1,2‑H Atom Rearrangements in Benzyloxyl Radicals

The rate constants for solvent-assisted 1,2-H atom rearrangements in para-substituted benzyloxyl radicals were studied with density functional theory. The rate of the radical rearrangement, calculated through transition state theory with Eckhart tunneling corrections, was shown to be drastically impacted by the presence of both implicit and explicit solvent molecules, with a quantitative agreement with laser flash photolysis studies for a variety of electron-donating and -withdrawing substituents. The rate of rearrangement was found to be correlated to the distance between the rearranging hydrogen atom and the α-carbon in the transition state, which could be modified through the para substituent and the type of assisting solvent molecule (e.g., water, ethanol, methanol, acetic acid, or a mixture of the latter). Natural bond orbital analysis showed that the rearrangement does not proceed through a hydrogen radical but through a quasi-proton exchange and charge transfer between the benzyl carbon and the adjacent oxygen atom. Energetic and spin population results indicated that electron-withdrawing groups induce faster rearrangement kinetics. Understanding 1,2-H atom shifts in benzyloxyl radicals are essential for tuning the rate of superoxide production in aqueous systems, as the resonance-stabilized carbon radical produced from the rearrangement can bind oxygen and decompose to produce superoxide radical anion, an important reactive intermediate in environmental and biological systems

Early Events in the Reductive Dehalogenation of Linear Perfluoroalkyl Substances

This work details the early events in the reductive defluorination of perfluoroalkyl substances (PFASs) and presents a straightforward methodology for predicting the reduction behavior of the perfluoroalkyl acids (PFAAs) using electronic structure calculations. Electron attachment to linear perfluorocarboxylic acids generally occurs at the α-carbon and is energetically not correlated to chain length, contrary to the case for linear perfluoroalkanesulfonates, where electrons generally insert into other positions. Perfluorooctanesulfonate and perfluorooctanoic acid, two widely studied and scrutinized PFAAs, are therefore predicted to be reduced through diverging pathways. Our protocol can predict the standard reduction potentials of PFAAs, provides a rational basis for probing reaction intermediates, establishes free energy relationships, and accounts for PFASs’ inherent structural diversity beyond the linear substrates

A Computational Study of the Ground and Excited State Structure and Absorption Spectra of Free-Base N-Confused Porphine and Free-Base N-Confused Tetraphenylporphyrin

Computational investigations into the ground and singlet excited-state structures and the experimental ground-state absorption spectra of N-confused tetraphenylporphyrin tautomers 1e and 1i and N-confused porphines (NCP) 2e and 2i have been performed. Structural data for the ground state, performed at the B3LYP/6-31G(d), B3LYP/6-31+G(d)//B3LYP/6-31G(d), and B3LYP/6-311+G(d)//B3LYP/6-31G(d) levels, are consistent with those performed at lower levels of theory. Calculations of the gas-phase, ground-state absorption spectrum are qualitatively consistent with condensed phase experiments for predicting the relative intensities of the Q(0,0) and Soret bands. Inclusion of implicit solvation in the calculations substantially improves the correlation of the energy of the Soret band with experiment for both tautomers (1e, 435 nm predicted, 442 nm observed in DMAc; 1i, 435 nm predicted, 437 nm observed in CH2Cl2). The x- and y-polarized Q-band transitions were qualitatively reproduced for 1e in both the gas phase and with solvation, although the low-energy absorption band in 1i was predicted at substantially higher energy (646 nm in the gas phase and 655 nm with solvation) than observed experimentally (724 nm in CH2Cl2). Franck−Condon state and equilibrated singlet excited-state geometries were calculated for unsubstituted NCP tautomers 2e and 2i at the TD-B3LYP/SVP and TD-B3LYP/TZVP//TD-B3LYP/SVP levels. Electronic difference density plots were calculated from these geometries, thereby indicating the change of electron density in the singlet excited states. Adiabatic S1 and S2 geometries of these compounds were also calculated at the TD-B3LYP/SVP level, and the results indicate that while 2i is a more stable ground-state molecule by ∼7.0 kcal mol−1, the energy difference for the S1 excited states is only ∼1.0 kcal mol−1 and is 6.1 kcal mol−1 for the S2 excited states

Dynamic and Solvation Behaviors of ALSEP Organic Ligands

The Actinide-Lanthanide Separation Process (ALSEP) is a solvent extraction approach for separating relevant trivalent minor actinides (e.g., americium and curium) from used nuclear fuel. However, relatively slow kinetics in the stripping step of the process restricts process throughput when scaled for industrial implementation. To assist in identifying specific kinetic barriers associated with the separation, the solvation and dynamic behaviors of the two organic extractants in the current ALSEP implementation, N,N,N′,N′-tetra­(2-ethylhexyl)­diglycolamide (T2EHDGA) and 2-ethylhexylphosphonic acid mono-2-ethylhexyl ester (HEHEHP), were probed through molecular dynamics (MD) simulations. The simulations examined the effects of extractant and nitric acid concentration on the interfacial behavior of the extractants in three solvent systems (n-dodecane, water, and n-dodecane + water). Solvation analyses of T2EHDGA revealed expected amphiphilic behavior in pure solvent systems. In a nitric-acid-free biphasic solvent, it was found that T2EHDGA expressed similar interfacial conformations as HEHEHP, suggesting that a parallel-like configuration, relative to the interface, is adopted at low concentrations. When HNO3 was introduced to biphasic systems containing a single molecule of extractant, HEHEHP was observed to retain a relatively parallel orientation while the T2EHDGA orientation was no longer affected by the presence of the interface. At bulk extractant concentrations, representative of the ALSEP process, the presence of nitric acid had minimal impact on the ligand orientation. Calculated diffusion constants showed that only some systems involving T2EHDGA were affected by the presence of acid

A charge-modified general amber force field for phospholipids: improved structural properties in the tensionless ensemble

<div><p>Accurately predicting the structural properties of phospholipid with a fully atomistic molecular model is critical for the study of pure phospholipid bilayers, mixed bilayer systems and bilayers containing proteins. The general amber force field (GAFF) has traditionally required the presence of a surface tension parameter to correctly model phospholipid bilayer properties such as area per lipid and order parameters. In this work, the GAFF partial charges for 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphate (POPA), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphochiline (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) were re-parameterised utilising high-level ab initio calculations and the restrained electrostatic potential method. Simulations of pure POPA, POPC and POPG bilayers using the charge-modified GAFF and no applied surface tension are compared with available experimental data, the original GAFF model and the recent Lipid14 variant. The results indicate a significant improvement in the accuracy of the lipid model for reproducing experimental observables without the need for a surface tension parameter. The successful application of modifying the lipid charge distributions represents an alternative to the use of a surface tension parameter within GAFF, and highlights the importance of the partial charge calculations when modelling lipid bilayers.</p></div

Kinetic Model for Predicting Perfluoroalkyl Acid Degradation During UV-Sulfite Treatment

Hydrated electron (eaq–) treatment processes show great potential in remediating recalcitrant water contaminants, including perfluoroalkyl and polyfluoroalkyl substances (PFAS). However, treatment efficacy depends upon many factors relating to source water composition, UV light source characteristics, and contaminant reactivity. Here, we provide critical insights into the complex roles of solution parameters on contaminant abatement through application of a UV-sulfite kinetic model that incorporates first-principles information on eaq– photogeneration and reactivity. The model accurately predicts decay profiles of short-chain perfluoroalkyl acids (PFAAs) during UV-sulfite treatment and facilitates quantitative interpretation of the effects of changing solution composition on PFAS degradation rates. Model results also confirm that the enhanced degradation of PFAAs observed under highly alkaline pH conditions results from changes in speciation of nontarget eaq– scavengers. Reverse application of the model to UV-sulfite data collected for longer chain PFAAs enabled estimation of bimolecular rate constants (k2, M–1 s–1), providing an alternative to laser flash photolysis (LFP) measurements that are not feasible due to the water solubility limitations of these compounds. The proposed model links the disparate means of investigating eaq– processes, namely, UV photolysis and LFP, and provides a framework to estimate UV-sulfite treatment efficacy of PFAS in diverse water sources

Role of Explicit Hydration in Predicting the Aqueous Standard Reduction Potential of Sulfate Radical Anion by DFT and Insight into the Influence of pH on the Reduction Potential

Sulfate radical anion (SO4•–) is a potent oxidant capable of destroying recalcitrant environmental contaminants such as perfluoroalkyl carboxylic acids. In addition, it is thought to participate in important atmospheric reactions. Its standard reduction potential (E°) is fundamental to its reactivity. Using theoretical methods to accurately predict the aqueous phase E° requires solvation with explicit water molecules. Herein, using density functional theory, we calculated the aqueous E° of SO4•– and evaluated sensitivity to explicit water count. The E° increased considerably with more waters until ca. 24 were included, after which change in E° was small. When a proton was added to these systems, the E° was similar regardless of the explicit water count and this value was similar to the E° for systems with a large number of explicit waters but no proton. This result agrees with literature evidence that the E° is pH independent. Natural Bond Orbital natural population analysis indicated that in the case of both SO42– and SO4•–, considerable charge was donated from the SO4 center to the explicit solvation shells

Periodic Trends behind the Stability of Metal Catalysts Supported on Graphene with Graphitic Nitrogen Defects

This study explored the fundamental chemical intricacies behind the interactions between metal catalysts and carbon supports with graphitic nitrogen defects. These interactions were probed by examining metal adsorption, specifically, the location of adsorption and the electronic structure of metal catalysts as the basis for the metal–support interactions (MSIs). A computational framework was developed, and a series of 12 transition metals was systematically studied over various graphene models with graphitic nitrogen defect(s). Different modeling approaches served to provide insights into previous MSI computational discrepancies, reviewing both truncated and periodic graphene models. The computational treatment affected the magnitudes of adsorption energies between the metals and support; however, metals generally followed the same trends in their MSI. It was found that the addition of the nitrogen dopant improved the MSI by promoting electronic rearrangement from the metals’ d- to s-orbitals for greater orbital overlap with the carbon support, shown with increased favorable adsorption. Furthermore, the study observed periodic trends that were adept descriptors of the MSI fundamental chemistries

Understanding Fragmentation of Organic Small Molecules in Atom Probe Tomography

In atom probe tomography of molecular organic materials, field ionization of either entire molecules or molecular fragments can occur, but the mechanism governing this behavior was not previously understood. This work explains when a doubly ionized small molecule organic material is expected to undergo fragmentation. We find that multiple detection events arising from post-ionization fragmentation of a parent molecular dication into two daughter ions is well explained by the free energy and geometries of the molecules computed using density functional theory. Of the systems studied, exergonic free energies for formation of the daughter ions, smaller activation energies for dissociation, and increases in bond length are all found to be quantitative predictors for ion fragmentation. This work expands the applicability of atom probe tomography to organic materials by increasing the fundamental understanding of processes occurring during this analysis technique

An Ab Initio Study of the Ground and Excited State Chemistry of Phenyldiazirine and Phenyldiazomethane

Phenyldiazirine and phenyldiazomethane were studied at the B3LYP/6-31+G(d) and RI-CC2/TZVP levels of theory, and the three lowest singlet excited states of both compounds were optimized at the RI-CC2/TZVP level. The calculations predict that the S1 state of phenyldiazirine is a σ → π* state, with a quinoidal structure, and the C−N bonds of the diazirine group are slightly deformed from the Cs symmetry of the ground state’s geometry. Both the S2 and S3 states are predicted to be π → π* states localized primarily on the phenyl group. The S1 state was predicted to have an exceedingly large dipole moment with a strong and distinct aromatic CC vibrational mode around ∼1600 cm−1, which is not present in any of the other electronic states examined in this study. The calculations are consistent with the assignment of the S1 state of phenyldiazirine to the polar intermediate recently observed by ultrafast time-resolved UV−vis and IR spectroscopic studies of arylhalo- and arylalkyldiazirines. The excited states of phenyldiazomethane were also studied, and the implications of interconversion between phenyldiazirine and phenyldiazomethane are discussed. The calculations predict that the chemistry of the ground state and the S1 excited state of phenyldiazirine are very different. Formation of phenylcarbene is favored on the ground state surface of phenyldiazirine, whereas the S1 excited state favors isomerization to the first excited state of phenyldiazomethane, which rapidly extrudes nitrogen and forms carbene