Peptide Isomerization is Suppressed at the Air-Water Interface

Ab Initio Characterization of the CO2-Water Interface Using Unsupervised Machine Learning for Dimensionality Reduction

Precise characterization of the supercritical CO2-water interface under high pressure and temperature conditions is crucial for the geological storage of carbon dioxide (CO2) in deep saline aquifers. Molecular dynamics (MD) simulations offer a valuable approach to gaining insight into the CO2-water interface at a microscopic level. However, no attempt has been made to characterize the CO2-water interface with the accuracy afforded by ab initio calculations. In this study, we performed ab initio MD (AIMD) simulations to investigate the structural and dynamical properties of the CO2-water interface, comparing the results with those obtained from classical force-field MD (FF-MD) simulations. Molecular orientation at the interface was well reproduced in both AIMD and FF-MD simulations. Characteristic structural fluctuations of water at the interface were unveiled by applying multidimensional scaling and time-dependent principal component analysis to the AIMD trajectories; however, they were not prominent in the FF-MD simulations. Furthermore, our study demonstrated a marked difference in the residence time of molecules in the interface region between AIMD and FF-MD simulations, indicating that time-dependent properties of the CO2-water interface strongly depend on the description of the intermolecular forces.

On the Statistical Mechanics of Mass Accommodation at Liquid-Vapor Interfaces

We propose a framework for describing the dynamics associated with the adsorption of small molecules to liquid-vapor interfaces using an intermediate resolution between traditional continuum theories that are bereft of molecular detail and molecular dynamics simulations that are replete with them. In particular, we develop an effective single particle equation of motion capable of describing the physical processes that determine thermal and mass accommodation probabilities. The effective equation is parametrized with quantities that vary through space away from the liquid-vapor interface. Of particular importance in describing the early time dynamics is the spatially dependent friction, for which we propose a numerical scheme to evaluate from molecular simulation. Taken together with potentials of mean force computable with importance sampling methods, we illustrate how to compute the mass accommodation coefficient and residence time distribution. Throughout, we highlight the case of ozone adsorption in aqueous solutions and its dependence on electrolyte composition.

Perspective: Path Sampling Methods Applied to Enzymatic Catalysis

This Perspective reviews the use of Transition Path Sampling methods to study enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic reaction over 15 years ago, the method has uncovered basic principles in enzymatic catalysis such as the protein promoting vibration, and it has also helped harmonize such ideas as electrostatic preorganization with dynamic views of enzyme function. It is now being used to help uncover principles of protein design necessary to artificial enzyme creation.

Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids

Amide bond formation, the essential condensation reaction underlying peptide synthesis, is hindered in aqueous systems by the thermodynamic constraints associated with dehydration. This represents a key difficulty for the widely held view that prebiotic chemical evolution leading to the formation of the first biomolecules occurred in an oceanic environment. Recent evidence for the acceleration of chemical reactions at droplet interfaces led us to explore aqueous amino acid droplet chemistry. We report the formation of dipeptide isomer ions from free glycine or L-alanine at the air-water interface of aqueous microdroplets emanating from a single spray source (with or without applied potential) during their flight toward the inlet of a mass spectrometer. The proposed isomeric dipeptide ion is an oxazolidinone that takes fully covalent and ion-neutral complex forms. This structure is consistent with observed fragmentation patterns and its conversion to authentic dipeptide ions upon gentle collisions and for its formation from authentic dipeptides at ultra-low concentrations. It also rationalizes the results of droplet fusion experiments that show that the dipeptide isomer facilitates additional amide bond formation events, yielding authentic tri- through hexapeptides. We propose that the interface of aqueous microdroplets serves as a drying surface that shifts the equilibrium between free amino acids in favor of dehydration via stabilization of the dipeptide isomers. These findings offer a possible solution to the water paradox of biopolymer synthesis in prebiotic chemistry.