Semiempirical PM3 Method Research Articles

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.

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.

Prediction of Antiglycation Activity by Calculating the Energies of Frontier Molecular Orbitals for New 4-Hydroxy-1,4-Dihydroazolo[5,1-c]-1,2,4-Triazines Used as an Example

Protein glycation and the formation of advanced glycation end products (AGEs) play an important role in the pathogenesis of diabetes mellitus (DM) complications, neurodegenerations, and age-related diseases. A model to predict antiglycation activity can reduce the costs and increase the productivity and quality of preclinical screening studies of new compounds. Azolo[5,1-c][1,2,4]triazines and azolo[1,5-a]pyrimidines are well known as biologically active compounds, which additionally have antiglycation properties. A number of 4-hydroxy-4H-azolo-1,4-dihydro[5.1-c]-1,2,4-triazines were selected for designing a prediction model. Azolotriazine derivatives were found to exert an antiglycation effect, inhibiting glycation of bovine serum albumin (BSA) with glucose and specific END fluorescence with equal or greater efficiency as compared with aminoguanidine. The activity range at 1000 μM was estimated at 23.0–71.6% for variously substituted derivatives (30.3 ± 1.2% for aminoguanidine). The highest activity was observed for 4-hydroxy-3-cyano-1,4-dihydro-1,2,4-triazolo[5.1-c]1,2,4-triazine. In all but one compound (aminoguanidine), antiglycation activity correlated with the energy difference ∆(HOMO – LUMO) between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO); the difference was established by a PM3 semiempirical method. Artificial neural network modeling was used to develop a mathematical model that describes the dependence of antiglycation activity on the calculated energies. The ELUMO and ∆(HOMO – LUMO) energies were found to make the largest contribution to the activity. The model can be used to predict antiglycation activity.

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.

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.

Accurate prediction of standard enthalpy of formation based on semiempirical quantum chemistry methods with artificial neural network and molecular descriptors

AbstractThis work investigates possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods for the prediction of standard enthalpy of formation (ΔfHo) through the use of an artificial neural network (ANN) with molecular descriptors. A total of 142 organic compounds with enough structural diversity has been considered in the training set. Standard enthalpy of formation for the selected compounds at the semiempirical PM3 and PM6 quantum chemistry methods is collected from literature and is calculated by using the semiempirical PM7 method in this work. The multiple stepwise regression is first used to screen effective molecular descriptors, which are highly correlated with the error terms of the standard enthalpy of formation compared with experimental values. The obtained seven effective molecular descriptors are then used as input set to establish three 7‐11‐1 neural network‐based correction models to improve the accuracy of SQC methods. By using the developed correction models, the mean absolute errors for ΔfHo of PM3, PM6, and PM7 methods are reduced from 22.36, 18.60, and 17.27 to 9.86, 9.83, and 8.95, respectively, in kJ/mol. Meanwhile, the results of the test set show that the neural network does not have the problem of overfitting. Detailed analysis of the seven effective molecular descriptors indicates that the major source of the correction models is the electron‐withdrawing effect. The developed ANN models for the three selected SQC methods provide an efficient method for the quick and accurate prediction of thermodynamic properties.

Theoretical study on ferrocenyl hydrazones inclusion complexes with β-cyclodextrin and its three methylated derivatives

Molecular interactions of ferrocenyl hydrazones (FcHZ) inclusion complexes with β-cyclodextrin (BCD), methyl-β-cyclodextrin (MEB), 2,6-di-O-methyl-β-cyclodextrin (DIMEB) and 2,3,6-tri-O-methyl-β-cyclodextrin (TRIMEB) in order to enhance their aqueous solubility and anti-mycobacterial efficiency were investigated by semi-empirical PM7 method and B3LYP/m6-31G* calculations. Simulation results suggest the complex formations of FcHZ with BCD, MEB, DIMEB and TRIMEB are possible with 1:1 host–guest molecular ratio. Two different binding modes of the FcHZ inside the BCD and MEB cavities were found. The ferrocene fragment of FcHZ molecule was entrapped in the cavity, located near the wider rim of BCD and MEB in both orientations (A and B). The hydrazone aromatic fragment of FcHZ cannot be completely embedded inside the hydrophobic cavity of BCD. It points downward from the narrower rim of BCD in orientation A and point upward from the wider rim of BCD in orientation B. Only orientation B was found in 1:1 inclusion complex of FcHZ agents with DIMEB and TRIMEB due to the effect of methyl group substitutions at the primary hydroxyl groups, which located at the narrower rim of cyclodextrins. The entering pathways of the FcHZ molecule into the molecular cavity of the BCD, MEB, DIMEB and TRIMEB were also discussed.

Calculation of Thermodynamic and Structural Characteristics of Gold and Silver Solvate Complexes

Gold and silver complexes with cyanide, thiocyanate, and thiosulfate ions have been considered. The potential energy surfaces of sorption complexes are shown. Quantum-chemical calculations of gold and silver complexes have been performed by the PM6 semi-empirical method as part of MOPAC. For eleven gold compounds, sets of potential energies have been obtained for various combinations. The potential energies for silver complexes have been calculated. As a result, data on the behavior of complex ions during sorption on anion exchange resin, the presence of energy minima, the pathways of the reaction, more accurate values of the binding energy, or the absence of sorption interaction in the system have been refined. Consideration of the sorption of gold and silver complexes from the classical standpoint of chemical kinetics made it possible to evaluate the activation energy and the nature of the interaction during the process. The thermodynamic parameters of the studied chemical processes have been calculated.

The inclusion behavior of 8-Anilino-1-naphthalene sulfonate into Cucurbit[7]uril: A DFT approach

A theoretical study has been conducted on the complexes (1,8-ANS/CB[7]), which formed between the guest 8-Anilinonaphthalene-1-sulfonate (1,8-ANS) and the host Cucurbit[7]uril (CB[7]) to determine the geometries, binding energies and the driving forces which governed its formation. The possible structures were investigated using semi-empirical PM3 method and density functional theory (DFT) incorporating various hybrid exchange-correlation functionals: B3LYP/6-31G(d), M06–2X/6-31G(d) and ωB97X-D/6-31G(d) levels of theory in vacuum and in water. It has been concluded that there is an exclusion of the 1,8-ANS molecule from the CB[7] cavity. Furthermore, the donor-acceptor interactions between host and guest were performed using Natural Bond Orbitals (NBO) and Quantum Theory of Atom In Molecule (QTAIM) analysis. Finally, and based on the Gauge-Including Atomic Orbital (GIAO) method, the 1H Proton Nuclear Magnetic Resonance (1H NMR) study has been used to confirm and give more information about the geometry of formed complexes. The results will be discussed in details.

Accuracy of the PM6 and PM7 Methods on Bare and Thiolate-Protected Gold Nanoclusters

Semiempirical quantum mechanical (SEQM) methods offer an attractive middle ground between fully ab initio quantum chemistry and force-field simulations, allowing for a quantum mechanical treatment of the system at a relatively low computational cost. However, SEQM methods have not been frequently utilized in the study of transition metal systems, mostly due to the difficulty in obtaining reliable parameters. This paper examines the accuracy of the PM6 and PM7 semiempirical methods to predict geometries, ionization potentials, and HOMO-LUMO energy gaps of several bare gold clusters (Aun) and thiolate-protected gold nanoclusters (AuSNCs). Contrary to PM6, the PM7 method can predict qualitatively correct geometries and ionization potentials when compared to DFT. PM6 fails to predict the characteristic gold core and gold-sulfur ligand shell (staple motifs) of the AuSNC structures. Both the PM6 and PM7 methods overestimate the HOMO-LUMO gaps. Overall, PM7 provides a more accurate description of bare gold and gold-thiolate nanoclusters than PM6. Nevertheless, refining the gold parameters could help achieve better quantitative accuracy.

Computer and Experimental Simulation of Alloxazine Synthesis from Gamma Irradiation of Amino Acids on Iceland Spar: A Prebiotic Chemistry Perspective.

On ancient Earth, environmental conditions favored prebiotic chemical reactions. In the Archean, some molecules with conjugated rings might have been synthesized, displaying structural stability in the Archean in the presence of ionizing radiation and hydration-dehydration events. Additionally, it is suggested that on ancient Earth, calcite was a common mineral promoting organic compound synthesis. In the present work a study of the interaction of amino acid mixtures with the (104) surface of calcite is presented. Our preliminary results show the abiotic synthesis of alloxazine (a flavin with relevant photochemical properties). Computer simulations were performed in HyperChem 8.0.1. by means of MM+ molecular mechanics and PM3 semi-empirical methods, in 27 possible amino acid trimers of alanine, glycine and lysine. Alloxazine formation is possible by the gamma irradiation of amino acids. The computer simulations show that trimers GGG and GGA promote the further transformation from diketopiperazines (DKP's) and KGK to alloxazine. The computer simulations with free radicals are not stable when alloxazine is interacting with the calcite surface. Experiments in anoxygenic environments with hydration-dehydration events in gamma irradiated samples allow the abiotic formation of flavins, DKP's and a heterocycle compound with possible relevance in prebiotic chemistry.

Theoretical Investigation of the Complexation Reaction of Procaine-hydrochloride by β-cyclodextrin

Abstract. . Quantum-chemical calculations were performed to study the complexation of drug molecule procaine hydrochloride with beta cyclodextrin (β-CD) in the gas phase and in water. The inclusion process was optimized by the semi empirical method PM3 and the obtained complex structure was further refined by ONIOM method (DFT: PM3). It is found that (B3LYP/6-31G(d,p) : PM3) provides the best energy minimum for the complex, compared to M06-2X and WB97XD functional. Given the energy profile, the configuration of the complex formed indicates that the benzene ring is completely included in the hydrophobic cavity of the β-CD. The thermodynamic parameters analysis has shown that the procaine/β-CD complexation is enthalpically favorable, and the complex is well structured. Natural bond orbital (NBO) analysis indicates that no hydrogen bond interaction exists, and the procaine/β-CD complex is mainly stabilized by Van der Waals forces. 1D 1H NMR spectra analysis shows that the procaine molecule penetrates into the cavity of this CD with the aromatic ring.

Quantitative Structure Activity Relationship Analysis of 1,3,4-Thiadiazole Derivatives as Anti-Inflamatory using Parameterized Model 3 Method

Quantitative Relationship Structure and Activity Relationship (QSAR) studies conducted on the anti-inflammatory activity of a series of 1,3,4-thiadiazole derivatives which aim to obtain an equation to predict the value of the anti-inflammatory activity of. As research material was experimental biological activity data of 28 1,3,4-thiadiazole derivatives which were divided into 25 fitting compounds and 3 test compounds. QSAR analysis was carried out based on multiple linear regression calculations of fitting compounds by plotting log BA as the dependent variable and the independent variable was the net charge of carbon and nitrogen atoms bound to the dressing group, dipole moment (µ), HOMO-LUMO, Log P, molecular weight, polarizability, hydration energy, and van der waals volume. The value of descriptors was obtained from calculations using the PM3 semi-empirical quantum mechanical method. The result of QSAR equation was:Log BA = 68.112 − 8.482 (qC1) + 14.764 (qC15) + 1.071 (Log P) − 0.018 (MW) − 0.484 (µ) − 4.427E-5 (Polarizability) − 0.561 (E. Hydration) + 7.843 (HOMO) − 1.489 (LUMO)n = 28, r = 0.861, SE = 0.170098, Fcalculate / Ftable = 2.02116, PRESS = 1.9665

PM3 Semi-Empirical Method on the Ring Opening Polymerization of ε-Caprolactone Using Bis (Benzoyltrifluoroacetone)Zirconium(IV) Chloride as catalyst

Polycaprolactone (PCL) is an interesting polymer because of its biodegradability, good mechanical properties, and the excellent miscibility with a large range of other polymers. PCL can be obtained via ring opening polymerization (ROP) of ε-caprolactone (ε-CL) by using Lewis acid as catalyst. The purpose of this study was to focus on the study of the plausible mechanism of the ROP of ε-CL using bis-(benzoyltrifluoroacetone)zirconium(IV) chloride as a catalyst. In this research, PM3 semi-empirical method was conducted to optimize the polymer and complex structure. After that, HyperChem 8.0 program package was used to calculate and to visualize the geometry structure. This program run on a personal computer with Windows 07 operating system. The results of the computational calculation indicate that, to obtain PCL using bis(benzoyltrifluoroacetone)zirconium (IV) chloride catalyst needed several reaction steps, that is coordination ε-CL on the zirconium complex, deprotonation of ε-CL, the ε-CL insertion, and the chain propagation.

Detection of Copper Ions by a Simple, Greener and Cost Effective Sensor with GCE Modified with L-Tryptophan

Metal ions contamination is the leading cause of many health and environmental problems. In order to rectify and remediate the environment from metal ions contamination, simple, efficient and easy to fabricate sensors for the onsite detection of metals ions is obligatory. However, devising a practically applicable sensor that could be compatible to the environment which contains a plethora of other ions than the target metal ions, is very challenging. In this work we report a highly sensitive and selective yet simple and greener electrode for copper ions detection by modifying GCE with amino acid-L-tryptophan. The modifier brings about increase in active surface area of the GCE and effectively binds to the metal ions through the process of chelation utilizing its amino and carboxylic acid functional groups. Cyclic voltammetry (CV), square wave voltammetry (SWV) and square wave anodic stripping voltammetry (SWASV) along with electrochemical impedance spectroscopy (EIS) was conducted to investigate the surface of the electrode and its sensitivity towards detection of Cu1+ and Cu2+ ions. A number of experimental parameters such as pH, supporting electrolyte, concentration of the modifier, accumulation time and deposition potential were investigated to achieve best response of the metal ions towards the modified electrode. The designed sensor exhibited excellent electrocatalytic activity and sensitivity towards Cu1+ ions even in the presence of 5-fold higher concentration of different interferents. The LOD (Limit of detection) of 3.13 pM as determined by the calibration curve was found to be much lower than permissible values suggested by the WHO (World Health Organization) and US EPA (Environmental Protection Agency). % age recoveries as estimated from real water samples was found to be within 3% RSD value and proved the validity of the proposed methodology for the designed sensor. Computational studies were carried out using hyperchem 7.5 software with semi empirical PM3 method. The negative value of binding energy of the merged molecule i.e., −3024.181 kcal mol−1 point towards significant interactions between L-tryptophan and Cu2+ ions which is evident from the change in physicochemical properties upon merging of L-tryptophan with Cu2+ ions. Our computational studies agree well with the experimental results.

Comparative Studies of Infrared Spectral Simulation of Some Benzoyl Derivatives of N-Heterocyclic Compounds Using Semi-Empirical Methods

Simulation studies based on ab initio, semi-empirical or density functional (DFT) calculations are now becoming common among the researchers who are pursuing their intereset in theoretical chemistry. These studies are based on quantum chemical softwares. These studies provide better insight for the structural and other parameters of the compounds. The present paper includes the studies on synthesis or procurement along with the simulated IR spectra of some benzoyl derivatives of N-heterocyclic compounds viz. 2-aminopyridine, 4-aminoantipyrine, 2-aminopyrimidine or 3-aminopyridine using four different AM1, PM3, MNDO and ZINDO1 semi-empirical methods. Among the methods used for the study, AM1 method is more reliable and more accurate so far as the prediction of spectral results is concerned.