Wavefunction and reactivity study of benzo[a]pyrene diol epoxide and its enantiomeric forms

Mechanistic insights into the lignin dissolution behavior in amino acid based deep eutectic solvents

Deep eutectic solvents (DESs) composed by amino acids (L-arginine, L-proline, L-alanine) as the hydrogen bond acceptors (HBAs) and carboxylic acids (formic acid, acetic acid, lactic acid, levulinic acid) as hydrogen bond donors (HBDs) were prepared and used for the dissolution of dealkaline lignin (DAL). The mechanism of lignin dissolution in DESs was explored at molecular level by combining the analysis of Kamlet-Taft (K-T) solvatochromic parameters, FTIR spectrum and density functional theory (DFT) calculations of DESs. Firstly, it was found that the formation of new hydrogen bonds between lignin and DESs mainly drove the dissolution of lignin, which were accompanied by the erosion of hydrogen bond networks in both lignin and DESs. The nature of hydrogen bond network within DESs was fundamentally determined by the type and number of functional groups in both HBA and HBD, which affected its ability to form hydrogen bond with lignin. One hydroxyl group and carboxyl group in HBDs provided active protons, which facilitated proton-catalyzed cleavage of β-O-4, thus enhancing the dissolution of DESs. The superfluous functional group resulted in more extensive and stronger hydrogen bond network in the DESs, thus decreasing the lignin dissolving ability. Moreover, it was found that lignin solubility had a closed positive correlation with the subtraction value of α and β (net hydrogen donating ability) of DESs. Among all the investigated DESs, L-alanine/formic acid (1:3) with the strong hydrogen-bond donating ability (acidity), weak hydrogen-bond accepting ability (basicity) and small steric-hindrance effect showed the best lignin dissolving ability (23.99 wt%, 60 °C). On top of that, the value of α and β of L-proline/carboxylic acids DESs showed some positive correlation with the global electrostatic potential (ESP) maxima and minima of the corresponding DESs respectively, indicating the analysis of ESP quantitative distributions of DESs could be an effective tool for DESs screening and design for lignin dissolution as well as other applications.

Activation persulfate for efficient tetrabromobisphenol A degradation via carbon-based materials: Synergistic mechanism of doped N and Fe

In this study, a novel carbon-based material (Fe-N-PGWBC) utilizing the garden waste, melamine and FeSO₄ as the precursor was successfully synthesized, efficiently activating peroxydisulfate (PDS) to degrade tetrabromobisphenol A (TBBPA). Under typical conditions (Fe-N-PGWBC dose of 100 mg·L^-1, PDS of 0.2 mM and TBBPA of 10 mg·L^-1), Fe-N-PGWBC/PDS system could achieve over 99% TBBPA removal (including adsorption and degradation) within 60 min, and the corresponding rate constant k_s was 0.0724 min^-1, which was almost 40.2 times higher than that of the pristine biochar. The extraction experiments implied that the excellent adsorption performance of Fe-N-PGWBC did not hinder the degradation of TBBPA. Abundant active sites (rich oxygen-containing functional groups, Fe-O and Fe₃C) of Fe-N-PGWBC could effectively promote PDS decomposition to produce reactive oxygen species. The probe-based kinetic modelling methods verified that approximately 87.6% TBBPA was degraded by SO₄^·-, 12.2% TBBPA was degraded by ¹O₂, and 0.2% TBBPA was degraded by ^·OH. Furthermore, based on the calculation of density functional theory and identification of products, TBBPA was mainly involved in three transformation pathways including hydroxylation, debromination and β-scission process. The study proposed a facile resource approach of garden waste and provided deeper understanding for the TBBPA degradation mechanisms in heterogeneous system.

Combination of Energetic Tetrazole and Triazole: Promising Materials with Exceptional Stability and Low Mechanical Sensitivity as Propellants and Gas Generators

An innovative synthesis of 5-((1H-tetrazol-5-yl)methyl)-4H-1,2,4-triazole-3,4-diamine (TMT) based on triazole and tetrazole frameworks bearing double amino groups was reported. It is worth mentioning that TMT is insensitive to impact and friction (IS > 40 J, FS > 360 N), thus enabling it to have an exceptional thermal decomposition behavior that is superior to RDX and TNT. Meanwhile, it also has relatively high energetic performance (D_v = 8.417 km/s). A series of energy-containing salts TMT-1-8 were also investigated for their potential applications. Except for TMT-4 and TMT-7, the remaining nitrogen-rich salts have initial decomposition temperatures above 200 °C. Furthermore, the salts with positive heat generation all have extraordinary gas production, especially for TMT-1 (V_o = 840.5 dm³/kg), TMT-2 (V_o = 803.9 dm³/kg), and TMT-7 (V_o = 844.3 dm³/kg). The low mechanical sensitivities of the TMT series were discovered, and a majority of them have impact sensitivities exceeding 40 J with friction sensitivities exceeding 360 N which are superior to TNT (IS = 15 J, FS = 353 N). The intermolecular and intramolecular interactions of the crystals TMT-1-3 were explored by Hirshfeld surfaces, 2D fingerprint plots, noncovalent interaction (NCI) analysis, and electrostatic potential surface analysis to understand the physicochemical property changes in relation to the structure. Consequently, this novel tri/tetrazole and polyamine system as a promising material provides the impetus for the development of gas generators and propellants.

Main/side chain asymmetric molecular design enhances charge transfer of two-dimensional conjugated polymer/g-C3N4 heterojunctions for high-efficiency photocatalytic sterilization and degradation

Heterojunctions based on conjugated polymers (PHJs) are of promise as photocatalysts. Here, we fabricate the two-dimensional benzodithiophene (BDT) and thieno[2,3-f]benzofuran (TBF) based conjugated polymers/g-C₃N₄ PHJs creatively using the symmetry-breaking strategy. PD1 and PD3 with the asymmetric backbone TBF have better crystallinity. Moreover, PD3 utilizing fluorinated benzotriazole as the electron acceptor unit possesses more compact π - π stacking and higher charge mobility. The conjugated polymer PD5 with asymmetric side chains in the donor unit BDT guarantees more efficient charge transfer in the corresponding PD5/g-C₃N₄ PHJ while maintaining comparable light utilization rate. Consequently, PD5/g-C₃N₄ shows the champion performance with photocatalytic sterilization rates reaching 99.1% and 97.3% for S. aureus and E. coli. Notably, the reaction rate constant for Rhodamine B degradation of PD5/g-C₃N₄ is 8 times that of g-C₃N₄, a record high among conjugated polymers/g-C₃N₄. This study aims to reveal the structure - property correlation of asymmetric conjugated polymers/g-C₃N₄ for potential photocatalysis applications.

Lead Sequestration in Perovskite Photovoltaic Device Encapsulated with Water-Proof and Adhesive Poly(ionic liquid)

The inevitable usage of toxic lead impedes the commercialization of lead halide perovskite solar cells, especially considering lead ions potentially unseals from the discarded and damaged devices and consequently contaminates the environment. In this work, we proposed a poly(ionic liquid) (PIL) cohered sandwich structure (PCSS) to realize lead sequestration in perovskite solar cells by a water-proof and adhesive poly([1-(3-propionic acid)-3-vinylimidazolium] bis(trifluoromethanesulphonyl)imide (PPVI-TFSI). A transparent ambidextrous protective shield manufactured from PPVI-TFSI was achieved and applied in lead sequestration for perovskite solar cells. PCSS provides robustness and water-resistance, which improves device stability toward water erosion and extreme situations (such as acid, base, salty water, and hot water). PPVI-TFSI exhibited excellent affinity toward lead with adsorption capacity of 516 mg·g^-1, which assisted to prevent lead leakage in abandoned devices as proved in the test of wheat germination vividly. PCSS provides a promising solution for complex lead sequestration and management issues, which contribute to the commercialization of perovskite solar cells.

Phosphorus-Enhanced and Calcium-Retarded Transport of Ferrihydrite Colloid: Mechanism of Electrostatic Potential Changes Regulated via Adsorption Speciation

The transport of ferrihydrite colloid (FHC) through porous media is influenced by anions (e.g., PO₄^3-) and cations (e.g., Ca²⁺) in the aqueous environment. This study investigated the cotransport of FHC with P and P/Ca in saturated sand columns. The results showed that P adsorption enhanced FHC transport, whereas Ca loaded onto P-FHC retarded FHC transport. Phosphate adsorption provided a negative potential on the FHC, while Ca added to P-FHC led to electrostatic screening, compression of the electric double layer, and formation of Ca₅(PO₄)₃OH followed by heteroaggregation at pH ≥ 6.0. The monodentate and bidentate P surface complexes coexisted, and Ca mainly formed a ternary complex with bidentate P (≡(FeO)₂PO₂Ca). The unprotonation bidentate P at the Stern 1-plane had a considerable negative potential at the Van der Waals molecular surface. Extending the potential effect to the outer layer of FHC, the potential at the Stern 2-plane and zeta potential exhibited a corresponding change, resulting in a change in FHC mobility, which was validated by comparison of experimental results, DFT calculations, and CD-MUSIC models. Our results highlighted the influence of P and Ca on FHC transport and elucidated their interaction mechanisms based on quantum chemistry and colloidal chemical interface reactions.

A Comprehensive Investigation into the Crystallology, Molecule, and Quantum Chemistry Properties of Two New Hydrous Long-Chain Dibasic Ammonium Salts CnH2n+8N2O6 (n = 35 and 37)

Through the salification reaction of carboxylation, successful attachment of the long-chain alkanoic acid to the two ends of 1,3-propanediamine was realized, which enabled the doubling of the long-chain alkanoic acid carbon chain. Hydrous 1,3-propanediamine dihexadecanoate (abbreviated as 3C16) and 1,3-propanediamine diheptadecanoate (abbreviated as 3C17) were synthesized afterward, and their crystal structures were characterized by the X-ray single crystal diffraction technique. By analyzing their molecular and crystal structure, their composition, spatial structure, and coordination mode were determined. Two water molecules played important roles in stabilizing the framework of both compounds. Hirshfeld surface analysis revealed the intermolecular interactions between the two molecules. The 3D energy framework map presented the intermolecular interactions more intuitively and digitally, in which dispersion energy plays a dominant role. DFT calculations were performed to analyze the frontier molecular orbitals (HOMO–LUMO). The energy difference between the HOMO–LUMO is 0.2858 eV and 0.2855 eV for 3C16 and 3C17, respectively. DOS diagrams further confirmed the distribution of the frontier molecular orbitals of 3C16 and 3C17. The charge distributions in the compounds were visualized using a molecular electrostatic potential (ESP) surface. ESP maps indicated that the electrophilic sites are localized around the oxygen atom. The crystallographic data and parameters of quantum chemical calculation in this paper will provide data and theoretical support for the development and application of such materials.

The Multiplicity of π-π Interactions of Fused-Ring Electron Acceptor Polymorphs on the Exciton Migration and Charge Transport

Efficient long-range exciton migration and charge transport are the key parameters for organic photovoltaic materials, which strongly depend on the molecular stacking modes. Herein, we extracted the stacked structures of the archetype fused-ring electron acceptor molecule, ITIC, based on the information on four polymorphic crystals and investigated the relationship between molecular stacking modes and exciton migration/charge transport properties through the intermolecular Coulomb coupling and charge transfer integral calculation. Experimentally, the thin film texture is crystallized through a post-annealing treatment through grazing-incidence wide-angle X-ray scattering (GIWAXS) measurements, which lead to the enhanced exciton migration through exciton-exciton annihilation in the femtosecond transient absorption (fs-TA) measurements. This work demonstrates the relationship between the molecular arrangement and the exciton migration and electron transport and highlights the significance of optimizing molecular stacking for the development of high-performance electron acceptor materials.

Simultaneous Stabilization of Lithium Anode and Cathode using Hyperconjugative Electrolytes for High-voltage Lithium Metal Batteries

Although great progress has been made in new electrolytes for lithium metal batteries (LMBs), the intrinsic relationship between electrolyte composition and cell performance remains unclear due to the lack of valid quantization method. Here, we proposed the concept of negative center of electrostatic potential (NCESP) and Mayer bond order (MBO) to describe solvent capability, which highly relate to solvation structure and oxidation potential, respectively. Based on established principles, the selected electrolyte with 1.7 M LiFSI in methoxytrimethylsilane (MOTMS)/ (trifluoromethyl)trimethylsilane (TFMTMS) shows unique hyperconjugation nature to stabilize both Li anode and high-voltage cathode. The 4.6 V 30 μm Li||4.5 mAh cm^-2 lithium cobalt oxide (LCO) (low N/P ratio of 1.3) cell with our electrolyte shows stable cycling with 91 % capacity retention over 200 cycles. The bottom-up design concept of electrolyte opens up a general strategy for advancing high-voltage LMBs.

Structural stability and the low-lying singlet and triplet states of BN-n-acenes, n = 1-7

The chemical stability and the low-lying singlet and triplet excited states of BN-n-acenes (n = 1-7) were studied using single reference and multireference methodologies. From the calculations, descriptors such as the singlet-triplet splitting, the natural orbital (NO) occupations and aromaticity indexes are used to provide structural and energetic analysis. The boron and nitrogen atoms form an isoelectronic pair of two carbon atoms, which was used for the complete substitution of these units in the acene series. The structural analysis confirms the effects originated from the insertion of a uniform pattern of electronegativity difference within the molecular systems. The covalent bonds tend to be strongly polarized which does not happen in the case of a carbon-only framework. This effect leads to a charge transfer between neighbor atoms resulting in a more strengthened structure, keeping the aromaticity roughly constant along the chain. The singlet-triplet splitting also agrees with this stability trend, maintaining a consistent gap value for all molecules. The BN-n-acenes molecules possess a ground state with monoconfigurational character indicating their electronic stability. The low-lying singlet excited states have charge transfer character, which proceeds from nitrogen to boron.

Computational Insights into Sensing Mechanism for Al3+ in a New Acylhydrazone Fluorescent Probe Based on Excited-State Intramolecular Proton Transfer (ESIPT) and Twisted Intramolecular Charge Transfer (TICT)

The work explored the fluorescent properties of probe N'-(2, 4-dihydroxy-benzylidene)pyridine-3-carbohydrazide (HL) and its sensing mechanism for the Al³⁺ ion in detail. HL has two competing deactivation processes: ESIPT and TICT. Upon light-excitation, only one proton can transfer, and the SPT1 structure is generated. The SPT1 form is highly emissive, which is inconsistent with the colorless emission observed in the experiment. Then a nonemissive TICT state was obtained by rotating the C-N single bond. The energy barrier of the TICT process is lower than that of the ESIPT process, which indicates that probe HL will decay to the TICT state and quench the fluorescence. When Al³⁺ is recognized by probe HL, strong coordinate bonds are formed between HL and Al³⁺, and then the TICT state is prohibited, and the fluorescence of HL is turned on. Al³⁺ as a coordinated ion can effectively remove the TICT state but cannot influence the photoinduced electron transfer (PET) process of HL.

Molecular level insight into the different interaction intensity between microplastics and aromatic hydrocarbon in pure water and seawater

The interaction of MPs and aromatic hydrocarbons in seawater and pure water was examined using experimental measurements, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations in light of the potential health risks posed by microplastic (MPs)-associated aromatic hydrocarbon pollutants. Isothermal studies and MD simulations suggested that MPs have a stronger affinity for aromatic hydrocarbons in seawater. To uncover the mechanism, MPs' surface characteristics and their intermolecular interactions with aromatic hydrocarbons were examined. According to the research, MPs in seawater have less compact structure, bigger pores, and a higher specific surface area, all of which contribute to more sorption sites. Analysis of the intermolecular interaction indicated that MPs have a greater ability for molecular interactions in seawater and the interaction energy between MPs and aromatic hydrocarbons in seawater is higher. Additionally, seawater cations may act as bridges, which also accelerate sorption in seawater. In summary, this study provides a molecular-level understanding of MPs-aromatic hydrocarbons interaction and demonstrates that the interaction is stronger in seawater.

Insensitive High-Energy Density Materials Based on Azazole-Rich Rings: 1,2,4-Triazole N-Oxide Derivatives Containing Isomerized Nitro and Amino Groups

It is an arduous and meaningful challenge to design and develop new energetic materials with lower sensitivity and higher energy. How to skillfully combine the characteristics of low sensitivity and high energy is the key problem in designing new insensitive high-energy materials. Taking a triazole ring as a framework, a strategy of N-oxide derivatives containing isomerized nitro and amino groups was proposed to answer this question. Based on this strategy, some 1,2,4-triazole N-oxide derivatives (NATNOs) were designed and explored. The electronic structure calculation showed that the stable existence of these triazole derivatives was due to the intramolecular hydrogen bond and other interactions. The impact sensitivity and the dissociation enthalpy of trigger bonds directly indicated that some compounds could exist stably. The crystal densities of all NATNOs were larger than 1.80 g/cm³, which met the requirement of high-energetic materials for crystal density. Some NATNOs (9748 m/s for NATNO, 9841 m/s for NATNO-1, 9818 m/s for NATNO-2, 9906 m/s for NATNO-3, and 9592 m/s for NATNO-4) were potential high detonation velocity energy materials. These study results not only indicate that the NATNOs have relatively stable properties and excellent detonation properties but also prove that the strategy of nitro amino position isomerization coupled with N-oxide is an effective means to develop new energetic materials.

Orbital Polarization-Dependent Fragment Twist-Induced Intramolecular Electric-Field-Driven Charge Transfer

Defects, such as twisting, in fused aromatic hydrocarbons disrupt the plane of the π orbital. The twisted structure induces an electric field in the system and affects the spectra. In this work, theoretical studies show that the intramolecular electric field within a distinctly twisted structure is larger than that of other molecules. In addition, the spectral study shows that the degree of charge transfer and the magnetic transition dipole in the electrostatic potential extremum region of the molecular electric field were significantly improved, which affected the optical absorption and chiral optical behavior of the molecule. The discovery of this theoretical regulation law will provide a solid foundation for the electric-field-induced regulation of optical properties and will promote the precise design and synthesis of optoelectronic molecules with inner electric fields.

Selective Chelation of the Exotic Meitner-Auger Emitter Mercury-197 m/g with Sulfur-Rich Macrocyclic Ligands: Towards the Future of Theranostic Radiopharmaceuticals

Mercury-197 m/g are a promising pair of radioactive isomers for incorporation into a theranostic as they can be used as a diagnostic agent using SPECT imaging and a therapeutic via Meitner-Auger electron emissions. However, the current absence of ligands able to stably coordinate ^197m/g Hg to a tumour-targeting vector precludes their use in vivo. To address this, we report herein a series of sulfur-rich chelators capable of incorporating ^197m/g Hg into a radiopharmaceutical. 1,4,7,10-Tetrathia-13-azacyclopentadecane (NS₄ ) and its derivatives, (2-(1,4,7,10-tetrathia-13-azacyclopentadecan-13-yl)acetic acid (NS₄ -CA) and N-benzyl-2-(1,4,7,10-tetrathia-13-azacyclopentadecan-13-yl)acetamide (NS₄ -BA), were designed, synthesized and analyzed for their ability to coordinate Hg²⁺ through a combination of theoretical (DFT) and experimental coordination chemistry studies (NMR and mass spectrometry) as well as ^197m/g Hg radiolabeling studies and in vitro stability assays. The development of stable ligands for ^197m/g Hg reported herein is extremely impactful as it would enable their use for in vivo imaging and therapy, leading to personalized treatments for cancer.

Revealing the incorporation of an NH2 group into the edge of carbon dots for H2O2 sensing via the C-N⋯H hydrogen bond interaction

We investigated hydrogen peroxide (H₂O₂) sensing on NH₂-functionalized carbon dots (Cdots) for three different -NH₂ positions, and the N atom was found to be the active site using a quantum computational approach. B3LYP and 6-31G(d,p) were used for density functional theory (DFT) ground state calculations, whereas CAM-B3LYP and the same basis set were used in time-dependent density functional theory (TD-DFT) excited state calculations. Structural optimization showed that the H₂O₂ is chemisorbed on 1-sim via a C-N⋯H hydrogen bond interaction with an adsorption energy of -10.61 kcal mol^-1. Mulliken atomic charge distributions and electrostatic potential (ESP) analysis were both used to determine reactivity of the molecules at the atomic level. For in-depth analysis of the ground states, we utilized Frontier molecular orbital (FMO) theory, quantum theory of atoms in molecules (QTAIM), and non-covalent interaction (NCI) index analysis. In addition, we also present UV-vis absorption spectra and charge transfer lengths to understand the mechanism of H₂O₂ sensing in excited states. Based on the molecular and electronic properties of the NH₂-Cdots, it was shown that 1-sim is a potential candidate for use as an electrochemical sensor for H₂O₂ sensing. Whereas 3-sim is believed to be a potential candidate for use as an optical sensor of H₂O₂ based on the UV-vis characteristics via photoinduced charge transfer.

Explaining the High Catalytic Activity in Bis(indenyl)methyl Zirconium Cation Using Combined EDA-NOCV/QTAIM Approach

The main purpose of this study is to elucidate some discrepancies already observed in the catalytic activity values of some zirconocene methyl cations. The EDA-NOCV scheme was employed for a theoretical description of the interactions between an ethylene molecule and five catalysts of zirconocene methyl cation. The nature of the chemical interactions has been elucidated through the QTAIM topological analysis. The steric hindrance due to the ligands was evaluated qualitatively by means of an IRI-based analysis and quantitively through Fisher information. The findings prove that the indenyl ligand seems to favor the orbital interaction between the ethylene molecule and the metal centre of zirconocene methyl cation. Both electrostatic and orbital contributions play a crucial role in stabilising the studied complexes. Based on the NOCV deformation density contributions, the strongest orbital interaction is reached with the bis(indenyl)methyl zirconium cation, which is the only one exhibiting covalent interactions. Especially, the strong contribution of π-back donation (occurring from the occupied orbitals of the zirconium atom to the π* anti-bonding orbital of ethylene) may be a key to understand why this catalyst has a higher polymerisation yield than the other studied catalysts. This work suggests a perspective for predicting values of catalytic activity when theoretically designing novel catalysts of zirconocene type.

Synthesis and characterization of potential polycyclic energetic materials using bicyclic triazole and azetidine structures as building blocks

Exploring the design strategy of new energetic materials is crucial to promote the development of energetic materials. In this study, a method for designing polycyclic energetic materials is proposed by combining the azetidine structure with azobis-1,2,4-triazole or bi-1,2,4-triazole. A series of typical triazolyl polycyclic compounds were designed and synthesized by simple nucleophilic reaction, which included 5,5'-dichloro-3,3'-bis(3,3'-difluoroazetidine)-4,4'-azobis-1,2,4-triazole (1), 5,5'-dichloro-3,3'-bis(3,3'-difluoroazetidine)-4,4'-bi-1,2,4-triazole (2), 5,5'-dichloro-3-(N,N-dimethyl)-3'-(3,3'-difluoroazetidine)-4,4'-bi-1,2,4-triazole (3) 5,5'-dichloro-3,3'-bis(3,3'-dinitroazetidine)-4,4'-bi-1,2,4-triazole (4), 5,5'-dichloro-3-(N,N-dimethyl)-3'-(3,3'-dinitroazetidine)-4,4'-bi-1,2,4-triazole (5), and 5,5'-diazido-3,3'-bis(3,3'-difluoroazetidine)-4,4'-azo-1,2,4-triazole (6). These designed and synthesized polycyclic compounds (1, 2, 3) have high decomposition temperatures (>200 °C). The molecular van der Waals surface electrostatic potentials suggested the reactivity of compounds 1, 2, and 3 when attacked by nucleophiles. The natural bond orbital and Hirshfeld surface analysis proved the essential reason for the stability of these compounds in theory. The formula design example suggests that some triazolyl polycyclic compounds (4, 5, and 6) are potentially explosives, suggesting that this strategy is feasible for constructing the triazolyl polycyclic energetic compounds.

Insights into the interactions between cellulose and biological molecules

Understanding the interactions between carbohydrate polymer molecules and biomolecules is of primary significance for its application. In this paper, the interaction between cellulose and biomolecules was studied using density functional theory method, in which cellobiose, nucleobases, and aromatic amino acids were employed as the structural models of cellulose, DNA, and protein, respectively. Quantitative molecular surface electrostatic potential (ESP) results well represented how cellulose perceived by organism during the recognition. The structural and energetic studies of cellulose with biomolecules complexes show that weak interactions, such as hydrogen bonding interaction, vdW interaction, and pi-H interaction, play an important role in stabilizing these complexes. Through systematic wavefunction analysis, including reduced density gradient (RDG) and natural bond orbital (NBO) methods, the nature of these weak interactions was revealed and further graphically visualized. In-depth understanding of the interaction between cellobiose with biological model molecules may shed lights on the application of carbohydrate polymer-based materials in biological fields.

Identification of potential inhibitors of omicron variant of SARS-Cov-2 RBD based virtual screening, MD simulation, and DFT

Emergence of the SARS-CoV-2 Omicron variant of concern (VOC; B.1.1.529) resulted in a new peak of the COVID-19 pandemic, which called for development of effective therapeutics against the Omicron VOC. The receptor binding domain (RBD) of the spike protein, which is responsible for recognition and binding of the human ACE2 receptor protein, is a potential drug target. Mutations in receptor binding domain of the S-protein have been postulated to enhance the binding strength of the Omicron VOC to host proteins. In this study, bioinformatic analyses were performed to screen for potential therapeutic compounds targeting the omicron VOC. A total of 92,699 compounds were screened from different libraries based on receptor binding domain of the S-protein via docking and binding free energy analysis, yielding the top 5 best hits. Dynamic simulation trajectory analysis and binding free energy decomposition were used to determine the inhibitory mechanism of candidate molecules by focusing on their interactions with recognized residues on receptor binding domain. The ADMET prediction and DFT calculations were conducted to determine the pharmacokinetic parameters and precise chemical properties of the identified molecules. The molecular properties of the identified molecules and their ability to interfere with recognition of the human ACE2 receptors by receptor binding domain suggest that they are potential therapeutic agents for SARS-CoV-2 Omicron VOC.

A study on the catalytic activity of polypeptides toward the hydrolysis of glucoside compounds gastrodin, polydatin and esculin

The self-assembly of a series of catalytically active polypeptides toward hydrolysis of glucoside compounds, namely, gastrodin, polydatin and esculin was investigated. These active peptides are composed of two functional fragments: one is the hydrophobic sequence LHLHLRL, which forms assembling segments in the presence of Zn ions (Zn²⁺); another functional sequence of active peptides are catalytic sites such as Glu (E), Asp (D) and His (H), where carboxylic acids (-COOH) or imidazole groups act like scissors to cleave glucoside bonds of the compounds (according to the acid-base coupling mechanism). The effects of the amino acid sequence of the peptide, Zn²⁺ concentration, pH and the size or steric hindrance of glucoside compounds on the hydrolytic activity were studied. It was found that the crystalline structure of assembled peptides was crucial to provide the peptide with catalytic hydrolytic activity. Noncovalent interaction index was used to analyse the noncovalent interaction of PEs with glucoside compounds, including hydrogen bonds, van der Waals, and steric effect in the complexes. The binding energy of complexes, the direction and site of nucleophilic attack during deglycosylation processes were also investigated by molecular docking and the electron density Laplace function. This revealed that the differences in the hydrolytic activity of peptides toward glucoside compounds with different sizes originated from different hydrogen bond interactions between the peptides and substrates. These active peptides may find application in the preparation of drugs by de-glycosylation of natural compounds.

Modelling the octanol-air partition coefficient of aromatic pollutants based on the solvation free energy and the dimer effect

In this study, generalized predictive models were developed to estimate K_OA of four kinds of aromatic pollutants based on the calculated solvation free energy and taking the dimer effect into account. Uncorrected log K_OA values, which were directly estimated from the calculated solvation free energy of individual molecules, underestimated experimental values, and the deviation increased with increasing log K_OA. Dimers were found to greatly affect the apparent K_OA values of these aromatic pollutants, which were driven by π-π interactions. London dispersion and exchange-repulsion terms were identified to be dominant components of the underlying π-π interactions. It is interesting to find that the π-π interactions of polybrominated diphenyl ethers correlate with not only the molecular polarizability but also the size of opposing aromatic surfaces, which leads to a different trend of π-π interactions from other aromatic pollutants. A universal quantitative structure-activity relationship model was developed to estimate the proportion of dimers based on five molecular structural descriptors relevant to the π-π interactions. After calibration with the dimer effect, estimations of log K_OA were consistent with experimental values. Therefore, the dimer effect should be taken into consideration when investigating the partition behavior of aromatic pollutants, and the solvation free energy model could be an alternative method for the prediction of K_OA.

Enhanced Built-in Electric Field Promotes Photocatalytic Hydrogen Performance of Polymers Derived from the Introduction of B←N Coordination Bond

High concentrations of active carriers on the surface of a semiconductor through energy/electron transfer are the core process in the photocatalytic hydrogen production from water. However, it remains a challenge to significantly improve photocatalytic performance by modifying simple molecular modulation. Herein, a new strategy is proposed to enhance the photocatalytic hydrogen evolution performance using boron and nitrogen elements to construct B←N coordination bonds. Experimental results show that polynaphthopyridine borane (PNBN) possessing B←N coordination bonds shows a hydrogen evolution rate of 217.4 µmol h^-1 , which is significantly higher than that of the comparison materials 0 µmol h^-1 for polyphenylnaphthalene (PNCC) and 0.66 µmol h^-1 for polypyridylnaphthalene (PNNC), mainly attributed to the formation of a strong built-in electric field that promotes the separation of photo-generated electrons/holes. This work opens up new prospects for the design of highly efficient polymeric photocatalysts at the molecular level.

Theoretical Exploration of Peculiar Sandwich-Type Clusters Formed by the Coordination of E92- (E = Si, Ge, Sn) Zintl Clusters: Structural Properties, Active Sites, and Hydrogen Storage

A peculiar heterogeneous metal sandwich fragment {(Ge₉)₂[η⁶-Ge(PdPPh₃)₃]}^4- anion cluster was synthesized for the first time by Xu et al. (Xu, H. L.; Tkachenko, N. V.; Wang, Z. C.; Chen, W. X.; Qiao, L.; Munoz-Castro, A.; Boldyrev, A. I.; Sun, Z. M. Nat. Commun.2020, 11, 5286). In this work, novel analogous sandwich compounds ({(E₉)₂[η⁶-E(PdPH₃)₃]}^4- (E = Si (1), Ge (2), Sn (3)) were studied using quantum chemical calculations and wave function analysis to determine the geometry, bonding nature, aromaticity, active sites, and hydrogen storage. Structural analysis revealed that the clusters were compounds formed by the coordination of two E₉^2- (E = Si, Ge, Sn) Zintl clusters with a central E@Pd₃ (E = Si, Ge, Sn) interlayer. The steric hindrance at both ends is small, facilitating facile attachment to other molecules. The valence states of the central atom E (E = Si, Ge, Sn) are close to zero, indicating that they are stable novel heterometallic sandwich compounds, and the Zintl ligands at both ends are negative, thus they can react with Lewis acids. Bonding analysis showed that the E₉^2- (E = Si, Ge, Sn) cluster has a delocalized framework bonding mode. For aromaticity analysis, we used AdNDP, ELF, LOL, ICSS, and NICS to qualitatively and quantitatively clarify that these clusters possess the characteristics of overall delocalization, σ aromaticity, and remarkable stability. By analyzing the unique structure and predicting the reaction sites, we concluded that the E₉^2- ligand reacts with Lewis acids. Finally, through the adsorption of hydrogen molecules, the average adsorption energies of 1-3 were 0.387, 0.374, and 0.325 eV per H₂ molecule, respectively, meeting the physical adsorption standard, with the adsorption effect of 3 being slightly more superior than that of 1 and 2. Our study represents a substantial step forward in the study of high-density materials for volumetric H₂ storage applications.

A combined QTAIM/IRI topological analysis of the effect of axial/equatorial positions of NH2 and CN substituents in the [(PY5Me2)MoO]+ complex

By means of the Interaction Region Indicator (IRI) and Quantum Theory of Atoms in Molecules (QTAIM), the influence exerted by NH₂ (amino) and CN (cyano) as electron donor and electron acceptor substituent groups, respectively, located at para-positions of axial and equatorial pyridine rings of derivatized complexes coming from the [(PY₅Me₂)MoO]⁺ complex during the hydrogen molecular release in the gas phase was analyzed. In any case, a H-H covalent bond is forming at the transition state, with a strengthening of the electron density of 5.5% when the substituent group involved is NH₂ at the para-position of the axial pyridine ring. However, there was no difference between NH₂ and CN when these substituent groups are located at the para-positions of the equatorial pyridine rings. The topological properties of electron densities from the QTAIM are not perturbed by the electron donor and electron acceptor nature of the substituents, even when these substituent groups are located at the axial or equatorial pyridine rings of the Mo-based complex.

Metal Confined in 2D Membranes for Molecular Recognition and Sieving towards Ethylene/Ethane Separation

Membranes with nanochannels have exhibited great potential in molecular separations, while it remains a great challenge to separate molecules with very close physical properties and kinetic diameters (e.g., ethylene/ethane) owing to the lack of size-sieving property and specific affinity. Herein, a metal confined 2D sub-nanometer channel is reported to successfully discriminate ethylene over ethane via molecular recognition and sieving. Transition metal cations are paired with polyelectrolyte anions to achieve high dissociation activity, forming reversible complexation with ethylene. Aberration-corrected transmission electron microscopy observes that the metals with size of ≈2 nm are uniformly confined in graphene oxide (GO) interlayer channels with average height of ≈0.44 nm, thereby cooperating the size-sieving effect with a molecular recognition ability toward ethylene and stimulating its selective transport over ethane. The resulting ultrathin (≈60 nm) membrane exhibits superior ethylene/ethane separation performance far beyond the polymeric upper-bound. Density functional theory (DFT) and molecular dynamic simulations reveal that the metal@2D interlayer channel provides a molecular recognition pathway for selective gas transport. The proposed metal confined in 2D channel with molecular recognition and sieving properties would have broad application in other related fields such as single-atom catalysis, sensor and energy conversion.

C-C bonded bis-5,6 fused triazole-triazine compound: an advanced heat-resistant explosive with high energy and low sensitivity

It is still an urgent problem in the field of energetic materials to explore the synthesis of heat-resistant compounds with balanced energy and thermal stability through simple synthetic routes. Recently, fused compounds are considered to provide a promising framework for the construction of ideal heat-resistant compounds. In this study, three novel C-C bonded bis-5,6 fused triazole-triazine compounds, 3,3'-dinitro-[7,7'-bi[1,2,4]triazolo[5,1-c][1,2,4]triazine]-4,4'-diamine (2), 4,4'-diamino-[7,7'-bi[1,2,4]triazolo[5,1-c][1,2,4]triazine]-3,3'-dicarbonitrile (3), and 3,3'-di(1H-tetrazol-5-yl)-[7,7'-bi[1,2,4]triazolo[5,1-c][1,2,4]triazine]-4,4'-diamine (4), were synthesized by a simple method. Compound 2 exhibited an approaching detonation velocity of 8837 m s^-1 compared with that of the traditional high energy explosive RDX velocity of 8795 m s^-1, while its thermal stability (T_d = 327 °C) was comparable to that of the heat-resistant explosive HNS (T_d = 318 °C). At the same time, the double fused compound 2 also realized high density (1.90 g cm^-3) and extremely low sensitivity (FS > 360 N, IS > 40 J). The above good comprehensive properties prove that compound 2 can be used as a potential insensitive high-energy heat-resistant explosive. In addition, the effects of the crystal structure on the sensitivity and thermal stability were studied using the quantum chemical methods. These results imply that the formation of double fused ring compounds by the ring closing reaction at symmetrical positions is an ideal strategy for the development of advanced heat-resistant explosives.

DFT calculations, structural analysis, solvent effects, and non-covalent interaction study on the para-aminosalicylic acid complex as a tuberculosis drug: AIM, NBO, and NMR analyses

In this study, the effect of non-covalent interactions on the para-aminosalicylic acid complex is explored using density functional theory (DFT) in the gas phase and the solution. Our findings exhibit that the achieved binding energies considerably change on going from the gas phase to the solution. Based on the obtained results, the absolute value of the binding energy of the complex in the polar solvents is lower than the non-polar ones while in the gas phase it is higher than the solution. The atoms in molecules (AIM) and the natural bond orbital (NBO) analyses are applied to estimate the topological properties and the charge transfer during complexation, respectively. The results indicate that the presence of the cation-π interaction increases the strength of the intramolecular hydrogen bond in the studied complex. Finally, the various electronic descriptors such as energy gap, hardness, softness, and electronic chemical potential are investigated to gain further insight into these interactions. According to the achieved results, the high energy gap of the complex in the water solvent indicates high chemical stability and low reactivity compared to the others. On the other hand, the most reactive as well as the softest complex belongs to the gas phase.

Unexpected catalytic influence of atmospheric pollutants on the formation of environmentally persistent free radicals

Environmentally persistent free radicals (EPFRs) have been recognized as harmful and persistent environmental pollutants. In polluted regions, many acidic and basic atmospheric pollutants, which are present at high concentrations, may influence the extent of the formation of EPFRs. In the present paper, density functional theory (DFT) and ab-initio molecular dynamics (AIMD) calculations were performed to investigate the formation mechanisms of EPFRs with the influence of the acidic pollutants sulfuric acid (SA), nitric acid (NA), organic acid (OA), and the basic pollutants, ammonia (A), dimethylamine (DMA) on α-Al₂O₃ (0001) surface. Results indicate that both acidic and basic pollutants can enhance the formation of EPFRs by acting as "bridge" or "semi-bridge" roles by proceeding via a barrierless process. Acidic pollutants enhance the formation of EPFRs by first transferring its hydrogen atom to the α-Al₂O₃ surface and subsequently reacting with phenol to form an EPFR. In contrast, basic pollutants enhance the formation of EPFRs by first abstracting a hydrogen atom from phenol to form a phenoxy EPFR and eventually interacting with the α-Al₂O₃ surface. These new mechanistic insights will inform in understanding the abundant EPFRs in polluted regions with high mass concentrations of acidic and basic pollutants.

Reconsideration of the Structures of Stemara-13(14)-en-18-ol and Related Diterpene Natural Products: Vinylic Hydrogen Chemical Shifts Are Key

The reported synthesis of stemara-13(14)-en-18-ol, which revealed that the structure of this natural product was misassigned, prompted an investigation using density functional theory methods into the structural reassignment of this natural product and related diterpenoids extracted from Calceolaria plants. ¹H and ¹³C chemical shift predictions led to the reassignment of relative configuration, and in one case the carbon skeleton, of several diterpenoids from Calceolaria. In many of these cases, the chemical shift of the vinylic hydrogen was found to be diagnostic.

Effect of polystyrene microplastics on the degradation of sulfamethazine: The role of persistent free radicals

Microplastic (MPs) pollution is increasingly becoming a global environmental problem. MPs entering the environment are subjected to various aging processes, among which photoaging is the most important process leading to MPs oxidation. Persistent free radicals (EPFRs) are formed on the surface of MPs during photoaging, but it is not clear whether EPFRs on the surface of MPs can produce reactive oxygen species (ROS) and thus degrade organic pollutants. In this study, with polystyrene (PS) as the representative plastic and sulfamethazine (SMT) degradation as the target pollutant, the effect and mechanism of light-induced PS on SMT degradation were investigated by experiment and theoretical calculation. It was found that PS can stimulate the production of ROS under sunlight, which can significantly improve the degradation rate of SMT. Through quenching experiment and free radical trapping experiment, it was found that the mechanism of PS promoting the degradation of SMT was mainly due to the production of hydroxyl radical (·OH) in the system, and ·OH was the main ROS species affecting the oxidative degradation of SMT. The characterization results show that the high reactive oxygen generation ability of PS under solar irradiation was due to the abundant photoactive oxidation functional groups on its surface. In addition, the key reaction sites of SMT were predicted by density functional theory (DFT) calculation. The results of different calculations consistently showed that the sulfonamide group of SMT, the pyrimidine heterocycle and the amino group of aniline are the reaction sites of ·OH priority attack. The main intermediates were determined by UHPLC-HRMS/MS. Combined with theoretical calculation, it was proposed that the oxidative degradation pathway of SMT mainly includes SN bond cleavage, SMILES rearrangement and SO₂ group removal. This study clarified the effect of PS on the degradation of organic pollutants under light, and provided theoretical guidance for the degradation mechanism.