分子电性作用矢量法定量预测单质子化肽段离子迁移谱碰撞截面

基于分子二维图形特征得到了一种新的结构参数化方法:分子电性作用矢量(MEIV)。将其应用于113个单质子化肽段样本集的结构表征及离子迁移谱碰撞截面模拟和预测当中,通过严格检验所得到3个回归模型的复相关系数Rcum及交叉验证Q分别为:0.984、0.981、0.980和0.979、0.979、0.978。结果表明MEIV对有机分子结构及其性质具有良好的表达和预测能力。     

Strategies to design pyrazolyl urea derivatives for p38 kinase inhibition: a molecular modeling study

The p38 protein kinase is a serine–threonine mitogen activated protein kinase, which plays an important role in inflammation and arthritis. A combined study of 3D-QSAR and molecular docking has been undertaken to explore the structural insights of pyrazolyl urea p38 kinase inhibitors. The 3D-QSAR studies involved comparative molecular field analysis (CoMFA) and comparative molecular similarity indices (CoMSIA). The best CoMFA model was derived from the atom fit alignment with a cross-validated r ² (q ²) value of 0.516 and conventional r ² of 0.950, while the best CoMSIA model yielded a q ² of 0.455 and r ² of 0.979 (39 molecules in training set, 9 molecules in test set). The CoMFA and CoMSIA contour maps generated from these models provided inklings about the influence of interactive molecular fields in the space on the activity. GOLD, Sybyl (FlexX) and AutoDock docking protocols were exercised to explore the protein–inhibitor interactions. The integration of 3D-QSAR and molecular docking has proffered essential structural features of pyrazolyl urea inhibitors and also strategies to design new potent analogues with enhanced activity.     

Quantitative Structure�CRetention Relationship Study on Nitrogen-Containing Polycyclic Aromatic Compounds by Using Molecular Electronegativity Interaction Vector

The molecular structures of 117 nitrogen-containing polycyclic aromatic compounds (N-PACs) were described by a method of molecular structural characterization (MSC) called molecular electronegativity interaction vector (MEIV). The samples were divided into a training set and a test set. For the training set, a quantitative structure?Cretention relationship (QSRR) model was built up by multiple linear regression (MLR) and the model was evaluated by performing the cross validation with the leave-one-out (LOO) procedure. The correlation coefficient (R) and the cross-verification correlation coefficient (R _CV) of the model were 0.992 and 0.991, respectively. Moreover, the model was evaluated by the test set and satisfactory results with a correlation coefficient (R _test) of 0.993 were obtained. The results suggested good stability and predictability of the model.     

Docking-based CoMFA and CoMSIA study of azaindole carboxylic acid derivatives as promising HIV-1 integrase inhibitors

Three-dimensional quantitative structure–activity relationship (3D-QSAR) studies were performed based on a series of azaindole carboxylic acid derivatives that had previously been reported as promising HIV-1 integrase inhibitors. Docking studies to explore the binding mode were performed based on the highly active molecule 36. The best docked conformation of molecule 36 was used as template for alignment. The comparative molecular field analysis (CoMFA) model (including steric and electrostatic fields) yielded the cross validation q ² = 0.655, non-cross validation r ² = 0.989 and predictive r ² _pred = 0.979. The best comparative molecular similarity indices analysis (CoMSIA) model (including steric, electrostatic, hydrophobic and hydrogen-bond acceptor fields) yielded the cross validation q ² = 0.719, non-cross validation r ² = 0.992 and predictive r ² _pred = 0.953. A series of new azaindole carboxylic acid derivatives were designed and the HIV-1 integrase inhibitory activities of these designed compounds were predicted based on the CoMFA and CoMSIA models.     

Holographic quantitative structure-activity relationship for prediction of the toxicity of polybrominated diphenyl ether congeners

Polybrominated diphenyl ether congeners (PBDEs) might activate the AhR (aromatic hydrocarbon receptor) signal transduction, and thus might have an adverse effect on the health of humans and wildlife. Because of the limited experimental data, it is important and necessary to develop structure-based models for prediction of the toxicity of the compounds. In this study, a new molecular structure representation, molecular hologram, was employed to investigate the quantitative relationship between toxicity and molecular structures for 18 PBDEs. The model with the significant correlation and robustness (r ² = 0.991, q ² _LOO = 0.917) was developed. To verify the robustness and prediction capacity of the derived model, 14 PBDEs were randomly selected from the database as the training set, while the rest were used as the test set. The results generated under the same modeling conditions as the optimal model are as follows: r ² = 0.988, q ² _LOO = 0.598, r ² _pred = 0.955, and RMSE (root-mean-square of errors) = 0.155, suggesting the excellent ability of the derived model to predict the toxicity of PBDEs. Furthermore, the structural features and molecular mechanism related to the toxicity of PBDEs were explored using HQSAR color coding.     

Two Reliable Simple Relationships between Flash Points of Hydrocarbon Kerosene Fuels and Their Molecular Structures

This study presents two new reliable simple correlations for predicting flash point of kerosene hydrocarbons using multiple linear regression method. The methodology assumes that the flash point of kerosene fuels can be expressed as a function of elemental composition and several structural parameters. The proposed correlations have determination coefficients of 0.910 and 0.977. Also, the first model has root mean square deviation (RMSD) and the average absolute deviations (AAD) of 10.6 and 8.2 K, respectively, for 111 kerosene fuels with different molecular structures as training set. The RMSD and AAD for the second improved model are 5.39 and 4.33 K, respectively. The predictive power of two correlations is checked using a cross validation method. (R² = 0.977, Q²_Ext = 0.975, and Q²_LMO = 0.979). Also, these correlations give good predictions for further 25 kerosene fuels as test set. The proposed model can also be applied for designing novel kerosene fuels.     

Combined 2D and 3D-QSAR,molecular modelling and docking studies of pyrazolodiazepinones as novel phosphodiesterase 2 inhibitors

Selective inhibition of phosphodiesterase 2 (PDE2) in cells where it is located elevates cyclic guanosine monophosphate (cGMP) and acts as novel analgesic with antinociceptive activity. Three-dimensional quantitative structure–activity relationship (QSAR) studies for pyrazolodiazepinone inhibitors exhibiting PDE2 inhibition were performed using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and Topomer CoMFA, and two-dimensional QSAR study was performed using a Hologram QSAR (HQSAR) method. QSAR models were generated using training set of 23 compounds and were validated using test set of nine compounds. The optimum partial least squares (PLS) for CoMFA-Focusing, CoMSIA-SDH, Topomer CoMFA and HQSAR models exhibited good ‘leave-one-out’ cross validated correlation coefficient (q²) of 0.790, 0.769, 0.840 and 0.787, coefficient of determination (r²) of 0.999, 0.964, 0.979 and 0.980, and high predictive power (r²_pred) of 0.796, 0.833, 0.820 and 0.803 respectively. Docking studies revealed that those inhibitors able to bind to amino acid Gln859 by cGMP binding orientation called ‘glutamine-switch’, and also bind to the hydrophobic clamp of PDE2 isoform, could possess high selectivity for PDE2. From the results of all the studies, structure–activity relationships and structural requirements for binding to active site of PDE2 were established which provide useful guidance for the design and future synthesis of potent PDE2 inhibitors.     

Study on the Quantitative Structure-toxicity Relationships for the Selected Esters by Using Molecular Electronegativity Interaction Vector （MEIV）

The molecular electronegativity interaction vector (MEIV) was used to describe the molecular structure of 30 selected esters. Two excellent QSTR models were built up by using multiple linear regression (MLR) and partial least-squares regression (PLS). The correlation coefficients (R) of the two models were 0.945 and 0.941, respectively. The models were evaluated by performing the cross validation with the leave-one-out (LOO) procedure. The cross-verification correlation coefficients (RCV) of the two models were 0.921 and 0.919, respectively. The results showed that the models constructed in this work could provide estimation stability and favorable predictive ability.     

A quantitative electron-microscopic study of a linear polyethylene fraction crystallized at different temperatures

Replica and thin-section electron microscopy was performed on a linear polyethylene fraction (M_w = 1.89 × 10⁵, M_n = 1.79 × 10 ⁵) which was either isothermally crystallized or quenched at difference temperatures. The results are numerically analyzed in such a manner so as to give the distribution of the total long spacing and of the crystallite and amorphous thicknesses. The quantitative information about the maximum and minimum values for these parameters at each crystallization temperature yields important clues as to possible molecular processes involved. Qualitative information regarding general morphology, molecular tilt with respect to the lamellar surface, and possible crystallographic faults are also discussed.     

Complexes of helium with neutral molecules: Progress toward a quantitative scale of bonding character

The complexes of helium with nearly 30 neutral molecules (M) were investigated by various techniques of bonding analysis and symmetry-adapted perturbation theory (SAPT). The main investigated function was the local electron energy density H( r ), analyzed, in particular, so to estimate the degree of polarization (DoP) of He in the various He(M). As we showed recently (Borocci et al., J. Comput. Chem., 2019, 40, 2318–2328), the DoP is a quantitative index that is generally informative about the role of polarization (induction plus charge transfer [CT]) and dispersion in noncovalent noble gas complexes. As further evidence in this regard, we presently ascertained quantitative correlations between the DoP(He) of the He(M) and indices based on the electron density ρ( r ), including the molecular electrostatic potential at the He M bond critical point, as well as the percentage contributions of induction and dispersion to the SAPT binding energies. Based also on the explicit evaluation of the CT, accomplished through the study of the charge-displacement function, we derived a quantitative scale that ranks the He(M) according to their dispersive, inductive, and CT bonding character. Our taken approach could be conceivably extended to other types of noncovalent complexes.     

Simultaneous chemical fingerprint and quantitative analysis of Ginkgo biloba extract by HPLC–DAD

A reverse-phase liquid chromatography method with diode array detection was developed to evaluate the quality of Ginkgo biloba extract through establishing chromatographic fingerprint and simultaneous determination of eight flavonoid compounds, namely rutin, myricetin, quercitrin, quercetin, luteolin, kaempferol, apigenin, and isorhamnetin. The chromatographic separation was performed on an Agilent SB-C18 column (250 × 4.6 mm, 5.0 μm) with a gradient elution program using a mixture of methanol and 0.1% formic acid (v/v) as mobile phase within 55 min at 360-nm wavelength. The correlation coefficients of similarity for different batches of G. biloba extract from the same manufacturer and G. biloba extract from different manufacturers were determined from the LC fingerprints, and they shared a close similarity. The eight flavonoid compounds showed good regression (R ² > 0.9995) within test ranges, and the recovery of the method was in the range of 94.1–101.4%. In addition, the content of those eight flavonoid compounds in G. biloba extract prepared by different manufacturers of China was determined to establish the effectiveness of the method. The results indicated that the developed method by having a combination of chromatographic fingerprint and quantification analysis could be readily utilized as a quality control method for G. biloba extract and its related traditional Chinese medicinal preparations.     

Developing 13C NMR quantitative spectrometric data-activity relationship (QSDAR) models of steroid binding to the corticosteroid binding globulin

We have developed four quantitative spectrometric data-activity relationship (QSDAR) models for 30 steroids binding to corticosteroid binding globulin, based on comparative spectral analysis (CoSA) of simulated ¹³C nuclear magnetic resonance (NMR) data. A QSDAR model based on 3 spectral bins had an explained variance (r ²) of 0.80 and a cross-validated variance (q ²) of 0.78. Another QSDAR model using the 3 atoms from the comparative structurally assigned spectral analysis (CoSASA) of simulated ¹³C NMR on a steroid backbone template gave an explained variance (r ²) of 0.80 and a cross-validated variance (q ²) of 0.73. Positions 3 and 14 from the steroid backbone template have correlations with the relative binding activity to corticosteroid binding globulin that are greater than 0.52. The explained correlation and cross-validated correlation of these QSDAR models are as good as previously published quantitative structure-activity relationship (QSAR), self-organizing map (SOM) and electrotopological state (E-state) models. One reason that the cross-validated variance of QSDAR models were as good as the other models is that simulated ¹³C NMR spectral data are more accurate than the errors introduced by the assumptions and approximations used in calculated electrostatic potentials, E-states, HE-states, and the molecular alignment process of QSAR modeling. The QSDAR models developed provide a rapid, simple way to predict the binding activity of a steroid to corticosteroid binding globulin.     

Rapid Simultaneous Determination of Andrographolides in Andrographis paniculata by Near-Infrared Spectroscopy

The potential of near-infrared spectroscopy (NIRS) for the quality control of traditional Chinese medicine has been evaluated. Seven quantitative parameters, andrographolide, deoxyandrographolide, dehydroandrographolide, neoandrographolide, moisture, ash content, and alcohol-soluble extract of Andrographis paniculata, were evaluated by NIRS. The reference values of andrographolides were determined by high-performance liquid chromatography, and the others were obtained using the standard methods of the 2015 Chinese Pharmacopoeia. The predicted values were determined by a quantitative model using NIRS based on partial least square regression. Different spectral preprocessing methods, spectral ranges, and optimum number of factors were selected to optimize the models. All models were estimated by the combination of various parameters, including the correlation coefficient of calibration for andrographolide, deoxyandrographolide, dehydroandrographolide, neoandrographolide, moisture, ash content, alcohol-soluble extract (values of 0.980, 0.984, 0.989, 0.983, 0.987, 0.988, 0.979, respectively), root mean square error of calibration (values of 0.156, 0.038, 0.050, 0.029, 0.604, 0.431, 0.135, respectively), root mean square error of prediction (values of 0.169, 0.041, 0.050, 0.033, 0.280, 0.493, 0.140, respectively), root mean square error of cross-validation (values of 0.626, 0.114, 0.158, 0.046, 1.145, 0.774, 0.508, respectively), and ratio of standard deviation to standard error of prediction (values of 4.583, 4.690, 4.796, 4.899, 4.899, 4.690, 5.099, respectively). The results show that the calibration models by NIRS are reliable and can be applied for the quantification for seven parameters from A. paniculata for quality control in traditional Chinese medicine production and processing.     

Mobility-sensitive fluorescence probes for quantitative monitoring of water sorption and diffusion in polymer coatings

The fluorescent molecular rotor probes 4-tricyanovinyl-[N-(2-hydroxyethyl)-N-ethyl]-aniline, tricyano-4-(dimethylamino) benzylidene, and tricyanovinyljulolidene have been used as extrinsic fluorescence probes for quantitative monitoring of water uptake in polymeric coatings. The presence of water causes plasticization of the polymer, which results in increased local mobility within the film. The nonradiative decay pathways of the rotor probes are increased as local mobility increases, and the resulting decrease in fluorescence intensity of the probes is directly proportional to the amount of water sorbed. Beyond allowing for the characterization of sorbent content, this fluorescence technique can be used to determine the diffusion coefficient of water in a polymer film. The relative change in fluorescence fits well to a Fickian diffusion model, yielding a diffusion coefficient for water of 3 × 10^-8 cm²/s in poly(vinyl acetate), and a value of 6 × 10^-9 cm²/s in a room-temperature cured epoxypolyamide, in excellent agreement with diffusion coefficient values determined from gravimetric analysis. Preliminary studies also demonstrate the utility of molecular rotor probes to monitor water uptake in individual layers of multilayered polymer systems. © 1995 John Wiley & Sons, Inc.