Building toward the future in chemical and materials simulation with accessible and intelligently designed web applications

Bylaska, Eric J.; Song, Duo; Ilton, Eugene S.; O’Leary, Shaun; Torralba–Sanchez, Tifany L.; Tratnyek, Paul G.

doi:10.1016/bs.arcc.2021.09.003

Cited by 8 publications

(12 citation statements)

References 150 publications

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“…All of the electronic structure calculations in this study were performed using the NWChem program suite (version 7.0; Kendall et al 2000, Valiev et al 2010, Apr à et al 2020 through Arrows, a new open access scientific service that facilitates running molecular modelling codes via a web Application Programming Interface (API) hosted at the Environmental Molecular Sciences Laboratory (EMSL, Richland, WA; Bylaska et al 2021). The calculations were performed using density functional theory (DFT) with the PBE96 (Perdew et al 1996), B3LYP (Lee et al 1988, Becke 1993), M06-2X (Zhao and Truhlar 2008) and PBE0 (Adamo and Barone 1999) exchange-correlation functionals.…”

Section: Methodsmentioning

confidence: 99%

“…2020) through Arrows, a new open access scientific service that facilitates running molecular modelling codes via a web Application Programming Interface (API) hosted at the Environmental Molecular Sciences Laboratory (EMSL, Richland, WA; Bylaska et al . 2021). The calculations were performed using density functional theory (DFT) with the PBE96 (Perdew et al .…”

Section: Methodsmentioning

confidence: 99%

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Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS/MS: Investigations with CO₂ as the Reaction Gas

Harouaka

Melby

Bylaska

et al. 2022

Geostandard Geoanalytic Res

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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 monoxides. The general reactivity was shown to be consistent with density functional theory (DFT)‐predicted reaction enthalpies, such that all predicted exothermic reactions produced product ions at levels of at least 1% of the unreacted ion. Most endothermic reactions observed had sufficient kinetic energy in excess of the reaction enthalpies. Our results suggest that reaction enthalpy is a reasonable predictor of reactivity with CO2 on the timescales of the interactions in non‐thermal ICP‐MS/MS systems. The ease and rapidity of data collection with the ICP‐MS/MS and DFT calculations using the NWChem suite has value given the scarcity of thermochemical data of CO2 reactions in the literature. These studies are especially useful for the identification of targeted reaction chemistries to be leveraged for analytical method development, such as for the inline separation of isobaric interferences from analytes of interest.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS/MS: Investigations with CO₂ as the Reaction Gas

Harouaka

Melby

Bylaska

et al. 2022

Geostandard Geoanalytic Res

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“…Arrows or early versions of capabilities in the Arrows have been used to carry out a variety of scientific studies. ,,− Most of these studies fall into two categories. In the first category, the reaction energies for all of the reactions contained in the reaction networks need to be estimated.…”

Section: Simulation Methods and Detailsmentioning

confidence: 99%

“…In short, estimating both the reaction energies and reaction pathways for reaction networks is time-consuming and difficult, and not surprisingly, automating calculations for reaction energies and reaction pathways (and related transition states) is an active area of research. − Recently, we have been developing a prototype open-source computational tool called Arrows, which can be used to carry out large numbers of electronic structure calculations and run complex workflows. With Arrows, it becomes more feasible to study reaction networks.…”

Section: Introductionmentioning

confidence: 99%

Computational Predictions of the Hydrolysis of 2,4,6-Trinitrotoluene (TNT) and 2,4-Dinitroanisole (DNAN)

et al. 2022

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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 2,4dinitroaniline (DNAN) were investigated with plane-wave density functional theory (DFT) combined with ab initio and classical molecular dynamics (AIMD/ MM) free energy simulations, Gaussian basis set DFT calculations, and correlated molecular orbital theory calculations. Most of the computations in this study were carried out using the Arrows web-based tools. For each mechanism, Meisenheimer complex formation, nucleophilic aromatic substitution, and proton abstraction reaction energies and activation barriers were calculated for the reaction at each relevant site. For TNT, it was found that the most kinetically favorable first hydrolysis steps involve Meisenheimer complex formation by attachment of OH − at the C1 and C3 arene carbons and proton abstraction from the methyl group. The nucleophilic aromatic substitution reactions at the C2 and C4 arene carbons were found to be thermodynamically favorable. However, the calculated activation barriers were slightly lower than in previous studies, but still found to be ΔG ‡ ≈ 18 kcal/mol using PBE0 AIMD/MM free energy simulations, suggesting that the reactions are not kinetically significant. For DNAN, the barriers of nucleophilic aromatic substitution were even greater (ΔG ‡ > 29 kcal/mol PBE0 AIMD/MM). The most favorable hydrolysis reaction for DNAN was found to be a two-step process in which the hydroxyl first attacks the C1 carbon to form a Meisenheimer complex at the C1 arene carbon C1−(OCH 3 )OH − , and subsequently, the methoxy anion (−OCH 3 ) at the C1 arene carbon dissociates and the proton shuttles from the C1−OH to the dissociated methoxy group, resulting in methanol and an aryloxy anion.

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“…The plane-wave calculations used a simple cubic box with L = 15 Å, and a cutoff energy of 40 Ry. The web application EMSL Arrows [88] was used to set up and perform the plane-wave calculations. The valence electron interactions with the atomic core are approximated with generalized norm-conserving Hamann [82] pseudopotentials modified to the separable form suggested by Kleinman and Bylander [81].…”

Section: Matrix Elements From the Two-electron Operatorsmentioning

confidence: 99%

Periodic Plane-Wave Electronic Structure Calculations on Quantum Computers

Song

Bauman

Prawiroatmodjo

et al. 2022

Preprint

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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 Microsoft's Azure Quantum service. This work is an extension to periodic systems of a new class of algorithms in which the virtual spaces were generated by optimizing orbitals from small pairwise CI Hamiltonians, which we term as correlation optimized virtual orbitals with the abbreviation COVOs. In this extension, the integration of the first Brillouin zone is automatically incorporated into the two-electron integrals. With these procedures we have been able to derive virtual spaces, containing only a few orbitals, that were able to capture a significant amount of correlation. The focus in this manuscript is on comparing the simulations of small molecules calculated with plane-wave basis sets with large periodic unit cells at the Γ-point, including images, to results for plane-wave basis sets with aperiodic unit cells. The results for this approach were promising as we were able to obtain good agreement between periodic and aperiodic results for an LiH molecule. Simulations performed on the Quantinuum H1-1 quantum computer were able to produce surprisingly good energies, reproducing the FCI values for the 1 COVO Hamiltonian to within 11 milliHartree (6.9 kcal/mol), when corrected for noise.

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Building toward the future in chemical and materials simulation with accessible and intelligently designed web applications

Cited by 8 publications

References 150 publications

Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS/MS: Investigations with CO₂ as the Reaction Gas

Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS/MS: Investigations with CO₂ as the Reaction Gas

Computational Predictions of the Hydrolysis of 2,4,6-Trinitrotoluene (TNT) and 2,4-Dinitroanisole (DNAN)

Periodic Plane-Wave Electronic Structure Calculations on Quantum Computers

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Building toward the future in chemical and materials simulation with accessible and intelligently designed web applications

Cited by 8 publications

References 150 publications

Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS/MS: Investigations with CO2 as the Reaction Gas

Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS/MS: Investigations with CO2 as the Reaction Gas

Computational Predictions of the Hydrolysis of 2,4,6-Trinitrotoluene (TNT) and 2,4-Dinitroanisole (DNAN)

Periodic Plane-Wave Electronic Structure Calculations on Quantum Computers

Contact Info

Product

Resources

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Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS/MS: Investigations with CO₂ as the Reaction Gas

Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS/MS: Investigations with CO₂ as the Reaction Gas