Reactions of Sulfur-Containing Organic Compounds and Peptides in 1-Ethyl-3-methyl-imidazolium Acetate

Concentrated ionic liquids for proteomics: Caveat emptor!

The use of concentrated ionic liquids (ILs) in the bioanalytical chemistry of proteins is sparse; typically, dilute aqueous IL solutions are used. Concentrated ILs have unique properties that may allow researchers to dissolve previously insoluble protein analytes, to increase the depth and robustness of sample preparation and the analysis of proteins. Previous research using concentrated ILs for this purpose is sparse and there is a need to systematically investigate the structure-activity relationship between the IL structure and its capacity to solubilise proteins. Here, bovine serum albumin was dissolved in various ionic liquids and monitored over time by light microscopy and SDS-PAGE. While qualitative, these measures provide a good estimate of, respectively, the dissolving power of an IL towards the given protein and the retained integrity of the protein. Hydrophilic ILs show the best solubilisation capacity and higher temperatures (in a restricted sense) improve the solubility of the protein. Higher temperatures and longer reaction times reduce the molecular weight of the protein, which could inhibit their applicability in proteomics, unless the conditions are judiciously controlled. Researchers should exercise caution when using concentrated ILs for protein analysis until the full scope and limitations are known, an aspect we are presently investigating.

Physics-based, neural network force fields for reactive molecular dynamics: Investigation of carbene formation from [EMIM+][OAc-]

Reactive molecular dynamics simulations enable a detailed understanding of solvent effects on chemical reaction mechanisms and reaction rates. While classical molecular dynamics using reactive force fields allows significantly longer simulation time scales and larger system sizes compared with ab initio molecular dynamics, constructing reactive force fields is a difficult and complex task. In this work, we describe a general approach following the empirical valence bond framework for constructing ab initio reactive force fields for condensed phase simulations by combining physics-based methods with neural networks (PB/NNs). The physics-based terms ensure the correct asymptotic behavior of electrostatic, polarization, and dispersion interactions and are compatible with existing solvent force fields. NNs are utilized for a versatile description of short-range orbital interactions within the transition state region and accurate rendering of vibrational motion of the reacting complex. We demonstrate our methodology for a simple deprotonation reaction of the 1-ethyl-3-methylimidazolium cation with acetate to form 1-ethyl-3-methylimidazol-2-ylidene and acetic acid. Our PB/NN force field exhibits ∼1 kJ mol^-1 mean absolute error accuracy within the transition state region for the gas-phase complex. To characterize the solvent modulation of the reaction profile, we compute potentials of mean force for the gas-phase reaction as well as the reaction within a four-ion cluster and benchmark against ab initio molecular dynamics simulations. We find that the surrounding ionic environment significantly destabilizes the formation of the carbene product, and we show that this effect is accurately captured by the reactive force field. By construction, the PB/NN potential may be directly employed for simulations of other solvents/chemical environments without additional parameterization.

Looking back: Developments in chemical protein synthesis in 2020

The world as we know it changed dramatically in the spring 2020 due to the Covid-19 pandemic. It was (and still is) a hard time for most of us. Luckily, the power of science enabled a good solution in form of a vaccine in less than 1 year. Of course, not only vaccine development boosted in 2020, but there were also several milestones in peptide chemistry. In this commentary, I would like to draw you away for a moment from the whole pandemic situation to discuss two exciting advances in chemical protein synthesis highlighted in 2020.

Native Chemical Ligation of Highly Hydrophobic Peptides in Ionic Liquid-Containing Media

The chemical synthesis of a highly hydrophobic membrane-associated peptide by native chemical ligation (NCL) in an ionic liquid (IL) [C₂mim][OAc]/buffer mixture was achieved by employing peptide concentrations up to 11 mM. NCL was studied at different pH and water content and compared to several “gold-standard” ligation protocols. The optimized reaction protocol for the NCL in IL required the addition of 40% water and pH adjustment to 7.0–7.5, resulting in ligation yields of up to 80–95% within 1 to 4 h. This new ligation protocol is generally applicable and outperforms current “gold-standard” NCL methods.

Regenerated Hoof Keratin from 1-Ethyl-3-Methylimidazolium Acetate and Insights into Disulfide-Ionic Liquid Interactions from MD Simulation

Regeneration of the hoof keratin from ionic liquids was never successful in the past because the ionic liquids were not strong enough. However, this biomaterial starts to play a central role for the preparation of biofilms in the future. In the present study, hoof keratin was regenerated for the first time from an ionic liquid by experiment and characterized by FTIR spectroscopy, Differential Scanning Calorimetry (DSC) and Scanning Electron Microscopy (SEM). As 1-Ethyl-3-methylimidazolium acetate is strong enough to dissolve hooves, which have a lot of disulfide bonds, a Molecular Dynamics (MD) simulation was performed with this ionic liquid and diphenyl disulfide. The MD simulation reveals that not only the cation as postulated after experiments were carried out, but also the anion is very important for the dissolution process. This complete picture was and is not accessible via experiments and is therefore valuable for future investigations. The anion always interacts with the disulfide bond, whereas the cation prefers in some situations a strong H-O interaction with the anion. If the cations and the anions are separated from each other so that the cation can not interact with the anion, both interact with the disulfide bond. The high solvation power of this solvent is shown by the fact that the cation interacts from the left and right side and the anion from above and below the disulfide bond.

Challenges and Perspectives in Chemical Synthesis of Highly Hydrophobic Peptides

Solid phase peptide synthesis (SPPS) provides the possibility to chemically synthesize peptides and proteins. Applying the method on hydrophilic structures is usually without major drawbacks but faces extreme complications when it comes to "difficult sequences." These includes the vitally important, ubiquitously present and structurally demanding membrane proteins and their functional parts, such as ion channels, G-protein receptors, and other pore-forming structures. Standard synthetic and ligation protocols are not enough for a successful synthesis of these challenging sequences. In this review we highlight, summarize and evaluate the possibilities for synthetic production of "difficult sequences" by SPPS, native chemical ligation (NCL) and follow-up protocols.

Unexpected Intrinsic Lability of Thiol-Functionalized Carboxylate Imidazolium Ionic Liquids

New thiol-functionalized carboxylate ionic liquids (ILs), varying both for the cation and for the anion structures, have been prepared as new potential redox switching systems by reacting either 3-mercapto propionic acid (3-MPA) or N-acetyl-cysteine (NAC) with commercially available methyl carbonate ILs. Different ratios of thiol/disulfide ILs were obtained depending both on the acid employed in the neutralization reaction and on the reaction conditions used. Surprisingly, the imidazolium ILs displayed limited thermal stability which resulted in the formation of an imidazole 2-thione and a new sulfide ionic liquid. Conversely, the formation of the imidazole 2-thione was not observed when phosphonium disulfide ILs were heated, thus confirming the involvement of the imidazolium ring in an unexpected side reaction. An insight into the mechanism of the decomposition has been provided by means of DFT calculations.

NHC in Imidazolium Acetate Ionic Liquids: Actual or Potential Presence?

Ionic liquids (ILs) are considered in the majority of cases green solvents, due to their virtually null vapor pressure and to the easiness in recycling them. In particular, imidazolium ILs are widely used in many fields of Chemistry, as solvents or precursors of N-heterocyclic carbenes (NHCs). The latter are easily obtained by deprotonation of the C2-H, usually using strong bases or cathodic reduction. Nevertheless, it is known that weaker bases (e.g., triethylamine) are able to promote C2-H/D exchange. From this perspective, the possibility of deprotonating C2-H group of an imidazolium cation by means of a basic counter-ion was seriously considered and led to the synthesis of imidazolium ILs spontaneously containing NHCs. The most famous of this class of ILs are N,N'-disubstituted imidazolium acetates. Due to the particular reactivity of this kind of ILs, they were appointed as “organocatalytic ionic liquids” or “proto-carbenes.” Many papers report the use of these imidazolium acetates in organocatalytic reactions (i. e., catalyzed by NHC) or in stoichiometric NHC reactions (e.g., with elemental sulfur to yield the corresponding imidazole-2-thiones). Nevertheless, the actual presence of NHC in N,N'-disubstituted imidazolium acetate is still controversial. Moreover, theoretical studies seem to rule out the presence of NHC in such a polar environment as an IL. Aim of this Mini Review is to give the reader an up-to-date overview on the actual or potential presence of NHC in such an “organocatalytic ionic liquid,” both from the experimental and theoretical point of view, without the intent to be exhaustive on N,N'-disubstituted imidazolium acetate applications.