Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session F31: Focus Session: Van der Waals Interactions in Complex Materials: Bridging Theory and Experiment II |
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Sponsoring Units: DMP Chair: Robert DiStasio, Princeton University Room: 607 |
Tuesday, March 4, 2014 8:00AM - 8:12AM |
F31.00001: Polymorphism and Elastic Response of Molecular Materials from First Principles: How Hard Can it Be? Anthony Reilly, Alexandre Tkatchenko Molecular materials are of great fundamental and applied importance in science and industry, with numerous applications in pharmaceuticals, electronics, sensing, and catalysis. A key challenge for theory has been the prediction of their stability, polymorphism and response to perturbations. While pairwise models of van der Waals (vdW) interactions have improved the ability of density functional theory (DFT) to model these systems, substantial quantitative and even qualitative failures remain. In this contribution we show how a many-body description of vdW interactions can dramatically improve the accuracy of DFT for molecular materials, yielding quantitative description of stabilities and polymorphism for these challenging systems. Moreover, the role of many-body vdW interactions goes beyond stabilities to response properties. In particular, we have studied the elastic properties of a series of molecular crystals, finding that many-body vdW interactions can account for up to 30\% of the elastic response, leading to quantitative and qualitative changes in elastic behavior. We will illustrate these crucial effects with the challenging case of the polymorphs of aspirin, leading to a better understanding of the conflicting experimental and theoretical studies of this system. [Preview Abstract] |
Tuesday, March 4, 2014 8:12AM - 8:24AM |
F31.00002: Structure and properties of fullerene molecular crystals with linear-scaling van der Waals density functional theory Arash Mostofi, Lampros Andrinopoulos, Nicholas Hine Fullerene molecular crystals are of technological promise for their use in heterojunction photovoltaic cells. An improved theoretical understanding of their structure and properties would be a step towards the rational design of new devices. Simulations based on density-functional theory (DFT) are invaluable for developing such insight, but standard semi-local functionals do not capture the important inter-molecular van der Waals (vdW) interactions in fullerene crystals. Furthermore the computational cost associated with the large unit cells needed are at the limit or beyond the capabilities of traditional DFT methods. In this work we overcome these limitations by using our implementation of a number of vdW-DFs in the ONETEP linear-scaling DFT code to study the structural properties of C$_{60}$ molecular crystals. Powder neutron diffraction shows that the low-temperature Pa-3 phase is orientationally ordered with individual C$_{60}$ units rotated around the [111] direction. We fully explore the energy landscape associated with the rotation angle and find two stable structures that are energetically very close, one of which corresponds to the experimentally observed structure. We further consider the effect of orientational disorder in very large supercells of thousands of atoms. [Preview Abstract] |
Tuesday, March 4, 2014 8:24AM - 8:36AM |
F31.00003: Van der Waals Interactions in Pyridine and Pyridine-like Molecular Crystals: An \textit{ab initio} Molecular Dynamics Study Hsin-Yu Ko, Robert A. DiStasio Jr., Biswajit Santra, Roberto Car Pyridine has recently been investigated as a potentially effective material for use in artificial light harvesting.\footnote{ EB Cole, PS Lakkaraju, DM Rampulla, AJ Morris, E Abelev, AB Bocarsly J. Am. Chem. Soc., \textbf{132}, 11539 (2010).} In this work, we propose the use of \textit{ab initio} molecular dynamics (AIMD) to gain valuable physical insight into the artificial photosynthetic processes occurring in condensed-phase pyridine, the study of which has been limited to semi-empirical force fields to date.\footnote{AT Anghel, GM Day, SL Price CrystEngComm., \textbf{4}, 348 (2002).} For this purpose, we introduce an accurate and efficient AIMD method, based on density functional theory (DFT) and a self-consistent pairwise description of van der Waals (vdW) interactions, for use in finite temperature and pressure (NPT) simulations on pyridine and several pyridine-like molecular crystals (PLMCs). Utilizing this approach, we demonstrate that vdW forces play a crucial role in the theoretical prediction of the structure and density of pyridine and PLMCs, and therefore must be accounted for in studies of these potential alternative energy materials. [Preview Abstract] |
Tuesday, March 4, 2014 8:36AM - 8:48AM |
F31.00004: Lowering the desorption temperature of Mg(BH$_4$)$_2$ through doping D. Harrison, T. Thonhauser Magnesium borohydride Mg(BH$_4$)$_2$ is a very promising hydrogen storage material due to its high gravimetric (14.9 mass\%) and volumetric density. However, it is limited for practical storage applications by its high hydrogen desorption temperature of 270$^\circ$C. Arguments have been made for both high thermodynamic stability and slow kinetics to be responsible for this high desorption temperature. In our study we show that doping of Mg(BH$_4$)$_2$ can address the thermodynamic stability issue and predictably lower its desorption enthalpy. We use ab initio calculations at the DFT level (utilizing vdW-DF) and calculate the change in desorption enthalpy from ground state energy and phonon contributions for several possible hydrogen release reactions. Note that van der Waals interactions are crucial to correctly describe the ground state of this complex hydride. We find that, depending on the reaction, the undoped phase has a desorption enthalpy of 50--75 kJ/mol H$_2$ and doping can lower this number by approximately 5~kJ/mol per 10\% doping at 300~K, making the desired range of 40~kJ/mol easily accessible. We argue that this lowering of desorption enthalpy will correspond to a lowering of the desorption temperature. [Preview Abstract] |
Tuesday, March 4, 2014 8:48AM - 9:00AM |
F31.00005: Ab initio study of hydrogen-halo rotation in ammonia borane Evan Welchman, T. Thonhauser The van der Waals crystal ammonia borane NH$_{3}$BH$_{3}$ is a promising hydrogen-storage material due to its large gravimetric storage density. In an isolated molecule, the H atoms reside in halos about either end of a central B--N backbone with \emph{three-fold} rotational symmetry. However, in the solid phase at ambient temperature and pressure, experiments reveal a tetragonal unit cell with a \emph{four-fold} rotational symmetry about the same axis, creating a geometric incompatibility. Using ab initio calculations at the DFT level (with vdW-DF to capture crucial van der Waals interactions), we elucidate this incompatibility by simulating the behavior of the hydrogen-halos and their substituent H atoms. We use Car-Parrinello molecular dynamics at several different temperatures to simulate behavior in the solid and NEB calculations to find barriers to rotation in solid and gas phase. We find that at room temperature the halos can rotate several degrees per fs and that the four-fold symmetry thus results from a time average. We further show that in the solid phase the complex network of dihydrogen bonds affects the torsional barrier for the halos, and thus their rate of rotation in the solid phase, contributing to the experimentally observed positional uncertainty. [Preview Abstract] |
Tuesday, March 4, 2014 9:00AM - 9:12AM |
F31.00006: \textit{Atoms in Solids} Perspective on Polarizabilities and van der Waals Coefficients in Semiconductors Guo-Xu Zhang, Anthony M. Reilly, Alexandre Tkatchenko, Matthias Scheffler The calculation of response properties of solids including their polarizabilities and van der Waals (vdW) coefficients usually requires the knowledge of the full electronic bandstructure. For non-covalently bound solids, such as noble-gas and ionic crystals, atoms-in-solids model can be successfully utilized to define their polarizabilities. Here we critically assess the atoms-in-solids model for covalently-bound solids, ranging from wide-gap ($\sim$10 eV) to narrow-gap ($\sim$1 eV) semiconductors. We model their response by assigning a single quantum harmonic oscillator to every atom, where the parameters of the oscillators are defined as functionals of the electron density, following the Tkatchenko-Scheffler method [1]. The response function is then calculated by solving self-consistent screening equations of classical electrodynamics, without any explicit information about the electronic bandstructure [2]. The calculated polarizabilities and vdW coefficients for 23 semiconductors are compared with TDDFT and experimental benchmark data, revealing an overall agreement within 10\%. We demonstrate the crucial role of vdW interactions in the cohesive properties of the 23 semiconductors.\\[4pt] [1] Tkatchenko and Scheffler, PRL (2009);\\[0pt] [2] Tkatchenko, DiStasio, Car, Scheffler, PRL (2012). [Preview Abstract] |
Tuesday, March 4, 2014 9:12AM - 9:24AM |
F31.00007: van der Waals interactions in MoS$_2$ and MoO$_3$ Hartwin Peelaers, Chris G. Van de Walle Molybdenum disulfide (MoS$_2$) is a layered material that attracted a lot of attention recently for use in electronic devices, such as field-effect transistors, as it has high electron mobilities and high on/off ratios. MoO$_3$ is a layered n-type semiconductor that shows good properties for energy applications. The layers in both materials are weakly bound by van der Waals interactions. A good theoretical description of these interactions is thus required. In this talk I will discuss different approaches to include van der Waals interactions in density-functional theory (DFT), focusing on MoS$_2$ and MoO$_3$. In particular, a combination of hybrid functionals, which correct for the DFT band gap problem, and explicit inclusion of van der Waals interactions, to correct for the long range interactions, shows a lot of promise. The validity of this approach will be demonstrated by comparing the structural parameters of MoS$_2$ under hydrostatic pressure with experimental data. [Preview Abstract] |
Tuesday, March 4, 2014 9:24AM - 9:36AM |
F31.00008: ABSTRACT WITHDRAWN |
Tuesday, March 4, 2014 9:36AM - 9:48AM |
F31.00009: The Structure, Density, and Local Environment Distribution in \emph{Ab Initio} Liquid Water Biswajit Santra, Robert A. DiStasio, Jr., Xifan Wu, Roberto Car We have performed extensive \emph{ab initio} molecular dynamics (AIMD) simulations of liquid water at ambient conditions in the canonical (NVT) and isothermal-isobaric (NPT) ensembles to understand the individual and collective importance of exact exchange, van der Waals interactions, and nuclear quantum effects on the structural properties of liquid water. AIMD simulations which include these effects result in oxygen-oxygen radial distribution functions which are in excellent agreement with experiments and a liquid water structure having an equilibrium density within 1\% of the experimental value of 1 g/cm$^3$. A detailed analysis of the distribution of local structure in ambient liquid water has revealed that the inherent potential energy surface is bimodal with respect to high- and low-density molecular environments, consistent with the existence of polymorphism in the amorphous phases of water. With these findings in mind, the methodology presented herein overcomes the well-known limitations of semi-local density functional theory (GGA-DFT) providing a detailed and accurate microscopic description of ambient liquid water. [Preview Abstract] |
Tuesday, March 4, 2014 9:48AM - 10:00AM |
F31.00010: Nuclear Zero Point Effects as a Function of Density in Ice-like Structures and Liquid Water from vdW-DF \textit{Ab Initio} Calculations Bet\"{u}l Pamuk, Philip B. Allen, Jose M. Soler, Marivi Fern\'andez-Serra The contributions of nuclear zero point vibrations to the structures of liquid water and ice are not negligible. Recently, we have explained the source of an anomalous isotope shift in hexagonal ice, representing itself as an increase in the lattice volume when H is replaced by D, by calculating free energy within the quasiharmonic approximation, with \textit{ab initio} density functional theory [1]. In this work, we extend our studies to analyze the zero point effect in other ice-like structures under different densities: clathrate hydrates, LDL and HDL-like amorphous ices with different densities, and a highly dense ice phase, ice VIII. We show that there is a transition from anomalous isotope effect to normal isotope effect as the density increases. We also analyze nuclear zero point effects in liquid water using different vdW-DFs and make connections to this anomalous-normal isotope effect transition in ice. [1] B. Pamuk \textit{et. al}, Phys. Rev. Lett. \textbf{108}, 193003 (2012). [Preview Abstract] |
Tuesday, March 4, 2014 10:00AM - 10:12AM |
F31.00011: Local order of liquid water at the electrochemical interface Marivi Fernandez Serra, Luana Pedroza Understanding the aqueous electrochemical interface in an atomic level is of fundamental importance in many areas, such as catalysis and materials science. In this work we analyze in detail the structural, dynamic and energetic properties of liquid-water interacting with (111) Pd and Au surfaces at ambient temperature, using first principles molecular dynamics, with and without van der Waals interactions. We show that, contrary to what was found when studying ice-like water layers, van der Waals interactions play a critical role in modeling the aqueous/electrode interface. We show the differences in the ordering of water at the interface for Pd and Au, and we explain the change in work functions of these two metals in aqueous solution. [Preview Abstract] |
Tuesday, March 4, 2014 10:12AM - 10:24AM |
F31.00012: 5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics Tahir Yusufaly, Wilma Olson, Yun Li Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile ``opening'' mode and two shear ``sliding'' and ``tearing'' modes in the orthogonal plane. The stacking interactions of the methyl groups are observed to globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. The results have implications for the epigenetic control of DNA mechanics. [Preview Abstract] |
Tuesday, March 4, 2014 10:24AM - 10:36AM |
F31.00013: Validation Challenge of Density-Functional Theory for Peptides: Example of Ac-Phe-Ala$_5$-LysH$^+$ Volker Blum, Mariana Rossi, Sucismita Chutia, Matthias Scheffler We assess the performance of a group of exchange-correlation functionals for predicting the secondary structure of peptide chains, up to a new many-body dispersion corrected hybrid density functional, coined PBE0+MBD*. For the purpose of validation, we first compare to published, high-level CCSD(T) benchmark conformational energy hierarchies for 73 conformers of small three-residue peptides, establishing that the van der Waals corrected PBE0 functional yields an average error of only $\approx$ 20 meV ($\approx$ 0.5 kcal/mol). This compares to $\approx$ 40-50~meV for non-dispersion corrected PBE0 and 50-100~meV for different empirical force fields. For longer peptide chains that form secondary structure, CCSD(T) level benchmark data are currently unaffordable. We thus turn to the experimentally well studied Ac-Phe-Ala$_5$-LysH$^+$ peptide, for which four closely competing conformers were experimentally established. For comparison, an exhaustive conformational space exploration yields at least eleven competing low energy minima. We show that (i) the many-body dispersion correction, (ii) the hybrid functional nature of PBE0+MBD*, and (iii) zero-point corrections are needed to reveal the four experimentally observed structures as the minima that would be populated at low temperature. [Preview Abstract] |
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