Short Peptide Self-Assembly in the Martini Coarse-Grain Force Field Family.

Pivotal to the success of any computational experiment is the ability to make reliable predictions about the system under study and the time required to yield these results. Biomolecular interactions is one area of research that sits in every camp of resolution vs the time required, from the quantum mechanical level to in vivo studies. At an approximate midpoint, there is coarse-grained molecular dynamics, for which the Martini force fields have become the most widely used, fast enough to simulate the entire membrane of a mitochondrion though lacking atom-specific precision. While many force fields have been parametrized to account for a specific system under study, the Martini force field has aimed at casting a wider net with more generalized bead types that have demonstrated suitability for broad use and reuse in applications from protein-graphene oxide coassembly to polysaccharides interactions.In this Account, the progressive (Martini versions 1 through 3) and peripheral (Sour Martini, constant pH, Martini Straight, Dry Martini, etc.) developmental trajectory of the Martini force field will be analyzed in terms of self-assembling systems with a focus on short (two to three amino acids) peptide self-assembly in aqueous environments. In particular, this will focus on the effects of the Martini solvent model and compare how changes in bead definitions and mapping have effects on different systems. Considerable effort in the development of Martini has been expended to reduce the "stickiness" of amino acids to better simulate proteins in bilayers. We have included in this Account a short study of dipeptide self-assembly in water, using all mainstream Martini force fields, to examine their ability to reproduce this behavior. The three most recently released versions of Martini and variations in their solvents are used to simulate in triplicate all 400 dipeptides of the 20 gene-encoded amino acids. The ability of the force fields to model the self-assembly of the dipeptides in aqueoues environments is determined by the measurement of the aggregation propensity, and additional descriptors are used to gain further insight into the dipeptide aggregates.

Martinoid: the peptoid martini force field.

Many exciting innovations have been made in the development of assembling peptoid materials. Typically, these have utilised large oligomeric sequences, though elsewhere the study of peptide self-assembly has yielded numerous examples of assemblers below 6-8 residues in length, evidencing that minimal peptoid assemblers are not only feasible but expected. A productive means of discovering such materials is through the application of in silico screening methods, which often benefit from the use of coarse-grained molecular dynamics (CG-MD) simulations. At the current level of development, CG models for peptoids are insufficient and we have been motivated to develop a Martini forcefield compatible peptoid model. A dual bottom-up and top-down parameterisation approach has been adopted, in keeping with the Martini parameterisation methodology, targeting the reproduction of atomistic MD dynamics and trends in experimentally obtained log D7.4 partition coefficients, respectively. This work has yielded valuable insights into the practicalities of parameterising peptoid monomers. Additionally, we demonstrate that our model can reproduce the experimental observations of two very different peptoid assembly systems, namely peptoid nanosheets and minimal tripeptoid assembly. Further we can simulate the peptoid helix secondary structure relevant for antimicrobial sequences. To be of maximum usefulness to the peptoid research community, we have developed freely available code to generate all requisite simulation files for the application of this model with Gromacs MD software.

An active machine learning discovery platform for membrane-disrupting and pore-forming peptides.

Membrane-disrupting and pore-forming peptides (PFPs) play a substantial role in bionanotechnology and can determine the life and death of cells. The control of chemical and ion transport through cell membranes is essential to maintaining concentration gradients. Likewise, the delivery of drugs and intracellular proteins aided by pore-forming agents is of interest in treating malfunctioning cells. Known PFPs tend to be up to 50 residues in length, which is commensurate with the thickness of a lipid bilayer. Accordingly, few short PFPs are known. Here we show that the discovery of PFPs can be accelerated via an active machine learning approach. The approach identified 71 potential PFPs from the 25.6 billion octapeptide sequence space; 13 sequences were tested experimentally, and all were found to have the predicted membrane-disrupting ability, with 1 forming highly stable pores. Experimental verification of the predicted pore-forming ability demonstrated that a range of short peptides can form pores in membranes, while the positioning and characteristics of residues that favour pore-forming behaviour were identified. This approach identified more ultrashort (8-residues, unmodified, non-cyclic) PFPs than previously known. We anticipate our findings and methodology will be useful in discovering new pore-forming and membrane-disrupting peptides for a range of applications from nanoreactors to therapeutics.

Mathematical and computational modeling of fats and triacylglycerides.

Fats and oils are found in many food products; however, their macroscopic properties are difficult to predict, especially when blending different fats or oils together. With difficulties in sourcing specific fats or oils, whether due to availability or pricing, food companies may be required to find alternative sources for these ingredients, with possible differences in ingredient performance. Mathematical and computational modeling of these ingredients can provide a quick way to predict their properties, avoiding costly trials or manufacturing problems, while, most importantly, keeping the consumers happy. This review covers a range of mathematical models for triacylglycerides (TAGs) and fats, namely, models for the prediction of melting point, solid fat content, and crystallization temperature and composition. There are a number of models that have been designed for both TAGs and fats and which have been shown to agree very well with empirical measurements, using both kinetic and thermodynamic approaches, with models for TAGs being used to, in turn, predict fat properties. The last section describes computational models to simulate the behavior of TAGs using molecular dynamics (MD). Simulation of TAGs using MD, however, is still at an early stage, although the most recent papers on this topic are bringing this area up to speed.

Triacylglyceride melting point determination using coarse-grained molecular dynamics.

This study is carried out using the COGITO force field to determine whether the thermodynamic melting point of pure triacylglyceride crystals can be predicted using molecular dynamics simulations. The triacylglycerides used in this study are both saturated and unsaturated, as well as symmetrical and asymmetrical, to test the robustness of both the force field and the direct heating methodology described in this paper. Given the nonequilibrium nature of a melting system, a larger number of simulations are required to ensure that the results are sufficiently converged, that is, with little fluctuation and a small confidence interval. The study also highlights the importance of the presence of defects, in this case as voids, to lower the melting nucleation energy barrier of the crystals and avoid superheating of the systems being tested. The size of these defects is much larger than what would be found in a physical crystal, however, the simple and robust procedure that was developed allows the accurate prediction of melting points of the different triacylglycerides.

[3+2]-Cycloaddition Reactions of gem-Difluorocyclopropenes with Azomethine Ylides - Access to Novel Fluorinated Scaffolds.

The introduction of fluorinated moieties into drugs as well as the increase of their overall three-dimensionality have become key strategies amongst medicinal chemists to generate sets of compounds with favorable drug-like properties. However, the introduction of fluorinated cyclopropane ring systems which combines both strategies is not widely exploited to date. This paper reports synthetic strategies exploiting the reactivity of gem-difluorocyclopropenes in dipolar cycloaddition reactions with azomethine ylides to afford sets of new fluorine-containing 3-azabicyclo[3.1.0]hexanes. In addition, the unexpected formation of complex trifluorinated scaffolds arising from proline esters and gem-difluorocyclopropenes is highlighted along with computational studies to elucidate the underlying mechanism. This study presents new avenues towards pharmaceutically relevant fluorinated 3-azabicyclo[3.1.0]hexanes that are accessible via robust and short synthetic sequences.

Solvent-controlled self-assembly of Fmoc protected aliphatic amino acids.

Self-assembly of modified amino acids facilitate the formation of various structures that have unique properties and therefore serve as excellent bio-organic scaffolds for diverse applications. Self-assembly of Fmoc protected single amino acids has attracted great interest owing to their ease of synthesis and applications as functional materials. Smaller assembly units enable synthetic convenience and potentially broader adoption. Herein, we demonstrate the ability to control the morphologies resulting from self-assembly of Fmoc modified aliphatic single amino acids (Fmoc-SAAs) namely, Alanine, Valine, Leucine, Isoleucine, and Proline. Controlled morphological transitions were observed through solvent variation and the mechanism that allows this control was investigated using coarse-grained molecular dynamics simulations. These show that FmocA can form well defined crystalline structures through uniform parallel Fmoc stacking and the optimization of ion concentrations, which is not observed for the other Fmoc-SAAs. We demonstrate that Fmoc protected aliphatic single amino acids are novel scaffolds for the design of distinct micro/nanostructures through a bottom-up approach that can be tuned by control of the environmental parameters.

Integrating Computation, Experiment, and Machine Learning in the Design of Peptide-Based Supramolecular Materials and Systems.

Interest in peptide-based supramolecular materials has grown extensively since the 1980s and the application of computational methods has paralleled this. These methods contribute to the understanding of experimental observations based on interactions and inform the design of new supramolecular systems. They are also used to virtually screen and navigate these very large design spaces. Increasingly, the use of artificial intelligence is employed to screen far more candidates than traditional methods. Based on a brief history of computational and experimentally integrated investigations of peptide structures, we explore recent impactful examples of computationally driven investigation into peptide self-assembly, focusing on recent advances in methodology development. It is clear that the integration between experiment and computation to understand and design new systems is becoming near seamless in this growing field.

Alkali Metal Dihydropyridines in Transfer Hydrogenation Catalysis of Imines: Amide Basicity versus Hydride Surrogacy.

Catalytic reduction of a representative set of imines, both aldimines and ketimines, to amines has been studied using transfer hydrogenation from 1,4-dicyclohexadiene. Unusually, this has been achieved using s-block pre-catalysts, namely 1-metallo-2-tert-butyl-1,2-dihydropyridines, 2-tBuC5 H5 NM, M(tBuDHP), where M=Li-Cs. Reactions have been monitored in C6 D6 and tetrahydrofuran-d8 (THF-d8 ). A definite trend is observed in catalyst efficiency with the heavier alkali metal tBuDHPs outperforming the lighter congeners. In general, Cs(tBuDHP) is the optimal pre-catalyst with, in the best cases, reactions producing quantitative yields of amines in minutes at room temperature using 5 mol % catalyst. Supporting the experimental study, Density Functional Theory (DFT) calculations have also been carried out which reveal that Cs has a pathway with a significantly lower rate determining step than the Li congener. In the postulated initiation pathways DHP can act as either a base or as a surrogate hydride.

Mechanistic insights of evaporation-induced actuation in supramolecular crystals.

Water-responsive materials undergo reversible shape changes upon varying humidity levels. These mechanically robust yet flexible structures can exert substantial forces and hold promise as efficient actuators for energy harvesting, adaptive materials and soft robotics. Here we demonstrate that energy transfer during evaporation-induced actuation of nanoporous tripeptide crystals results from the strengthening of water hydrogen bonding that drives the contraction of the pores. The seamless integration of mobile and structurally bound water inside these pores with a supramolecular network that contains readily deformable aromatic domains translates dehydration-induced mechanical stresses through the crystal lattice, suggesting a general mechanism of efficient water-responsive actuation. The observed strengthening of water bonding complements the accepted understanding of capillary-force-induced reversible contraction for this class of materials. These minimalistic peptide crystals are much simpler in composition compared to natural water-responsive materials, and the insights provided here can be applied more generally for the design of high-energy molecular actuators.

Hydrocarbon Soluble Alkali-Metal-Aluminium Hydride Surrog[ATES].

A series of group 1 hydrocarbon-soluble donor free aluminates [AM(t BuDHP)(TMP)Al(i Bu)2 ] (AM=Li, Na, K, Rb) have been synthesised by combining an alkali metal dihydropyridyl unit [(2-t BuC5 H5 N)AM)] containing a surrogate hydride (sp3 C-H) with [(i Bu)2 Al(TMP)]. These aluminates have been characterised by X-ray crystallography and NMR spectroscopy. While the lithium aluminate forms a monomer, the heavier alkali metal aluminates exist as polymeric chains propagated by non-covalent interactions between the alkali metal cations and the alkyldihydropyridyl units. Solvates [(THF)Li(t BuDHP)(TMP)Al(i Bu)2 ] and [(TMEDA)Na(t BuDHP)(TMP)Al(i Bu)2 ] have also been crystallographically characterised. Theoretical calculations show how the dispersion forces tend to increase on moving from Li to Rb, as opposed to the electrostatic forces of stabilization, which are orders of magnitude more significant. Having unique structural features, these bimetallic compounds can be considered as starting points for exploring unique reactivity trends as alkali-metal-aluminium hydride surrog[ATES].

Rapid Automated Quantification of Triacylglyceride Crystallinity in Molecular Dynamics Simulations.

The relative stability of crystalline polymorphs and the transition between crystalline and melt phases are key parameters in determining the physical properties of triacylglycerides used in food. However, while the determination of properties experimentally is well-defined, the ability to predict the onset of melting and discriminate between polymorphs is less well-defined within a molecular dynamics simulation environment. In this work, we present metrics for measuring the crystallinity, including a new metric, the near-neighbor occupancy time, giving a rapid determination of how many, and which, molecules are found in a crystal over a simulation trajectory, and the polymorphic determination of triacylglycerides over a simulation trajectory.

Expanding the Conformational Landscape of Minimalistic Tripeptides by Their O-Glycosylation.

We report on the supramolecular self-assembly of tripeptides and their O-glycosylated analogues, in which the carbohydrate moiety is coupled to a central serine or threonine flanked by phenylalanine residues. The substitution of serine with threonine introduces differential side-chain interactions, which results in the formation of aggregates with different morphology. O-glycosylation decreases the aggregation propensity because of rebalancing of the π interactions. The glycopeptides form aggregates with reduced stiffness but increased thermal stability. Our results demonstrate that the designed minimalistic glycopeptides retain critical functional features of glycoproteins and therefore are promising tools for elucidation of molecular mechanisms involved in the glycoprotein interactome. They can also serve as an inspiration for the design of functional glycopeptide-based biomaterials.

Radical and Ionic Mechanisms in Rearrangements of o-Tolyl Aryl Ethers and Amines Initiated by the Grubbs-Stoltz Reagent, Et3SiH/KOtBu.

Rearrangements of o-tolyl aryl ethers, amines, and sulfides with the Grubbs-Stoltz reagent (Et3SiH + KOtBu) were recently announced, in which the ethers were converted to o-hydroxydiarylmethanes, while the (o-tol)(Ar)NH amines were transformed into dihydroacridines. Radical mechanisms were proposed, based on prior evidence for triethylsilyl radicals in this reagent system. A detailed computational investigation of the rearrangements of the aryl tolyl ethers now instead supports an anionic Truce-Smiles rearrangement, where the initial benzyl anion can be formed by either of two pathways: (i) direct deprotonation of the tolyl methyl group under basic conditions or (ii) electron transfer to an initially formed benzyl radical. By contrast, the rearrangements of o-tolyl aryl amines depend on the nature of the amine. Secondary amines undergo deprotonation of the N-H followed by a radical rearrangement, to form dihydroacridines, while tertiary amines form both dihydroacridines and diarylmethanes through radical and/or anionic pathways. Overall, this study highlights the competition between the reactive intermediates formed by the Et3SiH/KOtBu system.

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.

Neutral Organic Super Electron Donors Made Catalytic.

Neutral organic super electron donors (SEDs) display impressive reducing power but, until now, it has not been possible to use them catalytically in radical chain reactions. This is because, following electron transfer, these donors form persistent radical cations that trap substrate-derived radicals. This paper unlocks a conceptually new approach to super electron donors that overcomes this issue, leading to the first catalytic neutral organic super electron donor.

Lithium-Aluminate-Catalyzed Hydrophosphination Applications.

Synthesized, isolated, and characterized by X-ray crystallography and NMR spectroscopic studies, lithium phosphidoaluminate iBu3 AlPPh2 Li(THF)3 has been tested as a catalyst for hydrophosphination of alkynes, alkenes, and carbodiimides. Based on the collective evidence of stoichiometric reactions, NMR monitoring studies, kinetic analysis, and DFT calculations, a mechanism involving deprotonation, alkyne insertion, and protonolysis is proposed for the [iBu3 AlHLi]2 aluminate catalyzed hydrophosphination of alkynes with diphenylphosphine. This study enhances further the development of transition-metal-free, atom-economical homogeneous catalysis using common sustainable main-group metals.

Concerted Nucleophilic Aromatic Substitution Reactions.

Recent developments in experimental and computational chemistry have identified a rapidly growing class of nucleophilic aromatic substitutions that proceed by concerted (cSN Ar) rather than classical, two-step, SN Ar mechanisms. Whereas traditional SN Ar reactions require substantial activation of the aromatic ring by electron-withdrawing substituents, such activating groups are not mandatory in the concerted pathways.

Electron Transfer Reactions: KO tBu (but not NaO tBu) Photoreduces Benzophenone under Activation by Visible Light.

Long-standing controversial reports of electron transfer from KO tBu to benzophenone have been investigated and resolved. The mismatch in the oxidation potential of KO tBu (+0.10 V vs SCE in DMF) and the first reduction potential of benzophenone (of many values cited in the literature, the least negative value is -1.31 V vs SCE in DMF), preclude direct electron transfer. Experimental and computational results now establish that a complex is formed between the two reagents, with the potassium ion providing the linkage, which markedly shifts the absorption spectrum to provide a tail in the visible light region. Photoactivation at room temperature by irradiation at defined wavelength (365 or 400 nm), or even by winter daylight, leads to the development of the blue color of the potassium salt of benzophenone ketyl, whereas no reaction is observed when the reaction mixture is maintained in darkness. So, no electron transfer occurs in the ground state. However, when photoexcited, electron transfer occurs within a complex formed from benzophenone and KO tBu. TDDFT studies match experimental findings and also define the electronic transition within the complex as n → π*, originating on the butoxide oxygen. Computation and experiment also align in showing that this reaction is selective for KO tBu; no such effect occurs with NaO tBu, providing the first case where such alkali metal ion selectivity is rationalized in detail. Chemical evidence is provided for the photoactivated electron transfer from KO tBu to benzophenone: tert-butoxyl radicals are formed and undergo fragmentation to form (acetone and) methyl radicals, some of which are trapped by benzophenone. Likewise, when KOC(Et)3 is used in place of KO tBu, then ethylation of benzophenone is seen. Further evidence of electron transfer was seen when the reaction was conducted in benzene, in the presence of p-iodotoluene; this triggered BHAS coupling to form 4-methylbiphenyl in 74% yield.

Dual Roles for Potassium Hydride in Haloarene Reduction: CSNAr and Single Electron Transfer Reduction via Organic Electron Donors Formed in Benzene.

Potassium hydride behaves uniquely and differently than sodium hydride toward aryl halides. Its reactions with a range of haloarenes, including designed 2,6-dialkylhaloarenes, were studied in THF and in benzene. In THF, evidence supports concerted nucleophilic aromatic substitution, CSNAr, and the mechanism originally proposed by Pierre et al. is now validated through DFT studies. In benzene, besides this pathway, strong evidence for single electron transfer chemistry is reported. Experimental observations and DFT studies lead us to propose organic super electron donor generation to initiate BHAS (base-promoted homolytic aromatic substitution) cycles. Organic donor formation originates from deprotonation of benzene by KH; attack on benzene by the resulting phenylpotassium generates phenylcyclohexadienylpotassium that can undergo (i) deprotonation to form an organic super electron donor or (ii) hydride loss to afford biphenyl. Until now, BHAS reactions have been triggered by reaction of a base, MO tBu (M = K, Na), with many different types of organic additive, all containing heteroatoms (N or O or S) that enhance their acidity and place them within range of MO tBu as a base. This paper shows that with the stronger base, KH, even a hydrocarbon (benzene) can be converted into an electron-donating initiator.