Electrostatic Potential Surface Research Articles

Structural basis for double-stranded RNA recognition by SID1.

The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 Å. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between β-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2'-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.

Supramolecular Assemblies in Mn (II) and Zn (II) Metal–Organic Compounds Involving Phenanthroline and Benzoate: Experimental and Theoretical Studies

Two new Mn(II) and Zn(II) metal–organic compounds of 1,10-phenanthroline and methyl benzoates viz. [Mn(phen)2Cl2]2-ClBzH (1) and [Zn(4-MeBz)2(2-AmPy)2] (2) (where 4-MeBz = 4-methylbenzoate, 2-AmPy = 2-aminopyridine, phen = 1,10-phenanthroline, 2-ClBzH = 2-chlorobenzoic acid) were synthesized and characterized using elemental analysis, TGA, spectroscopic (FTIR, electronic) and single crystal X-ray diffraction techniques. The crystal structure analysis of the compounds revealed the presence of various non-covalent interactions, which provides stability to the crystal structures. The crystal structure analysis of compound 1 revealed the formation of a supramolecular dimer of 2-ClBzH enclathrate within the hexameric host cavity formed by the neighboring monomeric units. Compound 2 is a mononuclear compound of Zn(II) where flexible binding topologies of 4-CH3Bz are observed with the metal center. Moreover, various non-covalent interactions, such as lp(O)-π, lp(Cl)-π, C–H∙∙∙Cl, π-stacking interactions as well as N–H∙∙∙O, C–H∙∙∙O and C–H∙∙∙π hydrogen bonding interactions, are found to be involved in plateauing the molecular self-association of the compounds. The remarkable enclathration of the H-bonded 2-ClBzH dimer into a supramolecular cavity formed by two [Mn(phen)2Cl2] complexes were further studied theoretically using density functional theory (DFT) calculations, the non-covalent interaction (NCI) plot index and quantum theory of atoms in molecules (QTAIM) computational tools. Synergistic effects were also analyzed using molecular electrostatic potential (MEP) surface analysis.

Dissolution behavior and thermodynamic study of N-ethyl-2,2-diisopropylbutylamide in fourteen mono solvents by experiments and molecular simulation

N-ethyl-2,2-diisopropylbutylamide (WS-27) is a new cooling agent with a soothing, long-lasting cooling effect, widely used in personal care and cosmetic products. The dissolution behavior of WS-27 in fourteen mono solvents (methanol, ethanol, n-propanol, isopropanol, n-butanol, n-pentanol, methyl acetate, ethyl acetate, isopropyl acetate, propyl acetate, butyl acetate, dichloromethane, cyclohexanone, and acetone) was measured using a dynamic laser monitoring method from 263.15 K to 298.15 K under 101.6 ± 1.2 kPa. In these selected solvents, the solubility of WS-27 increased with increasing temperature. The van't Hoff equation, λh equation, modified Apelblat equation, Wilson model, and NRTL (non-random two-liquid) model were applied to correlate the experimental solubility data of WS-27, and the modified Apelblat equation showed the best-fitting results. In addition, the intermolecular interactions and solvent effect were analyzed using the Hirshfeld surface analysis, molecular electrostatic potential surface analysis, and KAT-LSER model analysis to understand the dissolution behavior of WS-27. The results indicate that the solubility of WS-27 is influenced by multiple factors, and there can be other factors as well. These fundamental data can provide essential information for the crystallization and purification process of WS-27.

[Ti{η5-1-(SiMe3)-3-(R)-C9H5}Cl2(OEt)] half-sandwich complexes: Synthesis, solid-state structure, hirshfeld surface analysis and theoretical studies

Indenyl-titanium trichloride complexes of type [Ti{η5-1-(SiMe3)-3-(R)-C9H5}Cl3] (R = SiMe3 (3a); R = tBu (3b)) were obtained by treatment of Li[1-(SiMe3)-3-(R)-C9H5] (R = SiMe3 (1a); R = tBu (1b)) with titanium tetrachloride (2) in a 1:1 molar ratio in the presence of isopropanol and SOCl2. Compounds [Ti{η5-1-(SiMe3)-3-(R)-C9H5}Cl2(OEt)] (R = SiMe3 (4a); R = tBu (4b)) are accessible by reacting 1a,b (R = SiMe3 (1a); R = tBu (1b)) with TiCl4 (2) in the presence of ethanol and SOCl2, or when 3a,b were treated with equimolar amounts of EtOH in refluxing benzene. Spectroscopic methods and single crystal X-ray diffraction analysis confirmed the piano-stool geometry of 3a and 4b in the solid state. Hirshfeld surface analysis using 2D fingerprint plots of 3a and 4b were conducted to elaborate non-covalent, intermolecular interactions existing in the solid state, which accounted for the strengthening of the crystal lattice. The molecular structures of the 3 and 4 were further investigated by quantum-chemical calculations. The geometries of the compounds were optimized at the B3LYP/6-31G(d)+LANL2DZ level of theory, and their related molecular parameters including frontier orbital energy gap and molecular electrostatic surface potential have also been calculated to better understand their properties.

Synthesis, structure, and small molecule in situ modification effects on proton conduction properties of triazine‐based triscarboxylic acid complexe

In this study, we synthesized and characterized a new Co(II)‐based coordination polymer, denoted as {[Co(HL)(dpa)]·H2O}n (1), derived from the H3L ligand and dpa co‐ligand. Single crystal X‐ray diffraction revealed that 1 forms a two‐dimensional (2D) layer and a three‐dimensional (3D) supramolecular structure via hydrogen bonding interactions. Presence of carboxylic acid groups in 1 was confirmed by X‐ray crystallography, prompting investigation into its proton transport properties. Additionally, electrostatic potential surface and nucleophilic index analyses were conducted to simulate potential proton transfer pathways. Furthermore, we prepared nine modified encapsulated materials using 1 as the base material (SDA@1, APH@1, APY@1, TA@1, BA@1, DIC@1, IDZ@1, SCA@1, and TYD@1), and tested their proton conductivity and activation energy compared to pure Nafion membrane and 1, analyzing the influence of different small molecule structures on proton conductivity. Comparative analysis revealed that only SDA@1 exhibited enhanced proton conductivity and reduced activation energy at 303 K, with an improvement rate of 220.8%. We hope that the methods presented herein can provide valuable insights for the design and development of high‐performance proton‐conducting materials, as well as for the exploration of proton conduction mechanisms.

Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist?

This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.

Insight into the solution thermodynamic properties of cimetidine form A and form B based on experiments and molecular simulations

Cimetidine (CIM) is an antagonist of the type II histamine receptors, and act as a significant agent in the treatment of stomach ulcers. In this work, the effect of polymorphism and solvent type on the thermodynamic properties of CIM was investigated based on experimental results and molecular simulations. The solubility data of two polymorphs for CIM (forms A and B) in organic solvents were measured and correlated with four thermodynamic models. It could be found that the solubility of CIM form A is higher compared to form B. In addition, molecular simulations were adopted to investigate the mechanism of the solubility and stability of the two forms. Hirshfeld surface analysis shows that strong H···N interaction contributes to better stability of form B. Meanwhile, molecular electrostatic potential surface and radial distribution function results indicate that the solubility behavior is significantly influenced by the intensity of the solute–solvent interactions. Finally, the dissolution thermodynamic properties, including the enthalpy change, the Gibbs energy change, and the entropy change, were calculated and the results show that the dissolution process of CIM is endothermic, entropy-driven and spontaneous.

Effect of TX-100 on solubilizing power of CTAB and CPC for H Acid: An experimental and computational analysis

The present research work investigates the solubility of an anionic dye 8-amino-1-naphthol-3,6-disulfonic acid (H Acid) within the micellar mediaof two cationic surfactants cetylpyridinium chloride (CPC) and cetyltrimethylammonium bromide (CTAB) as well as in the mixed micellar mediaof each cationic surfactant with Triton X-100 (TX-100). The data from differential absorption spectroscopy across a concentration range spanning from pre-micellar to post-micellar regions was used to determine the degree of solubilization by calculating the partition coefficient (Kx), binding constant (Kb) and Gibbs free energy associated with the relevant processes. Electrical conductivity of each cationic surfactant in the presence of H Acid was recorded in aqueous media and used to determine the CMC and subsequent thermodynamic parameters including entropy (ΔSm), enthalpy (ΔHm) and Gibbs free energy change (ΔGm) associated with the process of micellization. The computational analysis was carried out with GAUSSIAN 09 using a 6-311G + basis set with a DFT/ B3LYP hybrid approach and each set of energy minimization was executed to perform frequency calculations for Frontier molecular orbital analysis and to evaluate absorption spectra. Moreover, the molecular electrostatic potential surfaces (MESP) were also computed to find their suitable hydrophobic and hydrophilic interactions.

Structural homology-based identification of BEN domain proteins in Poxviruses

BEND family transcription factors directly interact with DNA through BEN domains and have been found across metazoan species. Interestingly, certain insect and mammalian viruses have also hijacked Bend genes into their genome. However, the phylogenetic classification and evolution of these viral BEN domains remain unclear. Building on our previous finding that in silico method accurately determine the 3D model of BEN domains, we used AlphaFold2 to predict the tertiary structures of poxviral BEN domains for comprehensive homologous comparison.We revealed that the majority of poxviral BEN modules exhibit characteristics of type II BEN. Additionally, electrostatic surface potential analysis found various poxviral BEN domains, including the first BEN of OPG067 in Orthopoxvirus, the third BEN of OPG067 in Yatapoxvirus and the third BEN of MC036R in MCV, have positively charged protein surfaces, indicating a structural basis for DNA loading. Notably, MC036R shares structural resemblance with human BEND3, as they both contain four BEN domains and an intrinsically disordered region. In summary, our discoveries provide deeper insights into the functional roles of BEN proteins within poxviruses.

Mechanism analysis and energy-saving intensified exploration of green mixed solvents extractive distillation to separate ether-containing azeotropes

2-Methoxyethanol is an important solvent with wide application prospects. Recovering 2-Methoxyethanol from wastewater has significant environmental and economic benefits. In this work, quantum chemistry methods are used to calculate the surface electrostatic potential, mutual penetration analysis, and reduced density gradient-independent gradient model of solvents and azeotrope. From the perspective of the mechanism of action, suitable extractants are selected. With the minimum total annual cost as the goal, the splendid process parameters and the excellent ratio of mixed solvents (30 % 1-ethyl-3-methylimidazole acetate + 70 % N, N-dimethyl acetamide) are acquired. Moreover, two reinforcing processes for energy saving and consumption reduction are also researched. All processes are appraised from three aspects: economy, environment and exergy. The results show that the total annual cost and gas emission of mixed solvent extraction distillation are reduced by 26.79 % and 35.45 %, respectively, compared with the process with NMP as an entrainer. Compared with the process with [EMIM][AC] as an entrainer, the total annual cost and gas emissions are reduced by 44.99 % and 25.04 %, respectively. Relative to mixed solvent, the total annual cost and gas emissions of the heat pump combined with mixed solvent extractive distillation technology decreased by 6.77 % and 21.78 % respectively, while that of the heat integration process decreased via 9.93 % and 12.30 % respectively. From the point of view of environmental sustainability, the process effect combined with the heat pump is better, and from the point of view of economic benefits, the heat integration process has better performance. This study reveals the intrinsic relationship between the structure of mixed solvents and explores the intensification of the process, which provides a theoretical basis for the industrial separation of 2-Methoxyethanol/water azeotrope.

Mutation of Disulfide Bond Sites Reduces the Immunoreactivity of Cra a 4 by Changing the Structural Characteristics.

Sarcoplasmic calcium-binding protein (Cra a 4) from Crassostrea angulata belongs to the EF-hand superfamily, and understanding of its structure-allergenicity relationship is still insufficient. In this study, chemical denaturants were used to destroy the structure of Cra a 4, showing that disruption of the structure reduced its IgG-/IgE-binding activity. To explore which critical amino acid site affects the allergenicity of Cra a 4, the mutants were obtained by site-directed mutations in the disulfide bonds site (C97), conformational epitopes (I105, D114), or Ca2+-binding region (D106, D110) and their IgG-/IgE-binding activity was reduced significantly using serological tests. Notably, C97A had the lowest immunoreactivity. In addition, two conformational epitopes of Cra 4 were verified. Meanwhile, the increase of the α-helical content, surface hydrophobicity, and surface electrostatic potential of C97A affected its allergenicity. Overall, the understanding of the structure-allergenicity relationship of Cra a 4 allowed the development of a hypoallergenic mutant.

Crystallographic and theoretical analysis of a spirohydantoin derivative: 3-(4‑tert-butylbenzoyl)-1,3-diazaspiro[4.5]decane-2,4‑dione

Providing structural information on drug-like compounds is a significant step in efforts to develop innovative drugs with balanced solubility, cell permeability and target binding. In this paper, a new cyclohexane-5-spirohydantoin tethered with a 4‑tert-butylbenzoyl group was synthesized and its crystal structure was determined using the single crystal X-ray diffraction. The Hirshfeld surface analysis was used to gain a preliminary insight into the proportion and nature of the intermolecular interactions in the crystal structure, while their quantitative description is further presented in terms of a systematic analysis of dimeric motifs representing different recognition modes. A combination of N–H∙∙∙O and C(sp3)–H∙∙∙O hydrogen bonds, C(sp3)–H∙∙∙π, lone-pair∙∙∙π and π∙∙∙π stacking interactions links the molecules into a bilayer having two carbonyl O atoms exposed to the exterior. Further stacking of the bilayers occurs through C(sp3)–H∙∙∙O hydrogen bonds involving these O atoms as acceptors, C(sp3)–H∙∙∙π and π∙∙∙π stacking interactions between the phenyl groups. The molecular electrostatic potential surface map reveals that the carbonyl O atoms of the hydantoin ring and the phenyl ring are electrophilic centers, while the N1–H1 group is a nucleophilic center. The calculated HOMO and LUMO energies were used to semiquantitatively estimate the global reactivity descriptors suggesting the soft nature of the molecule.

Synthesis, spectroscopic analysis (FT-IR, FT-Raman, UV, NMR), non-covalent interactions (RDG, IGM) and dynamic simulation on Bis(8‑hydroxy quinoline) salicylate salicylic acid

Using spectrum techniques and density functional theory (DFT) reckonings, structural, vibrational and electrical characteristics of Bis(8‑hydroxy quinoline) salicylate salicylic acid (8HQSA) were determined. Characterizing the chemical under inquiry involved employing FT-IR, FT-Raman, UV–vis spectral studies and single crystal X-ray diffraction (SCXRD). For the characterization, the B3LYP approach inside the structure of DFT was employed, with a 6–311++G(d,p) basis set. The structural study shows that the stability of 8HQSA crystalline structure arising from N–H⋯O, C–O⋯H and O–H⋯O hydrogen bonding interactions. The 1H and 13C NMR chemical shifts were calculated using Gauge Independent Atomic Orbital (GIAO) technical. Vibrational frequencies and molecular geometry were computed and likened with experimental data. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, van der Waals and steric effect in 8HQSA were visualized and quantified by the independent gradient density (IGM) based on the trimolecular density. The hyper-conjugative and the delocalization of charge in 8HQSA have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MEP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The positions of the molecule's nucleophilic and electrophilic groups were ascertained using Fukui analysis. To describe the size, structure, and reactive sites of the molecules, the molecular electrostatic potential and total electron density are calculated. With a band gap (2.58 eV), FMO study indicates that the material is both bioactive and stable. The ADMET factor and drug similarity are used to predict 8HQSA's pharmokinetic characteristics. Based on the findings, it can be concluded that the 8HQSA particle is optimally crystallised and recommended as a preventative measure against bacterial and fungal infections. The stability of the title compound has been investigated via molecular dynamics simulations. In-vitro antimicrobial activity results clearly reveal that in all the four strains, activity increases with increase in compound concentration and the inhibition of the strains also increases. From both molecular docking and In-vitro Antimicrobial Activity the title compound can be certified that it inhibits antimicrobial activity.

Synthesis, structural, multitargeted molecular docking analysis of anti-cancer, anti-tubercular, DNA interactions of benzotriazole based macrocyclic ligand

Biologically important macromolecule 1, 1′, 3, 3′ Bis − [2,3,5,6-Tetramethyl-p-phenylenebis(methylene)] dibenzotriazlinium dibromide hydrate (BTD) was synthesized and characterized using FT-IR, NMR and single-crystal XRD (SCXRD). SCXRD revealed that the compound was crystallized as a monoclinic system and associated through weak intermolecular interactions like H-bonding and π- π stacking interactions. These weak intermolecular interactions in BTD were studied using Crystal Explorer and Gaussian. The calculated energies for the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) showed the stability and reactivity of the title compound. Molecular electrostatic potential (MEP) surface analysis was used to investigate the crystal’s nucleophilic and electrophilic reactive sites. The molecular shape and intermolecular interactions in the crystal structure were determined using Hirshfeld surface analysis and fingerprint plots. Anticancer, anti-bacterial and DNA binding ability of BTD were investigated by experimental and theoretical techniques. The obtained results suggest that BTD possesses better anti-cancer, anti-bacterial and DNA binding abilities. The mode of action of antibiotic and anticancer approach was discussed. This provides promising therapeutic advantages for further development.

Experimental and simulation study on the solubility of 1-naphthylamine in twelve neat solvents

To meet the demand of separating and purifying 1-naphthylamine from the reaction production and filling the solubility data gap, the solubility of 1-naphthylamine in twelve pure solvents (acetone, acetonitrile, ethyl acetate, n-butyl acetate, cyclohexane, n-heptane, methanol, ethanol, n-propanol, iso-propanol, n-butanol, and iso-butanol) was experimentally investigated in the range from 273.15 K to 308.15 K. It was found that the solubility of 1-naphthylamine increases markedly with increasing temperature in all solvent systems. The maximum solubility was 0.8978 (in the solvent of acetone,T = 308.15 K) and the minimum solubility was 0.005485 (in the solvent of n-heptane, T = 273.15 K). Then the experimental solubility data was correlated by the modified Apelblat model, Van't Hoff model, NRTL model, Wilson model, and Margules model. ARD% was calculated to assess the accuracy of the five equations and the results indicated that the modified Apelblat model fits optimally with an average ARD% value of 1.62 %. The effects of various physicochemical properties such as solvent polarity, hydrogen bond donor, hydrogen bond acceptor, and cohesive energy density on solute dissolution behavior were explored. In addition, the apparent thermodynamic properties of 1-naphthylamine in different solvents were analyzed based on modified Van’t Hoff model, which indicated the dissolution process of 1-naphthylamine in selected solvents is endothermic and entropy-driving. Finally, the effect of intermolecular interactions on the dissolution behavior was investigated at the molecular scale through molecular dynamics simulation studies, including molecular electrostatic potential surface, solvation free energy and radial distribution function analysis. This work will provide a fundamental guidance for the crystallization, separation, and purification of 1-naphthylamine.

Engineering a photothermal responsive cellulose carbon capture material for solar-driven CO2 desorption

The utilization of the solar-driven CO2 desorption of carbon capture materials opens a promising avenue to reduce energy consumption in the carbon capture process. A crucial aspect is the careful coordination of materials' adsorption capacity and regeneration temperature. In this study, a photothermal responsive carbon capture material was developed by incorporating a photothermal responsive cellulose nanofiber matrix skeleton with a temperature-sensitive Pluronic® F-127 and polyethyleneimine. These components formed a staggered network through crosslinking with epichlorohydrin. The devised preparation strategy demonstrated a remarkable conversion rate of 99 % for the reaction reagents. The resulting carbon capture material exhibited a high amino density of 14.18 mmol/g and a substantial adsorption capacity of 6.92 mmol/g. Notably, the shrinkage of Pluronic® F-127 molecular chains at elevated temperatures led to an increased surface electrostatic potential and the passivation of amino groups. This transformation endowed the material with a solar-driven regeneration temperature as low as 55 °C, representing an efficient approach to reduce energy consumption during the regeneration process of carbon capture materials.

Synthesis, NMR, electronic properties using DFT study and anticancer activity of 3-methyl-6-(m-tolylamine) quinazolin-4(3H)-one

3-methyl-6-(m-tolylamine) quinazolin-4(3H)-one (MTAQ) was synthesized. Its formation was ascertained with the help ESI mass spectroscopy in conjunction with 1HNMR spectroscopy. Anticancer activity of MTAQ was measured experimentally, for human carcinoma cell line pertaining to cervix (HeLa). Optimized structure parameters, Frontier molecular orbital (FMO) behavior, non linear optical (NLO) profile, molecular electrostatic potential surface (MESP), Fukui functions (FF) and thermodynamic parameters were evaluated for the molecule of interest employing DFT/B3LYP/6–311++G(d,p) formalism. TD-DFT was made use of to calculate absorption maxima (λmax) of electronic transitions for the molecule in CDCl3 solvent. Frontier molecular orbitals revealed the origin of UV–Vis spectrum and to comprehend chemical reactivity of the molecule. Good coincidence was noticed between measured and computed structure parameters, UV–Vis spectra, and 1HNMR signals. Fukui functions helped in identifying electrophilic and nucleophilic centers of MTAQ. The calculations showed that MTAQ exhibits significant NLO activity in addition to predicting existence of intramolecular hydrogen bond.

Fascinating inclusion of metal–organic complex moieties in dinuclear Mn(II) and Zn(II) compounds involving pyridinedicarboxylates and phenanthroline: Experimental and theoretical studies

In the present study, we have reported the synthesis of two new dinuclear Mn(II) and Zn(II) metal–organic compounds, [Mn(2,5-PDC)(phen)2][Mn(phen)2(H2O)2]2Cl·10H2O (1) and [Zn(phen)3][Zn(2,6-PDC)2]·11.5H2O (2) (where, 2,5-PDC = 2,5-pyridinedicarboxylate, 2,6-PDC = 2,6-pyridinedicarboxylate, phen = 1,10-phenanthroline) at room temperature which have been characterized by elemental analysis, TGA, spectroscopic (FTIR, electronic) and single crystal X-ray diffraction techniques. A fascinating chloride-water supramolecular cluster in 1 and (H2O)13 H-bonded cluster in 2 along with π-stacked assemblies stabilize the solid state structures. The most interesting aspect of the crystal structure of 1 is the inclusion of complex cationic moieties within the infinite self-assembled chloride-water cluster. Similarly the inclusion of cationic complex moieties in compound 2 inside the supramolecular cavity formed by the anionic complex provides rigidity to the crystal structure. DFT calculations, molecular electrostatic potential (MEP) surface analysis, quantum theory of atoms-in-molecules (QTAIM) and the non-covalent index plot (NCI plot) analysis were performed to investigate the supramolecular assemblies of the compounds. The studies reveal that the antiparallel π-stacking interactions are energetically significant synthons for the assemblies. However, the assemblies in 2 have been dominated mostly by Columbic attraction of the cationic and anionic complex moieties.

Purification, crystallization and preliminary crystallographic analysis of Chlamydophila pneumoniae AP endonuclease IV

Base excision is a crucial DNA repair process mediated by endonuclease IV in nucleotide excision. In Chlamydia pneumoniae, CpendoIV is the exclusive AP endonuclease IV, exhibiting DNA replication error-proofreading capabilities, making it a promising target for anti-chlamydial drug development. Predicting the structure of CpendoIV, molecular docking with DNA was performed, analyzing complex binding sites and protein surface electrostatic potential. Comparative structural studies were conducted with E. coli EndoIV and DNA complex containing AP sites.CpendoIV was cloned, expressed in E. coli, and purified via Ni-NTA chelation and size-exclusion chromatography. Low NaCl concentrations induced aggregation during purification, while high concentrations enhanced purity.CpendoIV recognizes and cleaving AP sites on dsDNA, and Zn2+ influences the activity. Crystallization was achieved under 8% (v/v) Tacsimate pH 5.2, 25% (w/v) polyethylene glycol 3350, and 1.91 Å resolution X-ray diffraction data was obtained at 100 K. This research is significant for provides a deeper understanding of CpendoIV involvement in the base excision repair process, offering insights into Chlamydia pneumoniae.

Photochemical properties and toxicity of fluoroquinolone antibiotics impacted by complexation with metal ions in different pH solutions

Acid-base dissociable antibiotic-metal complexes are known to be emerging contaminants in the aquatic environments. However, little information is available on the photochemical properties and toxicity of these complex forms. This study investigated the spectral properties of three fluoroquinolones (FQs) with and without metal ions Fe(III), Cu(II), and Al(III) in solutions under different pH conditions, as well as evaluated the changes in toxicity due to the complex with these metal ions using luminescent bacteria (vibrio fischeri). FQs showed a higher tendency to coordinate metal ions under alkaline conditions compared to neutral and acidic conditions, and the formation of complexes weakened the ultraviolet-absorbing ability of FQs. At pH = 7.0, Cu(II) quenched the fluorescence intensity of FQs. Moreover, their Fourier-transform infrared spectroscopy and X-ray photoelectron spectroscopy were explored, revealing that the coordination sites of Cu(II) in three FQs were situated in a bidentate manner through the oxygen atom of the deprotonated carboxyl group and cyclic carbonyl oxygen atom. This conclusion was further verified by the theory of molecular surface electrostatic potential. In addition, except for complexes of ciprofloxacin-metals, enhanced toxicity of FQs upon coordination with Fe(III) was observed, while reduced toxicity was found for coordination with Cu(II) and Al(III). These results are important for accurately evaluating the photochemical behavior and risk of these antibiotics in aquatic environments contaminated with metal ions.