Statewide Users Group Meeting Agenda - June 4, 2015

Metallic glass, a metal without an ordered atomic structure, may represent the next generation of engineering material. Despite having properties not accessible with current alloys, applications are limited by long-standing challenges in design and fabrication. Using the LAMMPS package, molecular dynamics simulations can probe properties of undercooled metallic liquids as they become glass. Some characteristics of this transition are attainable only through computer simulation, providing new insights for the deliberate design of new alloys that readily form glass. Experimentalists can apply this information to new alloy design by targeting promising systems and compositions that behave like the simulations.

Developing improved deformation models for polycrystalline Ni-based superalloys requires a deeper understanding of the rate controlling processes at higher temperatures. Compression creep tests on specially prepared single crystals of an exploratory Ni-base superalloy were conducted at 760°C in the [001] orientation in order to promote precipitate shearing by stacking faults. Scanning transmission electron microscopy imaging using high angle annular dark field imaging was coupled with state-of-the-art energy dispersive x-ray spectroscopy (EDS) to reveal for the first time to an ordered compositional variation along the extrinsic faults inside the Ni3Al precipitates. The local structure and chemistry is consistent with the eta phase, a D024 hexagonal structure. Density Functional Theory (DFT) computations are used to assess the energetics of this segregation and discuss implications of eta phase formation on deformation mechanisms.

Organophosphorus nerve agents (OPs) are a toxic class of compounds that have been used as pesticides and chemical warfare agents, and compounds for which there is a great need of effective therapeutics. Gated molecular baskets conjugated to aliphatic amino acid functionalities have been examined for the binding and hydrolysis of the toxic nerve agent upon entering the bloodstream. A computational protocol was developed for the molecular baskets including a Monte Carlo conformational search, Molecular Dynamics simulations, and docking calculations. The results of the computational studies of the baskets and the critical features for encapsulation of OPs will be presented.

Hydrogen bonding plays an important role in structural biology and supramolecular chemistry. We have obtained the free energies of association of nearly 50 hydrogen bonded complexes which belong to medium and large size both in the gas phase and solution at the M06-2X/cc-pvdz and SMD/M06-2X/cc-pvdz level of theory. This represents the first comprehensive solution phase evaluation of free energies of association of H-bonded complexes covering all the H-bonding interaction patterns of doubly and triply H-bonded complexes. We have justified that our computational protocol can give reliable binding free energies of hydrogen bonded complexes in organic solvent chloroform and dichloromethane.

Acknowledgement: Gratitude is expressed to Central State University, NSF and Ohio Supercomputer Center for support of this work

Atomic resolution scanning transmission electron microscopy (STEM) is often used to analyze deformation mechanisms and properties. Strong contrast has been observed around dislocation cores using medium-angle annular dark field STEM, but not in high-angle conditions. Atomic resolution image simulations using μSTEM have been employed with atomistic simulations on model FCC alloys to explain the nature of the contrast variation as a function of scattering angles for these HEAs in thin foil geometries necessary for high resolution imaging. Only through the use of HPC, especially with GPU acceleration, can such large systems be reasonably studied.

In high-resolution electron microscopy and spectroscopy, quantification of sample thickness is very important for interpretation of results. Until recently there were very few reliable experimental techniques for measuring sample thickness. Position average convergent beam electron diffraction (PACBED) has been shown to be very sensitive to sample thickness, giving thickness values to within 10%; however, experimental PACBED patterns are only useful when compared with simulation. Initial attempts at simulating PACBED were computationally expensive, until GPU acceleration and creative code writing allowed the average experimentalist to run complete simulations in a matter of minutes with little to no help from theorists.

Ionic liquids (ILs) are a unique class of highly tunable solvents. The IL cation and anion may virtually be altered to change their physical and chemical properties, allowing a near infinite number of IL candidates for particular tasks. However, exploring such a massive chemical compound space using experimentation is highly challenging. Given this situation, atomistic molecular simulation is a promising design tool to help understand the structure-property relationships governing the phase-behavior of solutes in ILs. In this work we studied the phase-behavior of acetaminophen in 21 ILs, and observed solubility enhancement on the order of million times that in water.

Accurate and efficient models to predict the phase-behavior of nonelectrolyte solids in a wide range of solvents are central to the design of novel separation processes. A promising design tool is the MOSCED limiting activity coefficient model which is parameterized for 133 solvents. However, before predictions may be made for a solute of interest, solute MOSCED parameters are required. For novel compounds of interest, the necessary MOSCED parameters are unavailable and sufficient data is likely unavailable to regress the necessary parameters. In this study we explore the use of molecular simulation to generate the necessary reference data.

A simple, molecular simulation framework to compute the pure liquid fugacity of low volatile liquids is presented and compared to reference Monte Carlo simulations. The method involves calculation of the residual chemical potential and the molar volume of the liquid at the conditions of interest. For substances that are solid at the conditions of interest, simulations may be performed at elevated temperatures and extrapolated to sub-cooled conditions because direct calculations at sub-cooled conditions provide erroneous results. Knowledge of the pure liquid fugacity is essential to compute activity coefficients defined with respect to a Lewis-Randall standard state for thermodynamic property modeling.

MOSCED is a promising model to predict the limiting activity coefficient of nonelectrolyte solids in solution. However, before it may used for a new solute, a limited set of reference data is needed to obtain the necessary solute MOSCED parameters. In this study we explore the use of electronic structure calculations to generate the reference data necessary to obtain solute MOSCED parameters. Specifically, we use the popular software package QChem which employs the SM8 solvation model. The method is applied to acetaminophen, acetanilide, phenacetin, anthracene, phenanthrene, naphthalene, pyrene and dibenzothiophene.

Acetylcholinesterase(AChE) is an essential enzyme in the human body, which hydrolyzes the neurotransmitter acetylcholine(ACh) at neurosynaptic junctions. Organophosphorus(OP) nerve agents such as Sarin and Tabun are covalent inhibitors of AChE. Following exposure to OPs, AChE is inhibited and undergoes a subsequent irreversible aging process in which the OP-AChE adduct is de-alkylated, destroying AChE’s ability to hydrolyze ACh. No known therapeutic is effective on aged AChE. Our research focuses on re-activation of the aged AChE using Quinone methides(QM), using computational methods to perform molecular dynamics on QMs and aged AChE.

Co-Authors: Ryan McCauslin

Olivine minerals ([Mg,Fe]2SiO4) in the deep earth could promote the generation of abiotic hydrocarbons. As a first step towards understanding CO2 surface chemistry at the aqueous surfaces in a Fisher-Tropsch Type (FTT) reaction, we examined the energetics of water adsorption on olivine(010) surface using density functional theory (DFT) calculations. Severals effects have been identified that lead to the different favorabilities of water adsorption with different metal dopants, including the common alkaline earth (AE) elements and transition metals (TM) seen in natural olivine. Our work provides a detailed picture of water interaction with olivines at molecular level.

Pollen analysis, or palynology, is useful for determining preferred pollinator forage, authenticating apicultural products and monitoring allergenic pollen dispersal. Metabarcoding could make palynology more tractable, however, comparative studies are needed to test the strengths and weaknesses of metabarcoding approaches. We applied metabarcoding, targeting the ITS2, matK and rbcL loci, alongside traditional microscopic palynology to characterize six samples of bee-collected pollen. We found significant rank-based associations between the relative abundance of pollen types within our samples as inferred by the two methods. Results suggest metabarcoding data from plastid loci, as opposed to ribosomal loci, are more reliable for quantitative palynology.

Atom Probe tomography can theoretically provide 3D, atom-by-atom characterization of samples. Having this capability would allow materials researchers to more easily link material properties to micro structure which has the potential to accelerate materials development. Unfortunately, a lack of understanding of the instrument process undermines current reconstruction algorithms, leading to the artifacts prevalent in current literature. We use supercomputer resources to examine atomic evaporation using density functional theory and develop a model for this process. Our models will be used in higher level simulations as part of developing a new, iterative reconstruction algorithm for atom probe data.

In this work, thermal reduction of PdO(101) surface is closely investigated. To do this study, the Density Functional Theory calculation (DFT) and kinetic Monte Carlo (kMC) simulation are used. From the DFT calculation, reaction mechanism of O2 on the surface is investigated and energetic data, including diffusion energy barrier, reaction energy barrier and desorption energy barrier, are obtained. Further, by conducting the kMC simulation with the energetic data from the DFT calculation, connection between energetic data and overall kinetic behavior on the surface is elucidated. The results make us understand the mechanism of thermal reduction of PdO(101) surface.