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Weare, John H.

Publications and source records attributed to Weare, John H..

8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Insights on the Alumina–Water Interface Structure by Direct Comparison of Density Functional Simulations with X-ray Reflectivity

Density functional theory molecular dynamics (DFT-MD) simulations are frequently used to predict the interfacial structures and dynamical processes at solid-water interfaces in efforts to gain a deeper understanding of these systems. However, the accuracy of these predictions of interfacial structure has not been rigorously quantified. Here, direct comparisons between large-scale DFT-MD simulations and high-resolution X-ray reflectivity (XR) measurements of the well-defined Al2O3(001)-water interface reveal the relative accuracy of these two methods to describe interfacial structure, a comparison that is enabled by XR’s high sensitivity to atomic-scale displacements. The DFT-MD simulated and XR model-fit structures are qualitatively similar, but XR signals calculated directly from the DFT-MD predictions deviate significantly from the experimental data, revealing discrepancies in these two approaches. Differences in the derived interfacial Al2O3 relaxation profiles of ~0.02 A within the top 5 layers are significant to XR but at the limit of the accuracy of DFT. Further differences are found in the surface hydration layer with a simulated average water layer height ~0.2 A higher than that observed experimentally. This is outside the accuracy of both XR and DFT and is not improved by the inclusion of a phenomenological correction for hydrogen bonding (e.g., Grimme).

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

First Principle Estimation of Geochemically Important Transition Metal Oxide Properties: Structure and Dynamics of the Bulk, Surface and Mineral/Aqueous Fluid Interface

Reactions in the mineral surface/reservoir fluid interface control many geochemical processes such as the dissolution and growth of minerals (Yanina and Rosso 2008), heterogeneous oxidation/reduction (Hochella 1990, Brown 2001, Hochella, Lower et al. 2008, Navrotsky, Mazeina et al. 2008), and inorganic respiration (Newman 2010). Key minerals involved in these processes are the transition metal oxides and oxyhydroxides (e.g., hematite, Fe2O3, and goethite, FeOOH)(Brown, Henrich et al. 1999, Brown 2001, Hochella, Lower et al. 2008, Navrotsky, Mazeina et al. 2008). To interpret and predict these processes, it is necessary to have a high level of understanding of the interactions between the formations containing these minerals and their reservoir fluids. However, these are complicated chemical events occurring under a wide range of T, P, and X conditions and the interpretation is complicated by the highly heterogeneous nature of natural environments (Hochella 1990, Hochella, Lower et al. 2008, Navrotsky, Mazeina et al. 2008) and the electronic and structural complexity of the oxide materials involved(Cox 1992, Kotliar and Vollhardt 2004, Navrotsky, Mazeina et al. 2008). In addition, also because of the complexity of the minerals involved and the heterogeneous nature of natural systems, the direct observation of these reactions at the atomic level is experimentally extremely difficult. Theoretical simulations will provide important support for analysis of the geochemistry of the mineral surface/fluid region as well as provide essential tools to extrapolate laboratory measurements to the field environment.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Computational Tools for Predictive Modeling of Properties in Complex Actinide Systems

In this chapter we focus on methodological and computational aspects that are key to accurately modeling the spectroscopic and thermodynamic properties of molecular systems containing actinides within the density functional theory (DFT) framework. Our focus is on properties that require either an accurate relativistic all-electron description or an accurate description of the dynamical behavior of actinide species in an environment at finite temperature, or both. The implementation of the methods and the calculations discussed in this chapter were done with the NWChem software suite (Valiev et al. 2010). In the first two sections we discuss two methods that account for relativistic effects, the ZORA and the X2C Hamiltonian. Section 1.2.1 discusses the implementation of the approximate relativistic ZORA Hamiltonian and its extension to magnetic properties. Section 1.3 focuses on the exact X2C Hamiltonian and the application of this methodology to obtain accurate molecular properties. In Section 1.4 we examine the role of a dynamical environment at finite temperature as well as the presence of other ions on the thermodynamics of hydrolysis and exchange reaction mechanisms. Finally, Section 1.5 discusses the modeling of XAS (EXAFS, XANES) properties in realistic environments accounting for both the dynamics of the system and (for XANES) the relativistic effects.

actinide↗
DOE OSTI2014

QM/MM Simulation (B3LYP) of the RNase A Cleavage-Transesterification Reaction Supports a Triester AN+DN Associative Mechanism with an O2´ H Internal Proton Transfer

The mechanism of the backbone cleavage transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report QM/MM free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2? oxygen on the neighboring diester phosphate bond and both reach the same product state (PS) (a O3??O2? cyclic phosphate and a O5? hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition state (TS) general acid (His 119)/base (His 12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2? migrates to the non-bridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN+DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 1011 difference in rate strongly supporting the less accepted triester mechanism.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2013

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H{sub 2}O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Automatic Transformation of MPI Programs to Asynchronous, Graph-Driven Form

The goals of this project are to develop new, scalable, high-fidelity algorithms for atomic-level simulations and program transformations that automatically restructure existing applications, enabling them to scale forward to Petascale systems and beyond. The techniques enable legacy MPI application code to exploit greater parallelism though increased latency hiding and improved workload assignment. The techniques were successfully demonstrated on high-end scalable systems located at DOE laboratories. Besides the automatic MPI program transformations efforts, the project also developed several new scalable algorithms for ab-initio molecular dynamics, including new massively parallel algorithms for hybrid DFT and new parallel in time algorithms for molecular dynamics and ab-initio molecular dynamics. These algorithms were shown to scale to very large number of cores, and they were designed to work in the latency hiding framework developed in this project. The effectiveness of the developments was enhanced by the direct application to real grand challenge simulation problems covering a wide range of technologically important applications, time scales and accuracies. These included the simulation of the electronic structure of mineral/fluid interfaces, the very accurate simulation of chemical reactions in microsolvated environments, and the simulation of chemical behavior in very large enzyme reactions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

First-principles simulation of solvation structure and deprotonation reactions of ore forming metal ions in very nonideal solutions

Advances in algorithms and computational performance achieved in this grant period have allowed the atomic level dynamical simulation of complex nanoscale materials using interparticle forces calculated directly from an accurate density functional solution to the electronic Schrödinger equation (ab-initio molecular dynamics, AIMD). Focus of this program was on the prediction and analysis of the properties of environmentally important ions in aqueous solutions. AIMD methods have provided chemical interpretations of these very complex systems with an unprecedented level of accuracy and detail. The structure of the solvation region neighboring a highly charged metal ion (e.g., 3+) in an aqueous solution is very different from that of bulk water. The many-body behaviors (polarization, charge transfer, etc.) of the ion-water and water-water interactions in this region are difficult to capture with conventional empirical potentials. However, a large numbers of waters (up to 128 waters) are required to fully describe chemical events in the extended hydrations shells and long simulation times are needed to reliably sample the system. Taken together this makes simulation at the 1 st principles level a very large computational problem. Our AIMD simulation results using these methods agree with the measured octahedral structure of the 1 st solvation shell of Al 3+ at the 1 st shell boundary and a calculated radius of 1.937 (exp. 1.9). Our calculated average 2 nd shell radius agrees remarkably well with the measured radius, 4.093 Å calculated vs. the measured value of 4.0-4.15 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗