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By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a blind test, the method is applied to the lateral chains of the 20 isolated amino acids. One demonstrates that the local softness of the lateral chain is a quantitative measure of the similarity of the amino acids. It predicts the separation of amino acids in different biochemical groups (aliphatic, basic, acidic, sulfur contained, and aromatic). The present approach may find applications in quantitative structure activity relationship methodology. [ABSTRACT FROM AUTHOR]

A new Hirshfeld partitioning of cluster polarizability into intrinsic polarizabilities and charge delocalization contributions is presented. For water clusters, density-functional theory calculations demonstrate that the total polarizability of a water molecule in a cluster depends upon the number and type of hydrogen bonds the molecule makes with its neighbors. The intrinsic contribution to the molecular polarizability is transferable between water molecules displaying the same H-bond scheme in clusters of different sizes, and geometries, while the charge delocalization contribution also depends on the cluster size. These results could be used to improve the existing force fields. [ABSTRACT FROM AUTHOR]

We apply a Monte Carlo technique specialized for the simulation of rare events to study the activated counterions motions in the aluminosilicate Na[sup +]-mordenite. Mean activation barriers are obtained from minimum energy paths calculated on realistic potential energy surfaces by using a Metropolis algorithm. Energy barriers for Na[sup +] hops calculated for lattices with various Si/Al ratio are found in good agreement with the Na[sup +] detrapping energies measured by thermally stimulated current spectroscopy. One shows that the dielectric activated motions of Na[sup +] proceed between degenerated many-body ground states with different dipolar moment by either sequential or collective hopping motions. This provides a first microscopic description of dielectric relaxation measured in zeolites. [ABSTRACT FROM AUTHOR]

The exact equations for the variations of the electronic density induced by an adiabatic external potential are derived to an arbitrary perturbation order in the framework of density-functional-theory. The formal solutions of these density perturbation equations are given and the exact relations between the electronic response functions and the Hohenberg–Kohn functional are derived. Using these relations, the static nonlinear electronic response functions are constructed from the linear one. Nonconserving electron number perturbations are also directly included in the formalism to all perturbation orders. In this way the well-known results of the density-functional reactivity theory are generalized beyond the first and the second-order. This makes it possible to derive the exact relations between the Hohenberg–Kohn functional and the linear and nonlinear Fukui responses, the nonlinear Fukui functions and the nonlinear hardnesses. These relations allow us to reformulate all the derivatives of the electronic energy relative to the external potential and to the particle number in terms of the linear response kernel and in terms of the linear Fukui function. The formalism is applied to the Thomas–Fermi–Dirac-λ von Weiszäcker model of the Hohenberg–Kohn functional. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Presents a Kohn-Sham orbital formulation of the chemical electronic responses. Band-structure formulation of the linear Fukui function; Orbital expression of the linear hardness; Comparison of the orbital expression of the linear hardness to the hardness matrix used in the construction of ab initio pseudo-potentials.

The structure and phonons of an ordered ice surface, prepared in situ under ultra high vacuum conditions, have been studied by high resolution helium atom scattering. The angular distributions are dominated by sharp hexagonal (1x1) diffraction peaks characteristic of a full bilayer terminated ice Ih crystal. Additional, very broad and weak, p(2.1x2.1) peaks may indicate the presence of small domains of antiphase oriented molecules. An eikonal analysis of the 1x1 peaks is compatible with either a proton disordered or a proton ordered surface with corrugations of 0.76 Å and 0.63 Å, respectively. Inelastic time-of-flight spectra reveal not only a dispersionless phonon branch reported previously at 5.9 meV, but also the first evidence for the surface Rayleigh phonons, which are reproduced well by a Born-von Kármán simulation of a full bilayer terminated ice surface using the unmodified force constants derived from neutron scattering bulk phonon measurements. Since the lattice dynamics simulations do not reproduce the dispersionless branch, it is attributed to the vibrations of single water molecules on the ice surface. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.

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.

The values of molecular polarizabilities and softnesses of the 20 amino acids were computed ab initio (MP2). By using the iterative Hirshfeld scheme to partition the molecular electronic properties, we demonstrate that the values of the softness of the side chain of the 20 amino acids are clustered in groups reflecting their biochemical classification, namely: aliphatic, basic, acidic, sulfur containing, and aromatic amino acids. The present findings are in agreement with previous results using different approximations and partitioning schemes [P. Senet and F. Aparicio, J. Chem. Phys. 126, 145105 (2007)]. In addition, we show that the polarizability of the side chain of an amino acid depends mainly on its number of electrons (reflecting its size) and consequently cannot be used to cluster the amino acids in different biochemical groups, in contrast to the local softness. Our results also demonstrate that the global softness is not simply proportional to the global polarizability in disagreement with the intuition that "a softer moiety is also more polarizable." Amino acids with the same softness may have a polarizability differing by a factor as large as 1.7. This discrepancy can be understood from first principles as we show that the molecular polarizability depends on a "softness dipole vector" and not simply on the global softness.