AM1 Method Research Articles

Adsorption of o-tolylthiourea on two polar-modified hyper-cross-linked resins: Equilibrium, thermodynamic and kinetic studies

Abstract Two polar monomers, Trimellitic anhydride and o-phthalic anhydride, are employed to copolymerize with the non-porous gel-type chloromethylated poly(styrene-divinylbenzene) (NP-CLPs), and synthesized two polar-modified hyper-cross-lined resins. The resins were efficient for adsorption of o-tolylthiourea, and possessed the largest equilibrium capacity (221.2 mg/g for TMAMR, and 206.7 mg/g for PAMR). The influences of adsorption temperature, solution pH, and salt content of the solution were studied by the static adsorption method. The Freundlich and Langmuir isotherm model were used to fit equilibrium data for all investigative temperatures (288–318 K). The Langmuir model was better than the Freundlich model at 288 K; however, with the increasing temperature the Freundlich and Langmuir models could all well describe the isotherm data. The thermodynamic parameters (ΔH0, ΔS0, and ΔG0) showed that the adsorption of o-tolylthiourea was feasible, exothermic, and spontaneous from 288 K to 318 K. The kinetic data were fitted by pseudo-first order, pseudo-second order, and intraparticle diffusion equations. Differences in adsorption of o-tolylthiourea between TMAMR and PAMR resins were interpreted by the frontier orbital energy level difference between resins and o-tolylthiourea calculated with the semi-empirical method AM1.

Development of Quantitative Structure-Property Relationship (QSPR) Models of Aspartyl-Derivatives Based on Eigenvalues (EVA) of Calculated Vibrational Spectra

In present study, validated linear quantitative structure-property (sweetness) relationship (QSPR) models were developed, based on an experimental sweetness index and the calculated vibrational spectra of 158 aspartyl-derivatives. The quantum chemical AM1 method was applied to calculate the vibrational spectra of the compounds. The EVA descriptors were derived from the vibrational spectra for a combination of various values of σ (2.5, 5, 10,20 and 40 cm−1) and L (5, 10, 20 and 40 cm−1), which were correlated with an experimental sweetness index of the compounds using the multiple linear regression method. Several QSPR equations were constructed and analyzed. Among the various combinations, the statistically best QSPR equations were achieved when σ =10 and L = 10 were chosen. Four equations were selected as QSPR models, namely, model_1, model_2, model_3 and model_4. Satisfactory statistical values were found for the fit of the training set, R2=0.618, 0.691, 0.605 and 0.604, internal validation Q2=0.540, 0.647, 0.550 and 0.548, and the external predictive measures for the test set, $$ {R}_{pre.}^2 $$=0.614, 0.616, 0.633 and 0.633 were obtained for dubbed 1 to 4 respectively. The application domain of the models was determined. The results of the Y-randomization test of the models support the finding that the statistical values obtained for the QSPR models were not due to just chance. Graphic visualizations of the EVA profiles of some of the selected compounds showed that the presence of hydrophobic moiety in the structure such as those of saturated hydrocarbons, e.g. heptane in ASP_215, tert-butyl in ASP_63, cyclohexane in ASP_201 and pentane in ASP_199, which is related to a high sweetness index, might be monitored in the EVA profiles of aspartyl-derivatives.

Novel 13,14‐dimethyl‐5,8‐dioxa‐2,11,13,14‐tetraaza‐1,12‐diphosphabicyclo [10.1.1] tetradecane 1,12‐dioxide ligand and its Ni(II), Co(II), and Cu(II) complexes: Synthesis, characterization, antimicrobial, DNA cleavage, and computational studies

A novel diazadiphosphetidine ligand derived from the reaction of 2,4‐dichloro‐1,3‐dimethyl‐1,3,2,4‐diazadiphosphetidine‐2,4‐dioxide and 2,2′‐(ethane‐1,2‐diylbis[oxy])bis(ethan‐1‐amine) and its Ni(II), Cu(II), and Co(II) complexes have been synthesized, characterized by spectroscopic, elemental analyses, magnetic susceptibility, and conductivity methods, and screened for antimicrobial, DNA binding, and cleavage properties. Spectroscopic analysis and elemental analyses indicate the formula [M(H2L)Cl2] for the Cu(II), Co(II), Ni(II), and Zn(II) complexes and octahedral geometry for all the complexes. The non‐electrolytic nature of the complexes in dimethyl sulfoxide (DMSO) was confirmed by their molar conductance values, which are in the range 12.32–6.73 Ω−1 cm2 mol−1. Computational studies have been carried out at the density functional theory (DFT)‐B3LYP/6‐31G(d) level of theory on the structural and spectroscopic properties of diazadiphosphetidine H2L and its binuclear Cu(II), Co(II), Ni(II), and Zn(II) complexes. Six tautomers and geometrical isomers of the diazadiphosphetidine ligand were confirmed using semiempirical AM1 and DFT method from DMOL3 calculations. The copper complex had the best antibacterial activity against Staphylococcus aureus (ATCC 29213). DNA cleavage activities of the compounds, evaluated on pBR322 DNA by agarose gel electrophoresis in the presence and absence of an oxidant (H2O2) and a free‐radical scavenger (DMSO), indicated no activity for the ligand and moderate activity for the complexes, with the copper complex cleaving pBR322 DNA more efficiently in the presence of H2O2.

Intramolecular Excited-State Proton Transfer in Biologically Active Flavones: A Combined Experimental and Theoretical Study

The absorption and fluorescence characteristics of two biologically active flavone derivatives 6-hydroxy-7,3’,4’,5’-tetramethoxyflavone (6HTMF) and 7-hydroxy-6,3’,4’,5’-tetramethoxyflavone (7HTMF) were studied as a function of acidity (pH/H0) of the solution. Dissociation constants were determined for ground and first excited singlet states and the results were compared with those obtained from Forster-Weller calculations. The acidity constants for these two compounds (6HTMF and 7HTMF) obtained from fluorimetric titrations are in poor agreement with those obtained from Forster-Weller data but are in good agreement with ground state pKa values indicated the deactivation of excited state (S1) before the prototropic equilibrium is complete. The broad band emission of both the flavones in acidic aqueous solution suggests their use as tuneable dye lasers. 6-Hydroxy-7,3’,4’,5’-tetramethoxyflavone undergoes adiabatic photo-dissociation in the singlet excited state indicating the formation of an exciplex or a photo-tautomer. The stability of photo-tautomer was confirmed by calculated value of enthalpy of formation using AM1 method.

Interaction of Dyes with Cationic Surfactants in Solutions: Determination of Critical Micelle Concentration

Interactions of sulforhodamine B or ethyl eosin (as the anionic dye) with cetylpyridinium bromide (as a cationic surfactant) have been investigated by visible spectroscopy in aqueous solution. The object of research is the association between an anion of dye and of cationic surfactant in aqueous solutions and its features. Computer simulation of these interactions was carried out with the use of AM1 and PM3 semi-empirical methods. A new spectrophotometric method was developed for determination of critical micelle concentration of cationic surfactants.

Interaction of Dyes with Cationic Surfactants in Solutions: Determination of Critical Micelle Concentration

Interactions of sulforhodamine B or ethyl eosin (as the anionic dye) with cetylpyridinium bromide (as a cationic surfactant) have been investigated by visible spectroscopy in aqueous solution. The object of research is the association between an anion of dye and of cationic surfactant in aqueous solutions and its features. Computer simulation of these interactions was carried out with the use of AM1 and PM3 semi-empirical methods. A new spectrophotometric method was developed for determination of critical micelle concentration of cationic surfactants.

Процеси утворення позитивних іонів при взаємодії електронів з молекулами тиміну

The work is aimed to solve the key problems of modern biophysics related to the study of fundamental mechanisms of interaction of ionizing radiation on living cells and stability of biological systems to its influence. The obtained data and their generalizations create a basis for understanding the interaction mechanisms and stability of biological systems to its influence. Investigation is aimed on the obtaining the new priority data about the characteristics of the life important biological molecules, establishing the mechanisms and features of dissociative capture, excitation and ionization under the slow electrons; the study of the influence of intermolecular interactions on these processes and solution of some applications concerning the definition of physical stability of biomolecules in different states of aggregation. The AM1 method that was used in research is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the neglect of differential diatomic overlap integral approximation and investigates the processes of formation of positive ions, which are formed during the interaction of thymine molecules with slow electrons. Fragmentation model of thymine molecules under electron ipmpact is proposed. Six most likely bond breaks in the cyclic structure of thymine molecular ion are identified. The obtained results are in good agreement with experimental data.

Photofading of Derivatives of Paraben (PHB) by AM1 and PM3 Methods: A Theoretical Study

Calculations of chemical structures and photofading of parabens (PHB—4 hydroxybenzoic acid), which are p-hydroxybenzoic acid alkyl esters were performed. These compounds are used as preservatives for the substances used in cosmetics. The reactivity of these derivatives with an oxidant—singlet oxygen—have been tested with a theoretical method of frontier orbitals. All-valence molecular orbital methods, AM1 and PM3, have been used to calculate frontier electron density for higher occupied HOMO and lower unoccupied LUMO orbitals, which might be sensitive to an electrophilic (with singleton oxygen atom 1O2) or nucleophilic ( superoxide anion radical) attack at a particular atom in a molecule. Using AM1 and PM3, we calculated the reactivity , superdelocalisability and electron density distributions. The obtained superdelocalisability rates allow you to explain the fastness values in different chemical molecules. The structure of parabens (PHB) was optimized by MM+, DM, AM1 or PM3, to achieve constant energy values at a convergence criterion of 0.01 kcal/mol. The performed calculations indicate that the electrophilic oxidation reaction should take place in the aromatic ring in the 2-position to the hydroxyl residue of PHB, whereas the superoxide radical reaction occurs mainly on the alkyl residues of the ester group. The reaction may take place according to superoxide mechanism or 1,2-addition, where the higher superdelocalisability values SN are located on neighboring atoms in aromatic systems.

Studies of the Association of Dyes with Surfactants in Aqueous Solutions: Spectrophotometry and Computer Simulation

The association of cationic dye (pinacyanol, PC) with anionic dyes (ethyleosin, EE, or rhodamine 200 C, R200C), and also the interaction “dye+surfactant” has been investigated in aqueous solutions by visible spectroscopy and computer simulation. Cetylpyridinium bromide (CPB), sodium dodecylsulfate (SDS) and triton X-100 (TX) were used as cationic, anionic and non-ionic surfactants respectively. The formation of “dye+surfactant” associates takes place at low dye concentrations (≥10‑6 M) and concentrations of surfactant, which are much smaller than the critical micelle concentrations (CMC). In contrast, similar concentrations (10‑6 – 10‑4 M) of small cations of tetramethylammonium or tetraethylammonium have no noticeable effect on the absorption spectra of the dye in the “dye+tetraalkylammonium salt” systems; it indicates the absence of formation of new compound between the dye and salt. The standard enthalpy of formation of “dye+dye” or “dye+surfactant” associates has been determined by AM1 and PM3 semiempirical methods. The computer simulation confirms that the formation of these associates is energetically beneficial.

NOTICE OF RETRACTION: EXPERIMENTAL AND QUANTUM STUDIES ON ADSORPTION AND CORROSION INHIBITION EFFECT OF IMIDAZOLE DERIVATIVES ON N80 STEEL IN HYDROCHLORIC ACID

The inhibition effect of synthesized N′-(phenylmethylidene)-2-(2-methyl-1H-benzimidazol-1-yl)acetohydrazides, N′-(4-methylphenylmethylidene)-2-(2-methyl-1H-benzimidazol-1-yl)acetohydrazides, and N′-(4-methoxyphenylmethylidene)-2-(2-methyl-1H-benzimidazol-1-yl)acetohydrazides on the corrosion behaviour of N80 steel in 15% hydrochloric acid solution was investigated using weight loss, potentiostatic polarization and electrochemical impedance spectroscopy methods. The inhibition efficiency increased as the concentration of the inhibitors was increased. The effect of temperature on corrosion inhibition was investigated by weight loss method and thermodynamic parameters were calculated. Potentiodynamic polarization measurements show that all the three studied inhibitors act as mixed inhibitor. The adsorption of inhibitors on N80 steel surface obeys Langmuir adsorption isotherm. The structure of inhibitors was optimized using semiemperical AM1 method. Theoretical parameters such as the highest occupied molecular orbital (EHOMO), lowest unoccupied molecular orbital (ELUMO) energy levels, energy gap (ΔE = ELUMO - EHOMO), dipole moment (μ), global hardness (γ), softness (σ), binding energy, molecular surface area and the fraction of electrons transferred (ΔN) were calculated and the adsorption mechanism was discussed. Scanning electron microscopy was used to characterize the surface marphology of the N80 steel.

Synthesis and X-ray Studies of Novel Azaphenanthrenes

Two azaphenanthrenes were synthesised by a facile synthetic pathway and characterised by X-ray crystallography. Molecular packing of 4-(2,4-dichlorophenyl)-2-methoxy-5,6-dihydrobenzo[ h]quinoline-3-carbonitrile exhibits C–H…N and C–H…Cl hydrogen bonds in addition to intermolecular C–H…π, Cl…π and π…π (π-ring) stacking interactions. However, molecules of the 2-ethoxy derivative are linked into chains by one hydrogen bond of the C–H…N type and the crystal structure reveals an intermolecular C–H…π (π-ring) interaction. Computational studies by AM1, PM3, and density functional theory (DFT) techniques provide good approximations to the experimental X-ray data. The root mean square errors between the experimental and calculated bond lengths using AM1, PM3 and DFT methods for the 2-methoxy and 2-ethoxy derivatives are 0.0187, 0.0193, 0.0120 and 0.0197, 0.0195 and 0.0116 respectively.

Analysis of a Quantitative Relationship Between the Structure and Analgesic Activity of Meperidin Derivatives Using Semi-Empirical AM1 Method

<p>This research aims were to analize a quantitative relationship between the structure and analgesic activity of meperidine derivatives and to determine the Hansch equation between meperidine derivatives and their analgesic activity. The study was done by computer calculation (in sillico) using semiempirical method of AM1. The first stage was molecules modelling of meperidine derivative compounds, followed with performing the process of geometric optimization. The second step was to determine the descriptor value in the form of electronic, steric, and hydrophobic descriptors. The last stage was done by statistics analysis using multiple regressions with backward model. The results showed that analgesic activity was significantly influenced by variation of descriptors, especially electronic descriptor which has more dominant influence than steric and hydrophobic descriptors. The most influential descriptor is the charge on N atoms, since N atoms are an important component in analgesic compounds.</p>

Molecular Modeling of An Analog Of Curcumin Compounds Pentagamavunon-0 (PGV-0) And Pentagamavunon-1 (PGV-1) Through Computational Chemistry Methods Ab-Initio HF/4-31G

Breast cancer is the second largest number of cancer cases in Indonesia, after cervical cancer. The growth of these cancer cells can be prevented with compounds Pentagamavunon-0 (PGV-0) and Pentagamavunon-1 (PGV-1). This compound is an analog of curcumin compounds that have anti breast cancer activity. Modeling the structure of compound PGV-0 and PGV-1 through computational chemistry methods Ab-initio HF/4-31G could be used to predict the geometry and structure elucidation spectra associated with pharmacological activity such as anticancer compounds theoretically.This research involves modeling the structures and spectra prediction calculation compounds PGV-0 and PGV-1 by computational chemistry methods Ab-initio HF/4-31G, using Gaussian03W. The result using Ab-initio HF/4-31G method then compared with data from experimental geometry and the results of calculations with AM1.The results showed that computational chemistry methods Ab-initio HF/4-31G calculations give better results for modeling the structure compared semiempirik method AM1.

Extended Zinc AMBER Force Field (EZAFF).

An empirical approach based on the previously developed zinc AMBER force field (ZAFF) is proposed for the determination of the parameters for bonds and angles involving zinc. We call it the extended ZAFF (EZAFF) model because the original ZAFF model was only formulated for four-coordinated systems, while EZAFF additionally can tackle five- and six-coordinated systems. Tests were carried out for six metalloproteins and six organometallic compounds with different coordination spheres. Results validated the reliability of the current model to handle a variety of zinc containing complexes. Meanwhile, benchmark calculations were performed to assess the performance of three bonded molecular mechanics models (EZAFF, Seminario, and Z-matrix models), four nonbonded parameter sets (the HFE, IOD, CM, and 12-6-4 models), and four semiempirical quantum mechanical methods (AM1, PM3, PM6, and SCC-DFTB methods) for simulating zinc containing systems. The obtained results indicate that, even with their increased computational cost, the semiempirical quantum methods only offered slightly better accuracy for the computation of relative energies and only afforded similar molecular geometries, when compared to the investigated molecular mechanics models.

Ground and excited state dipole moments of some flavones using solvatochromic methods: An experimental and theoretical study

The absorption and fluorescence characteristics of biologically active flavone derivatives 6-Hydroxy-7,3′,4′,5′-tetramethoxyflavone (6HTMF) and 7-Hydroxy-6,3′,4′,5′-tetramethoxyflavone (7HTMF) are studied at room temperature (298 K) in solvents of different polarities. Excited state dipole moments of these compounds have been determined using the solvatochromic shift method based on the microscopic solvent polarity parameter ETN. Dipole moments in excited state were found to be higher than those in the ground state in both the molecules. A reasonable agreement has been observed between experimental and theoretically calculated dipole moments (using AM1 method). Slightly large value of ground and excited state dipole moments of 7HTMF than 6HTMF are in conformity with predicted electrostatic potential maps. Our results would be helpful in understanding use of these compounds as tunable dye lasers, optical brighteners and biosensors.

Quantitative Structure-Activity Relationship Analysis of Organophosphate Insecticides Using Electronic and Molecular Parameters

Quantitative Structure-Activity Relationship (QSAR) analysis of organophosphate derivatives, and their insecticide activities, was performed using electronic and molecular parameters. The series of organophosphate derivatives and their activities were obtained from literature. The semi-empirical AM1 method was used to model the structure of organophosphate derivatives and calculate the parameters of QSAR. Multiple linear regression (MLR) analysis was performed on the electronic and molecular parameters as well as the activities of the organophosphate insecticides to derive the QSAR model. The best QSAR equation model was used to design, in silico, new insecticide molecules of organophosphate derivatives with higher insecticidal activity. A new insecticide molecule, 4-(diethoxy phosphoryloxy) benzene sulfonic acid, -Log LD 50 = 7.344, had the highest insecticidal activity. Lastly, we recommend synthesizing and testing the new insecticide molecule further in the laboratory.

DETERMINATION OF THE DISSOCIATION CONSTANTS OF SOME p-SUBSTITUTED AROMATIC HYDRAZONES

A b s t r a c t: The acid-base behavior of five p-substituted aromatic hydrazones has been studied, using UV spectrophotometric method. The influence of the acidity of the medium on the absorption spectra is followed in aqueous sodium hydroxide solutions in pH region from 7 to 14. The measurements are performed at room temperature, and at ionic strength of 0.1, 0.25 and 0.5 mol dm–3. A batochromic shift of the absorption band that appears in neutral media is observed, when pH is up to 7. It suggests that the dissociation process of the amide and hydroxyl group takes place. Deprotonation enthalpies and total energy values are calculated by using the semiempirical methods AM1 and PM3. Using the changes in the UV spectra with pH of the solution, the determination of dissociation constants, pKBH, at three different ionic strengths, as well as, the thermodynamic dissociation constants at zero ionic strength, is performed. In order to obtain more precise results, the calculations are made from the absorbance values at four selected wavelengths. Furthermore, the pKBH values were determined graphically from the intercept of the dependence of logI on pH. The results showed that the numerically calculated pKBH values are identical to those graphically obtained.

MODELAGEM MOLECULAR DE COPOLÍMEROS ACEITADORES E DOADORES DE ELÉTRONS

Com a descoberta de que alguns polímeros poderiam conduzir eletricidade houve uma forte demanda por novos sistemas que pudessem reproduzir ou melhorar as propriedades de materiais metálicos, objetivando principalmente facilidade de síntese, menor custo, e leveza. Atualmente, mais de 85% da produção mundial de células fotovoltaicas envolve a utilização de silício cristalino. A introdução de novos materiais orgânicos com características doadoras e aceitadoras tem sido utilizada para melhorar as propriedades de gap dos materiais. Foram estudados teoricamente os copolímeros formados de benzotiadiazole, fluoreno e tiofeno com promissoras propriedades fotovoltaicas. As propriedades energéticas, estruturais, eletrônicas e ópticas foram obtidas com o método semi empírico AM1 e as propriedades ópticas foram obtidas com o método semi empírico ZINDO. Observa-se do estudo teórico que as propriedades eletrônicas e ópticas das moléculas melhoram quando combinados a molécula doadora e aceitadora de elétrons.

A combination of experiment and molecular simulation studies on a new metal-organic framework showing pH-triggered drug release

A new Co(II)-based complex { [Co2(L)(4,4'-Bipy)2] · CH3CN} n (I) (H4L = 5,5'-(biphenyl-4,4'- diyl-bis(methylene))bis(oxy)diisophthalic acid, 4,4'-Bipy = 4,4'-bipyridine) has been synthesized and structurally characterized. Single-crystal X-ray analysis (CIF file CCDC no. 1406388) reveals that compound I has 3D pcu topology. The incorporation of the drug 5-fluorouracil (5-FU) into the desolvated I was around 15.0 wt % of dehydrated I. Complex I also shows a pH-triggered controlled drug release property. In addition, we used semiempirical AM1 method to investigate the adsorption of 5-FU to I at the molecular level.

Effect of chain structure on hydrogen bonding in vinyl acetate – vinyl alcohol copolymers

FTIR spectroscopy and semi-empirical AM1 method are used to study hydrogen bonding in multiblock and random equimolar copolymers of vinyl acetate and vinyl alcohol. An energetically beneficial zip-holder complex, built on multiple inter- and intrachain hydroxyl-hydroxyl bonds and an intrachain hydroxyl-acetyloxy bond, can be formed between two vinyl alcohol sequences. As a result, multiblock copolymers reveal stronger degree of association that affects crystallinity, as well as various rheological and relaxation properties discussed in the literature. Macromolecular complexes in random copolymers are weak and tend to be destroyed in the presence of residual DMF solvent and adsorbed water. Nevertheless, a rather stable interchain quaternary complex can be formed that includes vinyl alcohol and vinyl acetate units and DMF and water molecules. For a single chain it is shown that an H-bond between neighboring vinyl alcohol and vinyl acetate monomer units mostly engages a carbonyl oxygen atom of the vinyl acetate, if the vinyl alcohol belongs to a short (<5 units) sequence, and an ether oxygen atom in the other case. On the whole, the quantum chemistry calculations shed much light on the origin of distinctions in the copolymer FTIR spectra, which may seem subtle when considered standalone.