PM3 Method Research Articles

Quantum-chemical studies of rutile nanoparticles toxicity II. Comparison of B3LYP and PM6 data

Abstract The relation between copper atomic charges and metal-ligand interaction energies obtained by PM6 and DFT-B3LYP methods for cytotoxicity prediction of model rutile nanoparticles [Ti40O124H81]7–, [Ti7O28H26]2–, [Ti2O10H10]2–, [Ti7O30H30]2– and their Cu(II) complexes is investigated. Except for Mulliken charges, very good statistical parameters were obtained for the linear relation between the results obtained by both methods if standard accuracy of quantum-chemical calculations is achieved.

Theoretical Study of the Complexation of Lidocaine by α- and β-Cyclodextrins

Structure and stability of an eventual inclusion complex formed by Lidocaine and two cyclodextrins (α- and β-CD) were investigated using molecular mechanics and quantum-chemical methods in the gas phase and in water. The molecular docking and quantum chemical calculations results show that no inclusion complex is formed between α-CD and Lidocaine molecule, while the conformational research allowed observing two minimum-energy structures between this molecule and β-CD. From a potential energy scan, a partial inclusion of the two ends of Lidocaine by the secondary face of the cavity of β-CD is observed with a better stability for the complex including the ((-N(C2H5)2) group in it. The minimum energy conformers, obtained by semi empirical method (PM3), have been exposed to fully geometry optimization employing ONIOM2 calculations by combining PM3 method with B3LYP, M06-HF and WB97XD functionals at 6-311G (d,p) basis set. The results show that complexation reactions are thermodynamically favored (Gand#176; ˂ 0) and the inclusion complexes are energetically stables and well structured (Sand#176; ˂ 0). According to the analysis of natural bond orbitals, the Van der Waals interactions are the sole driving forces that ensure the stability of the formed complexes.

Prediction of Antagonistic Activity of <i>β</i>-Carboline and Its Derivatives Using Topological Descriptors

Prediction of antagonistic activity of β-carboline and its thirteen derivatives has been made using topological descriptors viz, connectivity index, and kappa shape index of different orders. For evaluation of values of descriptor, molecular modeling and geometry optimization of all the compounds were carried out with CAChe Pro software by opting semiempirical PM3 method using MOPAC 2002. For prediction of activity multiple linear regression analysis (MLR) was performed. MLR analysis has been made by Project Leader Software associated with CAChe by using the above descriptors as independent variables and biological activity as dependent variables. We were performed leave-one-out methods and the result reflected a direct relationship between biological activity and connectivity index of zero order, while indirect relationship with connectivity index of second order and thus connectivity index is a reliable descriptor to predict the biological activity of β-carboline and its various derivatives.

Theoretical Study of the Complexation of Lidocaine by α- and β-Cyclodextrins

Structure and stability of an eventual inclusion complex formed by Lidocaine and two cyclodextrins (α- and β-CD) were investigated using molecular mechanics and quantum-chemical methods in the gas phase and in water. The molecular docking and quantum chemical calculations results show that no inclusion complex is formed between α-CD and Lidocaine molecule, while the conformational research allowed observing two minimum-energy structures between this molecule and β-CD. From a potential energy scan, a partial inclusion of the two ends of Lidocaine by the secondary face of the cavity of β-CD is observed with a better stability for the complex including the ((-N(C2H5)2) group in it. The minimum energy conformers, obtained by semi empirical method (PM3), have been exposed to fully geometry optimization employing ONIOM2 calculations by combining PM3 method with B3LYP, M06-HF and WB97XD functionals at 6-311G (d,p) basis set. The results show that complexation reactions are thermodynamically favored (Gand#176; ˂ 0) and the inclusion complexes are energetically stables and well structured (Sand#176; ˂ 0). According to the analysis of natural bond orbitals, the Van der Waals interactions are the sole driving forces that ensure the stability of the formed complexes.

Quantum chemical assessment of the molecular area corresponding to the onset of the LE-LC phase transition for amphiphilic 2D monolayers at the air/water interface.

An approach for the assessment of the area per surfactant molecule in a monolayer at the onset of the LE-LC phase transition (Ac) is proposed based on the quantum chemical approach and a thermodynamic model for amphiphilic monolayers, which takes into account the nonideality of the mixing entropy. The values of the Gibbs' clusterization energy for small surfactant associates, as well as the geometric parameters of the monolayer unit cells, were used, previously calculated using the semiempirical PM3 method for eight classes of amphiphilic compounds: saturated and ethoxylated alcohols, saturated and unsaturated cis-carboxylic acids, α-hydroxylic and α-aminoacids, N-acyl-substituted alanine and dialkyl-substituted melamine. The obtained Ac values are in satisfactory agreement with the available experimental data. This allows using the proposed approach for prognostic purposes in the cases where there are no corresponding π-A isotherms for necessary surfactants, but there are calculated thermodynamic and structural parameters of its clusterization.

Molecular modeling of intermolecular interaction between macromolecules of polyvinyl alcohol and polyaniline in polymer composite

Quantum-chemical modeling of macromolecules of polyvinyl alcohol (PVA), emeraldine salt of polyaniline (PANI) and its composite was performed using the semi-empirical PM7 method taking into account the dielectric constant of water (EPS=78.4) as a solvent using the MOPAC2016 program and the WINMOSTAR graphical interface. Thermodynamic calculations of the models were performed using the key parameter THERMO (290,330,10). An X-ray examination of the original polymers and composites with different PANI content was performed. It is shown that intermolecular hydrogen bonds of different strength are formed between PVA and PANI macromolecules, which affect the physicochemical properties of the obtained composites. Quantum chemical calculations indicate that PANI macromolecules can assume different conformational states. Depending on the size of the dihedral angle, the PANI molecule can form a spiral structure (folded or unfolded spiral) or a rigid rod. It should be noted that during the formation of PPC due to intermolecular interaction may change the conformation of PVA and PANI. The calculated values of the heat of formation (Δ f H o ) for the composite are smaller than the sum of the corresponding values of the fragments of the studied polymers. The decrease in Δ f H o energy is associated with the formation of hydrogen bonds between the fragments of PVA and PANI. The difference between the corresponding values of Δ f H o is about 78 kJ/mol, which corresponds to the formation of 4 ̶ 6 intermolecular hydrogen bonds of the fragments N-H…O and С-Н…О. A further confirmation of the formation of hydrogen bonds in the composite between PVA and PANI molecules can be a decrease in the numerical values of entropy. The decrease in entropy is 382.6 ̶ 388.1 J/mol . K. Keywords : polyvinyl alcohol, polyaniline, quantum chemical calculations, intermolecular interaction, hydrogen bonds.

Prediction of photofading of N‐β‐hydroxyethylamino‐o‐nitrophenyl derivatives: a theoretical study

AbstractUntil now, the lightfastness of hair dyes had not been investigated using all‐valence molecular orbital methods. The results of calculations are used to obtain the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) frontier electron density, which can reflect the propensity for electrophilic or nucleophilic attack at an atom in a molecule. Using semi‐empirical quantum chemical methods AM1 and PM3, we have calculated the reactivity rates , superdelocalisability and electron density distribution in the tested dyes. We have found that the photooxidation of hair dyes (photochemical decomposition of hair dyes) and derivatives of N‐β‐hydroxyethylamino‐o‐nitrobenzene occurs through the degradation of the N‐β‐hydroxyethylamine substituent and on C2 or C4 atom (C4–NO2) in the process of electrophilic reaction with singlet oxygen 1O2 or nucleophilic reaction on the C1 carbon atom of the aromatic ring, with the use of superoxide anion radical O2●. The structures of the dyes were optimised using MM+, DM and AM1 or PM3 until constant energy value was realised with a 0.01 kcal/mol convergence criterion.

Synthesis, Characterization and Thermal Studies of Cr (III), Co (II) and Ni (II) Complexes with Schiff Base

The physiologically active compounds of Schiff bases find application in the treatment of several diseases. This biological activity of Schiff base is attributed to the formation of stable chelates with a transition metal, and they are known to exhibit a wide variety of pharmacological properties and carcinostatic activities. Cr (III), Co (II), and Ni (II) complexes of Schiff base were chosen for the present experimental work and theoretical treatment and characterized by different spectroscopies such as elemental analysis CHN, infrared, ultra visible spectroscopies, magnetic susceptibility, molar conductivity measurements, and thermal analysis The results of this research, indicate that the complexes have a type composition [M (NL)]. Schiff base NL: derived from 2-aminobenzoic acid and Benzil, M: Cr (III), Co (II), and Ni (II) transition metal ions. Schiff base acts as a tetradentate ligand with ions through the hydroxyl groups and imine groups. The work was included theoretical calculations of NL and its complexes, which were done by the program of hyperchem8. 0.7 using semi-empirical calculations. The PM3 method used to calculate the heat of formation (ΔH○f), binding energy (ΔEb), total energy (ΔEtot), and geometric properties of the compounds.

Synthesis, spectral characterization, DFT studies and antimicrobial activities of amino-methylbenzoic acid based azo dyes

Novel derivatives of azo dyes (6–9) were synthesized by diazotization of different amino-methylbenzoic acid (1–4) and followed by coupling with common coupling component 8-hydroxy quinoline(5) under suitable experimental condition. The azo dyes obtained are orange-red in color and they are characterized by various physic-chemical methods like IR, UV–Vis, NMR spectral techniques etc. metal complexes of the selected azo dyes were also prepared and characterized. The synthesized compounds were screened for their biological activities and the result was compared with the standards. Various density functional parameters-energies were evaluated for the selected azodyes from Hyper Chem Software PM3 method and optimized geometry of compound 6, electrostatic potential map, HOMO-LUMO energy states of the same compound were displayed.

COMPUTER MODELLING OF A VERY HEAT RESISTANT Hf6C3N2 FOR COVER OF HYPERSONIC FLIGHT VEHICLES

The creation of a very heat resistant cover for returnable orbiters and for hypersonic flying aircrafts is an actual problem in modern science and technics. Therefore, computer modelling and investigations molecular structure of various multicomponent compounds are important tasks. In the paper, based on the computer model the molecular structure and a very heat resistant of carbonitride hafnium Hf6C3N2 have been investigated by using of the semiempirical quantum mechanical method PM3. Some mechanical, electrical, optical and thermodynamic parameters of this material have been researched. Debye temperature and melting temperature have been calculated. The found theoretical value of melting temperature of carbonitride hafnium Hf6C3N2 is approximated to obtained experimental results. The block diagram of carried out investigations has been presented. The results of investigations indicate that these materials can be applied as a very heat resistant cover for hypersonic flight vehicles and returnable orbiter.

Relationship between the Bulk and Surface Basicity of Aliphatic Amines: A Quantum Chemical Approach.

To assess the surface basicity constant (pKb) of aliphatic amine films, the use of a theoretical approach recently developed to evaluate the pKa of carboxylic acid monolayers on the water surface is tested. The present paper gives a new full picture of the change of acid–base properties of surfactants during their aggregation at the air/water interface. The exploited approach is simple because it does not involve the construction of thermodynamic cycles but uses the Gibbs energies of the formation and dimerization of surfactant monomers in neutral and ionized forms in the aqueous and gaseous phases. The quantum chemical semiempirical PM3 method is applied to perform calculations using a conductor-like screening model, which takes into account the aqueous phase. The calculation shows that aliphatic amines, as well as carboxylic acids, are characterized by a change of the value of the basicity/acidity constant during the film formation. The film formation of surfactants leads to a decrease in their acid–base properties, i.e., the surface pKa values of carboxylic acids and pKb values of amines increase. However, unlike carboxylic acids, there is practically no dependence of the surface pKb value on the alkyl chain length of the aliphatic amine, which is caused by almost identical contributions of one CH2 fragment to the solvation Gibbs energy of neutral and ionized monomers within the calculation error. The obtained results agree with existing experimental data.

Quantum Chemical Calculations of Carbon Nanoscroll Energy Rolled from Zigzag Graphene Nanoribbon

Using the semi-empirical quantum chemical PM3 method the energies of carbon nanoscrolls formed from flat zigzag graphene nanoribbons 46zGNR and 70zGNR are calculated. For this purpose a simple algorithm to define the Cartesian coordinates of the atoms of a carbon nanoscroll is proposed. The dependences of the energy of the nanoscrolls relative to the energy of the corresponding flat nanoribbon on the inner radius of nanoscroll obtained using both the quantum chemical calculations and the semi-classical analytical model shows the bistability of the system. This shows promise for nanoscroll-based nanoelectromechanical systems.

Исследование механических свойств материалов на основе графена C-=SUB=-62-=/SUB=-H-=SUB=-20-=/SUB=- и полиэтилена (-CH-=SUB=-2-=/SUB=--CH-=SUB=-2-=/SUB=--)-=SUB=-n-=/SUB=-

In the paper, the mechanical properties of the materials based on graphene С62Н20 and polyethylene (-СН2-СН2-)n have been investigated by using semiempirical PM3 method, and the visual models of molecules have been constructed (-СН2-СН2-)n. The calculated values of mechanical parameters show that these materials possess a high elasticity and strength. The orbital energies, potentials of ionization, full energies of electrons, strengths, etc. for given material have been calculated. Opportunity of using these light materials in engineering industry for making of superstrong protective thin coating on car bumpers have been considered. The necessary minimal thickness of protective coating during two cars collision with given mass and speed has been calculated that bumpers do not damage.

PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties

We report on optimized molecular geometries and electronic properties calculated by the PM6 method for 94.0% of the 91.6 million molecules cataloged in PubChem Compounds retrieved on August 29, 2016. In addition to neutral states, we also calculated those for cationic, anionic, and spin flipped electronic states of 56.2%, 49.7%, and 41.3% of the molecules, respectively. Thus, the grand total of the PM6 calculations amounted to 221 million. We compared the resulting molecular geometries with B3LYP/6-31G* optimized geometries for 2.6 million molecules. The root-mean-square deviations in bond length and bond angle were approximately 0.016 Å and 1.7°, respectively. Then, using linear regression to examine the HOMO energy levels E(HOMO) in the B3LYP and PM6 calculations, we found that EB3LYP(HOMO) = 0.876EPM6(HOMO) + 1.975 (eV) and calculated the coefficient of determination to be 0.803. Likewise, we examined the LUMO energy levels and found EB3LYP(LUMO) = 1.069EPM6(LUMO) - 0.420 (eV); the coefficient of determination was 0.842. We also generated four subdata sets, each of which was composed of molecules with molecular weights less than 500. Subdata set i contained C, H, O and N, ii contained C, H, N, O, P, and S, iii contained C, H, N, O, P, S, F, and Cl, and iv contained C, H, N, O, P, S, F, Cl, Na, K, Mg, and Ca. The data sets are available at http://pubchemqc.riken.jp/pm6_datasets.html under a Creative Commons Attribution 4.0 International license.

IRMOF‐8: Theoretical evaluation of aluminum doping on hydrogen, methane, and hydrogen sulfide adsorption

AbstractThe use of porous materials, aimed at increasing gas storage capacity at lower pressures, exploits physical adsorption and is an emerging strategy that is being widely investigated. In this scope, porous materials such as metal organic frameworks (MOFs) are a viable alternative, where structural modifications can enhance the properties of these materials and improve the degree of adsorption for a given gas. In this work, we evaluated the adsorption of methane, hydrogen, and hydrogen sulfide gases on pure isoreticular MOF (IRMOF)‐8 and aluminum‐doped IRMOF‐8 using density functional theory Perdew‐Burke‐Ernzerhof/DZVP and semiempirical AM1, PM3, PM6, PM6‐DH+, PM6‐DH2, PM6‐D3, and PM7 methods. Adsorption isotherms were calculated by means of Grand Canonical Monte Carlo simulations. It was found that doping did not provide a significant increase in the amount of adsorbed methane and hydrogen gases. Conversely, doping led to a considerable increase for hydrogen sulfide capture.

A Cyclic Periodic Wave Function Approach for the Study of Infinitely Periodic Solid-State Systems. I. Application to the C-H···π(C≡C) Hydrogen Bonding Systems.

The cyclic periodic wave function (CPWF) approach is applied at the AM1 and PM3 semiempirical levels of approximation to infinitely periodic solid-state systems stabilized by weak CH–pi (C–H···π) interactions between repeat units. The reliability of the AM1 and PM3 methods for modeling C–H···π bonding is first demonstrated using two representative dimer systems: the T-shaped ethyne dimer and the T-shaped propyne dimer. The CPWF method is then applied to two different crystal systems that are stabilized by C–H···π interactions: (1) pent-4-ynoic acid solid and (2) a series of three infinite crystal systems—tetrakis(4-ethynylphenyl)methane solid, tetraethynylmethane solid, and tetrabutadiynylmethane solid. A comparison of our results with available data demonstrates that the use of the CPWF approach at the AM1 and PM3 levels of approximation provides a convenient and reliable method for the study of infinitely periodic systems containing very weak C–H···π bonding.

Design New Compound of Meisoindigo Derivative as Anti Breast Cancer Based on QSAR Approach

Design new compounds of Meisoindigo using the QSAR approach with semiempirical methods have been successfully made with better biological activity as anti-breast cancer results. The research method used to design the new compound of meisoindigo derivatives uses the semiempirical methods. The research procedure divide into tree step, molecular modeling, QSAR equation analysis, and design of new compounds. The PM3 method was chosen as a better method because it has model results that are more representative of physicochemical aspects. The selection of the best model is made by multilinear regression statistical analysis. New compounds derived from the design are expected to bind to the Cyclin-Dependent Kinase 4 (CDK4) enzyme that helps in the cell cycle to prevent cell division. Based on the design, the compound of (E)-2-(2-oxo-1-(2-(trifluoromethyl) benzyl)indolin-3-ylidene)-N-(quinoline-7-yl) acetamide choose as a new compound with more better biological activity (log 1/IC50 = 6.992) than before (log 1/IC50 = 5.823)

Study of the Interaction of Zinc Cation with Azithromycin and its Significance in the COVID-19 Treatment: A Molecular Approach

Introduction: On account of the current COVID-19 pandemic, we have explored the importance of azithromycin and zinc in the treatment of the coronavirus disease by studying the interaction between the cation Zn++ and azithromycin with the tools of the semi-empirical quantum mechanics PM3 method. Methods: By this approach, the niche in which Zn++ is located was determined. Zn++ creates a strong clastic binding between an amine and a hydroxyl group located on the amino-hexose side-chain. Such an interaction serves as a shuttle and allows zinc cation to invade endocellular structures. Results: In this triple collaborative association, the role of hydroxychloroquine would be more that of a chaotropic agent at plasmic membranes, which facilitates access to the azithromycin-Zn++ equipage into key internal compartments. Conclusion: Finally, we show that both azithromycin and Zn++ are susceptible to play a direct role against the replication and the assembly of SARS-CoV-2 particles.

Structural, electronic, and thermodynamic properties of TiO2/organic clusters: performance of DFTB method with different parameter sets

AbstractThe clusters of bare TiO2 and TiO2 with linked organic ligands modeling polyorganic composites used as photocatalytic materials were studied using the density functional based tight binding (DFTB) electronic structure method with three parameter sets (trans3d, tiorg, and matsci) in comparison with results of B3LYP/6‐31G(d,p) calculations, semiempirical methods PM6 and PM7, and available experimental data. It was found that the highly scalable DFTB method shows results that are close to the B3LYP/6‐31G(d,p) level of theory. The corrected version of the tiorg DFTB parameter set (tiorg‐smooth) has better performance for the estimations of structural parameters, whereas the trans3d set better reproduces energies of the composite material formation in polycondensation reactions. Performance of the matsci set is somehow in the middle of the tiorg‐smooth and trans3d sets. The tiorg‐smooth and matsci sets can be used for the studies of adsorption complexes of bare TiO2 clusters. All three DFTB parameter sets well estimate the electronic parameters of clusters (HOMO‐LUMO gap, ionization potential, and dipole moment). DFTB results are closer to the estimates made with DFT (B3LYP/6‐31G(d,p)) than the results of PM6 and PM7 methods. DFTB calculations of large (up to 448 atoms) bare TiO2 and TiO2/organic clusters (72 structures in total) confirm the robustness and computational efficiency of the method.

Conformational analysis and QSAR modeling of 14-membered macrolide analogues against mycobacterium tuberculosis

Electronic structures, effect of the substitution and structure physical-chemistry properties relationship for macrolide derivatives, have been studied by PM3 and ab initio methods. In the present work, the calculated values, namely net charges, bond lengths, MESP, dipole moments, electron-affinities, heats of formation, then, we treated the structural, physical and chemical relationships for a series of macrolide derivatives with inhibition activity against Mycobacterium tuberculosis. QSAR studies were done for these macrolide derivatives using a combination of various physicochemical descriptors. A multiple linear regression procedure was used to design the relationships between molecular descriptor and the activity of macrolide derivatives. Results validate the derived QSAR model.