Molecular pair potential of chiral amino acid amphiphile in Langmuir monolayers on the basis of an atomistic model

In the present work, the pair potential of enantiomeric N-palmitoyl aspartic acid amphiphile monolayer at the air/water interface is calculated based on an atomistic model. The molecular structure and partial charges are calculated using two semi empirical (PM3, AM1) and one empirical (Gasteiger and Marcili) methods. A distance-dependent dielectric function is used to represent the interfacial dielectric constant at the aqueous subphase. The present study indicates that a pair of molecules have favorable interaction at specific ranges of mutual orientations. Other orientations are favorable but at larger separations. Favorable electrostatic interaction at a specific combination of orientation and short separations of the head groups significantly contribute to the total energy. The curvature of the domain boundary is suggested to be driven by the favorable arrangement which is dependent on the pair potential of molecules. The use of charges obtained by the PM3 and GM do not lead to a significant variation of the orientation-dependent features, while the AM1 predicts higher partial charges and interactions are stronger than the former two methods. However, orientation-dependent features remain the same. The variations in the LJ parameters and charges indicate that the conclusions made are insensitive to the choice of parameters. The mutual favorable interaction predicted by calculation agree with the handedness of curvature of domains.     

Pharmacophore modelling of structurally unusual diltiazem mimics at L-type calcium channels

The purpose of this theoretical study was to investigate the molecular features of some structurally unusual calcium antagonists with experimentally proved affinity to the diltiazem-binding site at L-type calcium channels. Therefore, sterical and electronic characteristics of cis-/trans-diclofurime, the verapamil-like derivatives McN-5691 and McN-6186 as well as the natural products papaverine, laudanosine, antioquine and tetrandrine were compared with the pharmacophoric requirements detected for classical diltiazem-like derivatives. This yielded a common pharmacophore model for all of these compounds. Based on this model, one single negative molecular electrostatic potential induced by the free electron pairs of the oxime oxygen of trans-diclofurime was detected that might be responsible for the stronger effects compared to the cis isomer. Furthermore, the dual diltiazem- and verapamil-like features of McN-5691 (and McN-6186) as well as the distinct pharmacophoric assignment of the laudanosine enantiomers may be interpreted on a molecular level. Finally, the crucial partial structure of the bis-benzylisoquinoline derivatives antioquine and tetrandrine being responsible for the calcium antagonistic effects could be revealed by superposition on the most active benzothiazepinone derivative 8-methoxydiltiazem. The results obtained for these unusual diltiazem mimics are discussed taking into consideration earlier findings for classical diltiazem-like derivatives.     

基于拉曼高光谱成像的乳粉真伪非定向筛查新方法研究

乳粉真伪问题是我国食品安全的突出问题之一,其非定向筛查是分析科学领域的前沿热点。该研究提出一种稳健建模驱动的拉曼高光谱成像方法(RMD-RHIM),借助其图谱合一的数据特征,将乳粉中未知掺杂物识别问题转化为奇异样本识别问题,有效解决了乳粉中掺杂物的不确定性问题。在RMD-RHIM中,首先采用自适应迭代重加权惩罚最小二乘算法(airPLS)扣除拉曼光谱的背景信息,再通过改进迭代自权重偏最小二乘法(mIRPLS)准确识别乳粉拉曼高光谱成像信号中的畸变像素点,并转化为可视化的二值图像,实现了乳粉真伪的非定向筛查。结果表明,RMD-RHIM方法对阳性和阴性样品的识别率分别达到了98.3%和93.3%,可满足乳粉工业快速筛查的需求,并为其它食品样本的非定向筛查提供了一种新手段。     

Partial least-squares path modelling with latent variables

A partial least-squares treatment of multivariate data related through a complex model allows simultaneous evaluation of the interactions between large numbers of features. Results are given for a model in which water sources flow together; each source is represented by water quality data to allow the influence of the various sources to be evaluated with respect to their importance on the resulting flow downstream.     

Evaluation of partial interference functions of solutes in dilute metallic liquid alloys

This paper concerns the evaluation of the partial interference function of solutes in a liquid metallic solvent. The free electron model and its assumption for the solvent enables the calculation of the value of the partial interference function of the solute for zero wave vector.Comparison of the result with those deducted from thermodynamic data is made and the agreement is found to be satisfactory.On the other hand the partial interference function calculated for the whole range of wave vectors is compared for one system to the hard sphere Percus—Yevick model and to a recent model which uses a quasi chemical treatment.     

Pervaporation of volatile organics from water: II. Influence of permeate pressure on partial fluxes

Hydrophobic pervaporation is being developed within the area of separation of volatile organic compounds from dilute aqueous solutions. Optimisation of the pervaporation process for these types of applications is often very complex due to the many different organic compounds which are to be separated simultaneously. The permeate pressure is one of the key process parameters that has a considerable impact on both selectivities and partial fluxes. In this study, a model for predicting the permeate pressure dependence of the partial fluxes of the organic compounds to be separated was developed. The model includes both the effect of external mass transfer and the effect of altered permeabilities due to membrane plasticisation for the various permeants. Both these effects were proved to effect the partial fluxes to a significant extent. The model was shown to be applicable to organic permeants within the groups of alcohols, esters and aldehydes. Adequate information about the membrane separation factor and the overall separation factor together with the total flux at one specific permeate pressure is all that is needed for the application of this model.     

Quantum molecular dynamics study of water on TiO2(110) surface

The adsorption of water on perfect TiO(2)(110) surface is studied by quantum molecular dynamics simulation adopting a periodic model formed by five water molecules on a (5 x 1) surface unit cell of a five layer slab of TiO(2). The total simulation time is 3.2 ps. At about 1.3 ps, one water molecule dissociates with the help of other adsorbed waters and surface bridging oxygens. During the remaining 1.9 ps, the waters and OH groups vibrate, but no more dissociation or recombination is observed. By comparing recent experimental O1s photoemission (x-ray photoelectron spectroscopy) spectra of H(2)O/TiO(2)(110) to the computed spectrum of the adsorbate in the configurations supplied by the molecular dynamics simulation, the observed peaks can be attributed to different oxygen species. The proposed assignment of the main spectral features supports the occurrence of partial water dissociation (approximately 20%) also on a perfect TiO(2) surface.     

Synthesis of Fluorinated Heteroaromatics through Formal Substitution of a Nitro Group by Fluorine under Transition‐Metal‐Free Conditions

An efficient and transition‐metal‐free approach was developed to access a series of fluorinated heteroaromatics in moderate to excellent yields. This one‐pot procedure features a triple‐relay transformation of rapid dearomatization, fluorination, and rearomatization processes, which represents a conceptually novel strategy of combining partial hydrogenation and electrophilic fluorination.     

Non-linear QSAR modeling by using multilayer perceptron feedforward neural networks trained by back-propagation

The use of multilayer perceptrons (MLP) feedforward neural networks trained by back-propagation (BP) for non-linear QSAR model building is presented and explained in detail through a case study. This method was compared with others often used in this field, such as multiple linear regression (MLR), partial least squares (PLS) and quadratic PLS (QPLS). The case study deals with a series of 18 alpha adrenoreceptors agonists belonging to three different classes (alpha-1, alpha-2 and alpha-1,2) according to their different pharmacological effects. Each of them is described by 15 chemical features (the X block). Six pharmacological responses were also measured for each one to build the matrix of biological responses (the Y block). The results obtained indicated a slightly better performance of MLP against the other procedures, when using the correlation coefficient of the observed versus predicted response plots as an indicator of the goodness of the fit.     

Analysis of the equilibrium and kinetics of the ankyrin repeat protein myotrophin

We apply the Wako-Saito-Mun?oz-Eaton model to the study of myotrophin, a small ankyrin repeat protein, whose folding equilibrium and kinetics have been recently characterized experimentally. The model, which is a native-centric with binary variables, provides a finer microscopic detail than the Ising model that has been recently applied to some different repeat proteins, while being still amenable for an exact solution. In partial agreement with the experiments, our results reveal a weakly three-state equilibrium and a two-state-like kinetics of the wild-type protein despite the presence of a nontrivial free-energy profile. These features appear to be related to a careful "design" of the free-energy landscape, so that mutations can alter this picture, stabilizing some intermediates and changing the position of the rate-limiting step. Also, the experimental findings of two alternative pathways, an N-terminal and a C-terminal one, are qualitatively confirmed, even if the variations in the rates upon the experimental mutations cannot be quantitatively reproduced. Interestingly, the folding and unfolding pathways appear to be different, even if closely related: a property that is not generally considered in the phenomenological interpretation of the experimental data.     

The influence of electrostatic forces on the structure and dynamics of molecular ionic liquids

The vast majority of molecular dynamics simulations are based on nonpolarizable force fields with fixed partial charges for all atoms. The traditional way to obtain these charges are quantum-mechanical calculations performed prior to simulation. Unfortunately, the set of the partial charges heavily relies on the method and the basis set used. Therefore, investigations of the influence of charge variation on simulation data are necessary in order to validate various charge sets. This paper elucidates the consequences of different charge sets on the structure and dynamics of the ionic liquid: 1-ethyl-3-methyl-imidazolium dicyanoamide. The structural features seem to be more or less independent of the partial charge set pointing to a dominance of shape force as modeled by Lennard-Jones parameters. This can be seen in the radial distribution and orientational correlation functions. The role of electrostatic forces comes in when studying dynamical properties. Here, significant deviations between different charge sets can be observed. Overall, dynamics seems to be governed by viscosity. In fact, all dynamical parameters presented in this work can be converted from one charge set to another by viscosity scaling.     

Near-Infrared Spectroscopy Analytical Model Using Ensemble Partial Least Squares Regression

A novel ensemble-based feature selection method was developed which is designated as ensemble partial least squares regression coeffientents (EPRC). It was composed of two steps: generating a series of different single feature selectors and aggregating them to reach a consensus. Specifically, the bootstrap resampling approach was used to generate a diversity of single feature selectors, and the absolute values of the regression coefficients of the partial least squares (PLS) model were used to rank the features. Next, these feature rankings out of single feature selectors were aggregated by the weighted-sum approach. Finally, coupled with the regression model, the features selected by EPRC were evaluated through cross validation and an independent test set. By experiments of constructing the spectroscopy analysis model on three near infrared spectroscopy (NIRS) datasets, it was shown that the EPRC located key wavelengths, gave a promotion to regression performance, and was more stable and interpretable to the domain experts.     

3D QSAR analyses of novel tyrosine kinase inhibitors based on pharmacophore alignment

In an effort to develop a quantitative ligand-binding model for the receptor tyrosine kinases, a pharmacophore search was first used to identify structural features that are common in two novel sets of 12 molecules of the 3-substituted indolin-2-ones and 19 compounds of the benzylidene malononitriles with low-to-high affinity for HER2, a kind of receptor tyrosine kinase. The common pharmacophore model based on these 31 compounds was used as a template to obtain the aligned molecular aggregate, which provided a good starting point for 3D-QSAR analysis of only the 19 benzylidene malononitriles. Two molecular field analysis (MFA) techniques, including CoMFA and CoMSIA, were used to derive the quantitative structure-activity relationships of the studied molecules. From the studied results, it was obvious that the 3D-QSAR models based on the pharmacophore alignment were superior to those based on the simple atom-by-atom fits. Considering the flexibility of the studied molecules and the difference between the active conformers and the energy-lowest conformers, the pharmacophore model can usually provide the common features for the flexible regions. Moreover, the best CoMSIA model based on the pharmacophore hypothesis gave good statistical measure from partial least-squares analysis (PLS) (q(2) = 0.71), which was slightly better than the CoMFA one. Our study demonstrated that pharmacophore modeling and CoMSIA research could be effectively combined. Results obtained from both methods helped with understanding the specific activity of some compounds and designing new specific HER2 inhibitors.     

A new productivity function and stability criterion in chemical vapor transport processes

The crystal growth rate in a chemical vapor transport process using a closed system is analyzed on the basis of a one-dimensional configuration. A simplified model of vapor transport enables one to obtain a set of equations yielding the rates of reaction without a complete evaluation of the partial pressure gradients. This linear set comprises as many equations as independent chemical reactions. The effect of finite interface kinetics is formally taken into account. The efficiency of a one-reaction process is given by a function involving the mole fractions of the gaseous species and the stoichiometric coefficients in the formula equation. The features of such a productivity function are discussed. Maximum growth rate is achieved if the gaseous components are present in stoichiometric quantities. The concept of the productivity function is illustrated by chemical vapor transport systems involving binary and ternary gaseous phases. Proceeding from a two-phase source material, stability criteria that define stable one-phase and stable two-phase crystal growth are given. The kind of deposit may be changed by altering the amount of transporting agent. It is shown that limited interface kinetics favors a two-phase deposit.     

A structure-preserving computational method in the simulation of the dynamics of cancer growth with radiotherapy

In this work, we consider a two-dimensional mathematical model that describes the growth dynamics of cancer when radiotherapy is considered. The mathematical model for the local density of the tumor is described by a parabolic partial differential equation with variable diffusion coefficient. The nonlinear reaction term considers both the logistic law of proliferation of tumor cells and the effect of a treatment against cancer. Suitable initial-boundary conditions are imposed on a bounded spatial domain, and a theorem on the existence and the uniqueness of solutions for the initial-boundary-value problem is proved. Motivated by this result, we design a finite-difference methodology to approximate the solutions of our mathematical model. The scheme is a linear method that is capable of preserving the positivity and the boundedness of the approximations. Some simulations are presented in order to illustrate the performance of the method. Among other conclusions, the numerical results show that the method is able to preserve the analytical features of the relevant solutions of the model.     

The INDO/2-AHP (average hole potential) method for excited states: Comparison with the simple INDO/2-HP (hole potential) method

The INDO/2 version of the average hole potential (AHP) model is analyzed. The model is applied to study the geometric features, molecular inversion barriers, singlet-triplet splittings, etc., of a few small carbonyl molecules (H₂CO, HFCO, F₂CO) in the ^1,3nπ* states with partial as well as complete optimization of all geometric parameters in the excited states. The results are compared with those obtained by a simple hole-potential (HP) model.     

Incorporating variable importance into kernel PLS for modeling the structure–activity relationship

Kernel partial least squares (KPLS) has become popular techniques for chemical and biological modeling, which is a nonlinear extension of linear PLS. Training samples are transformed into a feature space via a nonlinear mapping, and then PLS algorithm can be carried out in the feature space. However, one of the main limitations of KPLS is that each feature is given the same importance in the kernel matrix, thus explaining the poor performance of KPLS for data with many irrelevant features. In this study, we provide a new strategy incorporated variable importance into KPLS, which is termed as the WKPLS approach. The WKPLS approach by modifying the kernel matrix provides a feasible way to differentiate between the true and noise variables. On the basis of the fact that the regression coefficients of the PLS model reflect the importance of variables, we firstly obtain the normalized regression coefficients by establishing the PLS model with all the variables. Then, Variable importance is incorporated into primary kernel. The performance of WKPLS is investigated with one simulated dataset and two structure–activity relationship (SAR) datasets. Compared with standard linear kernel PLS and Gaussian kernel PLS, The results show that WKPLS yields superior prediction performances to standard KPLS. WKPLS could be considered as a good mechanism by introducing extra information to improve the performance of KPLS for modeling SAR.