Characterization and reactivity of the weakly bound complexes of the [H, N, S](-) anionic system with astrophysical and biological implications

We investigate the lowest electronic states of doublet and quartet spin multiplicity states of HNS(-) and HSN(-) together with their parent neutral triatomic molecules. Computations were performed using highly accurate ab initio methods with a large basis set. One-dimensional cuts of the full-dimensional potential energy surfaces (PESs) along the interatomic distances and bending angle are presented for each isomer. Results show that the ground anionic states are stable with respect to the electron detachment process and that the long range parts of the PESs correlating to the SH(-) + N, SN(-) + H, SN + H(-), NH + S(-), and NH(-) + S are bound. In addition, we predict the existence of long-lived weakly bound anionic complexes that can be formed after cold collisions between SN(-) and H or SH(-) and N. The implications for the reactivity of these species are discussed; specifically, it is shown that the reactions involving SH(-), SN(-), and NH(-) lead either to the formation of HNS(-) or HSN(-) in their electronic ground states or to autodetachment processes. Thus, providing an explanation for why the anions, SH(-), SN(-), and NH(-), have limiting detectability in astrophysical media despite the observation of their corresponding neutral species. In a biological context, we suggest that HSN(-) and HNS(-) should be incorporated into H2S-assisted heme-catalyzed reduction mechanism of nitrites in vivo.

Ab initio study of the reaction of ozone with bromide ion

Surface level ozone destruction in polar environments may be initiated by oxidation of bromide ions by ozone, ultimately leading to Br2 production. Ab initio calculations are used to support the development of atmospheric chemistry models, but errors can occur in study of the bromide-ozone reaction due to inappropriate treatment of the many-electron species and the ionic nature of the reaction. In this work, a high level ab initio study is used to take into account the electronic correlation and the polarization effects. Our results show three possible pathways for the reaction. In particular, we find that this process, though endothermic on the singlet spin state surface, can be energetically feasible on the triplet surface. The triplet surface can be reached through photoexcitation of ozone or by the spin crossing of the potential energy surface. Because this process is known to occur in the dark, it may be that it occurs after intersystem crossing to a triplet surface. This paper also provides a starting point calibration for any future ab initio calculation studies of the bromide-ozone reaction, from the gas to the condensed phase.

Theoretical spectroscopic investigations of HNS(q) and HSN(q) (q = 0, +1, -1) in the gas phase

We performed accurate ab initio investigations of the geometric parameters and the vibrational structure of neutral HNS/HSN triatomics and their singly charged anions and cations. We used standard and explicitly correlated coupled cluster approaches in connection with large basis sets. At the highest levels of description, we show that results nicely approach those obtained at the complete basis set limit. Moreover, we generated the three-dimensional potential energy surfaces (3D PESs) for these molecular entities at the coupled cluster level with singles and doubles and a perturbative treatment of triple excitations, along with a basis set of augmented quintuple-zeta quality (aug-cc-pV5Z). A full set of spectroscopic constants are deduced from these potentials by applying perturbation theory. In addition, these 3D PESs are incorporated into variational treatment of the nuclear motions. The pattern of the lowest vibrational levels and corresponding wavefunctions, up to around 4000 cm(-1) above the corresponding potential energy minimum, is presented for the first time.

Interconnection of reactive oxygen species chemistry across the interfaces of atmospheric, environmental, and biological processes

Oxidation reactions are ubiquitous and play key roles in the chemistry of the atmosphere, in water treatment processes, and in aerobic organisms. Ozone (O3), hydrogen peroxide (H2O2), hydrogen polyoxides (H2Ox, x > 2), associated hydroxyl and hydroperoxyl radicals (HOx = OH and HO2), and superoxide and ozonide anions (O2(-) and O3(-), respectively) are the primary oxidants in these systems. They are commonly classified as reactive oxygen species (ROS). Atmospheric chemistry is driven by a complex system of chain reactions of species, including nitrogen oxides, hydroxyl and hydroperoxide radicals, alkoxy and peroxy radicals, and ozone. HOx radicals contribute to keeping air clean, but in polluted areas, the ozone concentration increases and creates a negative impact on plants and animals. Indeed, ozone concentration is used to assess air quality worldwide. Clouds have a direct effect on the chemical composition of the atmosphere. On one hand, cloud droplets absorb many trace atmospheric gases, which can be scavenged by rain and fog. On the other hand, ionic species can form in this medium, which makes the chemistry of the atmosphere richer and more complex. Furthermore, recent studies have suggested that air-cloud interfaces might have a significant impact on the overall chemistry of the troposphere. Despite the large differences in molecular composition, concentration, and thermodynamic conditions among atmospheric, environmental, and biological systems, the underlying chemistry involving ROS has many similarities. In this Account, we examine ROS and discuss the chemical characteristics common to all of these systems. In water treatment, ROS are key components of an important subset of advanced oxidation processes. Ozonation, peroxone chemistry, and Fenton reactions play important roles in generating sufficient amounts of hydroxyl radicals to purify wastewater. Biochemical processes within living organisms also involve ROS. These species can come from pollutants in the environment, but they can also originate endogenously, initiated by electron reduction of molecular oxygen. These molecules have important biological signaling activities, but they cause oxidative stress when dysfunction within the antioxidant system occurs. Excess ROS in living organisms can lead to problems, such as protein oxidation-through either cleavage of the polypeptide chain or modification of amino acid side chains-and lipid oxidation.

Probing the radical and base dual properties of peptide sulfinyl radicals via mass spectrometry

Heteroatom-centered radicals are known to play critical roles in atmospheric chemistry, organic synthesis, and biology. While most studies have focused on the radical reactivity such as hydrogen abstraction, the base properties of heteroatom-centered radicals have long been overlooked, despite the profound consequences, such as their ability to participate in hydrogen-bonding networks. In this study, we use the sulfinyl radical (-SO(•)) as a model to show that the dual properties of heteroatom-centered radicals, that is, their ability to function as a radical and a base, can coexist in peptides and be differentiated by examining the loss of hydrosulfinyl radical (SOH) upon unimolecular dissociation of the peptide sulfinyl radical ions in the gas phase. The loss of SOH can result from two channels; one involves hydrogen atom abstraction, which reflects the radical property; the other is initiated by proton transfer to the sulfinyl radical, manifesting its base property. Tuning of the two properties of peptide sulfinyl radicals can be achieved by varying the chemical properties of the neighboring functional groups, which demonstrates the influence of the local chemical environment on the behavior of the radical species. The experimental approach established in this study to probe the dual chemical property of the peptide sulfinyl radical can be potentially applied to studying other types of heteroatom-centered radical species of biological significance.

Hydroxyalkoxy radicals: importance of intramolecular hydrogen bonding on chain branching reactions in the combustion and atmospheric decomposition of hydrocarbons

During both the atmospheric oxidation and combustion of volatile organic compounds, sequential addition of oxygen can lead to compounds that contain multiple hydrogen-bonding sites. The presence of two or more of these sites on a hydrocarbon introduces the possibility of intramolecular H-bonding, which can have a stabilizing effect on the reactants, products, and transition states of subsequent reactions. The present work compares the absolute energies of two sets of conformations, those that contain intramolecular H-bonds and those that lack intramolecular H-bonds, for each reactant, product, and transition state species in the 1,2 through 1,7 H-migrations and Cα-Cβ, Cα-H, and Cα-OH-bond scission reactions in the n-hydroxyeth-1-oxy through n-hydroxyhex-1-oxy radicals, for n ranging from 1 to 6. The difference in energy between the two conformations represents the balance between the stabilizing effects of H-bonds and the steric cost of bringing the two H-bonding sites together. The effect of intramolecular H-bonding and the OH group is assessed by comparing the net intramolecular H-bond stabilization energies, the reaction enthalpies, and barrier heights of the n-hydroxyalkoxy radical reactions with the corresponding alkoxy radicals values. The results suggest that there is a complex dependence on the location of the two H-bonding groups, the location of the abstraction or bond scission, and the shape of the transition state that dictates the extent to which intramolecular H-bonding effects the relative importance of H-migration and bond scission reactions for each n-hydroxyalkoxy radical. These findings have important implications for future studies on hydrocarbons with multiple H-bonding sites.

Spontaneous formation of one-dimensional hydrogen gas hydrate in carbon nanotubes

We present molecular dynamics simulation evidence of spontaneous formation of quasi-one-dimensional (Q1D) hydrogen gas hydrates within single-walled carbon nanotubes (SW-CNTs) of nanometer-sized diameter (1-1.3 nm) near ambient temperature. Contrary to conventional 3D gas hydrates in which the guest molecules are typically contained in individual and isolated cages in the host lattice, the guest H2 molecules in the Q1D gas hydrates are contained within a 1D nanochannel in which the H2 molecules form a molecule wire. In particular, we show that in the (15,0) zigzag SW-CNT, the hexagonal H2 hydrate tends to form, with one H2 molecule per hexagonal prism, while in the (16,0) zigzag SW-CNT, the heptagonal H2 hydrate tends to form, with one H2 molecule per heptagonal prism. In contrast, in the (17,0) zigzag SW-CNT, the octagonal H2 hydrate can form, with either one H2 or two H2 molecules per pentagonal prism (single or double occupancy). Interestingly, in the hexagonal or heptagonal ice nanotube, the H2 wire is solid-like as the axial diffusion constant is very low (<5 × 10(-10) cm(2)/s), whereas in the octagonal ice nanotube, the H2 wire is liquid-like as its axial diffusion constant is comparable to 10(-5) cm(2)/s.

A mass spectrometric approach for probing the stability of bioorganic radicals

Glycyl radicals are important bioorganic radical species involved in enzymatic catalysis. Herein, we demonstrate that the stability of glycyl-type radicals (X-(.) CH-Y) can be tuned on a molecular level by varying the X and Y substituents and experimentally probed by mass spectrometry. This approach is based on the gas-phase dissociation of cysteine sulfinyl radical (X-Cys SO .-Y) ions through homolysis of a Cα Cβ bond. This fragmentation produces a glycyl-type radical upon losing CH2 SO, and the degree of this loss is closely tied to the stability of the as-formed radical. Theoretical calculations indicate that the energy of the Cα Cβ bond homolysis is predominantly affected by the stability of the glycyl radical product through the captodative effect, rather than that of the parent sulfinyl radical. This finding suggests a novel experimental method to probe the stability of bioorganic radicals, which can potentially broaden our understanding of these important reactive intermediates.