First-principles molecular structure search with a genetic algorithm

The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment of the conformation space of molecules. The algorithm is designed to work with first-principles methods, facilitated by the incorporation of local optimization and blacklisting conformers to prevent repeated evaluations of very similar solutions. The aim of the search is not only to find the global minimum, but to predict all conformers within an energy window above the global minimum. The performance of the search strategy is: (i) evaluated for a reference data set extracted from a database with amino acid dipeptide conformers obtained by an extensive combined force field and first-principles search and (ii) compared to the performance of a systematic search and a random conformer generator for the example of a drug-like ligand with 43 atoms, 8 rotatable bonds and 1 cis/trans bond

Density Functional Theory screening of gas-treatment strategies for stabilization of high energy-density lithium metal anodes

To explore the potential of molecular gas treatment of freshly cut lithium foils in non-electrolyte based passivation of high energy-density Li anodes, density functional theory (DFT) has been used to study the decomposition of molecular gases on metallic lithium surfaces. By combining DFT geometry optimization and Molecular Dynamics, the effects of atmospheric (N2, O2, CO2) and hazardous (F2, SO2) gas decomposition on Li(bcc) (100), (110), and (111) surfaces on relative surface energies, work functions, and emerging electronic and elastic properties are investigated. The simulations suggest that exposure to different molecular gases can be used to induce and control reconstructions of the metal Li surface and substantial changes (up to over 1 eV) in the work function of the passivated system. Contrary to the other considered gases, which form metallic adlayers, SO2 treatment emerges as the most effective in creating an insulating passivation layer for dosages <= 1 mono-layer. The substantial Li->adsorbate charge transfer and adlayer relaxation produce marked elastic stiffening of the interface, with the smallest change shown by nitrogen-treated adlayers

Applied Symmetry for Crystal Structure Prediction

This thesis presents an original open-source Python package called PyXtal (pronounced pi-crystal ) that generates random symmetric crystal structures for use in crystal structure prediction (CSP). The primary advantage of PyXtal over existing structure generation tools is its unique symmetrization method. For molecular structures, PyXtal uses an original algorithm to determine the compatibility of molecular point group symmetry with Wyckoff site symmetry. This allows the molecules in generated structures to occupy special Wyckoff positions without breaking the structure\u27s symmetry. This is a new feature which increases the space of search-able structures and in turn improves CSP performance. It is shown that using already-symmetric initial structures results in a higher probability of finding the lowest-energy structure. Ultimately, this lowers the computational time needed for CSP. Structures can be generated for any symmetry group of 0, 1, 2, or 3 dimensions of periodicity. Either atoms or rigid molecules may be used as building blocks. The generated structures can be optimized with VASP, LAMMPS, or other computational tools. Additional options are provided for the lattice and inter-atomic distance constraints. Results for carbon and silicon crystals, water ice crystals, and molybdenum clusters are presented as usage examples

Ab Initio Studies of Cellulose I: Crystal Structure, Intermolecular Forces, and Interactions with Water

We have studied the structural, energetic, and electronic properties of crystalline cellulose I using first-principles density functional theory (DFT) with semiempirical dispersion corrections. The predicted crystal structures of both Iα and Iβ phases agree well with experiments and are greatly improved over those predicted by DFT within the local and semilocal density approximations. The cohesive energy is analyzed in terms of interchain and intersheet interactions, which are calculated to be of similar magnitude. Both hydrogen bonding and van der Waals (vdW) dispersion forces are found to be responsible for binding cellulose chains together. In particular, dispersion corrections prove to be indispensable in reproducing the equilibrium intersheet distance and binding strength; however, they do not improve the underestimated hydrogen bond length from DFT. The computed energy gaps of crystalline cellulose are 5.7 eV (Iα) and 5.4 eV (Iβ), whereas localized surface states appear within the gap for surfaces. The interaction of cellulose with water is studied by investigating the adsorption of a single water molecule on the hydrophobic Iβ(100) surface. The formation of hydrogen bond at the water/cellulose interface is shown to depend sensitively on the adsorption site for example above the equatorial hydroxyls or the CH moieties pointing out of the cellulose sheets. VdW dispersion interactions also contribute significantly to the adsorption energy

Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion

We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular interaction model from dispersion and electrostatics for more than 1,300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine---intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. The mean absolute error made by the combination of static electrostatics with many-body dispersion reduces at larger distances, while it plateaus for two-body dispersion, in conflict with the common assumption that the simple $1/R^6$ correction will yield proper dissociative tails. Overall, the method achieves an accuracy well within conventional molecular force fields while exhibiting a simple parametrization protocol.Comment: 13 pages, 8 figure

Development of a Transferable Reactive Force Field of P/H Systems: Application to the Chemical and Mechanical Properties of Phosphorene

ReaxFF provides a method to model reactive chemical systems in large-scale molecular dynamics simulations. Here, we developed ReaxFF parameters for phosphorus and hydrogen to give a good description of the chemical and mechanical properties of pristine and defected black phosphorene. ReaxFF for P/H is transferable to a wide range of phosphorus and hydrogen containing systems including bulk black phosphorus, blue phosphorene, edge-hydrogenated phosphorene, phosphorus clusters and phosphorus hydride molecules. The potential parameters were obtained by conducting unbiased global optimization with respect to a set of reference data generated by extensive ab initio calculations. We extend ReaxFF by adding a 60{\deg} correction term which significantly improves the description of phosphorus clusters. Emphasis has been put on obtaining a good description of mechanical response of black phosphorene with different types of defects. Compared to nonreactive SW potential [1], ReaxFF for P/H systems provides a huge improvement in describing the mechanical properties the pristine and defected black phosphorene and the thermal stability of phosphorene nanotubes. A counterintuitive phenomenon is observed that single vacancies weaken the black phosphorene more than double vacancies with higher formation energy. Our results also show that mechanical response of black phosphorene is more sensitive to defects for the zigzag direction than for the armchair direction. Since ReaxFF allows straightforward extensions to the heterogeneous systems, such as oxides, nitrides, ReaxFF parameters for P/H systems build a solid foundation for the reactive force field description of heterogeneous P systems, including P-containing 2D van der Waals heterostructures, oxides, etc