Eric J. Bylaska

Pacific Northwest National Laboratory | PNNL

The transformative impact of modern computational paradigms and technologies, such as high-performance computing (HPC), quantum computing, and cloud computing, has opened up profound new opportunities for scientific simulations. Scalable computational chemistry is one beneficiary of this technological progress. The main focus of this paper is on th...

This study investigated the reaction pathway of 2,4-dinitroanisole (DNAN) on the pyrogenic carbonaceous matter (PCM) to assess the scope and mechanism of PCM-facilitated surface hydrolysis. DNAN degradation was observed at pH 11.5 and 25 °C with a model PCM, graphite, whereas no significant decay occurred without graphite. Experiments were performe...

Many important chemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular simulation have limitations in terms of scales of time, lengt...

Many important geochemical and biogeochemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular simulation have limitations in terms of...

This paper summarizes developments in the NWChem computational chemistry suite since the last major release (NWChem 7.0.0). Specifically, we focus on functionality, along with input blocks, that is accessible in the current stable release (NWChem 7.2.0) and in the "master" development branch, interfaces to quantum computing simulators, interfaces t...

Chloroform (CF) is a widely used chemical reagent and disinfectant and a probable human carcinogen. The extensive literature on halocarbon reduction with zerovalent iron (ZVI) shows that transformation of CF is slow, even with nano, bimetallic, sulfidated, and other modified forms of ZVI. In this study, an alternative method of ZVI modification─inv...

A procedure for defining virtual spaces, and the periodic one-electron and two-electron integrals, for plane-wave second quantized Hamiltonians has been developed, and it was validated using full configuration interaction (FCI) calculations, as well as executions of variational quantum eigensolver (VQE) circuits on Quantinuum’s ion trap quantum com...

The SCAN (strongly constrained and appropriately normed) meta-generalized gradient approximation (meta-GGA), which satisfies all 17 exact constraints that a meta-GGA can satisfy, accurately describes equilibrium bonds that are normally correlated. With symmetry breaking, it also accurately describes some sd equilibrium bonds that are strongly corre...

Hydrolysis is a common transformation reaction that can affect the environmental fate of many organic compounds. In this study, three proposed mechanisms of alkaline hydrolysis of 2,4,6-trinitrotoluene (TNT) and 2,4-dinitroaniline (DNAN) were investigated with plane-wave density functional theory (DFT) combined with ab initio and classical molecula...

The SCAN (strongly constrained and appropriately normed) meta-generalized gradient approximation (meta-GGA), which satisfies all 17 exact constraints that a meta-GGA can satisfy, accurately describes equilibrium bonds that are normally correlated. With symmetry breaking, it also accurately describes some sd equilibrium bonds that are strongly corre...

Characterizing the chemical state and physical disposition of uranium that has persisted over geologic time scales is key for modeling the long-term geologic sequestration of nuclear waste, accurate uranium-lead dating, and the use of uranium isotopes as paleo redox proxies. X-ray absorption spectroscopy coupled with molecular dynamics modeling dem...

A procedure for defining virtual spaces, and the periodic one-electron and two-electron integrals, for plane-wave second quantized Hamiltonians has been developed and demonstrated using full configuration interaction (FCI) simulations and variational quantum eigensolver (VQE) circuits on Quantinuum's ion trap quantum computers accessed through Micr...

Carbon dioxide (CO2) was used as a reaction gas to investigate the gas‐phase ion‐molecule interactions using the Agilent 8900 ICP‐MS/MS. A solution containing forty‐five elements representative of the periodic table was used to supply the ions to react with CO2 in the collision/reaction cell (CRC). The only significant product ions formed were mono...

Nitrous oxide (N2O) was used as a reaction gas to investigate the gas-phase ion-molecule interactions using the Agilent 8900 QQQ-ICP-MS. A multi-element standard containing 45 elements, from Be to Pb, was used for the measurement of ions with QQQ-ICP-MS in the presence and absence of N2O. The main product ion species observed were oxides and nitrid...

Hematite (α-Fe2O3) exerts a strong control over the transport of minor but critical metals in the environment and is used in multiple industrial applications; the photocatalysis community has explored the properties of hematite nanoparticles over a wide range of transition metal dopants. Nonetheless, simplistic assumptions are used to rationalize t...

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s a...

For many-body methods such as MCSCF and CASSCF, in which the number of one-electron orbitals is optimized and independent of the basis set used, there are no problems with using plane-wave basis sets. However, for methods currently used in quantum computing such as select configuration interaction (CI) and coupled cluster (CC) methods, it is necess...

This paper explores the utility of the quantum phase estimation (QPE) algorithm in calculating high-energy excited states characterized by the promotion of electrons occupying core-level shells. These states have been intensively studied over the last few decades, especially in supporting the experimental effort at light sources. Results obtained w...

The bulk behavior of materials is often controlled by minor impurities that create nonperiodic localized defect structures due to ionic size, symmetry, and charge balance mismatches. Here, we used transmission electron microscopy (TEM) of atom-resolved dynamics to directly map the topology of Fe vacancy clusters surrounding structurally incorporate...

For many-body methods such as MCSCF and CASSCF, in which the number of one-electron orbitals are optimized and independent of basis set used, there are no problems with using plane-wave basis sets. However, for methods currently used in quantum computing such as select configuration interaction (CI) and coupled cluster (CC) methods, it is necessary...

This paper explores the utility of the quantum phase estimation (QPE) in calculating high-energy excited states characterized by promotions of electrons occupying inner energy shells. These states have been intensively studied over the last few decades especially in supporting the experimental effort at light sources. Results obtained with the QPE...

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven me...

A key reaction underlying the charge transport in iron containing oxides, clays, micas is the Fe²⁺-Fe³⁺ exchange reaction between edge-sharing iron octahedra. These reactions facilitate conduction in these minerals by the thermally-activated hopping of small polarons across the lattice. Depending on the mineral and local charge state the small pola...

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principledriven met...

Abstract An efficient and accurate approach for calculating exact exchange and other two-electron integrals has been developed for periodic electronic structure methods. Traditional approaches used for integrating over the Brillouin zone in band structure calculations, e.g. trapezoidal or Monkhorst-Pack, are not accurate enough for two-electron int...

The alanine transaminase (ALT) enzyme catalyzes the transfer of an amino group from alanine to α-ketoglutarate to produce pyruvate and glutamate. Isotope fractionation factors (IFFs) for the reaction ⁺H₃NCH(CH₃)COO⁻ + ⁻OOCCH₂CH₂C(O)COO⁻ ↔ CH₃C(O)COO⁻ + ⁻H₃NCH(CH₂CH₂COO⁻)COO⁻ (zwitterionic neutral alanine + doubly deprotonated α-ketoglutarate ↔ pyru...

The characteristic pathway for degradation of halogenated aliphatic compounds in groundwater or other environments with relatively anoxic and/or reducing conditions is reductive dechlorination. For 1,2-dichalocarbons, reductive dechlorination can included hydrogenolysis and dehydrohalogenation, the relative significance of which depends on various...

Zn is an essential micronutrient that is often limited in tropical, lateritic soils in part because it is sequestered in nominally refractory iron oxide phases. However, stable phases such as goethite and hematite can undergo reductive recrystallization without a phase change under circumneutral pH conditions and release metal impurities such as Zn...

In this paper, we discuss the extension of the recently introduced subsystem embedding subalgebra coupled cluster (SES-CC) formalism to unitary CC formalisms. In analogy to the standard single-reference SES-CC formalism, its unitary CC extension allows one to include the dynamical (outside the active space) correlation effects in an SES induced com...

Fault-tolerant quantum computation promises to solve outstanding problems in quantum chemistry within the next decade. Realizing this promise requires scalable tools that allow users to translate descriptions of electronic structure problems to optimized quantum gate sequences executed on physical hardware, without requiring specialized quantum com...

In this paper we outline the extension of recently introduced the sub-system embedding sub-algebras coupled cluster (SES-CC) formalism to the unitary CC formalism. In analogy to the standard single-reference SES-CC formalism, its unitary CC extension allows one to include the dynamical (outside the active space) correlation effects in an SES induce...

closo-Borate anions [closo-BnXn]²⁻ are part of the most famous textbook examples of polyhedral compounds. Substantial differences in their reactivity and interactions with other compounds depending on the substituent X and cluster size n have been recognized, which favors specific closo-borates for different applications in cancer treatment, chemic...

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...

Non-equilibrium chemical phenomena are known to play an important role in single molecule microscopy and spectroscopy. Herein, we explore these effects through ab initio molecular dynamics (AIMD)-based Raman spectral simulations. We target an isolated aromatic thiol (thiobenzonitrile, TBN) as a prototypical molecular system. We first show that the...

An approach for modeling electron transfer in solids and at surfaces of iron - (oxyhydr)oxides and other redox active solids has been developed for electronic structure methods (i.e., plane-wave Density Functional Theory) capable of performing calculations with periodic cells and large system sizes efficiently while at the same time being accurate...

Radiotoxic uranium contamination in natural systems and nuclear waste containment can be sequestered by incorporation into naturally abundant iron (oxyhydr)oxides such as hematite (α-Fe₂O₃) during mineral growth. The stability and properties of the resulting uranium-doped material are impacted by the local coordination environ...

Electrocatalysis at a transition metal oxide (TMO) electrode in aqueous electrolyte is controlled in part by the behavior of interfacial water. Atomically precise measurements of TMO-electrolyte interfaces under electrocatalytic working conditions are therefore prerequisite for developing accurate models of interfacial reactions. We present the mos...

Ab-initio Molecular Dynamics (AIMD) methods are an important class of algorithms, as they enable scientists to understand the chemistry and dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. Many-core architectures such as the Intel® Xeon Phi™ processor are an interesting an...

The characterization of trace elements in minerals using extended X-ray absorption fine structure (EXAFS) spectroscopy constitutes a first step toward understanding how impurities and contaminants interact with the host phase and the environment. However, limitations to EXAFS interpretation complicate the analysis of trace concentrations of impurit...

Background Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous i...

Quantitative structure-activity relationships (QSARs) have long been used in the environmental sciences. More recently, molecular modeling and chemoinformatic methods have become widespread. These methods have the potential to expand and accelerate advances in environmental chemistry because they complement observational and experimental data with...

Hiding communication behind useful computation is an important performance programming technique but remains an inscrutable programming exercise even for the expert. We present Bamboo, a code transformation framework that can realize communication overlap in applications written in MPI without the need to intrusively modify the source code. We refo...

Phenols and anilines have been studied extensively as reductants of environmental oxidants (such as manganese dioxide) and as reductates (e.g., model contaminants) that are transformed by environmental oxidants (ozone, triple organic matter, etc.). The thermodynamics and kinetics of these reactions have been interpreted using oxidation potentials f...

A detailed description of modern plane-wave density functional theory (DFT) methods and software (contained in the NWChem package) is described that allows for both geometry optimization and ab initio molecular dynamics simulations. Significant emphasis is placed on aspects of these methods that are of interest to computational chemists and useful...

The presence of counter ions in solutions containing highly charged metal cations can trigger processes such as ion-pair formation, hydrogen bond breakages and subsequent reformation, and ligand exchanges. In this work, it is shown how halide (Cl⁻, Br⁻) and perchlorate (ClO4⁻) anions affect the strength of the primary solvent coordination shells ar...

Incorporation of economically or environmentally consequential polyvalent metals into iron (oxyhydr)oxides has applications in environmental chemistry, remediation, and materials science. A primary tool for characterizing the local coordination environment of such metals, and therefore building models to predict their behavior, is extended X-ray ab...

Reactions in the mineral surface/reservoir fluid interface control many geochemical processes such as the dissolution and growth of minerals, heterogeneous oxidation/reduction, and inorganic respiration. Transition metal oxides are one of the mineral involved in these processes. This chapter describes the usage of first principles dynamical simulat...

New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate/effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide...

Lithium clusters Lin (n = 1–20) have been investigated with density functional theory (DFT) and coupled-cluster (CC) methods. The global minima are located via an improved basin-hopping algorithm. Simulated polarizabilities are in good agreement with the measured data generally. The simulated polarizabilities for Li6, Li12 and Li19 are in reasonabl...

We probe, at high energy resolution, the double electron excitation (KLII&II) x-ray absorption region that lies approximately 115 eV above the main Al K-edge (1566 eV) of α-alumina and sodium aluminate. The two solid standards, α-alumina (octahedral) and sodium aluminate (tetrahedral) are compared to aqueous species that have the same Al coordinati...

The evaluation of new energetic nitroaromatic compounds (NACs) for use in green munitions formulations requires models that can predict their environmental fate. Previously invoked linear free energy relationships (LFER) relating the log of the rate constant for this reaction (log(k)) and one-electron reduction potentials for the NAC (E1NAC) normal...

This chapter focuses 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. It discusses two methods that account for relativistic effects, the zeroth-order regular approximation (ZO...

The atom-centered density-matrix propagation method is used to illustrate how time-dependent conformational changes affect the electronic structure and derived spectroscopic properties of a prototypical finite metal cluster-bound π-conjugated organic complex, Ag7-benzenethiol. We establish that there is considerable conformational flexibility to th...

Divalent cation-rich silicate minerals such as olivines have a high potential for carbonation reaction and thus their reactivity with water/carbon dioxide mixed fluids is critical to understanding chemical interactions relevant to carbon dioxide capture and sequestration. Therefore, plane-wave density functional theory (DFT) calculations were perfo...

Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics and the first hydrolysis constants of Pu3+, Pu4+, PuO2+ and PuO22+ ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with availabl...

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 ti (trajectory positions and velocities xi = (ri, vi)) to...

Using density functional theory based ab initio molecular dynamics and metadynamics, we show that counterions can trigger noticeable changes in the hydration shell structure of the curium ion. On the basis of the free energies of curium–water coordination, the eight-fold coordination state is dominant by at least 98% in the absence of counteranions...

Enthalpies of formation for the ThX₄ and UX₄ (X = F, Cl, OH) species have been investigated with density functional theory and coupled-cluster methods. ThX₄ molecules are all confirmed as tetrahedral while all UX₄ molecules are predicted to adopt D_2d symmetry using density functional theory. Mu...

Herein, we report on the structure and dynamics of the aqueous Ca2+ system studied by using abinitio molecular dynamics (AIMD) simulations. Our detailed study revealed the formation of well-formed hydration shells with characteristics that were significantly different to those of bulk water. To facilitate a robust comparison with state-of-the-art X...

The environmental impacts of energetic compounds can be minimized through the design and selection of new energetic materials with favorable fate properties. Building predictive models to inform this process, however, is difficult because of uncertainties and complexities in in the major fate-determining transformation reactions, such as the alkali...

A one-year Study Topic project was funded at PNNL to investigate the state-of-the-art in modeling CdZnTe (CZT) melt-solid interface, or solid-liquid interface (SLI), with an emphasis on knowledge and method gaps. The Study Topic culminates with this report to DNDO regarding the current modeling capabilities and outlining the known gaps in our capab...

We present Bamboo, a custom source-to-source translator that transforms MPI C source into a data-driven form that automatically overlaps communication with available computation. Running on up to 98304 processors of NERSC's Hopper system, we observe that Bamboo's overlap capability speeds up MPI implementations of a 3D Jacobi iterative solver and C...

The Car-Parrinello-based molecular dynamics (CPMD) method was used to investigate the ion-pairing behavior between Cl(-) and Al(3+) ions in an aqueous AlCl(3) solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, with the internuclear separation (r(Al-Cl)) between the Al(3+) ion a...

DFT-MD simulations (PBE96 and PBE0) with MD-XAFS scattering calculations (FEFF9) show near quantitative agreement with new and existing XAFS measurements for a comprehensive series of transition metal ions which interact with their hydration shells via complex mechanisms (high spin, covalency, charge transfer, etc.). This work was supported by the...

A detailed plane-wave density functional theory investigation of the solid-state properties of the extended organometallic system PbâCâXâ 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 PbâCâXâ extended solid mole...

Ab initio molecular dynamics simulations at 300 K, based on density functional theory, are performed to study the hydration shell geometries, solvent dipole, and first hydrolysis reaction of the uranium(IV) (U(4+)) and uranyl(V) (UO(2)(+)) ions in aqueous solution. The solvent dipole and first hydrolysis reaction of aqueous uranyl(VI) (UO(2)(2+)) a...

ABSTRACTFrom 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 (UO22+) using the primary hydration number of U as the reaction coordinate. The free energy and activation barrier of the wate...

NWChem is the highly scalable computational chemistry software package developed by the Molecular Sciences Software group for the Environmental Molecular Sciences Laboratory. The software provides a wide range of capabilities for quantum mechanical and classical mechanical modeling and simulation of chemical and biological systems. The software inf...