Semiempirical PM3 Method Research Articles

METFORMIN-SENSITIVE POTENTIOMETRIC SENSOR

Metformin (N,N-dimethylbiguanidine) in its protonated form as metformin hydrochloride is used worldwide as an advanced antidiabetic drug for type 2 diabetes. Hyperinsulinemia and insulin resistance of cells are the main causes of this disease. For patients with diabetes, metformin hydrochloride (hereinafter – MET) works by improving cell sensitivity to insulin. It has been shown that metformin with tropeolin 00 (T00) forms an ionic associate that can be isolated in solid form and is suitable for the creation of plasticized membrane potentiometric metformin-sensitive sensors. The energy efficiency of ionic associate formation is substantiated by the method of mathematical modeling. Molecular modeling of T00- + MET+ systems and related calculations were performed using the HyperChem 8.0 package for various initial variants of counter ion relative to each other (single point procedure). Geometric optimization of ions was performed by the method of molecular mechanics MM+. The standard enthalpy (ΔH0) of ion formation and the association “MET+ + T00-” was determined by the semi-empirical method PM3. The difference in the energy of formation of the ionic associate and the sum of the energies of formation of its components is 312 kJ/mol. Therefore, the process of ionic associate formation is thermodynamically advantageous. Modeling and optimization of membrane composition is carried out. The results of the study of the influence of the nature of plasticizers on the electroanalytical properties of the developed sensors indicate that the best plasticizer for the system is TCP or DNF. For these solvents, the product of the dielectric constant and Rorschneider polarity (ε × PR) is 123,5 and 175 respectively. For plasticizers that were less effective (DBF and DEF), these values are 235,6 and 326 respectively. For membranes with the same content of plasticizer of one homologous series (DEF, DBF, DOF, DNF), the slope of the Nernst function decreases with increasing dielectric constant of the plasticizer solvent. It is shown that the working pH range of the electrode is from 2 to 11. The drift potential does not exceed 1–3 mV/day. Stable values of electrode potentials are set for 5–15 s. The stability of the electroanalytical characteristics of the optimized membranes can be traced for at least three months. The developed sensors show satisfactory selectivity in relation to a number of substances and ions. The 300 and 1000 times the amount of glucose, starch, polyvinyl alcohol, Na+, K+, Mg2+, Ca2+, Ba2+ ions do not interfere with MET determination. This, in turn, allows the practical use of developed MET-sensitive sensors in a variety of objects. A method of potentiometric determination of metformin has been developed, which has been tested in its determination in dosage forms.

Polyurethane/single wall carbon nanotube/polymethylmethacrylate nanocomposite: PM3 semi-empirical method, Monte Carlo applied

Firstly, this work shows the crosslinking of the Polyurethane/Single Wall Carbon Nanotube/ Polymethyl Methacrylate (PU/SWCNT/PMMA) nanocomposite at 298.15K using the PM3 semi-empirical method (Parameterized Model number 3), where the reaction was spontaneous and endothermic. The log P indicated a hydrophobic character. Subsequently, the Monte Carlo simulation was carried out at 303.15, 313.15 and 323.15K, where the Gibbs free energy and the dipole moment increased. However, the reactions were spontaneous and endothermic. The log P had hydrophobic character. Additionally, the entropy decreased due to the increase in intermolecular forces in the nanocomposite. Furthermore, FTIR analysis had similar vibrational frequencies, which was verified with the electronic distribution. Thus, this nanocomposite would have excellent physical and thermal stability, and it does not have reactions to polar solvents such as water so that it could be used in the human body.

QSAR MODELING AND DESIGN OF A NEW MODEL OF ANTIHIV DRUG 1-ARYL-TETRAHYDROISOQUINOLINE DERIVED USING THE PM3 SEMIEMPIRICAL METHOD

Quantitative Structure-Activities Relationship Analysis (QSAR) on the 1-aryl-tetrahydroisoquinoline derivative as a candidate for the anti-HIV drug (Human Immunodeficiency Virus) has been done. The analysis using an electronic descriptor of atomic net charge, dipole moment, polarization, HOMO-LUMO energy, and log P was calculated using the PM3 semiempirical method. The best equation model is determined using multilinear regression analysis. The QSAR analysis show that the best QSAR equation model of 1-aryl-tetrahydroisoquinoline derivatives: pEC50= -23.019-10.867(qC3)-162.911(qC4)-107.057(qC6) + 53.621(qC8) - 0.047 (µ) + 0.158 (α) + 0.175 (log P); (n = 36; r = 0.935; r2 = 0.875; SE= 0.135927366; Fcount/Ftable= 7.945277618; PRESS = 2.857943). The compound with the higher activity value is the best theoretically derivative compound for the anti-HIV drug candidate. The new model of the 1-aryl-tetrahydroisoquinoline derivative from the design is expected to have better activity than the 1-aryltetrahydroisoquinoline derivative compound that already exists is 1-(6-acetylpyridine-2-yl)-7,8-methoxy-quinoline.

Non-covalent interactions atlas benchmark data sets 4: σ-hole interactions.

The SH250×10 dataset presented here extends the Non-Covalent Interactions Atlas database (https://www.nciatlas.org) to complexes bound by σ-hole interactions - halogen, chalcogen and pnictogen bonds. It comprises 250 complexes where Cl, Br, I, S, Se, P and As interact with diverse electron donors. An accurate CCSD(T)/CBS benchmark is provided for ten points along a dissociation curve of each complex. The SH250×10 set is used in testing a wide variety of DFT functionals and semiempirical quantum-mechanical methods. In DFT calculations, the new data set exposes large errors of some functionals related to exaggerated charge transfer. The size and diversity of the data set have also been exploited in the reparametrization of a halogen-bond correction for the PM6 semiempirical method.

Computational Exploration of Charge Transfer Dynamics in Dye Sensitized SnO2 and ZnS for Photocatalytic Applications

A computational study of some novel charge transfer complexes, prepared by the adsorption of dyes on SnO2 and ZnS was carried out using semiempirical PM3 method. The two natural dyes, 1S,3R,4R,5R-3-(3,4-dihydroxyphenyl)acryloyloxy)-1,4,5-trihydroxycyclohexane carboxylic acid (DTC) and 2-Phenyl-4H-chromen-4-one (PHC) were adsorbed independently on to 1×1×1 SnO2 and ZnS crystals to form SnO2-DTC, SnO2‌-DTC-PHC and ZnS-DTC adsorption complexes. The theoretical electronic absorption spectra calculated via PM3 method revealed a large bathochromic shift to 958 nm and 577 nm for SnO2-DTC and SnO2-DTC-PHC, respectively, indicating the formation of charge transfer complex. Moreover, the bandgap was reduced to 1.29 and 2.15 eV as compared to 3.4 eV of pristine SnO2. Subsequently the adsorption of DTC on ZnS was accomplished and calculations were performed to determine the spectroscopic properties of the complex, where a considerable red shift was observed for ZnS-DTC as well. The semiempirical PM3 calculations evidenced stability of SnO2-DTC, SnO-DTC-PHC and ZnS-DTC as predicted from negative adsorption energy values. The positions of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) as obtained from single point energy calculations, were concomitant with proposed photocatalytic mechanisms.

Molecular structure, spectral and thermal properties and in silico biological activity of new bis-phthalimidopropylalkylammonium conjugates of bile acids

• Nine novel quaternary bis-phthalimidopropylalkylammonium conjugates of bile acids were synthesized. • 1 H NMR, 13 C NMR, FT-IR and ESI-MS were performed for the characterization. • Computational study was done at PM5 method level for comparative analysis. • In silico study was done to facilitate the search for pharmacological activity. New quaternary bis-phthalimidopropylalkylammonium conjugates of lithocholic, deoxycholic and cholic acids were obtained by reaction of bile acids with bromoacetic acid bromide to give bile acid 3α-bromoacetates. These intermediates were subjected to nuclephilic substitution with N,N -bis-(phthalimidopropyl)- N -ethylamine, N,N -bis-(phthalimidopropyl)- N -decylamine and N,N -bis-(phthalimidopropyl)- N -hexadecylamine to give the final quaternary ammonium salts. The structures of products were confirmed by spectral ( 1 H NMR, 13 C NMR, 2D NMR and FT-IR) analysis, mass spectrometry (ESI-MS) as well as PM5 semiempirical methods and B3LYP ab initio methods. In addition, differential scanning calorimetric (DSC) studies were performed for compounds of different hydrocarbon chain length. Estimation of the pharmacotherapeutic potential has been accomplished for synthesized compounds on the basis of Prediction of Activity Spectra for Substances (PASS).

Study of Stability and Reactivity of Cyclopolic Acid Compounds and Their Derivatives Using Semi-empirical Methods AM1 and PM3

The semi-empirical method is a method can be selected in computational chemistry. This method can be used to study the stability and reactivity of cyclopolic acid compounds and their derivatives. This method is simple method in optimizing a compound in calculating the parameters possessed by the atom. Cyclopolic acid is an organic compound that can be found in corn and beans. Analysis using two methods on HyperChem Professional application are AM1 and PM3. Analysis Result has shown the that total energy and gradient of each compound do not have significant differences in calculations. As in the structure of 2-formyl-3-(hydroxymethyl)-6-methoxy-5-methylterephthalic acid has a total energy of -80608.1868567 (kcal/mol) and a gradient of 0.0898817 (kcal/mol/Ang) with the AM1 method and total energy of -74935.9180118 (kcal/mol) and a gradient of 0.0874369 (kcal/mol/Ang) with the PM3 method. The stable structure is in the structure of the 2-formyl-3-(hydroxymethyl)-6-methoxy-5-methylterephthalic acid based on the calculation of the total energy and gradient. Meanwhile, according to the calculation of the difference between LUMO-HOMO, it has different results. Where according to the calculation of the energy difference between LUMO-HOMO, the most stable compound structure is the structure of 2-formyl-3-(hydroxymethyl)-4-isocyano-6-metoxy-5-methylbenzoic acid but is not reactive. Likewise, the 2-formyl-4-hidroxy-3-(hydroxymethyl)-6-methoxy-5-methylbenzoic acid, 2-formyl-3-(hydroxymethyl)-6-methoxy-5-methyl-4-(oxo-λ6-methyl)benzoic acid and 2-formyl-3-(hydroxymethyl)-6-methoxy-5-methylterephthalic acid are reactive but unstable compound structure.

Design, synthesis, spectral and theoretical study of new bile acid–sterol conjugates linked via 1,2,3-triazole ring

New four steroid conjugates have been prepared from bile acids and sterol derivatives using click chemistry method. The azide-alkyne Huisgen cycloaddition (intermolecular 1,3-dipolar cycloaddition) of the propargyl ester of lithocholic, deoxycholic, cholic acid as well as dehydrocholic acids and azide derivatives of cholesterol gave a new bile acid–sterol conjugates linked with a 1,2,3-triazole ring. Previously, bile acids were converted into bromoacetyl substituted derivatives by the reaction of propargyl esters of lithocholic, deoxycholic, cholic with bromoacetic acid bromide in toluene with TEBA and sodium hydride. All conjugates were obtained in good yields using an efficient synthesis method. The structures of all products were confirmed by spectral (1H- and 13C NMR, and FT-IR) analysis, mass spectrometry (ESI-MS), as well as PM5 semiempirical methods. Estimation of the pharmacotherapeutic potential has been accomplished for the synthesized compounds on the basis of Prediction of Activity Spectra for Substances (PASS).

Physicochemical characterization of the DNA complexes with different surfactants

DNA complexes with cetyltrimethylammonium chloride (CTMA), benzyldimethylhexadecylammonium chloride (BAC) and hexadecylpyridinium chloride (HDP) surfactants as powder samples were studied by Fourier-transform middle infrared spectroscopy, X-ray diffraction and dielectric spectroscopy methods. Complexation as electrostatic interactions was confirmed by FT-MIR spectroscopy. The width of DNA-surfactant complexes was estimated to 61–73 Å based on modeling with the semi-empirical PM7 method. Based on SAXS results we propose the packing model for the complex molecules as hexagonal or slightly distorted hexagonal depending on the surfactant. For the first time the dielectric process registered in the low frequency range for all complexes was interpreted as oscillation of surfactant ions (BAC+, HDP+ or CTMA+), analogous to the oscillation of ions (e.g. Na+) in solutions of pure DNA. The influence of the structure of the complex-forming surfactant molecule on the value of the relaxation time distribution parameter is discussed.

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations.

The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.

Spectroscopic Determination of Dissociation Constants of Some 4- nitrobenzaldehyde-4-substituted phenyl-1-carbonylhydrazones in Sodium Hydroxide Media

Purpose: Hydrazones are a class of azomethines with a wide spectrum of pharmacological properties which are influenced by pH of the media. The purpose of this study was investigation of acid-base properties of five 4-nitrobenzaldehyde-4-substitutedphenyl1-carbonylhydrazones in sodium hydroxide media (14>pH>7). Method: The dissociation process was followed by UV-Vis spectroscopy, in the ethanol-water (V/V, 1:1) solutions, at room temperature. Semiempirical methods AM1 and PM3 were applied for determination of the deprotonation enthalpies. Results: The changes in the UV-Vis spectra, as well as the deprotonation enthalpies, suggested that the dissociation process for four investigated hydrazones with an amide group took place in one step. The exception with two dissociation steps was hydrazone with amide and hydroxyl group. The pH region of dissociation was from pH 10.8 to pH 11.6 for the first step and between pH 11.7 and pH 12.1 for the second step of dissociation. The influence of the ethanol on the UV-Vis spectra was eliminated by the method of Characteristic Vector Analyses (CVA). The stoichiometric dissociation constants were determined numerically (pKHA = n·pH + logI) and graphically (intercept of the dependence of logI on pH) from the absorbance data using experimental and reconstructed UV-Vis spectra, at three different ionic strengths. Thermodynamic dissociation constants were estimated graphically as an intercept of dependence of dissociation constant on the square root of the ionic strength. Conclusion: The obtained results demonstrated that the influence of the substituents on pKHA values was not significant, except for hydrazone with amide and hydroxyl group. Namely, the dissociation of the amide group of this hydrazone was retarded due to the influence of the phenolic group.

An approach of quantum chemical methods for the development and substantiation of the structure of new piperidine compounds

The main research direction uses computational computer programs that establish the structural features of new modified piperidine compounds. The analysis of molecular models of piperidine derivatives using the semiempirical PM3 method of the HyperChem program (version 8.0.8) shows the practicality of synthesizing seven drugs and thermodynamic stability for the structures. All compounds have one nucleophilic reaction (oxygen in benzoyl radical) based on the calculations of the piperidine charges and their derivatives. The chemical stability of piperidine derivatives directly depends on the highest occupied molecular orbital (HOMO) energy gap and the lowest unoccupied molecular orbital (LUMO). All investigated model structures 4, 6, 7, 10 are nucleophiles. Compounds 2, 3, and 15 acts as electrophiles, attributed to the absence of benzyloxy radical in their structure. Based on the calculations of dipole moments, all the considered compounds have high polarity and will be readily soluble in almost all polar solvents: water and alcohol. This confirms the possibility of obtaining various dosage forms based on the investigated compounds on an industrial scale.

Predicting water solubility in ionic liquids using machine learning towards design of hydro-philic/phobic ionic liquids

In this work, a database containing the solubility data for water in 16,137 ionic liquids (ILs), which were formed by a combination of the most commonly used 163 cations (in nine groups) and 99 anions, were analyzed using machine learning. The water solubility in ILs was computed by COnductor-like Screening MOdel for Realistic Solvents (COSMO-RS) while the molecular descriptors for the individual cations and anions were determined by semi-empirical PM3 method. Association rule mining, decision tree and multilayer fully connected neural network (a deep learning model) were employed as machine learning techniques. The association rule mining analysis clearly identified the descriptors leading to low water solubility in ILs, while the decision tree analysis provided heuristic rules for the selection of cations and anions to form ILs with low water capacity. The prediction accuracy of fully connected neural network model was also high; even the model constructed from a small fraction of data was successful to predict the water solubility in other ILs in the dataset indicating that the anionic and cationic descriptors used were sufficient to represent the performance of ILs. The classification ability of decision trees was verified by the experimental water solubility data for 49 ILs extracted from 13 published papers in literature; the decision tree model correctly classified the experimental solubility of 46 of these ILs. The deep learning predictions of solubility were also in agreement with the experimental data within the accuracy level of COSMO-RS calculations. It was generally found that the anionic descriptors were more influential to predict the water capacity of ILs, while the cationic descriptors made limited contribution.

Ring-opening Polymerization Reaction Mechanism of ε-Caprolactone Catalyzed by Bis(dibenzoylmethanato) zirconium(IV) Using PM3 Semi-Empirical Method

Polycaprolactone (PCL) is a semi-crystalline polymer and belongs to a biodegradable plastic. PCL also can naturally degraded, has a high degree of adjustment with other polymer, and has great mechanical and thermal properties. By using the Lewis acid catalyst, PCL can be yielded through the ring opening polymerization (ROP) of caprolactone (ε-CL). The objective of this study was to explore the most likely reaction mechanism of the ROP of ε-CL using bis(dibenzoylmethanato) zirconium(IV) chloride as a catalyst. Here, the Hyper Chem 8.0 program was performed to compute the monomer molecule, intermediate molecules, and polymer molecule. The program can be launch on the Windows 07 systems. The method used was the PM3 semi-empirical method. This program also used to show the results of optimized structures. The calculation results show that to generate PCL required bis(dibenzoylmethanato) zirconium (IV) catalyst. The ROP reaction mechanism of ε-CL can be occurs through direct coordination ε-CL on the Zr complex. After that, deprotonation and insertion monomer. Last step was chain propagation of the χ–CL.

The Reaction Mechanism of Ring-opening Polymerization of ε-Caprolactone Using Bis(benzoylacetonato)zirconium(IV) Catalyst With PM3 Semi-Empirical Method

Acknowledged that polycaprolactone (PCL) is one of the prospective polymer category. This is due to PCL has a great mechanical properties, biodegradability, and excellent mixing ability with various other polymers. The effective technique to get PCL is through the ring opening polymerization (ROP) of caprolactone (ε-CL) using metal catalyst. The aims of this research was to determine a reasonable reaction mechanism of the ROP of ε-CL using bis(benzoylacetonato)zirconium(IV) chloride catalyst. In this investigation the PM3 semi-empirical method was assigned to calculate the monomer, intermediate structures, and polymer structure. Then, to compute and visualize geometry structure was employed by using the HyperChem 8.0 program. This software operates on the Windows 07 system. The calculation results imply that to get PCL using bis(benzoylacetonato)zirconium(IV) catalyst required a few steps i.e. coordination ε-CL in metal center, χ-CL deprotonation, the insertion of ε–CL, and propagation of the chain.

Quantum computational, linear and non-linear optical properties of spin-coated nickel (II)-tetraphenylporphyrin/FTO thin films

The out of a plane (OOP) distortions in the geometric structure of Nickel (II) tetraphenylporphyrin (NiTPP) were calculated by quantum chemical calculation using semi-empirical PM3, PM6, and DFT methods. NiTPP thin films were deposited onto FTO substrates using the spin coating method on different thicknesses (80, 120, and 170 nm). The x-ray diffraction (XRD) patterns for all thicknesses exposed that NiTPP/FTO films were in the tetragonal phase structure. As the thickness grows, the crystallite size rises, and film morphology looks to be uniform and the small grains start to agglomerate to form big grains. The Raman spectra were checked and assigned for the powder and various thicknesses NiTPP/FTO thin films in the spectral range between 200−1800 cm−1. According to Tauc’s relation, the indirect energy bandgaps values were decreased as the film thickness rises. The optical constants (n& k), electronic polarizability αe the complex dielectric constant (ε1& ε2), and optical conductivity σopt were calculated as a function in film thickness. In addition, the nonlinear susceptibility χ(3), non-linear refractive index χ(3), and nonlinear absorption coefficient (βc) were estimated in the wavelength range 300−1000 nm by semi-empirical calculation. The findings obtained indicate that the spin-coated NiTPP/FTO thin films exhibit strong nonlinear optical (NLO) properties that are probable candidates for optoelectronic devices fabrication.

Repositioning Adequate Antibiotics to Treat/Cure the Coronavirus Disease 2019 (COVID-19): Current Treatments and Future Directions

Repositioning Adequate Antibiotics to Treat/Cure the Coronavirus Disease 2019 (COVID-19): Current Treatments and Future Directions

Quantum-Chemical Calculation of Alkoxy(hydroxy)(ethylacetoacetate)alumoxane Geometry

Geometric parameters of two probable molecular structures of amorphous alkoxy(hydroxy)(ethylacetoacetate)alumoxane were calculated using self-consistent field (Hartree–Fock) and semiempirical PM3 methods in the HyperChem 6.01 software package. Bond lengths, bond angles, and calculated total energies for two molecular structures of amorphous alkoxy(hydroxy)(ethylacetoacetate)alumoxane are presented.

First-principles investigation of dimethyl-functionalized MIL-53(Al) metal–organic framework for adsorption and separation of xylene isomers

Functionalization of organic linker in metal–organic frameworks (MOFs) has been a popular method to utilize the porous material for a wide range of applications. In xylene separation, dimethyl functionalization of MOFs had demonstrated improved adsorptions properties. However, the effect of different xylene isomers on the organic linker is still not fully understood. In this work, the MIL-53(Al) MOF was functionalized with two methyl groups in ortho-, meta- and para-positions. The energy and thermochemical properties of xylene isomers when complexed dimethyl functionalized MIL-53(Al) MOFs were investigated using semiempirical quantum chemical PM6 method. The adsorption model of xylene isomers over meta-dimethyl-MIL-53(Al) (MDM) produced the lowest energy and the most thermochemically stable complex. The electronic properties, natural charge, nuclear magnetic resonance, aromaticity and molecular electrostatic potential of MDM complexes were further characterized using density functional theory (DFT) calculations at B3LYP/6-31G(d) level. DFT calculations revealed that the complex of MDM with m-xylene had the lowest adsorption energy and the highest reactivity, caused by the oxygen atoms surrounding the Al metal ion. In contrast, the complex of MDM with o-xylene had the highest energy of adsorption and the lowest reactivity, mostly governed by weak π interactions. Based on the results, we propose the use of MDM MOF for adsorption and separation of xylene isomers.

Quantum chemical calculation of piperidine-based synthesized compounds using the PM-3 semiempirical method

The article provides estimates of the geometry of molecules, calculation of the stability of intermediate products and transition states. Calculation of the results for the majority of reactions is carried out experimentally. Along with a multi-stage process, difficulties are inherent in the appearance of intermediate stages and the presence of intermediate reaction products in an extremely short time.