Exploring kinetics and thermodynamics in fast-ion conductors and hydrogen-storage materials using ab-initio molecular dynamics

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2007.Includes bibliographical references (p. 173-190).We investigate the interplay between various kinetic processes and thermodynamic factors in three materials--silver iodide (AgI), cesium hydrogen sulfate (CsHSO4), and sodium alanate (NaAlH4)-using ab-initio molecular dynamics simulations. The time-averaged and instantaneous silver substructure in the fast-ion conductor AgI is analyzed, resulting in a set of ordering rules that govern the distribution of the mobile silvers in the first coordination shell surrounding an iodine. We find evidence of an independent phase transition of the silver ions which drives the structural transformation to the high-mobility phase. A thermodynamic motivation for the existence of fast-ion conduction is suggested in terms of an entropic stabilization associated with the decrease in silver mobility upon melting. We also find a unique chemical signature for the fourth nearest-neighbor silver to an iodine. This fourth silver is weakly bound and relatively unconstrained, and we isolate it as the predominant agent in the diffusion process. Next, a detailed statistical analysis is performed on simulations of the fuel-cell electrolyte CsHSO4 to isolate the interplay between the dynamics of the O-H chemical bonds, the ... H hydrogen bonds, and the SO4 tetrahedra in promoting proton conduction. A high reversal rate limits the apparent success rate of the otherwise rapid chemical-bond dynamics, which are dominated by the Grotthuss mechanism of proton transfer. Rapid angular hops in concert with small reorientations of the SO4 tetrahedra constitute a new dominant mechanism for hydrogen-bond network reorganization. The SO4 dynamics are found to control the attempt rate of chemical-bond dynamical events and the success rate of hydrogen-bond dynamical events; this enables a novel interpretation of the diminished CsHSO4/CsDSO4 isotope effect.(cont.) Two distinct timescales for SO4 reorientation events are linked to different diffusion mechanisms along different crystal directions. Finally, a graph-theoretic analysis of the hydrogen-bond network topology demonstrates an increased likelihood for diffusion in connectivity configurations favoring linear network chains over closed rings. We have discovered and characterized a new phase (-y) of the hydrogen-storage material NaAlH4 that is energetically close to the known ground state. The manifestation of this phase is kinetically inhibited in the bulk but is favored in a (001) surface slab above 225 K. The transition involves first activating the surface AlH4 rotational modes. This is followed by a lattice expansion perpendicular to the slab and a shear of successive lattice planes. A possible connection between 7-NaAlH4 and the dehydrogenation product Na3aAH6 is suggested. We also show that hydrogen transport in NaAlH4 can be treated independently from the observed phase transition, and that the presence of certain point defects can enable transport of hydrogen via a structural diffusion mechanism. A link between long-range hydrogen migration and the rotational mobility of A1Hz groups is demonstrated.by Brandon C. Wood.Ph.D

Proceedings of the Thirteenth International Conference on Time-Resolved Vibrational Spectroscopy

The thirteenth meeting in a long-standing series of “Time-Resolved Vibrational Spectroscopy” (TRVS) conferences was held May 19th to 25th at the Kardinal Döpfner Haus in Freising, Germany, organized by the two Munich Universities - Ludwig-Maximilians-Universität and Technische Universität München. This international conference continues the illustrious tradition of the original in 1982, which took place in Lake Placid, NY. The series of meetings was initiated by leading, world-renowned experts in the field of ultrafast laser spectroscopy, and is still guided by its founder, Prof. George Atkinson (University of Arizona and Science and Technology Advisor to the Secretary of State). In its current format, the conference contributes to traditional areas of time resolved vibrational spectroscopies including infrared, Raman and related laser methods. It combines them with the most recent developments to gain new information for research and novel technical applications. The scientific program addressed basic science, applied research and advancing novel commercial applications. The thirteenth conference on Time Resolved Vibrational Spectroscopy promoted science in the areas of physics, chemistry and biology with a strong focus on biochemistry and material science. Vibrational spectra are molecule- and bond-specific. Thus, time-resolved vibrational studies provide detailed structural and kinetic information about primary dynamical processes on the picometer length scale. From this perspective, the goal of achieving a complete understanding of complex chemical and physical processes on the molecular level is well pursued by the recent progress in experimental and theoretical vibrational studies. These proceedings collect research papers presented at the TRVS XIII in Freising, German

Predicting Skin Permeability by means of Computational Approaches : Reliability and Caveats in Pharmaceutical Studies

© 2019 American Chemical Society.The skin is the main barrier between the internal body environment and the external one. The characteristics of this barrier and its properties are able to modify and affect drug delivery and chemical toxicity parameters. Therefore, it is not surprising that permeability of many different compounds has been measured through several in vitro and in vivo techniques. Moreover, many different in silico approaches have been used to identify the correlation between the structure of the permeants and their permeability, to reproduce the skin behavior, and to predict the ability of specific chemicals to permeate this barrier. A significant number of issues, like interlaboratory variability, experimental conditions, data set building rationales, and skin site of origin and hydration, still prevent us from obtaining a definitive predictive skin permeability model. This review wants to show the main advances and the principal approaches in computational methods used to predict this property, to enlighten the main issues that have arisen, and to address the challenges to develop in future research.Peer reviewedFinal Accepted Versio

Mapping energy transport networks in proteins

The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the evolution of protein structural change following ligand photolysis, and time-resolved IR and Raman techniques, e.g., have provided detailed pictures of the nature and rate of energy transport in peptides and proteins, including recent advances in identifying transport through individual amino acids of several heme proteins. Computational tools to locate energy transport pathways in proteins have also been advancing. Energy transport pathways in proteins have since some time been identified by molecular dynamics (MD) simulations, and more recent efforts have focused on the development of coarse graining approaches, some of which have exploited analogies to thermal transport in other molecular materials. With the identification of pathways in proteins and protein complexes, network analysis has been applied to locate residues that control protein dynamics and possibly allostery, where chemical reactions at one binding site mediate reactions at distance sites of the protein. In this chapter we review approaches for locating computationally energy transport networks in proteins. We present background into energy and thermal transport in condensed phase and macromolecules that underlies the approaches we discuss before turning to a description of the approaches themselves. We also illustrate the application of the computational methods for locating energy transport networks and simulating energy dynamics in proteins with several examples

Recent achievements in ab initio modelling of liquid water

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.Comment: 23 pages, 17 figure