Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences

Unraveling the Transport Properties of RONS across Nitro-Oxidized Membranes

The potential of cold atmospheric plasma (CAP) in biomedical applications has received significant interest, due to its ability to generate reactive oxygen and nitrogen species (RONS). Upon exposure to living cells, CAP triggers alterations in various cellular components, such as the cell membrane. However, the permeation of RONS across nitrated and oxidized membranes remains understudied. To address this gap, we conducted molecular dynamics simulations, to investigate the permeation capabilities of RONS across modified cell membranes. This computational study investigated the translocation processes of less hydrophilic and hydrophilic RONS across the phospholipid bilayer (PLB), with various degrees of oxidation and nitration, and elucidated the impact of RONS on PLB permeability. The simulation results showed that less hydrophilic species, i.e., NO, NO₂, N₂O₄, and O₃, have a higher penetration ability through nitro-oxidized PLB compared to hydrophilic RONS, i.e., HNO₃, s-cis-HONO, s-trans-HONO, H₂O₂, HO₂, and OH. In particular, nitro-oxidation of PLB, induced by, e.g., cold atmospheric plasma, has minimal impact on the penetration of free energy barriers of less hydrophilic species, while it lowers these barriers for hydrophilic RONS, thereby enhancing their translocation across nitro-oxidized PLB. This research contributes to a better understanding of the translocation abilities of RONS in the field of plasma biomedical applications and highlights the need for further analysis of their role in intracellular signaling pathways.

Mechanistic Insight into Permeation of Plasma-Generated Species from Vacuum into Water Bulk

Due to their potential benefits, cold atmospheric plasmas (CAPs), as biotechnological tools, have been used for various purposes, especially in medical and agricultural applications. The main effect of CAP is associated with reactive oxygen and nitrogen species (RONS). In order to deliver these RONS to the target, direct or indirect treatment approaches have been employed. The indirect method is put into practice via plasma-activated water (PAW). Despite many studies being available in the field, the permeation mechanisms of RONS into water at the molecular level still remain elusive. Here, we performed molecular dynamics simulations to study the permeation of RONS from vacuum into the water interface and bulk. The calculated free energy profiles unravel the most favourable accumulation positions of RONS. Our results, therefore, provide fundamental insights into PAW and RONS chemistry to increase the efficiency of PAW in biological applications.

The Fate of Molecular Species in Water Layers in the Light of Power-Law Time-Dependent Diffusion Coefficient

In the present paper, we propose two methods for tracking molecular species in water layers via two approaches of the diffusion equation with a power-law time-dependent diffusion coefficient. The first approach shows the species densities and the growth of different species via numerical simulation. At the same time, the second approach is built on the fractional diffusion equation with a time-dependent diffusion coefficient in the sense of regularised Caputo fractional derivative. As an illustration, we present here the species densities profiles and track the normal and anomalous growth of five molecular species OH, H2O2, HO2, NO3-, and NO2- via the calculation of the mean square displacement using the two methods.

Free Energy Prediction of Ion-Induced Nucleation of Aqueous Aerosols

Ion-induced nucleation (IIN) is thought to be an important nucleation pathway of atmospheric aerosols. We present a combined polarizable molecular dynamics (MD) simulation and the classic ion-induced nucleation theory (IINT) approach to predict the free energy profiles of the ion-induced nucleation of aqueous aerosols in a qualitative or semiquantitative way. The dependence of both cluster structure and thermodynamic properties on cluster sizes and ion species is also systemically studied. It is confirmed the ions can significantly enhance the cluster stability, and thereby increase the nucleation rate. The ability of the common atmospheric ions to enhance the nucleation rate follows the order SO₄^2- > H₃O⁺ > NH₄⁺ > NO₃^-, coinciding with the order of their solvation free energies. Therefore, the solvation energy can be employed as a rough index for evaluating the INN ability. Overall, the consistency between the present predictions and previous experimental and theoretical observations demonstrates the combination of MD simulation and the IINT appears to be a promising approach for exploring the IIN process and understanding the microscopic mechanism of atmospheric-related ions.

Solubilities in aqueous nitrate solutions that appear to reverse the law of mass action

Non-ideal aqueous electrolyte solutions have been studied since the start of the application of thermodynamics to chemistry in the late 19th century. The present study examines some of the most extreme non-ideal behavior ever observed: solubilities of alkali and NH₄⁺ nitrate salts in water that appear to behave the opposite of how the Law of Mass Action would predict. A literature review discovered that the solubilities of NH₄NO₃ and many alkali nitrate salts increases when another nitrate-bearing electrolyte is added to solution. These occurrences were in concentrated solutions with insufficient water to provide all ions their preferred hydration number without sharing waters between ions. This water deficit results in the formation of contact ion-pairs as well as larger ion-clusters. These ion-clusters may be favored when there is more than one type of monovalent cation present.

Electrification of water interface

The surface charge of a water interface determines many fundamental processes in physical chemistry and interface science, and it has been intensively studied for over a hundred years. We summarize experimental methods to characterize the surface charge densities developed so far: electrokinetics, double-layer force measurements, potentiometric titration, surface-sensitive nonlinear spectroscopy, and surface-sensitive mass spectrometry. Then, we elucidate physical ion adsorption and chemical electrification as examples of electrification mechanisms. In the end, novel effects on surface electrification are discussed in detail. We believe that this clear overview of state of the art in a charged water interface will surely help the fundamental progress of physics and chemistry at interfaces in the future.

Hydroxide promotes ion pairing in the NaNO2-NaOH-H2O system

Nitrite (NO2-) is a prevalent nitrogen oxyanion in environmental and industrial processes, but its behavior in solution, including ion pair formation, is complex. This solution phase complexity impacts industries such as nuclear waste treatment, where NO2- significantly affects the solubility of other constituents present in sodium hydroxide (NaOH)-rich nuclear waste. This work provides molecular scale information into sodium nitrite (NaNO2) and NaOH ion-pairing processes to provide a physical basis for later development of thermodynamic models. Solubility isotherms of NaNO2 in aqueous mixtures with NaOH and total alkalinity were also measured. Spectroscopic characterization of these solutions utilized high-field nuclear magnetic resonance spectroscopy (NMR) and Raman spectroscopy, with additional solution structure detailed by X-ray total scattering pairwise distribution function analysis (X-ray PDF). Despite the NO2- deformation Raman band's insensitivity to added NaOH in saturated NaNO2 solutions, 23Na and 15N NMR studies indicated the Na+ and NO2- chemical environments change likely due to ion pairing. The ion pairing correlates with a decrease in diffusion coefficient of solution species as measured by pulsed field gradient 23Na and 1H NMR. Two-dimensional correlation analyses of the 2800-4000 cm-1 Raman region and X-ray PDF indicated that saturated NaNO2 and NaOH mixtures disrupt the hydrogen network of water into a new structure where the length of the OO correlations is contracted relative to the typical H2O structure. Beyond describing the solubility of NaNO2 in a multicomponent electrolyte mixture, these results also indicate that nitrite exhibits greater ion pairing in mixtures of concentrated NaNO2 and NaOH than in comparable solutions with only NaNO2.

Solvation Shell of the Nitrite Ion in Water: An Ab Initio Molecular Dynamics Study

We performed ab initio molecular dynamics simulation of a nitrite ion in water to investigate the structural and dynamical properties of its hydration shell. The nitrite ion is found to exhibit strong asymmetry toward hydrogen bonding due to its two different types of hydrogen bond acceptor sites. This difference is better captured through further partitioning of the hydration shell into its proximal and distal regions. The frequency shifts of the stretch modes of hydration shell water reveal that the nitrogen site forms a stronger hydrogen bond than its oxygen sites with the latter forming hydrogen bonds, which are similar in strength to that between a pair of water molecules. The escape dynamics of water from the hydration shell is found to be rather slow, which seems to classify the nitrite ion as a structure-maker. However, the dynamics of orientational and hydrogen bond relaxation reveal a faster mobility of water molecules in the hydration shell than bulk water in spite of strong ion-water interactions. It is found that the nitrite ion can hold water molecules in its solvation shell and still make them rotate fast in its vicinity through switching of their hydrogen bonds between its nitrogen and oxygen acceptor sites. The dipole moment of the solute in water is also calculated in the present study.