Semiempirical Calculation Method Research Articles

Determination of Relative Counterion Binding Constant to Cationic Micelles.

The efficiency of counterion affinity towards ionic micelles is often described in terms of the degree of counterion binding (β X ) to ionic micelles or the conventional ion-exchange constant ([Formula: see text]) or relative binding constant ([Formula: see text]) of X - and Br- counterions. This review describes the use of ionized phenyl salicylate ions, PSa-, as a new probe to determine [Formula: see text] values using a semiempirical spectrophotometric method. The value of [Formula: see text] is found to be comparable to reported values obtained using different probes by the semiempirical kinetic method as well as different physical methods. Application of semiempirical methods for calculation of [Formula: see text] or [Formula: see text] values involves an inherent assumption that these values are independent of the physicochemical characteristics of the probe molecule.

Changes in diad sequence distribution by preferential chain scission during the thermal hydrolysis of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate)

Specific hydrolysis properties of microbial copolyester P(3HB-co-6%-3HHx) was found during super-heated steam treatment in a temperature range of 130–190 °C. From changes in diad sequences on 13C nuclear magnetic resonance spectra, preferential and suppressive chain scission of HHx*HB and HB*HHx sequences, respectively, were determined. These specific reaction properties were considered to be contributed by higher steric propyl group in HHx unit than methyl group in HB unit, that is, promoting effect due to the concentration of HHx units in amorphous regions and suppressive effect due to steric hindrance and hydrophobicity of propyl group. Further, it was validated by the lowest-unoccupied molecular orbital analysis using a semi-empirical molecular orbital calculation method.

Statistical Analysis of the Impact of Molecular Descriptors on Cytotoxicity of Thiourea Derivatives Incorporating 2-Aminothiazole Scaffold.

Chemical reactivity descriptors and lipophilicyty (log P) were evaluated via semi-empirical method for the quantum calculation of molecular electronic structure (PM3) in order to clarify the structure-cytotoxic activity relationships of disubstutited thioureas. Analysed compounds were obtained by the linkage of 2-aminothiazole ring, thiourea and substituted phenyl ring. The detailed examination was carried out to establish correlation between descriptors and cytotoxic activity against the MT-4 cells for 11 compounds. For the most active compounds (6 compounds) cytotoxic activity against three cancer cell lines (CCRF-CEM, WIL-2NS, CCRF-SB) and normal human cell (HaCaT) was determined. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction and lactate dehydrogenase (LDH) release were assessed. Regression analysis revealed that electrophilicity index and chemical potential significantly contributed to expain the thioureas cytotoxic potential.

Calculation of the rate of constrained precipitation of monodisperse solid particles

In this paper, the authors derived generalized formula for calculating of the ratio of the rate of constrained precipitation to the rate of free precipitation for monodisperse particles of arbitrary shape based on analysis of known empirical relationships and semi-empirical method of calculation.

Multivariate Modeling of Cytochrome P450 Enzymes for 4- Aminoquinoline Antimalarial Analogues using Genetic- Algorithms Multiple Linear Regression

Purpose: To develop QSAR modeling of the inhibition of cytochrome P450s (CYPs) by chloroquine and a new series of 4-aminoquinoline derivatives in order to obtain a set of predictive in-silico models using genetic algorithms-multiple linear regression (GA-MLR) methods. Methods: Austin model 1 (AM1) semi-empirical quantum chemical calculation method was used to find the optimum 3D geometry of the studied molecules. The relevant molecular descriptors were selected by genetic algorithm-based multiple linear regression (GA-MLR) approach. In silico predictive models were generated to predict the inhibition of CYP 2B6, 2C9, 2C19, 2D6, and 3A4 isoforms using a set of descriptors. Results: The results obtained demonstrate that our model is capable of predicting the potential of new drug candidates to inhibit multiple CYP isoforms. A cross-validated Q 2 test and external validation showed that the models were robust. By inspection of R 2 pred , and RMSE test sets, it can be seen that the predictive ability of the different CYP models varies considerably. Conclusion : Apart from insights into important molecular properties for CYP inhibition, the findings may also guide further investigations of novel drug candidates that are unlikely to inhibit multiple CYP sub-types. Keywords : Antimalarial, Chloroquine, Cytochrome P450, Genetic algorithm-based multiple linear regression, QSAR.

Sources of PM in an Industrial Area: Comparison between Receptor Model Results and Semiempirical Calculations of Source Contributions

Source apportionment of PM_(10) and PM_(2.5) samples collected in an industrial area of the Po Valley was performed by using the Positive Matrix Factorization (PMF) model and a semiempirical calculation of five macro-source contributions. Samples were collected during four monitoring periods, January-February 2011, June 2012, January-February 2012, May-June 2012, resulting in a total of 720 samples (360 for PM_(10) and 360 for PM_(2.5)). PMF variables included major elements, ions, elemental carbon and organic compounds and minor and trace elements. In order to increase the selectivity of minor and trace elements as source tracers, a chemical fractionation methodology based on the elemental solubility was employed; it was thus possible to include the extractable, the residual or both thefractions of the minor and trace elements in the database. PMF resolved six factors for PM_(10) (crustal matter, marine aerosol, industry, secondary/oil combustion, secondary nitrate/biomass burning/exhaust particles, brake/tyre wear/re-suspended road dust) and seven factors for PM_(2.5) (crustal matter, marine aerosol, industry, secondary nitrate, biomass burning, other secondary components, secondary sulphate/oil combustion). Mixing properties of the lower atmosphere were monitored by using natural radioactivity. The lack in the separation of some sources was shown to be due to their co-variation during periods of high atmospheric stability in the cold months. Seasonal variations of the source contributions were evaluated and discussed. PMF results were compared with those obtained by a semiempirical calculation method in which analytical results are grouped into five macro-sources (crustal matter, marine aerosol, secondary inorganic compounds, combustion products from vehicular emissions and organics). Although similar trends in the temporal variation of the main PM sources were obtained, the absolute magnitude of the concentrations varied in some cases, especially for crustal matter and marine aerosol sources.

A Novel Method for Limiting Current Calculation in Electrodialysis Modules

The purpose of this work was to develop a novel semi-empirical method for calculation of limiting currents in electrodialysis modules. Experiments were carried out at pilot-scale module with five electrolytes. Current-voltage curves were measured and limiting currents were determined. Subsequently, dependence of the mass transfer coefficient on linear flow velocity was evaluated and its parameters a, b were estimated. The main advance of this work is that comparison of electrolytes showed the clear relationship between parameter a, electrolyte diffusion coefficient and the difference of cation transport numbers in membrane and solution. The semi-empirical relationship between the mass transfer coefficient and linear flow velocity was set up, and the limiting current calculation run was proposed. At the same time, dependence of the diffusion layer thickness on linear flow velocity was examined and the way of its calculation was established. The proposed method is unique thanks to its applicability in a broad range of experimental conditions; its use is not limited neither by electrolyte type nor electrodialysis module size.

Research for the adjustable performance of the thermal vapor compressor in the MED–TVC system

As the expansion in the desalination industry, multiple-effect distillation (MED) with thermal vapour compression (TVC) system becomes more attractive than other thermal systems due to effectiveness, easier operation and maintenance, and good economic characteristics and is expected to take a considerable portion in the desalination field in the near future. The TVC is an essential part that governs the overall process in the MED–TVC system. The flow and heat transfer in the TVC is very complex due to the strong compressibility and supersonic turbulent flow of the stream. In this paper, based on gas-dynamic theory, a kind of semi-empirical calculation method of ejector, including calculation of the design point and variable operating condition of ejector, has been presented. The model gives the variation of the performance of the ejector as a function of the discharge pressure for different area values of throat and provides a foundation for the research for the performance of the adjustable ejector under variation condition. Furthermore, the necessity for the utilization of the adjustable TVC in the MED–TVC system and the performance for the adjustable TVC have been researched.

Theoretical investigation of the Cl and CH3 substitutions effect on structural and energy behavior of benzodiazepine

In this study, heat energy, atomic charges and dipole moments permit qualitative predictions about the substituent effects by a chlorine or methyl group on the benzodiazepine properties in the ground state. AM1 and MNDO semi-empirical methods of calculation are used to obtain information on the structural and energy properties for some benzodiazepine derivatives.

Assembly and organization of poly(3-hexylthiophene) brushes and their potential use as novel anode buffer layers for organic photovoltaics

Buffer layers that control electrochemical reactions and physical interactions at electrode/film interfaces are key components of an organic photovoltaic cell. Here the structure and properties of layers of semi-rigid poly(3-hexylthiophene) (P3HT) chains tethered at a surface are investigated, and these functional systems are applied in an organic photovoltaic device. Areal density of P3HT chains is readily tuned through the choice of polymer molecular weight and annealing conditions, and insights from optical absorption spectroscopy and semiempirical quantum calculation methods suggest that tethering causes intrachain defects that affect co-facial π-stacking of brush chains. Because of their ability to modify oxide surfaces, P3HT brushes are utilized as an anode buffer layer in a P3HT-PCBM (phenyl-C₆₁-butyric acid methyl ester) bulk heterojunction device. Current-voltage characterization shows a significant enhancement in short circuit current, suggesting the potential of these novel nanostructured buffer layers to replace the PEDOT:PSS buffer layer typically applied in traditional P3HT-PCBM solar cells.

Antimicrobial, anti-inflammatory, and antinociceptive activities of triazole, pyrazole, oxadiazine, oxadiazole, and sugar hydrazone-5-nitroindoline-2-one derivatives and a study of their computational chemistry ( part II)

Objective The aim of this study (part II) is to evaluate the antibacterial, anti-inflammatory, and antinociceptive activities of a series of 1H-1,2,4-triazol-3-yl)phenylimino)(methylbenzyl)-5-nitroindolin-2-ones, 1H-pyrazole-1-carbonyl)phenylimino)-1-(p-methylbenzyl)-5-nitroindolin-2-ones, 3-(4-(1,3,4-oxadizine-6-one)phenylimino)-1-(p-methylbenzyl)-5-nitroindolin-2-ones, 1,3,4-oxadiazol-2-yl)phenylimino)-1-(p-methylbenzyl)-5-nitroindolin-2-ones and 4-(-1-(p-methylbenzyl)-5-nitro-2-oxoindolin-3-ylideneamino) sugar hydrazone derivatives (1–13) and, in addition, to investigate their computational chemistry. Methods The synthesized compounds in (part I) 1–9 were evaluated for their antibacterial and antifungal activities using different strains of Gram-positive bacteria (Bacillus subtilis), Gram-negative bacteria (Pseudomonas aeruginosa), yeast (Candida albicans), and four mold fungi (Fusarium solani, Aspergillus niger, Colletotrichum gloeosporioides, and Phomopsis obscurans). The anti-inflammatory and antinociceptive activities of compounds 1–13 were evaluated using a hot-plate test, acetic acid-induced writhing in mice, formalin-induced nociception, a tail immersion test, and carrageenan-induced hind paw edema. For computational chemistry, a semiempirical MNDO method (Modified Neglect of Differential Overlap is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry) associated with HyperChem professional 7.5 programs was adapted. Results and conclusion Compounds 4-[(1-(p-methylbenzyl)-5-nitro-2-oxoindolin-3-ylideneamino)] benzohydrazide (3) and 3-(4-(5-methyl-1,3,4-oxadiazol-2-yl)phenylimino)-1-(p-methylbenzyl)-5-nitroindolin-2-one (9) showed the highest antibacterial and antifungal activities compared with clotrimazole and sulfamethoxazole as reference drugs. In contrast, compounds ethyl 4-(5-nitro-2-oxoindolin-3-ylideneamino) benzoate (1), 3-(4-(3-methyl-5-oxo-4,5-dihydro-1H-pyrazole-1-carbonyl) phenylimino)-1-(p-methylbenzyl)-5-nitroindolin-2-one (8), D-glucose-4-(-1-(p-methylbenzyl)-5-nitro-2-oxoindolin-3-ylideneamino) hydrazone derivative (10), and D-arabinose-4-(-1-(p-methylbenzyl)-5-nitro-2-oxoindolin-3-ylideneamino) hydrazone derivative (12) showed significantly high anti-inflammatory and antinociceptive activities when compared with indomethacin and morphine as reference drugs. From the computational chemistry compounds, ethyl 4-(5-nitro-2-oxoindolin-3-ylideneamino) benzoate (1), ethyl 4-[(1-(p-methylbenzyl)-5-nitro-2-oxoindolin-3-ylideneamino)] benzoate (2), and 4-[(1-(p-methylbenzyl)-5-nitro-2-oxoindolin-3-ylideneamino)] benzohydrazide (3) yielded the lowest values of total energy and heat of formation, and had higher stability than other molecules.

Settlement Calculation and Analysis of Ground Improved by Dynamic Compaction at RSGT Project

Red Sea coral reefs in Saudi Arabia were dredged and reclaimed firstly, and then were treated by dynamic compaction as non-cohesive soil ground. Consolidated condition of improved ground within different depth is in different. Calculating settlements for different state ground should consider actual condition. Several semi-theoretical and semi-empirical settlement calculation methods mainly including Terzaghi’s method(1996), Teng’s method(1969), Meyerhof’s method（1956）are applied and analyzed to investigate the actual condition of improved ground according to the RSGT project test results, and the differences are proposed among these three methods.

Settlement Calculation and Analysis of Ground Improved by Dynamic Compaction at RSGT Project

Red Sea coral reefs in Saudi Arabia were dredged and reclaimed firstly, and then were treated by dynamic compaction as non-cohesive soil ground. Consolidated condition of improved ground within different depth is in different. Calculating settlements for different state ground should consider actual condition. Several semi-theoretical and semi-empirical settlement calculation methods mainly including Terzaghi’s method(1996), Teng’s method(1969), Meyerhof’s method（1956）are applied and analyzed to investigate the actual condition of improved ground according to the RSGT project test results, and the differences are proposed among these three methods.

Quantitative Structure-Activity Relationship Analysis of the Anticonvulsant Activity of Some Benzylacetamides Based on Genetic Algorithm-Based Multiple Linear Regression

Purpose: To develop the quantitative structure-activity relationship (QSAR) for predicting the anticonvulsant activity of α-substituted acetamido-N-benzylacetamide derivatives.Methods: AM1 semiempirical quantum chemical calculation method was used to find the optimum 3D geometry of the studied molecules. Two types of molecular descriptors, including the 2D autocorrelation and GETAWAY descriptors, were used to derive a quantitative relation between anticonvulsant activity and structural properties. The relevant molecular descriptors were selected by genetic algorithm-based multiple linear regression (GA-MLR) approach.Results: The high value of the correlation coefficient, R2 (0.900), indicate that the model was satisfactory.Conclusion: The proposed model has good stability, robustness and predictability when verified by internal and external validation.Keywords: Anticonvulsant, Benzylacetamides, 2D Autocorrelation, Quantitative structure-activity relationships, Multiple linear regression.

Hydrophobicity of Peptides Containing D‐Amino Acids

Several types of L-amino acid residues (Ser, Asp) in proteins are sometimes converted to D-amino acid residues by posttranslational isomerization. This phenomenon leads to an increase in hydrophobicity and results in their deposition from aqueous media. This research involves the hydrophobicity of oligopeptides containing D-amino acid residues, which may be generated by posttranslational isomerization (racemization or epimerization), to clarify the relationship between normal peptide residues composed of L-amino acids and the peptides containing D-amino acid residues. Calculated log P (log P(calc), where P is the octan-1-ol/H(2)O partition coefficient) values for many amino acids and oligopeptide diastereoisomers have been obtained by a semiempirical calculation method based on the PM5 Hamiltonian and compared with the experimental values (log P(exp)) reported in the literatures. A linear correlation was found between log P(calc) and log P(exp) except for basic and aromatic amino acids, and peptides. Calculations on homo-oligopeptide diastereoisomers composed of alanine, valine, leucine, and aspartic acid showed differences in log P(calc) values between diastereoisomers. Pentapeptides containing Asp residues that are most racemized or even inverted in alpha A-crystallin were also calculated to show that log P(calc) values of pentapeptides differ depending on the configuration (D or L) and kinds of linkage (alpha or beta) to their C-terminal amino acid residues.

Semi-empirical calculation of quenching factors for ions in scintillators

Semi-empirical method of calculation of quenching factors for scintillators is described. It is based on classical Birks formula with the total stopping powers for electrons and ions which are calculated with the ESTAR and SRIM codes, respectively. Method has only one fitting parameter (the Birks factor kB) which can have different values for the same material in different conditions of measurements and data treatment. A hypothesis is used that, once the kB value is obtained by fitting data for particles of one kind and in some energy region (e.g. for a few MeV α particles from internal contamination of a detector), it can be applied to calculate quenching factors for particles of another kind and for another energies (e.g. for low energy nuclear recoils) if all data are measured in the same experimental conditions and are treated in the same way. Applicability of the method is demonstrated on many examples including materials with different mechanisms of scintillation: organic scintillators (solid C 8 H 8 , and liquid C 16 H 18 , C 9 H 12 ); crystal scintillators (pure CdWO 4 , PbWO 4 , ZnWO 4 , CaWO 4 , CeF 3 , and doped CaF 2 (Eu), CsI(Tl), CsI(Na), NaI(Tl)); liquid noble gases (LXe). Estimations of quenching factors for nuclear recoils are also given for some scintillators where experimental data are absent ( CdWO 4 , PbWO 4 , CeF 3 , Bi 4 Ge 3 O 12 , LiF, ZnSe).

A semi-empirical method for calculation of true coincidence corrections for the case of a close-in detection in γ-ray spectrometry

In this paper, a semi-empirical method is proposed to determine true coincidence-summing (TCS) correction factors for high resolution γ-ray spectrometry. It needs the knowledge of both full energy peak (FEP) efficiency and total-to-peak (TTP) efficiency curves. The TTP efficiency curve is established from the measurements with a set of coincidence-free point sources. Whereas for a volume source, the coincidence-free FEP efficiency curve is obtained iteratively by using the peaks from almost the coincidence-free nuclides and those from the coincident nuclides in the mixed standard sources. Then the fitting parameters obtained for both TTP and FEP efficiency curves are combined in a freely-available TCS calculation program called TrueCoinc, which yields the TCS correction factors required for any nuclide. As an application, the TCS correction factors were determined for the particular peaks of 238U, 226Ra and 232Th in the reference materials, measured in the case of a close-in detection geometry using a well-type Ge detector. The present TCS correction method can be applied without difficulty to all Ge detectors for any coincident nuclide.

Determination of the effective nuclear charge for free ions of transition metals from experimental spectra

The refined set of values of the effective nuclear charge ( $$ \bar Z_{ef} $$ ) and the set of one-electron spin-orbital constants (ξ 3 teor ) are obtained for ions of transition metals with the help of a semiempirical method of calculation of the spectrum of free ions with allowance for the spin-orbital interaction. The effective nuclear charge, which is a variable theoretical parameter, was determined from a comparison of theoretically calculated ion absorption spectra with experimental ones. The form of the potential for the calculation of the spin-orbital constant was chosen such that the calculated value ξ 3 teor would coincide with the experimental one ξ 3 exp . The calculated set of values $$ \bar Z_{ef} $$ , ξ 3 teor } can be used in semiempirical calculations of energy levels of 3d ions (ions with an incomplete 3d shell).

Partial Charge Calculation Method Affects CoMFA QSAR Prediction Accuracy

The 3D-QSAR method comparative molecular field analysis (CoMFA) involves the estimation of atomic partial charges as part of the process of calculating molecular electrostatic fields. Using 30 data sets from the literature the effect of using different common partial charge calculation methods on the predictivity (cross-validated R2) of CoMFA was studied. The partial charge methods ranged from the popular Gasteiger and the newer MMFF94 electronegativity equalization methods, to the more complex and computationally expensive semiempirical charges AM1, MNDO, and PM3. The MMFF94 and semiempirical MNDO, AM1, and PM3 methods for computing charges were found to result in statistically significantly more predictive CoMFA models than the Gasteiger charges. Although there was a trend toward the semiempirical charges performing better than the MMFF94 charges, the difference was not statistically significant. Thus, semiempirical partial charge calculation methods are suggested for the most predictive CoMFA models, but the MMFF94 charge calculation method is a very good alternative if semiempirical methods are not available or faster calculation speed is important.

IINS, MIR, and DFT Investigations of Vibrational Spectra of 3, 3-Dimethyl-1-Butanol and 3, 3-Dimethyl-2-Butanol

Molecular vibrational spectra in 3,3-dimethyl-1-butanol, (CH3)3CCH2CH2OH, and 3,3-dimethyl-2-butanol, (CH3)3CCHOHCH3, were measured by the inelastic incoherent neutron scattering and mid infrared spectroscopy and for 3,3-dimethyl-2-butanol additionally by the far infrared absorption method. Experimental results were discussed and compared with the results of the quantum chemical calculations performed by the density functional theory (DFT/B3LYP/6-311G∗∗) and semi-empirical PM3 calculation methods assuming the isolated molecule approximation.