Influence of solvent in controlling peptide−surface interactions

Protein binding to surfaces is an important phenomenon in biology and in modern technological applications. Extensive experimental and theoretical research has been focused in recent years on revealing the factors that govern binding affinity to surfaces. Theoretical studies mainly focus on examining the contribution of the individual amino acids or, alternatively, the binding potential energies of the full peptide, which are unable to capture entropic contributions and neglect the dynamic nature of the system. We present here a methodology that involves the combination of nonequilibrium dynamics simulations with strategic mutation of polar residues to reveal the different factors governing the binding free energy of a peptide to a surface. Using a gold-binding peptide as an example, we show that relative binding free energies are a consequence of the balance between strong interactions of the peptide with the surface and the ability for the bulk solvent to stabilize the peptide

Predicting the reducing power of organic super electron donors

The utilization of computational methods to predict reactivity is an increasingly useful tool for chemists to save time and materials by screening compounds for desirable reactivity prior to testing in the laboratory. In the field of electron transfer reactions, screening can be performed through the application of Marcus Hush theory to calculate the activation free energy of any potential reaction. This work describes the most accurate and efficient approach for modelling the electron transfer process. In particular, the importance of using an electron transfer complex to model these reactions rather than considering donor and acceptor molecules as separate entities is highlighted. The use of the complex model is found to produce more accurate calculation of the electron transfer energy when the donor and acceptor spin densities are adequately localised

Reductive cleavage of sulfones and sulfonamides by neutral organic super electron-donor (S.E.D.) reagent

The sulfonyl group finds extensive applications in organic and medicinal chemistry both in sulfonamides, popular as robust protecting groups for amines, and in sulfones. Frequently, sulfones are introduced into synthetic schemes to assist particular transformations; further progress along the synthetic route can later require the removal of a sulfone group, and this can be achieved by reductive desulfonylation or, in the special cases of α-halo- or ß-acyloxysulfones, by elimination to an alkene

Tripeptide emulsifiers

Traditional, surfactant based emulsions have applications in the food, cosmetic, encapsulation and materials industries. The majority of the surfactants that are currently in use are based on lipids that are extracted from natural sources, however, other surfactants, based on polypeptides, copolymers and solid particles (Pickering emulsions)are also used. The process by which traditional amphiphilic surfactants stabilize biphasic mixtures by interfacial assembly and the consequent reduction of surface tension is well understood. Although these surfactants are well-suited to stabilize emulsions, they are not always biocompatible or biodegradable. In addition, they may not have sufficient stability at elevated temperatures or extremes of pH, which can limit their utility in a variety of applications. Therefore, it is desirable to identify a class of surfactants that can be tuned, or tailored, to match the application for which they are used

Supramolecular fibers in gels can be at thermodynamic equilibrium : a simple packing model reveals preferential fibril formation versus crystallization

Low molecular weight gelators are able to form nanostructures, typically fibers, which entangle to form gel-phase materials. These materials have wide-ranging applications in biomedicine and nanotechnology. While it is known that supramolecular gels often represent metastable structures due to the restricted molecular dynamics in the gel state, the thermodynamic nature of the nanofibrous structure is not well understood. Clearly, 3D extended structures will be able to form more interactions than 1D structures. However, self-assembling molecules are typically amphiphilic, thus giving rise to a combination of solvophobic and solvophilic moieties where a level of solvent exposure at the nanostructure surface is favorable. In this study, we introduce a simple packing model, based on prisms with faces of different nature (solvophobic and solvophilic) and variable interaction parameters, to represent amphiphile self-assembly. This model demonstrates that by tuning shape and "self" or "solvent" interaction parameters either the 1D fiber or 3D crystal may represent the thermodynamic minimum. The model depends on parameters that relate to features of experimentally known systems: The number of faces exposed to the solvent or buried in the fiber; the overall shape of the prism; and the free energy penalties associated with the interactions can be adjusted to match their chemical nature. The model is applied to describe the pH-dependent gelation/precipitation of well-known gelator Fmoc-FF. We conclude that, despite the fact that most experimentally produced gels probably represent metastable states, one-dimensional fibers can represent thermodynamic equilibrium. This conclusion has critical implications for the theoretical treatment of gels

Iridium-catalysed ortho-directed deuterium labelling of aromatic esters – an experimental and theoretical study on directing group chemoselectivity

Herein we report a combined experimental and theoretical study on the deuterium labelling of benzoate ester derivatives, utilizing our developed iridium N-heterocyclic carbene/phosphine catalysts. A range of benzoate esters were screened, including derivatives with electron-donating and -withdrawing groups in the para- position. The substrate scope, in terms of the alkoxy group, was studied and the nature of the catalyst counter-ion was shown to have a profound effect on the efficiency of isotope exchange. Finally, the observed chemoselectivity was rationalized by rate studies and theoretical calculations, and this insight was applied to the selective labelling of benzoate esters bearing a second directing group

Enzymatically activated emulsions stabilised by interfacial nanofibre networks

We report on-demand formation of emulsions stabilised by interfacial nanoscale networks. These are formed through biocatalytic dephosphorylation and self-assembly of Fmoc(9-fluorenylmethoxycarbonyl)-dipeptide amphiphiles in aqueous/organic mixtures. This is achieved by using alkaline phosphatase which transforms surfactant-like phosphorylated precursors into self-assembling aromatic peptide amphiphiles (Fmoc-tyrosine-leucine, Fmoc-YL) that form nanofibrous networks. In biphasic organic/aqueous systems, these networks form preferentially at the interface thus providing a means of emulsion stabilisation. We demonstrate on-demand emulsification by enzyme addition, even after storage of the biphasic mixture for several weeks. Experimental (Fluorescence, FTIR spectroscopy, fluorescence microscopy, electron microscopy, atomic force microscopy) and computational techniques (atomistic molecular dynamics) are used to characterise the interfacial self-assembly process

Thiazole-induced rigidification in substituted dithieno-tetrathiafulvalene : the effect of planarisation on charge transport properties

Two novel tetrathiafulvalene (TTF) containing compounds 1 and 2 have been synthesised via a four-fold Stille coupling between a tetrabromo-dithienoTTF 5 and stannylated thiophene 6 or thiazole 4. The optical and electrochemical properties of compounds 1 and 2 have been measured by UV-vis spectroscopy and cyclic voltammetry and the results compared with density functional theory (DFT) calculations to confirm the observed properties. Organic field effect transistor (OFET) devices fabricated from 1 and 2 demonstrated that the substitution of thiophene units for thiazoles was found to increase the observed charge transport, which is attributed to induced planarity through S-N interactions of adjacent thiazole nitrogen atoms and TTF sulfur atoms and better packing in the bulk

KOtBu : a privileged reagent for electron transfer reactions?

Many recent studies have used KOtBu in organic reactions that involve single electron transfer; in the literature, the electron transfer is proposed to occur either directly from the metal alkoxide or indirectly, following reaction of the alkoxide with a solvent or additive. These reaction classes include coupling reactions of halobenzenes and arenes, reductive cleavages of dithianes and SRN1 reactions. Direct electron transfer would imply that alkali metal alkoxides are willing partners in these electron transfer reactions, but the literature reports provide little or no experimental evidence for this. This paper examines each of these classes of reaction in turn, and contests the roles proposed for KOtBu; instead, it provides new mechanistic information that in each case supports the in situ formation of organic electron donors. We go on to show that direct electron transfer from KOtBu can however occur in appropriate cases, where the electron acceptor has a reduction potential near the oxidation potential of KOtBu, and the example that we use is CBr4. In this case, computational results support electrochemical data in backing a direct electron transfer reaction

Computational study on the boundary between the concerted and stepwise mechanism of bimolecular SNAr reactions

The text-book mechanism of bimolecular nucleophilic aromatic substitutions (SNAr) reactions is a stepwise process that proceeds via a so-called Meisenheimer intermediate. Only recently the alternative, concerted version of this mechanism has gained acceptance as more and more examples thereof have been reported. But so far only isolated examples of concerted SNAr reactions have been described and a coherent picture of when a SNAr reaction proceeds via a stepwise and when via a concerted mechanism has not yet been established. Here key factors are identified that influence the mechanistic choice of SNAr reactions. Moreover, the electron affinity is used as a simple descriptor to make a prediction on whether a given aryl fluoride substrate favors a concerted or stepwise mechanism