The electron attachment effect on the structure and properties of ortho-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 reaction in a Schiff base occurs as an ordinary hydrogen transfer from a donor to an acceptor, while in a Mannich base the transfer of hydrogen occurs simultaneously with a C-N bond scission leading to an intermolecular complex. The attachment of electrons preserves the overall structural topology of the reactants; however, due to differences in electron affinities, reactions switch from endothermic to exothermic and reaction rates in the anionic systems are significantly higher. The difference in electron affinities for particular reactants comes from the fundamental differences in electron binding mechanisms, leading to the valence-bound or dipole-bound states. The observed mechanisms are closely related to the nature and size of the LUMOs of the parent molecules. The transition state of the Mannich base corresponds to the σ and π orbital conversion and possesses the characteristics of the valence-bound state and the dipole-bound electronic state.

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. There are similarities in the nature of eight low-frequency fundamentals of these two dimers, and the in-plane bending and stretch-bend fundamentals of the different dimers of these two species (in this low-frequency region) have specific roles in their relative stability order. The computed linear correlations were further verified against the results from coupled cluster calculations including triple excitation (CCSD(T)), Gaussian-G4 (G4), Gaussian-G2-MP2 (G2MP2) and complete basis set (CBS-QB3) methods of high accuracy energy calculations. As a consequence of such linear correlations, an additive property of local fragment energies (responsible for hydrogen bonding) was found to be a valid approximation to predict the binding energies of such dimers and the idea was found to be extendable to the other homologues of these acids/amides.

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. The least studied case of C/Be substitution offers an attractive possibility in this respect. The interactions of Be2 with Be or C atoms are dominated by the large repulsive Pauli exchange contributions, which in turn offsets the attractive interactions leading to relatively small binding energies. The Be2 dimer, e.g., after being doped inside a planar carbon network, undergoes orbital adjustments due to charge transfer and unusual intermolecular interactions and is oriented perpendicular to the plane of the carbon network with the Be-Be bond center located inside the plane. The present theoretical investigation on the nature of bonding in C/Be2 exchange complexes, using state of the art quantum chemical techniques, reveals a sp(2) carbon-like bonding scheme in Be2 arising due to the molecular hybridization of σ and two π orbitals. The perturbations imposed by doped Be2 dimers exhibit a local character of the structural and electronic properties of the complexes, and the separation by two carbon atoms between beryllium active centers is sufficient to consider these centers as independent sites.

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 P21/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. Such a structure was confirmed by 1H and 13C NMR studies as well as IR, Raman, UV-Vis, and emission spectra. The results were analysed using the quantum-chemical DFT calculations. The paper reports the vibrational characteristics and discusses dynamical properties of this moiety. The full set of the normal modes typical of the hydrazo bridge was identified and assigned to respective IR and Raman bands. The results of structural and spectroscopic studies were used to find the dependence between the conformation of the θ-NH-NH-ϕ system and its optic properties. The experimental UV-Vis and emission spectra were discussed in terms of the calculated singlet and triplet states that allowed assigning the unique spectral pattern originating from the electrons of the hydrazo-bridge system.

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.

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. An analysis of the charge sharing between the donor (the π-systems) and the acceptors (the cations) together with the partitioning of total interaction energies revealed that the strong and weak cation-π interactions have similar electrostatic interaction properties. Further decomposition of such electrostatic terms into their multipolar components showed the importance of the charge-dipole, charge-quadrupole, and charge-octopole terms in shaping the electrostatic forces in such interactions. The computed vibrational spectra of the complexes were analyzed for the specific cation-π interaction modes and have been shown to contain the signature of higher order electrostatic interaction energy components (quadrupole and octopole) in such interactions.

Schaftoside inhibits 3CLpro and PLpro 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 (3CLpro) and papain-like protease (PLpro) 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 3CLpro and PLpro with IC50 values of 1.73 ± 0.22 and 3.91 ± 0.19 µmol/L, respectively, and inhibited SARS-CoV-2 virus in Vero E6 cells with EC50 of 11.83 ± 3.23 µmol/L. Hydrogen-deuterium exchange mass spectrometry analysis, quantum mechanics/molecular mechanics calculations, together with site-directed mutagenesis indicated the antiviral activities of schaftoside were related with non-covalent interactions with H41, G143 and R188 of 3CLpro, and K157, E167 and A246 of PLpro. Moreover, proteomics analysis and cytokine assay revealed that schaftoside also regulated immune response and inflammation of the host cells. The anti-inflammatory activities of schaftoside were confirmed on lipopolysaccharide-induced acute lung injury mice. Schaftoside showed good safety and pharmacokinetic property, and could be a promising drug candidate for the prevention and treatment of COVID-19.

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. The energetic and electronic consequences for the increased size of structures differ significantly, which leads to representatives of the ground electronic state from different structural groups. The ab initio calculated thermal functions allow enhancements to the available atomization energies and improve the agreement between the calculated and experimental heat content.

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 B(6)Si molecule represents a geometrical transition with a quasi-planar geometry, and the first 3D global minimum is found for the B(7)Si cluster. The small neutral B(n)Si clusters can be formed by substituting the single boron atom of B(n+1) by silicon. The Si atom prefers the external position of the skeleton and tends to form bonds with its two neighboring B atoms. The larger B(7)Si cluster is constructed by doping Si-atoms on the symmetry axis of the B(n) host, which leads to the bonding of the silicon to the ring boron atoms through a number of hyper-coordination. Calculations of the thermochemical properties of B(n)Si(0/-) clusters, such as binding energies (BE), heats of formation at 0 K (ΔH(f)(0)) and 298 K (ΔH(f)([298])), adiabatic (ADE) and vertical (VDE) detachment energies, and dissociation energies (D(e)), are performed using the high accuracy G4 and complete basis-set extrapolation (CCSD(T)/CBS) approaches. The differences of heats of formation (at 0 K) between the G4 and CBS approaches for the B(n)Si clusters vary in the range of 0.0-4.6 kcal mol(-1). The largest difference between two approaches for ADE values is 0.15 eV. Our theoretical predictions also indicate that the species B(2)Si, B(4)Si, B(3)Si(-) and B(7)Si(-) are systems with enhanced stability, exhibiting each a double (σ and π) aromaticity. B(5)Si(-) and B(6)Si are doubly antiaromatic (σ and π) with lower stability.

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. Also the electrical properties of obtained films confirm the good potential of these novel aryl-based π-conjugated polymers for the development of various electrical and electrochemical solid-state devices.

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...Au(4), CaO...Au(4), TiO(2)...Au(4), Al(2)O(3)...Au(4), M(16)O(16)...Au(8), and [M(16)O(15)...Au(8)](2+), M = Ca, Mg) clusters. All of these clusters and the DFP-bound clusters are fully optimized, and the computed energetics shows that DFP attaches itself weakly to these clusters. The normal Raman spectra calculations on these clusters show that there is substantial enhancement of the -P=O stretching mode of DFP compared to the isolated species. This enhancement has been found to be due to the polarization of the -P=O bond of DFP when bound to the clusters. Significant enhancement in intensity has been observed in the case of Au(n)...DFP (n = 8, 20), M(16)O(16)...Au(8)...DFP, and [M(16)O(15)...Au(8)](2+)...DFP (M = Ca, Mg) clusters. The resonance Raman calculations on the Au(n)...DFP (n = 8, 20) reveals that this enhancement could be made quite large and selective, which is a feature that is unique to the nerve agents and could be used as a property for detecting them.

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.

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. The Hg0 oxidation efficiency was increased ranging from 30% to 60%, and the gaseous Hg removal efficiency was 62.16% in APCDs when wastewater evaporated before SCR. However, the Hg0 oxidation efficiency was 18.99% and the gaseous Hg removal efficiency was 40.19% in APCDs when wastewater evaporated before ESP. The results show that WFGD wastewater evaporation before SCR is beneficial to improve the efficiency of Hg oxidized and removed in APCDs. Because Hg2+ can be easily removed in ACPDs and WFGD wastewater in power plants is enriched with chlorine ions, this method realizes WFGD wastewater zero discharge and simultaneously enhances Hg removal in APCDs.

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. The present contribution was focused on experimental and theoretical studies of the 1H and 13C NMR chemical shifts and nuclear magnetic shielding parameters of daidzein and puerarin. Experimental data were gained by exploring standard one-dimensional spectra and a set of two-dimensional measurements: COSY, HSQC, and HMBC. The theoretical gauge independent atomic orbital density functional theory supporting studies, were performed to determine shielding constants and chemical shifts in vacuum and methanol-d4 solvent. The correlation between experimental and theoretical data was fairly good, especially when the DFT/PBE0 approach was used. The molecular properties of daidzein and puerine related to antiradical activity were studied in the context of a single-step hydrogen atom transfer mechanism and its correlation with 13C NMR chemical shifts. Graphical abstract Electron spin density distribution for daidzein radical.

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...O(P) hydrogen bond, and the P-C bond cleavage from the resulting protonated structure. Explicit inclusion of water molecules indicated that two waters are needed for the P-C bond cleavage, and the calculated mechanistic paths in this hydrated model are similar to those of the aqueous solvation model.

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

Applicability of Hammett parameters (σ m and σ p ) was tested in extended π-systems in gas phase. Three different model graphene systems, viz. 5,5-graphene (GR), 3-B-5,5-graphene (3BGR), and 3-N-5,5-graphene (3NGR), were designed as extended π-systems, and interactions of various nitrobenzene derivatives (mainly m- and p-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. Offset face to face (OSFF) stackings were found to be the favored orientations, and reasonable correlations were found between binding energies (ΔE B) and the ∑|σ m | values of the substituted nitrobenzenes. It was proposed previously that |σ m | contains information about the substituents' polarizability and controls electrostatic and dispersion interactions. The combination of ∑|σ m | and molar refractivity (as ∑M r) or change in polarizability (Δα: with respect to benzene) of nitrobenzene derivatives generated statistically significant correlation with respect to ΔE B, thereby supporting the hypothesis related to the validity of |σ m | correlations. The |σ p | parameters also maintain similar correlations for the various p-substituted nitrobenzene derivatives together with several multiply-substituted nitrobenzene derivatives. The correlation properties in such cases are similar to the |σ m | cases, and the energy partition analysis for both the situations reveled importance of electrostatic and dispersion contributions in such interactions. The applicability of Hammett parameters was observed previously on the restricted parallel face to face orientation of benzene···substituted benzene systems, and the present results show that such an idea could be used to predict ΔE B values in OSFF orientations, if the scaffolds are designed in such a way that substituted benzene systems cannot escape their π-clouds.

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. In contrast to carboplatin hydrolysis, representing a typical two stage SN2 mechanism, the postulated electron-driven reactions proceed under the dissociative electron attachment (DEA) mechanism. The reaction profiles predict endothermic effect in both stages of hydrolytic course and final exothermic effects for electron-driven processes. The most effective are hybrid processes including two-stages: water and subsequent electron impact on transformed carboplatin. The aqua-products, manifesting strong electron-affinity, can be the active form of drug capable to cytotoxic interaction with DNA, not only as alkylating agent but also as electron-acceptor. Concluding, the hybrid transformation of carboplatin is more favourable than hydrolytic.

Probing the acetylcholinesterase inhibition of sarin: a comparative interaction study of the inhibitor and acetylcholine with a model enzyme cavity.

Interaction energies have been estimated between sarin and a model enzyme cavity of acetylcholinesterase (ACHE) using the density functional and Møller-Plesset second-order perturbation (MP2) levels of theories. The calculated interaction energies have been compared with those of acetylcholine and the same model ACHE cavity. The ACHE...sarin and ACHE...acetylcholine (Ach) structures have been optimized using DFT based two-layer ONIOM hybrid calculations. The nature of interactions has been investigated in detail using an interaction energy partitioning technique. The effects of solvation on the interaction energies have also been taken into account. An inhibition mechanism during the uptake of sarin inside the ACHE cavity has been proposed from the comparison of the energetics of the ACHE...sarin and ACHE...Ach complexes.

Comprehensive global energy minimum modeling of the sarin-serine adduct.

DFT-based molecular dynamics and quantum chemistry theory approaches are combined to investigate the various conformers of sarin-serine adduct. Twenty different conformers have been located as the local minima on the potential energy surface. They are categorized into five classes based on the relative orientation of sarin moiety. The energy properties of the twenty sarin-serine conformers revealed in the present study suggest that at least four of the conformers (1-1, 4-1, 4-2, and 5-1) are expected to have crucial contributions to the phosphonylation and dealkylation reactions of the sarin-serine adduct at low temperature. Among them, the 1-1 conformer which has both the lowest energy and the highest Boltzman distribution relative probability is expected to be the most important. However, as the temperature rises, the 4-1 conformer plays a more important role than 1-1 in the sarin-serine adductation reactions. Under the relatively high temperatures, the contribution of conformer 5-1 decreases in the phosphonylation and dealkylation reactions while at least eight other conformers (1-2, 1-3, 3-1, 3-4, 3-7, 4-2, 4-3, and 4-4) are expected to have larger contributions in these reactions.

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. To determine the nature of interactions between hydrogen and the metallic center, variation-perturbational decomposition of interaction energy was applied together with ETS-NOCV analysis. The results obtained suggest that the aromatic character comes from three π orbitals located mainly on the C5H5(-) fragment. The high hydrogen adsorption energy (up to 6.5 kcal mol(-1)) results from two types of interaction. In C5H6Be2, adsorption is controlled by interactions between the empty metal orbital and the σ orbital of the hydrogen molecule (Kubas interaction) together with corresponding back-donation interactions. Other C5H6M2 compounds adsorb H2 due to Kubas interactions enhanced by H2-π interactions.