QSAR of chemical polarizability and nerve toxicity. 2

Polarizability is a property of molecules that has long been of interest to scientists from a variety of viewpoints. However, in the area of the QSAR of chemical-biological interactions, it has received little attention. Recently we have shown that one can use the simple summation of the valence electrons (H = 1, C = 4, O = 6, etc.) in a molecule as a measure of its polarizability. We have found this parameter to correlate nerve toxicity of a wide variety of chemicals acting on nerves of frogs, rabbits, cockroaches, and humans.     

(Hyper)polarizability density analysis for open-shell molecular systems based on natural orbitals and occupation numbers

We have developed a method for analyzing the (hyper)polarizabilities of open-shell molecular systems. This method employs the (hyper)polarizability densities based on the natural orbitals and occupation numbers, which enables us to analyze the contributions of odd electrons having various open-shell (diradical) characters. Within broken-symmetry, i.e., spin-unrestricted, single-determinant molecular orbital and density functional theory approaches, we can also remove the spin contamination effects on these quantities through spin projection. To do that, an approximate spin projected method has been elaborated and applied to the analysis of the (hyper)polarizability of multi-radical systems. As examples, typical open-shell singlet systems, 1,3-dipoles and rectangular graphene nanoflakes, are examined.     

Exchange effects on electronic states in jellium clusters

Hartree-Fock calculations are done for finite number of valence electrons (8, 20, 40, and 58) in a positively charged uniform background (jellium) with the density of bulk sodium. Differences and similarities with the results of Kohn-Sham local-density calculations are discussed. State-dependence and suppression of the wave functions are the two important effects coming from the nonlocality of the Hartree-Fock potential. These two effects, however, cancel in the density profile of electrons. The Kohn-Sham calculations consequently produce similar density profiles as in the Hartree-Fock calculations. The dipole polarizability is also calculated for 8-mers. The calculated value is still smaller than the measured one and is not an improvement of the insufficient Kohn-Sham result.deceased     

Fast approaches for molecular polarizability calculations

Molecular polarizability of a molecule characterizes the capability of its electronic system to be distorted by the external field, and it plays an important role in modeling many molecular properties and biological activities. In this paper, a set of fast empirical models have been developed to predict molecular polarizability using two types of approaches. The first type of approaches is based on Slater's rules of calculating the effective atomic nuclear shielding constants. The best model (model 1A) of this category has achieved an average unsigned error (AUE), root-mean square error (RMSE), and average percent error (APE) of 2.23 au, 3.29 au, and 2.77%, respectively. The second type of model is based on an additive hypothesis of molecular polarizability. Five models have been constructed using different schemes of atom types. The best model that applies 14 atom types, model 2e, achieves AUE, RMSE, and APE of 0.99 au, 1.48 au, and 1.24%, respectively. This performance is much better than those of the models purely based upon chemical composition (model 2A and the Bosque and Sales model), for which errors are about 2-fold higher. It is expected that both model 1A and model 2E will have broad applications in QSAR and QSPR studies.     

On the parametrization of the toxicity of organic chemicals to Tetrahymena pyriformis. The problem of establishing a uniform activity

In this report we illustrate the importance of making an effort to ensure that all of the dependent variables in a QSAR are associated with one mechanism of action. If this cannot be established, it will not be possible to compare the QSAR with others acting on different biological systems. That is, such information cannot be used to develop a science of chemical-biological interactions. A study of the action of a large set of phenols acting on Tetrahymena pyriformis made by Cronin and Schultz is analyzed to illustrate the problem.     

QSAR and Docking Studies of Thiazolidine-4-carboxylic Acid Derivatives as Neuraminidase Inhibitors

In order to understand the chemical-biological interactions governing their activities toward neuraminidase(NA), QSAR models of 28 thiazolidine-4-carboxylic acid derivatives with inhibitory influenza A virus were developed. Here a quantitative structure activity relationship(QSAR) model was built by three-dimensional holographic atomic vector field(3 D-HoVAIF) and multiple linear regression(MLR). The estimation stability and prediction ability of the model were strictly analyzed by both internal and external validations. The correlation coefficient(R2) of established MLR model was 0.984, and the cross-validated correlation coefficient(Q2) of MLR model was 0.947. Furthermore, the cross-validated correlation coefficient for the test set(Qext2) was 0.967. The binding mode pattern of the compounds to the binding site of integrase enzyme was confirmed by docking studies. The results of present study indicated that this model can aid in designing more potent neuraminidase inhibitors.     

Invited review solvatochromic shifts: The influence of the medium on the energy of electronic states

The displacement of electronic absorption and luminescence spectra (solvatochromic shifts) are related to the solute—medium interactions. These interactions can be non-specific (dielectric interactions) when they depend only on multiple and polarizability properties of the solute and solvent molecules; but specific associations such as hydrogen bonding can also be important.

A number of examples of solvatochromic shifts are shown and discussed according to the various solute—medium interactions. The properties of solvent mixtures and those of rigid media are considered, as well as the “thermochromic shifts” which result from the change in the temperature of the medium.

The use of solvatochromic shifts for the determination of the dipole moment and of the polarizability of electronically excited molecules has been important for an understanding of electron distribution changes in such states; examples of such determinations are given, together with references to the original literature.

In the final section some limitations of the theories of solvent shifts and possible improvements are discussed.     

Ca2B2O5的电子结构和能带结构

合成了标题化合物,在已测晶体结构的基础上,利用含组态作用的INDO/S方法计算了其他电子能带结构;利用态求和方法计算了微结构分子的线性极化率及其晶体的平均折射率。分析结果表明,价带主要由B^3^+和O^2^-离子的价轨道的贡献,导带底部主要由Ca^2^+离子轨道的贡献,从O^2^-离子到Ca^2^+离子的电荷转移对线性极化率起主要贡献。     

Molecular structure–biological activity relationships on the basis of quantum-chemical calculations

Detailed quantum-chemical calculations by means of semiempirical all-valence electrons methods and a generalized (multivariable) rank correlation analysis are the fundamentals of a novel strategy of search for QSAR within homologous series of compounds. The set of molecular parameters (describing the electronic and conformational properties as well as potential interactions of the drugs) is calculated theoretically. Owing to the rank correlation method, no linear model (like LFER ) for the dependence of the biological activity upon the molecular parameters is presumed. The computed correlation coefficients are valued by carefully determined levels of statistical significance. Significant correlations are used to predict unknown activities in terms of ranks relative to the basic sample.     

A conceptual framework for predicting the toxicity of reactive chemicals: modeling soft electrophilicity

Although the literature is replete with QSAR models developed for many toxic effects caused by reversible chemical interactions, the development of QSARs for the toxic effects of reactive chemicals lacks a consistent approach. While limitations exit, an appropriate starting-point for modeling reactive toxicity is the applicability of the general rules of organic chemical reactions and the association of these reactions to cellular targets of importance in toxicology. The identification of plausible "molecular initiating events" based on covalent reactions with nucleophiles in proteins and DNA provides the unifying concept for a framework for reactive toxicity. This paper outlines the proposed framework for reactive toxicity. Empirical measures of the chemical reactivity of xenobiotics with a model nucleophile (thiol) are used to simulate the relative rates at which a reactive chemical is likely to bind irreversibly to cellular targets. These measures of intrinsic reactivity serve as correlates to a variety of toxic effects; what's more they appear to be more appropriate endpoints for QSAR modeling than the toxicity endpoints themselves.     

QSAR and Pharmacophore Studies of Thiazolidine-4-carboxylic Acid Derivatives as Novel Influenza Neuraminidase Inhibitors Using HQSAR, Topomer CoMFA and CoMSIA

In order to understand the chemical-biological interactions governing their activities toward neuraminidase (NA), QSAR models of 28 thiazolidine-4-carboxylic acid derivatives with inhibitory influenza A virus were developed. The obtained HQSAR (hologram quantitative structure activity relationship), Topomer CoMFA and CoMSIA (comparative molecular similarity indices analysis) models were robust and had good exterior predictive capabilities. Moreover, QSAR modeling results elucidated that hydrogen bonds highly contributed to the inhibitory activity, then electrostatic and hydrophobic factors. Squared multiple correlation coefficients (R2) of HQSAR, Topomer CoMFA and CoMSIA models were 0.994, 0.978 and 0.996, respectively. Squared cross-validated correlation coefficients (Q2) of HQSAR, Topomer CoMFA and CoMSIA models were in turn 0.951, 919 and 0.820. Furthermore, squared multiple correlation coefficients for the test set (R2test) of HQSAR, CoMFA and CoMSIA models were 0.879, 0.912 and 0.953, respectively. Squared cross-validated correlation coefficients for the test set (Q2ext) of HQSAR, Topomer CoMFA and CoMSIA models were 0.867, 0.884 and 0.899, correspondingly.     

Self-consistent approach for simplifying the molecular interpretation of nonlinear optical and multiphoton phenomena

A method is developed for simplifying molecular interpretations of nonlinear optical phenomena. General sum-over-states expressions derived from perturbation theory can be written identically and self-consistently as simple products of lower-order effects. Electric dipole-allowed expressions for the nonlinear polarizability reduce to straightforward formulas directly connected to intuitive molecular properties without sacrificing mathematical rigor. This approach is sufficiently general to allow its application in treating electronic, vibrational, and vibronic interactions for both parametric (passive) processes (e.g., wave-mixing spectroscopies, sum- and difference-frequency generation, harmonic generation, etc.) and nonparametric (active) processes (e.g., hyper-Raman spectroscopy, multiphoton absorption, etc.). Explicit examples for sum-frequency generation and for four-wave mixing provide a convenient context for interpreting higher order nonlinear optical processes.     

Effect of ionic van der Waals forces on the diffuse potential of model colloids

In this work, the role of ionic dispersion forces in specific ion effects is evaluated through Monte Carlo simulations in the primitive model. More specifically, we assess the effect of such forces on the diffuse potential, since this property is essential to understand the electrokinetic behavior of colloids. In this way, ion specificity arises naturally since ion dispersion forces depend on ionic polarizability, which differs for ions with the same valence. This property is included in the primitive model by means of the Lifshitz theory. The results for different ions are summarized with the help of a nondimensional parameter characterizing the relative weight of ionic van der Waals interactions. Our data reveal that for small ions with high polarizability the ionic dispersion forces can considerably contribute to the specificity of the diffuse potential. In any case, the specific ion effects due to ion polarizability are strongly influenced by ion size.     

Effects of resonance occupation on dynamical electronic properties of adsorbates

A great variety of phenomena encountered in the studies of adsorption systems is, in one way or another, determined by the dynamics and the energetics of electronic transitions in adsorbates. Being intrinsically of a quantum nature, these transitions reflect the properties of the unperturbed species, as well as those of the interactions between the adsorbates and substrates that lead to adsorption. A typical feature of chemisorption systems is the occurrence of adsorbate valence electronic resonances which are degenerate to the substrate valence bands. The presence of a resonance may give rise to changes in the properties of the adsorbate electronic transitions relative to the corresponding gas phase characteristics. These changes should, in turn, manifest themselves in a number of the properties of adsorbates, which can be studied by modern surface sensitive experimental methods. In this article, we first briefly review the characteristics of the adsorbate electronic transitions involving valence resonances. Using this as a prerequisite, we present examples of the physical phenomena and events, such as van der Waals scattering from adsorbates and the measurements of the adsorbate spectra by electronic spectroscopies, which can be interpreted by invoking the effects of fractionally occupied valence resonances on the electronic transitions in chemisorbed species.     

A conceptual framework for predicting the toxicity of reactive chemicals: modeling soft electrophilicity

Although the literature is replete with QSAR models developed for many toxic effects caused by reversible chemical interactions, the development of QSARs for the toxic effects of reactive chemicals lacks a consistent approach. While limitations exit, an appropriate starting-point for modeling reactive toxicity is the applicability of the general rules of organic chemical reactions and the association of these reactions to cellular targets of importance in toxicology. The identification of plausible “molecular initiating events” based on covalent reactions with nucleophiles in proteins and DNA provides the unifying concept for a framework for reactive toxicity. This paper outlines the proposed framework for reactive toxicity. Empirical measures of the chemical reactivity of xenobiotics with a model nucleophile (thiol) are used to simulate the relative rates at which a reactive chemical is likely to bind irreversibly to cellular targets. These measures of intrinsic reactivity serve as correlates to a variety of toxic effects; what's more they appear to be more appropriate endpoints for QSAR modeling than the toxicity endpoints themselves.