Semiempirical Level Research Articles

Supramolecular complex of fluoxetine with β-cyclodextrin: An experimental and theoretical study

In this work the complex formed between β-cyclodextrin (βCD) and fluoxetine (FLU) was investigated by experimental and computational methods. From Horizontal Attenuated Total Reflectance (HATR) was possible to verify a strong modification in the vibrational modes of βCD and FLU, indicating interactions between them. The Nuclear Magnetic Resonance (NMR) experiments confirm these interactions through the change in chemical shifts in 1H spectra, reduction in longitudinal relaxation times values, and the Nuclear Ouverhauser Effect confirm the inclusion of aromatic rings of FLU into the βCD. The structures of the proposed inclusion compounds were optimized at PM3 semiempirical level of theory. In addition, single point calculations at the Density Functional Theory (DFT) level, using the Becke, Lee, Yang, and Parr functional and 6-31G(d,p) basis set, were used to determine the interaction energy for these structures. The DFT calculations identified the aromatic ring, which contains the CF 3 group as the most stable into the βCD by an amount of, 11.7 kcal mol −1, in the gas phase. Polarized continuum model, at the DFT level mentioned, was used to investigate the solvent effect, and the results corroborated the gas phase analysis. A high equilibrium constant ( K ≈ 6921 ± 316) and the stoichiometry, 1:1, were obtained by Isothermal Titration Calorimetry (ITC) experiments.

An intermolecular hydrogen transfer process inducing triplet biradical photochromism of 1-methyl-2,4,4,6-tetraphenyl-1,4-dihydropyridine in the solid state

An intermolecular hydrogen transport process, as a source of photochromism in a crystal, was identified in 1-methyl-2,4,4,6-tetraphenyl-1,4-dihydropyridine (DHP). The photochromic form of that compound, dark violet in color, according to EPR measurements is triplet biradical in nature. According to photoluminescence measurements, the lowest excited triplet state (T 1) as well as the excited singlet state (S 1) of the DHP molecule is of π,π* type. Two active non-symmetrical biradical forms, absorbing at 400 nm and 550 nm, are proposed connected with a hydrogen transfer process created by transformation of the forms on mutual terms (‘hydrogen cascade’). Optical generation of the photochromic form was followed by steady-state UV–vis spectroscopy. The rate constants are equal to k 400 = 4.36 ± 0.17 × 10 −3 s −1 and k 550 = 5.87 ± 0.56 × 10 −4 s −1, respectively. The values of energy of activation of these two parallel processes obtained by analysis of non-isothermal kinetics of the bleaching process are equal to 10.96 kJ/mol and 31.2 kJ/mol, respectively. The IR spectra together with EPR measurements as well as X-ray structural analysis and calculations on the semi-empirical AM1 level method seem to support the intermolecular hydrogen transfer chain process.

Molecular modeling of polymer–clay nanocomposite precursors: Lysine in montmorillonite interlayers

The layered structure of clays with interlayer cations leads to unique chemical and mechanical properties, which have been capitalized on in the field of polymer/layered silicate nanocomposites. Hydrophilic silica surfaces can become organophilic with the inclusion of alkylammonium cations, which improve the wetting characteristics of the polymer matrix. In fact, the molecular level interactions of amino acids, either natural or non-natural, with clay surfaces are at the heart of fields of study as diverse as nanocomposites fabrication, drug delivery, bio-remediation of soils and catalysis of biological polymers, to name a few. The ubiquity of these systems and the potential uses to which they could be put suggests the necessity of a deeper understanding of the interplay of bonds, conformations, and configurations between the molecules and the hosts. The interactions of the amino acid lysine with sodium montmorillonite were studied using theoretical molecular modeling methods. The interlayer spacing of montmorillonite was increased by incorporating water molecules and allowing the system to evolve with molecular mechanics. Care was taken to retain the sodium cations in the interlayer. The initial amino acid conformation was obtained surrounding the molecule with numerous discrete water molecules and minimizing the system at the semi empirical level. The optimized amino acid was then placed in the interlayer space in a series of initial positions. Molecular mechanics calculations were performed and the final positions were analyzed. The results tended to indicate the preponderance of configurations which included surface-sodium-amino acid complexes with a variety of spatial arrangements. These results were compared with molecular dynamics calculations of similar systems from the literature.

Quantum Chemical Study on Molecular and Electronic Structures of Methyl and Methoxyl Substituted Cu(II) and Ni(II) Benzoic Acid Hydrazides Ions

The electronic structures of model methyl and methoxyl substituted benzoic acid hydrazides of Ni(II) and Cu(II) complexes have been studied both at semi empirical level (PM3). The ortho‐methoxyl is relatively stable which may be due to the formation of hydrogen bonds between methoxyl oxygen and hydrogen on hydrazide (CH30‐‐‐HNNH; 1.817Å for Cu(II) and 1.806∼1.839∼ for Ni(II)). The change in torsion in the complexes affect π‐electrons delocalization (complexes containing π‐electrons system) and consequently affect the band gap which is a measure of electronic properties that control the reactivity of the complexes. The curves for ortho and para methoxyl substituted Cu(II) complexes intercept at 50° and 135°‐144°, this could suggest that both complex ions can co‐exist and react in very similar ways in solution under certain conditions.

Kinetics of hydrogen abstraction O( 3P) + alkane → OH + alkyl reaction class: An application of the reaction class transition state theory

This paper presents an application of the reaction class transition state theory (RC-TST) for prediction of thermal rate constants of the O( 3P) + alkane → OH + alkyl reaction class. Parameters of the RC-TST were derived from first principles from a set of 19 reactions representing hydrogen abstractions from primary, secondary, and tertiary carbon atoms so that rate constants of any reaction in this class can be estimated without any further information or with its reaction energy calculated either at the density functional theory BH&HLYP/cc-pVDZ level or the semiempirical AM1 level. Detailed error analyses show that when compared to explicit theoretical calculations, the systematic errors in the calculated rate constants arising from the use of analytical expressions to approximate different reaction class factors in the RC-TST method are less than 40% on the average over the temperature range from 300 to 3000 K. In addition, we found that the rate constants estimated using either approach are in good agreement with available data in the literature.

Synthesis and dynamics of atropisomeric ( S)- N-(α-phenylethyl)benzamides

The synthesis of atropisomeric 2-substituted benzamides 2a– e, 3a– e, and 4a– e, and characterization by X-ray structure analysis of 2d, 2e, 3c, 3e, 4c, and 4e are reported. Dynamic 1H NMR spectroscopic studies of benzamides 2b– d, 3b– d, and 4b– d indicate that only two of the four possible rotamers are present in solution, with population ratios ranging between 1.5:1 and 4.1:1. The measured free energy of activation to interconversion of the rotamers ranged from 12.4 to 18.9 kcal mol −1. Benzamides ArCON[( S)-phenethyl] 2 ( 2e, 3e, and 4e), exhibited atropisomer ratios between 1.7:1 and 1:1, and free energies of interconversion of the rotamers ranged from 11.5 to 17.6 kcal mol −1. The highest rotation barriers were observed for the ortho-nitro derivatives 2a– e. Molecular calculations at the semiempirical level (PM3MM) gave free energies of activation for benzamides 2e and 3e of 23.6 and 12.4 kcal mol −1, respectively, which are comparable to the experimental values.

One‐Pot Synthesis of Core‐Modified Rubyrin, Octaphyrin, and Dodecaphyrin: Characterization and Nonlinear Optical Properties

AbstractModified 26π rubyrin, 36π octaphyrin, and 54π dodecaphyrin systems have been synthesized in moderately good yields through acid‐catalyzed condensations of terthiophene diols and tripyrranes. The product distributions are decided both by the acid catalyst concentration and by the nature of the meso substituents. For example, a new isomer of [26]hexaphyrin(1.1.1.1.0.0) (rubyrin) was obtained with 0.3 equiv. of p‐toluenesulfonic acid, when the meso substituent was mesityl in at least one of the precursors. A change of the mesityl substituent for a p‐methoxy substituent in terthiophene diol resulted in the formation of a [3 + 3 + 3 + 3] condensation product – [54]dodecaphyrin(1.1.1.1.0.0.1.1.1.1.0.0) – in addition to the expected rubyrin. Furthermore, an increase in the acid concentration to 0.6 equiv. resulted in the formation of a new [36]octaphyrin(1.1.1.1.1.1.0.0), in addition to the rubyrin and dodecaphyrin. A single‐crystal X‐ray analysis of octaphyrin represents the first example of a planar conformation of an octaphyrin with six meso links. In rubyrin 19, one thiophene ring, opposite to the terthiophene subunit, is inverted, while in octaphyrin 30 one pyrrole ring and two thiophene rings are inverted. The various conformational possibilities tested for the unsubstituted dodecaphyrin 28, at semiempirical level, suggest that the most stable conformation is a figure‐eight. The final geometry optimization of figure‐eight dodecaphyrin was done at the B3LYP/6‐31G* level of DFT. Octaphyrins and dodecaphyrins bind trifluoroacetate anion effectively in their diprotonated forms, the binding constants (K) being 638 M–1 for dodecaphyrin 28, and 415 M–1 for octaphyrin 30. Electrochemical data reveal HOMO destabilization with increasing π electron conjugation, consistently with the large red shifts of the absorption bands. Preliminary studies on the use of these expanded porphyrins as third‐order NLO materials were followed by measurements of their two‐photon absorption (TPA) cross‐sections [σ(2)]. The σ(2) values increase upon going from the 26π rubyrins to the 54π dodecaphyrins, confirming our earlier observation that increases in π‐conjugated electrons increase the TPA values.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)

Introduction of Modified Electronic Parameters – Searching for a Unified Ligand Properties Scale through the Electrophilicity Index Concept

AbstractIn order to quantify the contribution of mainly, but not only, diimine ligands to the electronic properties of the corresponding complexes, two novel indices, namely modified electronic parameters (ModEP) and electrophilicity, ω, are introduced and discussed in this report. First, we introduce the concept of ModEP, a novel scale relating to the electronic properties of diimine ligands. Mainly on the basis of well‐characterized M(diimine)(dithiolato) complexes (M = Pt, Pd, or Ni), we derive the contribution of the diimine ligand to the reduction potentials of the complexes, and incorporating its contribution to the main charge‐transfer band of the UV/Vis spectra, we obtain our ModEP values. The applicability of the introduced scale to several other classes of diimine compounds (W, Re, and Ru) is then tested. The performance of our scale in predicting the values of the reduction potentials and the position of the charge‐transfer bands is very satisfactory. With this approach, some interesting aspects of ligand coordination were revealed. Next, we employ the recently introduced electrophilicity index ω, in order to correlate our ModEP scale with various other empirical scales that are already known and extensively used. This permits us to unify most known scales, which were primarily derived for different types of ligands (e.g. ModEP for diimines, Tolman's for phosphanes). The proposed method of ω calculation (at the semiempirical AM1 level) avoids any experimental limitation and can be employed even for ligands that are not yet experimentally available, whereas its correlation to the known scales would immediately provide the properties of the compound. This supports the idea that the electrophilicity index could become a powerful tool in coordination and organometallic chemistry.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)

The structural, electronic and transport properties of monatomic chains deposited onto silicon surfaces: A study at semi-empirical level

The purpose of this study is the assessment of the properties of deposited nanostructures with a perspective on the 1D limit. Therefore linear, single-atom chains deposited onto the Si(100) surface and onto monolayer steps of this surface have been considered. The elements forming the chains are covalent and metallic atoms, i.e. As, Al, Ni, Ag and Co, and the properties analyzed are the chain structure, its electronic charge and conductance. The calculations are based on a simple semi-empirical Hamiltonian, which is applied to the evaluation of both the electronic structure and the conductance, and on a cluster model of the exposed surface. The study of the structural properties shows that the linear structure is, in essence, maintained in all cases though some fuzziness is observed in the deposited structures. The binding energies and the density of states show a subtle, but appreciable, dependence on the structure of the exposed surface and on the chain composition. These differences are of paramount importance for the conductance and lead to the formation of well-defined resonances.

The Photocatalytic Degradation of Imazapyr

The degradation of imazapyr, an imidazolinone herbicide, in aqueous solution has been investigated with TiO2 slurry as photocatalyst at 30°C under UV radiation. The depletion of imazapyr concentration in an aqueous suspension followed 1st order kinetic behavior. The influence of pH and the charge densities of imazapyr geometries were calculated at the semi-empirical AM1 level, and the effect of temperature was investigated. The addition of electron acceptors such as potassium persulfate and hydrogen peroxide showed that the rate constant doubled at least. At higher persulfate concentrations the herbicide degradation was more efficient in direct photolysis than TiO2-photocatalysis. The degradation rate constant increased by 38% upon variation of the temperature between 20.0 and 50.0°C and displayed non-Arrhenius behavior.

Calorimetric and Computational Study of Enthalpy of Formation of Diperoxide of Cyclohexanone

A thermochemical rather simple experimental technique is applied to determinethe enthalpy of formation of Diperoxide of ciclohexanone. The study is complemented withsuitable theoretical calculations at the semiempirical and ab initio levels. A particularsatisfactory agreement between both ways is found for the ab initio calculation at the 6-311G basis This set level. Some possible extensions of the present procedure are pointedout.

A theoretical investigation on the absorption and emission properties of isomeric benzofuran trimers

The influence of isomeric conformation and substituent on the luminescent properties of two series of linear benzofuran trimers are studied. The structures, ionization potentials (IPs), electron affinities (EAs), and HOMO–LUMO gaps (ΔH–L) of the trimers are studied by the density functional theory with B3LYP functional. The calculation of the lowest excitation energies (Egs) and the maximal absorption wavelength λabs of trimers are performed employing time dependent density functional theory (TDDFT) and semi-empirical level ZINDO.

Molecular Recognition in an Organic Host–Guest Complex: CH···O and CH···π Interactions Completely Control the Crystal Packing and the Host–Guest Complexation

Abstract The synthesis, crystal structure analysis, theoretical modeling at DFT and semiempirical PM3 levels, and molecular electrostatic potential analysis of an organic host–guest system containing an azapolycyclic system 3 and ethyl acetate are presented. The structure of 3 was charaterized by the presence of seven-connected five-membered rings. Though 3 contained six-saturated nitrogen atoms capable of CH···N interactions, its crystal structure and the host–guest complexation were completely governed by CH···O and CH···π interactions. Further, an aromatic pocket consisting of four phenyl rings from four molecules of 3 existed located in the crystal structure. The guest molecule ethyl acetate trapped inside this aromatic pocket was found to interact with it via three CH···π and two CH···O interactions. A model structure for this host–guest complex was also optimized at DFT level, which showed good agreement with the experimental structure.

Synthesis and molecular orbital calculations of some benzo-substituted macrocyclic diamides and their corresponding macrocyclic dithiodiamides

A new series of benzo-substituted macrocyclic diamides were prepared by nucleophilic reaction of the appropriate dipotassium salts with the corresponding bis(halo) compounds in refluxing DMF. Treatment of the novel macrocyclic diamides with Lawesson's reagent in refluxing toluene led to the formation of the corresponding macrocyclic dithiodiamides in good yields. Molecular orbital calculations were performed at the semi-empirical level AM1 on some of the studied macrocycles. Thermodynamic functions show that the most stable structures in gas phase that have internal amine groups are less in energy than the other ones that have internal carbonyl groups. The solvent polarity does not appreciably affect the stability trend of the three conformers of each compound due to their comparable dipole moments. A complete and thorough survey of proton affinity (PA) and proton detachment energies (PDE) on each of the possible sites has been performed.

Semiempirical Molecular Orbital Scheme To Study Lanthanide(III) Complexes: PM3 Parameters for Europium, Gadolinium, and Ytterbium.

Semiempirical parameters for europium, gadolinium, and ytterbium have been developed for use in the PM3 method to allow the structure and energetics of complexes containing lanthanide(III) ions to be accurately modeled. At the semiempirical level, the lanthanide(III) ion is represented by a +3 core and has a minimal basis of 6s5d6p (9 atomic orbitals), the 4f electrons being included within the electronic core. Training sets containing up to 19 lanthanide complexes, with data computed at the density functional theory (DFT) level, have been employed for each lanthanide(III) ion. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure of the complexes and demonstrate improvements in the prediction of water binding energies compared to the AM1/sparkle model. For the 28 Eu(III), 28 Gd(III), and 29 Yb(III) complexes optimized at the DFT level, the PM3 average unsigned mean errors for all interatomic distances between the lanthanide(III) ion and the ligand atoms of the first coordination sphere are 0.04, 0.03, and 0.03 Å, respectively. The derived parameters are shown to be comparable to small-basis set DFT calculations in predicting the experimental structures of various lanthanide(III) complexes. The derived parameter sets provide a starting point should greater accuracy for a more restricted range of compounds be required.

A computational study of substituted flavylium salts and their quinonoidal conjugate-bases: S0 -> S1 electronic transition, absolute pKa and reduction potential calculations by DFT and semiempirical methods

The electronic transitions for flavylium cations and quinonoidal bases of 17 substituted flavylium salts have been studied at semiempirical and DFT (density functional theory) levels. Solvent effect on electronic spectra was included by Polarizable Continuum Model, PCM. We assigned longest-wavelength absorption maxima to HOMO ® LUMO transition. Both levels of theory gave good results for electronic transitions of flavylium cations whereas only TDDFT-PCM calculations could be used for electronic transitions of their quinonoidal bases. We also performed absolute pKa calculations of nine flavylium salts at DFT level. The pKa calculated values by our PCM parameterization gave excellent results with mean absolute deviation less than a half of one pKa unit. One-electron reduction potentials were carried out for 5 flavylium cations at DFT level. The theoretical results found were in good agreement with experimental values after adjustment for a systematic deviation.

Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules

Semi-empirical calculations including an empirical dispersive correction are used to calculate intermolecular interaction energies and structures for a large database containing 156 biologically relevant molecules (hydrogen-bonded DNA base pairs, interstrand base pairs, stacked base pairs and amino acid base pairs) for which MP2 and CCSD(T) complete basis set (CBS) limit estimates of the interaction energies are available. The dispersion corrected semi-empirical methods are parameterised against a small training set of 22 complexes having a range of biologically important non-covalent interactions. For the full molecule set (156 complexes), compared to the high-level ab initio database, the mean unsigned errors of the interaction energies at the corrected semi-empirical level are 1.1 (AM1-D) and 1.2 (PM3-D) kcal mol(-1), being a significant improvement over existing AM1 and PM3 methods (8.6 and 8.2 kcal mol(-1)). Importantly, the new semi-empirical methods are capable of describing the diverse range of biological interactions, most notably stacking interactions, which are poorly described by both current AM1 and PM3 methods and by many DFT functionals. The new methods require no more computer time than existing semi-empirical methods and therefore represent an important advance in the study of important biological interactions.

Push-pull benzoxazole based stilbenes as new promising electrooptics materials

Photoinduced linear electrooptics effect (EOE) was discovered for three push-pull benzoxazole based stilbenes with different electron withdrawing and donating substituents at the phenylene and methane groups. The ground state geometry optimization for trans-stilbene has been performed using molecular mechanic geometry optimization within a framework of MM + force field method. We have done simulations of the optical absorption spectra and we have compared them with the experimental spectra. Quantum chemical simulations of UV-absorption spectra were done within a framework of semi-empirical restricted Hartree-Fock level (RHF) by AM1 (Austin Model 1) and PM3 (Parametric Method 3) methods. In addition, semi-empirical quantum mechanical calculations were carried out to verify reliability of theoretical simulations with respect to experimental data. Furthermore, semi-empirical quantum mechanical calculations indicated substantial difference of absorption obtained for the stilbenes possessing the in-plane and out-of-plane benzoate complexes. The maximally achieved value of photoinduced EOE coefficient was equal to 11.7 pm/V during illumination by λ = 1060 nm and λ = 530 nm coherent wavelengths. Correlation between the AFM morphological structure and EOE coefficients for the three investigated stilbenes was demonstrated.

A theoretical vibrational spectroscopic investigation on free Ethyl 2- and 3-aminobenzoate molecules

The possible stable conformers of free Ethyl 2- and 3-aminobenzoate molecules were searched via subsequent single point energy calculations carried out at semi-empirical PM3 theory level. The final equilibrium geometrical parameters for the obtained stable conformers were defined by performing geometry optimizations with B3LYP hybrid DFT method and basis sets of different size and type. The harmonic vibrational normal modes of the two molecules and their corresponding wavenumbers and IR intensities were calculated at the obtained equilibrium geometries using the same method and basis sets used in the geometry optimizations. In the light of these calculated spectral data, a successful assignment for the fundamental bands in the IR spectra of the two molecules was given. In order to fit the calculated harmonic wavenumbers to the experimentally observed ones, two different scaling procedures, called “scaling wavenumbers in Scaled Quantum Mechanics Force Field (SQM FF) methodology” and “scaling wavenumbers with dual empirical scale factors”, were proceeded independently.

Quantum chemical and spectroscopic analysis of calcium hydroxyapatite and related materials

Amorphous calcium hydroxyapatite was examined by vibrational spectroscopy (Raman and infra-red (IR)) and quantum chemical simulation techniques. The structures and vibrational (IR, Raman and inelastic neutron scattering) spectra of PO 4 3− ion, Ca 3(PO 4) 2, [Ca 3(PO 4) 2] 3, Ca 5(PO 4) 3OH, CaHPO 4, [CaHPO 4] 2, Ca 3(PO 4) 2·H 2O, Ca 3(PO 4) 2·2H 2O and Ca 3(PO 4) 2·3H 2O clusters were quantum chemically simulated at ab initio and semiempirical levels of approximation. A complete coordinate analysis of the vibrational spectra was performed. The comparison of the theoretically simulated spectra with the experimental ones allows to identify correctly the phase composition of the amorphous calcium hydroxyapatite and related materials. The shape of the bands in the IR spectra of the hydroxoapatite can be used in order to characterize the structural properties of the material, e.g., the PO 4 3− ion status, the degree of hydrolysis of the material and the presence of hydrolysis products.