### 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 |