Semiempirical PM3 Calculations Research Articles

A Hypothetical Study on the Structural Properties of Limonene Compounds Using Semi-Empirical (PM3) Method with Arguslab Software

Limonene, in its racemic form (+/-), is a naturally occurring cyclic monoterpene and a primary constituent of citrus peel oil, known for its chemopreventive and antitumor properties. The conformational analysis and geometric optimization of certain limonene compounds were performed using the PM3 semi-empirical quantum mechanical calculations in ArgusLab 4.0.1 software. The compounds' geometries, geometric, and thermodynamic parameters were obtained using their most stable structures. The HOMO-LUMO frontier orbital energies, molecular electrostatic potential (MEP), solvent surface distribution, and UV spectrum values of the optimized compounds were also calculated.

Synthesis, crystal structure and dielectric properties of a hybrid dihydrogen arsenate salt: (C9H11N4)H2AsO4

The use of the organic aromatic amine molecule 5-amino-3-methyl-1-phenyl-1H-1,2,4-triazole to synthesize a dihydrogen arsenate hybrid salt leads to a supramolecular structure type. Single crystals of (C9H11N4)H2AsO4 were grown through slow evaporation in solution. The synthesized compound crystallizes in the monoclinic system with the non-centrosymmetric P21 space group according to the following parameters; a = 9.655 (3) Å, b = 4.7090 (15) Å, c = 14.022 (4) Å, β = 108.147 (5)° and Z = 4. The mineral part building from dihydrogen arsenate anions [H2AsO4]− is linked together and to the organic cations [C9H11N4]+ by hydrogen bonds only. The results of Hirshfeld’s analysis show that in all possible molecular contacts, the hydrogen–hydrogen and the oxygen–hydrogen are the most important interaction in the crystal (37.5 and 31.9%, respectively). The Fourier transform infrared (FT-IR) confirms the existence of vibrational modes corresponding to the organic amine molecule and mineral arsenate tetrahedron. The optimized molecular structure and the vibrational spectra were calculated by the density functional theory DFT methods and the semi-empirical PM3 calculations. Dielectric study of this compound has been measured in order to determine the electrical conductivity type giving rise to an activation energy of ΔEσ = 0.17 eV.

Theoretical Investigation on Inclusion Complex of (s)-2-Isopropyl-1-(o-nitrophenyl) Sulfonyl) Aziridine with β-Cyclodextrin

The present work aims to study the theoretical chemistry applied to organic systems such as host / guest inclusion complexes. In literature different molecular modeling computation methods have been used to study the complexation of the host β-cyclodextrin molecule, with the guest (S) -2-Isopropyl-1- (o-nitrophenyl) sulfonyl) aziridine molecule, as semi-empirical PM3 and DFT (Density Functional Theory) calculations in gas and aqueous phases. The present paper focus on complexation, interaction and deformation energies determination, besides geometries, electronic structure, and chemical reactivity in order to describe the changes that AZ during encapsulation in two phases and two orientations. The results obtained with the Long-range corrected hybrid functional (WB97X-D / Base 6-31G (d))clearly indicate that the formed complex is energetically preferred in both phases, and the inclusion complex in the orientation A is more favorable than in the orientation B and shows good compatibility with the experimental results. NBO and NCI analysis were performed on the β - CD / AZ complex to understand the different interactions. The 1H nuclear magnetic resonance (NMR) of the complex was studied using the Gauge-Including Atomic Orbital (GIAO).

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

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

Preparation of encapsulated α-tocopherol acetate and study of its physico-chemical and biological properties

The article discusses the results of research for obtaining encapsulated vitamin E using a water-soluble oligosaccharide (cyclodextrin). The inclusion complexes of β-CD with α-tocopherol were obtained in an aqueousalcoholic medium by coprecipitation and microwave activation. The highest yields of target clathrate inclusion complexes of vitamin E with cyclodextrin were obtained under microwave synthesis conditions. Molecular modeling of inclusion complexes of α-tocopherol acetate with β-cyclodextrin in the ratios of 1:1, 1:2, 1:3, and 1:4 was performed using the MM+ method. Based on semi-empirical PM3 calculations, without taking into account the influence of the environment, the total energy of the systems under study was estimated. Data on the study of the structure of the clathrate complex of α-tocopherol acetate with β-cyclodextrin was presented. The surface morphology of the resulting “guest-host” clathrate complex was described using a scanning electron microscope. The spectral properties of the inclusion complex were characterized by FT-IR and 1H and 13C NMR spectroscopy data. The study of the 1H NMR and 13C NMR spectra of β-CD in the free and bound state in the form of the β-CD: VE clathrate made it possible to reveal the displacements of the signals of the nuclei (± ∆δ) 1H and 13C of the host molecule both in the region of weak and strong fields. The experimental results confirmed the possibility of the formation of inclusion complexes of α-tocopherol acetate with β-cyclodextrin at various ratios. The data on the study of the effect of encapsulated α-tocopherol acetate on the safety of food meat products was presented.

Quantum-Chemical Calculations for the Electronic Absorption Spectra of Certain Anthocyanidins

Semi-empirical PM3 calculations are made for the electronic absorption spectra of colored forms of nonmethylated anthocyanidins (aurantinidin, pelargonidin, cyanidin, and delphinidin). The position of the absorption band peak is shown to depend on the orientation of hydroxyl groups in the aglycone structure. The observed tendency toward a bathochromic shift after ОН groups are added to the ring generally corresponds to experimental data. The results for the uncharged quinonoid forms of pelargonidin (a hypsochromic shift of absorption bands) do not in this case agree with the prevailing opinion of specialists about the bathochromic shift. While this opinion is confirmed by DFT calculations, there are still no reliable experimental data on their validity. The formation of single-charged (negatively) quinonoid structures is clearly the reason for the bathochromic shift of absorption bands, which is consistent with the experimental data. When the charge multiplicity increases (to −2), a hypsochromic shift of absorption bands to the experimentally observed yellow color of anthocyanins in alkaline solutions is again predicted.

Computational Investigations of a Novel Charge Transfer Complex for Potential Application in Dye-Sensitized Solar Cells

The computational study of a novel charge-transfer complex as a photoactive blend for potential application in dye-sensitized solar cells was carried out using the semi-empirical method. The adsorption of two natural dyes, 1S,3R,4R,5R-3-(3,4-dihydroxyphenyl)acryloyloxy)-1,4,5-trihydroxycyclohexane carboxylic acid (DHTH) and 2-Phenyl-4H-chromen-4-one (PCO) was achieved independently on to 1×1×1 TiO2 crystal to form TiO2-DHTH and TiO2-PCO adsorption complexes. Semiempirical calculations were performed on the optimized molecules, as well as on the adsorption complexes, to obtain the total energies and EHOMO/ELUMO values, manifesting a flow of electrons from DHTH/PCO to TiO2. The theoretical electronic absorption spectra calculated via ZINDO/s method revealed a large bathochromic shift to 810 nm and 526 nm for TiO2-DHTH and TiO2-PCO, respectively, indicating the formation of a charge-transfer complex. Subsequently, the co-adsorption of PCO and DHTH on TiO2 was accomplished with the aim to minimize the possible charge recombination in the photoactive blend. The semiempirical PM3 calculations evidenced the high stability of the co-adsorption complex, TiO2-PCO-DHTH, with the total energy of -200678.578 kcal/mol. The positions of HOMO and LUMO orbitals as obtained from single-point energy calculations, coincided accurately with our proposition of electron flow in a cascade manner from DHTH to PCO and finally to TiO2. The theoretical electronic absorption spectrum ofTiO2-PCO-DHTH evinced absorption range of 351.8-800 nm demonstrating the high potential of TiO2-PCO-DHTH to be used as a photoactive blend for solar cells.

Studies of a Tripodal Biomimetic Siderophore Analog: An Efficient Encapsulation for Fe(III) Ion

A new tris-(2-aminoethyl)amine (TREN) capped tripodal Schiff base ligand has been developed by mimicking structural features of a natural siderophore, Bacillibactin, by substituting the catechol units with salicylaldehyde and employing amino acid as a spacer. Synthesis of the ligand N-[2-[bis[2-[[2-[(2-hydroxyphenyl)methylamino]acetyl] amino]ethyl]amino]ethyl]-2-[(2-hydroxyphenyl)methylamino]acetamide(TRENglySAL) includes condensation of salicylaldehyde and amino acid (glycine) followed by an in-situ reduction of the produced Schiff base, followed by further condensation with TREN. The complexation behavior of the ligand with Fe(III) has been investigated by potentiometric and UV-Vis spectrophotometric method at temperature 25±1oC and 0.1 M ionic strength. Seven protonation constants were obtained of the ligand: three each for secondary amine and phenolic protons and one for tertiary nitrogen of capping TREN moiety. The formation constants (log β11n) of different complex species MLH3, MLH2, MLH, ML and MLH-1 are found to be 35.15, 32.09, 27.91, 25.32 and 17.32 respectively. These results indicate that the ligand is an excellent iron-binding chelator. Significant electronic spectral variations during complex formation at higher pH also provide a scope for the ligand to act as an optical pH sensor towards Fe (III) metal ion in biological systems. Structures of the ligand and metal complexes are proposed through experimental findings along with the theoretical semi-empirical PM3 calculation. The theoretical spectroscopic results are found to be comparable with the experimental finding.

Alkaloid from Colchicum species in complexes with lithium, sodium, potassium and magnesium cations– spectroscopic characterization, semiempirical and theoretical calculation, fungicidal and cytotoxic activity

The colchicine (1:1) complexes with monovalent cations: Li+, Na+ and K+ as well as divalent cation Mg2+ of nitrate salts were synthesized and characterized by 1H and 13C NMR, FT-IR, UV–Vis, ESI-MS, spectroscopic methods and elemental analysis. In the ESI-MS mass spectra (in ES+ mode) formation of complexes of different stoichiometry 1:1, 2:1, 3:1, (colchicine – metal cation) was detected and in complexation process nitrate anions are also involved. Stoichiometry 1:1:1, 1:2:1, 2:1:1 and 2:2:1 (colchicine – metal cation – nitrate anion) of colchicine complexes with nitrate salts were also detected. The structures of the colchicine complexes with Li+, Na+, K+ and Mg2+ cations are discussed in details by PM5 semiempirical calculations, DFT, M06-2X theoretical calculations, molecular dynamics (MD) simulations and molecular modelling. Complexes were also screened against fungicidal and cytotoxic activity. The antifungal activity of colchicine and all complexes was assayed in vitro against eight fungi species. Cytotoxic activity of all complexes was tested against ovarian cancer cell SKOV-3 line.

Stable ferrocenyl-NHC Pd(II) complexes: Evidence of C-H ⋯H/π interaction and M-O bonding in solution

New air stable palladium(II)-NHC complexes where carbene ligand is substituted with a bulky ferrocenylmethyl and pyranylmethyl groups viz. PdI(Phpy){FcCH2-C3H2N2-Me} (3), PdI2{FcCH2-C3H2N2-C6H11O} (4) and PdI2{FcCH2-NHC}(L) (5–10) (NHC = C3H2N2-Me or C6H11O; L = pyridine, imidazole and thiazole) are reported. The presence of C-H⋯H/π interactions has been confirmed for complex 3 by NOE interaction and multinuclear NMR experiments. In addition, for this complex, a quantum chemical analysis was performed using PM3 semi-empirical calculations to find the possible conformers. The conformation with minimal energy confirms the NMR interpretation for complex 3. The M-O bond in complex 4 was ruptured by the reaction of an extra pyridine ligand to afford PdI2{FcCH2-C3H2N2-C6H11O}(py) (5) which was synthetized differently by reacting NHC ligand, Pd(OAc)2 and pyridine. Molecular structure of complex 5 was determined by X-ray diffraction. The catalytic activity of these complexes was checked in Suzuki-Miyaura reaction. Complex 5 exhibits excellent conversions and selectivities (up to 99%).

Optical Band Gap Alteration of Graphene Oxide via Ozone Treatment

Graphene oxide (GO) is a graphene derivative that emits fluorescence, which makes GO an attractive material for optoelectronics and biotechnology. In this work, we utilize ozone treatment to controllably tune the band gap of GO, which can significantly enhance its applications. Ozone treatment in aqueous GO suspensions yields the addition/rearrangement of oxygen-containing functional groups suggested by the increase in vibrational transitions of C-O and C=O moieties. Concomitantly it leads to an initial increase in GO fluorescence intensity and significant (100 nm) blue shifts in emission maxima. Based on the model of GO fluorescence originating from sp2 graphitic islands confined by oxygenated addends, we propose that ozone-induced functionalization decreases the size of graphitic islands affecting the GO band gap and emission energies. TEM analyses of GO flakes confirm the size decrease of ordered sp2 domains with ozone treatment, whereas semi-empirical PM3 calculations on model addend-confined graphitic clusters predict the inverse dependence of the band gap energies on sp2 cluster size. This model explains ozone-induced increase in emission energies yielding fluorescence blue shifts and helps develop an understanding of the origins of GO fluorescence emission. Furthermore, ozone treatment provides a versatile approach to controllably alter GO band gap for optoelectronics and bio-sensing applications.

Molecular Modeling of an Electrophilic Addition Reaction with “Unexpected” Regiochemistry

The electrophilic addition of a hydrohalic acid (HX) to an alkene is often one of the first reactions learned in second-year undergraduate organic chemistry classes. During the ensuing discussion of the mechanism, it is shown that this reaction follows Markovnikov’s rule, which states that the hydrogen atom will attach to the carbon with fewer substituents while the halogen atom will attach to the carbon with more substituents. However, in the preparation of tropic acid, the reaction of HCl with atropic acid (2-phenylpropenoic acid) does not follow this rule because it is a conjugated system. Molecular modeling of the possible carbocation intermediates suggests that the reaction follows a conjugate addition mechanism involving a 1,4-addition of HCl across the conjugated alkene and carboxyl group rather than addition across the alkene as students often first propose. PM3 semiempirical calculations are used to determine the energies of three possible carbocation intermediates. The energies obtained from the modeling suggest that the carbocation intermediate produced by the 1,4-addition is the most stable.

Synthesis, Structure and Antimicrobial Properties of Novel Benzalkonium Chloride Analogues with Pyridine Rings.

Quaternary ammonium compounds (QACs) are a group of compounds of great economic significance. They are widely used as emulsifiers, detergents, solubilizers and corrosion inhibitors in household and industrial products. Due to their excellent antimicrobial activity QACs have also gained a special meaning as antimicrobials in hospitals, agriculture and the food industry. The main representatives of the microbiocidal QACs are the benzalkonium chlorides (BACs), which exhibit biocidal activity against most bacteria, fungi, algae and some viruses. However, the misuses of QACs, mainly at sublethal concentrations, can lead to an increasing resistance of microorganisms. One of the ways to avoid this serious problem is the introduction and use of new biocides with modified structures instead of the biocides applied so far. Therefore new BAC analogues P13–P18 with pyridine rings were synthesized. The new compounds were characterized by NMR, FT-IR and ESI-MS methods. PM3 semiempirical calculations of molecular structures and the heats of formation of compounds P13–P18 were also performed. Critical micellization concentrations (CMCs) were determined to characterize the aggregation behavior of the new BAC analogues. The antimicrobial properties of novel QACs were examined by determining their minimal inhibitory concentration (MIC) values against the fungi Aspergillus niger, Candida albicans, Penicillium chrysogenum and bacteria Staphylococcus aureus, Bacillus subtilis, Escherichia coli and Pseudomonas aeruginosa. The MIC values of N,N-dimethyl-N-(4-methylpyridyl)-N-alkylammonium chlorides for fungi range from 0.1 to 12 mM and for bacteria, they range from 0.02 to 6 mM.

The formation, structure, and electronic properties of Lansoprazol drug and cucurbit [7]urils complex (Theoretical Study)

The current study deals with host-guest complex formation between cucurbit [7] urils as host and lansoprazole as guesti using PM3 (semi empirical molecules orbital calculations) also DFT calculations. In this complex, the formation of hydrogen bonding may be occurred through portal oxygen atoms(O2) of cucurbit [7] urils and amine groups (NH 2 )of the drug. The energies of HOMO and LUMO orbital’s have been computed for the host guest complex and its components. The result of the stabilization energy explained a complex formation.

The formation, structure, and electronic properties of Lansoprazol drug and cucurbit [7]urils complex (Theoretical Study)

The current study deals with host-guest complex formation between cucurbit [7] urils as host and lansoprazole as guesti using PM3 (semi empirical molecules orbital calculations) also DFT calculations. In this complex, the formation of hydrogen bonding may be occurred through portal oxygen atoms(O2) of cucurbit [7] urils and amine groups (NH 2 )of the drug. The energies of HOMO and LUMO orbital’s have been computed for the host guest complex and its components. The result of the stabilization energy explained a complex formation.

Theoretical and Molecular Docking Study of Ketoconazole on Heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin as Chiral Selector.

A molecular docking study, using molecular mechanics calculations with AutoDock and semi-empirical PM3 calculations, was used to predict the enantiodiscrimination of heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMβCD) and ketoconazole (KTZ) enantiomers. A Density Functional Theory (DFT) single-point calculation at the level of B3LYP/6-311G (d,p) was performed for the PM3-optimized complexes to obtain more accurate binding energy and the electronic structures of the complexes. The difference in energies of the inclusion complexes between the KTZ enantiomers and TMβCD is probably a measure of chiral discrimination, which results in the separation of the enantiomers as observed in the experimental studies.

Theoretical study of nonlinear optical properties of some azoic dyes

In this paper we presented semi-empirical PM3, ab-initio (HF, MP2) and DFT (B3LYP, B3PW91) calculation of the dipole moment, polarizability, and first hyperpolarizability of some azoics dyes derivatives which have electron donor and electron acceptor groups on either sides. The first hyperpolarizability of these molecules was calculated with PM3 method, HF/6-31G**, HF/6-31+G**, HF/6-31++G**, DFT with B3LYP and B3PW91 functional, and MP2/6-31++G** based on finite field approach using GAUSSIAN03 program. The effects of the intramolecular charge transfer (ICT) from the donor to the acceptor groups on the molecular geometry and atomic charge distribution of these NLO chromophores are derived from its HF, MP2 and DFT calculations. The variation of this property has also been correlated to E (HOMO-LUMO) gap and to the nature of the highest occupied molecular orbital HOMO and the lowest unoccupied molecular orbital HOMO. The study reveals that the azoics dyes derivatives have large hyperpolarizability values; hence they may be used in the development of nonlinear optical materials.

Bioferroelectricity in Nanostructured Glycine and Thymine: Molecular Modeling and Ferroelectric Properties at the Nanoscale

Nanostructured aminoacid glycine and nucleobase thymine are very important for various biomedical applications. Experimentally, these structures demonstrate piezoelectric and polar properties. But the value of polarization and its switching behavior are not clear yet. In this work, computational modeling of glycine polymorphic phases (α and β) and thymine nanostructures was performed using a combined method with LDA first principle calculations of atomic optimized crystal structures in AIMPRO code on Linux cluster combined with molecular semi-empirical PM3 calculations by HyperChem 8.0. The developed molecular model and calculated parameters are compared with recent measurements using piezoresponse force microscopy (PFM) at the nanoscale.

Generalizing thermodynamic properties of bulk single-walled carbon nanotubes.

The enthalpy and Gibbs free energy thermodynamical potentials of single walled carbon nanotubes were studied of all types (armchairs, zig-zags, chirals (n>m), and chiral (n<m)). Bulk values of these thermodynamic potentials were obtained using a previously demonstrated robust method based on semi-empirical PM3 calculations and an extrapolated cluster approach. Those values were used to study the relationship between the thermodynamic potentials and the diameter of the nanotube. Results of this study led to the proposal of a single equation for the thermodynamical potential of [Formula: see text] or [Formula: see text] (assembly of nanotubes from atoms) versus the chiral vector indexes n and m for any given nanotube. The equations show a good level of accuracy in predicting thermodynamic potentials for practical applications.

Nanostructures formed by cyclodextrin covered procainamide through supramolecular self assembly – Spectral and molecular modeling study

Inclusion complexation behavior of procainamide (PCA) with two cyclodextrins (α-CD and β-CD) were analyzed by absorption, fluorescence, scanning electron microscope (SEM), transmission electron microscope (TEM), Raman image, FT-IR, differential scanning colorimeter (DSC), Powder X ray diffraction (XRD) and 1H NMR. Blue shift was observed in β-CD whereas no significant spectral shift observed in α-CD. The inclusion complex formation results suggest that water molecules also present in the inside of the CD cavity. The present study revealed that the phenyl ring of the PCA drug is entrapped in the CD cavity. Cyclodextrin studies show that PCA forms 1:2 inclusion complex with α-CD and β-CD. PCA:α-CD complex form nano-sized particles (46nm) and PCA:β-CD complex form self-assembled to micro-sized tubular structures. The shape-shifting of 2D nanosheets into 1D microtubes by simple rolling mechanism were analysed by micro-Raman and TEM images. Thermodynamic parameters (ΔH, ΔG and ΔS) of inclusion process were determined from semiempirical PM3 calculations.