Patrick Senet

A Hirshfeld partitioning of polarizabilities of water clusters

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.

Effect of Structural Parameters on the Polarizabilities of Methanol Clusters: A Hirshfeld Study

The polarizabilities of fifty methanol clusters (CH3OH)n, n = 1 to 12, were calculated at the B3LYP/6-311++G** level of theory and partitioned into molecular contributions using the Hirshfeld-I method. The resulting molecular polarizabilities were found to be determined by the polarizabilities of the two parts of the molecule, the hydrophilic hydroxyl group and the hydrophobic methyl group, each exhibiting a different dependency upon the local environment. The polarizability of the hydroxyl group was found to be dependent on the number, type, and strength of the hydrogen bonds a methanol molecule makes, whereas the polarizability of the methyl groups is mostly influenced by sterical hindrance. The findings were compared with the results obtained in a previous study on water clusters. The influence of the BSSE correction was investigated and found to increase polarizability values by up to 8.5%.

Influence of structure on the polarizability of hydrated methane sulfonic acid clusters

The relationship between polarizability and structure is investigated in methane sulfonic acid (MSA) and in 36 hydrated MSA clusters. The polarizabilities are calculated at B3LYP and MP2 level and further partitioned into molecular contributions using classic and iterative Hirshfeld methods. The differences in the two approaches for partitioning of polarizabilities are thoroughly analyzed. The polarizabilities of the molecules are found to be influenced in a systematic way by the hydrogen bond network in the clusters, proton transfer between MSA and water molecules, and weak interactions between water molecules and the methyl group of MSA.

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.

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

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.

Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent

Human 70 kDa heat shock protein (hHsp70) is an ATP-dependent chaperone and is currently an important target for developing new drugs in cancer therapy. Knowledge of the conformations of hHsp70 is central to understand the interactions between its nucleotide-binding domain (NBD) and substrate-binding domain (SBD) and is a prerequisite to design inhibitors. The conformations of ADP-bound (or nucleotide-free) hHsp70 and ATP-bound hHsp70 was investigated by using unbiased all-atom molecular dynamics (MD) simulations of homology models of hHsp70 in explicit solvent on a timescale of .5 and 2.7 μs, respectively. The conformational heterogeneity of hHsp70 was analyzed by computing effective free-energy landscapes (FELs) and distance distribution between selected pair of residues. These theoretical data were compared with those extracted from single-molecule Förster resonance energy transfer (FRET) experiments and to small-angle X-ray scattering (SAXS) data of Hsp70 homologs. The distance between a pair of residues in FRET is systematically larger than the distance computed in MD which is interpreted as an effect of the size and of the dynamics of the fluorescent probes. The origin of the conformational heterogeneity of hHsp70 in the ATP-bound state is due to different binding modes of the helix B of the SBD onto the NBD. In the ADP-bound (or nucleotide-free) state, it arises from the different closed conformations of the SBD and from the different positions of the SBD relative to the NBD. In each nucleotide-binding state, Hsp70 is better represented by an ensemble of conformations on a μs timescale corresponding to different local minima of the FEL. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:30

Activated cation motions in zeolites

We apply a Monte Carlo technique specialized for the simulation of rare events to study the activated counterions motions in the aluminosilicate Na+-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+ hops calculated for lattices with various Si/Al ratio are found in good agreement with the Na+ detrapping energies measured by thermally stimulated current spectroscopy. One shows that the dielectric activated motions of Na+ 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.

Density functional theory fragment descriptors to quantify the reactivity of a molecular family: Application to amino acids

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.

Dependence of the Energy of Water Molecules in Clusters upon Hydrogen Bonds: A Hirshfeld Study

The energy of water clusters, containing up to 20 water molecules, are partitioned into molecular contributions using the Hirshfeld method at the DFT level. The molecular energies are analyzed with respect to the hydrogen bonding network in the clusters.

Angstrom-Size Defect Creation and Ionic Transport through Pores in Single-Layer MoS2

Atomic-defect engineering in thin membranes provides opportunities for ionic and molecular filtration and analysis. While molecular-dynamics (MD) calculations have been used to model conductance through atomic vacancies, corresponding experiments are lacking. We create sub-nanometer vacancies in suspended single-layer molybdenum disulfide (MoS2) via Ga+ ion irradiation, producing membranes containing ∼300 to 1200 pores with average and maximum diameters of ∼0.5 and ∼1 nm, respectively. Vacancies exhibit missing Mo and S atoms, as shown by aberration-corrected scanning transmission electron microscopy (AC-STEM). The longitudinal acoustic band and defect-related photoluminescence were observed in Raman and photoluminescence spectroscopy, respectively. As the irradiation dose is increased, the median vacancy area remains roughly constant, while the number of vacancies (pores) increases. Ionic current versus voltage is nonlinear and conductance is comparable to that of ∼1 nm diameter single MoS2 pores, proving that the smaller pores in the distribution display negligible conductance. Consistently, MD simulations show that pores with diameters <0.6 nm are almost impermeable to ionic flow. Atomic pore structure and geometry, studied by AC-STEM, are critical in the sub-nanometer regime in which the pores are not circular and the diameter is not well-defined. This study lays the foundation for future experiments to probe transport in large distributions of angstrom-size pores.