Semiempirical AM1 Method Research Articles

Accurate prediction of enthalpy of formation combined with AM1 method and molecular descriptors

An error correction model is established by combining the experimental values and the calculated values obtained by the semi-empirical method AM1, and using the multiple stepwise regression (MSR) method on the training set to obtain five descriptors that have a large effect on the error term, and the linear equation of the correction model is derived. The test set is used to verify the reliability of the calibration model. In the training set, the new corrected regression model increased the square of the coefficient of determination (R2) from 0.688 to 0.966 and reduced the root mean square error (RMSE) from 98.563 to 27.249. In the test set, the R2 increased from 0.872 to 0.884, and the RMSE decreased from 43.337 to 37.736. It has good fitting ability and stability. According to the results of multiple stepwise regression, the main atomic structure that causes errors is 〉S==, which indicates that we should take the electrical environment of highly electronegative atoms into consideration, which can provide guidance for accurate calculation of thermodynamic properties.

Comparative Studies of Infrared Spectral Simulation of Some Benzoyl Derivatives of N-Heterocyclic Compounds Using Semi-Empirical Methods

Simulation studies based on ab initio, semi-empirical or density functional (DFT) calculations are now becoming common among the researchers who are pursuing their intereset in theoretical chemistry. These studies are based on quantum chemical softwares. These studies provide better insight for the structural and other parameters of the compounds. The present paper includes the studies on synthesis or procurement along with the simulated IR spectra of some benzoyl derivatives of N-heterocyclic compounds viz. 2-aminopyridine, 4-aminoantipyrine, 2-aminopyrimidine or 3-aminopyridine using four different AM1, PM3, MNDO and ZINDO1 semi-empirical methods. Among the methods used for the study, AM1 method is more reliable and more accurate so far as the prediction of spectral results is concerned.

Quantitative structure activity relationship (qsar) study and biological evaluation on mono-ketone analogs of curcumin as antioxidant

The objective of this study was to design new mono-ketone analogs of curcumin and determine its lipid peroxidation inhibition. Molecular modeling studies were carried out by using the semi-empirical quantum chemical algorithm AM-1 method in MOE 2018.01.01 software. Build QSAR was used to generate an equation model that will be used to design new mono-ketone analogs of curcumin. Synthesis of new compounds produced from an aldol condensation reaction. Thiobarbituric acid reactive substance (TBARS) method was used to determine antioxidant activity by measuring lipid peroxide concentration. Promising predictions values of lipid peroxidation the QSAR study obtained inhibitory activity. The in vitro lipid peroxidation inhibition of 2,6-bis-(3’-ethoxy, 4’-hydroxybenzylidene)-cyclohexanone; 2,6-bis-(3’-Bromo,4’-methoxybenzylidene)-cyclohexanone; and 2,6-bis-(3’,4’-dimethoxybenzylidene)-cyclohexanone indicates good inhibitory with IC50 values of 2.95; 0.95; and 2.45μM respectively. The new mono-ketone analogs of curcumin compound from the QSAR study has been shown to have antioxidant activity by inhibiting lipid peroxidation by scavenging free radicals.

UV Spectrophotometric Determination of Thermodynamic Dissociation Constants of Some Aromatic Hydrazones in Acid Media

The spectral behavior of some p-nitro-p-substituted benzoylhydrazones in the perchloric acid media was followed, applying the UV spectroscopy. The position of the absorption maximum in the spectra was defined in acidic media and the electronic transitions were discussed, as well (7<pH<1). The equilibrium between neutral and protonated form was investigated in the ethanol-water (V/V, 1:1) solutions. The observed changes in the UV spectra suggested that protonation process took place in one step. The pH region of protonation ranges between 1.4 and 2.9. Using the changes in the UV spectra which appear as a result of the protonation reaction the stoichiometric dissociation constants were determined numerically (pKBH+ = n·pH + logI) and graphically (intercept of the dependence of logI on pH). Thermodynamic dissociation constants were estimated as an intercept of dependence of pKBH+ on square root of the ionic strength. In order to achieve that, measurements were performed at different ionic strengths: 0.1, 0.25 and 0.5 mol/dm3, adjusted with sodium perchlorate. The obtained thermodynamic pKBH+ values ranged between 2.07 and 2.58. In order to predict proton transfer at a given pH, semiempirical methods AM1 and PM3 were applied. The influence of the substituents present in the p-position of the benzene ring on pKBH+ values of investigated hydrazones was discussed, too. Total energy, binding energy, enthalpy of formation, Gibbs energies of formation, atomic charge and proton affinity values were used to predict protonation site in hydrazone molecule. Furthermore, the stability and the proton affinity of the isomers (E and Z) in which hydrazones exist and their protonated forms were defined.

Microwave Assisted Synthesis Characterization and Study of Some Novel Chalcones Compounds Derived From Mefenamic Acid

New chalcones compounds were synthesis by reaction mefenamyl chloride with P-aminoacetophenone to from N–(4-acetyl phenyl)-2-(2/3- dimethyl phenyl) amino benzamide(A). The chalcones produced by Claisen – Schmidt condensation of compound A with substituted benzaldehydes [(2,4-dihydroxy(1), 3-NH2(2) and 4- OMe (3)] in ethanollic KOH solvent by using microwave irradiation. The new compounds were characterized by M.P, TLC, CHN, FT-IR, 1HNMR and 13CNMR. The biological screening data of the synthesized compounds were also presented. The theoretical study by using AM1 semi-empirical method emphasizes these compounds exists as trans configuration.

Simulation of the Adsorption of Polychlorinated Aromatic Hydrocarbons on Graphitized Thermal Carbon Black for Predicting Chromatographic Retention Values

The adsorption of polychlorinated aromatic hydrocarbons on graphitized thermal carbon black was simulated by a molecular-statistical method. The results of calculations were compared with data on chromatographic retention under gas chromatography conditions. A version that took into account the conformational flexibility of molecules was used for polychlorinated biphenyls. Different computational chemistry methods (classical molecular dynamics and semiempirical quantum methods) for evaluating the internal energy of a molecule were considered. It was found that the use of a molecular-statistical method and the AM1 semiempirical method for estimating the internal energy of molecules makes it possible to correctly predict the order of elution of isomeric dichlorobiphenyls. It was demonstrated that this approach can be used to confirm the assignment of peaks in a chromatogram to particular isomers.

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.

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.

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.

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.

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>

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.

Retention prediction of low molecular weight anions in ion chromatography based on quantitative structure-retention relationships applied to the linear solvent strength model

Quantitative Structure-Retention Relationships (QSRRs) represent a popular technique to predict the retention times of analytes, based on molecular descriptors encoding the chemical structures of the analytes. The linear solvent strength (LSS) model relating the retention factor, k to the eluent concentration (log k=a−blog [eluent]), is a well-known and accurate retention model in ion chromatography (IC). In this work, QSRRs for inorganic and small organic anions were used to predict the regression parameters a and b in the LSS model (and hence retention times) for these analytes under a wide range of eluent conditions, based solely on their chemical structures. This approach was performed on retention data of inorganic and small organic anions from the “Virtual Column” software (Thermo Fisher Scientific). These retention data were recalibrated via a “porting” methodology on three columns (AS20, AS19, and AS11HC), prior to the QSRR modeling. This provided retention data more applicable on recently produced columns which may exhibit changes of column behavior due to batch-to-batch variability. Molecular descriptors for the analytes were calculated with Dragon software using the geometry-optimized molecular structures, employing the AM1 semi-empirical method. An optimal subset of molecular descriptors was then selected using an evolutionary algorithm (EA). Finally, the QSRR models were generated by multiple linear regression (MLR). As a result, six QSRR models with good predictive performance were successfully derived for a- and b-values on three columns (R2>0.98 and RMSE<0.11). External validation showed the possibility of using the developed QSRR models as predictive tools in IC (Qext(F3)2>0.7 and RMSEP<0.4). Moreover, it was demonstrated that the obtained QSRR models for the a- and b-values can predict the retention times for new analytes with good accuracy and predictability (R2 of 0.98, RMSE of 0.89min, Qext(F3)2 of 0.96 and RMSEP of 1.18min).

A BOX-MODEL APPROACH TO MOLECULAR SHAPE

In this work, using the length-width-height ratios of a rectangular box in which the molecule under study is enclosed, two descriptors for the characterization of molecular shape are introduced. The molecular shape analysis of the set of molecules under study is facilitated by the introduction of a diagram where the extreme cases (i.e. cubic-box, prolate-box and oblate-box) are clearly located. The method is illustrated by the analysis of fifty molecules including normal alkanes, acenes, alkynes, oblate molecules and the eighteen octane isomers. The geometry of each molecule was optimized by AM1 semiempirical method, and van der Waals molecular surface was used to define the molecular shape contour. The length, the width, and the height of the enclosing box were extracted using VEGA ZZ software. A regular behaviour of the shape descriptors for homologous series was observed. Finally, using the present descriptors, a molecular shape similarity analysis of the octane isomer molecules was included.

Study of Ribavirin–Nucleic Acids Interaction

The UV–Vis absorption spectra of ribavirin in the absence and presence of calf thymus DNA are presented and discussed in this paper. The molecular structure of ribavirin was investigated by the semiempirical AM1 method, which triggered two polymorphic modifications of the antiviral drug also reported in the literature. Our experimental results point out two types of the binding. The first type involves a non-electrostatic (internal) binding, consisting of the intercalation of drug between the nitrogenous bases of nucleic acid. The second type (an external binding) involves the drug binding to the nucleic acid grooves. In addition, the binding constant of the second process has an order of magnitude greater than the binding constant for the first process, calculated by the Benesi–Hildebrand, Scott, and Scatchard methods, which supposes a 1:1 binding ratio. Also, the interactions of two polymorphic modifications of ribavirin (V1 and V2) with nucleic acids by the molecular mechanic and semiempirical AM1 methods were analyzed. The experimental data pointed out that in the ribavirin–nucleic acid complexes, the 1,2,4-triazole-3-carboxamide chromophore is intercalated between the bases of the nucleic acid sequences, the carboxamidic group is set outside of the nucleic acid sequence toward the major groove, and the 2-hydroxymethyl-tetrahydrofuran-3,4-diol fragment is located in the minor groove. In order to stress the sequence specificity of ribavirin, different models of the nucleic acid sequences containing adenine (A), thymine (T), cytosine (C), and guanine (G) in AAAAAA, TTTTTT, CCCCCC, GGGGGG, ATATAT, CGCGCG, ATCGAT, and CGATCG were used. The theoretical results outline the differences in the contributions of the electrostatic and van der Waals interactions to the total binding energy and the preference of ribavirin for the binding at the sequences of nucleic acids containing adenine and thymine bases.