‐white‐light luminescence was detected. The synthesis of Ba₃P₅N₁₀Br:Eu²⁺ was carried out using the multianvil technique. The crystal structure of Ba₃P₅N₁₀Br:Eu²⁺ was solved and refined by single‐crystal X‐ray diffraction analysis and confirmed by Rietveld refinement and FTIR spectroscopy. Furthermore, spectroscopic luminescence measurements were performed. Through the synthesis of Ba₃P₅N₁₀Br:Eu²⁺, we have shown the great potential of nitridophosphate zeolites to serve as high‐performance luminescence materials.     

Characterizing Pressure‐Induced Uranium CH Agostic Bonds

The diuranium(III) compound [UN′′₂]₂(μ‐η⁶:η⁶‐C₆H₆) (N′′=N(SiMe₃)₂) has been studied using variable, high‐pressure single‐crystal X‐ray crystallography, and density functional theory . In this compound, the low‐coordinate metal cations are coupled through π‐ and δ‐symmetric arene overlap and show close metal? CH contacts with the flexible methyl CH groups of the sterically encumbered amido ligands. The metal–metal separation decreases with increasing pressure, but the most significant structural changes are to the close contacts between ligand CH bonds and the U centers. Although the interatomic distances are suggestive of agostic‐type interactions between the U and ligand peripheral CH groups, QTAIM (quantum theory of atoms‐in‐molecules) computational analysis suggests that there is no such interaction at ambient pressure. However, QTAIM and NBO analyses indicate that the interaction becomes agostic at 3.2 GPa.     

Locating Gases in Porous Materials: Cryogenic Loading of Fuel‐Related Gases Into a Sc‐based Metal–Organic Framework under Extreme Pressures

An alternative approach to loading metal organic frameworks with gas molecules at high (kbar) pressures is reported. The technique, which uses liquefied gases as pressure transmitting media within a diamond anvil cell along with a single‐crystal of a porous metal–organic framework, is demonstrated to have considerable advantages over other gas‐loading methods when investigating host–guest interactions. Specifically, loading the metal–organic framework Sc₂BDC₃ with liquefied CO₂ at 2 kbar reveals the presence of three adsorption sites, one previously unreported, and resolves previous inconsistencies between structural data and adsorption isotherms. A further study with supercritical CH₄ at 3–25 kbar demonstrates hyperfilling of the Sc₂BDC₃ and two high‐pressure displacive and reversible phase transitions are induced as the filled MOF adapts to reduce the volume of the system.