Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session T26: Computational Applications and Methods I |
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Sponsoring Units: DCP Chair: Bruce Garrett, Pacific Northwest National Laboratory Room: 204A |
Thursday, March 5, 2015 11:15AM - 11:27AM |
T26.00001: Attenuated second order Møller-Plesset perturbation theory: correcting finite basis set errors and infinite basis set inaccuracies Matthew Goldey, Martin Head-Gordon Second order M{\o}ller-Plesset perturbation theory (MP2) in finite basis sets describes several classes of noncovalent interactions poorly due to basis set superposition error (BSSE) and underlying inaccurate physics for dispersion interactions. Attenuation of the Coulomb operator provides a direct path toward improving MP2 for noncovalent interactions. In limited basis sets, we demonstrate improvements in accuracy for intermolecular interactions with a three to five-fold reduction in RMS errors. For a range of inter- and intermolecular test cases, attenuated MP2 even outperforms complete basis set estimates of MP2. Finite basis attenuated MP2 is useful for inter- and intramolecular interactions where higher cost approaches are intractable. Extending this approach, recent research pairs attenuated MP2 with long-range correction to describe potential energy landscapes, and further results for large systems with noncovalent interactions are shown. [Preview Abstract] |
Thursday, March 5, 2015 11:27AM - 11:39AM |
T26.00002: Vapor liquid equilibria of hydrofluorocarbons via first principles Monte Carlo simulations Neeraj Rai, Himanshu Goel The Kohn-Sham density functional theory (DFT)~ is a popular approach to compute condensed phase properties. In Kohn-Sham DFT, the local or semi local density functionals do not~ capture van der Waals interactions accurately. An accurate description of van der Waals interactions is essential in determing~ thermodyanmic properties of molecules. The development of fully non local van der Waals density functional adequatey describe dispersion interactions.~ In this work, we present first principles Monte Carlo simulations to obtain vapor liquid coexistence curves for hydrofluorocarbons by using Becke-Lee-Yang-Parr (BLYP)~ functional, dispersion corrected functionals, and with rVV10 nonlocal van der Waals density functional. [Preview Abstract] |
Thursday, March 5, 2015 11:39AM - 11:51AM |
T26.00003: Optical spectra and quasiparticle energies of molecules using a local basis set Mathias Ljungberg, Peter Koval, Francesco Ferrari, Dietrich Foerster, Daniel S\'anchez-Portal The Bethe-Salpeter equation (BSE) is the state of the art for computing optical spectra for solids and molecular clusters. Here we present an implementation of BSE for clusters that scales asymptotically like O(N$^{3})$ with the number of atoms, achieved by exploiting the locality of the problem in the local basis set representation and by using the Haydock recursion method to compute the spectrum. Using a pseudo-Hermitian Lanczos algorithm we can go beyond the Tamm-Dancoff approximation within our iterative scheme. As a starting point for the BSE we compute quasiparticle energies with our low-scaling GW implementation [1], retaining the frequency dependence of all quantities and thus avoiding the plasmon-pole model or similar schemes. The initial wave functions are taken from a preceding SIESTA calculation. We discuss the influence of self-consistency on the quasiparticle energies [2] and its effect on the BSE spectra. We also investigate the satellite peaks that are present in the GW density of states. Computed GW/BSE spectra are shown for some organic molecules of medium size that are relevant for photovoltaic applications. \\[4pt] [1] D. Foerster et al. J. Chem. Phys. 135 (2011) 074105\\[0pt] [2] P. Koval et al. Phys. Rev. B 89 (2014) 155417 [Preview Abstract] |
Thursday, March 5, 2015 11:51AM - 12:03PM |
T26.00004: Computational XPS from Koopmans compliant Functionals Nicolas Poilvert, Nathan Keilbart, Ismaila Dabo X-Ray Photo-emission Spectroscopy (XPS) is one of the most accurate experimental probe when it comes to deciphering the \textbf{chemical composition} of materials like Transition-Metals and Transition-Metal Oxides. Because of the sensitivity of \textit{electron binding energies} to the local chemistry surrounding an atom, XPS can also help identify atomic \textbf{oxidation states}. Nevertheless the complexity of XPS signals makes it a hard task to go from a spectra to a list of chemical species and their associated oxidation states. Electronic structure methods such as Density Functional Theory fall short when it comes to predicting electron binding energies because of large self-interaction errors. The recent introduction of Koopmans-compliant functionals\footnote{I. Dabo et al., \textbf{Phy. Rev. B} 82, 115121 (2010)}\footnote{I. Dabo et al., \textbf{Phys. Chem. Chem. Phys.}, 15, 685-695 (2013)} on the other hand has led to the conclusion that UPS spectra can be accurately predicted at the level of \textbf{Many-Body Perturbation Theory} and beyond, while retaining most of the conceptual and computational simplicity of DFT. In this talk, we will more particularly focus our attention on assessing the accuracy of predicted Transition-Metal XPS spectra. [Preview Abstract] |
Thursday, March 5, 2015 12:03PM - 12:15PM |
T26.00005: Computational studies of the acid catalysts and solvent effects on Diels-Alder cycloaddition and dehydration reactions: Maleic anhydride and 2,5 dimethylfuran Taha Salavati-fard, Stavros Caratzoulas, Douglas Doren Using DFT calculations, we present a detailed gas-phase mechanism for the conversion of DMF and maleic anhydride to 3,6 dimethyl phthalic anhydride. The conversion includes Diels-Alder cycloaddition followed by dehydration of cycloadduct. In addition, we consider the effects of solvent by making use of the PCM. We provide free energies of uncatalyzed, Lewis acid and Br\"{o}nsted acid catalyzed reactions in vacuum and in a broad range of solvents. Our calculations show that a Lewis acid catalyzes the reaction through decreasing HOMO-LUMO gap of the addends. Also, a Br\"{o}nsted acid changes the mechanism of reaction and is able to lower the activation free energy of cycloaddition, effectively. Furthermore, we show that as Lewis acids lower the activation barrier of dehydration reaction which is originally too high, a Br\"{o}nsted acid changes the mechanism and is extremely effective in catalyzing the dehydration. Also, increasing dielectric constant of solvent decreases the activation barrier of uncatalyzed and Lewis acid catalyzed Diels-Alder reaction. For both the Lewis and Br\"{o}nsted acid catalyzed Diels-Alder reaction, the dependency of activation free energy to increasing dielectric constant is much stronger when the acid is coordinated to DMF. [Preview Abstract] |
Thursday, March 5, 2015 12:15PM - 12:27PM |
T26.00006: First-principles Study of the Removal of Boron by Co-precipitation with Hydroxyapatite Using Dolomite as a Starting Material Chenyang Li, Lazaro Calderin, Keiko Sasaki, Ismaila Dabo Boron is a toxic chemical in drinking water and a major health concern worldwide. One method to reduce boron concentration in water consists of co-precipitating boron with hydrated minerals. Nevertheless, little is known about the chemical mechanisms underlying boron reactions with complex minerals. In this work, we have applied first-principles calculations based on density-functional theory (DFT) to characterize boron-bearing hydroxyapatite (HAp) resulting from co-precipitation with hydrated dolomite. DFT calculations have been performed to interpret X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) experiments and to characterize solid residues after boron removal with a focus on determining the absorption sites of B(OH)$_{3}$ and B(OH)$_{4}$ in the formed minerals. The computed results indicate that the absorption takes place at phosphate (PO$_4$) sites. In addition, changes in the lattice parameters of B-bearing HAp as a function of boron concentration have been calculated and compared with experimental results. Good agreement of the decreasing trend in $a$-direction and the increasing trend in $c$-direction has been observed by our calculations. Raman and infrared (IR) spectra have been studied as well to achieve a better understanding the B-HAp structures. [Preview Abstract] |
Thursday, March 5, 2015 12:27PM - 12:39PM |
T26.00007: Effective Many-Body Interactions in Dipolar Fluids and their Effect on Structure: Can the Dipole-Dipole Interaction be Modelled as a Short-Ranged 3-Body Interaction? Julien Sindt, Philip Camp In the 1970s, Stell {\it et al.} showed that it is possible to map the partition function of a system of particles interacting via anisotropic dipolar pairwise interactions to that of a hypothetical system with isotropic many-body interactions. It follows that ``polar and nonpolar fluids have the same critical exponents'' irrespective of long-ranged Coulombic interactions. We have calculated the structural properties of a system of soft spheres with the leading-order 2- and 3-body terms of the isotropic many-body potential. We have compared radial distribution functions and structure factors obtained from $NVT$ Monte Carlo simulations with those from molecular dynamics simulations of dipolar soft spheres (DSSs) under the same physical conditions. We find that the many-body potential overemphasises chaining when compared to the equivalent DSS system. The chain-inducing component is the three-body Axilrod-Teller potential, and by adjusting its contribution, it is possible to match the structure with that of the DSS fluid, showing that the many-body potential can be used as a proxy for the dipolar potential. We conclude by studying the gas-liquid phase transition, finding that the phase transition disappears beyond a threshold degree of chaining. [Preview Abstract] |
Thursday, March 5, 2015 12:39PM - 12:51PM |
T26.00008: A new lattice Monte-Carlo simulation for the dielectric inhomogeneity of ion-containing liquids Xiaozheng Duan, Issei Nakamura We develop a novel lattice Monte-Carlo method to capture the effects of the reorganization of solvent dipoles under external electrostatic fields. Our simulation accounts for the effects of saturated dipoles near ions on the angstrom scale and hence spatial variations in the dielectric function. We will discuss the substantial disparity in the dielectric functions between like and unlike charges. Importantly, a contacting cation-anion pair cannot be literally taken as ``charge-neutral species'' in terms of the solvation energy. On the other hand, even when the two charges are separated by 1 [nm], a significant correlation in the dielectric function may arise. Our simulation also provides the dependence of the bulk dielectric value on the ionic strength, which is consistent with experimental data. [Preview Abstract] |
Thursday, March 5, 2015 12:51PM - 1:03PM |
T26.00009: Energy levels of a particle confined in an ellipsoidal potential well Roman Kezerashvili, Tamaz Kereselidze, Tamar Tchelidze The Schrodinger equation is solved for a particle confined within the ellipsoidal potential well using the perturbation theory and the Hamiltonian diagonalization method. The explicit expressions are obtained for the energy levels that are the size and shape dependent and appropriate wave functions. The calculated energy levels are in a good qualitative and quantitative agreement with the result obtained by numerical solution of the Schrodinger equation. It is revealed that for the lowest states of a given symmetry the region of validity of the perturbation approximation is much larger than it follows from the usual condition of applicability of the perturbation theory. The optical properties of nanoparticles of a prolate and oblate ellipsoidal shape are discussed. [Preview Abstract] |
Thursday, March 5, 2015 1:03PM - 1:15PM |
T26.00010: Potential and kinetic energetic analysis of phonon modes in varied molecular solids Brent Kraczek We calculate partitioned kinetic and potential energies of the phonon modes in molecular solids to illuminate the dynamical behavior of the constituent molecules. This enables analysis of the relationship between the characteristics of sets of phonon modes, molecular structure and chemical reactivity by partitioning the kinetic energy into the translational, rotational and vibrational motions of groups of atoms (including molecules), and the potential energy into the energy contained within interatomic interactions[1]. We consider three solids of differing size and rigidity: naphthalene (C$_10$ H$_6$), nitromethane (CH$_3$NO$_2$) and $\alpha$-HMX (C$_4$H$_8$N$_8$O$_8$). Naphthalene and nitromethane mostly act in the semi-rigid manner often expected in molecular solids. HMX exhibits behavior that is significantly less-rigid. While there are definite correlations between the kinetic and potential energetic analyses, there are also differences, particularly in the excitation of chemical bonds by low-frequency lattice modes. This suggests that in many cases computational and experimental methods dependent on atomic displacements may not identify phonon modes active in chemical reactivity. 1. Kraczek, Chung, \textit{J. Chem. Phys.} 138:074505 (2013). [Preview Abstract] |
Thursday, March 5, 2015 1:15PM - 1:27PM |
T26.00011: Switching mechanisms and role of entropy in chemically controlled hydrazone-based switches Rene Derian, Ivan Stich Chemically controlled synthetic rotary switches are important as they resemble rotary motors found in nature. In order to elucidate the recent experiments [1], using hybrid QM/MM methods we have studied chemically controlled hydrazone-based switches in a strongly polar solvent. The experiments indicate a controlled E$\to $Z-H$^{+}$ switching by addition of acid and thermal backward isomerization. We have studied the Z$\to $E switching mechanisms and the role of entropy. We find use of explicit MM solvent crucial for understanding the huge dipole moments (\textgreater 10D) in the Z conformation and significantly smaller ($\approx $5D) in the E conformation and at the transition state, pointing toward very different ordering in those states. Furthermore, the internal and free energy surfaces from thermodynamic integration are qualitatively very different with the free energy surface exhibiting much smaller energy differences between E and Z. In addition, the solvent causes a pronounced shift ($\approx $30$^{\circ}$) in the position of the Z states from internal and free energies. Both finding highlight the role of the entropy in the switching process and help a quantitative understanding of the switching in the solvent.\\[4pt] [1] S. M. Landge et al., J. Am. Chem. Soc. \textbf{133}, 9812 (2011). [Preview Abstract] |
Thursday, March 5, 2015 1:27PM - 1:39PM |
T26.00012: Determination of the Torsional Potential Energy Surfaces of the Ortho- Meta-, and Para-Isomers of Dinitrobenzene Paul Smith, Mario Borunda The three unique isomers of dinitrobenzene, the ortho-, meta-, and para-isomers, have widely varying steric hindrances and bond hybridizations. The steric effects and the hybridized bonds cause the molecular energy to be dependent on the rotation of the nitro groups. We have calculated the torsional potential energy surfaces of each of the three dinitrobenzene isomers using density functional theory, obtaining a 33x33 plot of the energy of each molecule as a function of the torsional angles of the C-N bonds. The accuracy of the method used is determined by comparsion with previous theoretical and experimental results. The potential energy surfaces provide valuable insight into the mechanics of conjugated molecules, and the method we present can be extended even to proteins, which have very complicated conformations and many conjugated bonds. This method makes the determination of the lowest energy conformations of complex molecules far more computationally accesible. [Preview Abstract] |
Thursday, March 5, 2015 1:39PM - 1:51PM |
T26.00013: Density Functional Plus Dynamical Mean Field Study of Spin Crossover Molecule Jia Chen, Andrew Millis, Chris Marianetti We report a density functional plus dynamical mean field study of spin crossover molecule Fe(phen)2(NCS)2. The temperature dependent magnetic susceptibility, Fe-d spectral and total energy were calculated and compared with experimental magnetization, metal L-edge x-ray adsorption spectroscopy. The importance of dynamic effect on energetics is demonstrated by comparison with density functional plus U method, and the role of full charge self-consistency is identified. Moreover, the local spin density plus U (LSDA+U) method with exchange interaction explicitly included is shown to dramatically overemphasize magnetic interaction. [Preview Abstract] |
Thursday, March 5, 2015 1:51PM - 2:03PM |
T26.00014: The Effect of Structure Variations on Transition State Scaling Relations Philipp Plessow, Frank Abild-Pedersen Linear scaling relations for adsorption as well as transition state (TS) energies have proven extremely useful in the quest to identify, understand and predict reactivity trends of catalysts [1]. The existence of linear scaling relations for reaction intermediates can be understood in terms of simple bond order arguments and hence their accuracy depends on the variations in the adsorbate-surface bond [2]. Since structure and bonding of TS can vary substantially for different surfaces, it is much less clear that TS scaling relations should behave linearly at all. We investigated how the TS structure influences scaling relations and how scaling parameters relate to bond-orders. A model that accounts for varying geometry and goes beyond the linear approach is developed and applied to industrially relevant surface reactions. \\[4pt] [1] Norskov, J. K.; Bligaard, T.; Hvolbaek, B.; Abild-Pedersen, F.; Chorkendorff, I.; Christensen, C. H. Chem. Soc. Rev. 2008, 37, 2163.\\[0pt] [2] Abild-Pedersen, F.; Greeley, J.; Studt, F.; Rossmeisl, J.; Munter, T.; Moses, P.; Skulason, E.; Bligaard, T.; Norskov, J. Phys. Rev. Lett. 2007, 99, 016105. [Preview Abstract] |
Thursday, March 5, 2015 2:03PM - 2:15PM |
T26.00015: Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics Rachael Mansbach, Andrew Ferguson The conformational states explored by proteins and polymers can be controlled by environmental conditions (e.g., temperature, pressure, solvent) or molecular chemistry (e.g., chain length, side chains). It is of fundamental interest to quantify the impact upon molecular structure and function, and a prerequisite to the rational engineering of proteins and polymers with desired properties. Using the diffusion map nonlinear manifold learning algorithm, we have developed an approach to: (i) extract from molecular simulations the single molecule free energy surface governing the microscopic molecular behavior, (ii) quantify changes in its topography as a function of environmental conditions and molecular chemistry, and (iii) relate these perturbations to changes in molecular structure and dynamics. In a first application to an \textit{n}-eicosane chain, we have quantified the thermally accessible chain configurations as a function of temperature and solvent conditions. In a second application to a family of polyglutamate-derivative decameric homopeptides, we quantify the stability of the helical state relative to the random coil as a function of side chain length and expose the molecular mechanism underpinning side chain-mediated helix stability. [Preview Abstract] |
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