Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session P18: Condensed Phase Dynamics, Structure and Thermodynamics |
Hide Abstracts |
Sponsoring Units: DCP Chair: Branka Ladanyi, Colorado State University Room: Colorado Convention Center 103 |
Wednesday, March 7, 2007 11:15AM - 11:27AM |
P18.00001: First-principles study of molecular point defects in ice Ih Maurice de Koning, Alex Antonelli, Antonio J.R. da Silva, Adalberto Fazzio We present a first-principles study of the structure and energetics of molecular point defects in ice Ih [1]. Our approach is based on a DFT-GGA description, utilizing a periodic supercell containing 96 water molecules. We compute the formation free energies and corresponding thermal equilibrium concentrations as a function of temperature for the molecular vacancy and 3 different interstitial structures: the Tc, Tu and Bc configurations. The latter involves bonding to the surrounding lattice, whereas the first two do not. The results indicate that, due to its bonding to the surrounding lattice, the equilibrium concentration of the Bc interstitial is larger than that of the Tc and Tu structures, suggesting that the Bc structure is the preferred interstitial configuration in ice Ih. Comparison with the molecular vacancy, on the other hand, indicates that the vacancy is expected to be the overall dominant molecular point defect in ice Ih, at least for temperatures below T $\approx $ 200 K. Due to the elevated formation entropy of the Bc interstitial, however, a crossover scenario in which the Bc interstitial becomes favored at temperatures below the melting point, as has been suggested experimentally, is conceivable. \newline [1] M. de Koning, A. Antonelli, A.J.R. da Silva and A. Fazzio, Phys. Rev. Lett. \textbf{97}, 155501 (2006). [Preview Abstract] |
Wednesday, March 7, 2007 11:27AM - 11:39AM |
P18.00002: Size- and Temperature- Dependent Crystal Growth Rates Xian-Ming Bai, Mo Li Using molecular dynamics simulations and a crystal/melt coexistence model, we have calculated the size-dependent crystal growth rates of a Lennard-Jones system over a wide range of undercooling temperatures. Our results show that the growth rate or interface moving velocity decreases substantially with the increasing system size. It is found that the system fluctuations are related to the finite-size effects. By treating the atomic site acceptance ratio as a function of temperature and system size rather than a constant, we modified the collision-controlled model which fits the simulation results well. [Preview Abstract] |
Wednesday, March 7, 2007 11:39AM - 11:51AM |
P18.00003: ESR Studies of a Reorienting Nickel Complex Bruce Kowert Electron spin resonance spectra of the planar bis(maleonitriledithiolato)nickel anion radical (BMNT) in the intermediate motional region have been simulated in several polar solvents using axially symmetric reorientation. The rotational diffusion about the long in-plane axis is three to four times faster than that about the two axes perpendicular to it. The reorientational model needed to produce agreement with experiment is either in or close to the Brownian rotational diffusion limit. The solvents are 4-allyl-2-methoxyphenol (eugenol), dimethyl phthalate, tri-$n$-butyl phosphate, tris(2-ethyl-hexyl)phosphate, and 2-methoxyethyl ether (diglyme), ethyl alcohol, and a dimethylformamide-chloroform mixed solvent. The reorientational rates from the simulations are in general agreement with those from line width analyses carried out from the fast to the slow motional regions. The temperature dependence of the diffusion rates is discussed in terms of the Stokes-Einstein-Debye (SED) model and the Vogel-Tammann-Fulcher equation. [Preview Abstract] |
Wednesday, March 7, 2007 11:51AM - 12:03PM |
P18.00004: Low coverage Neon adsorption on HiPCo$^{TM}$ nanotube bundles Subramanian Ramachandran, Oscar Vilches We present heat capacity measurements of Ne adsorbed on single-walled closed-end carbon nanotube bundles (HiPCo$^{TM})$ between 2 and 20 K. Limited adsorption isotherms measurements for 17K$<$T$<$28K allow us to estimate the isosteric heat of adsorption for these films. Particular emphasis is on the results at very low coverage, between 0.02 monolayer to 0.3 monolayer where Ne may form single-line and three-lines of atoms in imperfect adsorption sites and grooves. The specific heat versus temperature at 0.02 -- 0.04 monolayer coverage shows qualitative agreement with a model of adsorption of Ne on grooves by Kostov et.al (PRB 68, 245403, (2003)). For 0.06 monolayer and higher coverages, however, the measured low temperature specific heat vs temperature has a T$^{2}$ dependence, which yields 2D Debye temperatures in the range of 44 to 47 K. [Preview Abstract] |
Wednesday, March 7, 2007 12:03PM - 12:15PM |
P18.00005: Structure and dynamics of levitated liquid aluminates Louis Hennet, Irina Pozdnyakova, Marie-Louise Saboungi, David L. Price We have used the aerodynamic levitation technique combined with CO$_{2}$ laser heating to study the structures of liquid CaAl$_{2}$O$_{4}$ and MgAl$_{2}$O$_{4}$ with x-ray and neutron diffraction. We determined the structure factors and corresponding pair correlation functions describing the short-range order in the liquids. The combination of the two scattering techniques makes it possible to derive information not accessible with a single measurement. We have also obtained information on the dynamics of liquid MgAl$_{2}$O$_{4}$ with inelastic x-ray scattering. [Preview Abstract] |
Wednesday, March 7, 2007 12:15PM - 12:27PM |
P18.00006: Thermal Fluctuations and Excitonic Interactions in Polyadenosine John Jean Interest in the electronic structure and photophysics of DNA has been sparked in recent years by increased awareness of the biological effects of non--ionizing UV radiation as well as the possibility of using short DNA oligomers as molecular conduits for efficient charge or energy transport in nanoscale devices. The optical properties of DNA in the near UV region are governed by dipole-allowed transitions localized on the aromatic bases, which have excited state lifetimes on the order of a few hundred femtoseconds. Recent time-resolved experiments on polyadenosine oligomers, however, provide clear evidence for stacking-induced long-lived, stacking-induced states and spectral shifts compared to those of the monomer bases. The origin of these states and their relation to stacking dynamics is still largely unknown. DNA is a highly dynamic structure undergoing large-amplitude structural fluctuations on timescales spanning many orders of magnitude and spatial correlation lengths, thus characterization of the excitonic states requires understanding how nearest-neighbor Coulombic and exchange interactions couple to picosecond motions of the bases. In this paper, we present results from hybrid QM/MD simulations of polyadenosine in solution that provide detailed insight into the time-dependent stacking interactions in these systems and the effects of dynamic disorder on the temporal and spatial properties of the low-lying excitons. [Preview Abstract] |
Wednesday, March 7, 2007 12:27PM - 12:39PM |
P18.00007: The activation of phosphoramide mustard anticancer drugs from ab initio simulations. Markus Allesch, Eric Schwegler, Mike Colvin, Francois Gygi, Giulia Galli The nitrogen mustard based DNA alkylating agents were the first nonhormonal drugs to be used effectively in the treatment of cancer and remain one of the most important drugs for the chemotherapeutic management of many common malignancies today. An understanding of the activation of these compounds is, in itself, of scientific interest, but also critical in designing improved analogs of greater selectivity and efficacy. We have investigated the activation pathways of one of the most active metabolites, phosphoramide mustard (PM), and its methylated ester (PMME). In particular, we have examined the activation barrier and reaction free energy for the intramolecular cyclization reaction using first principles molecular dynamics simulations with explicit and continuum solvation models. Structural, dynamical and electronic properties along the reaction path have been computed mainly to address the question why de-esterification is required to activate these drugs. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48. [Preview Abstract] |
Wednesday, March 7, 2007 12:39PM - 12:51PM |
P18.00008: Use of light scattering data to determine free energies of ternary mixtures George Thurston, David Ross, Carl Lutzer, Seth Fraden We demonstrate a method that uses light scattering data to determine the free energy of ternary liquid mixtures, through solving a second-order nonlinear partial differential equation appropriate for single isotropic phases. We show that forward light scattering efficiency data, together with boundary condition data, permit integration of the second derivative of the intensive free energy along curves tangent to the local dielectric coefficient gradient vector. With suitable information about phase boundaries the method also accommodates the presence of phase-separated regions next to single-phase regions in which the governing equation is an appropriate model. In the presence of composition-dependent optical dielectric dispersion, light scattering at more than one wavelength can help augment and check such free energy determination. In summary, light scattering provides a non-invasive method of determining ternary liquid mixture free energies without adopting specific free energy models in advance. [Preview Abstract] |
Wednesday, March 7, 2007 12:51PM - 1:03PM |
P18.00009: Proton momentum distributions in water: A path integral molecular dynamics study Varadharajan Srinivasan, Joseph A. Morrone, Daniel Sebastiani, Roberto Car Recent neutron Compton scattering experiments have detected the proton momentum distributions of water. This density in momentum space is a quantum mechanical property of the proton, due to the confining anharmonic potential from covalent and hydrogen bonds. The theoretical calculation of this property can be carried out via ``open'' path integral expressions. In this work, we present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize the SPC/F2 empirical force field to model the system's interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton. [Preview Abstract] |
Wednesday, March 7, 2007 1:03PM - 1:15PM |
P18.00010: Calculation of Proton Transfer Rates in Liquids Using Molecular Dynamics Simulations Yin Guo We have been investigating a computational method that incorporates WKB tunneling calculations within the framework of classical molecular dynamics (MD) simulations. The computational cost is at the same level as the usual MD simulation, thus providing a practical and efficient dynamical approach for treating quantum tunneling. Building upon the earlier gas-phase studies, we extend the method to condensed phase materials. As a test case, the method is applied to a model system that represents proton transfer AH--B$\leftrightarrow $A$^{-}$--H$^{+}$B in liquid methyl chloride, where AH--B is a linear complex with parameters chosen to model a typical phenol-amine complex. The calculated results are compared with those of earlier studies on the same system by Azzouz and Borgis and by Hammes-Schiffer and Tully using different methods. [Preview Abstract] |
Wednesday, March 7, 2007 1:15PM - 1:27PM |
P18.00011: Local structure and the intermediate-energy fine structure in x-ray Raman scattering from ice Ih G.T. Seidler, T.T. Fister, C. Hamner, F.D. Vila, J.O. Cross The structure of the various different equilibrium and nonequilibrium phases of water ice is a topic of considerable interest, with strong relevance for geophysics, atmospheric sciences, and space sciences.~ Recent advances in non-resonant x-ray Raman scattering (XRS) provide a new method for studying local structure of water ices in extreme environments including especially in high-pressure cells.~ Here, we investigate two pragmatic issues: the optimum choice of momentum transfer $q$ for these measurements and the usefulness of the intermediate-energy fine structure as a strong fingerprint of local atomic structure out to several coordination shells.~ To this end, we present new XRS measurements of ice Ih with greatly improved statistics over earlier work, and also present extensive full-multiple calculations of the dependence of the intermediate-energy fine structure on local structure.~ We find that XRS measurements at high $q$, where the XRS cross-section is largest but where multipole transitions can be important, show little difference from dipole-limited soft x-ray absorption studies.~ In addition, our calculations predict significant sensitivity of the XRS intermediate-energy fine structure to different ice structures. [Preview Abstract] |
Wednesday, March 7, 2007 1:27PM - 1:39PM |
P18.00012: Covalency in Actinide and Lanthanide Hexachloride Anions Ping Yang, Enrique Batista, Richard Martin, Christin Carlson, David Clark, Steven Conradson, Daniel Schwarz, Marinne Wilkerson Whether actinide atoms form covalent or ionic bonds is still a matter of debate after many years of study and it remains a challenge for experimentalists and theoreticians. From the experimental side, synchrotron-based ligand K-edge X-ray absorption spectroscopy appears as a promising technique for probing this issue. From the theoretical perspective, quantum chemical simulations should be able to add on a first principle understanding. To tackle this problem, we have applied these techniques on a series of octahedral uranium and lanthanide chloride salts, MCl$_{6}^{n-}$ (M= U, Ce, Pr) in various oxidation states (n=1, 2, 3). We will show hybrid density functional theory calculations that give evidence of the covalent nature of the M-Cl bond in a quantitative manner. This covalency was found to increase for higher oxidation states. [Preview Abstract] |
Wednesday, March 7, 2007 1:39PM - 1:51PM |
P18.00013: Site Sensitivity and local electronic symmetries in carboranes T.T. Fister, G.T. Seidler, F.D. Vila, J.O. Cross, J.C. Linehan Icosohedral carboranes containing ten boron and two carbon atoms are seeing renewed interest because of their potential use in new cancer and AIDS therapies.~ These molecules have flexible geometries which allow bonding to three types of carbon sites (e.g. \textit{ortho}-, \textit{para}-, and \textit{meta}- configurations).~ Using a new multielement spectrometer, we present the first x-ray Raman scattering (XRS) study on each isomer with excited state spectra taken from the both the carbon and boron 1$s$ states.~ The change in the electronic structure between the isomers is most pronounced in the carbon spectrum, where the position in the edge confirms prior density functional theory calculations.~ With the boron spectra, we used the unique momentum transfer dependence of XRS to extract the symmetry components of the density of unoccupied states, i.e. the $l$-DOS.~ These results give an improved picture of the local electronic properties of the carboranes. [Preview Abstract] |
Wednesday, March 7, 2007 1:51PM - 2:03PM |
P18.00014: The electronic structure of Co and Ni tetraazaannulenes Jing Liu, Jie Xiao, P. Jeppson, P.A. Dowben, Seok-Bong Choi, L. Jarabek, A.N. Caruso, Ya.B. Losovyj We compare two metal centered tetraazaannulene (TMTAA) macrocyclic complex molecules: 5,7,12,14- tetramethyl -2,3:9,10- dibenzo [b,i] -1,4,8,11- tetraazacyclotetradecine nickel (II) and 5,7,12,14- tetramethyl -2,3:9,10- dibenzo [b,i] -1,4,8,11- tetraazacyclotetradecine cobalt (II). The highest occupied molecular orbital to the lowest unoccupied molecular orbital gap, obtained from combined ultraviolet photoemission and inverse photoemission studies, is close to the expected value of 6.6 eV expected from simple model calculations. While both the Co(II) (s=1/2) and Ni(II) (s=0) tetramethyldibenzo-tetraazaannulene molecular electronic structures are very similar, the Ni(II) adopts a high symmetry molecular configuration upon adsorption, with a strong preferential orientation. The role of an unpaired electron upon molecular symmetry and stability is discussed. [Preview Abstract] |
Wednesday, March 7, 2007 2:03PM - 2:15PM |
P18.00015: Pump-Probe Photoionization Spectroscopy of penta methyl cyclopentadiene Peter Weber, Fedor Rudakov The ultrafast curve crossing from the excited electronic state to the ground state in cyclic dienes often proceeds via conical intersections.~ Time-resolved experiments were performed by exciting the first excited state of pentamethylcyclopentadiene, as well as other methylated cyclopentadiene derivatives, with femtosecond pulses at 260 nm.~ Photoionization with a time-delayed probe pulse yields delay-time dependent mass and photoelectron spectra that reveal the ultrafast character of the curve crossing dynamics.~ [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700