Workshop on Computational Chemistry and its Applications (CCA) Session 1

Time and Date: 10:35 - 12:15 on 1st June 2015

Room: V102

Chair: Jerry Bernholc

600 Calculations of molecules and solids using self-interaction corrected energy functionals and unitary optimization of complex orbitals [abstract]
Abstract: The Perdew-Zunger self-interaction correction to DFT energy functionals can improve the accuracy of calculated results in many respects. The long range effective potential for the electrons then has the correct -1/r dependence so Rydberg excited states of molecules and clusters of molecules can be accurately treated [1,2]. Also, localized electronic states are brought down in energy so defects in semi-conductors and insulators with defect states in the band gap can be characterized [3,4]. The calculations are, however, more challenging since the energy functional is no longer unitary invariant and each step in the self-consistent procedure needs to include an inner loop where unitary optimization is carried out [5,6]. As a result, the calculations produce a set of optimal orbitals which are generally localized and correspond well to chemical intuition. It has become evident that the optimal orbital need to be complex valued functions [7]. If they are restricted to real valued functions, the energy of atoms and molecules is less accurate and structure of molecules can even be incorrect [8]. [1] 'Self-interaction corrected density functional calculations of Rydberg states of molecular clusters: N,N-dimethylisopropylamine', H. Gudmundsdóttir, Y. Zhang, P. M. Weber and H. Jónsson, J. Chem. Phys. 141, 234308 (2014). [2] 'Self-interaction corrected density functional calculations of molecular Rydberg states', H. Gudmundsdóttir, Y. Zhang, P. M. Weber and H. Jónsson, J. Chem. Phys. 139, 194102 (2013). [3] `Simulation of Surface Processes', H. Jónsson, Proceedings of the National Academy of Sciences 108, 944 (2011). [4] 'Solar hydrogen production with semiconductor metal oxides: New directions in experiment and theory', Á. Valdés et al., Phys. Chem. Chem. Phys. 14, 49 (2012). [5] 'Variational, self-consistent implementation of the Perdew–Zunger self-interaction correction with complex optimal orbitals', S. Lehtola and H. Jónsson, Journal of Chemical Theory and Computation 10, 5324 (2014). [6] 'Unitary Optimization of Localized Molecular Orbitals', S. Lehtola and H. Jónsson, Journal of Chemical Theory and Computation 9, 5365 (2013). [7] 'Importance of complex orbitals in calculating the self-interaction corrected ground state of atoms', S. Klüpfel, P. J. Klüpfel and H. Jónsson, Phys. Rev. A Rapid Communication 84, 050501 (2011). [8] 'The effect of the Perdew-Zunger self-interaction correction to density functionals on the energetics of small molecules', S. Klüpfel, P. Klüpfel and H. Jónsson, J. Chem. Phys. 137, 124102 (2012).
Hannes Jónsson
629 Towards An Optimal Gradient-Dependent Energy Functional of the PZ-SIC Form [abstract]
Abstract: too high atomization energy (overbinding of the molecules), the application of PZ-SIC gives a large overcorrection and leads to significant underestimation of the atomization energy. The exchange enhancement factor that is optimal for the generalized gradient approximation within the Kohn-Sham (KS) approach may not be optimal for the self-interaction corrected functional. The PBEsol functional, where the exchange enhancement factor was optimized for solids, gives poor results for molecules in KS but turns out to work better than PBE in PZ-SIC calculations. The exchange enhancement is weaker in PBEsol and the functional is closer to the local density approximation. Furthermore, the drop in the exchange enhancement factor for increasing reduced gradient in the PW91 functional gives more accurate results than the plateaued enhancement in the PBE functional. A step towards an optimal exchange enhancement factor for a gradient dependent functional of the PZ-SIC form is taken by constructing an exchange enhancement factor that mimics PBEsol for small values of the reduced gradient, and PW91 for large values. The average atomization energy is then in closer agreement with the high-level quantum chemistry calculations, but the variance is still large, the F2 molecule being a notable outlier.
Elvar Örn Jónsson, Susi Lehtola, Hannes Jónsson
686 Correlating structure and function for nanoparticle catalysts [abstract]
Abstract: Metal nanoparticles of only ~100-200 atoms are synthesized using a dendrimer encapsulation technique to facilitate a direct comparison with density functional theory (DFT) calculations in terms of both structure and catalytic function. Structural characterization is done using electron microscopy, x-ray scattering, and electrochemical methods. Combining these tools with DFT calculations is found to improve the quality of the structural models. DFT is also successfully used to predict trends between structure and composition of the nanoparticles and their catalytic function for reactions including the reduction of oxygen and the oxidation of formic acid. This investigation demonstrates some remarkable properties of the nanoparticles, including facile structural rearrangements and nanoscale tuning parameters which can be used to optimize catalytic rates.
Graeme Henkelman
199 The single-center multipole expansion (SCME) model for water: development and applications [abstract]
Abstract: Despite many decades of force field developments, and the proliferation of efficient first principles molecular dynamics simulation techniques, a universal microscopic model for water in its various phases has not yet been achieved. In recent years, progress in force field development has shifted from optimizing in ever greater detail the parameters of simple pair-wise additive empirical potentials to developing more advanced models that explicitly include many-body interactions through induced polarization and short-range exchange-repulsion interactions. Such models are often parametrized to reproduce as closely as possible the Born-Oppenheimer surface from highly accurate quantum chemistry calculations; the best models often outperform DFT in accuracy, yet are orders of magnitude more computationally efficient. The SCME model was recently suggested as a physically rigorous and transparent model where the dominant electrostatic interaction is described through a single-center multipole expansion up to the hexadecapole moment, and where many-body effects are treated by induced dipole and quadrupole moments. In this paper, recent improvements of SCME are presented along with selected applications. Monomer flexibility is included via an accurate potential energy surface, a dipole moment surface is used to describe the geometric component of the dipole polarizability, and several formulations of the anisotropic short-range exchange-repulsion interaction are compared. The performance of this second version of the model, SCME2, is demonstrated by comparing to experimental results and high-level quantum chemistry calculations. Future perspectives for applications and developments of SCME2 are presented, including an outline for how the model can be adapted to describe mixed systems of water with other small molecules and how it can be used as a polarizable solvent in QM/MM simulations.
Kjartan Thor Wikfeldt and Hannes Jonsson
8 Quantum Topology of the Charge density of Chemical Bonds. QTAIM analysis of the C-Br and O-Br bonds. [abstract]
Abstract: The present study aims to explore the quantum topological features of the electron density and its Laplacian of the understudied molecular bromine species involved in ozone depletion events. The characteristics of the C-Br and O-Br bonds have been analyzed via quantum theory of atom in molecules (QTAIM) analysis using the wave functions computed at the B3LYP/aug-cc-PVTZ level of theory. Quantum topology analysis reveal that the C-Br and O-Br bonds show depletion of charge density indicating the increased ionic character of these bonds. Contour plots and relief maps have been analyzed for regions of valence shell charge concentrations (VSCC) and depletions (VSCD) in the ground state
Rifaat Hilal, Saadullah Aziz, Shabaan Elrouby, Abdulrahman Alyoubi

Workshop on Computational Chemistry and its Applications (CCA) Session 2

Time and Date: 14:30 - 16:10 on 1st June 2015

Room: V102

Chair: Hannes Jonsson

608 Computational study of electrochemical CO2 reduction at transition metal electrodes [abstract]
Abstract: Density functional theory calculations were used to model the electrochemical reduction of CO2 on various transition metals, in particular Cu(111) and Pt(111) surfaces. The minimum energy paths for sequential protonation by either Tafel or Heyrovsky mechanism were calculated using the nudged elastic band method for applied potentials comparable to those used in experimental studies, ranging from -0.7 V to -1.7 V. A mechanism for CO2 reduction on Cu(111) has been identified where the highest activation energy is 0.4 eV. On Pt(111) a different mechanism is found to be optimal but it involves a higher barrier, 0.7 eV. Hydrogen production is then a competing reaction with activation barrier of only 0.3 eV, while on Cu(111) hydrogen production has a barrier of 0.6 eV. These results are consistent with experimental findings where copper electrodes are found to lead to relatively high yield of CH4 while H2 forms almost exclusively at platinum electrodes. A detailed understanding of the mechanism of electrochemical reduction of CO2 to hydrocarbons can help design improved catalysts for this important reaction.
Javed Hussain, Egill Skúlason, Hannes Jónsson
147 Petascale Calculations of Electronic Structure and Electron Transport [abstract]
Abstract: We describe new developments and applications of the Real Space Multigrid (RMG) electronic structure family of codes. RMG uses real-space grids, a multigrid pre-conditioner, and subspace diagonalization to solve the Kohn-Sham equations. It is designed for use on massively parallel computers and has shown excellent scalability and performance, reaching 6.5 PFLOPS on 18k Cray compute nodes with 288k CPU cores and 18k GPUs. We discuss (i) New developments in parallel subspace diagonalization, which speeds of the diagonalization part of the calculations by a factor of three or more; and (ii) Linear-scaling quantum transport methodology, which enable calculations for several thousand atoms. As examples, we consider: (iii) Molecular sensors based on carbon nanotubes, with configurations based both on direct attachment (physisorption and chemisorption) and indirect functionalization via covalent and non-covalent linkers; and (iv) Electron transport in DNA and the effects of base-pair matching, solvent and counterions. All of these dramatically affect the conductivity of DNA strands, which explains the wide range of results observed experimentally. If time permits, we will also discuss (v) fully quantum simulations of solvated biomolecules, in which Kohn-Sham (KS) DFT is used to describe the biomolecule and its first solvation shells, while the orbital-free (OF) DFT is employed for the rest of the solvent. The OF part is fully O(N) and capable of handling 10^5 solvent molecules on current parallel supercomputers, while taking only ~10% of the total time. RMG is now an open source code, running on Linux, Windows and MacIntosh systems. The current release of the code may be downloaded at In collaboration with E. Briggs, Y. Li, B. Tan, M. Hodak, and W. Lu.
Jerry Bernholc
239 Dynamic Structural Disorder in Supported Pt Clusters Under Operando Conditions [abstract]
Abstract: Supported nanoparticle catalysts are ubiquitous in heterogeneous catalytic processes, and there is broad interest in their physical and chemical properties. However, global probes such as XAS and XPS generally reveal their ensemble characteristics, obscuring details of their fluctuating internal structure. We have previously shown [1] that a combination of theoretical and experimental techniques is needed to understand the intra-particle heterogeneity of these systems [2], and their changes under operando conditions [3]. For example, ab initio DFT/MD simulations revealed that the nanoscale structure and charge distribution are inhomogeneous and dynamically fluctuating over several time-scales, ranging from fast (200-400 fs) bond vibrations to slow fluxional bond breaking (>10 ps). In particular the anomalous behavior of the mean-square relative displacement is not static, but rather is driven by stochastic motion of the center of mass over 1-4 ps time-scales. The resulting large scale fluctuations are termed “dynamic structural disorder” (DSD) [2]. Moreover, the nanoparticles tend to exhibit a semi-melted cluster surface, which for alloy clusters can be atomically-segregated. Recent studies of CO- and H-covered Pt nanoclusters on C and SiO2 supports show a variety of spectral and structural trends as a function of temperature. DFT simulations show that adsorption drives local electronic structure changes that are responsible for the opposite energy shifts vs temperature, of the absorption edge and off-resonant emission line. Moreover, desorption results in local bond contraction, thus explaining the negative thermal expansion observed in XAS experiments. For example, upon single CO adsorption, the Pt-Pt bonds formed by coordinated Pt atoms are locally expanded by ~5%, with little change in the rest of the particle. Coordination also has a large effect on the net charge of the Pt atoms (Figure 1), with a net loss of charge upon adsorption. Finally, we show how high coverage inverts the charging structure of the cluster, turning the negative surface (positive interior) of the clean cluster to positive surface (negative interior) in the fully covered case. Supported by DOE grant DE-FG02-03ER15476, with computer support from DOE-NERSC. [1] F. D. Vila, J. J. Rehr, J. Kas, R. G. Nuzzo and A. I. Frenkel, Phys. Rev. B 78, 121404(R) (2008). [2] J. J. Rehr and F. D. Vila, J. Chem. Phys. 140, 134701 (2014). [3] F. D. Vila, J. J. Rehr, S. D. Kelly and S. R. Bare J. Phys. Chem. C 117, 12446 (2013).
John Rehr, Fernando Vila and Anatoly Frenkel
359 Long time scale simulations of amorphous ice [abstract]
Abstract: Amorphous ice, or amorphous solid water (ASW), is the most common form of ice in astrophysical environments and is believed to be the dominant com- ponent of comets, planetary rings and dust grains in interstellar molecu- lar clouds. The surface of ASW catalyzes chemical reactions in interstellar space ranging from H 2 to complex organic molecules, and a deeper under- standing of ASW is thus crucial for better models of chemical evolution in the universe. ASW is disordered and metastable with respect to crystalline hexagonal ice, and forms when water molecules are deposited on surfaces at temperatures below 140 K. However, the structure, morphology and for- mation mechanisms of ASW are poorly understood and have received much attention across many disciplines. Indeed, the structure and morphology of ASW depend sensitively on how it forms, where key parameters are temper- ature, deposition rate and deposition angle. While atomistic simulations of ASW are extremely challenging due to slow kinetics and the long timescales involved, state-of-the-art long timescale methods provide a possible means to study the atomistic mechanisms involved on relevant timescales. Here we will discuss atomistic simulations of the growth and long timescale evolution of ASW through the use of the adaptive kinetic Monte Carlo (AKMC) tech- nique coupled to different interaction potentials for water molecules. The influence of temperature and deposition parameters is studied in detail and compared to available experimental results. Our results elucidate the struc- ture and formation mechanisms of ASW under astrophysical environments and provide realistic structure models that can be used in further studies of chemical reactivity of ASW surfaces.
Ramya Kormath Madam

Workshop on Computational Chemistry and its Applications (CCA) Session 3

Time and Date: 16:40 - 18:20 on 1st June 2015

Room: V102

Chair: John Rehr

404 Modelling Molecular Crystals by QM/MM [abstract]
Abstract: Computational modelling of chemical systems is most easily carried out in the vacuum for single molecules. Accounting for environmental effects accurately in quantum chemical calculations, however, is often necessary for computational predictions of chemical systems to have any relevance to experiments carried out in the condensed phases. I will discuss a quantum mechanics/molecular mechanics (QM/MM) based method to account for solid-state effects on geometries and molecular properties in molecular crystals. The method in its recent black-box implementation in Chemshell can satisfactorily describe the crystal packing effects on local geometries in a molecular crystals and account for the electrostatic effects that affects certain molecular properties such as transition metal NMR chemical shifts, electric field gradients, Mössbauer and other spectroscopic properties.
Ragnar Bjornsson
437 A Quaternion Method for Removing Translational and Rotational Degrees of Freedom from Transition State Search Methods [abstract]
Abstract: In finite systems, such as nanoparticles and gas-phase molecules, calculations of minimum energy paths connecting initial and final states of transitions as well as searches for saddle points are complicated by the presence of external degrees of freedom, such as overall translation and rotation. A method based on quaternion algebra for removing the external degrees of freedom is presented and applied in calculations using two commonly used methods: the nudged elastic band (NEB) method for finding minimum energy paths and DIMER for minimum-mode following to find transition states. With the quaternion approach, fewer images in the NEB are needed to represent MEPs accurately. In both the NEB and DIMER calculations, the number of iterations required to reach convergence is significantly reduced.
Marko Melander
438 Drag Assisted Simulated Annealing Method for Geometry Optimization of Molecules [abstract]
Abstract: One of the methods to find the global minimum of a potential energy surface of a molecular system is simulated annealing. The main idea of simulated annealing is to start you system at a high temperature and then slowly cool it down so that there is a chance for the atoms in the system to explore the different degrees of freedom and ultimately find the global minimum. Simulated annealing is traditionally used in classical Monte Carlo or in classical molecular dynamics. One of the methods to find the global minimum of a potential energy surface of a molecular system is simulated annealing. The main idea of simulated annealing is to start you system at a high temperature and then slowly cool it down so that there is a chance for the atoms in the system to explore the different degrees of freedom and ultimately find the global minimum. Simulated annealing is traditionally used in classical Monte Carlo or in classical molecular dynamics. In molecular dynamics, one of the traditional methods was first implemented by Woodcock in 1971. In this method the velocities are scaled down after a given number of molecular dynamics steps, let the system explore the potential energy surface and scale down the velocities again until a minimum is found. In this work we propose to use a viscous friction term, similar to the one used in Langevin dynamics, to slowly bring down the temperature of the system in a natural way. We use drag terms that depend linearly or quadraticaly on the velocity of the particles. These drag terms will naturally bring the temperature the system down and when the system reaches equilibrium they will vanish. Thus, imposing a natural criterion to stop the simulation. We tested the method in Lenard-Jones clusters of up to 20 atoms. We started the system in different initial conditions and used different values for the temperature and the drag coefficients and found the global minima of every one of the clusters. This method demonstrated to be conceptually very simple, but very robust, in finding the global minima.
Bilguun Woods, Paulo Acioli
597 Modeling electrochemical reactions at the solid-liquid interface using density functional calculations [abstract]
Abstract: Charged interfaces are physical phenomena found in various natural systems and artificial devices within the fields of biology, chemistry and physics. In electrochemistry, this is known as the electrochemical double layer, introduced by Helmholtz over 150 years ago. At this interface, between a solid surface and the electrolyte, chemical reactions can take place in a strong electric field. In this presentation, a new computational method is introduced for creating charged interfaces and to study charge transfer reactions on the basis of periodic DFT calculations. The electrochemical double layer is taken as an example, in particular the hydrogen electrode as well as the O2, N2 and CO2 reductions. With this method the mechanism of forming hydrogen gas, water, ammonia and methane/methanol is studied. The method is quite general and could be applied to a wide variety of atomic scale transitions at charged interfaces.
Egill Skúlason
601 Transition Metal Nitride Catalysts for Electrochemical Reduction of Nitrogen to Ammonia at Ambient Conditions [abstract]
Abstract: Computational screening for catalysts that are stable, active and selective towards electrochemical reduction of nitrogen to ammonia at room temperature and ambient pressure is presented from a range of transition metal nitride surfaces. Density functional theory (DFT) calculations are used to study the thermochemistry of cathode reaction so as to construct the free energy profile and to predict the required onset potential via the Mars-van Krevelen mechanism. Stability of the surface vacancy as well as the poisoning possibility of these catalysts under operating conditions are also investigated towards catalyst engineering for sustainable ammonia formation. The most promising candidates turned out to be the (100) facets of rocksalt structure of VN, CrN, NbN and ZrN that should be able to form ammonia at -0.51 V, -0.76 V, -0.65 V and -0.76 V vs. SHE, respectively. Another interesting result of the current work is that for the introduced nitride candidates hydrogen evolution is no longer the competing reaction; thus, high formation yield of ammonia is expected at low onset potentials.
Younes Abghoui, Egill Skúlason