Formation Of Molecular Complexes Research Articles

Analytic and In Silico Methods to Understand the Interactions between Dinotefuran and Haemoglobin.

This work lies in the growing concern over the potential impacts of pesticides on human health and the environment. Pesticides are extensively used to protect crops and control pests, but their interaction with essential biomolecules like haemoglobin remains poorly understood. Spectrofluorometric, electrochemical, and simulations investigations have been chosen as potential methods to delve into this issue, as they offer valuable insights into the molecular-level interactions between pesticides and haemoglobin. The research aims to address the gaps in knowledge and contribute to the development of safer and more sustainable pesticide practices. The interaction was studied by spectroscopic techniques (UV-Visible & Fluorescence), in silico studies (molecular docking & molecular dynamics simulations) and electrochemical techniques (cyclic voltammetry and tafel). The studies showed effective binding of dinotefuran with the Hb and will cause toxicity to human. The formation of a stable molecular complex between ofloxacin and hemoglobin was shown via molecular docking and the binding energy was found to -5.37 kcal/mol. Further, molecular dynamics simulations provide an insight for the stability of the complex (Hb-dinotefuran) for a span of 250 ns with a binding free energy of -53.627 kJ/mol. Further, cyclic voltammetry and tafel studies for the interaction of dinotefuran with Hb effectively.

Retraction Note: Verteporfin-induced formation of protein cross-linked oligomers and high molecular weight complexes is mediated by light and leads to cell toxicity

Retraction Note: Verteporfin-induced formation of protein cross-linked oligomers and high molecular weight complexes is mediated by light and leads to cell toxicity

Biophysical and Structural Characterization of the Interaction between Human Galectin-3 and the Lipopolysaccharide from Pseudomonas aeruginosa.

Given the significant involvement of galectins in the development of numerous diseases, the aim of the following work is to further study the interaction between galectin-3 (Gal3) and the LPS from Pseudomonas aeruginosa. This manuscript focused on the study of the interaction of the carbohydrate recognition domain of Gal3 with the LPS from Pseudomonas aeruginosa by means of different complementary methodologies, such as circular dichroism; spectrofluorimetry; dynamic and static light scattering and evaluation of the impact of Gal3 on the redox potential membranes of Escherichia coli and P. aeruginosa cells, as well as ITC and NMR studies. This thorough investigation reinforces the hypothesis of an interaction between Gal3 and LPS, unraveling the structural details and providing valuable insights into the formation of these intricate molecular complexes. Taken together, these achievements could potentially prompt the design of therapeutic drugs useful for the development of agonists and/or antagonists for LPS receptors such as galectins as adjunctive therapy for P. aeruginosa.

Thermodynamic properties of an artificial molecule quantum rings: Geometric and external field effects

A systematic study of the thermal properties of an artificial molecule formed by a single electron embedded in two laterally coupled quantum rings under external probes: magnetic and static electric fields was carried out. The eigen-states and eigen-values of the Hamiltonian in the effective mass approximation were obtained numerically. By varying the distance between the centers of the rings, it was possible to establish the equilibrium length required by the formation of a giant stable artificial molecular complex and its dissociation energy. These features were corroborated by studying the effects of the distance between centers of the rings, the magnetic and electric field on the entropy and heat capacity of the system. At low temperatures, the equilibrium condition of the artificial molecule is linked to the formation of a minimum value of the entropy and a peak in the heat capacity. The temperature’s rising modifies substantially these conditions.

Photosensitizing effects and physicochemical properties of chlorophyll a derivatives with hydrophilic oligoethylene glycol fragments at the macrocycle periphery.

In this work, screening studies of the cytotoxic effect of chlorins with fragments of di-, tri-, and pentaethylene glycol at the macrocycle periphery in relation to HeLa, A549, and HT29 cells were performed. It is shown that, despite different hydrophobicity, all the compounds studied have a comparable photodynamic effect. The conjugate of chlorin e6 with pentaethylene glycol, which has the lowest tendency to association among the studied compounds with tropism for low density lipoproteins and the best characteristics of the formation of molecular complexes with Tween 80, has a significant difference in dark and photoinduced toxicity (ratio IC50(dark)/IC50(photo) approximately 2 orders of magnitude for all cell lines), which allows to hope for a sufficiently large "therapeutic window". A study of the interaction of this compound with HeLa cells shows that the substance penetrates the cell and, after red light irradiation induces ROS appearance inside the cell, associated, apparently, with the photogeneration of singlet oxygen. These data indicate that photoinduced toxic effects are caused by damage to intracellular structures as a result of oxidative stress. Programmed type of cell death characterized with caspase-3 induction is prevailing. So, the conjugate of chlorin e6 with pentaethylene glycol is a promising antitumor PS that can be successfully solubilized with Tween 80, which makes it suitable for further in vivo studies.

THERMODYNAMICS OF COMPLEXATION WITH 18-CROWN-6 WITH L-CARNOSINE AND ITS CONFORMATIONAL ANALYSIS

The study of model biological "guest-host" processes between dipeptides and crown ethers allows us to understand the nature of molecular recognition in living systems. The reaction of the formation of the molecular complex of the crown ether 18-crown-6 (18K6) with L-carnosine (L-Carn) in water at T = 298.15 K was studied using isothermal titration calorimetry. The mixing heats of aqueous solutions of L-carnosine with aqueous solutions of 18-Carn-6 were determined on a TAM III titration calorimeter system (TA Instruments) equipped with a 20 mL titration cell. In the main experiment, the heat of mixing of aqueous 18K6 solution with aqueous L-Carn solution was determined. In separate experiments the heat effect of dilution of L-Carn solution in water was measured, which was taken into account in determining the thermal effect of complex formation. From the thermochemical data, the thermodynamic parameters of the molecular complex formation reaction were calculated. It was found that the presence of a histidine fragment in the L-Carn structure leads to an increase in the stability of the molecular complex L-Carn with 18K6 and to a decrease in the exothermicity of complex formation as compared to the complex formation of alanine with 18K6. Thermodynamic parameters of [L-Carn 18K6] formation reaction are similar to thermodynamics of 18K6 complex formation with histidine. Quantum-chemical calculations were performed within the framework of the electron density functional theory using the GAUSSSIAN 03 software package. The results were visualized using the ChemCraft software. We performed the conformational analysis of L-Carn within the framework of the density functional theory (version B3LYP/6-31G**) to analyze the reactivity of L-Carn structural fragments. For three stable conformers in the M062X/ aug-cc-pVTZ approximation the geometric parameters were obtained and the electron density distribution was analyzed within the framework of the QTAIM method as well as the NBO scheme. For citation: Usacheva T.R., Belova N.V., Saturina E.V., Krutova O.N., Lukanov M.M., Pavlova E.A. Thermodynamics of complexation with 18-crown-6 with l-carnosine and its conformational analysis. ChemChemTech [Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol.]. 2023. V. 66. N 5. P. 21-31. DOI: 10.6060/ivkkt.20236605.6781.

A phage-encoded RNA-binding protein inhibits the antiviral activity of a toxin-antitoxin system.

Bacteria harbor diverse mechanisms to defend themselves against their viral predators, bacteriophages. In response, phages can evolve counter-defense systems, most of which are poorly understood. In T4-like phages, the gene tifA prevents bacterial defense by the type III toxin-antitoxin (TA) system toxIN, but the mechanism by which TifA inhibits ToxIN remains unclear. Here, we show that TifA directly binds both the endoribonuclease ToxN and RNA, leading to the formation of a high molecular weight ribonucleoprotein complex in which ToxN is inhibited. The RNA binding activity of TifA is necessary for its interaction with and inhibition of ToxN. Thus, we propose that TifA inhibits ToxN during phage infection by trapping ToxN on cellular RNA, particularly the abundant 16S rRNA, therebypreventing cleavage of phage transcripts. Taken together, our results reveal a novel mechanism underlying inhibition of a phage-defensive RNase toxin by a small, phage-encoded protein.

Intermolecular Interactions in Liquid Propionic Acid and Its Solutions: Raman and DFT Study

The mechanism of molecular complex formation in liquid propionic acid and its solutions is investigated. The anisotropic component of the Raman band of the C=O stretching vibration of pure propionic acid consists of three bands with maxima at 1661, 1700, and 1753 cm−1. The effect of varying the concentrations of solvents such as CCl4, acetonitrile, and water on this vibration mode is studied. The mechanism of formation of molecular complexes in solutions is determined using DFT calculations at the B3LYP/6-311++G(d,p) level of theory. The AIM, RDG, and NCI topological analyses are also performed to investigate the intermolecular interactions in the complexes.

Generalized Michaelis-Menten rate law with time-varying molecular concentrations.

The Michaelis-Menten (MM) rate law has been the dominant paradigm of modeling biochemical rate processes for over a century with applications in biochemistry, biophysics, cell biology, systems biology, and chemical engineering. The MM rate law and its remedied form stand on the assumption that the concentration of the complex of interacting molecules, at each moment, approaches an equilibrium (quasi-steady state) much faster than the molecular concentrations change. Yet, this assumption is not always justified. Here, we relax this quasi-steady state requirement and propose the generalized MM rate law for the interactions of molecules with active concentration changes over time. Our approach for time-varying molecular concentrations, termed the effective time-delay scheme (ETS), is based on rigorously estimated time-delay effects in molecular complex formation. With particularly marked improvements in protein-protein and protein-DNA interaction modeling, the ETS provides an analytical framework to interpret and predict rich transient or rhythmic dynamics (such as autogenously-regulated cellular adaptation and circadian protein turnover), which goes beyond the quasi-steady state assumption.

Development of Visible Spectrophotometric Methods for the Determination of Tricyclic Antidepressants Based on Formation of Molecular Complexes with p-Benzoquinones

Tricyclic antidepressants are commonly employed in the management of major depressive disorders. The present work describes two visible (VIS) spectrophotometric techniques that utilize the formation of charge transfer complexes between four antidepressant compounds, namely, amitriptyline hydrochloride (AMI), imipramine hydrochloride (IMI), clomipramine hydrochloride (CLO), and trimipramine maleate (TRI) acting as electron donors and two p-benzoquinones, namely, p-chloranilic acid (pCA) and 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), serving as electron acceptors. The stoichiometry of the compounds produced exhibited a consistent 1:1 ratio in all instances, as established by Job’s method. Molar absorptivities, equilibrium association constants, and several other spectroscopic properties were determined for all complexes. The developed spectrophotometric techniques were validated intra-laboratory and successfully applied for quantitative assessment of the four antidepressant active ingredients in several commercial pharmaceutical formulations. The methods are relatively simple, fast, and use readily available laboratory instrumentation, making them easily applicable by most quality control laboratories worldwide.

Caveolin-1 forms a complex with P2X7 receptor and tunes P2X7-mediated ATP signaling in mouse bone marrow-derived macrophages.

The ionotropic purinergic P2X7 receptor responds to extracellular ATP and can trigger proinflammatory immune signaling in macrophages. Caveolin-1 (Cav-1) is known to modulate functions of macrophages and innate immunity. However, it is unknown how Cav-1 modulates P2X7 receptor activity in macrophages. We herein examined P2X7 receptor activity and macrophage functions using bone marrow-derived macrophages (BMDMs) from wild-type (WT) and Cav-1 knockout (KO) mice. ATP (1 mM) application caused biphasic increase in cytosolic [Ca2+] and sustained decrease in cytosolic [K+]. A specific P2X7 receptor blocker, A-740003, inhibited the maintained cytosolic [Ca2+] increase and cytosolic [K+] decrease. Total internal reflection fluorescent imaging and proximity ligation assays revealed a novel molecular complex formation between P2X7 receptors and Cav-1 in WT BMDMs that were stimulated with lipopolysaccharides. This molecular coupling was increased by ATP application. Specifically, the ATP-induced Ca2+ influx and K+ efflux through P2X7 receptors were increased in Cav-1 KO BMDMs, even though the total and surface protein levels of P2X7 receptors in WT and Cav-1 KO BMDMs were unchanged. Cell-impermeable dye (TO-PRO3) uptake analysis revealed that macropore formation of P2X7 receptors was enhanced in Cav-1 KO BMDMs. Cav-1 KO BMDMs increased ATP-induced IL-1β secretion, reactive oxygen species production, Gasdermin D (GSDMD) cleavage, and lactate dehydrogenase release indicating pyroptosis. A-740003 completely prevented ATP-induced pyroptosis. In combination, these datasets show that Cav-1 has a negative effect on P2X7 receptor activity in BMDMs and that Cav-1 in macrophages may contribute to finely tuned immune responses by preventing excessive IL-1β secretion and pyroptosis.NEW & NOTEWORTHY In bone marrow-derived macrophages, Cav-1 suppresses the macropore formation of P2X7 receptors through their direct or indirect interactions, resulting in reduced membrane permeability of cations (Ca2+ and K+) and large cell-impermeable dye (TO-PRO3) induced by ATP. Cav-1 also inhibits ATP-induced IL-1β secretion, ROS production, GSDMD cleavage, and pyroptosis. Cav-1 contributes to the maintenance of proper immune responses by finely tuning IL-1β secretion and cell death in macrophages.

The molecular structure of 4-substituted pyridine N-oxides–boron trifluoride triel bonded complexes: Peculiarities and regularities

Pyridine N-oxides are widely used in medicine, organic synthesis and design of functional coordination compounds and supramolecular systems. However, at present, issues related to the complex formation and stereochemistry of pyridine N-oxide molecular complexes as well as the nature of the complexing bond and the substituent effect remain relevant. In this paper the substituent effect on geometric, electronic, thermodynamic and spectral properties was established by quantum chemical calculations (DFT/M062-X/aug-cc-pvTZ) for the series of 4-substituted pyridine N-oxides with boron trifluoride as model complexes. Theoretical insights into the nature of OB triel bond was considered in terms of QTAIM and NBO analysis. A conformational analysis has been performed to resolve the contradictions in the literature data concerning the stereochemistry of such complexes. The calculated structural parameters, as well as complex formation energy, binding energy, thermodynamic characteristics, vibrational frequencies and chemical shifts reveal high correlation with the empirical Hammett substituent constants.

A Molecular Electron Density Theory Study of the Domino Reaction of N-Phenyl Iminoboranes with Benzaldehyde Yielding Fused Bicyclic Compounds.

The reaction of N-phenyl iminoborane with benzaldehyde yielding a fused aromatic compound, recently reported by Liu et al., has been studied within the Molecular Electron Density Theory (MEDT). Formation of the fused aromatic compound is a domino process that comprises three consecutive reactions: (i) formation of a weak molecular complex between the reagents; (ii) an intramolecular electrophilic attack of the activated carbonyl carbon of benzaldehyde on the ortho position of the N-phenyl substituent of iminoborane; and (iii) a formal 1,3-hydrogen shift yielding the final fused aromatic compound. The two last steps correspond to a Friedel-Crafts acylation reaction, the product of the second reaction being the tetrahedral intermediate of an electrophilic aromatic substitution reaction. However, the presence of the imino group adjacent to the aromatic ring strongly stabilizes the corresponding intermediate, being the reaction product when the ortho positions are occupied by t-butyl substituents. This domino reaction shows a great similitude with the Brønsted acid catalyzed Povarov reaction. Although N-phenyl iminoborane can experience a formal [2+2] cycloaddition reaction with benzaldehyde, its higher activation Gibbs free energy compared to the intramolecular electrophilic attack of the activated carbonyl carbon of benzaldehyde on the ortho position of the N-phenyl substituent, 6.6 kcal·mol-1, prevents the formation of the formal [2+2] cycloadduct. The present MEDT study provides a different vision of the molecular mechanism of these reactions based on the electron density.

Cyclodextrin - Essential Oil Complexes Studied by Thermal Gravimetry Analysis - Differential Scanning Calorimetry

Background: The structural features allow cyclodextrins to form solid inclusion complexes (host–guest complexes) with wide variety of solid, liquid, and gaseous compounds as a guest. It is the utmost an astounding property of the cyclodextrins, and is commonly termed as molecular recognition. The process of formation of an inclusion complex of the cyclodextrins has been associated with the substitution of the water inside the hydrophobic cavity and the non–covalent bonding interactions of the guest in the hydrophobic host cavity. Objective: To study the thermal gravimetry analysis behaviour for α–cyclodextrin–clove oil, α–cyclodextrin–neem oil and β–cyclodextrin–clove oil adducts using TGA–DSC. : To compute specific heat capacity at constant pressure, as a function of temperature for the studied systems. Methods: The thermal gravimetry analysis and differential scanning calorimetry techniques are used. Results: It is observed that the calculated Cp values from DSC curves are of low magnitude for α–CD–neem oil adduct as compared to that of individual constituents over the temperature range studied. An interesting pattern for the Cp values is found to emerge in case of α– CD–clove oil and β–CD–clove oil adducts wherein the calculated Cp values are higher in magnitude than for pure clove oil but are lower than that of the pure cyclodextrins. Conclusion: Using thermal methods, the attempt to understand the possibilities of molecular complex formation between cyclodextrins and medicinally important neem oil and clove oil is described. The crystals of inclusion compounds for clove oil and neem oil with α–CD and β–CD are synthesized. The results of TGA–DSC for the crystals are presented and analysed. Other: The results of neem oil–adducts have been explained in terms of binding of part of tri–glyceride linkages by 2–3 cyclodextrin molecules as neem oil is tri–glyceride and the adduct is having lower stability.

Inclusion Complexes of β-Cyclodextrin with Salvia officinalis Bioactive Compounds and Their Antibacterial Activities

In the present study, the formation of molecular inclusion complexes of Salvia officinalis (sage) bioactive compounds with β-cyclodextrin (β-CD) was evaluated. Sage essential oil (SEO)/β-CD inclusion complexes (ICs) were prepared by co-precipitation at iso-molecular concentrations, and Fourier transform infrared spectroscopy (FT-IR) was applied for the confirmation of the ICs’ formation. Quantification of the SEO in the inclusion complexes was performed spectrophotometrically at 273 nm using an SEO standard curve. The SEO and its inclusion complexes were evaluated for their antimicrobial activity against Escherichia coli, Staphylococcus aureus and Listeria monocytogenes. The results showed that β-CD effectively formed inclusion complexes with SEO in satisfactory yields. The antimicrobial activity of the SEO in prepared complexes with β-CD was exhibited against L. monocytogenes and S. aureus and was proportional to their concentrations but was less pronounced.

Formation and Structure Research of a Molecular Conjugate in the L-Ascorbic Acid – Isomaltite System

The formation of L-ascorbic acid molecular complexes with various biologically active substances opens the way to the production of a new drug type promising for the pharmaceutical, food and cosmetic industries use. The research concerns the possibility study of obtaining a conjugate of L-ascorbic acid with isomaltite in an aqueous ethanol (40 %) medium. The method of the target product isolating involves thermostating a solution containing equimolar amounts (0.001 mmol) of components (50 °C, 1 hour), followed by slow solvent removal for 24 hours (25 °C). The authors examined formation processes dynamics by molecular spectroscopy methods through sequential sampling. The optical density values at 350 Nm in the electronic spectra and 1,674 and 1,754 cm−1 bands position in the IR-Fourier solution spectra indicate the components destruction absence during thermostate control. When treated with carbon tetrachloride or diethyl ether, the syrupy mass obtained after solvent removal containing significant solvent amounts crystallizes a yellowish powder (0.32 g, ice point at 146.6 °C). A man studied its structure by the IR-Fourier spectroscopy. The authors recorded the spectra in the transmission mode (in the KBr tablets) and using the diffusion reflection method enabling to record changes in the absorption bands characteristic positions of the molecular complex formation. The transmission spectra of the high-frequency area indicate the 1-O-glycosylated isomaltite component involvement in the conjugation with ascorbic acid. The shifts of the C=C, C−O and C−O−H bond oscillation bands in the diffusion reflection spectrum of the isolated product relative to their position in the initial component spectra in the low-frequency area indicate the endiol ascorbic acid fragment interaction with the secondary OH groups of the acyclic isomaltite component. Structural analogues of the studied molecular conjugate are promising antioxidant preparations. This determines the further study relevance of its properties.

Estimation of the Controlled Release of Antioxidants from β-Cyclodextrin/Chamomile (Matricaria chamomilla L.) or Milk Thistle (Silybum marianum L.), Asteraceae, Hydrophilic Extract Complexes through the Fast and Cheap Spectrophotometric Technique.

This is the first study on the modeling of the controlled release of the estimated antioxidants (flavonoids or flavonolignans) from β-cyclodextrin (β-CD)/hydrophilic vegetable extract complexes and the modeling of transdermal pharmaceutical formulations based on these complexes using an overall estimation by the spectrophotometric method. The Korsmeyer-Peppas model was chosen for evaluating the release mechanisms. β-CD/chamomile (Matricaria chamomilla L., Asteraceae) ethanolic extract and β-CD/milk thistle (Silybum marianum L., Asteraceae) ethanolic extract complexes were obtained by the co-crystallization method with good recovering yields of 55-76%, slightly lower than for β-CD/silibinin or silymarin complexes (~87%). According to differential scanning calorimetry (DSC) and Karl Fischer water titration (KFT), the thermal stability of complexes is similar to β-CD hydrate while the hydration water content is lower, revealing the formation of molecular inclusion complexes. In the Korsmeyer-Peppas model, β-CD/M. chamomilla flower extract complexes reveal Case II transport mechanisms, while the corresponding complexes with leaf extracts indicate non-Fickian diffusion for the controlled release of antioxidants in ethanol 60 and 96%. The same non-Fickian diffusion was revealed by β-CD/S. marianum extract and β-CD/silibinin complexes. On the contrary, almost all model transdermal pharmaceutical formulations based on β-CD/M. chamomilla extract complexes and all those based on β-CD/S. marianum extract complexes revealed non-Fickian diffusion for the antioxidant release. These results indicate that H-bonding is mainly involved in the diffusion of antioxidants into a β-CD based matrix, while the controlled release of antioxidants in model formulations is mainly due to hydrophobic interactions. Results obtained in this study can be further used for studying the particular antioxidants (namely rutin or silibinin, quantified, for example, by liquid chromatographic techniques) for their transdermal transport and biological effects in innovatively designed pharmaceutical formulations that can be obtained using "green" methods and materials.

THERMODYNAMICS OF INTERMOLECULAR INTERACTION REACTIONS OF BIOMOLECULES IN WATER AND WATER-ORGANIC SOLVENTS

The paper summarizes the results of our own research into the formation of molecular complexes of cyclodextrins with biologically active polyphenol compounds in water-organic solvents, chemical equilibria in the solutions of hydrazones and Schiff bases and their metal complexes in the solutions of DNA and proteins. It was found that an increase in the content of the non-aqueous component in the binary solvent leads to a decrease in the stability of molecular complexes of cyclodextrins with polyphenols and a decrease in the exothermicity of their formation reactions. It has been shown that metal complexes in an aqueous buffer solution containing also DNA or protein dissociate, and the released cation and free ligand bind to the biomolecule. For citation: Usacheva T.R., Gamov G.A., Kuranova N.N., Zavalishin M.N., Kabirov D.N., Alister D.A., Grazhdan K.V., Gushchina A.S., Isaeva V.A., Kashina O.V., Kuzmina I.A., Tukumova N.V., Sharnin V.A. Thermodynamics of intermolecular interaction reactions of biomolecules in water and water-organic solvents. ChemChemTech [Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol.]. 2023. V. 66. N 7. P. 59-75. DOI: 10.6060/ivkkt.20236607. 6842j.

Competitive formation of molecular inclusion complexes of chlordecone and β-hexachlorocyclohexane with natural cyclodextrins: DFT and molecular dynamics study.

Chlordecone (CLD) and β-hexachlorocyclohexane (β-HCH) are chlorinated pesticides that coexist as persistent organic pollutants in the groundwater of several countries in the Caribbean, being an environmental issue. This work evaluates theoretically the competitive formation of host-guest complexes pesticides@cyclodextrines (CDs) as an alternative for water purification and selective separation of pesticides. Quantum mechanical calculations based on density functional theory (DFT) and classical molecular dynamics (MD) simulations were used to achieve information on geometries, energies, structure, and dynamics of guest-host complexes in the gas phase, implicit solvent medium, and in aqueous solutions. DFT studies showed that interactions of both pesticides with CDs are mediated by steric factors and guided by maximization of the hydrophobic interactions either with the other pesticide or with the CD cavity's inner atoms. MD results corroborate the formation of stable complexes of both pesticides with the studied CDs. α-CD exhibited a preference for the smaller β-HCH molecule over the CLD that could not perturb the formed complex. The simulation of competitive formation with γ-CD illustrated that this molecule could accommodate both pesticides inside its cavity. These results suggest that CDs with smaller cavity sizes such as α-CD could be used for selective separation of β-HCH from CLD in water bodies, while γ-CD could be used for methods that aim to remove both pesticides at the same time.

MolClustPy: a Python package to characterize multivalent biomolecular clusters.

Low-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become supply-limited large clusters. In stochastic simulations, such clusters display a wide range of sizes and compositions. We have developed a Python package, MolClustPy, which performs multiple stochastic simulation runs using NFsim (Network-Free stochastic simulator); MolClustPy characterizes and visualizes the distribution of cluster sizes, molecular composition, and bonds across molecular clusters. The statistical analysis offered by MolClustPy is readily applicable to other stochastic simulation software, such as SpringSaLaD and ReaDDy. The software is implemented in Python. A detailed Jupyter notebook is provided to enable convenient running. Code, user guide, and examples are freely available at https://molclustpy.github.io/.