Monomer Dynamics of Alzheimer Peptides and Kinetic Control of Early Aggregation in Alzheimer's Disease

The rate of reconfiguration—or intramolecular diffusion—of monomeric Alzheimer (Aβ) peptides is measured and, under conditions that aggregation is more likely, peptide diffusion slows down significantly, which allows bimolecular associations to be initiated. By using the method of Trp–Cys contact quenching, the rate of reconfiguration is observed to be about five times faster for Aβ₄₀, which aggregates slowly, than that for Aβ₄₂, which aggregates quickly. Furthermore, the rate of reconfiguration for Aβ₄₂ speeds up at higher pH, which slows aggregation, and in the presence of the aggregation inhibitor curcumin. The measured reconfiguration rates are able to predict the early aggregation behavior of the Aβ peptide and provide a kinetic basis for why Aβ₄₂ is more prone to aggregation than Aβ₄₀, despite a difference of only two amino acids.     

The Catalytic Mechanism of the Marine‐Derived Macrocyclase PatGmac

Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including antitumor and antiviral (including anti‐HIV). Despite their desirability, efficient design and production of these compounds has not been achieved to date. The catalytic mechanism of patellamide macrocyclization by the PatG macrocyclase domain has been computationally investigated by using quantum mechanics/molecular mechanics methodology, specifically ONIOM(M06/6‐311++G(2d,2p):ff94//B3LYP/6‐31G(d):ff94). The mechanism proposed herein begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 on the substrate leads to the formation of an acyl–enzyme covalent complex. The leaving group Ala‐Tyr‐Asp‐Gly (AYDG) of the substrate is protonated by the substrate's N terminus, leading to the breakage of the P1?P1′ bond. Finally, the substrate's N terminus attacks the P1 residue, decomposing the acyl–enzyme complex forming the macrocycle. The formation and decomposition of the acyl–enzyme complex have the highest activation free energies (21.1 kcal mol^?1 and 19.8 kcal mol^?1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.     

How Epigallocatechin‐3‐gallate and Tetracycline Interact with the Josephin Domain of Ataxin‐3 and Alter Its Aggregation Mode

Epigallocatechin‐3‐gallate (EGCG) and tetracycline are two known inhibitors of amyloid aggregation able to counteract the fibrillation of most of the proteins involved in neurodegenerative diseases. We have recently investigated their effect on ataxin‐3 (AT3), the polyglutamine‐containing protein responsible for spinocerebellar ataxia type 3. We previously showed that EGCG and tetracycline can contrast the aggregation process and toxicity of expanded AT3, although by different mechanisms. Here, we have performed further experiments by using the sole Josephin domain (JD) to further elucidate the mechanism of action of the two compounds. By protein solubility assays and FTIR spectroscopy we have first observed that EGCG and tetracycline affect the JD aggregation essentially in the same way displayed when acting on the full‐length expanded AT3. Then, by saturation transfer difference (STD) NMR experiments, we have shown that EGCG binds both the monomeric and the oligomeric JD form, whereas tetracycline can only interact with the oligomeric one. Surface plasmon resonance (SPR) analysis has confirmed the capability of the sole EGCG to bind monomeric JD, although with a K_D value suggestive for a non‐specific interaction. Our investigations provide new details on the JD interaction with EGCG and tetracycline, which could explain the different mechanisms by which the two compounds reduce the toxicity of AT3.     

Force‐Induced Reversal of β‐Eliminations: Stressed Disulfide Bonds in Alkaline Solution

Understanding the impact of tensile forces on disulfide bond cleavage is not only crucial to the breaking of cross‐linkers in vulcanized materials such as strained rubber, but also to the regulation of protein activity by disulfide switches. By using ab initio simulations in the condensed phase, we investigated the response of disulfide cleavage by β‐elimination to mechanical stress. We reveal that the rate‐determining first step of the thermal reaction, which is the abstraction of the β‐proton, is insensitive to external forces. However, forces larger than about 1 nN were found to reshape the free‐energy landscape of the reaction so dramatically that a second channel is created, where the order of the reaction steps is reversed, turning β‐deprotonation into a barrier‐free follow‐up process to C?S cleavage. This transforms a slow and force‐independent process with second‐order kinetics into a unimolecular reaction that is greatly accelerated by mechanical forces.     

Hydroxypalladation Precedes the Rate‐Determining Step in the Wacker Oxidation of Ethene

The complete reaction mechanism and kinetics of the Wacker oxidation of ethene in water under low [Cl^?], [Pd^II], and [Cu^II] conditions are investigated in this work by using ab initio molecular dynamics. These extensive simulations shed light on the molecular details of the associated individual steps, along two different reaction routes, starting from a series of ligand‐exchange processes in the catalyst precursor PdCl₄^2? to the final aldehyde‐formation step and the reduction of Pd^II. Herein, we report that hydroxylpalladation is not the rate‐determining step and is, in fact, in equilibrium. The newly proposed rate‐determining step involves isomerization and follows the hydroxypalladation step. The mechanism proposed herein is shown to be in excellent agreement with the experimentally observed rate law and rate. Moreover, this mechanism is in consensus with the observed kinetic isotope effects. This report further confirms the outer‐sphere (anti) hydroxypalladation mechanism. Our calculations also ratify that the final product formation proceeds through a reductive elimination, assisted by solvent molecules, rather than through β‐hydride elimination.     

Unraveling the Role of Water in the Stereoselective Step of Aqueous Proline‐Catalyzed Aldol Reactions

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self‐condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First‐principles molecular dynamics simulations were used to study the free‐energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high‐level static first‐principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths.     

Numerical Simulation of the Effect of Solvent Viscosity on the Motions of a β‐Peptide Heptamer

This report examines the effect of a decrease in solvent viscosity on the simulated folding behaviour of a β‐peptide heptamer in methanol. Simulations of the molecular dynamics of the heptamer H‐β³‐HVal‐β³‐HAla‐β³‐HLeu‐(S,S)‐β³‐HAla(αMe)‐β³‐HVal‐β³‐HAla‐β³‐HLeu‐OH in methanol, with an explicit representation of the methanol molecules, were performed for 80 ns at various solvent viscosities. The simulations indicate that at a solvent viscosity of one third of that of methanol, only the dynamic aspects of the folding process are altered, and that the rate of folding is increased. At a viscosity of one tenth of that of methanol, insufficient statistics are obtained within the 80 ns period. We suggest that 80 ns is an insufficient time to reach conformational equilibrium at very low viscosity because the dependence of the folding rate of a β‐peptide on solvent viscosity has two regimes; a result that was observed in another computational study for α‐peptides.     

FMO‐MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics

Full‐quantum mechanical fragment molecular orbital‐based molecular dynamics (FMO‐MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized continuum model reaction field predicted that the hydration prefers a concerted mechanism. Because the calculated activation barriers were too high for free FMO‐MD simulations to give reactive trajectories spontaneously, a More O’Ferrall–Jencks‐type diagram was constructed from the statistical analysis of the FMO‐MD simulations with constraint dynamics. The diagram showed that the hydration proceeds through a zwitterionic‐like (ZW‐like) structure. The free energy changes along the reaction coordinate calculated by means of the blue moon ensemble for the hydration and the amination of formaldehyde indicated that the hydration proceeds through a concerted process through the ZW‐like structure, whereas the amination goes through a stepwise mechanism with a ZW intermediate. In inspection of the FMO‐MD trajectories, water‐mediated cyclic proton transfers were observed in both reactions on the way from the ZW‐like structure to the product. These proton transfers also have an asynchronous character, in which deprotonation from the nucleophilic oxygen atom (or nitrogen atom for amination) precedes the protonation of the carbonyl oxygen atom. The results showed the strong advantage of the FMO‐MD simulations to obtain detailed information at a molecular level for solution reactions.     

Thermal characterization and kinetic analysis of nano‐ and micro‐Al/NiO thermites: Combined experimental and molecular dynamics simulation study

In the experimental part of this study, thermal properties of the Al and NiO composites in micro‐ and nano‐sized Al are investigated. Differential scanning calorimetry (DSC) analysis of the onset temperatures of ignition, activation energy (E_a), frequency factor (A), rate constant (k), critical ignition temperature of thermal explosion (T_b), and self‐accelerating decomposition temperature (T_SADT), as well as the thermodynamic parameters (ΔS^≠ , ΔH^≠ , and ΔG^≠ ) are used to explore the thermal behavior and analyze the kinetics. Thermal analysis suggests that the mechanism is based on solid–solid diffusion and liquid–gas for the nano‐ and micro‐Al/NiO composite, respectively. Our results indicate that the incorporation of nano‐Al particles can significantly reduce the ignition temperature, E_a, A, k, T_b, and T_SADT. In the second part of this work, molecular dynamics (MD) simulation is used to investigate the behavior of Al/NiO thermite reaction using the Reaxff force field to evaluate the experimental results. Theoretically, MD results show 1,154 K as the reaction ignition temperature, which is in reasonably good agreement with experimental temperature of 893°C (1,166 K). The radial distribution function (RDF) shows that no reaction occurs at 500 K but it is complete at 1,200 K.     

Experimental and Theoretical Studies on the Bismuth‐Triflate‐Catalysed Cycloisomerisation of 1,6,10‐Trienes and Aryl Polyenes

Cycloisomerisation of polyenes such as diethyl geranylprenylmalonate [(E)‐ 1 a ], diethyl geranylphenylmalonate [(E)‐ 2 a ] and diethyl cinnamylgeranylmalonate [(E,E)‐ 3 a ] catalysed by bismuth triflate was studied from experimental and theoretical viewpoints. Several intermediates were isolated and characterised, and calculated transition‐state structures are proposed for the three reactions. The diastereoselectivity observed during the reaction of (E)‐ or (Z)‐ 2 a in favour of the formation of trans‐fused bicyclic products is discussed in detail. The nature of the active catalytic species derived from bismuth triflate was also investigated, and the formation of a hybrid Lewis acid/Brønsted acid catalyst with water molecules is proposed, supported by experimental and theoretical data.     

Synthesis of Peptides by Silver‐Promoted Coupling of Carboxylates and Thioamides: Mechanistic Insight from Computational Studies

The mechanism of the recently described N→C direction peptide synthesis through silver‐promoted coupling of N‐protected amino acids with thioacetylated amino esters was explored by using density functional theory. Calculation of the potential energy surfaces for various pathways revealed that the reaction proceeds through silver‐assisted addition of the carboxylate to the thioamide, which is followed by deprotonation and silver‐mediated extrusion of sulfur as Ag₂S. The resulting isoimide is the key intermediate, which subsequently rearranges to an imide through a concerted pericyclic [1,3]‐acyl shift (O–sp²N 1,3‐acyl migration). The proposed mechanism clearly emphasises the requirement of two equivalents of Ag^I and basic reaction conditions, which is in full agreement with the experimental findings. Alternative rearrangement pathways involving only one equivalent of Ag^I or through O–sp³N 1,3‐acyl migration can be excluded. The computations further revealed that peptide couplings involving thioformamides require significant conformational changes in the intermediate isoformimide, which slow down the rearrangement process.     

Isomerization‐ and Temperature‐Jump‐Induced Dynamics of a Photoswitchable β‐Hairpin

Conformational changes in proteins and peptides can be initiated by diverse processes. This raises the question how the variation of initiation mechanisms is connected to differences in folding or unfolding processes. In this work structural dynamics of a photoswitchable β‐hairpin model peptide were initiated by two different mechanisms: temperature jump (T‐jump) and isomerization of a backbone element. In both experiments the structural changes were followed by time‐resolved IR spectroscopy in the nanosecond to microsecond range. When the photoisomerization of the azobenzene backbone switch initiated the folding reaction, pronounced absorption changes related to folding into the hairpin structure were found with a time constant of about 16 μs. In the T‐jump experiment kinetics with the same time constant were observed. For both initiation processes the reaction dynamics revealed the same strong dependence of the reaction time on temperature. The highly similar transients in the microsecond range show that the peptide dynamics induced by T‐jump and isomerization are both determined by the same mechanism and exclude a downhill‐folding process. Furthermore, the combination of the two techniques allows a detailed model for folding and unfolding to be presented: The isomerization‐induced folding process ends in a transition‐state reaction scheme, in which a high energetic barrier of 48 kJ mol^?1 separates unfolded and folded structures.     

On the Importance of Decarbonylation as a Side‐Reaction in the Ruthenium‐Catalysed Dehydrogenation of Alcohols: A Combined Experimental and Density Functional Study

We report a density functional study (B97‐D2 level) of the mechanism(s) operating in the alcohol decarbonylation that occurs as an important side‐reaction during dehydrogenation catalysed by [RuH₂(H₂)(PPh₃)₃]. By using MeOH as the substrate, three distinct pathways have been fully characterised involving either neutral tris‐ or bis‐phosphines or anionic bis‐phosphine complexes after deprotonation. α‐Agostic formaldehyde and formyl complexes are key intermediates, and the computed rate‐limiting barriers are similar between the various decarbonylation and dehydrogenation paths. The key steps have also been studied for reactions involving EtOH and iPrOH as substrates, rationalising the known resistance of the latter towards decarbonylation. Kinetic isotope effects (KIEs) were predicted computationally for all pathways and studied experimentally for one specific decarbonylation path designed to start from [RuH(OCH₃)(PPh₃)₃]. From the good agreement between computed and experimental KIEs (observed k_H/k_D=4), the rate‐limiting step for methanol decarbonylation has been ascribed to the formation of the first agostic intermediate from a transient formaldehyde complex.     

The Three‐Component Biginelli Reaction: A Combined Experimental and Theoretical Mechanistic Investigation

Biginelli reactions have been monitored by direct infusion electrospray ionization mass spectrometry (ESI‐MS) and key cationic intermediates involved in this three‐component reaction have been intercepted and further characterized by tandem MS experiments (ESI‐MS/MS). Density functional theory calculations were also used to investigate the feasibility of the major competing mechanisms proposed for the Biginelli reaction. The experimental and theoretical results were found to corroborate the iminium mechanism proposed by Folkers and Johnson, whereas no intermediates directly associated with either the more energy demanding Knoevenagel or enamine mechanisms could be intercepted.