Engineering topics

Bylaska, Eric J

Publications and source records attributed to Bylaska, Eric J.

9 records

DOE OSTI2013

The Aqueous Ca2+ System, in Comparison with Zn2+, Fe3+, and Al3+: An Ab Initio Molecular Dynamics Study

Results of Ab Initio Molecular Dynamics (AIMD) simulations of a Ca2+ ion in an aqueous environment (64 waters, 38ps=5ps equilibration + 33ps data collection, 300K) are reported. The 1st hydration shell contains 6-7 waters with d(OH) = 0.97Å (identical to our bulk water estimate) and average tilt angle, I = 32º. The 1st maximum in the radial distribution function occurs at GCaO(r) = 2.45Å. Our results compare well with published experimental structural data from X-Ray Absorption (XAFS) and Neutron Diffraction. We also generate simulated XAFS spectra using a 1st principles MD-XAFS procedure and show quantitative agreement with experimental XAFS data from a 0.2m Ca(ClO4)2 aqueous solution. The Ca2+ 1st shell water dipole moment of 3.1D is identical to our bulk water estimate (3.1D). The structured 2nd hydration shell, composed of ~16.5 waters, has a maximum at GCaO(r) =4.6Å. The average 2nd shell dipole moment = 2.9D, is suppressed relative to bulk water values. Detailed H-bond analysis demonstrates the waters in this shell predominately coordinate 1st shell waters with a trigonally structured H-bond network. Two exchanges between the 1st hydration shell and the bulk were observed. These were consistent with a dissociative and dissociative interchange Eigen-Wilkins ligand exchange mechanism. Many transfers between the 2nd shell and bulk are detected for Ca2+ allowing an estimation of the 2nd shell mean residence time (MRT) of 4.6ps. Comparison of the Ca2+ hydration shell structure and dynamics with those of the recently reported Zn2+, Fe3+ and Al3+ cation species show that the 1st and 2nd hydration shell parameters, d(M-OI) distance, CNII, H-bond d(OI-OII) distance and %Tetrahedral structure are correlated with cation charge density, the ratio of cation charge (Z) and size (Rion). However, important exceptions are d(M-OII) and the 2nd shell Mean Residence Time (MRT). These differences are explained in terms of the 1st shell structure parameters (d(M-OI) distance and tilt angle I which are strongly influenced by the valence electronic structure of the Ca2+, Zn2+, Fe3+, and Al3+ cation species. The average 2nd shell dipole moment for all cations are found to be suppressed relative to bulk water.

Ab Initio Molecular Dynamics↗

DOE OSTI2012

Ion Association in AlCl3 Aqueous Solutions from Constrained First-Principles Molecular Dynamics

Ab initio molecular dynamics was used to investigate the ion pairing behavior between Cl- and the Al3+ ion in an aqueous AlCl3 solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, by fixing the inter-nuclear separation (rAl-Cl) between the Al3+ ion and one of the Cl- ions. The calculated potential of mean force of the Al3+-Cl- ion pair shows a pronounced minimum at rAl-Cl = 2.3 Å corresponding to a contact ion pair (CIP). Two local minima assigned to solvent separated ion pairs (SSIP) are identified at rAl-Cl= 4.4 and 6.0 Å. The positions of the free energy minima coincide with the hydration shell intervals of the Al3+ cation suggesting that the Cl- ion is inclined to reside in regions of low concentration of waters, i.e. between the 1st and 2nd shells of Al3+ and between the 2nd shell and bulk. A detailed analysis of solvent structure around the Al3+ and Cl- ions as a function of rAl-Cl is presented. The results are compared to structure data from X-ray measurements and unconstrained AIMD simulations of single ions Al3+ and Cl- and AlCl3 solutions. The dipole moment of the water molecules inside the 1st and 2nd hydration shells of Al3+ and in the bulk region and those of the Clion were calculated as a function of rAl-Cl. Major changes in the electronic structure of the system result from the removal of Cl- from the 1st hydration shell of the Al3+ cation. Finally, two unconstrained AIMD simulations of aqueous AlCl3 solutions corresponding to CIP and SSIP configurations were performed (17 ps, 300 K). Only minor structural changes are observed in these systems, confirming their stability.

ab initio↗

DOE OSTI2012

Tuning Band Gap Energies in Pb3(C6X6) Extended Solid-State Structures

A detailed plane-wave density functional theory investigation of the solid-state properties of the extended organometallic system Pb{sub 3}C{sub 6}X{sub 6} for X = O, S, Se, and Te has been performed. Initial geometry parameters for the Pb-X and C-X bond distances were obtained from optimized calculations on molecular fragment models. The Pb{sub 3}C{sub 6}X{sub 6} extended solid molecular structures were constructed in the space group P6/mmm on the basis of the known structure for X = S. Ground-state geometries, band gap energies, densities of states, and charge densities were calculated with the PBE-generalized gradient exchange-correlation functional and the HSE06 hybrid exchange-correlation functional. The PBE band gap energies were found to be lower than the HSE06 values by >0.7 eV. The band energies at points of high symmetry along the first Brillouin zone in the crystal were larger than the overall band gap of the system. Pb{sub 3}C{sub 6}O{sub 6} was predicted to be a direct semiconductor ({Lambda} point) with a PBE band gap of 0.28 eV and an HSE06 band gap of 1.06 eV. Pb{sub 3}C{sub 6}S{sub 6} and Pb{sub 3}C{sub 6}Se{sub 6} were predicted to have indirect band gaps. The PBE band gap for Pb{sub 3}C{sub 6}S{sub 6} was 0.98 eV, and the HSE06 band gap was 1.91 eV. The HSE06 value is in good agreement with the experimentally observed band gap of 1.7 eV. Pb{sub 3}C{sub 6}Se{sub 6} has a PBE band gap of 0.56 eV and a HSE06 band gap of 1.41 eV. Pb{sub 3}C{sub 6}Te{sub 6} was predicted to be metallic with both of the PBE and HSE06 functionals. A detailed analysis of the PBE band structure and partial density of states at two points before and after the metallic behavior reveals a change in orbital character indicative of band crossing in Pb{sub 3}C{sub 6}Te{sub 6}. These results show that the band gap energies can be fine-tuned by changing the substituent X atom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Structure and Hydrolysis of the U(IV), U(V), and U(VI) Aqua Ions from Ab Initio Molecular Simulations

Ab initio molecular dynamics simulations at 300 K based on density functional theory have been used to study the hydration shell geometries, solvent dipole, and first hydrolysis of the Uranium(IV) (U{sup 4+}) and Uranyl(V) (UO{sub 2}{sup +}) ions in aqueous solution. The solvent dipole and first of hydrolysis of aqueous Uranium(VI) (UO{sub 2}{sup 2+}) has also been probed. The first shell of U{sup 4+} is coordinated by 8-9 water ligands with an average U-O distance of 2.42 {angstrom}. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 {angstrom} respectively. The simulated EXAFS spectra of U{sup 4+} matched well with recent experimental data. The first shell of UO{sub 2}{sup +} is coordinated by 5 water ligands in the equatorial plane, with the average U=O{sub ax} and U-O distances being 1.85 {angstrom} and 2.54 {angstrom} respectively. Overall, the hydration shell structure of UO{sub 2}{sup +} matches closely with that of UO{sub 2}{sup 2+} except for small expansions in the average U=O{sub ax} and U-O distances. Each ion strongly polarizes their respective first shell water ligands. The computed acidity constant (pK{sub a}) of U{sup 4+} and UO{sub 2}{sup 2+} are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24 respectively. The predicted pK{sub a} of UO{sub 2}{sup +} is 8.5.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Free energies and mechanisms of water exchange around Uranyl from first principles molecular dynamics

From density functional theory (DFT) based ab initio (Car-Parrinello) metadynamics, we compute the activation energies and mechanisms of water exchange between the first and second hydration shells of aqueous Uranyl (UO{sub 2}{sup 2+}) using the primary hydration number of U as the reaction coordinate. The free energy and activation barrier of the water dissociation reaction [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) {yields} [UO{sub 2}(OH{sub 2})4]{sup 2+}(aq) + H{sub 2}O are 0.7 kcal and 4.7 kcal/mol respectively. The free energy is in good agreement with previous theoretical (-2.7 to +1.2 kcal/mol) and experimental (0.5 to 2.2 kcal/mol) data. The associative reaction [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) + H{sub 2}O {yields} [UO{sub 2}(OH{sub 2})6]{sup 2+}(aq) is short-lived with a free energy and activation barrier of +7.9 kcal/mol and +8.9 kca/mol respectively; it is therefore classified as associative-interchange. On the basis of the free energy differences and activation barriers, we predict that the dominant exchange mechanism between [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) and bulk water is dissociative.

36 MATERIALS SCIENCE↗

DOE OSTI2011

NWChem: scalable parallel computational chemistry

NWChem is a general purpose computational chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree-Fock and density functional theory methods for both plane-wave basis sets as well as Gaussian basis sets, tensor contraction engine based coupled cluster capabilities and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message passing approaches could offer. In response a global address space library, the Global Array Toolkit, was developed. The programming model it offers is based on using predominantly one-sided communication. This model underpins most of the functionality in NWChem and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper the core capabilities of NWChem are described as well as their implementation to achieve an efficient computational chemistry code with high parallel scalability. NWChem is a modern, open source, computational chemistry code1 specifically designed for large scale parallel applications2. To meet the challenges of developing efficient, scalable and portable programs of this nature a particular code design was adopted. This code design involved two main features. First of all, the code is build up in a modular fashion so that a large variety of functionality can be integrated easily. Secondly, to facilitate writing complex parallel algorithms the Global Array toolkit was developed. This toolkit allows one to write parallel applications in a shared memory like approach, but offers additional mechanisms to exploit data locality to lower communication overheads. This framework has proven to be very successful in computational chemistry but is applicable to any engineering domain. Within the context created by the features above NWChem has grown into a general purpose computational chemistry code that supports a wide variety of energy expressions and capabilities to calculate properties based there upon. The main energy expressions are classical mechanics force fields, Hartree-Fock and DFT both for finite systems and condensed phase systems, coupled cluster, as well as QM/MM. For most energy expressions single point calculations, geometry optimizations, excited states, and other properties are available. Below we briefly discuss each of the main energy expressions and the critical points involved in scalable implementations thereof.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2011

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.

09 BIOMASS FUELS↗

DOE OSTI2011

Hydration Shell Structure and Dynamics of Curium(III) in Aqueous Solution: First Principles and Empirical Studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM) and classical molecular dynamics (CMD) simulations of Cm3+ in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm3+ and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted a average first shell and second shell Cm-O bond distances of 2.49-2.53 Å and 4.67-4.75 Å respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 Å and 4.65 Å. The average geometric arrangement of the eight-fold and nine-fold coordinated first shell structures corresponded to the square anti-prism and tricapped trigonal prisms respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell over-coordination compared to recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time is predicted to be on the nanosecond timescale. The computed diffusion constants of Cm3+ and water are in good agreement with experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2011

NWChem

Computational atomistic modeling has emerged as a powerful approach for fundamental studies in chemistry, materials science, geosciences, and biology. It has the ability to provide detailed insights into complex phenomena and over the years has grown into a powerful tool not only to validate experiment, but also to predict new phenomena. In order to harness computational modeling to the fullest, superior computational tools are required that not only offer a broad spectrum of capabilities, but are also capable of taking advantage of modern massively parallel computer architectures efficiently to solve real world problems. The NWChem program suite is an example along these lines. It offers a range of capabilities to perform first-principles electronic structure calculations on molecular and periodic systems, classical molecular dynamics simulations and hybrid QM/MM simulations that permits one to combine quantum and classical methods within a calculation. The code is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters with the goal to provide scalable solutions for large scale atomistic simulations. It has been ported to almost all high-performance computing platforms, workstations, PCs running LINUX, as well as clusters of desktop platforms or workgroup servers. The package is scalable, both in its ability to treat large problems efficiently, and in its utilization of available parallel computing resources. The parallel framework for NWChem is provided by the Global Array (GA) toolkit developed at PNNL. NWChem is developed and maintained by the Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific Northwest National Laboratory (PNNL) in Washington State. The latest release (version 6.0) of the code is distributed under the terms of the Educational Community License (ECL) version 2.0.

99 GENERAL AND MISCELLANEOUS↗