Environmental Molecular Sciences Laboratory

A DOE Office of Science User Facility

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Molecular Science Computing

Environmental molecular research is enhanced when combined with advance data analytics and visualization, computational modeling and simulation, and efficient parallel software. Users are encouraged to combine computation with EMSL's state-of-the-art experimental tools to make an integrated platform for scientific discovery. See a complete list of Molecular Science Computing instruments.

Resources and Techniques

*NEW* EMSL's new supercomputer, Tahoma, is planned to be available for research starting October 1. This system will support computational research requiring significant memory as well as processing speed to enable data mining, image processing, and multiscale modeling.

  • Tahoma provides 160 CPU nodes and 24 GPU nodes, with an estimated peak performance of 0.57 PetaFLOPs.
  • The 160 CPU nodes each have 36 3.1 GHz Intel Xeon processor cores, 384 GB of memory and 2 TB of flash storage.
  • The 24 GPU nodes each have 36 processor cores and 2 NVIDIA v100 GPGPUs, 1536 GB of memory and 7 TB of flash storage.
  • Tahoma’s 10 PB global file system is capable of 100 Gigabyte/sec bandwidth.

Additional flagship computing resources also offered include:

  • Cascade, a 1440-node supercomputer with theoretical peak performance of 3.4 petaflops; Cascade came online in December 2013.
  • Aurora, a 17 Petabyte HPSS data storage system
  • NWChem, a molecular modeling software. NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum-mechanical descriptions of the electronic wave-function or density.
  • Data Analysis & Visualization, a web-based front end for visualizations of data generated in EMSL.

EMSL employs a forward-looking strategy to maintain leading-edge supercomputing capabilities and encourages users to combine computational and state-of-the-art experimental tools, providing a cross-disciplinary environment to further research.

Additional Information

Description

Molecular Science Computing – EMSL offers sophisticated and integrated computational capabilities, including scientific consultants, software, Cascade supercomputer and the Aurora data archive, to enable the following:

  • Quantum chemistry and molecular dynamics simulations of molecules, surface interfaces, nanoparticles and biological systems
  • Subsurface flow and reactive transport modeling
  • Simulations of aerosols and atmospheric particles
  • Agent-based modeling framework for simulation of biological systems
  • Data analysis and visualization tools to enable exploration of complex data sets from experimental platforms.

Instruments

No instruments are available at this time.

Publications

Periodic self-consistent density functional theory (DFT-GGA) calculations were used to study the adsorption of several atomic species, molecular...
The heats of formation and the normalized clustering energies (NCEs) for the group 4 and group 6 transition metal oxide (TMO) trimers and tetramers...
Nearly free electron (NFE) states with density maxima in nonnuclear (NN) voids may have remarkable electron transport properties ranging from...
Cyclobutanetetrone, (CO)4, has a triplet ground state. Here we predict, based on electronic structure calculations, that the B2N2O4 molecule also has...
The presence of Cu in reactions of triphenylene (TRPH) and 1,4-C4F8I2 at 360 °C led to regiospecific substitution of TRPH ortho C(β) atoms to form...

Science Highlights

Posted: August 02, 2019
Pacific Northwest National Laboratory web feature Ammonia, the primary ingredient in nitrogen-based fertilizers, has helped feed the world since...
Posted: July 25, 2019
The Science Inert gases like argon typically do not form chemical bonds except under extreme conditions, such as the icy cold of outer space. As...
Posted: January 23, 2019
From Pacific Northwest National Laboratory's Physical Sciences Division Dissolved aluminum formed during industrial processing has perplexed chemists...
Posted: January 04, 2019
From Pacific Northwest National Laboratory's Physical Sciences Division A team of researchers led by PNNL computational scientist Simone Raugei have...
Posted: August 13, 2018
The Science One promising approach to stabilize uranium contamination in soils is to envelop the radioactive uranium into iron-bearing minerals like...

Instruments

There are no related projects at this time.

Environmental molecular research is enhanced when combined with advance data analytics and visualization, computational modeling and simulation, and efficient parallel software. Users are encouraged to combine computation with EMSL's state-of-the-art experimental tools to make an integrated platform for scientific discovery. See a complete list of Molecular Science Computing instruments.

Resources and Techniques

*NEW* EMSL's new supercomputer, Tahoma, is planned to be available for research starting October 1. This system will support computational research requiring significant memory as well as processing speed to enable data mining, image processing, and multiscale modeling.

  • Tahoma provides 160 CPU nodes and 24 GPU nodes, with an estimated peak performance of 0.57 PetaFLOPs.
  • The 160 CPU nodes each have 36 3.1 GHz Intel Xeon processor cores, 384 GB of memory and 2 TB of flash storage.
  • The 24 GPU nodes each have 36 processor cores and 2 NVIDIA v100 GPGPUs, 1536 GB of memory and 7 TB of flash storage.
  • Tahoma’s 10 PB global file system is capable of 100 Gigabyte/sec bandwidth.

Additional flagship computing resources also offered include:

  • Cascade, a 1440-node supercomputer with theoretical peak performance of 3.4 petaflops; Cascade came online in December 2013.
  • Aurora, a 17 Petabyte HPSS data storage system
  • NWChem, a molecular modeling software. NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum-mechanical descriptions of the electronic wave-function or density.
  • Data Analysis & Visualization, a web-based front end for visualizations of data generated in EMSL.

EMSL employs a forward-looking strategy to maintain leading-edge supercomputing capabilities and encourages users to combine computational and state-of-the-art experimental tools, providing a cross-disciplinary environment to further research.

Additional Information

Effects of van der Waals Density Functional Corrections on Trends in Furfural Adsorption and Hydrogenation on Close-Packed

Abstract: 

The hydrogenation of furfural to furfuryl alcohol on Pd(111), Cu(111) and Pt(111) is studied with both standard Density Functional Theory (DFT)-GGA functionals and with van der Waals-corrected density functionals. VdWDF
functionals, including optPBE, optB88, optB86b, and Grimme's method, are used to optimize the adsorption configurations of furfural, furfuryl alcohol, and related intermediates resulting from hydrogenation of furfural, and the results are compared to corresponding values determined with GGA functionals, including PW91 and PBE. On Pd(111) and Pt(111), the adsorption geometries of the intermediates are not noticeably different between the two classes of functionals, while on Cu(111), modest changes are seen in both the erpendicular distance and the orientation of the aromatic ringwith respect to the planar surface. In general, the binding energies increase substantially in magnitude as a result of van derWaals contributions on all metals. In contrast, however, dispersion effects on the kinetics of hydrogenation are relatively small. It is found that activation barriers are not significantly affected by the inclusion of dispersion effects, and a Brønsted–Evans–Polanyi relationship developed solely fromPW91 calculations on Pd(111) is capable of describing corresponding results on Cu(111) and Pt(111), even when the dispersion effects are included. Finally, the reaction energies and barriers derived from the
dispersion-corrected and pure GGA calculations are used to plot simple potential energy profiles for furfural hydrogenation to furfuryl alcohol on the three considered metals, and an approximately constant downshift of the
energetics due to the dispersion corrections is observed.

Citation: 
Liu B, L Cheng, LA Curtiss, and JP Greeley.2014."Effects of van der Waals Density Functional Corrections on Trends in Furfural Adsorption and Hydrogenation on Close-Packed Transition Metal Surfaces ."Surface Science 622:51-59. doi:10.1016/j.susc.2013.12.001
Authors: 
B Liu
L Cheng
LA Curtiss
JP Greeley

Impact of Lattice Mismatch and Stoichiometry on the Structure and Bandgap of (Fe,Cr)2O3 Epitaxial Thin Films.

Abstract: 

The structural properties of high-quality epitaxial (Fe1-xCrx)2O3 thin films are investigated across the composition range. Epitaxial films are deposited on a-Al2O3(0001) substrates by oxygen-plasma-assisted molecular beam epitaxy. Corundum (Fe1-xCrx)2O3 supercells relaxed by density functional theory confirm that the non-linear behavior of the bulk lattice parameters originates in the magnetic structure of the alloy films. High-resolution x-ray diffraction reveals the degree of epitaxial strain relaxation in the films, with Cr-rich films remaining partially strained to the Al2O3 substrate. For intermediate compositions, a lattice expansion and non-Poisson-like tetragonal distortion are found. Scanning transmission electron microscopy and electron energy loss spectroscopy reveal a columnar grain structure in the films, with uniform mixing of cations on the nanometer scale. Oxygen non-stoichiometry is quantified by non-Rutherford resonant elastic scattering measurements utilizing 3.04 MeV He+. Intermediate-composition films are found to be slightly over-stoichiometric, resulting in the observed lattice expansion. Cr-rich films, in contrast, appear to be slightly oxygen deficient. A model is proposed to explain these results based on the energetics of oxygen defect formation and rate of oxygen diffusion in the corundum lattice. Compressive biaxial strain is found to reduce the bandgap of epitaxial Cr2O3 relative to the bulk value. The relationships which are elucidated between epitaxial film structure and optical properties can be applied to bandgap optimization in the (Fe,Cr)2O3 system.

Citation: 
Kaspar TC, SE Chamberlin, ME Bowden, RJ Colby, V Shutthanandan, S Manandhar, Y Wang, P Sushko, and SA Chambers.2014."Impact of Lattice Mismatch and Stoichiometry on the Structure and Bandgap of (Fe,Cr)2O3 Epitaxial Thin Films."Journal of Physics: Condensed Matter 26(13):Article No. 135005. doi:10.1088/0953-8984/26/13/135005
Authors: 
TC Kaspar
SE Chamberlin
ME Bowden
RJ Colby
V Shutthanan
S Manhar
Y Wang
P Sushko
SA Chambers
Facility: 

Impact of subgrid-scale radiative heating variability on the stratocumulus-to-trade cumulus transition in climate models.

Abstract: 

Subgrid-scale interactions between turbulence and radiation are potentially important for accurately reproducing marine low clouds in climate models. To better understand the impact of these interactions, the Weather Research and Forecasting (WRF) model is configured for large eddy simulation (LES) to study the stratocumulus-to-trade cumulus (Sc-to-Cu) transition. Using the GEWEX Atmospheric System Studies (GASS) composite Lagrangian transition case and the Atlantic Trade Wind Experiment (ATEX) case, it is shown that the lack of subgrid-scale turbulence-radiation interaction, as is the case in current generation climate models, accelerates the Sc-to-Cu transition. Our analysis suggests that in cloud-topped boundary layers subgrid-scale turbulence-radiation interactions contribute to stronger production of temperature variance, which in turn leads to stronger buoyancy production of turbulent kinetic energy and helps to maintain the Sc cover.

Citation: 
Xiao H, WI Gustafson, Jr, and H Wang.2014."Impact of subgrid-scale radiative heating variability on the stratocumulus-to-trade cumulus transition in climate models."Journal of Geophysical Research. D. (Atmospheres) 119(7):4192–4203. doi:10.1002/2013JD020999
Authors: 
H Xiao
WI Gustafson
Jr
H Wang

CO2 Reduction on Supported Ru/Al2O3 Catalysts: Cluster Size Dependence of Product Selectivity.

Abstract: 

The catalytic performance of a series of Ru/Al2O3 catalysts with Ru content in the 0.1-5% range was examined in the reduction of CO2 with H2. At low Ru loadings (≤0.5 %) where the active metal phase is highly dispersed (mostly atomically) on the alumina support CO is formed with high selectivity. With increasing metal loading the selectivity toward CH4 formation increases, while that for CO production decreases. In the 0.1% Ru/Al2O3 catalyst Ru is mostly present in atomic dispersion as STEM images obtained from the fresh sample prior to catalytic testing reveal. STEM images recorded form this same sample following temperature programmed reaction test clearly show the agglomeration of small metal particles (and atoms) into 3D clusters. The clustering of the highly dispersed metal phase is responsible for the observed dramatic selectivity change during elevated temperature tests: dramatic decrease in CO, and large increase in CH4 selectivity. Apparent activation energies, estimated from the slopes of Arrhenius plots, of 82 kJ/mol and 62 kJ/mol for CO and CH4 formation were determined, respectively, regardless of Ru loading. These results suggest that the formation of CO and CH4 follow different reaction pathways, or proceed on active centers of different nature. Reactions with CO2/H2 and CO/H2 mixtures (under otherwise identical reaction conditions) reveal that the onset temperature of CO2 reduction is about 150 ºC lower than of CO reduction. We thank Dr. Feng Gao for carrying out the H2 chemisorption measurements on all the Ru/Al2O3 catalysts discussed in this work. The catalyst preparation and catalytic measurements were supported by a Laboratory Directed Research and Development (LDRD) project, while the TEM work was supported by the Chemical Imaging Initiative at the Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US Department of Energy by Battelle under contract number DE-AC05-76RL01830. JHK also acknowledges the support of this work by the 2013 Research Fund of UNIST (Ulsan National Institute of Science and Technology, Ulsan, Korea).

Citation: 
Kwak JH, L Kovarik, and J Szanyi.2013."CO2 Reduction on Supported Ru/Al2O3 Catalysts: Cluster Size Dependence of Product Selectivity."ACS Catalysis 3(11):2449-2455. doi:10.1021/cs400381f
Authors: 
JH Kwak
L Kovarik
J Szanyi
Facility: 

Level Alignment of a Prototypical Photocatalytic System: Methanol on TiO2(110).

Abstract: 

Photocatalytic activity depends on the optimal alignment of electronic levels at the molecule− semiconductor interface. Establishing the level alignment experimentally is complicated by the uncertain chemical identity of the surface species. We address the assignment of the occupied and empty electronic levels for the prototypical photocatalytic system consisting of methanol on a rutile TiO2(110) surface. Using many-body quasiparticle (QP) techniques, we show that the frontier levels measured in UV photoelectron and two-photon photoemission spectroscopy experiments can be assigned to molecularly chemisorbed methanol rather than its dissociated product, the methoxy species. We find that the highest occupied molecular orbital of the methoxy species is much closer to the valence band maximum, suggesting why it is more photocatalytically active than the methanol molecule. We develop a general semiquantitative model for predicting many-body QP energies based on the
electronic screening within the bulk, molecular, or vacuum regions of the wave functions at molecule−semiconductor interfaces.

Citation: 
Migani A, DJ Mowbray, A Iacomino, J Zhao, and H Petek.2013."Level Alignment of a Prototypical Photocatalytic System: Methanol on TiO2(110)."Journal of the American Chemical Society 135(31):11429–11432. doi:10.1021/ja4036994
Authors: 
A Migani
DJ Mowbray
A Iacomino
J Zhao
H Petek

Role of Point Defects on the Reactivity of Reconstructed Anatase Titanium Dioxide (001) Surface.

Abstract: 

The chemical reactivity of different surfaces of titanium dioxide (TiO2) has been the subject of extensive studies in recent decades. The anatase TiO2(001) and its (1x4) reconstructed surfaces were theoretically considered to be the most reactive and have been heavily pursued by synthetic chemists. However, the lack of direct experimental verification or determination of the active sites on these surfaces has caused controversy and debate. Here we report a systematic study on an anatase TiO2(001)-(1x4) surface by means of microscopic and spectroscopic techniques in combination with first-principles calculations. Two types of intrinsic point defects are identified, among which only the Ti3+ defect site on the reduced surface demonstrates considerable chemical activity. The perfect surface itself can be fully
oxidized, but shows no obvious activity. Our findings suggest that the reactivity of the anatase TiO2(001) surface should depend on its reduction status, similar to that of rutile TiO2 surfaces.

Citation: 
Wang Y, H Sun, S Tan, H Feng, Z Cheng, J Zhao, A Zhao, B Wang, Y Luo, J Yang, and JG Hou.2013."Role of Point Defects on the Reactivity of Reconstructed Anatase Titanium Dioxide (001) Surface."Nature Communications 4:2214. doi:10.1038/ncomms3214
Authors: 
Y Wang
H Sun
S Tan
H Feng
Z Cheng
J Zhao
A Zhao
B Wang
Y Luo
J Yang
JG Hou

Coordination and Hydrolysis of Plutonium Ions in Aqueous Solution using Car-Parrinello Molecular Dynamics Free Energy

Abstract: 

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 available experimental estimates. The hexavalent PuO22+ species is coordinated to 5 aquo ligands while the pentavalent PuO2+ complex is coordinated to 4 aquo ligands. The Pu3+ and Pu4+ ions are both coordinated to 8 water molecules. The first hydrolysis constants obtained for Pu3+ and PuO22+ are 6.65 and 5.70 respectively, all within 0.3 pH units of the experimental values (6.90 and 5.50 respectively). The hydrolysis constant of Pu4+, 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2+, 9.51, supports the experimental results of Bennett et al. (Radiochim. Act. 1992, 56, 15). A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.

Citation: 
Odoh SO, EJ Bylaska, and WA De Jong.2013."Coordination and Hydrolysis of Plutonium Ions in Aqueous Solution using Car-Parrinello Molecular Dynamics Free Energy Simulations."Journal of Physical Chemistry A 117(47):12256-12267. doi:10.1021/jp4096248
Authors: 
SO Odoh
EJ Bylaska
WA De Jong

High-energy radiation damage in zirconia: modeling results .

Abstract: 

Zirconia has been viewed as a material of exceptional resistance to amorphization by radiation damage, and was consequently proposed as a candidate to immobilize nuclear waste and serve as a nuclear fuel matrix. Here, we perform molecular dynamics simulations of radiation damage in zirconia in the range of 0.1-0.5 MeV energies with the account of electronic energy losses. We find that the lack of amorphizability co-exists with a large number of point defects and their clusters. These, importantly, are largely disjoint from each other and therefore represent a dilute damage that does not result in the loss of long-range structural coherence and amorphization. We document the nature of these defects in detail, including their sizes, distribution and morphology, and discuss practical implications of using zirconia in intense radiation environments.

Citation: 
Zarkadoula E, R Devanathan, WJ Weber, M Seaton, I Todorov, K Nordlund, MT Dove, and K Trachenko.2014."High-energy radiation damage in zirconia: modeling results ."Journal of Applied Physics 115(8):083507. doi:10.1063/1.4866989
Authors: 
E Zarkadoula
R Devanathan
WJ Weber
M Seaton
I Todorov
K Nordlund
MT Dove
K Trachenko

Cation-Cation Interactions in [(UO2)2(OH)n](4-n) Complexes.

Abstract: 

The structures and bonding of gas-phase [(UO2)2(OH)n]4-n (n=2-6) complexes have been studied using density functional theory (DFT), MP2 and CCSD(T) methods with particular emphasis on ground state structures featuring cation-cation interactions (CCIs) between the uranyl groups. An interesting trend is observed in the stabilities of members of this series of complexes. The structures of [(UO2)2(OH)2]2+, [(UO2)2(OH)4] and [(UO2)2(OH)6]2- featuring CCIs are found at higher energies (by 3-20 kcal/mol) in comparison to their conventional μ2-dihydroxo structures. In contrast, the CCI structures of [(UO2)2(OH)3]+ and [(UO2)2(OH)5]- are respectively almost degenerate with and lower in energy than the structures with the μ2-dihydroxo format. The origin of this trend lies in the ‘symmetry’-based need to balance the coordination numbers and effective atomic charges of each uranium center. The calculated IR vibrational frequencies provide signature probes that can be used in differentiating the lowenergy structures and in experimentally confirming the existence of the structures featuring CCIs. Analysis of the bonding in the structures of [(UO2)2(OH)3]+ and [(UO2)2(OH)5]- shows that the CCIs and bridging hydroxo between the dioxo-uranium units are mainly electrostatic in nature.

Citation: 
Odoh SO, N Govind, G Schreckenbach, and WA De Jong.2013."Cation-Cation Interactions in [(UO2)2(OH)n](4-n) Complexes."Inorganic Chemistry 52(19):11269-11279. doi:10.1021/ic4015338
Authors: 
SO Odoh
N Govind
G Schreckenbach
WA De Jong

A Simple, Accurate Model for Alkyl Adsorption on Late Transition Metals.

Abstract: 

A simple model that predicts the adsorption energy of an arbitrary alkyl in the high-symmetry sites of late transition metal fcc(111) and related surfaces is presented. The model makes predictions based on a few simple attributes of the adsorbate and surface, including the d-shell filling and the matrix coupling element, as well as the adsorption energy of methyl in the top sites. We use the model to screen surfaces for alkyl chain-growth properties and to explain trends in alkyl adsorption strength, site preference, and vibrational softening.

Citation: 
Montemore MM, and JW Medlin.2013."A Simple, Accurate Model for Alkyl Adsorption on Late Transition Metals."Journal of Physical Chemistry C 117(6):2835-2843. doi:10.1021/jp310533e
Authors: 
MM Montemore
JW Medlin

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Leads

Dr. McCue develops and implements computational strategy for data analysis, storage and retrieval as well as develops, acquires, and provides software and hardware to enable EMSL Sciences Areas. Responsible for infrastructure health, development,...