Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session P10: Focus Session: Frontiers in Computational Chemical Physics IV |
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Sponsoring Units: DCP Chair: Andrew Rappe, University of Pennsylvania Room: Baltimore Convention Center 302 |
Wednesday, March 15, 2006 11:15AM - 11:51AM |
P10.00001: First Principles Dynamics Beyond the Born-Oppenheimer Approximation Invited Speaker: The dynamics of molecules in excited electronic states almost invariably involves breakdown of the Born-Oppenheimer approximation, necessitating treatment of quantum mechanical effects for both electrons and nuclei. The ab initio multiple spawning (AIMS) method has been developed in order to model molecular dynamics in excited states from first principles, solving both the electronic and nuclear Schr\"{o}dinger equations ``on the fly.'' We discuss some recent developments in the AIMS methodology and applications to photodamage in DNA bases. Theoretical results are compared directly to femtosecond spectroscopy experiments. Recent attempts to couple the AIMS approach with optimization algorithms to redesign fluorescent proteins will also be discussed, if time allows. [Preview Abstract] |
Wednesday, March 15, 2006 11:51AM - 12:03PM |
P10.00002: First principles studies of CO adsorption and oxidation on the Cu$_{2}$O(100) surface Sergey Stolbov, Duy Le, Talat S. Rahman This work is motivated by the experimental results [1] indicating that the rate of CO oxidation on Cu$_{2}$O surface is much higher than that on Cu and CuO surfaces. To gain insight into the nature of this effect we study from first principles the energetics of adsorption and oxidation of CO on Cu$_{2}$O(100). Applying the \textit{ab initio} thermodynamics approach [2] to the surface in contact with gaseous O$_{2}$, we find that the O-termination of Cu$_{2}$O(100) is preferred for all reasonable range of temperature and the O$_{2}$ pressure. We find that CO adsorbed on surface O associates with it to form CO$_{2}$ without any activation barrier. On the other hand, CO adsorbing on a surface Cu atom, it is found to slide first towards the neighboring O atom to form CO$_{2}$ as in the previous case. We analyze the local densities of electronic states and valence charge densities of the systems to rationalize the obtained results. \begin{enumerate} \item T.-J. Huang and D.-H. Tsai, Catal. Lett. 87, 173 (2003). \item K. Reuter and M. Scheffler, Phys. Rev. B \textbf{65}, 035406 (2002). \end{enumerate} [Preview Abstract] |
Wednesday, March 15, 2006 12:03PM - 12:15PM |
P10.00003: Electronic structure and bonding properties of K and K $^{+}$ on graphite under external electric field Alejandro Tapia, Romeo de Coss, Gabriel Canto The effect of an external electric field on the adsorption of K and K$^{+}$ on the graphite (0001) surface, are studied by means of first- principles total-energy calculations. The results were obtained with the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. The structural parameters, bonding properties, and electronic structure of the K and K$^{+}$-graphite system are studied in the triangular (2x2) overlayer phase as a function of the external electric field magnitude. We find an important change in the K and K$^{+}$-graphite bonding as a consequence of the charge transfer from the adatom towards the substrate induced by the electric field. However, we find that none of the investigated systems show diffusion of K or K$^{+}$ into graphite even with a strong electric field. The results are discussed in the light of the experimental observed diffusion of K into graphite, presumably induced by external electric fields. [Preview Abstract] |
Wednesday, March 15, 2006 12:15PM - 12:27PM |
P10.00004: Carbon-based nanostructured materials for enhanced H$_{2}$ production M.K. Kostov, E.E. Santiso, A.M. George, K.E. Gubbins, M.B. Nardelli A key fundamental limit of the thermal splitting of bulk water is the fact that the ground state of oxygen is paramagnetic, whereas the ground state of water is diamagnetic. Here, we propose to explore a new paradigm in H$_{2}$ production: a process in which the system remains on the spin singlet potential surface throughout the reaction, by exploiting the catalytic role of defective carbon substrates. Using first principles modeling techniques, we found evidence that mono-vacancy defects in graphite and carbon nanotubes give rise to a rich chemistry, yielding many possible water dissociation pathways, some of which have activation barriers lower than half the value for the dissociation of bulk water. This reduction is caused by spin selection rules that allow the system to remain on the same spin surface throughout the reaction. These novel reactions enhance the hydrogen yield and the reaction rate. In the presence of water only, this reaction is self-limiting: when all of the defects are oxidized, the reaction is complete, and no further H$_{2}$ is produced. There are several possibilities to achieve regeneration of the active surface sites, such as photo-excitation, vibrational excitations or further reaction with other molecules. We will discuss this exploration in the context of a complete cycle of energy storage and release through the production of H$_{2}$. [Preview Abstract] |
Wednesday, March 15, 2006 12:27PM - 12:39PM |
P10.00005: Quantum dynamics with wavepackets and density matrices: A novel computational tool with applications to biological enzymes. Srinivasan Iyengar A recently developed computational approach for simultaneous dynamics of electrons and nuclei is discussed. The approach is based on a synergy between quantum wavepacket dynamics and ab initio molecular dynamics. The quantum dynamics is performed using an efficient banded, sparse and Toeplitz representation for the discretized free propagator that is formally exact. Ab initio molecular dynamics is achieved by using (a) an extended Lagrangian formalism, known as atom-centered density matrix propagation, that effects an adjustment of time-scales of the electronic motion, (b) Born-Oppenheimer dynamics. The quantum dynamics and ab initio dynamics schemes are coupled through a time-dependent self consistent field-like procedure. Higher order coupling between the subsystems is inherent when the Born-Oppenheimer procedure is used as opposed to atom-centered density-matrix propagation. A fundamental computational bottleneck associated with the computation of the interaction potential between the ab initio and quantum dynamical subsystem are overcome through a novel importance sampling approach and this aspect is also discussed. Further generalization for periodic quantum dynamical treatment in extended systems is outlined. [Preview Abstract] |
Wednesday, March 15, 2006 12:39PM - 12:51PM |
P10.00006: First-Principles pH Theory Yong-Hyun Kim, S. B. Zhang Despite being one of the most important macroscopic measures and a long history even before the quantum mechanics, the concept of pH has rarely been mentioned in microscopic theories, nor being incorporated computationally into first-principles theory of aqueous solutions. Here, we formulate a theory for the pH dependence of solution formation energy by introducing the proton chemical potential as the microscopic counterpart of pH in atomistic solution models. Within the theory, the general acid-base chemistry can be cast in a simple pictorial representation. We adopt density-functional molecular dynamics to demonstrate the usefulness of the method by studying a number of solution systems including water, small solute molecules such as NH$_3$ and HCOOH, and more complex amino acids with several functional groups. For pure water, we calculated the auto- ionization constant to be 13.2 with a 95 \% accuracy. For other solutes, the calculated dissociation constants, i.e., the so- called pK$_{\rm a}$, are also in reasonable agreement with experiments. Our first-principles pH theory can be readily applied to broad solution chemistry problems such as redox reactions. [Preview Abstract] |
Wednesday, March 15, 2006 12:51PM - 1:03PM |
P10.00007: Efficiency and accuracy in transition-metal chemistry: a self-consistent GGA+U approach Heather Kulik, Matteo Cococcioni, Nicola Marzari Transition-metal centers are the active sites for a broad variety of biological and inorganic chemical reactions. Notwithstanding this central importance, density-functional theory calculations based on local-density or generalized gradient approximations often fail qualitatively and quantitatively in describing energetics, multiplet structures, reaction barriers, and geometries around the active sites. We suggest here an alternative approach, mutuated from the Hubbard U correction to solid-state problems, that provides an excellent agreement with accurate, correlated-electron quantum chemistry calculations in paradigmatic test cases that range from the ground state of the Fe$_2$ dimer to the potential energy surfaces for the addition-elimination of molecular hydrogen on FeO$^+$. The Hubbard U is determined with a novel self-consistent procedure based on a linear-response approach. [Preview Abstract] |
Wednesday, March 15, 2006 1:03PM - 1:15PM |
P10.00008: First principles calculation of the x-ray absorption spectra of ice and liquid water David Prendergast, Giulia Galli Recent interpretations of x-ray absorption spectra (XAS) of ice and liquid water propose that the standard, tetrahedral model of the liquid should be replaced with a model where each water molecule possesses two stronger and two weaker hydrogen bonds to nearest neighbor molecules. We have investigated this issue and find no conclusive evidence to discount the standard model. Using density functional theory (DFT) calculations we find an excellent agreement with experiment for the XAS of ice I. We perform TIP4P classical molecular dynamics simulations of the liquid at 300K. Using 10 statistically uncorrelated snapshots of 32 molecules in our DFT calculations, we compute the XAS of this standard liquid model and also find a reasonable agreement with experiment. The spectral differences between liquid and solid arise from both structural disorder and the presence of dangling hydrogen bonds. [Preview Abstract] |
Wednesday, March 15, 2006 1:15PM - 1:27PM |
P10.00009: Exploiting unitary invariance in ab initio molecular dynamics: Applications to spectral decomposition and surface reactions Mark Tuckerman The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated using forces computed ``on the fly'' from electronic structure calculations, has benefited significantly from its combination with maximally localized electronic orbitals. The latter exploit the unitary invariance of the total energy to generate orbitals with maximum spatial locality. These orbitals resemble the classic textbook picture of molecular orbitals and, hence, are useful tools for analyzing electronic structure. In addition, maximally localized orbitals, expanded in localized basis sets, are a key component in linear scaling methods. In this talk, it will be shown how techniques from quantum field theory can be used to reformulate ab initio molecular dynamics in such a way that maximally localized orbitals are generated automatically and dynamically as the calculation proceeds. As an application of the technique, it will be shown how IR spectra can be decomposed to reveal particular structures in aqueous solutions. A second application will focus on the addition of organic molecules to the Si(100)-2x1 surface. [Preview Abstract] |
Wednesday, March 15, 2006 1:27PM - 1:39PM |
P10.00010: Engineering protein structure and function with computational protein design Jeffery Saven Understanding molecular folding has important applications to understanding biology and to developing new therapeutics and new materials.~ Protein design also opens new ways to probe the determinants of folding and to facilitate the study of proteins. Such design is complicated, however, by~the conformational complexity of proteins and by the large numbers of possible sequences. Recent computational methods for identifying the properties of amino acid sequences likely to fold to a given three-dimensional structure will be presented. Several examples of structures so designed, which have been experimentally synthesized and characterized, will be presented. [Preview Abstract] |
Wednesday, March 15, 2006 1:39PM - 1:51PM |
P10.00011: First-Principles Calculations of van't Hoff Plots for Novel Hydrogen-Storage Materials Nikolai Zarkevich, D.D. Johnson A van't Hoff plot, log(P) vs. 1/T, provides information on the free-energy change in a reaction and is widely used to characterize hydrogen-storage materials. Recently, a new reaction of LiBH$_4$ destabilized by MgH$_2$ (yielding over 11 wt.\% of H$_2$) was proposed.\footnote{J.J. Vajo et al., J. of Phys. Chem. B 109, p.3719 (2005)} Here we investigate this reaction and its products by first-principles calculations and construct the van't Hoff plot for a direct comparison to experiment. Although it is often assumed that there is a constant slope in the van't Hoff plot for ease of interpretation, we find an important non-linearity arising from temperature-dependent vibrational entropy difference, etc. This non-linearity can be critical for an accurate comparison to experimental data, and between various reactions to determine optimal hydrogen-storage systems. Including these effects, we find agreement with recent measurements. [Preview Abstract] |
Wednesday, March 15, 2006 1:51PM - 2:03PM |
P10.00012: Application of Generalized Sturmians to the Bound States of Two-Electron Atoms and Molecules Eddie Red, Albert Wynn III, Charles Weatherford A variation on the method of Generalized Sturmians [J. Avery, $\underline {Hyperspherical\ Harmonics and \ GeneralizedSturmians}$, Kluwer, 2000], is applied to the calculation of the ground and excited states of two-electron atoms and molecules (etc. He, H$_2$). In the present implementation of this method, each determinant formed from a set of primitive one-electron Sturmians, is required to separately solve the Sch\"odinger equation. In the process, the screening constant of each one- electron Sturmian orbital is non-iteratively uniquely determined. The resultant generalized eigenvalue problem however has a non-positive- definite overlap matrix. The method of \lq corresponding orbitals\rq\ [H.F. King et. al. J. Chem. Phys. 47, 1936 (1967)] is used to produce a positive-definite overlap matrix. A CI calculation is then performed whereby the Hartree-Fock calculation is avoided. Results will be presented and compared with Hartree-Fock based CI calculations. [Preview Abstract] |
Wednesday, March 15, 2006 2:03PM - 2:15PM |
P10.00013: Characterizing the potential energy landscape by its geodesic paths Chengju Wang, Richard M. Stratt We suggest that the time evolution of a condensed-matter system is related to a unique exploration path in its multidimensional potential energy surface. We show that sampling from what we call the potential energy landscape filling ensemble, we can study the potential energy landscape of a monatomic Lennard-Jones system without the complications of barrier hopping processes. The ensemble defined to include all the configurations with potential energy less than a specified value, allows us to sample the geodesic path between two randomly selected configurations. The geodesics were tentatively related to the dynamics of the system under the assumption that the geodesic path corresponds to the most efficient exploration route on its potential energy surface. The derived dynamic parameters were compared with those obtained from a molecular dynamics simulation. The agreement we found offers us a new method for relating the dynamics of a system to the topology of its static potential energy surface. [Preview Abstract] |
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