ArcaNN: automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials.

The emergence of artificial intelligence is profoundly impacting computational chemistry, particularly through machine-learning interatomic potentials (MLIPs). Unlike traditional potential energy surface representations, MLIPs overcome the conventional computational scaling limitations by offering an effective combination of accuracy and efficiency for calculating atomic energies and forces to be used in molecular simulations. These MLIPs have significantly enhanced molecular simulations across various applications, including large-scale simulations of materials, interfaces, chemical reactions, and beyond.

Prebiotic chemical reactivity in solution with quantum accuracy and microsecond sampling using neural network potentials.

While RNA appears as a good candidate for the first autocatalytic systems preceding the emergence of modern life, the synthesis of RNA oligonucleotides without enzymes remains challenging. Because the uncatalyzed reaction is extremely slow, experimental studies bring limited and indirect information on the reaction mechanism, the nature of which remains debated. Here, we develop neural network potentials (NNPs) to study the phosphoester bond formation in water.

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling.

The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges.

Adsorption Studies at the Graphene Oxide-Liquid Interface: A Molecular Dynamics Study.

The adsorption of organic aromatic molecules, namely aniline, onto graphene oxide is investigated using molecular simulations. The effect of the oxidation level of the graphene oxide sheet as well as the presence of two different halide salts, sodium chloride and sodium iodide, were examined. The aniline molecule in the more-reduced graphene oxide case, in the absence of added salt, showed a slightly greater affinity for the graphene oxide-water interface as compared to the oxidized form.

Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations.

Electrostatic interactions play a significant role in regulating biological systems and have received increasing attention due to their usefulness in designing advanced stimulus-responsive materials. Polypeptoids are highly tunable N-substituted peptidomimetic polymers that lack backbone hydrogen bonding and chirality. Therefore, polypeptoids are suitable systems to study the effect of noncovalent interactions of substituents without complications of backbone intramolecular and intermolecular hydrogen bonding.

Acids at the Edge: Why Nitric and Formic Acid Dissociations at Air-Water Interfaces Depend on Depth and on Interface Specific Area.

Whether the air-water interface decreases or increases the acidity of simple organic and inorganic acids compared to the bulk is critically important in a broad range of environmental and biochemical processes. However, a consensus has not yet been achieved on this key question. Here we use machine learning-based reactive molecular dynamics simulations to study the dissociation of paradigmatic nitric and formic acids at the air-water interface.

A bio-inspired heterodinuclear hydrogenase CoFe complex.

Herein, a new heterobimetallic CoFe complex is reported with the aim of comparing its performance in terms of H production within a series of related MFe complexes (M = Ni, Fe). The fully oxidized [(L)Co(CO)FeCp] complex (CoIIFeII, L = 2,2'-(2,2'-bipyridine-6,6'-diyl)bis(1,1'-diphenylethanethiolate), Cp = cyclopentadienyl anion) can be (electro)chemically reduced to its CoIFeII form, and both complexes have been isolated and fully characterized by means of classic spectroscopic techniques and theoretical calculations. The redox properties of CoIIFeII have been investigated in DMF, revealing that this complex is the easiest to reduce by one-electron among the analogous MFe complexes (M = Ni, Fe, Co).

Reactive events at the graphene oxide-water interface.

Graphene oxide exhibits interesting reactive events at its interface with water, with water as an active participant. The reactive events are influenced by the level of oxidation of the graphene oxide sheet. The fully oxidized sheet tends to make the interfacial water media acidic leaving the sheet negatively charged, whereas the reduced sheet can form comparatively long lived carbocations as well as split water forming two alcohol groups on the sheet.

Effect of anion identity on ion association and dynamics of sodium ions in non-aqueous glyme based electrolytes-OTf vs TFSI.

Sodium-based rechargeable battery technologies are being pursued as an alternative to lithium, in part due to the relative abundance of sodium compared to lithium. Despite their low dielectric constant, glyme-based electrolytes are particularly attractive for these sodium-based batteries due to their ability to chelate with the sodium ion and their high electrochemical stability. While the glyme chain length is a parameter that can be tuned to modify solvation properties, charge transport behavior, reactivity, and ultimately battery performance, anion identity provides another tunable variable.

Effect of Oxidation Level on the Interfacial Water at the Graphene Oxide-Water Interface: From Spectroscopic Signatures to Hydrogen-Bonding Environment.

The interfacial region of the graphene oxide (GO)-water system is nonhomogenous due to the presence of two distinct domains: an oxygen-rich surface and a graphene-like region. The experimental vibrational sum-frequency generation (vSFG) spectra are distinctly different for the fully oxidized GO-water interface as compared to the reduced GO-water case. Computational investigations using ab initio molecular dynamics were performed to determine the molecular origins of the different spectroscopic features.

Ion Pairing in HCl-Water Clusters: From Electronic Structure Investigations to Multiconfigurational Force-Field Development.

In the bulk, condensed-phase HCl exists as a dissociated Cl ion and a proton that is delocalized over solvating water molecules. However, in the gas phase, HCl is covalent, and even on the introduction of hydrating water molecules, the HCl covalent state dominates small clusters and is relevant at larger clusters including 21 water molecules. Electronic structure calculations (at the MP2 level) and ab initio metadynamics simulations (at the DFT level) have been carried out on HCl-(HO) clusters with = 2-22 to investigate distinct solvation environments in clusters from covalent HCl structure, to contact ion pairs and solvent-separated ion pairs.

Interfacial Water at Graphene Oxide Surface: Ordered or Disordered?

The graphene oxide (GO)-water interface was simulated using Born-Oppenheimer molecular dynamics (BOMD) simulations with two different functionals, namely, revPBE-D3 and BLYP-D2, as well as a commonly used classical force field, namely, OPLS-AA. A number of different order parameters, including the orientation of the interfacial water molecules near the aromatic region of the GO surface as well as those near the oxygenated defects, were examined and compared. The BOMD interfacial waters are clearly much less structured as compared to the classical force field that shows a strongly ordered interface.

Effect of Monoelectronic Oxidation of an Unsymmetrical Phenoxido-Hydroxido Bridged Dicopper(II) Complex.

A (μ-hydroxido, μ-phenoxido)CuCu complex 1 has been synthesized using an unsymmetrical ligand bearing an N, N-bis(2-pyridyl)methylamine (BPA) moiety coordinating one copper and a dianionic bis-amide moiety coordinating the other copper(II) ion. Electrochemical mono-oxidation of the complex in DMF occurs reversibly at 213 K at E = 0.12 V vs Fc/Fc through a metal-centered process.

Influence of Asymmetry on the Redox Properties of Phenoxo- and Hydroxo-Bridged Dicopper Complexes: Spectroelectrochemical and Theoretical Studies.

The redox properties and electronic structures of a series of phenoxo- and hydroxo-bridged dicopper(II) complexes have been explored. Complexes (1a-c) are based on symmetrical ligands with bis(2-methylpyridyl)aminomethyl as complexing arms bearing different substituting R groups (CH, OCH, or CF) in the para position of the phenol moiety. Complex 2a is based on a symmetrical ligand with bis(2-ethylpyridyl)aminomethyl arms and R = CH, while complex 3a involves an unsymmetrical ligand with two different complexing arms (namely bis(2-ethylpyridyl)aminomethyl and bis(2-methylpyridyl)aminomethyl).

Iron Hydroperoxide Intermediate in Superoxide Reductase: Protonation or Dissociation First? MM Dynamics and QM/MM Metadynamics Study.

Superoxide reductase is a mononuclear iron enzyme involved in superoxide radical detoxification in some bacteria. Its catalytic mechanism is associated with the remarkable formation of a ferric hydroperoxide Fe-OOH intermediate, which is specifically protonated on its proximal oxygen to generate the reaction product HO. Here, we present a computational study of the protonation mechanism of the Fe-OOH intermediate, at different levels of theory.

Room-Temperature Characterization of a Mixed-Valent μ-Hydroxodicopper(II,III) Complex.

Bis(μ-hydroxo)dicopper(II,II) bearing a naphthyridine-based ligand has been synthesized and characterized in the solid state and solution. Cyclic voltammetry at room temperature displays a reversible redox system that corresponds to the monoelectronic oxidation of the complex. Spectroscopic and time-resolved spectroelectrochemical data coupled to theoretical results support the formation of a charge-localized mixed-valent Cu(II,III)2 species.

Rethinking tenure in dental education.

In the midst of changes in the environment of academic dentistry over the past two decades, reform of traditional tenure is one way for dental schools to respond to these changes while maintaining scholarly, evidence-based learning environments. Challenges facing academic dentistry today and in the future include a crisis in workforce capacity, difficulty attracting recent graduates into academic positions, overburdened faculty members with limited time for scholarly activity, loss of tenured faculty members due to retirement, and a potentially diminished voice for dental schools within the parent university. The purpose of this opinion article is to suggest ways to reform the current tenure system in dental education as a means of improving recruitment and retention of new faculty members while maintaining or increasing scholarly activity within dental schools.