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.

Conformation of the hydrazo bond in new 2-methyl-3,5-dinitro-6-(2-phenylhydrazinyl)pyridine and its influence on the structural and optic properties - Quantum chemical DFT calculations.

A new methyl-dinitro-phenylhydrazinyl-pyridine derivative [2-methyl-3,5-dinitro-6-(2-phenylhydrazinyl)pyridine] was synthesised and characterised by means of structural and spectroscopic measurements. The X-ray diffraction studies revealed that the compound crystallises in the centrosymmetric monoclinic space group P2/n, with two symmetry-independent molecules in the asymmetric unit with Z = 8. Hydrazo bridge C-NH-NH-C links two fragments composed of phenyl ring and pyridine unit substituted with methyl and nitro groups.

Schaftoside inhibits 3CL and PL of SARS-CoV-2 virus and regulates immune response and inflammation of host cells for the treatment of COVID-19.

It is an urgent demand worldwide to control the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The 3-chymotrypsin-like protease (3CL) and papain-like protease (PL) are key targets to discover SARS-CoV-2 inhibitors. After screening 12 Chinese herbal medicines and 125 compounds from licorice, we found that a popular natural product schaftoside inhibited 3CL and PL with IC values of 1.

The electron attachment effect on the structure and properties of -hydroxyaryl Schiff and Mannich bases - the hydrogen/proton transfer processes.

The attachment of electrons is known to significantly influence some chemical and biological processes. The chemical differences between Schiff and Mannich bases are characterized by strong intramolecular hydrogen bonds, resulting from the presence of, respectively, single or double carbon-nitrogen bonds in the chelate rings. Differences are especially visible in the hydrogen transfer processes from molecular (O-H⋯N) to the proton transfer (O⋯H-N) forms.

The hybrid models, containing hydrolytic and electron-driven processes, in theoretical study of oxaliplatin biotransformation.

The results of theoretical simulations of reaction paths for oxaliplatin from pro-drug into its active form responsible for cytostatic effect are presented. The studies based on the quantum-chemical density functional theory approach were performed considering environmental influence resulting from the aquation or electron donation. The hybrid mechanisms: hydrolytic mixed with electron driven were found to be the energetically favourable.

NMR studies of daidzein and puerarin: active anti-oxidants in traditional Chinese medicine.

Radix puerariae-a popular traditional Chinese medicine-is used for the treatment of diarrhea, acute dysentery, deafness, and cardiovascular diseases. It can also be used as an effective antioxidant and has been tested as an anticancer drug. Daidzein and puerarin are its main active compounds.

Interactions of Substituted Nitroaromatics with Model Graphene Systems: Applicability of Hammett Substituent Constants To Predict Binding Energies.

Applicability of Hammett parameters (σ and σ ) was tested in extended π-systems in gas phase. Three different model graphene systems, viz. 5,5-graphene (), 3-B-5,5-graphene (), and 3-N-5,5-graphene (), were designed as extended π-systems, and interactions of various nitrobenzene derivatives (mainly - and -substituted together with some multiple substitutions) on such platforms were monitored using density functional theory (M06/cc-pVDZ, M06/cc-pVTZ, M06/sp-aug-cc-pVTZ) and Møller-Plesset second-order perturbation (MP2/cc-pV-DZ) theory.

Enhancing mercury removal across air pollution control devices for coal-fired power plants by desulfurization wastewater evaporation.

Desulfurization wastewater evaporation technology is used to enhance the removal of gaseous mercury (Hg) in conventional air pollution control devices (APCDs) for coal-fired power plants. Studies have affirmed that gaseous Hg is oxidized and removed by selective catalytic reduction (SCR), an electrostatic precipitator (ESP) and wet flue gas desulfurization (WFGD) in a coal-fired thermal experiment platform with WFGD wastewater evaporation. Effects of desulfurization wastewater evaporation position, evaporation temperature and chlorine ion concentration on Hg oxidation were studied as well.

Understanding the influence of low-frequency vibrations on the hydrogen bonds of acetic acid and acetamide dimers.

Low-frequency vibrations coupled to high-frequency modes are known to influence the hydrogen bond strengths in a weakly interacting dimer. In this context, various acetic acid and acetamide dimers were analyzed using Møller-Plesset second-order perturbation (MP2) and density functional theory (DFT)-based approaches with explicit anharmonicity corrections. The computed low-frequency fundamentals as well as the high-frequency modes, which were found to be related to hydrogen bonding (OH/NH stretching modes), were analyzed and their computed intensities were correlated with their hydrogen-bond strengths/binding energies.

Comparative study of hydrolytic and electron-driven processes in carboplatin biotransformation.

The results of computational simulation of reaction courses mimicking the transformation of carboplatin from pro-drug into its active shape, responsible for cytotoxic effect, are reported. Implementing the density functional theory (DFT) calculations and the supermolecular approach, we explored the pathways representing two disparate models of carboplatin bioactivation: (1) based on paradigm of carboplatin aquation, and (2) based on new hypothesis that transformation is controlled by electron-transfer processes. The calculated geometrical and thermodynamic parameters were used for evaluation of pathways.

Synthesis and Electrochromic Properties of Conducting Polymers Based on Highly Planar 2,7-Disubstituted Xanthene Derivatives.

On the basis of preliminary DFT calculations, p-type semiconducting polymers based on 2,7-substituted xanthene building blocks that show a high degree of planarity were designed. The synthesis, electrochemical characterization, and theoretical modeling of 2,7-bis(thiophen-2-yl)-9,9-dimethylxanthene (1) and 2,7-bis(3-hexylthiophen-2-yl)-9,9-dimethylxanthene (2) is described. The synthetic procedure is based on the incorporation of thiophene rings by means of Pd-catalyzed cross-coupling reactions, which lead to monomers 1 and 2.

s-Block metallabenzene: aromaticity and hydrogen adsorption.

Second group metal dimers can replace the carbon atom in benzene to form metallabenzene (C5H6M2) compounds. These complexes possess some aromatic character and promising hydrogen adsorption properties. In this study, we investigated the aromatic character of these compounds using aromaticity indices and molecular orbital analysis.

Unique bonding nature of carbon-substituted Be2 dimer inside the carbon (sp(2)) network.

Controlled doping of active carbon materials (viz., graphenes, carbon nanotubes etc.) may lead to the enhancement of their desired properties.

Alkaline hydrolysis of organophosphorus pesticides: the dependence of the reaction mechanism on the incoming group conformation.

The fundamental mechanism of organophosphate hydrolysis is the subject of a growing interest resulting from the need for safe disposal of phosphoroorganic pesticides. Herein, we present a detailed ab initio study of the gas-phase mechanisms of alkaline hydrolysis of P-O and P-S bonds in a number of organophosphorus pesticides, including paraoxon, methyl parathion, fenitrothion, demeton-S, acephate, phosalone, azinophos-ethyl, and malathion. Our main finding is that the incoming group conformation influences the mechanism of decomposition of organophosphate and organothiophosphate compounds.

Role of the multipolar electrostatic interaction energy components in strong and weak cation-π interactions.

Density functional and Møller-Plesset second-order perturbation (MP2) calculations have been carried out on various model cation-π complexes formed through the interactions of Mg(2+), Ca(2+), and NH4(+) cations with benzene, p-methylphenol, and 3-methylindole. Partial hydration of the metal cations was also considered in these model studies to monitor the effect of hydration of cations in cation-π interactions. The binding energies of these complexes were computed from the fully optimized structures using coupled cluster calculations including triple excitations (CCSD(T)) and Gaussian-G4-MP2 (G4MP2) techniques.

Theoretical studies of structure, energetics and properties of Ca²⁺ complexes with alizarin glucoside.

The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations.

Exploring Relative Thermodynamic Stabilities of Formic Acid and Formamide Dimers - Role of Low-Frequency Hydrogen-Bond Vibrations.

The low-frequency fundamentals together with the high-frequency modes, responsible for hydrogen bonding (OH/NH stretching modes), were analyzed to correlate the intensities with the hydrogen-bond strengths/binding energies of the formic acid and formamide dimers using Møller-Plesset second-order perturbation (MP2) and coupled cluster computations with explicit anharmonicity corrections. Linear correlations were observed for both the formic acid and formamide dimers, and as consequence of such correlation an additive properties of binding energies with respect to the local hydrogen-bond energies of fragments involved (for these dimers) has been proposed. It has been further observed that (i) the nature of their six low-frequency fundamentals are very similar, and (ii) the in-plane bending and stretch-bend fundamentals of different dimers of these two species (depending on the dimer structure), in this low-frequency region, modulate their strength of hydrogen-bond/binding hence their relative stability order.

Electronic structures and thermochemical properties of the small silicon-doped boron clusters B(n)Si (n=1-7) and their anions.

We perform a systematic investigation on small silicon-doped boron clusters B(n)Si (n=1-7) in both neutral and anionic states using density functional (DFT) and coupled-cluster (CCSD(T)) theories. The global minima of these B(n)Si(0/-) clusters are characterized together with their growth mechanisms. The planar structures are dominant for small B(n)Si clusters with n≤5.

The evolution of bonding and thermodynamic properties of boron-doped small carbon clusters: an ab initio study.

Theoretical studies on BC(n) (n=1-6) clusters are carried out using density functional theory, Møller-Plesset second-order perturbation theory (MP2), coupled-cluster calculations including up to triple excitations (CCSD(T)), and higher-level approaches. All possible isomers depending on the positions of the boron atom are generated and the lowest-energy isomers are determined for doublet and quartet electronic states. The three potential evolution paths of the clusters are determined as a function of their size.

Comparative study of alternating low-band-gap benzothiadiazole co-oligomers.

The benzothiadiazole-arylene alternating conjugated oligomers have been designed and synthesized via Suzuki coupling reaction. The structures and properties of the conjugated oligomers were characterized by (1)HNMR, (13)CNMR, UV-vis absorption spectroscopy, photoluminescence (PL) spectroscopy. The luminescent measurements demonstrate that polybenzothiadiazoles are good chromophores able to form thin films by Langmuir-Blodgett (LB) technique, making them suitable for further applications.

Density functional theory based studies on the nature of Raman and resonance Raman scattering of nerve agent bound to gold and oxide-supported gold clusters: a plausible way of detection.

A detailed theoretical investigation has been carried out at the density functional level of theories to investigate the nature of Raman intensities of the -P=O stretching mode of a model nerve agent DFP (diisopropylfluorophosphate) when bound to different gold (Au(8), Au(20)) and oxide-supported gold (MgO...

Theoretical study of spin-spin coupling across the hydrogen (O-H...N) bond in adenosine derivatives.

The study of spin-spin coupling constants across hydrogen bond provides useful information about configuration of complexes. The interesting case of such interactions was observed as a coupling across an intramolecular hydrogen bond in 8-bromo-2',3'-O-isopropylideneadenosine between the -CH2OH (at 5'' proton) group and the nitrogen atom of adenine. In this paper we report theoretical investigations on the 4hJNH coupling across the H''-C-O-H.

Theoretical studies on the bonding and thermodynamic properties of Ge n Si m (m+n=5) clusters: the precursors of germanium/silicon nanomaterials.

Theoretical studies on the Ge n Si m clusters have been carried out using advanced ab initio approaches. The lowest energy isomers were determined for the clusters with compositions n+m=2-5. All possible isomers arising due to permutations of Ge and Si atoms were investigated.

The decomposition of alpha-aminophosphine oxides to phosphonic acid derivatives (PIII).

Aminophosphine oxides and aminophosphonates are, in general, very stable compounds. However, following phosphorus-carbon bond cleavage in aqueous acidic media these compounds sometimes decompose to phosphonic acids derivatives (P(III)). Despite some controversy in the literature, careful analysis supported by theoretical studies leads to the conclusion that decomposition to P(III) derivatives proceeds via an elimination reaction.

Theoretical studies on the mechanism of C-P bond cleavage of a model alpha-aminophosphonate in acidic condition.

Various reaction paths of the P-C bond cleavage of alpha-aminophosphonates in acidic media, resulting in the derivatives of phosphonic acid, has been investigated using density functional level of theories in the gas phase as well as in aqueous medium. Dimethyl (alpha-anilinobenzyl)phosphonate has been used as the model molecule and our investigation confirms a three steps process including protonation, P-C bond cleavage, and the transformation of the products from the final transition state (imine cation and H-phosphonate) through hydrolysis. The most favorable reaction path starts from the amino group protonation, followed by a proton transfer through N-H.