Clustering files of chemical structures using the Szekely-Rizzo generalization of Ward's method

Ward's method is extensively used for clustering chemical structures represented by 2D fingerprints. This paper compares Ward clusterings of 14 datasets (containing between 278 and 4332 molecules) with those obtained using the Szekely–Rizzo clustering method, a generalization of Ward's method. The clusters resulting from these two methods were evaluated by the extent to which the various classifications were able to group active molecules together, using a novel criterion of clustering effectiveness. Analysis of a total of 1400 classifications (Ward and Székely–Rizzo clustering methods, 14 different datasets, 5 different fingerprints and 10 different distance coefficients) demonstrated the general superiority of the Székely–Rizzo method. The distance coefficient first described by Soergel performed extremely well in these experiments, and this was also the case when it was used in simulated virtual screening experiments

Hamiltonian Dynamics of Yang-Mills Fields on a Lattice

We review recent results from studies of the dynamics of classical Yang-Mills fields on a lattice. We discuss the numerical techniques employed in solving the classical lattice Yang-Mills equations in real time, and present results exhibiting the universal chaotic behavior of nonabelian gauge theories. The complete spectrum of Lyapunov exponents is determined for the gauge group SU(2). We survey results obtained for the SU(3) gauge theory and other nonlinear field theories. We also discuss the relevance of these results to the problem of thermalization in gauge theories.Comment: REVTeX, 51 pages, 20 figure

Development and Validation of ReaxFF Reactive Force Field for Hydrocarbon Chemistry Catalyzed by Nickel

To enable the study of hydrocarbon reactions catalyzed by nickel surfaces and particles using reactive molecular dynamics on thousands of atoms as a function of temperature and pressure, we have developed the ReaxFF reactive force field to describe adsorption, decomposition, reformation and desorption of hydrocarbons as they interact with the nickel surface. The ReaxFF parameters were determined by fitting to the geometries and energy surfaces from quantum mechanics (QM) calculations for a large number of reaction pathways for hydrocarbon molecules chemisorbed onto nickel (111), (100) and (110) surfaces, supplemented with QM equations of state for nickel and nickel carbides. We demonstrate the validity and accuracy of ReaxFF by applying it to study the reaction dynamics of hydrocarbons as catalyzed by nickel particles and surfaces. For the dissociation of methyl on the (111), (100), and stepped (111) surfaces of nickel, we observe the formation of chemisorbed CH plus subsurface carbide. We observe that the (111) surface is the least reactive, the (100) surface has the fastest reaction rates, and the stepped (111) surface has an intermediate reaction rate. The importance of surface defects in accelerating reaction rates is highlighted by these results

Structures, Energetics, and Reaction Barriers for CH_x Bound to the Nickel (111) Surface

To provide a basis for understanding and improving such reactive processes on nickel surfaces as the catalytic steam reforming of hydrocarbons, the decomposition of hydrocarbons at fuel cell anodes, and the growth of carbon nanotubes, we report quantum mechanics calculations (PBE flavor of density functional theory, DFT) of the structures, binding energies, and reaction barriers for all CH_x species on the Ni(111) surface using periodically infinite slabs. We find that all CH_x species prefer binding to μ3 (3-fold) sites leading to bond energies ranging from 42.7 kcal/mol for CH_3 to 148.9 kcal/mol for CH (the number of Ni-C bonds is not well-defined). We find reaction barriers of 18.3 kcal/mol for CH_(3,ad) → CH_(2,ad) + H_(ad) (with ΔE = +1.3 kcal/ mol), 8.2 kcal/mol for CH_(2,ad) → CH_(ad) + H_(ad) (with ΔE = -10.2 kcal/mol) and 32.3 kcal/mol for CH_(ad) → C_(ad) + H_(ad) (with ΔE = 11.6 kcal/mol). Thus, CH_(ad) is the stable form of CH_x on the surface. These results are in good agreement with the experimental data for the thermodynamic stability of small hydrocarbon species following dissociation of methane on Ni(111) and with the intermediates isolated during the reverse methanation process

Natural linewidth analysis of d-band photoemission from Ag(110)

We report a high-resolution angle-resolved study of photoemission linewidths observed for Ag(110). A careful data analysis yields k$-resolved upper limits for the inverse inelastic lifetimes of$d$-holes at the X-point of the bulk band structure. At the upper$d$-band edge the hole-lifetime is$\tau_h \geq 22 $fs, i.e. more than one order of magnitude larger than predicted for a free-electron gas. Following calculations for$d$-hole dynamics in Cu (I.\ Campillo et al., Phys. Rev. Lett., in press) we interpret the lifetime enhancement by a small scattering cross-section of $d$- and $sp$-states below the Fermi level. With increasing distance to $E_F$ the $d$-hole lifetimes get shorter because of the rapidly increasing density of d-states and contributions of intra-$d$-band scattering processes, but remain clearly above free-electron-model predictions.Comment: 14 pages, 7 figure

Competing, Coverage-Dependent Decomposition Pathways for C_2H_y Species on Nickel (111)

Competing, coverage-dependent pathways for ethane (CH_3CH_3) decomposition on Ni(111) are proposed on the basis of quantum mechanics (QM) calculations, performed by using the PBE flavor of density functional theory (DFT), for all C_2H_y species adsorbed to a periodically infinite Ni(111) surface. For CH_2CH_3, CHCH_3, and CCH_3, we find that the surface C is tetrahedral in each case, with the surface C forming bonds to one, two, or three Ni atoms with bond energies scaling nearly linearly (E_(bond) = 32.5, 82.7, and 130.8 kcal/mol, respectively). In each of the remaining six C_2H_y species, both C atoms are able to form bonds to the surface. Three of these (CH_2CH_2, CHCH_2, and CCH_2) adsorb most favorably at a fcc-top site with the methylene C located at an on-top site and the other C at an adjacent fcc site. The bond energies for these species are E_(bond) = 19.7, 63.2, and 93.6 kcal/mol, respectively. The remaining species (CHCH, CCH, and C_2) all prefer binding at fcc-hcp sites, where the C atoms sit in a pair of adjacent fcc and hcp sites, with binding energies of E_(bond) = 57.7, 120.4, and 162.8 kcal/mol, respectively. We find that CHCH_(ad) is the most stable surface species (ΔH_(eth) = −18.6), and an important intermediate along the lowest-energy decomposition pathway for ethane on Ni(111). The second most stable species, CCH_3, is a close competitor (ΔH_(eth) = −18.2 kcal/mol), lying along an alternative decomposition pathway that is preferred for high-surface-coverage conditions. The existence of these competing, low- and high-coverage decomposition pathways is consistent with the experiments. The QM results reported here were used as training data in the development of the ReaxFF reactive force field describing hydrocarbon reactions on nickel surfaces [Mueller, J. E.; van Duin, A: C. T.; Goddard, W. A. J. Phys. Chem. C 2010, 114, 4939−4949]. This has enabled Reactive dynamics studying the chemisorption and decomposition of systems far too complex for quantum mechanics. Thus we reported recently, the chemisorption and decomposition of six different hydrocarbon species on a Ni_(468) nanoparticle catalysts using this ReaxFF description [Mueller, J. E.; van Duin, A: C. T.; Goddard, W. A. J. Phys. Chem. C 2010, 114, 5675−5685]

Characteristics of Separated Flow Regions Within Altitude Compensating Nozzles Final Report

Characteristics of separated flow regions within altitude compensating nozzle