Semiempirical AM1 Research Articles

Quantitative Structure Property Relationship Modeling for Prediction of Retention Index for a Set of Some Organic Compounds

One of the most ubiquitous challenges of the scientists is the theoretical evaluation of experimental parameters to validate and improve their ability. Plant essential oils and their extracts have been greatly employed in folk medicine, food flavoring, fragrance and pharmaceutical industries. This work is a part of our comprehensive investigation to correlate the experimental and calculated retention indices (RI) of the some organic compounds from K. Javidnia et al. The structures of all organic compounds were drawn into the HYPERCHEM program and optimized using semi-empirical AM1 method, applying a gradient limit of 0.01 kcal/A as a stopping criterion for optimized structures prior to geometry optimization step. Then molecular descriptors were calculated for each compound by the DRAGON software on the minimal energy conformations. The Stepwise SPSS was used for the selection of the variables that resulted in the best fitted models. By molecular modeling and calculation of descriptors, four significant descriptors (XMOD, PCD, MATS2e, GATS2e) related to the retention indices values of the essential oils, were identified. After the variables selection, the MLR method used for building the regression models. The statistical figures obtained by the proposed model are R 2 =0.989, RMSEP=53.08, REP =3.83 and SEP =54.94. In the final step, models generated were used to predict the retention index for a set of test compounds.

Application of Artificial Neural Networks for the Prediction of Antitumor Activity of a Series of Acridinone Derivatives

Artificial neural networks (ANNs) have been applied for the quantitative structure-activity relationships (QSAR) studies of antitumor activity of acridinone derivatives. Molecular modeling studies were performed with the use of HyperChem and Dragon computer programs and molecular geometry optimization using MM+ molecular mechanics and semi-empirical AM1 method, and several molecular descriptors of agents were obtained. A high correlation resulted between the ANN predicted antitumor activity and that one from biological experiments for the data used in the testing set of acridinones was obtained with correlation coefficient on the level of 0.9484. Moreover, the sensitivity analysis indicated that molecular parameters describing geometrical properties as well as lipophilicity of acridinone derivative molecule are important for acridinones antitumor activity.

Retracted: Computational study of hydrogen adsorption on potassium-decorated boron nitride nanotubes

We have investigated the potassium-decorated boron nitride nanotubes for hydrogen storage using semi-empirical AM1 method. The ultra narrow (3,3) and (5,0) boron nitride nanotubes of same diameter but of different chirality have been used. Both of them show hydrogen storage greater than 8 % by weight. Density of states have been calculated, and it is found that the presence of alpha density of state of potassium results in smaller energy gap; as a result of which, the conductivity of the potassium-decorated boron nitride nanotubes is enhanced as compared to pristine boron nitride nanotubes. Charge decomposition analysis showed that there is significant transfer of charge from adsorbate potassium to boron nitride nanotubes; the same is also confirmed by Mulliken population analysis. For same diameter, due to different electronic configuration, zigzag tube is found to be slightly more favorable for hydrogen adsorption. The results of the present simulation study suggest that the potassiumdecorated boron nitride nanotubes are good candidate for hydrogen adsorption.

Quantum-chemical investigation of the mechanism of trans-cis photoisomerization of 4-[2-(2-chlorophenyl)vinyl]-6,6-dimethyl-2-oxo-1,2,5,6-tetrahydropyridine-3-carbonitrile

A quantum-chemical investigation has been carried out by the semiempirical AM1 method of the trans-cis photoisomerization mechanism of 4-[2-(2-chlorophenyl)vinyl]-6,6-dimethyl-2-oxo-1,2,5,6-tetra- hydropyridine-3-carbonitrile. It was shown that the isomerization process proceeds in the excited singlet state S1 by rotation of the 2-chlorophenyl substituent around the C(2)–C(3) bond. Electronic absorption spectra of the isomers were calculated by the INDO/S method Transitions caused by exitation of an electron from HOMO to LUMO were characterized by the greatest intensity.

A Novel and Simple Molecular Probe Sensing Hg(II) in Living Cells by Chelation‐enhanced Fluorescence

AbstractMercury is currently widely used in industries which leads to various means of Hg(II) waste exposure and its accumulation in organisms will cause neurological damages. Thus, there is a great need for the design of probes or sensors with high sensitivity and selectivity for detecting and monitoring Hg(II) at physiological pH. Thus a novel and simple molecular probe P1 was prepared from 1,1′‐(1,3‐phenylene)‐bis(2,4‐pentanedionato) for sensing Hg(II) via chelation‐enhanced fluorescence (CHEF) mechanism. The probe indicated a selectively fluorescent response to Hg(II) in aqueous media excited by the ultraviolet light of 254 nm. The recognition mechanism was further studied by semi‐empirical AM1 and molecular mechanics MM+ methods in HyperChem 8.0. The calculation indicated a tetrahedron coordination geometry for Hg(II) and a chair‐like configuration for the total molecule. The fluorescent images sensing Hg(II) in living mouse fibroblast cells by the probe were obtained by fluorescence microscope.

Development and validation of quantitative structure-activity relationship models for compounds acting on serotoninergic receptors.

A quantitative structure-activity relationship (QSAR) study has been made on 20 compounds with serotonin (5-HT) receptor affinity. Thin-layer chromatographic (TLC) data and physicochemical parameters were applied in this study. RP2 TLC 60F254 plates (silanized) impregnated with solutions of propionic acid, ethylbenzene, 4-ethylphenol, and propionamide (used as analogues of the key receptor amino acids) and their mixtures (denoted as S1–S7 biochromatographic models) were used in two developing phases as a model of drug-5-HT receptor interaction. The semiempirical method AM1 (HyperChem v. 7.0 program) and ACD/Labs v. 8.0 program were employed to calculate a set of physicochemical parameters for the investigated compounds. Correlation and multiple linear regression analysis were used to search for the best QSAR equations. The correlations obtained for the compounds studied represent their interactions with the proposed biochromatographic models. The good multivariate relationships (R 2 = 0.78–0.84) obtained by means of regression analysis can be used for predicting the quantitative effect of biological activity of different compounds with 5-HT receptor affinity. “Leave-one-out” (LOO) and “leave-N-out” (LNO) cross-validation methods were used to judge the predictive power of final regression equations.

Effect of amidine derivatives on Leishmania amazonensis axenic amastigotes. Preliminary studies of structure-activity relationships

In a previous work, searching for new drugs with high efficiency and low toxicity, the in vitro antileishmanial activity of a series of seven amidine derivatives against Leishmania amazonensis promastigotes was reported. In order to compare the potential difference in the susceptibility between the two developmental stages of the parasite to these compounds, an analysis of the effects of these amidine derivatives on promastigotes and axenically grown amastigotes of L. amazonensis was carried out. Among the N,N'-diphenyl-4-R-benzamidine (where R = H, Cl, Br, CN, NO2, CH3 and OCH3) derivatives studied, the most active compounds in both developmental stages were those with -Br, -Cl, -NO2, and -OCH3 substituents, the nonsubstituted ones being the least active. However, the susceptibility to the drugs varied in these forms, being higher in promastigotes. The electronic theoretical parameters calculated by molecular modelling using the semi-empirical AM1 method showed good correlation with substituent constant (sigma para, sigma 1 and F). The chemical structure and biological activity relationships were investigated in all compounds, although a small but significant correlation was observed. The obtained results suggest that other factors than the electronic parameters have an influence on the biological response.

Theoretical Study of the Mechanism of an Inverse-Demand Diels–Alder Reaction

Quantum mechanical calculations (AM1, PM3, ab initio HF/3-21G, DFT(B3LYP/6-31G*) and MP2//(B3LYP/6-31G*) have been used to study the inverse-demand synchronous concerted Diels–Alder reactions between dimethyl-1,2,4,5-tetrazine-3,6-dicarboxylate (diene) and a variety of dienophiles (ethylene, cyclopentadiene, 1-hexene, cyclohexene). All the molecular structures (reactants, transition states, intermediates and adducts) were optimized using the semi-empirical AM1 method. The calculated energies and volumes showed that the cycloaddition reaction followed a mechanism involving the formation of an intermediate, elimination of N2, and a 1,3-hydrogen shift adduct. The reaction energies of the systems were obtained by using semi-empirical AM1 calculations and showed good agreement with the experimental data. In contrast, calculations of the reaction energies using PM3, HF/3-21G, DFT (B3LYP/6-31G*) and MP2//(B3LYP/6-31G* were in poor agreement with the experimental data. Compared to the experimental data, the activation energies were overestimated using AM1, PM3 and HF/3-21G, while they were underestimated using DFT (B3LYP/6-31G*) and MP2//(B3LYP/6-31G*).

Determination of the Association Constants of Charge-Transfer Complexes Between N,N-Diethylaniline and Nitro Explosives Using High Performance Thin Layer Chromatography with Scanning Video Densitometry and Spectrophotometry

Charge-transfer (CT) or electron donor-acceptor (EDA) complex formation between organic donors and acceptors has been extensively studied by spectrophotometry and other methods. High performance thin layer chromatography (HPTLC), although extensively used for the identification and quantification of drugs and explosives, has not been used until now to determine the extent of association and the association constants K DA of charge transfer or EDA complexes between donor (D) and acceptor (A). This paper describes the use of the HPTLC technique with scanning densitometry to identify and determine the association constants K DA of charge-transfer complexes of N,N-diethylaniline (DEA) with different nitro explosives, namely 1,4-dinitrobenzene (DNB), 2,4-dinitrotoluene (DNT) and 2,4,6-trinitrotoluene (TNT), in chloroform. Advantages of the HPTLC method are highlighted. The association constants K DA of the complexes determined using the HPTLC method have been verified and validated spectrophotometrically when the concentrations of D and A are in their stoichiometric ratio. The thermodynamics of the complex formation reaction were obtained spectrophotometrically from measurements of the association constants K DA at five different temperatures ranging from 293 to 313 K, when D and A are in their stoichiometric ratio and also when A≫D. The vertical ionization potential ( $I_{\mathrm{D}}^{\mathrm{V}}$ ) and vertical electron affinity ( $E_{\mathrm{A}}^{\mathrm{V}}$ ) of DEA were also calculated using Mulliken’s theory employing the semi-empirical AM1 method.

Theoretical study of β and γ-cyclodextrins inclusion complexes with nineteen atropisomeric polychlorobiphenyls

Inclusion complexes of β and γ-cyclodextrins (CDs), chirally selective macrocycles, with 19 atropisomeric polychlorinated biphenyls (PCBs), stable at physiological temperatures, were studied by molecular mechanics optimized potential for liquid simulations and semi-empirical quantum AM1 methods. Bimodal manual docking, geometry optimization and single point calculations were done. PCB:CD complex formation was studied considering two ways of entry in the large base of CD cavity: with biphenyl C1–C1′ bond axis of PCBs oriented parallel and anti-parallel with the CD trunk height axis. A distance dependent dielectric constant was used to account for the solvent effect. The values of complexation and binding energies were calculated, confirming the existence of a specific van der Waals (vdW) type interaction. β and/or γ-CD chiral recognition of the 19 atropisomeric PCBs, is described by means of the complexation and binding energy values. The binding energy is a better discriminator of PCBs enantiomers than complexation energy considering the average energy differences between (+) and (−) PCB:β/γ-CD complexes. The chromatographic elution order of several PCB enantiomers from literature was correlated with the complexation and binding energies. The molecular modeling of inclusion complexes is recommended to be used as enantiomer identification tool in correlation with chromatographic data.

Intramolecular and intermolecular OH …O and OH …F interactions in perfluoropolyethers with polar end groups: IR spectroscopy and first-principles calculations

Perfluoropolyether (PFPE) fluids constitute a class of polymers that fulfil a wide range of requirements for hi-tech applications, due to their pefluorinated backbone. For some of these applications they are requested to bear polar end groups, and the combination of a chemical inert backbone and a reactive end group can produce peculiar conformations and supramolecular structures. The molecular structure and the vibrational properties of the ethoxyl-terminated PFPE FLUOROLINK®E10H in solution are here investigated by means of IR spectroscopy. It is shown that the complex spectral features of the OH-stretching region cannot be explained without a thorough computational study, involving the investigation of the conformational space of an isolated model molecule by means of semiempirical AM1 calculations and DFT calculations. The most relevant conformers were singled out, showing a high degree of conformational disorder for FLUOROLINK®E10H. Furthermore, it is shown that intra- and intermolecular H-bonding affects significantly the molecular structure and the vibrational spectrum. Several interactions are shown to be relevant, such as OH …F interactions and complexes with residual water. Theoretical values of the absolute intensities of OH stretching IR bands, relevant for the analytical applications, are obtained.

Importance of some classes of molecular descriptors on classification of antitumor acridinones using factor analysis

Factor analysis method has been applied to determine the relationships between some classes of structural descriptors series of acridinones drugs differing in chemical structures and their antileukemia activity. Molecular modeling studies were performed with the use of HyperChem and Dragon computer programs, and molecular geometry optimization using MM+ molecular mechanics and semi-empirical AM1 method. Sixteen classes of molecular descriptors include over 1200 descriptors were calculated and taken for factor analysis. Importantly, among the classes of molecular structural descriptors studied, the most significant influence was recognized for descriptors from classes of constitutional descriptors as well as topological charge indices descriptors, and allowed to distribution of individual compounds on the plane determined by two principal components (factors 1 and 2) produced patterns in good agreement with their ability to antitumor activity as well as with their chemical structures.

A G4MP2 theoretical study on the gas phase enthalpies of formation for various polycyclic aromatic hydrocarbons (PAHs) and other C~10~ through C~20~ unsaturated hydrocarbons

AbstractGas phase enthalpies of formation at 298.15 and 1 atm (Δ~f~H~(g),298K~) were calculated using the atomization approach at the G4MP2 composite method level of theory for 86 polyaromatic hydrocarbons (PAHs) and other C~10~ through C~20~ unsaturated hydrocarbons. Where available, good agreement with prior experimental data and/or high level theoretical estimates was obtained. Linear regressions between semiempirical MNDO, MNDO-d, AM1, PM3, RM1, and PM6 estimated Δ~f~H~(g),298K~ and the corresponding G4MP2 values were employed to obtain G4MP2 corrected semiempirical Δ~f~H~(g),298K~ for a suite of 156 C~11~ through C~42~ unsaturated hydrocarbons and PAHs.

Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface.

Dihydrofolate reductase (DHFR) catalyzes the reduction of 7,8-dihydrofolate by nicotinamide adenine dinucleotide phosphate hydride (NADPH) to form 5,6,7,8-tetrahydrofolate and oxidized nicotinamide. DHFR is a small, flexible, monomeric protein with no metals or SS bonds and serves as one of the enzymes commonly used to examine basic aspects in enzymology. In the current work, we present extensive benchmark calculations for several model reactions in the gas phase that are relevant to the DHFR catalyzed hydride transfer. To this end, we employ G4MP2 and CBS-QB3 ab initio calculations as well as numerous density functional theory methods. Using these results, we develop two specific reaction parameter (SRP) Hamiltonians based on the semiempirical AM1 method. The first generation SRP Hamiltonian does not account for dispersion, while the second generation SRP accounts for dispersion implicitly via the AM1 core-repulsion functions. These SRP semiempirical Hamiltonians are subsequently used in hybrid quantum mechanics/molecular mechanics simulations of the DHFR catalyzed reaction. Finally, kinetic isotope effects are computed using a mass-perturbation-based path-integral approach.

Evaluation of some functionalized imidazoles and 1,2,4-triazoles as antioxidant additives for industrial lubricating oils and correlating the results with the structures of additives using empirical AM1 calculations

Functionalized 4,5-diphenyl-imidazoles, 4,5-diphenyl-1,2,4-triazoles and 5-(o-hydroxyphenyl)-4-phenyl-1,2,4-triazoles at the 2-position with thiol, thiomethyl and thiobenzyl groups, have been tested as antioxidant additives for lubricating oils. Whereas the thiomethyl groups in such compounds increased the antioxidant property than the thiol group, the corresponding thiobenzyl groups did the reverse. The results can be explained, based on correlating the electron donating and withdrawing abilities of the substituents with the oxidation stability. The triazoles carrying a phenolic hydroxyl group have more antioxidant power than those without such a group. The imidazoles gave the oils more oxidation stabilities than the two types of triazoles with the same functionalities. The 4,5-diphenyl-2-thiomethyl-imidazole (2), as an additive, has the highest antioxidant property, reaching the level of standard one when its concentration is 1.0% wt. instead of the 0.8% wt. of the standard. The correlation of the antioxidant character of the heterocyclic additives with their structures has been investigated using the semiempirical gas phase AM1 calculations for the studied heterocycles. The relative stability of the imidazoles 1 and 3 compared to 2 were in the order 2>1>3. Similarly, the relative stability of the triazoles are in the same order where 5>4>6 and 8>7>9.

NONLINEAR OPTICAL PROPERTIES OF NOVEL AND EFFECTIVE H-SHAPED CHROMOPHORES CONTAINING THREE PARALLEL AND NON-CONJUGATED D-π-A UNITS

H-shaped chromophores containing three parallel non-conjugated D-π-A units are effective chromophores with high hyperpolarizability and good optical transparency. The semi-empirical methods ZINDO, AM1, MNDO and PM3 were employed to study the effect of strength of acceptors and donors, and steric repulsion between substituents on static first hyperpolarizabilities (β0) and enhancements of β0 of the H-shaped chromophores. The results show that the H-shaped chromophore would exhibit the largest β0 and/or the largest enhancement of β0 of the chromophore when combination of a donor (D) and an acceptor (A) in a D-π-A unit is suitable.

Protein–Ligand Interaction Energies with Dispersion Corrected Density Functional Theory and High-Level Wave Function Based Methods

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.

Prediction of the Dissociation Constant pKa of Organic Acids from Local Molecular Parameters of Their Electronic Ground State

A quantum chemical method has been developed to estimate the dissociation constant pK(a) of organic acids from their neutral molecular structures by employing electronic structure properties. The data set covers 219 phenols (including 29 phenols with intramolecular H-bonding), 150 aromatic carboxylic acids, 190 aliphatic carboxylic acids, and 138 alcohols, with pK(a) varying by 16 units (0.38-16.80). Optimized ground-state geometries employing the semiempirical AM1 Hamiltonian have been used to quantify the site-specific molecular readiness to donate or accept electron charge in terms of both charge-associated energies and energy-associated charges, augmented by an ortho substitution indicator for aromatic compounds. The resultant regression models yield squared correlation coefficients (r(2)) from 0.82 to 0.90 and root-mean-square errors (rms) from 0.39 to 0.70 pK(a) units, corresponding to an overall (subset-weighted) r(2) of 0.86. Simulated external validation, leave-10%-out cross-validation and target value scrambling demonstrate the statistical robustness and prediction power of the derived model suite. The low intercorrelation with prediction errors from the commercial ACD package provides opportunity for a consensus model approach, offering a pragmatic way for further increasing the confidence in prediction significantly. Interestingly, inclusion of calculated free energies of aqueous solvation does not improve the prediction performance, probably because of the limited precision provided by available continuum-solvation models.

QSPR probing of Na+ complexation with 15-crown-5 ethers derivatives using artificial neural network and multiple linear regression

A quantitative structure–property relationship (QSPR) study is performed to develop a model, relating to Na+ complex stability constant (log K) and the structure of 74 derivatives of 1,4,7,10,13-pentaoxacyclo-pentadecane ethers (15C5). Stepwise Multiple Linear Regression (SMLR) and Artificial Neural Network (ANN) methods have been exploited as linear and nonlinear methods, respectively to build the QSPR model. MOPAC software embedded in ChemOffice 2004 package was used for the minimizing energy using semi-empirical AM1 method. The optimum structures have been applied to generate more than 50 descriptors using available servers in ChemOffice 2004. The five most important constitutional, steric, electronic, thermodynamic and molecular descriptors were selected using the common preselection method combined by SMLR method. SMLR and ANN models were constructed based on the five selected descriptors. Both proposed models efficiently predict log K of 15C5 complexes. However, the results of ANN were more effective respect to SMLR model. This phenomenon reveals that log K of 15C5 complexes have a deviation from linear behavior related to the selected descriptors.

QM and QM/MD simulations of the Vinca alkaloids docked to tubulin

Abstract The Vinca alkaloids are a class of pharmaceutically relevant binary indole-indoline alkaloids based on and including natural extracts of the periwinkle plant, Catharanthus rosea. Two natural products, vinblastine and vincristine, have been in clinical use as important chemotherapy agents for over four decades. Two semi-synthetic Vinca alkaloids, vindesine and vinorelbine, are currently in investigational chemotherapy programs, and a third semi-synthetic, vinflunine, is in advanced clinical trials. In addition to these five compounds studied in the present work, there are hundreds of other natural and semi-synthetic Vinca alkaloids known, although most are not clinically advantageous. The Vinca alkaloids are anti-mitotic agents that affect the cellular protein tubulin and bind to a specific site known as the Vinca domain located on β-tubulin. While the Vinca domain is well established, the specific binding mode of each drug is not. However, there is much insight into the binding mode and this has provided a strong base of information to begin simulations and to make comparisons against. Complicating the issue, however, is the large size of the Vinca alkaloids and their complex molecular structure, including a rotatable single bond joining the indole and indoline portions of each compound. The differential geometric and tubulin-binding properties of the drugs are not fully known. In the present work, the projection of the potential energy surface on the major torsional angle was calculated at the semi-empirical AM1 level, through in vacuo geometry optimizations. QM/MD simulations were performed, with the drugs at the AM1 level, of each Vinca alkaloid free in TIP3P water, and also bound to β-tubulin. A single equilibrium structure, resembling a known crystallographic vinblastine structure [1], for the free drugs was found. Further, the 1Z2B crystal structure [2] of vinblastine bound to tubulin appears to be a valid starting point for simulations of all five Vinca alkaloids studied here.