A density functional theory-based chemical potential equalisation approach to molecular polarizability

The electron density changes in molecular systems in the presence of external electric fields are modeled for simplicity in terms of the induced charges and dipole moments at the individual atomic sites. A chemical potential equalisation scheme is proposed for the calculation of these quantities and hence the dipole polarizability within the framework of density functional theory based linear response theory. The resulting polarizability is expressed in terms of the contributions from individual atoms in the molecule. A few illustrative numerical calculations are shown to predict the molecular polarizabilities in good agreement with available results. The usefulness of the approach to the calculation of intermolecular interaction needed for computer simulation is highlighted.     

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.     

Transition metal NMR chemical shifts and polarizability effect in organometallic complexes

The literature data on substituent influence on the ⁵¹V, ⁵⁵Mn, ⁵⁷Fe, ⁵⁹Co, ⁶¹Ni, ⁹⁵Mo, ¹⁰³Rh, ¹⁸³W, ¹⁸⁷Os and ¹⁹⁵Pt NMR chemical shifts (δ) and on J (M, P; M = Mn, Fe, Mo, Rh, W, Os) coupling constants have been analyzed for 30 series of the organometallic complexes. It has been established for the first time that the δ and J values depend on the inductive, resonance and polarizability effects of substituents. The polarizability effect is caused by the partial charge on the central M atom. The contribution of this effect ranges from 3 to 86%. Copyright © 2009 John Wiley & Sons, Ltd.     

Correlation analysis of quantum chemical data and the polarizability effect in H-complexes

The study is concerned with analysis of the energies of formation (E), frequency shifts (Δν) in IR spectra, ionization potentials (IP) of H-complexes, hydrogen bond lengths (r), and spin densities (sd) in H-complexes involving radical cations, obtained from quantum chemical calculations for 20 series of H-complexes. It was for the first time established that the E, IP, r, and sd values and the changes in enthalpy (δH) depend not only on the inductive and resonance effects but also on the polarizability effect of the substituents bound to the donor and acceptor centers in the H-complexes. Interrelations between the polarizability effect and the molecular structure of H-complexes are considered. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 602–608, April, 2006.     

Calculation of polarizability derivatives using analytic gradient methods

Expressions are given for polarizability derivatives calculated using closed-shell SCF wavefunctions, and their implementation is discussed. Example calculations are given for H₂O and (H₂O)₂.     

On molecular polarizability. 4. Evaluation of the ionization potential for alkanes and alkenes with polarizability

To express the influence of polarizability effect on ionization potential (Ip), the Geometric Mean Polarizability Effect Index (GMPEI) and Geometric Mean Polarizability Effect Index of pi Bond (GMPEIpi) were proposed for alkanes and alkenes, respectively. Taking a few of the compounds as a model, we obtained the correlation equations between the experimental Ip and GMPEI or GMPEI pi and then, with the obtained equations, we evaluated the Ip for the title compounds. The estimated Ip values by this work are in good agreement with the measured ones. Furthermore, the ab initio (#HF/6-31G** OPT, Gaussian 98 program) and semiempirical (AM1) Ip computation are finished, and other topological index correlations with the Ip of alkane are discussed.     

Improved exchange-correlation potential for polarizability and dissociation in density functional theory

The authors propose a novel approach to the problem of polarizabilities and dissociation in electric fields from the static limit of the Vignale-Kohn (VK) functional. The response to the purely scalar part of the VK response potential is considered. This potential has ground-state properties that notably improve over the full VK response density and over usual (semi-)local functionals. The correct qualitative behavior of our potentials means that it is expected to work well for polarizabilities in cases such as the H(2) chain, and it will also correctly dissociate open-shell fragments in a field.     

Variable scaling and nearest neighbor methods

When employing nearest neighbor classifiers scaling of input variables is often useful. In this paper we propose a small modification in usual data preprocessing: scaling of variables should be done by use of pooled variances instead of overall ones. Thus prediction accuracy is distinctly improved in some situations. Copyright © 2008 John Wiley & Sons, Ltd.     

Choice of quantum chemical methods and the calculation of the structure,dipole moment,and polarizability of phosphoryl compounds in the gas phase

Journal of Structural Chemistry - Molecules of phosphoryl compounds (H3PO, HF2PO, F3PO, Cl3PO, CH3POF2, CH3POCl2, and (CH3)3PO) are calculated at the Hartree-Fock, density functional theory with...     

Effect of crystal potential on dynamic polarizability of negative ions

Summary We combine a time-dependent approach with a crystal potential model to study environment-specific optical linear response of closed-shell ions within crystals under the influence of an external time-varying field. It is shown how the dynamic dipole polarizability of free halogen anions within the normal dispersion region is altered due to the crystal potentials felt by the anions in environments appropriate for different binary cubic ionic lattices. The pole-positions of the in-crystal anion polarizability are found to be consistent with the vacuum ultraviolet absorption edges of the corresponding alkali halides and to vary linearly with the lattice potentials at the anion sites in these salts. It is observed that the crystal potential induces quite a large enhancement in the anionic absorption oscillator strengths of these dipole transitions, thereby making these values conform well with those of the first excitonic absorptions in such crystals.     

Structure and molecular polarizability of mesogenic Shiff bases from quantum chemical calculation data

The molecular polarizability of a number of Shiff bases and compounds with similar structures is calculated by B3LYP/6-311G(d,p) (d ⁵) method. The comparison of calculated data with available experimental illustrates the stable correlation between the calculated and experimental polarization tensor components. The calculation results confirm the applicability of the additivity approximation to estimate the polarizability of azomethines with terminal substituents. The relation between the molecular anisotropy of polarizability of azomethines and the temperature of the phase transition nematic-isotropic liquid is examined. Also the effect of acoplanarity degree of azomethines on the molecular polarizability is considered.     

Strategies for kinome profiling in cancer and potential clinical applications: chemical proteomics and array-based methods

Kinases are key enzymes involved in deregulated signal transduction associated with cancer development and progression. The advent of personalized medicine drives the development of new diagnostic tools for patient stratification and therapy selection Ginsburg and Willard (Transl Res 154:277-287, 2009). Since deregulation of kinase-mediated signal transduction is implied in tumorigenesis, the analysis of all kinases (the kinome) active in a particular tumor may yield tumor-specific information on aberrant cell signalling pathways. Tumor tissue kinase activity profiles may correlate with response to therapy and therefore may be used for future therapy selection. In this Trend paper we describe peptide array and mass spectrometry-based technologies and new developments for kinome profiling, and we present an outlook towards future implementation of therapy selection based on kinome profiling in clinical practice.     

Relations between coordinate and potential scaling in the high-density limit

Exact relations are derived between scaling to the high-density limit of density functional theory and taking Z to infinity for nondegenerate atoms. Gorling-Levy perturbation results are deduced for hydrogenic densities. The kinetic contribution to the correlation energy is also studied, and estimates given for its value for neutral atoms. Popular approximate functionals are tested against these benchmarks.     

Efficient multipole model and linear scaling of NDDO-based methods

Fast growth of computational costs with that of the system's size is a bottleneck for the applications of traditional methods of quantum chemistry to polyatomic molecular systems. This problem is addressed by the development of linear (or almost linear) scaling methods. In the semiempirical domain, it is typically achieved by a series of approximations to the self-consistent field (SCF) solution. By contrast, we propose a route to linear scalability by modifying the trial wave function itself. Our approach is based on variationally determined strictly local one-electron states and a geminal representation of chemical bonds and lone pairs. A serious obstacle previously faced on this route were the numerous transformations of the two-center repulsion integrals characteristic for the neglect of diatomic differential overlap (NDDO) methods. We pass it by replacing the fictitious charge configurations usual for the NDDO scheme by atomic multipoles interacting through semiempirical potentials. It ensures invariance of these integrals and improves the computational efficiency of the whole method. We discuss possible schemes for evaluating the integrals as well as their numerical values. The method proposed is implemented for the most popular modified neglect of diatomic overlap (MNDO), Austin model 1 (AM1), and PM3 parametrization schemes of the NDDO family. Our calculations involving well-justified cutoff procedures for molecular interactions unequivocally show that the proposed scheme provides almost linear scaling of computational costs with the system's size. The numerical results on molecular properties certify that our method is superior with respect to its SCF-based ancestors.     

Exploring potential energy surfaces for chemical reactions: an overview of some practical methods

Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described.     

Scientific foundations and effective chemical methods of combustion,explosion, and gas detonation control

The competition between the branching and termination of reaction chains is shown to determine all general laws of gas combustion and explosion not only at pressures much lower that atmospheric, but also at atmospheric and increased pressures upon self-heating. It is established that the role of any elementary reaction in combustion is determined primarily by its effect on the relation between the rates of chain branching and termination. Scientific foundations and effective chemical methods of combustion, explosion, and combustible gas detonation control are developed.     

Origin of threefold methyl torsional potential in methylindoles

In this article, we present a systematic study on mono-methylindoles to investigate the electronic origin of the threefold symmetric component (V ₃) of the methyl torsional potential barrier in the ground electronic state (S ₀). The structures and the torsional potential parameters of these molecules were evaluated from ab initio calculation using Hartree-Fock (HF), second order Mollar Plesset perturbation (MP2) and B3LYP density functional level of theories and Gaussian type basis set 6-31G(d, p). Natural bond orbital (NBO) analysis of these molecules were carried out using B3LYP/6-31G(d, p) level of calculation to understand the formation of the threefold V ₃ term arising from the changes of various non-covalent interactions during methyl rotation. Our analysis reveals that the contributions from π orbitals play a dominant role in the barrier height determination in this class of molecules. The threefold term in the barrier arises purely from the interactions non-local to the methyl group in case when the methyl group has two single bonds vicinal to it. On the other hand, it is the local interaction that determines the potential energy barrier when the methyl group has one single bond and one double bond vicinal to it. However, in all these cases, the magnitude of the energy barrier depends on the resonance structure formation in the benzene ring frame upon rotation of the methyl group and, therefore, the energetics of the barrier cannot be understood without considering the molecular flexing during methyl rotation.     

Origin of the size-dependence of the polarizability per atom in heterogeneous clusters: The case of AlP clusters

An analysis of the atomic polarizabilities α in stoichiometric aluminum phosphide clusters, computed at the MP2 and density functional theory (DFT) levels, the latter using the B3LYP functional, and partitioned using the classic and iterative versions of the Hirshfeld method, is presented. Two sets of clusters are examined: the ground-state Al(n)P(n) clusters (n=2-9) and the prolate clusters (Al(2)P(2))(N) and (Al(3)P(3))(N) (N≤6). In the ground-state clusters, the mean polarizability per atom, i.e., α/2n, decreases with the cluster size but shows peaks at n=5 and at n=7. We demonstrate that these peaks can be explained by a large polarizability of the Al atoms and by a low polarizability of the P atoms in Al(5)P(5) and Al(7)P(7) due to the presence of homopolar bonds in these clusters. We show indeed that the polarizability of an atom within an Al(n)P(n) cluster depends on the cluster size and the heteropolarity of the bonds it forms within the cluster, i.e., on the charges of the atoms. The polarizabilities of the fragments Al(2)P(2) and Al(3)P(3) in the prolate clusters were found to depend mainly on their location within the cluster. Finally, we show that the iterative Hirshfeld method is more suitable than the classic Hirshfeld method for describing the atomic polarizabilities and the atomic charges in clusters with heteropolar bonds, although both versions of the Hirshfeld method lead to similar conclusions.     

Dynamic scaling and slowing down in chemical reactions of the critical triethylamine-water system

Between 100 kHz and 1 MHz, special ultrasonic attenuation measurements of the triethylamine-water mixture of critical composition have been performed for the determination of the Bhattacharjee-Ferrell scaling function. The experimental data are evaluated considering two noncritical Debye-type relaxation terms as revealed by broadband ultrasonic spectra. Shear viscosity and dynamic light scattering data from the literature are re-evaluated to yield the relaxation rate of order parameter fluctuations of the critical system as a function of temperature. The power law behavior found for the relaxtion rate fits to the scaling function in the ultrasonic spectra. The relaxation times of the noncritical Debye terms display a non-Arrhenius temperature dependence, pointing at effects of slowing in the chemical reactions associated with the relaxations.