Comparative molecular field analysis of artemisinin derivatives: Ab initio versus semiempirical optimized structures

Based on the belief that structural optimization methods, producing structures more closely to the experimental ones, should give better, i.e. more relevant, steric fields and hence more predictive CoMFA models, comparative molecular field analyses of artemisinin derivatives were performed based on semiempirical AM1 and HF/3-21G optimized geometries. Using these optimized geometries, the CoMFA results derived from the HF/3-21G method are found to be usually but not drastically better than those from AM1. Additional calculations were performed to investigate the electrostatic field difference using the Gasteiger and Marsili charges, the electrostatic potential fit charges at the AM1 level, and the natural population analysis charges at the HF/3-21G level of theory. For the HF/3-21G optimized structures no difference in predictability was observed, whereas for AM1 optimized structures such differences were found. Interestingly, if ionic compounds are omitted, differences between the various HF/3-21G optimized structure models using these electrostatic fields were found.     

Steric and electrostatic effects in dye-cellulose interactions by the MTD and CoMFA approaches

This paper presents the application of the MTD (minimal steric difference) analysis and CoMFA (comparative molecular field analysis) to series of anthraquinone vat, mono and disazo and disperses dyes with known affinities for cellulose fiber. A comparison of the results demonstrates that these methods usually agree with the prediction of structural features favorable for dyeing. A series of n = 49 anthraquinone vat dyes was studied by MTD with r2 between 0.903 and 0.941 and r2CV values in the range of 0.827-0.878. For CoMFA, r2 = 0.992, r2CV = 0.841 were obtained; the CoMFA field is in rather good agreement with vertex attributions, by MTD for attractive and repulsive vertices. Anionic disazo dyes were studied by the CoMFA method (n = 21, r2 = 0.999, r2CV = 0.703). Monoazo dyes (several series) were studied by CoMFA and MTD. The effect of lipophilicity on dye fiber affinity was, also, studied for these dyes. Disperse dye adsorption was analyzed by MTD and CoMFA (n = 27, r2 = 0.925, r2CV = 0.776). Conclusions refer to the effect of structural features of dye molecules upon adsorption on cellulose fibers.     

Steric and electrostatic effects in dye-cellulose interactions by the MTD and CoMFA approaches

This paper presents the application of the MTD (minimal steric difference) analysis and CoMFA (comparative molecular field analysis) to series of anthraquinone vat, mono and disazo and disperses dyes with known affinities for cellulose fiber. A comparison of the results demonstrates that these methods usually agree with the prediction of structural features favorable for dyeing. A series of n =49 anthraquinone vat dyes was studied by MTD with r 2 between 0.903 and 0.941 and r CV 2 values in the range of 0.827-0.878. For CoMFA, r 2 =0.992, r CV 2 =0.841 were obtained; the CoMFA field is in rather good agreement with vertex attributions, by MTD for attractive and repulsive vertices. Anionic disazo dyes were studied by the CoMFA method ( n =21, r 2 =0.999, r CV 2 =0.703). Monoazo dyes (several series) were studied by CoMFA and MTD. The effect of lipophilicity on dye fiber affinity was, also, studied for these dyes. Disperse dye adsorption was analyzed by MTD and CoMFA ( n =27, r 2 =0.925, r CV 2 =0.776). Conclusions refer to the effect of structural features of dye molecules upon adsorption on cellulose fibers.     

镍铁类水滑石对偶氮阴离子染料的吸附脱色作用

采用镍铁类水滑石作为吸附剂,对偶氮阴离子染料酸性大红G、活性艳红X-3B和直接耐酸大红4BS废水进行脱色处理,研究了时间、镍与铁的物质的量之比、初始pH和无机电解质添加剂等因素对脱色率的影响,并结合红外光谱和X射线衍射分析结果讨论了其吸附脱色机理.结果表明,三种染料在镍铁类水滑石上的吸附均为层间的阴离子交换吸附和外表面的吸附.通过阴离子交换进入层间后,不同于直接耐酸大红4BS阴离子,酸性大红G和活性艳红X-3B两种阴离子与水滑石层间水分子之间产生氢键作用;在化学键合过程中,染料分子被镍铁类水滑石表面Fe3+氧化,同时偶氮键断裂导致脱色.     

A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands

The Comparative Molecular Field Analysis (CoMFA) was developed to investigate a three-dimensional quantitative structure activity relationship (3D-QSAR) model of ligands for the sigma 1 receptor. The starting geometry of sigma-1 receptor ligands was obtained from the Tripos force field minimizations and conformations were decided from DISCOtech using the SYBYL 6.8. program. The structures of 48 molecules were fully optimized at the ab initio HF/3-21G* and semiempirical AM1 calculations using GAUSSIAN 98. The electrostatic charges were calculated using several methods such as semiempirical AM1, density functional B3LYP/3-21G*, and ab initio HF/3-21G*, MP2/3-21G* calculations within GAUSSIAN 98. Using the optimized geometries, the CoMFA results derived from the HF/3-21G method were better than those from AM1. The best CoMFA was obtained from HF/3-21G* optimized geometry and charges (R2 = 0.977). Using the optimized geometries, the CoMFA results derived from the HF/3-21G methods were better than those from AM1 calculations. The training set of 43 molecules gave higher R2 (0.989-0.977) from HF/3-21G* optimized geometries than R2 (0.966-0.911) values from AM1 optimized geometries. The test set of five molecules also suggested that HF/3-21G* optimized geometries produced good CoMFA models to predict bioactivity of sigma 1 receptor ligands but AM1 optimized geometries failed to predict reasonable bioactivity of sigma 1 receptor ligands using different calculations for atomic charges.     

Synthesis of azobenzenes: the coloured pieces of molecular materials

Azobenzenes are ubiquitous motifs very important in many areas of science. Azo compounds display crucial properties for important applications, mainly for the chemical industry. Because of their discovery, the main application of aromatic azo compounds has been their use as dyes. These compounds are excellent candidates to function as molecular switches because of their efficient cis-trans isomerization in the presence of appropriate radiation. The classical methods for the synthesis of azo compounds are the azo coupling reaction (coupling of diazonium salts with activated aromatic compounds), the Mills reaction (reaction between aromatic nitroso derivatives and anilines) and the Wallach reaction (transformation of azoxybenzenes into 4-hydroxy substituted azoderivatives in acid media). More recently, other preparative methods have been reported. This critical review covers the various synthetic methods reported on azo compounds with special emphasis on the more recent ones and their mechanistic aspects (170 references).     

Mapping the binding site of a large set of quinazoline type EGF-R inhibitors using molecular field analyses and molecular docking studies

In the current work, three-dimensional QSAR studies for one large set of quinazoline type epidermal growth factor receptor (EGF-R) inhibitors were conducted using two types of molecular field analysis techniques: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). These compounds belonging to six different structural classes were randomly divided into a training set of 122 compounds and a test set of 13 compounds. The statistical results showed that the 3D-QSAR models derived from CoMFA were superior to those generated from CoMSIA. The most optimal CoMFA model after region focusing bears significant cross-validated r(2)(cv) of 0.60 and conventional r(2) of 0.92. The predictive power of the best CoMFA model was further validated by the accurate estimation to these compounds in the external test set, and the mean agreement of experimental and predicted log(IC(50)) values of the inhibitors is 0.6 log unit. Separate CoMFA models were conducted to evaluate the influence of different partial charges (Gasteiger-Marsili, Gasteiger-Hückel, MMFF94, ESP-AM1, and MPA-AM1) on the statistical quality of the models. The resulting CoMFA field map provides information on the geometry of the binding site cavity and the relative weights of various properties in different site pockets for each of the substrates considered. Moreover, in the current work, we applied MD simulations combined with MM/PBSA (Molecular mechanics/Possion-Boltzmann Surface Area) to determine the correct binding mode of the best inhibitor for which no ligand-protein crystal structure was present. To proceed, we define the following procedure: three hundred picosecond molecular dynamics simulations were first performed for the four binding modes suggested by DOCK 4.0 and manual docking, and then MM/PBSA was carried out for the collected snapshots. The most favorable binding mode identified by MM/PBSA has a binding free energy about 10 kcal/mol more favorable than the second best one. The most favorable binding mode identified by MM/PBSA can give satisfactory explanation of the SAR data of the studied molecules and is in good agreement with the contour maps of CoMFA. The most favorable binding mode suggests that with the quinazoline-based inhibitor, the N3 atom is hydrogen-bonded to a water molecule which, in turn, interacts with Thr 766, not Thr 830 as proposed by Wissner et al. (J. Med. Chem. 2000, 43, 3244). The predicted complex structure of quinazoline type inhibitor with EGF-R as well as the pharmacophore mapping from CoMFA can interpret the structure activities of the inhibitors well and afford us important information for structure-based drug design.     

Probability issues in molecular design: predictive and modeling ability in 3D-QSAR schemes

In the current work we investigated 3D-QSAR data by the use of the coupled leave-several-out (LSO) and leave-one-out (LOO) cross-validation (CV) procedures. We verified the above mentioned scheme using both simulated data and real 3D QSAR data describing a series of CoMFA steroids, heterocyclic azo dyes and styrylquinoline HIV integrase inhibitors. Unlike in standard analyses, this technique characterizes individual method not by a single performance metrics but screens a whole possible modeling space by sampling different molecules into the training and test sets, respectively. This allowed us for the discussion of the information included in the estimators validating cross-validation procedures, as well as the comparison of the efficiency of several 3D QSAR schemes, in particular, Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Surface Analysis (CoMSA). Moreover, it allows one to acquire some general knowledge about predictive and modeling ability in 3D QSAR method.     

QSAR and 3D-QSAR studies of the diacyl-hydrazine derivatives containing furan rings based on the density functional theory

QSAR studies of 27 diacyl-hydrazine derivatives containing furan rings were conducted and compared with the DFT method and AM1-MOPAC method. q ² values of 0.61 and 0.40 validated the predictability and reliability of eq. (5) from the DFT method were higher than those of eq. (6) from the AM1-MOPAC method. The DFT-optimized conformations and ESP-fitting charges of the target compounds were also used for 3D-QSAR analysis, including CoMFA and CoMSIA. The leave-one-out cross-validation correlation coefficient and the good correlation between the predicted and experimental activities of excluded test compounds revealed that CoMFA and CoMSIA models were robust. The QSAR results were consistent with the 3D-QSAR results, indicating that the electrostatic and hydrophobic properties of the target compounds were significant to the biological activity. These models are useful tools for predicting the larvicidal activities of new compounds and designing new specific insect growth regulators.     

3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors

The urgent need for novel HCV antiviral agents has provided an impetus for understanding the structural requisites of NS5B polymerase inhibitors at the molecular level. Toward this objective, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of 67 HCV NS5B polymerase inhibitors were performed using two methods. First, ligand-based 3D QSAR studies were performed based on the lowest energy conformations employing the atom fit alignment method. Second, receptor-based 3D QSAR models were derived from the predicted binding conformations obtained by docking all NS5B inhibitors at the allosteric binding site of NS5B (PDB ID: 2dxs). Results generated from the ligand-based model were found superior (r2cv values of 0.630 for CoMFA and 0.668 for CoMSIA) to those obtained by the receptor-based model (r2cv values of 0.536 and 0.561 for CoMFA and CoMSIA, respectively). The predictive ability of the models was validated using a structurally diversified test set of 22 compounds that had not been included in a preliminary training set of 45 compounds. The predictive r2 values for the ligand-based CoMFA and CoMSIA models were 0.734 and 0.800, respectively, while the corresponding predictive r2 values for the receptor-based CoMFA and CoMSIA models were 0.538 and 0.639, respectively. The greater potency of the tryptophan derivatives over that of the tyrosine derivatives was interpreted based on CoMFA steric and electrostatic contour maps. The CoMSIA results revealed that for a NS5B inhibitor to have appreciable inhibitory activity it requires hydrogen bond donor and acceptor groups at the 5-position of the indole ring and an R substituent at the chiral carbon, respectively. Interpretation of the CoMFA and CoMSIA contour maps in context of the topology of the allosteric binding site of NS5B provided insight into NS5B-inhibitor interactions. Taken together, the present 3D QSAR models were found to accurately predict the HCV NS5B polymerase inhibitory activity of structurally diverse test set compounds and to yield reliable clues for further optimization of the benzimidazole derivatives in the data set.     

Effect of cooperative hydrogen bonding in azo-hydrazone tautomerism of azo dyes

Azo-hydrazone tautomerism in azo dyes has been modeled by using density functional theory (DFT) at the B3LYP/6-31+G(d,p) level of theory. The most stable tautomer was determined both for model compounds and for azo dyes Acid Orange 7 and Solvent Yellow 14. The effects of the sulfonate group substitution and the replacement of the phenyl group with naphthyl on the tautomer stability and on the behavior in solvent have been discussed. Intramolecular hydrogen bond energies have been estimated for the azo and hydrazone tautomers to derive a relationship between the tautomer stability and the hydrogen bond strength. The transition structures for proton transfer displayed resonance assisted strong hydrogen bonding properties within the framework of the electrostatic-covalent hydrogen bond model (ECHBM). Evolution of the intramolecular hydrogen bond with changing structural and environmental factors during the tautomeric conversion process has been studied extensively by means of the atoms-in-molecules (AIM) analysis of the electron density. The bulk solvent effect was examined using the self-consistent reaction field model. Special solute-solvent interactions were further investigated by means of quantum mechanical calculations after defining the first-solvation shell by molecular dynamics simulations. The effect of cooperative hydrogen bonding with solvent molecules on the tautomer stability has been discussed.     

Diazo compounds of the heterocyclic series. 6. Amination of methoxy-substituted 2-naphthyl- and 2-arylazobenzimidazoles

The amination of azo compounds inactivated by quaternization was carried out for the first time using 4-methoxyphenyl-, 2- and 4-methoxynaphthylazobenzimidazoles as examples. In contrast to the quaternary salts of 2-arylazobenzimidazoles, during the amination of the above bases of azo compounds, the substitution of the methoxy group rather than of the hydrogen atom was observed. The anomalous ease of substitution of the methoxy group, located in the naphthalene ring in a position adjacent to the azo bridge was attributed to the manifestation of an ortho-effect, discovered in the series of azo compounds for the first time.For Communication 5, see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1209–1214, September, 1991.     

Effect of tautomerization on the fast-atom bombardment tandem mass spectra of azo dyes

The effect of tautomerization on the collision-induced dissociation of negative ions produced from sulfonated azo dyes by fast-atom bombardment (FAB) was studied by analyzing the product ion spectra of several related compounds. The mechanisms by which azo dyes fragment were found to depend on the formation and stability of tautomers. The extent of tautomerization was affected by the number and location of hydroxy groups on the dye, as well as by the FAB matrix. Ions that retained a sodium were often inhibited from forming tautomers and gave different product ions. Substitution of deuterium for hydrogen on the hydroxy groups aided in the identification of ions having more than one possible structure and provided verification of proposed mechanisms. Mechanisms involving ions retaining a sodium were verified by substituting potassium for the sodium.     

Photochromic properties of thienylpyrrole azo dyes in solution

The photochromic behaviour of thienylpyrrole azo dyes in THF solutions was studied for the first time. The photochromic properties are strongly dependent on the substitution pattern on the dyes. Nitro-substituted thienylpyrrole azo dyes are particularly interesting since they exhibit very fast colouration/decolouration processes. The activation energies of these compounds are among the lowest values reported for heterocyclic azo dyes. These compounds show aggregation phenomena in freshly prepared solutions of THF, which lead to variable photochromic behaviours. Only after 1-5 h the solutions reach equilibrium and then reproducible photochromic behaviour can be observed.     

Specific interaction between polyethylenimine and azo dyes carrying hydroxyl groups

The binding of acid azo dyes having phenolic hydroxyl groups such as orange I ( I ), orange II ( II ), chrome violet ( III ), 4-hydroxyazobenzene-4′-sulfonate ( IV ), and 2,4-dihydroxyazobenzene-4′-sulfonate ( V ) by polyethylenimine was studied by equilibrium dialysis and spectroscopic methods. The results obtained indicate that dyes ( III ) and ( V ) with two OH groups are bound much more strongly than dyes ( I ), ( II ), and ( IV ) with one OH group. Also polyethylenimine is far superior to any other polymers which have been examined, including bovine serum albumin, polyvinylpyrrolidone, and poly-L -lysine, in its ability to form complexes with these dyes ( III ) and ( V ). The OH groups involved participate preferentially in complex formation with polyethylenimine. The unusual affinity of polyethylenimine for the dyes carrying OH groups is discussed.     

Voltammetric,spectroscopic and thermal studies on the binding of some heterocyclic azo compounds with α- and β-cyclodextrins: pH effect and association affinity

The binding abilities of α- and β-cyclodextrins (α-CD and β-CD) with some heterocyclic azo compounds (1,1'-(azodicarbonyl)dipiperidine (ADP) and azodicarboxylic dimorpholide (ADM)) were studied at different pHs (4, 7.4 and 10) by UV-Vis spectroscopy and square-wave voltammetry techniques. The association constants (K _i) and stoichiometries of the binding of these azo compounds with α-CD and β-CD were determined by using square-wave voltammetry technique. These bindings were formed with a stoichiometry of 1: 1 in solution. The solid samples, obtained from the mixtures (molar ratio of 1: 1) of these azo dyes and CDs in aqueous phase were analyzed by FT-IR spectroscopy and thermal analysis methods. Thermal analysis results showed that ADP and ADM formed the inclusion complexes with α-CD; however, the binding of the azo dyes with β-CD gave non-inclusion complexes.     

Characterization of sulfonated azo dyes and aromatic amines by pyrolysis gas chromatography/mass spectrometry

Sixteen sulfonated and unsulfonated azo dyes as well as eleven sulfonated and unsulfonated aromatic amines were analyzed and qualitatively characterized by means of pyrolysis gas chromatography/mass spectrometry at different temperatures. Aniline and aminonaphthalene were found to be the dominant pyrolysis products of sulfonated aromatic amines and dyes. Azo dye and dye class specific key compounds such as benzidine, vinyl-p-base and 4-aminoazobenzene could be identified by pyrolysis gas chromatography/mass spectrometry of commercial acid, cationic, direct, reactive and solvent dyes. 500 degrees C was the optimal pyrolysis temperature for most of the pyrolyzed compounds. The method was applied to a dried sample of a textile wastewater concentrate from a dyeing process. Reactive azo dyes of the group of Remazol dyes and anthraquinone dyes could be identified as the major compounds of the sample. The finding of caprolactam (a printing additive) suggests that the wastewater contained effluent from a process of heat-activated printing with reactive dyes. p-Chloraniline, a banned aromatic amine, was identified. Chemical reduction of the wastewater sample prior to pyrolysis resulted in the release of volatile aromatic amines and aided the classification of several products of pyrolysis.