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Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels

Peptides that self-assemble into nanostructures are of tremendous interest for biological, medical, photonic and nanotechnological applications. The enormous sequence space that is available from 20 amino acids probably harbours many interesting candidates, but it is currently not possible to predict supramolecular behaviour from sequence alone. Here, we demonstrate computational tools to screen for the aqueous self-assembly propensity in all of the 8,000 possible tripeptides and evaluate these by comparison with known examples. We applied filters to select for candidates that simultaneously optimize the apparently contradicting requirements of aggregation propensity and hydrophilicity, which resulted in a set of design rules for self-assembling sequences. A number of peptides were subsequently synthesized and characterized, including the first reported tripeptides that are able to form a hydrogel at neutral pH. These tools, which enable the peptide sequence space to be searched for supramolecular properties, enable minimalistic peptide nanotechnology to deliver on its promise.

Organic super-electron-donors : initiators in transition metal-free haloarene-arene coupling

Recent papers report transition metal-free couplings of haloarenes to arenes to form biaryls, triggered by alkali metal tert-butoxides in the presence of various additives. These reactions proceed through radical intermediates, but understanding the origin of the radicals has been problematic. Electron transfer from a complex formed from potassium tert-butoxide with additives, such as phenanthroline, has been suggested to initiate the radical process. However, our computational results encouraged us to search for alternatives. We report that heterocycle-derived organic electron donors achieve the coupling reactions and these donors can form in situ in the above cases. We show that an electron transfer route can operate either with phenanthrolines as additives or using pyridine as solvent, and we propose new heterocyclic structures for the respective electron donors involved in these cases. In the absence of additives, the coupling reactions are still successful, although more sluggish, and in those cases benzynes are proposed to play crucial roles in the initiation process.

The Electronic Structure of Iron Corroles: A Combined Experimental and Quantum Chemical Study

There is a longstanding debate in the literature on the electronic structure of chloroiron corroles, especially for those containing the highly electron-withdrawing meso-tris(pentafluorophenyl)corrole (TPFC) ligand. Two alternative electronic structures were proposed for this and the related [FeCl(tdcc)] (TDCC=meso-tris(2,6-dichlorophenyl)corrole) complex, namely a high-valent ferryl species chelated by a trianionic corrolato ligand ([Fe(IV)(Cor)(3-)](+)) or an intermediate-spin (IS) ferric ion that is antiferromagnetically coupled to a dianionic pi-radical corrole ([Fe(III)(Cor)(.2-)](+)) yielding an overall triplet ground state. Two series of corrole-based iron complexes ([Fe(L)(Cor)], in which L=F, Cl, Br, I, and Cor=TPFC, TDCC) have been investigated by a combined experimental (Mössbauer spectroscopy) and computational (DFT) approach in order to differentiate between the two possible electronic-structure descriptions. The experimentally calibrated conclusions were reached by a detailed analysis of the Kohn-Sham solutions, which successfully reproduce the experimental structures and spectroscopic parameters: the electronic structures of [Fe(L)(Cor)] (L=F, Cl, Br, I, Cor=TPFC, TDCC) are best formulated as ([IS-Fe(III)(Cor)(.2-)](+)), similar to chloroiron corrole complexes containing electron-rich corrole ligands. The antiferromagnetic pathway is composed of singly occupied Fe d(z(2) ) and corrole a(2u)-like pi orbitals, with coupling constants that exceed those of analogous porphyrin systems by a factor of 2-3. In the corroles, the combination of lower symmetry, extra negative charge, and smaller cavity size (relative to the porphyrins) leads to exceptionally strong iron-corrole sigma bonds. Hence, the Fe d(x(2)-y(2) )-based molecular orbital is unavailable in the corrole complexes (contrary to the porphyrin case), and the local spin states are S(Fe)=3/2 in the corroles versus S(Fe)=5/2 in the porphyrins. The consequences of this qualitative difference are discussed for spin distributions and magnetic properties.

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.

Identifying the Roles of Amino Acids, Alcohols and 1,2-Diamines as Mediators in Coupling of Haloarenes to Arenes

Coupling of haloarenes to arenes has been facilitated by a diverse range of organic additives in the presence of KO(t)Bu or NaO(t)Bu since the first report in 2008. Very recently, we showed that the reactivity of some of these additives (e.g., compounds 6 and 7) could be explained by the formation of organic electron donors in situ, but the role of other additives was not addressed. The simplest of these, alcohols, including 1,2-diols, 1,2-diamines, and amino acids are the most intriguing, and we now report experiments that support their roles as precursors of organic electron donors, underlining the importance of this mode of initiation in these coupling reactions.

OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

The semiempirical methods of the OMx family (orthogonalization models OM1, OM2, and OM3) are known to describe biochemical systems more accurately than standard semiempirical approaches such as AM1. We investigate the benefits of augmenting these methods with an empirical dispersion term (OMx-D) taken from recent density functional work, without modifying the standard OMx parameters. Significant improvements are achieved for non-covalent interactions, with mean unsigned errors of 1.41 kcal/mol (OM2-D) and 1.31 kcal/mol (OM3-D) for the binding energy of the complexes in the JSCH-2005 data base. This supports the use of these augmented methods in quantum mechanical/molecular mechanical (QM/MM) studies of biomolecules, for example during system preparation and equilibration. As an illustrative application, we present QM and QM/MM calculations on the binding between antibody 34E4 and a hapten, where OM3-D performs better than the methods without dispersion terms (AM1, OM3).

Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly.

Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.

Aromatic peptide amphiphiles: significance of the Fmoc moiety

Aromatic peptide amphiphile hydrogelators commonly utilise the fluorenyl-9-methoxycarbonyl moiety as an N-terminal capping group. Material properties and spectroscopic techniques show the influence of alternative linkers between the fluorenyl moiety and the peptide. This study establishes whether methoxycarbonyl is an optimal or mainly convenient linker, for this class of self-assembling systems.

Reductions of Challenging Organic Substrates by a Nickel Complex of a Noninnocent Crown Carbene Ligand

The first crown-tetracarbene complex of Ni(II) has been prepared, and its crystal structure determined. The complex can be reduced by Na/Hg, with an uptake of two electrons. The reduced complex reductively cleaves arenesulfonamides, including those derived from secondary aliphatic amines, and effects Birch reduction of anthracenes as well as reductive cleavage of stilbene oxides. Computational studies show that the orbital that receives electrons upon reduction of the complex 2 is predominantly based on the crown carbene ligand and also that the HOMO of the parent complex 2 is based on the ligand.

Exploiting CH-π interactions in supramolecular hydrogels of aromatic carbohydrate amphiphiles

A novel class of supramolecular hydrogels derived from amino sugars is reported, where the self-assembly of aromatic carbohydrate amphiphiles is driven by CH-π interactions, rather than π–π stacking and H-bonding associated with gelators based on aromatic peptide amphiphiles. Spectroscopic data is provided as evidence for this mode of self-assembly and in silico studies revealed that a combination of CH-π and T-stacking of the fluorenyl groups contribute to the formation of the aggregated structures.