Semiempirical PM3 Research Articles

An Innovative Vortex-Assisted Liquid-Liquid Microextraction Approach Using Deep Eutectic Solvent: Application for the Spectrofluorometric Determination of Rhodamine B in Water, Food and Cosmetic Samples.

A new green and highly sensitive method for the determination of rhodamine B (RhB) by deep eutectic solvent-based vortex-assisted liquid-liquid microextraction with fluorescence detection (DES-VALLME-FLD) was developed. The extraction efficiency of conventional solvents and different deep eutectic solvent (DES) systems composed of tetrabutylammonium bromide (TBAB) and an alcohol (hexanol, octanol, or decanol) in different ratios were compared. DFT calculations of intermolecular electrostatic and non-covalent interactions of the most stable RhB forms with DES and water explain the experimental DESs' extraction efficiency. Semiempirical PM7 computations were used to obtain Hansen solubility parameters, which supported the good solubility of the monocationic RhB form in selected DESs. The dependence of the linear calibration of microextraction into 100 µL DES was observed in the RhB calibration range from 0.2 to 10.0 µg L-1 with a correlation coefficient of R2 = 0.9991. The LOD value was calculated to be 0.023 µg L-1. The accuracy and precision of the proposed method were verified over two days with RSD values of 2.9 to 4.1% and recovery of 94.6 to 103.7%. The developed method was applied to the determination of RhB in real samples (tap water, energy drink, and lipstick).

CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods.

Quantum mechanical (QM) treatments, when combined with molecular mechanical (MM) force fields, can effectively handle enzyme-catalyzed reactions without significantly increasing the computational cost. In this context, we present CHARMM-GUI QM/MM Interfacer, a web-based cyberinfrastructure designed to streamline the preparation of various QM/MM simulation inputs with ligand modification. The development of QM/MM Interfacer has been achieved through integration with existing CHARMM-GUI modules, such as PDB Reader and Manipulator, Solution Builder, and Membrane Builder. In addition, new functionalities have been developed to facilitate the one-stop preparation of QM/MM systems and enable interactive and intuitive ligand modifications and QM atom selections. QM/MM Interfacer offers support for a range of semiempirical QM methods, including AM1(+/d), PM3(+/PDDG), MNDO(+/d, +/PDDG), PM6, RM1, and SCC-DFTB, tailored for both AMBER and CHARMM. A nontrivial setup related to ligand modification, link-atom insertion, and charge distribution is automatized through intuitive user interfaces. To illustrate the robustness of QM/MM Interfacer, we conducted QM/MM simulations of three enzyme-substrate systems: dihydrofolate reductase, insulin receptor kinase, and oligosaccharyltransferase. In addition, we have created three tutorial videos about building these systems, which can be found at https://www.charmm-gui.org/demo/qmi. QM/MM Interfacer is expected to be a valuable and accessible web-based tool that simplifies and accelerates the setup process for hybrid QM/MM simulations.

الدراسة التركيبية والطاقية لأيونات الليثيوم مع الأحماض الدهنية ميثيل استر [[FAME (9Z-18:1) + Li+ باستخدام الطريقة الكيميائية الكمومية (PM3)

Lithium (Li) ions are being used in a variety of fields ranging from energy storage to the treatment of mental illnesses including bipolar disorder and schizophrenia. Lithium caton (Li+) is able to form cationic adducts with various compounds and they can stabilize the biomacromolecules that interact with. Here, the interaction of lithium ions with fatty acid methyl ester [FAME (9Z-18:1)] has been theoretically investigated to gain insight into the structure and energetics of [FAME (9Z-18:1) + Li+]. All theoretical calculations were performed using Gaussian09 software via a graphic user interface. Geometry optimisations with harmonic vibrational analysis of conformations for chelated and extended forms of [FAME (9Z-18:1) + Li+] were carried out using semi-empirical method PM3. To obtain accurate energetic, zero-point energy (ZPE) corrections were included in all optimized energies and relative energies between conformers. The calculations indicated that the chelated form is relatively more stable than extended forms by 25 and 118 kJmol-1 when lithium is bound to the carbonyl oxygen (O-Li+) or olefin (C=C-Li+), respectively. The comparison between the relative stabilization energies of extended (O-Li+) versus extended (C=C-Li+) reveals that the lithium cation energetically prefers to bind to with carbonyl oxygen over the carbon-carbon double bond. Keywords: lithium ions, geometry optimization, sim-empirical method, Gaussian 09.

Chemical and electrochemical nanofabrication of polyaminothiazole/graphene oxide composites

Poly(2-aminothiazole) is a little-studied conducting polymer with sulfur and nitrogen heteroatoms in the aromatic ring, which reveals prospects for application in various fields. We studied the conditions of chemical synthesis of poly(2-aminothiazole) and its composite with graphene oxide in an aqueous solution, as well as electrochemical deposition on electrode surfaces – Pt and SnO2. The structure of the polymer was investigated by SEM and FT-IR spectroscopy. A quantum-chemical calculation using the semi-empirical PM7 method was carried out. The electrochemical activity of polymer films was examined. Increasing effective parameters of charge transport for poly(2-aminothiazole)/graphene oxide films were detected.

Design, synthesis, explorations of DFT, PM6, molecular docking with SAR-CoV-2 Mpro and anticancer properties of novel indolo[2,3-c]isoquinoline analogues

A novel series of indolo[2,3-c]isoquinoline derivatives, coupled with pyrazole and pyrazolo[3,4-d]pyrimidinone rings bearing substituted Cl, OCH3, CH3, and H groups II, II(a-d), were successfully synthesized, exhibiting significant biological and pharmacological relevance. Computational chemistry using the semiempirical method PM6 via MOPAC software was employed to investigate their thermochemical properties. Compound IIIb displayed a lower heat formation (ΔHf) value of 68.89873 kcal/mole, indicating enhanced stability, whereas compound IId exhibited a higher ΔHf value of 151.32004 kcal/mole, suggesting lesser stability. Density functional theory (DFT) at B3LYP/def2-TZVP def2/J was utilized for analyzing electronic structures and geometric optimization. The HOMO-LUMO energy gap (ΔEg) followed an ascending order in the pyrimidinone>pyrazole series, with IIIb possessing the lowest energy gap (ΔEg = 2.994 eV) and IIc having the highest (ΔEg = 3.433 eV). Compound IIa displayed the highest electrophilicity index (χ = 3.540 eV) and exhibited potent anti-cancer activity, as observed in derivatives II and III(a-d). Additionally, compounds IIa, IIb, and IIc demonstrated promising interactions with amino acids of the SARS-CoV-2 main protease (PDB:7e18).

Ferroelectric Thin Films and Composites Based on Polyvinylidene Fluoride and Graphene Layers: Molecular Dynamics Study

This work is devoted to the study of nanosized polymer polyvinylidene fluoride (PVDF) thin ferroelectric films (two-dimensional ferroelectrics) and their composites with graphene layers, using molecular dynamics methods to (1) study and calculate the polarization switching time depending on the electric field and film thickness, (2) study and calculate the polarization switching time depending on changes of the PVDF in PVDF-TrFE film, and (3) study the polarization switching time in PVDF under the influence of graphene layers. All calculations at each MD run step were carried out using the semi-empirical quantum method PM3. A comparison and analysis of the results of these calculations and the kinetics of polarization switching within the framework of the Landau–Ginzburg–Devonshire theory for homogeneous switching in ferroelectric polymer films is carried out. The study of the composite heterostructures of the “graphene-PVDF” type, and calculations of their polarization switching times, are presented. It is shown that replacing PVDF with PVDF-TrFE significantly changes the polarization switching times in these thin polymer films, and that introducing various graphene layers into the PVDF layered structure leads to both an increase and a decrease in the polarization switching time. It is shown that everything here depends on the position and displacement of the coercive field depending on the damping parameters of the system. These phenomena are very important for various ferroelectric coatings.

A General Model of Impact Sensitivity for Nitrogen-Rich Energetic Materials: A Combined Incremental Theory and Genetic Function Approximation Study.

In this paper, we report the first example of impact sensitivity prediction based on the genetic function approximation (GFA) as a regression method. The prediction is applicable for a wide variety of chemical families, which include nitro compounds, peroxides, nitrogen-rich salts, heterocycles, etc. Within this work, we have obtained 7 empirical models (with 27-32 basis functions), which all provide 0.80≤R2≤0.83 and 7.2 J≤RMSE≤7.8 J (for 450 training set compounds) and 0.64≤R2≤0.70 and 11.2 J≤RMSE≤12.4 J (for 170 test set compounds). The models were developed using Friedman Lack-of-Fit as a scoring function, which allows avoiding an overfitting. All the models have simple descriptors as basis functions and include linear splines. Furthermore, the applied descriptors do not require expensive calculation procedures, namely, non-empirical quantum-chemical calculations, complex iterative procedures, real space electron density analysis, etc. Most descriptors are based on structural and topological analysis and a part of them require very cheap semi-empirical PM6 calculations. The prediction takes a few minutes as an average, and most of the time is for the structure preparation and manual calculation of the descriptor "Increment", which is based on our recent incremental theory.

Computer aided design of novel antibiotic drug candidate against multidrug resistant strains of Salmonella typhi from pyridine-substituted coumarins

BackgroundThe rising cases of resistance to existing antibiotics by Salmonella typhi, has made the development of novel drug candidates a necessity. In this study, a data set of antibacterial pyridine substituted coumarins were subjected to Virtual Screening against SipA effector protein of the bacterium. The compounds were geometry-optimized using Semi-empirical (pm3) method in Spartan 14 software, docked against the active sites of SipA using AutoDock Vina software. The molecule with the best docked score was selected as template and subjected to structural modifications leading to the design of a novel coumarin based drug candidate codenamed Y-1.ResultsThe docking of Y-1 against SipA revealed that it binds to the target with ΔG value of − 9.1 kcal/mol. This value is better than − 6.8 kcal/mol obtained for ciprofloxacin used herein for quality assurance. Additionally, quantum mechanical calculations on Y-1 using DFT (B3LYP/6-31G* basis set) shows a wide energy gap of 3.44 eV and ω value of 1.47 eV, indicating its sound kinetic and thermodynamic stabilities. Y-1 was also found to possess good oral bioavailability and positive pharmacokinetic profiles.ConclusionThis is the first time coumarin derivatives are screened against an effector protein of Salmonella typhi. It is envisaged that the findings of this research will provide an excellent blueprint toward the development of novel antibiotics against Salmonella typhi.

Theoretical and Experimental In-vitro Studies of Novel Thiophene Based Organotellurium(IV) Complexes.

Schiff bases are one of the important classes of organic compounds containing imine or azomethine functional groups with potential biological applications in medicinal chemistry. Nowadays, these compounds have attracted the scientific community's attention due to their ability to act as ligands in the formation of stable metal complexes with significant biological activity. In this connection, we have designed and synthesized six novel thiophene-based organoltellurium (IV) complexes using a novel N-((5-methylthiophen-2-yl) methylene)-2-nitroaniline (5MTCONA) schiff base. These complexes underwent analytical investigation (TGA, Powder XRD, SEM, EDAX) as well as spectral analysis (FT-IR, NMR, Mass spectrometry, UV-Vis). The in-vitro pharmacological evaluation of these compounds has been carried out as antimicrobial and antioxidant agents. To further corroborate our findings, we have implemented computational analyses (Semi empirical PM3 method, Molecular Docking, and ADMET) of all the compounds with Spartan-14, Hex-8.0., Swiss ADME software. Precisely, our study integrates experimental and theoretical aspects, offering innovative insights in the field of pharmaceutical sciences.

Tenability on schiff base Hydrazone derivatives and Frontier molecular orbital

Context hydrazine compounds based on 1,3,5-triazine were synthesised and their molecular structures were characterised by elemental analysis, Electronic, IR and 1H NMR spectra. The spectral behaviour of the newly prepared compounds in organic solvents of different polarities was extensively studied and correlated to the molecular structure. In this study, 1,3,5-Triazine derivatives (L1, L6, L7, L8) have been subjected to theoretical studies using the Semi-empirical PM3 quantum chemical method. The physical-chemical properties of some Hydrazone derivatives are determined theoretically. The molecular geometry, the Highest Occupied Molecular Orbital (HOMO) - Lowest Unoccupied Molecular Orbital (LUMO) energy gap, molecular hardness (η), ionisation energy (IE), Electron affinity and total energy were analysed, and applications as biological effects were done.

Investigation of the Adsorption Properties of Electrically Conductive Pyrolyzed Polyacrylonitrile Modified with Chromium (III) Oxide to Obtain Highly Efficient Gas Sensors

Introduction. Obtaining highly sensitive gas sensors is an urgent task, the solution to which will allow you to accurately and quickly assess changes in the air-gas composition of a given medium. Gas sensors based on metal-containing pyrolyzed polyacrylonitriles (Me-pPAN) are among the cheapest and most environmentally friendly gas-sensitive materials with a fast response. One of the types of sensor materials included in the Me-pPAN list is pyrolyzed polyacrylonitrile (pPAN) modified with a chromium (III) oxide molecule. The reasons for selective adsorption of pPAN and Me-pPAN to pollutant gases, which would allow controlling this process and obtaining sensory materials with increased sensitivity to gases, are not enough studied. Therefore, the aim of this work was to establish the main causes of selective adsorption of semiconductor electrically conductive films by modeling methods in the framework of molecular and quantum mechanics. Materials and Methods. The authors used modeling methods in the framework of molecular and quantum mechanics (MM2), the density functional theory (COSMO) method and the semi-empirical PM7 method in the MOPAC software package. Results. MM2 and PM7 methods were used to obtain models of adsorption complexes of "Cr-pPAN – gas-pollutant" systems. Thermodynamic parameters of the system were calculated for standard environmental conditions. The dependence of the adsorption of pollutant gases on the surface of Cr-pPAN on temperature has been established. Discussion and Conclusion. As a result of calculating the thermodynamic parameters of gas-pollutant–pPAN/Me-pPAN systems and obtaining positive values of Gibbs energies of these systems, it was confirmed that the adsorption of polluting gases on the surface of Cr-pPAN was not a spontaneous phenomenon and was effective at high temperatures. Considering that when chromium (III) oxide was introduced into the pPAN matrix, the charge on nitrogen atoms increased. It could be concluded that a chromium (III) oxide molecule had a positive effect on the semiconductor properties of pPAN. It was found that the adsorption of polluting gases (SO2 and NO2) was most likely on the surfaces of pPAN and Cr-pPAN. The results obtained in the work can be used to obtain gas-sensitive materials with specified metrological characteristics.

Comparison between Schiff-base and its iron complex as steel corrosion inhibitors used by the petroleum industry in marine environments

ABSTRACT The Schiff-base N,N-bis(2-furaldehyde)−1,3-diaminopropane (FDP) and its complex with iron (FDPIC) were prepared and used as corrosion inhibitors for mild-steel (MS) in a 3.5% NaCl medium as an artificial marine environment to evaluate the functional groups’ efficiency within the structure of the compounds for corrosion inhibition. To predict the effect of the researched inhibitors’ ability to suppress corrosion, weight loss measurements and a variety of complex analytical techniques, including potentiodynamic-polarisation and electrochemical-impedance tests, were applied. Experimental results revealed that (FDPIC) has a higher corrosion inhibition efficacy than (FDP). According to electrochemical measurements, inhibitors showed significant resistance to charge transfer through the electrolyte–metal interface and mixed-type inhibitor behaviour. Furthermore, the film formed on the surface of the mild steel was examined using a scanning electron microscope (SEM). Quantum chemical calculations using semi-empirical molecular orbital PM3 and Molecular Dynamics (MD) were used to investigate inhibitor adsorption and inhibition on the mild-steel surface. The geometry of the Schiff-base and its complex structures, as well as electron density distribution in LUMO, HOMO, and QSAR properties of each atom for their conceivable interaction mode with the mild-steel surface, were used in chemical quantum calculations. According to molecular dynamic simulations, all of the inhibitor molecules adhered to the surface in a parallel direction.

Monolayers of amino acid-type amphiphiles

The monolayer characteristics of selected N-alkanoyl substituted α-amino acid are studied with the objective to demonstrate the specific effect of the chemical structure of the polar head group which is highlighted with the D- and L-enantiomers of the following selected examples: R-alanine, R-serine, R-threonine, R-allo-threonine, and R-aspartic acid (R = C16, C18). The thermodynamic effect of the head group variation is studied. Experimental π-A isotherms of the N-tetradecyl-L-alanine monolayers show similar behavior as those of usual amphiphiles. The -CH3-group in R-alanine with the simplest head group structure is substituted by a -CH2-OH group in R-serine and serine methylester and by a -CH- CH3-OH group in R-threonine (or allo-threonine) and threonine methylester. The introduction of the methyl group in 3-position of serine (serine to 3-methyl-serine = threonine) shifts the characteristic temperatures by >20 K to lower values determined for N-C16-Dl-serine. The formation of the corresponding methylester decreases these temperatures by 15 K for serine with the shorter (C16) alkyl chain and only by ∼5 K for threonine with the longer chain (C18). The π–A curves of the enantiomeric and racemic allo-forms show similar features to those of N-stearoyl-threonine. The absolute T0-values (disappearance of the LE/LC-transition) are 4–5 K larger compared with the corresponding N-stearoyl-threonines, but the ΔT0 between the enantiomeric (D) and the racemic (DL) forms is only slightly larger than that of N-stearoyl-threonine.Monolayers of different N-alkanoyl substituted α-amino acid amphiphiles have been mesoscopically characterized. Substantial topological differences are observable at the condensed phase domains of several amino acid amphiphiles, such as, N-palmitoyl aspartic acid, N-palmitoyl- or N-stearoyl serine methyl ester, N-stearoyltyrosine, N-palmitoyl or N-myristoyl alanine. Many fascinating domain shapes are found, but always the curvatures of the two enantiomeric forms are directed in an opposite sense. The domain shape of the 1:1 racemic mixtures is usually different, but very often oppositely curved texture elements are observable.GIXD is used to study the characteristic features of the lattice structure of condensed monolayer phases on the Angstrom scale. Specific for all structures is the large tilt angle with respect to the surface normal, which decreases only marginally by compression. The large size of the head groups and strong interactions between them dominate the monolayer structure. As presented for NC16 and N-C18-threonine, N-C16-DL -serine, N-C16-L -serine, NC16 DL -serine-ME, NC16 L -serine-ME, NC18 DL -threonine-ME, and NC18 L -threonine-ME the enantiomers form an oblique lattice structure (3 diffraction peaks), whereas two peaks are observed for the racemates forming NNN tilted orthorhombic structures. A complete phase diagram of mixed monolayers of the D- and L-enantiomers of N-stearoyl-threonine with two eutectic points at xD ≈ 0.25 and xD ≈ 0.75 is proposed.The quantum chemical semiempirical PM3 method is applied to calculate the thermodynamic and structural parameters of clusterization in finite and infinite clusters for N-alkanoyl-substituted alanine with n = 8–17 carbon atoms in the chain at the air/water interface with the aim to obtain a new theoretical verification of the experimental results.

2D-QSAR, Docking, Molecular Dynamics Simulations with the MM/GBSA Approaches against Graves' Disease and PTPN22

Graves' disease (GD) is an autoimmune condition that frequently causes hyperthyroidism and thyrotoxicosis. Protein tyrosine phosphatase, non-receptor type 22 (lymphoid) isoform 1 (PTPN22), is a promising therapeutic candidate for treating GD, rheumatoid arthritis, type 1 diabetes, and other autoimmune disorders. In this dataset, 31 molecular compounds and two standard drugs were optimized using the semi-empirical PM7 theory method via MOPAC v22.0.4 to reveal the key influencing factors contributing to their grave's disease inhibition activity and selectivity. Using QSARIN software, the acquired properties/descriptors were used to create a quantitative structural activities relationship (QSAR) model, and the similarities between the observed and predicted pIC50 values were examined. A molecular docking simulation study also uncovers non-covalent interactions between the investigated compounds and the receptors. The observed ligand-protein interactions with GD proteins (PDB ID 2XPG and 4QT5) and PTPN22 (PDB ID 3BRH) were investigated. The pharmacokinetics (ADMET) properties were also investigated. Finally, molecular dynamics (MD) simulation and MM/GBSA studies that demonstrated stable trajectory and molecular properties with a consistent interaction profile were used to validate the stability of the compounds in the complex with PTPN22.

Spontaneous elimination of halides from β-halo carbanions upon geometry optimizations: Computational predictions of the outcomes from elimination reactions proceeding via an E1cb-Like mechanism

The geometries of many β-halocarbanions are not stationary points on the potential energy surface. Computational optimization of these geometries can lead to spontaneous elimination of the halogen as a halide ion and formation of alkene products. Computational optimizations might, therefore, be used to predict the experimental behavior of β-halocarbanions according to an E1cb-like elimination reaction mechanism. We compare the optimization behavior of a variety of β-halocarbanions according to DFT (ωB97X-D and B3LYP), MP2, and semi-empirical PM3 models. For most optimizations, there was agreement about the general order of leaving group preference (Br– > Cl– > F–). Also observed was a general preference for loss of the leaving group from the least substituted carbon atom when options were presented.

The Effect of Acyl Chain Position on the 2D Monolayer Formation of Monoacyl-sn-Glycerol at the Air/Water Interface: Quantum Chemical Modeling

This paper deals with the results of quantum chemical modeling of the monoacyl-sn-glycerol 2D cluster formation at the air/water interface using a semi-empirical PM3 method. The impact of the 2 or 3 positions of the acyl substituent on the thermodynamics of the monolayer formation is assessed for surfactants with an acyl substituent CnH2n+1COO chain length of n = 6–17 carbon atoms. The calculation shows a significant change in the spontaneous clusterization threshold for isomeric compounds, which differs only in the position of the acyl substituent with respect to the glycerol backbone. This change is almost equal to substituent shortening by approximately two methylene fragments. At the same time, the geometric parameters of the unit cell for resulting monolayers are not affected so drastically. The 2D films in question possess an oblique or orthorhombic unit cell with parameters for 2 and 3-monoacyl-sn-glycerol monolayers, as follows: a = 4.91 Å and 4.82 Å and b = 5.00 Å and 4.92 Å, with hydrocarbon chains tilted at t = 23.0° and 23.5°. The calculated results are in accordance with existing experimental data obtained using grazing incidence X-ray diffraction measurements and the π-A isotherm technique.

STUDY OF THE EFFECT OF MODIFICATION OF THE STRUCTURE OF A NEW DERIVATIVE OF QUINAZOLINE–4(3H)–ONE ON FATTY ACID SYNTHASE (FAS) MYCOBACTERIUM

Relevance. Tuberculosis remains one of the main causes of disability and mortality from infectious diseases worldwide. The discovery of phenotypi-cally tolerant subpopulations of pathogen persisters has called into question the possibilities of known anti-tuberculosis drugs. In this connection, the search and development of new effective anti-tuberculosis drugs is an important direction in the development of modern pharmacology. Currently, it is relevant to consider substances of the quinazoline nature as antimicrobial agents that exhibit antitubercular activity. The aim of the work is computer modeling of the interaction of new derivatives of quinazoline–4(3H)–oh with NAD(H) in order to predict the possibility of influencing the fatty acid synthase (FAS) Mycobacterium. Material and methods. Modeling of intermolecular complexes in the interaction system of new derivatives of quinazoline-4(3H)–on – VMA–17–04 and VMA–13–05 with the oxidized form of NAD+ was carried out using the quantum chemical semi-empirical PM7 method implemented in the MOPAC 2016 program. Conclusions. The VMA–13–05 derivative, being in stable conformation I, forms an adduct with NAD+ having optimal energy characteristics. This inter-action can be considered as one of the stages of the biochemical pathway of suppressing the activity of FAS synthase, which takes part in the synthe-sis of mycolic acids and leads to the death of Mycobacterium cells.

Molecular modeling study of natural products as potential bioactive compounds against SARS-CoV-2.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of vaccines, research interest in the emergence of new variants is still prominent. Currently, the focus is on the search for effective and safe drugs, given the limitations and side effects observed for the synthetic drugs administered so far. In this sense, bioactive natural products that are widely used in the pharmaceutical industry due to their effectiveness and low toxicity have emerged as potential options in the search for safe drugs against COVID-19. Following this line, we screened 10 bioactive compounds derived from cholesterol for molecules capable of interacting with the receptor-binding domain (RBD) of the spike protein from SARS-CoV-2 (SC2Spike), responsible for the virus's invasion of human cells. Rounds of docking followed by molecular dynamics simulations and binding energy calculations enabled the selection of three compounds worth being experimentally evaluated against SARS-CoV-2. The 3D structures of the cholesterol derivatives were prepared and optimized using the Spartan 08 software with the semi-empirical method PM3. They were then exported to the Molegro Virtual Docking (MVD®) software, where they were docked onto the RBD of a 3D structure of the SC2Spike protein that was imported from the Protein Data Bank (PDB). The best poses obtained from MVD® were subjected to rounds of molecular dynamics simulations using the GROMACS software, with the OPLS/AA force field. Frames from the MD simulation trajectories were used to calculate the ligand's free binding energies using the molecular mechanics - Poisson-Boltzmann surface area (MM-PBSA) method. All results were analyzed using the xmgrace and Visual Molecular Dynamics (VMD)software.

Host–Guest Inclusion Systems of Vanillic Acid into α-Cyclodextrin: Structures, Electronic Properties, QTAIM, NCI and IGM Analyses with Dispersion Corrected Calculations

In this work, a theoretical study of the host–guest inclusion process involving the vanillic acid (VA) into α-cyclodextrin (α-CD) was investigated by the semi empirical methods PM6 and its modern variant PM6-D3H4 and density functional theory with the BP86-D3/6-31G+(d,p) functional to elucidate the relationship between host, guest and their molecular structures. According to the results from theoretical calculation, the model in which the VA molecule points it’s the carboxylic acid group toward the wider rim of α–CD is energetically preferred. The global reactivity descriptors were calculated and analyzed. The electronic transitions of the two complexes computed with the TD-DFT approach on the optimized geometries at BP86-D3/6-31G+ (d, p) level of theory including the CPCM model were investigated. Finally, quantum theory of atoms in molecules (QTAIM) analysis, the non-covalent interactions analysis (NCI) and the independent gradient model (IGM) results confirms that the van der Waals interactions and hydrogen bonds play a major role in the stabilization of the complexes.

2D-monolayer formation of 3-monoacyl-sn-glycerols at the air/water interface. A comprehensive quantum chemical approach

Thermodynamic and structural aspects of the monolayer film formation of 3-monoacyl-sn-glycerol homologous series with the alkyl chain length n = 7–18 at the air/water interface are considered. The calculations are carried out within the framework of the semiempirical quantum chemical method PM3 and supported experimentally using surface pressure-area per molecule (π–A) isotherms, Brewster angle microscopy (BAM), as well as grazing incidence X-ray diffraction analysis (GIXD). A conformational analysis of 3-monoacyl-sn-glycerol monomers reveals three stable conformations of monomers with Monomer 1 as the possible basis for the construction of the most energetically advantageous structures of small clusters, which subsequently can form a 2D monolayer. Optimized tetramer structure of 3-monoacyl-sn-glycerol is considered as a unit cell of the 2D film with geometric parameters: a= 4.82 Å, b= 4.92 Å, and the angle between them θ = 91°. The molecular tilt angle of surfactant molecules with respect to the normal to the interface is 23.5°. These structural parameters are in good agreement with existing experimental data. The spontaneous clusterization threshold of 3-monoacyl-sn-glycerol at the air/water interface is 16 carbon atoms in the alkyl chain at standard temperature. The temperature dependences of the Ac area per film molecule at the beginning of the liquid-expanded–liquid-condensed (LE–LC) phase transition are analyzed. The values of the Ac change per 1 °C for 3-monoacyl-sn-glycerol are commensurable with corresponding values of other surfactant classes confirming the dominating role of intermolecular CH···HC interactions in the clusterization energy of surfactants.