Semiempirical PM3 Method Research Articles

Effect of intramolecular hydrogen bond in unsaturated dicarboxylic acid molecules on the formation of cobalt(II) and nickel(II) carboxylates

The energies of formation of intramolecular hydrogen bonds (IHB) in unsaturated dicarboxylic acid molecules in aqueous solutions were calculated by the DFT method (B3LYP hybrid functional, 6-31G** basis set) using the GAMESS software, Version 1, May 2013 (R1). The medium effect was taken into account in terms of the Polarized Continuum Model (PCM). In the case of allylmalonic, itaconic, and maleic acids, fairly weak IHB with an energy of 5.8–13.9 kJ/mol were found to form. The enthalpies of formation of acid and normal cobalt and nickel salts of carboxylic acids in aqueous solutions were calculated by the semiempirical PM3 method using the HyperChem 8.0.8 software (Hypercube Inc.). The results indicate that in aqueous solutions, the formation of cobalt and nickel acid salts of allylmalonic, itaconic, and cis,cis-muconic acids is energetically more favorable than the formation of normal carboxylates, which is consistent with experimental data.

Global chemical reactivity parameters for several chiral beta-blockers from the Density Functional Theory viewpoint.

Background and aimBeta-adrenergic antagonists have been established as first line treatment in the medical management of hypertension, acute coronary syndrome and other cardiovascular diseases, as well as for the prevention of initial episodes of gastrointestinal bleeding in patients with cirrhosis and esophageal varices, glaucoma, and have recently become the main form of treatment of infantile hemangiomas.The aim of the present study is to calculate for 14 beta-blockers several quantum chemical descriptors in order to interpret various molecular properties such as electronic structure, conformation, reactivity, in the interest of determining how such descriptors could have an impact on our understanding of the experimental observations and describing various aspects of chemical binding of beta-blockers in terms of these descriptors.MethodsThe 2D chemical structures of the beta-blockers (14 molecules with one stereogenic center) were cleaned in 3D, their geometry was preoptimized using the software MOPAC2012, by PM6 method, and then further refined using standard settings in MOE; HOMO and LUMO descriptors were calculated using semi-empirical molecular orbital methods AM1, MNDO and PM3, for the lowest energy conformers and the quantum chemical descriptors (HLG, electronegativity, chemical potential, hardness and softness, electrophilicity) were then calculated.ResultsAccording to HOMO-LUMO gap and the chemical hardness the most stable compounds are alprenolol, bisoprolol and esmolol. The softness values calculated for the study molecules revolve around 0.100. Propranolol, sotalol and timolol have among the highest electrophilicity index of the studied beta-blocker molecules. Results obtained from calculations showed that acebutolol, atenolol, timolol and sotalol have the highest values for the electronegativity index.ConclusionsThe future aim is to determine whether it is possible to find a valid correlation between these descriptors and the physicochemical behavior of the molecules from this class. The HLG could be correlated to the experimentally recorded electrochemical properties of the molecules. HOMO could be correlated to the observed oxidation potential, since the required voltage is related to the energy of the HOMO, because only the electron from this orbital is involved in the oxidation process.

Quantum chemical study of the structure and properties of isotopically pure lead chalcogenides

Background/Objectives: In the present work the theoretical methods B3LYP/SDD, GGA and BP86/TZ2P were used for quantum-chemical calculations of lead chalcogenides. Methods/Statistical Analysis: Calculations were carried out using a hybrid method of a functional of density of B3LYP, with an exchange functional to Becke В3 and a correlation functional Lee, Wang and Parr (LYP). As a basic condition were used the SDD pseudo potential for an atom of lead and the D95 double-dzeta as the basis for other atoms. To estimate the enthalpy of formation the semi-empirical method PM3 was used. Findings: It is shown that there are correlations between the experimental and calculated characteristics of lead sulphide, selenide and telluride. The influence of different isotopes of lead, sulphur, selenium and tellurium on the thermodynamic parameters and the Raman spectra for the lead chalcogenides is shown. Applications/Improvements: The results suggest that the use of the density functional method in various versions with different functional and basic conditions.

Spectroscopic (FT-IR, FT-Raman, FT-NMR and UV–Vis) investigation on benzil dioxime using quantum computational methods

The spectral analysis of benzil dioxime is carried out using the FTIR, FT Raman, FT NMR and UV–Vis spectra of the compound with the help of quantum computations by density functional theories. The FT-IR (4000 – 400 cm−1) and FT-Raman (4000–100 cm−1) spectra are recorded in solid phase, the 1H and 13C NMR spectra in DMSO phase and the UV spectrum (200–400 nm) in ethanol phase. The different conformers of the compound and their minimum energies are studied by potential energy surface scan, using semi-empirical method PM6. The computed wavenumbers from different methods are scaled so as to agree with the experimental values and the scaling factors are reported. All the fundamental modes have been assigned based on the potential energy distribution (PED) values and the structure the molecule is analyzed interms of parameters like bond length, bond angle and dihedral angles predicted byB3LYP and CAM-B3LYP methods with cc-pVDZ basis sets. The values of dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the molecule are reported, using which the non -linear optical property of the molecule is discussed. The HOMO-LUMO mappings are reported which reveals the different charge transfer possibilities within the molecule. The isotropic chemical shifts predicted for 1H and 13C atoms using gauge invariant atomic orbital (GIAO) theory show good agreement with experimental shifts and the same is discussed in comparison with atomic charges, predicted by Mullikan and APT charge analysis. NBO analysis is carried out to picture the probable electronic transitions in the molecule.

Encapsulation of monomers, homodimers and heterodimers of amides and carboxylic acids in three non-covalent assemblies

A structural study has been carried out involving geometry optimization of different capsules and encapsulated complexes of single monomers, homodimers and heterodimers of benzoic acid and benzamide and substituted dimers, as well as hydrogen-bonded networks of benzamide addressing experimental observation, where cages offering similar cavities but made up of slightly different cavitands result in strikingly different dimer distributions. This is attributed, according to the present results, mainly to the fact that the two cages have different formation energy and different dimer encapsulation energy. The generation of hydrogen-bonded networks of the amide in solution acts competitively to encapsulation. In addition, the trends of the different quantities associated with encapsulation such as dimerization energy, % dimer distribution and encapsulation energies, as the size of the dimers is increased, are examined. Furthermore, the efficacy of the ONIOM(DFT or MP2 and CCSD:PM6) method with respect to the calculation of % distribution of encapsulated dimers in limited cavities is studied. The results show that when the interaction of the guests with the cage is significant, the ONIOM % distributions do not agree with the experimental finding, as full DFT does, due to PM6 method, where the use of semi-empirical PM6 method changes the ordering of the low in energy encapsulated complexes.

Design and Synthesis of New Bile AcidSterol Conjugates Linked via 1,2,3‐Triazole Ring

AbstractA new steroid conjugates have been obtained from bile acids and sterol derivatives using ‘click chemistry’. Intermolecular 1,3‐dipolar cycloaddition of the propargyl ester of bile acids (lithocholic, deoxycholic, and cholic acid) and azide derivatives of sterols (ergosterol and cholesterol) gave a new bile acidsterol conjugates linked with a 1,2,3‐triazole ring. The structures of all products were confirmed by spectroscopic (1H‐ and 13C‐NMR, and FT‐IR) analyses, mass spectrometry (ESI‐MS), and in silico biological activity evaluation methods (PASS), as well as PM5 semiempirical methods.

Self-assembly of Metallamacrocycles Employing a New Benzil-based Organometallic Bisplatinum(II) Acceptor.

A benzil-based semi-rigid dinuclear-organometallic acceptor 4,4'-bis[trans-Pt(PEt(3))(2)(NO(3))(ethynyl)]benzil (bisPt-NO(3)) containing a Pt-ethynyl functionality was synthesized in good yield and characterized by multinuclear NMR ((1)H, (31)P, and (13)C), electrospray ionization mass spectrometry (ESI-MS), and single-crystal X-ray diffraction analysis of the iodide analogue bisPt-I. The stoichiometric (1:1) combination of the acceptor bisPt-NO(3) separately with four different ditopic donors (L(1)-L(4); L(1) = 9-ethyl-3,6-di(1H-imidazol-1-yl)-9H-carbazole, L(2) = 1,4-bis((1H-imidazol-1-yl)methyl)benzene, L(3) = 1,3-bis((1H-imidazol-1-yl)methyl)benzene and L(4) = 9,10-bis((1H-imidazol-1-yl) methyl)anthracene) yielded four [2 + 2] self-assembled metallacycles M(1)-M(4) in quantitative yields, respectively. All these newly synthesized assemblies were characterized by various spectroscopic techniques (NMR, IR, ESI-MS) and their sizes/shapes were predicted through geometry optimization employing the PM6 semi-empirical method. The benzil moiety was introduced in the backbone of the acceptor bisPt-NO(3) due to the interesting structural feature of long carbonyl C-C bond (∼1.54 Å), which enabled us to probe the role of conformational flexibility on size and shapes of the resulting coordination ensembles.

Erratum to: Molecular Modeling of Ammonium, Calcium, Sulfur, and Sodium Lignosulphonates in Acid and Basic Aqueous Environments

Lignosulphonates (LS), also known as lignin sul- fonates or lignin, are lignins in sulfonated forms, obtained from the sulfite liquors, a residue of the wood pulp extraction process. Their main utility lies in its wide range of properties, they can be used as additives, disper- sants, binders, fluxing, binder agents, etc. in fields ranging from food to fertilizer manufacture and even as agents in the preparation of ion exchange membranes. Since they can be manufactured relatively easy and quickly, and that its molecular size can be manipulated to obtain fragments of very low molecular weight, they are used as transport agents in the food industry, cosmetics, pharmaceutical and drug development, and as molecular elements for the treatment of health problems. In this paper, we study the electronic structural and optical characteristics of LS incorporating ammonium, sulfur, calcium, and sodium ions in acidic and basic aqueous media in order to gain a better understanding of their behavior and the very interesting properties exhibit. The studies were performed using the molecular model- ing program HyperChem 5 using the semiempirical method PM3 of the NDO Family (neglect of differential overlap), to calculate the structural properties. We calculated the electronic and optical properties using the semiempirical method ZINDO / CI.

QSAR models for antioxidant activity of new coumarin derivatives

This study presents 37 new antioxidant coumarin derivatives and strategies for structural modification to improve their antioxidant activities, the main ferric-reducing antioxidant power (FRAP) assay used to evaluate their antioxidant properties and the generation of validated quantitative structure–activity (antioxidant activity) relationship (QSAR) models. In an attempt to generate QSAR models, structures of all coumarin derivatives in the data set were fully optimized by semi-empirical PM6 method using SPARTAN 10 software. Descriptors were calculated by DRAGON 6.0 software. Multiple linear regression (MLR) models were developed with different training/test set combinations using QSARINS 2.2.1 software. Robustness, reliability and predictive power of the models were tested by internal and external validations. Applicability domain of the best two-descriptor model (nTR = 30; r2 = 0.924; RMSETR = 0.213; nTEST = 7; r2ext = 0.887; RMSEext = 0.255; CCCext = 0.939) was determined. Descriptors appeared in the model revealed that complexity, H-bond donor and lipophilic character are important parameters in describing the antioxidant activity. Apart from the compounds in the data set, we also designed 31 new antioxidant coumarin derivatives and predicted their antioxidant activity using the best two-descriptor model. Most of these compounds are promising antioxidants

Quantum chemical analysis of the molecular structure and vibrational spectrum of arglabin

Results of a theoretical study of the molecular structure of arglabin are pesented. Quantum chemical calculations of the geometry and physicochemical characteristics of arglabin are performed by the semi-empirical PM6 method, the non-empirical Hartree–Fock method, and the hybrid B3LYP DFT method with 6-31G and 6-31G(d) basis sets. By the B3LYP/6-31G(d) method the vibrational frequencies and intensities of IR absorption bands of arglabin are also calculated and the detailed interpretation of the IR spectrum is given. The theoretical frequencies are well consistent with the experimental data.

Theoretical description of 2D-cluster formation of nonionic surfactants at the air/water interface

Recent progress in modeling of the surfactant behavior from atomistic to continuous at the air/water interface across different space-time scales is reviewed. Advantages and disadvantages of modern quantum mechanical, molecular dynamical, and mesoscale methods are discussed for description of interactions between amphiphilic molecules leading to formation of 2D films. The use of nonempirical and semiempirical methods for assessment of the thermodynamic and structural parameters of large van der Waals complexes is of particular interest. An approach for calculation of the thermodynamic and structural parameters of clusterization for nonionic surfactants at the air/water interface is proposed on the basis of the quantum chemical semiempirical PM3 method. This approach implicitly takes into account the influence of the interface on the surfactant molecules via stretching and orienting effect. The calculations are carried out in the supermolecule approximation for a limited number of small amphiphilic aggregates with different alkyl chain. The correlation analysis of the calculated data array provides the increments contributing by the intermolecular CH · · · HC interactions and interactions between hydrophilic parts into the thermodynamic parameters of formation and clusterization. Obtained increments are further used for constructing the dependencies of the thermodynamic clusterization parameters per one monomer on the alkyl chain length for large clusters up to 2D films. In the framework of the proposed theoretical approach, the next parameters are calculated as follows: enthalpy, entropy, and Gibbs’ energy of clusterization for 11 homologous series of nonionic surfactants, threshold chain length enabling the process of monolayer formation at standard conditions, the “temperature effect” of clusterization, and the structural parameters of the monolayer unit cell (particularly the tilt angle) depending on the size of the hydrophilic headgroup of the amphiphilic compound.

Structural and vibrational study of the sulphate anion within the

We used the semi-empirical methods AM1 and PM3 and density functional theory (DFT) B3LYP/6-311 G to analyse the structure and position of the sulphate anion intercalated between the layers of the zinc and aluminium layered double hydroxide [Al-Zn-SO 4 ]. We determined the interlayer distances, vibration frequencies, force constants and enthalpies of formation and showed that the anion is intercalated in the interlayer space through the formation of hydrogen bonds with water molecules. Results calculated are similar to those obtained experimentally.

Synthesis and characterization of some arylhydrazone ligand and its metal complexes and their potential application as flame retardant and antimicrobial additives in polyurethane for surface coating

Hydrazones are versatile organic ligands and can be synthesized by condensation of hydrazides with carbonyl compounds (aldehydes/ketones). These compounds coordinate to the metal ions via azomethine nitrogen. Hydrazone Schiff's base ligands and their transition metal complexes possess a number of biological and flame retardant applications. Some selected divalent metal (CuII and NiII) complexes of hydrazone Schiff base ligand, namely o-methoxybenzaldehyde benzoylhydrazone (MBH) was synthesized and fully characterized by elemental analysis, FTIR, 1HNMR and mass spectra. This work summarizes the application of the prepared MBH ligand and its metal complexes. The prepared MBH ligand and its metal complexes were physically incorporated in polyurethane coating and evaluated for their flame retardancy and antimicrobial activity for surface coating. The flame retardancy of these materials was characterized by the limiting oxygen index (LOI) test. The antimicrobial activity of these materials was screened against Gram-positive bacteria, Gram-negative bacteria and fungi. The physical, mechanical and chemical properties were studied to ascertain any drawbacks. On the basis of experimental results of an oxygen index (LOI) and the biological activity, the synthesized MBH ligand and its metal complexes showed excellent flame retardancy and antimicrobial activity. In addition, the metal complexes were much more active than the original MBH ligand. Quantum chemical calculations were also performed by Semiempirical PM3 method to find the optimum geometry of the ligand and its metal complexes. The calculated pharmacokinetic parameters in silico, showed promising futures for application of the MBH ligand and its metal complexes as high antimicrobial potency agents.

Structural modifications of graphyne layers consisting of carbon atoms in the sp- and sp 2-hybridized states

A model scheme is proposed for obtaining layered compounds consisting of carbon atoms in the sp- and {vnsp}2-hybridized states. This model is used to find the possibility of existing the following seven basic structural modifications of graphyne: α-, β1-, β2-, β3-, γ1-, γ2-, and γ3-graphyne. Polymorphic modifications β3 graphyne and γ3 graphyne are described. The basic structural modifications of graphyne contain diatomic polyyne chains and consist only of carbon atoms in two different crystallographically equivalent states. Other nonbasic structural modifications of graphyne can be formed via the elongation of the carbyne chains that connect three-coordinated carbon atoms and via the formation of graphyne layers with a mixed structure consisting of basic layer fragments, such as α-β-graphyne, α-γ-graphyne, and β-γ-graphyne. The semiempirical quantum-mechanical MNDO, AM1, and PM3 methods and ab initio STO6-31G basis calculations are used to find geometrically optimized structures of the basic graphyne layers, their structural parameters, and energies of their sublimation. The energy of sublimation is found to be maximal for γ2-graphyne, which should be the most stable structural modification of graphyne.

Molecular Pockets, Umbrellas and Quasi Podands from Steroids: Synthesis, Structure and Applications

A new methods for the synthesis of molecular pockets, molecular umbrellas as well as quasi podands of steroids derivatives have been described. Moreover, a molecular umbrellas and pockets derived from biogenic precursors and their applications are described. Intermolecular 1,3- dipolar cycloaddition gave a quasi podands with 1,2,3-triazole rings. The structures of the products were confirmed by spectral analysis, mass spectrometry and PM5 semiempirical methods. Estimation of the pharmacotherapeutic potential of synthesized compounds has been accomplished on the basis of Prediction of Activity Spectra for Substances (PASS).

D-Xylose-based surfactants: Synthesis, characterization and molecular modeling studies

Pentose-derived surfactants were easily synthesized and fully characterized through classical analytical methods. The interfacial behaviors revealed the importance of both the length of the hydrophobic chain and the nature of the anomeric form. Finally, the spatial conformation of four xylosides was obtained by molecular modeling with software Hyperchem ® 4 using the semi-empirical method PM3, which demonstrated the role of hydrophobic interactions in the stability of the compounds.

Molecular modeling of bioorganometallic compounds: thermodynamic properties of molybdocene-glutathione complexes and mechanism of Peptide hydrolysis.

The computational study of bioinorganic complexes between transition metals and flexible ligands is still challenging, given that, besides requiring extensive conformational searches, the treatment of metal-ligand bonds demands the application of quantum chemical methods. Herein, the adducts formed between molybdocene, which exhibits antitumor activity and reacts with thiol groups to give stable water-soluble complexes, and the tripeptide glutathione, which is a major source of biological thiols, are studied. Conformational searches are performed using the semiempirical PM6 method followed by geometry optimizations and single-point calculations using density functional theory methods. In addition, molecular dynamics simulations of the molybdocene-glutathione complex involved in the regioselective hydrolysis of the Cys-Gly linkage are performed in explicit solvent. The reactive process is also studied theoretically on cluster models of both the molybdocene-bound and the free peptide.

Synthesis, characterization and molecular modeling of new ruthenium(II) complexes with nitrogen and nitrogen/oxygen donor ligands

Ru(II) complexes with some dinitrogen ligands; 3,4-diamino benzoic acid (DABA), 2-hydazinopyridine (hzpy), 2,2′-bipyridyl (bipy) and anthranilic acid (anth) have been synthesized and characterized by using IR, mass, and UV–Vis spectrometry and thermal analysis. The thermodynamic parameters (ΔE, ΔH, ΔS and ΔG) have been calculated by using Coats–Redfern and Horowitz–Metzger methods. The electrochemical properties of these complexes have been studied by using cyclic voltammetry. The evaluated energies of the HOMO and LUMO are in the range of −4.94 to −4.85eV and −2.86 to −2.68eV, respectively. The complexes have been proven to have an octahedral geometry with DABA, hzpy and bipy as N2 donor ligands and NSC as monodentate ligand. The structure of the Ru(II) complexes has been geometrically optimized by using parameterized PM3 semiempirical method.

Evaluation of Homolytic Dissociation Energies by Quantum Mechanical Methods

In this paper we propose a quantum mechanical evaluation model for homolytic dissociation energies. Using AM1 and PM3 semi-empirical methods we have characterized molecular structures and fragments that resulted from the chemical bond dissociation. Total binding energies were determined for the geometrically optimized molecular structures of fragments that resulted due to the breaking of chemical bonds, as well as for transitional states. The reaction enthalpy and activation energies were correlated with homolytic dissociation energies. Accuracy of the method and application elds of di erent evaluation modalities were achieved by the intercomparison of obtained values with experimental ones found in literature. More than 74 organic and inorganic compounds were analyzed.

Spectroscopic and structural studies of new mononucleating tetradentate Schiff base metal chelates derived from 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)-dione and 1,3-diaminopropane

Metal complexes with the general formula Some newly transition metal complexes, [ML(H2O)x(NO3)y], x=1–2 and y=0–1, [M=Cr(III), Fe(III), Co(II), Ni(II), Cu(II), Ce(III), Cd(II), Zn(II) or UO2(VI)], L= of the Schiff base (H2L) derived from the reaction of 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)-dione with 1,3-diaminopropane have been prepared and characterized by physical, spectral and analytical data. The structure of the Schiff–base acts as dibasic tetradentate N2O2 for the complexation reaction with Cr(III), Fe(III), Co(II), Cu(II), Ni(II), Ce(III), Cd(II), and UO2(II) ions via phenolates oxygen and nitrogen of azomethine groups. Based on spectral data and magnetic moments, an octahedral geometry may be proposed for the synthesized complexes except cerium(III) complex which has pentagonal bipyramidal arrangement. The low values of the molar conductance indicate non-electrolyte nature of complexes, while 1:1 electrolyte for cerium(III)- and chromium(III)-complexes. The Coats–Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. All the synthesized compounds were tested for in vitro antibacterial activity against some Gram-positive and Gram-negative bacteria, yeast and fungus. Molecular structure of the Schiff base ligand and its complexes were optimized for the proposed structures on the basis of semiempirical PM3 method.