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.

Degradation of NTO induced by superoxide and hydroperoxyl radicals: a comprehensive DFT study.

Reactive oxygen species, produced in the aquatic environment under sunlight irradiation, actively take part in degradation of environmental pollutants. NTO (5-nitro-1,2,4-triazol-3-one), being a primary ingredient in a suite of insensitive munitions formulations, may be released into training range soils after incomplete detonations and dissolved in surface water and groundwater due to good water solubility. A detailed investigation of a possible mechanism for NTO decomposition in water induced by superoxide and hydroperoxyl radicals as one of the pathways for NTO environmental degradation was performed with a computational study at the PCM(Pauling)/M06-2X/6-311++G(d,p) level. Superoxide causes rapid deprotonation of NTO. Decomposition of NTO induced by hydroperoxyl radicals was found to be a multistep process leading to mineralization of the nitrocompound. The reaction process may begin with hydroperoxyl radical attachment to carbon atom of the CN double bond of NTO, then proceeds through rupture of C-N bonds and addition of water molecules leading to the formation of nitrous acid, ammonia, nitrogen gas, hydrazine, and carbon(IV) oxide. The obtained results indicate that the anionic form of NTO shows a higher reactivity towards hydroperoxyl radicals than its neutral form. Excitation of NTO by sunlight enables complete mineralization of NTO induced by superoxide. The calculated activation energies and exergonicity of the studied processes support the contribution of hydroperoxyl radicals and superoxide to the degradation of NTO in the environment into low-weight inorganic compounds.

Role of Hydroxyl Radical in Degradation of NTO: DFT Study.

Hydroxyl radicals are important reactive oxygen species produced in the aquatic environment under sunlight irradiation. Many organic pollutants may be decomposed as they encounter hydroxyl radicals, due to their high oxidative ability. NTO (5-nitro-1,2,4-triazol-3-one), an energetic material used in military applications, may be released to the environment and dissolved in surface water and groundwater due to its good water solubility. A detailed investigation of the possible mechanism for NTO decomposition in water induced by hydroxyl radical as one of the pathways for NTO environmental degradation was performed by computational study at the PCM/M06-2X/6-311++G(d,p) level. Decomposition of NTO was found to be a multistep process that may begin with an addition of hydroxyl radical to the carbon atom of C═N double bond and consequent release of a nitrite radical. The formed intermediate undergoes a series of chemical transformations that include the attachments of hydroxyl radical to carbon atoms, the transfer of hydrogen to hydroxyl radical, isomerization, and bond cleavage, leading to low-weight inorganic compounds, such as ammonia, nitrogen gas, nitrous acid, nitric acid, and carbon(IV) oxide. The anionic form of NTO is more reactive toward interaction with the hydroxyl radical as compared with its neutral form. Calculated activation energies and high exergonicity of the studied process support the significant contribution of the hydroxyl radical to NTO mineralization in environment.

Expanding the applicability domain of QSPRs for predicting water solubility and vapor pressure of PFAS.

This work aimed to verify whether it is possible to extend the applicability domain (AD) of existing QSPR (Quantitative Structure-Property Relationship) models by employing a strategy involving additional quantum-chemical calculations. We selected two published QSPR models: for water solubility, logSW, and vapor pressure, logVP of PFAS as case studies. We aimed to enlarge set of compounds used to build the model by applying factorial planning to plan the augmentation of the set of these compounds based on their structural features (descriptors). Next, we used the COSMO-RS model to calculate the logSW and logVP for selected chemicals. This allowed filling gaps in the experimental data for further training QSPR models. We improved the published models by significantly extending number of compounds for which theoretical predictions are reliable (i.e., extending the AD). Additionally, we performed external validation that had not been carried out in original models. To test effectiveness of the AD extension, we screened 4519 PFAS from NORMAN Database. The number of compounds outside the domain was reduced comparing the original model for both properties. Our work shows that combining physics-based methods with data-driven models can significantly improve the performance of predictions of phys-chem properties relevant for the chemical risk assessment.

The structure of DNA fragments: Quantum-chemical modelling.

In this review, we analyze and systematize our computational studies of the nucleic acid duplex formations and thermodynamic stability under the different factors of investigation. The proposed structural models of mini-helix contains N nucleobase pairs (N = 3-5); QM structural data suggest that the helical conformations of mini-helix adopt geometrical parameters comparable to those of natural A- and B-DNA forms under specific conditions as micro hydration and charge compensation. The gas-phase models adopt non regular conformations between the helical form and a ladder form.. The natural helical shape of DNA mini-helix is stabilized by the presence of counterions or by explicit micro-hydration of the major and minor groves. The presence of aqueous solution is shown as a minor factor for the helical shape formation. The studies are performed at the level of density functional theory.

Role of Molecular Singlet Oxygen in Photochemical Degradation of NTO: DFT Study.

NTO (5-nitro-1,2,4-triazol-3-one), an energetic material used in military applications, may be released to the environment and dissolved in surface water and groundwater due to its good water solubility. Singlet oxygen is an important reactive oxygen species produced in the aquatic environment under sunlight irradiation. A detailed investigation of the possible mechanism for NTO decomposition in water induced by singlet oxygen as one of the pathways for NTO environmental degradation was performed by a computational study at PCM(Pauling)/M06-2X/6-311++G(d,p) level. Decomposition of NTO was found to be a multistep process that may begin with singlet oxygen attachment to the carbon atom of the C═N double bond. The formed intermediate undergoes cycle opening, and nitrogen gas, nitrous acid, and carbon (IV) oxide elimination. Isocyanic acid, arisen transiently, hydrolyzes into ammonia and carbon (IV) oxide. The obtained results show a significant increase in reactivity of the anionic form of NTO as compared to its neutral form. The calculated activation energies and high exothermicity of the studied processes support the contribution of singlet oxygen to NTO degradation into low-weight inorganic compounds in the environment.

Manifestations of intramolecular H-bonds of CH O and OH C type in quercetin molecule: Analysis of IR spectra by mean of density functional theory.

The IR spectra of 48 conformers of quercetin which represent full conformation space of its tautomers have been modeled at B3LYP/6-311++G(d,p) level of the density functional theory. The presence of intramolecular H-bonds C2'H/C6'H…O3 and O3H…C2'/C6' was characterized by their spectral manifestations. The C2'H/C6'H…O3 contacts were found to have a spectral blue-shift. The O3H…C2'/C6' contacts were mostly red-shifted. The stretching vibrations of H-bonds C2'H/C6'H…O3 demonstrate an increase in the intensity of the modes of stretching vibrations ν(C2'H)/ν(C6'H) and an increase in the frequency of their out-of-plane vibrations γ(C2'H)/γ(C6'H). Most of the spectral parameters correlate a little with the energy of the H-bonds.

Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes.

HIV-1 RNA dimerization is a critical step in viral life cycle. It is a prerequisite for genome packaging and plays an important role in reverse transcription and recombination. Dimerization is promoted by the DIS (dimerization initiation site) hairpin located in the 5' leader of HIV-1 genome. Despite the high genetic diversity in HIV-1 group M, only five apical loops (AAGCGCGCA, AAGUGCGCA, AAGUGCACA, AGGUGCACA and AGUGCAC) are commonly found in DIS hairpins. We refer to the parent DISes with these apical loops as DISLai, DISTrans, DISF, DISMal, and DISC, respectively. Based on identity or similarity of DIS hairpins to parent DISes, we distributed HIV-1 M genomes into five dimerization groups. Comparison of the primary and secondary structures of DIS, SD and Psi hairpins in about 3000 HIV-1 M genomes showed that the mutation frequencies at particular nucleotide positions of these hairpins differ among the dimerization groups, and DISF may be an origin of other parent DISes. We found that DIS, SD and Psi hairpins have hundreds of variants, only some of them occurring rather frequently. The lower part of DIS hairpin with G x AGG internal loop is highly conserved in both HIV-1 and SIV genomes. We supposed that the G-quadruplex, located 56 nts downstream of the Gag start codon, may participate in switching of HIV-1 leader RNA from BMH (branched multiple hairpins) to LDI (long distance interaction) conformation.

NTO Degradation by Nitroreductase: A DFT Study.

NTO (5-nitro-1,2,4-triazol-3-one), an energetic material used in military applications, may be released to the environment during manufacturing, transportation, storage, training, and disposal. A detailed investigation of the possible mechanism for all steps of reduction of NTO by oxygen-insensitive nitroreductase, as one of the pathways for NTO environmental degradation, was performed by computational study at the PCM(Pauling)/M06-2X/6-311++G(d,p) level. Obtained results reveal an overall sequence for NTO transformation into ATO (5-amino-1,2,4-triazol-3-one) with the flavin mononucleotide (FMN) cofactor of nitroreductase. Reduction of the nitro group to the nitroso group and the nitroso group to the hydroxylamino group follow a similar mechanism that consists of the sequential electron and proton transfer from the flavin cofactor. The hydride transfer mechanism may contribute to reduction of the nitroso group by the anionic form of the reduced flavin cofactor. Reduction of 5-(hydroxylamino)-1,2,4-triazol-3-one by the neutral form of the reduced flavin is impossible, whereas reduction of the hydroxylamino group to the amino group occurs with the anionic form of the reduced cofactor by a mechanism involving an initial proton transfer from the hydroxonium ion followed by two electrons and one proton transfers from the flavin cofactor. Small activation energies and high exothermicity support the significant contribution of oxygen-insensitive nitroreductase and other enzymes, containing FMN as a cofactor, to NTO degradation in the environment.

Decomposition of 2,4,6-trinitrotoluene (TNT) and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) by Fe13O13 nanoparticle: density functional theory study.

To obtain more insight into the mechanisms of the decomposition of energetic compounds, we performed a computational study of the interaction of Fe13O13 nanoparticles with two energetic molecules such as 2,4,6-trinitrotoluene (TNT) and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO). The density functional theory using M06-2X, B3LYP, and BLYP density functionals was applied. We found that the reactivity of these molecules strongly depends on the place of adsorption (so-called top and bottom planes of Fe13O13). Namely, only the interaction with the bottom plane results in the thermodynamic characteristics of the decomposition that provide a medium reaction rate for the studied processes. Several pathways for such decomposition were found. One of them is the inter-complex oxygen transfer of nitro-group oxygen to Fe13O13. This pathway results in the formation of adsorbed nitroso compounds. The second pathway describes a more complex decomposition that includes the transfer of the nitro-group oxygen accompanied by the hydrogen transfer. In all cases, the interaction of energetic molecules with Fe13O13 nanoparticles takes place along with a barrier-less electron transfer from Fe13O13 to TNT or NTO species.

Effect of Microenvironment on the Geometrical Structure of d(A)5 d(T)5 and d(G)5 d(C)5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study.

We report a comprehensive quantum-chemical study on d(A)5·d(T)5 and d(G)5·d(C)5 DNA mini-helixes and the Dickerson dodecamer d[CGCGAATTCGCG]. The research was performed to model the evolution of the spatial structure of d(A)5·d(T)5 and d(G)5 d(C)5 DNA mini-helixes all the way from vacuum to water bulk. The influence of external factors such as the presence of counterions and the extent of hydration was included. Also, for comparison, limited calculations have been carried out on the Dickerson dodecamer. The study has been performed at the density functional theory level using B97D3 and ωB97XD exchange-correlation functionals augmented by the Def2SVP basis set. We found that the (dA)5·(dT)5 anion when placed in vacuum forms a DNA duplex, which possesses an intermediate form between a helix and a ladder. The presence of compensating Na+ counterions or explicit microhydration of minor and major grooves stabilizes a DNA mini-helix of B-shape. Factors such as water bulk play a minor role. Somewhat different behavior has been found in the case of the (dG)5·(dC)5 duplex. In this case, we observe the formation of B-type mini-helixes even for the (dG)5·(dC)5 anion placed in vacuum. This is due to an additional stabilization originated from the appearance of an extra hydrogen bond, compared to an AT base pair. To assess whether the obtained results are transferable to different sizes of mini-helixes, similar calculations have been performed for the duplex formed by the Dickerson dodecamer which contains a total of 12 dG·dC and dA·dT base pairs. It has been found that in vacuum, analogous to the d(A)5·d(T)5 duplex, this system possesses a shape which is also quite close to a ladder. However, the presence of factors such as hydration restores the B-type geometry. Also, our results completely in line with the results of electrospray-ionization experiments suggest that uncompensated by counterions the DNA backbone preserves the duplex geometry in vacuum. We present arguments that this state is kinetically unstable.

A density functional theory study of simplest nanocomposites formed by graphene oxide and polyvinyl alcohol: geometry, interaction energy and vibrational spectrum.

A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate sandwich structures consist of nanocomposites between graphene oxide and polyvinyl alcohol. We predicted the interaction energies and discuss the contribution of electrostatic and dispersion components. Also, we computationally generated IR spectra of intercalates and compared them with those experimentally obtained. Two sources of interaction energy to stabilize the intercalates between graphene oxide and PVA are suggested. They are the electrostatic and dispersion (van-der-Waals) components. We also revealed that ωB97XD density functional in conjunction with 6-31G(d,p) basis set is qualitatively able to describe IR spectra of considered species.

A density functional theory investigation of degradation of Nitroguanidine in the photoactivated triplet state.

It is well known that nitroguanidine (NQ) undergoes photodegradation when exposed to UV-radiation. However, the mechanism of NQ photolysis is not fully understood. Earlier investigations have shown that nitrocompounds undergo to their triplet state population through crossing of electronic singlet and triplet excited state potential energy surfaces due to the nitrogroup rotation and nonplanarity under electronic excitation. Therefore, it is expected that under electronic excitation, the presence of nitrogroup in NQ would also lead to the population of electronic lowest energy triplet state. To shed a light on the degradation of NQ in alkaline solution under electronic excitation, we performed a detailed investigation of a possible degradation mechanism at the IEFPCM/B3LYP/6-311++G(d,p) level in the electronic lowest energy triplet state. We found that degradation ability of NQ in the electronic triplet state would be significantly larger than in the electronic ground singlet state. It was revealed that the photodecomposition of nitroguanidine might occur through several pathways involving N-N and C-N bond ruptures, nitrite elimination, and hydroxide ion attachment. Nitrogen of nitrogroup would be released in the form of nitrite and nitrogen (I) oxide. Computationally predicted intermediates and products of nitroguanidine photolysis such as nitrite, hydroxyguanidine, cyanamide, and urea correspond to experimentally observed species.

Role of Singlet Oxygen in the Degradation of Selected Insensitive Munitions Compounds: A Comprehensive, Quantum Chemical Investigation.

DNAN (2,4-dinitroanisole), NTO (3-nitro-1,2,4-triazol-5-one), and NQ (nitroguanidine) are important energetic materials used in military applications. They may find their way to the environment during manufacturing, transportation, storage, training, and disposal. A detailed investigation of possible mechanisms for reactions of the nitrocompounds with singlet oxygen, one of the potential methods for their degradation, was performed by computational study using the PCM(Pauling)/M06-2X/6-311++G(d,p) approach. Obtained results suggest that reactivity of the investigated munitions compounds toward singlet oxygen follows the order: DNAN > NTO(anion) > NQ ≫ NTO. DNAN is involved in [4 + 2]-addition with oxygen, and further formation of diepoxide or epoxyketone through diradical intermediates have been predicted. The NTO may undergo intramolecular rearrangement with formation of peroxide compound or nitrite radical elimination, and NQ may be transformed into urea.

Temperature-induced phase transitions in the rock-salt type SiC: a first-principles study.

The phase transitions in the rock-salt type SiC (B1-SiC) under decompression are studied in the framework of first-principles molecular dynamics simulations up to room temperature. The transformation pathways were determined based on an analysis of the symmetry and phonon spectra of high-symmetry transient structures identified in the simulations. The plausible pathways of the transformation of B1-SiC into the 3C-, 2H-, 4H-, 12R-SiC polytypes were suggested. The transformation paths were found to depend on both the availability of soft phonon modes in an unreconstructed phase and the initial conditions of the simulation. It is shown that an increase in cell volume at decompression leads to the condensation of a certain phonon mode. As a result, an intermediate state forms due to the atomic displacements and to subsequent strains related to this mode. All the decompressed structures were compressed back under pressure of 120-250 GPa depending on the type of the decompressed phase and simulation temperature that was in the range of 300-1200 K. The suggested scheme of structural identification can be used to determine the transition paths for the structural transformations of other similar structures under pressure.

Diffusion of energetic compounds through biological membrane: Application of classical MD and COSMOmic approximations.

Computational studies of the potential biological impact of several energetic compounds were performed. The most commonly used explosives were considered in the present studies: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,4-dinitroanisole (DNAN), and 5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO). The effect of such factors as ionic strength and presence of DMSO in the water solution on the structure of the membrane were considered using the POPC lipid bilayer as an example. Molecular dynamics (MD) simulations revealed that, even on a short-time scale, the influence of those additives is noticeable, and therefore those factors should always be taken into account. The MD and the COSMOmic approaches were used to elucidate the ability of the energetic compounds to penetrate the living cell. Calculated free energy profiles and partitioning coefficients revealed distributions of the compounds in the lipid bilayer as well as an overall ability to enter the cell. MD in this case provides a better representation of the free energy profile, while the COSMOmic approach works better to predict log(Klipw) values. The effect of the functional group was observed for the profiles that were obtained using the MD method.

Adsorption of nitrogen-containing compounds on hydroxylated α-quartz surfaces.

Adsorption energies of various nitrogen-containing compounds (specifically, 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAn), and 3-nitro-1,2,4-triazole-5-one (NTO)) on the hydroxylated (001) and (100) α-quartz surfaces are computed. Different density functionals are utilized and both periodic as well as cluster approaches are applied. From the adsorption energies, partition coefficients on the considered α-quartz surfaces are derived. While TNT and DNT are preferably adsorbed on the (001) surface of α-quartz, NTO is rather located on both α-quartz surfaces.

d(A)3d(T)3 and d(G)3d(C)3 B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics.

We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra-molecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)3d(T)3 and d(G)3d(C)3 duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.