Mechanism-Based Redesign of GAP to Activate Oncogenic Ras.

Ras GTPases play a crucial role in cell signaling pathways. Mutations of the Ras gene occur in about one third of cancerous cell lines and are often associated with detrimental clinical prognosis. Hot spot residues Gly12, Gly13, and Gln61 cover 97% of oncogenic mutations, which impair the enzymatic activity in Ras. Using QM/MM free energy calculations, we present a two-step mechanism for the GTP hydrolysis catalyzed by the wild-type Ras.GAP complex. We found that the deprotonation of the catalytic water takes place via the Gln61 as a transient Brønsted base. We also determined the reaction profiles for key oncogenic Ras mutants G12D and G12C using QM/MM minimizations, matching the experimentally observed loss of catalytic activity, thereby validating our reaction mechanism. Using the optimized reaction paths, we devised a fast and accurate procedure to design GAP mutants that activate G12D Ras. We replaced GAP residues near the active site and determined the activation barrier for 190 single mutants. We furthermore built a machine learning for ultrafast screening, by fast prediction of the barrier heights, tested both on the single and double mutations. This work demonstrates that fast and accurate screening can be accomplished via QM/MM reaction path optimizations to design protein sequences with increased catalytic activity. Several GAP mutations are predicted to re-enable catalysis in oncogenic G12D, offering a promising avenue to overcome aberrant Ras-driven signal transduction by activating enzymatic activity instead of inhibition. The outlined computational screening protocol is readily applicable for designing ligands and cofactors analogously.

Charge transfer and polarisability in ionic liquids: a case study.

The practical use of ionic liquids (ILs) is benefiting from a growing understanding of the underpinning structural and dynamic properties, facilitated through classical molecular dynamics (MD) simulations. The predictive and explanatory power of a classical MD simulation is inextricably linked to the underlying force field. A key aspect of the forcefield for ILs is the ability to recover charge based interactions. Our focus in this paper is on the description and recovery of charge transfer and polarisability effects, demonstrated through MD simulations of the widely used 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C4C1im][NTf2] IL. We study the charge distributions generated by a range of ab initio methods, and present an interpolation method for determining atom-wise scaled partial charges. Two novel methods for determining the mean field (total) charge transfer from anion to cation are presented. The impact of using different charge models and different partial charge scaling (unscaled, uniformly scaled, atom-wise scaled) are compared to fully polarisable simulations. We study a range of Drude particle explicitly polarisable potentials and shed light on the performance of current approaches to counter known problems. It is demonstrated that small changes in the charge description and MD methodology can have a significant impact; biasing some properties, while leaving others unaffected within the structural and dynamic domains.

N-Heterocyclic Carbene Organocatalysis: With or Without Carbenes?

In this work the mechanism of the aldehyde umpolung reactions, catalyzed by azolium cations in the presence of bases, was studied through computational methods. Next to the mechanism established by Breslow in the 1950s that takes effect through the formation of a free carbene, we have suggested that these processes can follow a concerted asynchronous path, in which the azolium cation directly reacts with the substrate, avoiding the formation of the carbene intermediate. We hereby show that substituting the azolium cation, and varying the base or the substrate do not affect the preference for the concerted reaction mechanism. The concerted path was found to exhibit low barriers also for the reactions of thiamine with model substrates, showing that this path might have biological relevance. The dominance of the concerted mechanism can be explained through the specific structure of the key transition state, avoiding the liberation of the highly reactive, and thus unstable carbene lone pair, whereas activating the substrate through hydrogen-bonding interactions. Polar and hydrogen-bonding solvents, as well as the presence of the counterions of the azolium salts facilitate the reaction through carbenes, bringing the barriers of the two reaction mechanisms closer, in many cases making the concerted path less favorable. Thus, our data show that by choosing the exact components in a reaction, the mechanism can be switched to occur with or without carbenes.

Can Nanoplastics Alter Cell Membranes?

Whilst the formation of plastic nanoparticles (nanoplastics) from plastic wastes has been unequivocally evidenced, little is known about the effects of these materials on living organisms at the subcellular or molecular levels. In the present contribution we show through molecular dynamics simulations that polyethylene nanoparticles dissolve in the hydrophobic core of lipid bilayers into a network of disentangled, single polymeric chains. The thereby induced structural and dynamic changes in the bilayer alter vital functions of the cell membrane, which if lacking a mechanism to decompose the polymer chains may result in the death of the cell.

Understanding the fluidity of condensed phase systems in terms of voids-novel algorithm, implementation and application.

Solvation processes, transport properties, and fluidity of condensed phases can be described considering the void space between the particles of the system. In this work a novel algorithm for the analysis of this void in molecular dynamics simulations is presented. Based on suitable void spheres which are fitted between the atoms a void domain is defined employing a Voronoi tessellation scheme. The algorithm is not only providing the distribution of the void sphere's radii, but also contains extensions to analyses details of the static structure and the dynamical behavior of the void space. The first extension is realized by recalculating the void domain neglecting void spheres of a certain size, the second by calculating autocorrelation functions of the probability to find certain grid-based points as part of the void domains. Furthermore, the performance of the new analyses is demonstrated on two suitable case studies. Thereby, the proper functionality of the new algorithm is shown by comparing the void radii distribution obtained by the new algorithm to results from the literature. The further analyses applying the extensions show a crucial influence of the density during the simulation, especially on the dynamical behavior.

Hydrogen Bonding of N-Heterocyclic Carbenes in Solution: Mechanisms of Solvent Reorganization.

Invited for the cover of this issue are Sascha Gehrke and Oldamur Hollóczki at the University of Bonn. The image depicts how N-heterocyclic carbenes exchange hydrogen bonding partners in solution. The "breakup" with the old partner happens either before or after forming a connection with the new. Read the full text of the article at 10.1002/chem.201802286.

Hydrogen Bonding of N-Heterocyclic Carbenes in Solution: Mechanisms of Solvent Reorganization.

The hydrogen-bond dynamics of N-heterocyclic carbenes plays a central role in their proton-transfer reactions, and the effects of hydrogen bonding are also often invoked in corresponding organocatalytic applications. In the present study, the structures and lifetimes of hydrogen bonds have been investigated for several carbenes in alcohol-containing solutions by classical molecular dynamics simulations. The basicity of the carbene was found to be of major importance; while the least basic carbenes are often in their free form in the solvent, by increasing the basicity the simulations show increased hydrogen bonding, often even with two alcohol molecules at a time. In the latter structure the single lone pair of the carbene is in interplay with two hydrogen bond donors. The exchange mechanism is different for carbenes with different basicities, with different substituents, and in different solvents, occurring through the free carbene for the least basic compounds, and through the aforementioned doubly-hydrogen-bonded structure in case of the most basic derivatives. Since this process plays a central role also in H/D exchange reactions, we argue that the pK values calculated from the related measurements have a varying physical meaning for the different carbenes. The lifetimes of the hydrogen bonds are apparently also clearly related to the basicity of the carbene, with gradually increasing lifetimes for the most basic compounds.

Structure and lifetimes in ionic liquids and their mixtures.

With the aid of molecular dynamics simulations, we study the structure and dynamics of different ionic liquid systems, with focus on hydrogen bond, ion pair and ion cage formation. To do so, we report radial distribution functions, their number integrals, and various time-correlation functions, from which we extract well-defined lifetimes by means of the reactive flux formalism. We explore the influence of polarizable force fields vs. non-polarizable ones with downscaled charges (±0.8) for the example of 1-butyl-3-methylimidazolium bromide. Furthermore, we use 1-butyl-3-methylimidazolium trifluoromethanesulfonate to investigate the impact of temperature and mixing with water as well as with the chloride ionic liquid. Smaller coordination numbers, larger distances, and tremendously accelerated dynamics are observed when the polarizable force field is applied. The same trends are found with increasing temperature. Adding water decreases the ion-ion coordination numbers whereas the water-ion and water-water coordination is enhanced. A domain analysis reveals that the nonpolar parts of the ions are dispersed and when more water is added the water clusters increase in size. The dynamics accelerate in general upon addition of water. In the ionic liquid mixture, the coordination number around the cation changes between the two anions, but the number integrals of the cation around the anions remain constant and the dynamics slow down with increasing content of the chloride ionic liquid.

NMR relaxometric probing of ionic liquid dynamics and diffusion under mesoscopic confinement within bacterial cellulose ionogels.

Bacterial cellulose ionogels (BCIGs) represent a new class of material comprising a significant content of entrapped ionic liquid (IL) within a porous network formed from crystalline cellulose microfibrils. BCIGs suggest unique opportunities in separations, optically active materials, solid electrolytes, and drug delivery due to the fact that they can contain as much as 99% of an IL phase by weight, coupled with an inherent flexibility, high optical transparency, and the ability to control ionogel cross-sectional shape and size. To allow for the tailoring of BCIGs for a multitude of applications, it is necessary to better understand the underlying principles of the mesoscopic confinement within these ionogels. Toward this, we present a study of the structural, relaxation, and diffusional properties of the ILs, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf2N]) and 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([bmpy][Tf2N]), using 1H and 19F NMR T1 relaxation times, rotational correlation times, and diffusion ordered spectroscopy (DOSY) diffusion coefficients, accompanied by molecular dynamics (MD) simulations. We observed that the cation methyl groups in both ILs were primary points of interaction with the cellulose chains and, while the pore size in cellulose is rather large, [emim]+ diffusion was slowed by ∼2-fold, whereas [Tf2N]- diffusion was unencumbered by incorporation in the ionogel. While MD simulations of [bmpy][Tf2N] confinement at the interface showed a diffusion coefficient decrease roughly 3-fold compared to the bulk liquid, DOSY measurements did not reveal any significant changes in diffusion. This suggests that the [bmpy][Tf2N] alkyl chains dominate diffusion through formation of apolar domains. This is in contrast to [emim][Tf2N] where delocalized charge appears to preclude apolar domain formation, allowing interfacial effects to be manifested at a longer range in [emim][Tf2N].

Ab initio simulations of bond breaking in sulfur crosslinked isoprene oligomer units.

Sulfur crosslinked polyisoprene (rubber) is used in important material components for a number of technical tasks (e.g., in tires and sealings). If mechanical stress, like tension or shear, is applied on these material components, the sulfur crosslinks suffer from homolytic bond breaking. In this work, we have simulated the bond breaking mechanism of sulfur crosslinks between polyisoprene chains using Car-Parrinello molecular dynamic simulations and investigated the maximum forces which can be resisted by the crosslinks. Small model systems with crosslinks formed by chains of N = 1 to N = 6 sulfur atoms have been simulated with the slow growth-technique, known from the literature. The maximum force can be thereby determined from the calculated energies as a function of strain (elongation). The stability of the crosslink under strain is quantified in terms of the maximum force that can be resisted by the system before the crosslink breaks. As shown by our simulations, this maximum force decreases with the sulfur crosslink length N in a step like manner. Our findings indicate that in bridges with N = 1, 2, and 3 sulfur atoms predominantly, carbon-sulfur bonds break, while in crosslinks with N > 3, the breaking of a sulfur-sulfur bond is the dominant failure mechanism. The results are explained within a simple chemical bond model, which describes how the delocalization of the electrons in the generated radicals can lower their electronic energy and decrease the activation barriers. It is described which of the double bonds in the isoprene units are involved in the mechanochemistry of crosslinked rubber.

Are There Carbenes in N-Heterocyclic Carbene Organocatalysis?

Azolium cations are widely employed in organocatalysis to catalyse highly valuable synthetic processes in the presence of a base. These reactions are called "N-heterocyclic carbene catalysis", based on the assumption that they are initiated by the formation of a free carbene through deprotonation, which can then react with the substrates and thereby affect their reactivity to obtain the desired products. However, we herein provide evidence that an electrophilic aromatic substitution mechanism is energetically more favourable, in which the azolium cation reacts directly with the substrate, avoiding the formation of the free carbene in solution.

A molecular mechanical model for N-heterocyclic carbenes.

In this work we present a set of force fields for nine synthetically relevant and/or structurally interesting N-heterocyclic carbenes, including imidazol-, thiazol-, triazol-, imidazolidin-, and pyridine-ylidenes. The bonding parameters were calculated by using a series of geometry optimizations by ab initio methods. For fitting the non-bonding interactions, a water molecule was employed as a probe. The interaction energy between the carbene and the probe molecule was sampled along two coordinates for each carbene, representing the interaction through the lone pair, or the π system of the molecule. The corresponding reference interaction energies were obtained by CCSD(T)/CBS calculations. To describe the direction dependence of the intermolecular potential energy, an extra, massless Coulombic interaction site was included for all carbenes, which represents the lone pair of the divalent carbon atom. The resulting fitted carbene force field (CaFF) showed a robust behavior regarding probe molecule, as changing the molecular mechanical water model, or employing, instead, an OPLS methanol molecule did not introduce significant deviations in the potential energies. The obtained CaFF models are easy to merge with standard OPLS or AMBER force fields, therefore the molecular simulations of a large number of N-heterocyclic carbenes becomes available.

Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor.

Patient symptom relief is often heavily influenced by the residence time of the inhibitor-target complex. For the human muscarinic receptor 3 (hMR3), tiotropium is a long-acting bronchodilator used in conditions such as asthma or chronic obstructive pulmonary disease (COPD). The mechanistic insights into this inhibitor remain unclear; specifically, the elucidation of the main factors determining the unbinding rates could help develop the next generation of antimuscarinic agents. Using our novel unbinding algorithm, we were able to investigate ligand dissociation from hMR3. The unbinding paths of tiotropium and two of its analogues, N-methylscopolamin and homatropine methylbromide, show a consistent qualitative mechanism and allow us to identify the structural bottleneck of the process. Furthermore, our machine learning-based analysis identified key roles of the ECL2/TM5 junction involved in the transition state. Additionally, our results point to relevant changes at the intracellular end of the TM6 helix leading to the ICL3 kinase domain, highlighting the closest residue L482. This residue is located right between two main protein binding sites involved in signal transduction for hMR3's activation and regulation. We also highlight key pharmacophores of tiotropium that play determining roles in the unbinding kinetics and could aid toward drug design and lead optimization.

Water in Protic Ionic Liquid Electrolytes: From Solvent Separated Ion Pairs to Water Clusters.

The large electrochemical and cycling stability of "water-in-salt" systems have rendered promising prospective electrolytes for batteries. The impact of addition of water on the properties of ionic liquids has already been addressed in several publications. In this contribution, we focus on the changes in the state of water. Therefore, we investigated the protic ionic liquid N-butyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide with varying water content at different temperatures with the aid of molecular dynamics simulations. It is revealed that at very low concentrations, the water is well dispersed and best characterized as shared solvent molecules. At higher concentrations, the water forms larger aggregates and is increasingly approaching a bulk-like state. While the librational and rotational dynamics of the water molecules become faster with increasing concentration, the translational dynamics are found to become slower. Further, all dynamics are found to be faster if the temperature increases. The trends of these findings are well in line with the experimental measured conductivities.

Ionic Liquids as Extractants for Nanoplastics.

Plastic waste in the ocean and on land in the form of nanoplastics is endangering food and drinking water supplies, raising the need for new strategies for the removal of plastic nanoparticles from complex media. In the present contribution we suggest considering ionic liquids as extractants, since they show several advantageous properties that may facilitate the design of efficient separation processes. Through varying the anion and the side chain at the cation, the interactions between the extractant and the polymer can be strengthened and tuned, and thereby the disintegration of the particle into separate polymer chains can be controlled. Oxidized moieties can also be efficiently solvated, given the amphiphilic nature of the considered ionic liquids, allowing also realistic particles to be extracted into these solvents. The phase transfer was found to be thermodynamically and kinetically possible, which is supported by the complicated structure of the ionic liquid-water interface through the rearrangement of the interfacial ions, and the formation of a micelle around the plastic already at the edge of the aqueous phase.

Combined Small-Angle Neutron Scattering, Diffusion NMR, and Molecular Dynamics Study of a Eutectogel: Illuminating the Dynamical Behavior of Glyceline Confined in Bacterial Cellulose Gels.

A deep eutectic solvent (DES) entrapped in a bacterial cellulose (BC) network gives rise to a gelatin-like, self-supported material termed a bacterial cellulose eutectogel (BCEG). Although this novel material holds potential for numerous industrial, environmental, energy, or medical applications, little is known about the structural features or dynamical behavior within a eutectogel. In this work, we employ X-ray diffraction (XRD), nuclear magnetic resonance (NMR), and small-angle neutron scattering (SANS) to probe the structural and diffusive behavior of the prevailing DES glyceline (1:2 molar ratio of choline chloride:glycerol) confined within bacterial cellulose. XRD investigations demonstrate that the bacterial cellulose maintains its crystallinity even as the glyceline content approaches 95 wt % in the BCEG, an outcome corroborated by molecular dynamics (MD) simulations, which suggest minimal changes in the structural features of the cellulose chains due to the presence of glyceline. SANS measurements reveal a significant reduction in the radius of gyration (Rg) for BC in a BCEG compared to its hydrogel analogue, indicating a collapse in the microfibrillar structure that we attribute to removal of waters from the interfibrillar space due to a higher affinity of DES for water than for cellulose. Furthermore, SANS experiments suggest that the vast majority of DES is hosted within large micropores in the BCEG (i.e., mesoscopic confinement). Interestingly, proton NMR experiments disclose faster diffusional rates for choline and glycerol entrapped in a BCEG compared to neat glyceline. MD simulations offer the possible explanation that this diffusional acceleration results from significant migration of chloride from the bulk to cellulose microfibrillar surfaces, thereby reducing hydrogen bonding with choline and glycerol partners. This study provides the first comprehensive investigation into the structure and diffusional dynamics of glyceline within a eutectogel, offering insights into mass transport that should be useful for tailoring these novel materials to potential applications.

Nanoplastics can change the secondary structure of proteins.

Submillimetre-sized plastic particles (microplastics and nanoplastics) of waste origin in the environment have been repeatedly suggested in recent years to have severe impact on living organisms. While the uptake of these materials has been unequivocally evidenced for animals, so far no adverse effects have been observed in the corresponding animal experiments. In this study, we show that nanoplastics are prone to interact with proteins, and this interaction fundamentally changes the functionally crucial secondary structure of these biomolecules, and thereby denaturates them. These results show, for the first time, that the interplay between plastic waste and biological matter can induce significant cellular and thereby ecological damages. Observing these remarkable microscopic level changes highlights the urgent need to extend investigating the effects of these materials through further modelling and molecular biological methods.

Water in Protic Ionic Liquids: Properties and Use of a New Class of Electrolytes for Energy-Storage Devices.

In this work, the properties of "water-in-PIL" (PIL=protic ionic liquid) electrolytes are reported based on 1-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide (PyrH4 TFSI). Taking advantage of experimental and theoretical investigations, it is shown that the amount of water inside the electrolyte has a dramatic effect on the viscosity, conductivity, density, cation-anion interplay, and electrochemical stability of PyrH4 TFSI. The impact of water on the properties of this ionic liquid also affects its use as an electrolyte for electrochemical double-layer capacitors (EDLCs). It is shown that the presence of water improves the transport properties of PyrH4 TFSI, with a beneficial effect on the capacitance retention of the devices in which these electrolytes are used. However, at the same time, water reduces the operative voltage of EDLCs containing this PIL as the electrolyte and, furthermore, it has a strong impact on the inactive components of these systems. To suppress this latter problem, and to realize EDLCs with high stability, the use of inactive components stable in aqueous environment appears necessary.

Tuning Solvent Miscibility: A Fundamental Assessment on the Example of Induced Methanol/ n-Dodecane Phase Separation.

In this work, we assess the fundamental aspects of mutual miscibility of solvents by studying the mixing of two potential candidates, methanol and n-dodecane, for nonaqueous solvent extraction. To do so, 1H NMR spectroscopy and molecular dynamics simulations are used jointly. The NMR spectra show that good phase separation can be obtained by adding LiCl and that the addition of a popular extractant (tri- n-butyl phosphate) yields the opposite effect. It is also demonstrated that in a specific case the poor phase separation is not due to the migration of n-dodecane into the more polar phase, but due to the transfer of the extractant into it, which is especially relevant when considering industrial applications of solvent extraction. With the aid of molecular dynamics simulations, explanations of this behavior are given. Specifically, an increase of all hydrogen-bond lifetimes is found to be consequent to the addition of LiCl which implies an indirect influence on the methanol liquid structure, by favoring a stronger hydrogen-bond network. Therefore, we found that better phase separation is not directly due to the presence of LiCl, but due to the "hardening" of the hydrogen-bond network.

How to Harvest Grotthuss Diffusion in Protic Ionic Liquid Electrolyte Systems.

Hydrogen is often regarded as fuel of the future, and there is an increasing demand for the development of anhydrous proton-conducting electrolytes to enable fuel-cell operation at elevated temperatures exceeding 120 °C. Much attention has been directed at protic ionic liquids as promising candidates, but in the search for highly conductive systems the possibility of designing Grotthuss diffusion-enabled protic ionic liquids has been widely overlooked. Herein, the mechanics of proton-transfer mechanism in the equimolar mixture of N-methylimidazole and acetic acid was explored using ab initio molecular dynamics simulations. The ionicity of the system is approximated with good agreement to experiments. This system consists mostly of neutral species but exhibits a high ionic conductivity through Grotthuss-like proton conduction. Chains of acetic-acid molecules and other species participating in the proton-transfer mechanisms resembling Grotthuss diffusion could be directly observed. Furthermore, based on these findings, a series of static quantum chemical calculations was conducted to investigate the effect of substituting the anion and cation with different functional groups. We predict whether a given combination of cation and anion will be a true ionic liquid or a molecular mixture and propose some systems as candidates for Grotthuss diffusion-enabled protic ionic liquids.