5-Amino-1,2,4-triazol-3-one Degradation by Indirect Photolysis: A Density Functional Theory Study.

Sunlight irradiation induces formation of reactive oxygen species (superoxide, hydroperoxyl radical, singlet oxygen, etc.), which readily take part in degradation of environmental pollutants. Being a primary ingredient in a suite of insensitive munition formulations, NTO (5-nitro-1,2,4-triazol-3-one) can be released onto training range soils and reduced to ATO (5-amino-1,2,4-triazol-3-one) by soil bacteria or iron-contained minerals. ATO can be dissolved in surface water and groundwater due to its good water solubility and then undergo further decomposition. A detailed investigation of possible mechanisms for ATO decomposition in water induced by superoxide, hydroperoxyl radical, and singlet oxygen as pathways for ATO environmental degradation was performed by computational study at the PCM(Pauling)/M06-2X/6-311++G(d,p) level. Hydrolysis and degradation of ATO induced by superoxide are unlikely to occur due to the high activation energy or endergonicity of the processes. The hydroperoxyl radical causes rapid and reversible hydrogen transfer from ATO, while an attachment of the hydroperoxyl radical to ATO can induce decomposition of ATO, leading to its mineralization. Singlet oxygen shows a higher reactivity toward ATO than the hydroperoxyl radical. Decomposition of ATO was found to be a multistep process that begins with singlet oxygen attachment to the carbon atom of the C═N double bond. The intermediate that is formed undergoes recyclization, cycle opening, and sequential elimination of nitrogen gas, ammonia, and carbon(IV) oxide. Isocyanic acid, which arises intermediately, hydrolyzes into ammonia and carbon(IV) oxide. Calculated activation energies and high exergonicity of the studied processes support the contribution of singlet oxygen and the hydroperoxyl radical to ATO degradation into low-weight inorganic compounds in the environment.

From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA.

In this computational study, we explore the folding of a particular sequence using various computational tools to produce two-dimensional structures, which are then transformed into three-dimensional structures. We then study the geometry, energetics and dynamics of these structures using full electron quantum-chemical and classical molecular dynamics calculations. Our study focuses on the SARS-CoV-2 RNA fragment GGaGGaGGuguugcaGG and its various structures, including a G-quadruplex and five different hairpins. We examine the impact of two types of counterions (K+ and Na+) and flanking nucleotides on their geometrical characteristics, relative stability and dynamic properties. Our results show that the G-quadruplex structure is the most stable among the constructed hairpins. We confirm its topological stability through molecular dynamics simulations. Furthermore, we observe that the nucleotide loop consisting of seven nucleotides is the most flexible part of the RNA fragment. Additionally, we find that RNA networks of intermolecular hydrogen bonds are highly sensitive to the surrounding environment. Our findings reveal the loss of 79 old hydrogen bonds and the formation of 91 new ones in the case when the G-quadruplex containing flanking nucleotides is additionally stabilized by Na+ counterions.

Environmental impact of PFAS: Filling data gaps using theoretical quantum chemistry and QSPR modeling.

Per- and polyfluorinated alkyl substances (PFAS), known for their widespread environmental presence and slow degradation, pose significant concerns. Of the approximately 10,000 known PFAS, only a few have undergone comprehensive testing, resulting in limited experimental data. In this study, we employed a combination of physics-based methods and data-driven models to address gaps in PFAS bioaccumulation potential. Using the COnductor-like Screening MOdel for Realistic Solvents (COSMO-RS) method, we predicted n-octanol/water partition coefficients (logKOW), crucial for PFAS bioaccumulation. Our developed Quantitative Structure-Property Relationship (QSPR) model exhibited high accuracy (R2 = 0.95, RMSEC = 0.75) and strong predictive ability (Q2LOO = 0.93, RMSECV = 0.83). Leveraging the extensive NORMAN, we predicted logKOW for over 4,000 compounds, identifying 244 outliers out of 4519. Further categorizing the database into eight Organisation for Economic Co-operation and Development (OECD) categories, we confirmed fluorine atoms role in enhanced bioaccumulation. Utilizing predicted logKOW, water solubility logSW, and vapor pressure logVP values, we calculated additional physicochemical properties that are responsible for the transport and dispersion of PFAS in the environment. Parameters such as Henry's Law (kH), air-water partition coefficient (KAW), octanol-air coefficient (KOA), and soil adsorption coefficient (KOC) exhibited favorable correlations with literature data (R2 > 0.66). Our study successfully filled data gaps, contributing to the understanding of ubiquitous PFAS in the environment and estimating missing physicochemical data for these compounds.