Heterogeneity and restricted state selection in FRET with fluorescent proteins

Most fluorescent proteins exhibit multi-exponential fluorescence decays, indicating the presence of a heterogeneous excited state population. In the analysis of FRET to and between fluorescent proteins, it is often convenient to assume that a single interaction pathway is involved. However, in recent work we have shown that this assumption does not hold. Moreover, certain pathways can be highly constrained, leading to the potential misinterpretation of experimental data concerning protein-protein interactions. FRET and single-photon absorption both obey the same global electric dipole selection rules but differ greatly in the mechanism of the acceptor photoselection. In an isotropic medium, single-photon excitation accesses all acceptor transition dipole moment orientations with an equal probability. However, the FRET rate depends on the relative orientation of the donor and acceptor through the κ2 orientation parameter. We show how time- and spectrally- resolved fluorescence intensity and anisotropy decay measurements following direct acceptor excitation, combined with those of the interacting FRET pair, can be used to identify restricted FRET state selection and thus provide accurate measurements of protein-protein interaction dynamics

A Mild Hydration of Nitriles Catalysed by Copper (ll) Acetate

A simple, mild and general procedure for the hydration of nitriles to amides using copper as catalyst and promoted by N,N-diethylhydroxylamine is described. The reaction can be conducted in water at low temperature in short reaction times. This new procedure allows amides to be obtained from a wide range of substrates in excellent yields

Continuous formation of N-chloro-N,N-dialkylamine solutions in well-mixed meso-scale flow reactors

The continuous flow synthesis of a range of organic solutions of N, N-dialkyl-N-chloramines is described using either a bespoke meso-scale tubular reactor with static mixers or a continuous stirred tank reactor. Both reactors promote the efficient mixing of a biphasic solution of N,N-dialkylamine in organic solvent, and aqueous sodium hypochlorite to achieve near quantitative conversions, in 72–100% in situ yields, and useful productivities of around 0.05 mol/h with residence times from 3 to 20 minutes. Initial calorimetric studies have been carried out to inform on reaction exotherms, rates and safe operation. Amines which partition mainly in the organic phase require longer reaction times, provided by the CSTR, to compensate for low mass transfer rates in the biphasic system. The green metrics of the reaction have been assessed and compared to existing procedures and have shown the continuous process is improved over previous procedures. The organic solutions of N,N-dialkyl-N-chloramines produced continuously will enable their use in tandem flow reactions with a range of nucleophilic substrates

Preparation of C2-Symmetric Biaryl Bisiminium Salts and Their Use as Organocatalysts for Asymmetric Epoxidation

Two C2-symmetric bisiminium salt species containing biphenylazepinium units and derived from two chiral diamines were prepared and tested as organocatalysts for asymmetric epoxidation

Computational studies explain the importance of two different substituents on the chelating bis(amido) ligand for transfer hydrogenation by bifunctional Cp*Rh(III) catalysts

A computational approach (DFT-B3PW91) is used to address previous experimental studies (Chem. Commun. 2009, 6801) that showed that transfer hydrogenation of a cyclic imine by Et3N·HCO2H in dichloromethane catalyzed by 16-electron bifunctional Cp*Rh III(XNC6H4NX') is faster when XNC 6H4NX' = TsNC6H4NH than when XNC6H4NX' = HNC6H4NH or TsNC 6H4NTs (Cp* = η5-C5Me 5, Ts = toluenesulfonyl). The computational study also considers the role of the formate complex observed experimentally at low temperature. Using a model of the experimental complex in which Cp* is replaced by Cp and Ts by benzenesulfonyl (Bs), the calculations for the systems in gas phase reveal that dehydrogenation of formic acid generates CpRhIIIH(XNC 6H4NX'H) via an outer-sphere mechanism. The 16-electron Rh complex + formic acid are shown to be at equilibrium with the formate complex, but the latter lies outside the pathway for dehydrogenation. The calculations reproduce the experimental observation that the transfer hydrogenation reaction is fastest for the nonsymmetrically substituted complex CpRh III(XNC6H4NX') (X = Bs and X' = H). The effect of the linker between the two N atoms on the pathway is also considered. The Gibbs energy barrier for dehydrogenation of formic acid is calculated to be much lower for CpRhIII(XNCHPhCHPhNX') than for CpRh III(XNC6H4NX') for all combinations of X and X'. The energy barrier for hydrogenation of the imine by the rhodium hydride complex is much higher than the barrier for hydride transfer to the corresponding iminium ion, in agreement with mechanisms proposed for related systems on the basis of experimental data. Interpretation of the results by MO and NBO analyses shows that the most reactive catalyst for dehydrogenation of formic acid contains a localized Rh-NH π-bond that is associated with the shortest Rh-N distance in the corresponding 16-electron complex. The asymmetric complex CpRhIII(BsNC6H4NH) is shown to generate a good bifunctional catalyst for transfer hydrogenation because it combines an electrophilic metal center and a nucleophilic NH group

Process-oriented approach towards catalyst design and optimisation

Translation of catalysts developed in academia to industrial end-users remains a challenge due to a lack of knowledge about the impact of catalyst attributes on the whole process and vice versa. A systematic methodology is proposed that assesses these in terms of Key Performance Indicators (KPIs). As a case study, the dehydration of butanol to butenes and dibutyl ether is considered over H-ZSM5 and H-Beta catalysts. It is demonstrated that catalysts should be designed for complete conversion and high butene selectivity, as removal of unreacted 1-butanol requires a complex separation due to the thermo-physical properties of the product mixture

Investigating State Restriction in Fluorescent Protein FRET Using Time-Resolved Fluorescence and Anisotropy

Most fluorescent proteins exhibit multiexponential fluorescence decays, indicating a heterogeneous excited state population. FRET between fluorescent proteins should therefore involve multiple energy transfer pathways. We recently demonstrated the FRET pathways between EGFP and mCherry (mC), upon the dimerization of 3-phosphoinositide dependent protein kinase 1 (PDK1), to be highly restricted. A mechanism for FRET restriction based on a highly unfavorable κ(2) orientation factor arising from differences in donor-acceptor transition dipole moment angles in a far from coplanar and near static interaction geometry was proposed. Here this is tested via FRET to mC arising from the association of glutathione (GSH) and glutathione S-transferase (GST) with an intrinsically homogeneous and more mobile donor Oregon Green 488 (OG). A new analysis of the acceptor window intensity, based on the turnover point of the sensitized fluorescence, is combined with donor window intensity and anisotropy measurements which show that unrestricted FRET to mC takes place. However, a long-lived anisotropy decay component in the donor window reveals a GST-GSH population in which FRET does not occur, explaining previous discrepancies between quantitative FRET measurements of GST-GSH association and their accepted values. This reinforces the importance of the local donor-acceptor environment in mediating energy transfer and the need to perform spectrally resolved intensity and anisotropy decay measurements in the accurate quantification of fluorescent protein FRET

A practical experiment to teach students continuous flow and physico-chemical methods: acetylation of ethylene diamine in liquid bi-phase

Despite growing applications being reported both in academia and industry, continuous flow chemistry remains a relatively untaught field across most chemistry undergraduate courses. This is particularly true in laboratory practical classes, where it is often deemed simpler to carry out synthetic reactions in traditional batch mode using round-bottomed flasks. Herein, we report the development of an undergraduate project that utilises cheap and readily available materials to construct continuous flow reactors. The students compare the performance of different types of reactors and conditions in a biphasic selective acetylation of a symmetrical diamine. Throughout the investigation, the students can vary multiple parameters as they optimise the reaction, thus actively learning and readjusting them based on their improved understanding. The experiments give the students an appreciation of continuous flow techniques in comparison to batch

Polarized Two-Photon Absorption and Heterogeneous Fluorescence Dynamics in NAD(P)H

Two-photon absorption (2PA) finds widespread application in biological systems, which frequently exhibit heterogeneous fluorescence decay dynamics corresponding to multiple species or environments. By combining polarised 2PA with time-resolved fluorescence intensity and anisotropy decay measurements, we show how the two-photon transition tensors for the components of a heterogeneous population can be separately determined, allowing structural differences between the two fluorescent states of the redox cofactor NAD(P)H to be identified. The results support the view that the two states correspond to alternate configurations of the nicotinamide ring, rather than folded and extended conformations of the entire molecule

Machine Learning with Physicochemical Relationships: Solubility Prediction in Organic Solvents and Water

Solubility prediction remains a critical challenge in drug development, synthetic route and chemical process design, extraction and crystallisation. Here we report a successful approach to solubility prediction in organic solvents and water using a combination of machine learning (ANN, SVM, RF, ExtraTrees, Bagging and GP) and computational chemistry. Rational interpretation of dissolution process into a numerical problem led to a small set of selected descriptors and subsequent predictions which are independent of the applied machine learning method. These models gave significantly more accurate predictions compared to benchmarked open-access and commercial tools, achieving accuracy close to the expected level of noise in training data (LogS ± 0.7). Finally, they reproduced physicochemical relationship between solubility and molecular properties in different solvents, which led to rational approaches to improve the accuracy of each models