Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na⁺-montmorillonite (001), Ca²⁺-montmorillonite (001), goethite (100), and Na⁺-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na⁺ -birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation

EMSL and Institute for Integrated Catalysis (IIC) Catalysis Workshop

Within the context of significantly accelerating scientific progress in research areas that address important societal problems, a workshop was held in November 2010 at EMSL to identify specific and topically important areas of research and capability needs in catalysis-related science

First-Principles Dynamics along the Reaction Path of CH3CH2 + O2 f H2C)CH2 + HOO: Evidence for Vibronic State Mixing and Neutral Hydrogen Transfer †

We employ Born-Oppenheimer molecular dynamics (BOMD), with forces derived from spin-polarized density functional theory using the B3LYP hybrid exchange-correlation functional, to explore the dynamics of oxidation of ethyl radical to produce ethylene, along the concerted-elimination path CH3CH2 + O2 f CH3CH2OO f CH2dCH2 + HOO. The transition state connecting CH3CH2OO to CH2dCH2 and HOO has a planar, fivemembered-ring structure ‚‚‚C-C-H-O-O‚‚ ‚ known as TS1. The electronic nature of this saddle point has been the subject of controversy. Recent ab initio calculations have indicated that TS1 has a 2 A′ ′ electronic ground state within Cs symmetry. In this state, intramolecular neutral hydrogen transfer from the methyl group of the intermediate ethylperoxy radical (CH3CH2OO‚) to the terminal oxygen is hindered by the lack of overlap between the 1s orbital of the in-plane hydrogen atom and the singly-occupied 2p (a′′) orbital of the terminal oxygen. Previous explanations invoked proton transfer, a rather unpalatable process for an alkylperoxy radical. Two other possibilities that both facilitate neutral H-transfer are explored in the present work, namely: (i) an O2 π*-resonance mechanism and (ii) 2 A′- 2 A′ ′ state mixing. First, we show that the structure of TS1 is a “late, ” loose transition state, consistent with a loosely coupled O2 that can shift π*-electrons to aid neutral hydrogen atom transfer. Second, our BOMD trajectories reveal that torsional motion in the ethylperoxy radical and at the transition state causes symmetry-breaking and 2 A′- 2 A′ ′ state mixing

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Quantification of High Temperature Transition Al2O3 and Their Phase Transformations

High temperature exposure of gamma-Al2O3 can lead to a series of polymorphic transformations, including the formation of delta-Al2O3 and theta-Al2O3. Quantification of the microstructure in the delta/theta-Al2O3 formation range represents a formidable challenge as both phases accommodate a high degree of structural disorder. In this work, we explore the use of XRD recursive stacking formalism for quantification of high temperature transition aluminas. We formulate the recursive stacking methodology for modelling of disorder in delta-Al2O3 and twinning in theta-Al2O3 and show that explicitly accounting for the disorder is necessary to reliably model the XRD patterns of high temperature transition alumina. In the second part, we use the recursive stacking approach to study phase transformation during high temperature (1050 ºC) treatment. We show that the two different intergrowth modes of delta-Al2O3 have different transformation characteristics, and that a significant portion of delta-Al2O3 is stabilized with theta-Al2O3 even after prolonged high-temperature exposures. In discussions, we outline the limitation of the current XRD approach and discuss a possible multimodal XRD and NMR approach which can improve analysis of complex transition aluminas.</p