Molecular Science Computing

Environmental molecular research is accelerated when combined with leading-edge hardware, efficient parallel software, accurate and predictive theories and visualization capabilities. Users are encouraged to combine computation with EMSL's state-of-the-art experimental tools that make an integrated platform for scientific discovery. See a complete list of Molecular Science Computing instruments.

The Molecular Science Computing (MSC) capability supports EMSL's flagship computing resources including:

  • Cascade, a supercomputer with theoretical peak performance of 3.4 petaflops, that came online in December 2013. See announcements about the current status of Cascade
  • NWChem, a molecular modeling software developed to take full advantage of the advanced computing systems installed. NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum-mechanical descriptions of the electronic wavefunction or density.
  • GA Tools
  • Ecce, a domain encompassing problem-solving environment for molecular modeling, analysis, and simulations, and
  • Aurora, a 15.8 Petabyte HPSS data storage system

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.

Additonal Information

Description

Resources and Techniques

Molecular Science Computing – Sophisticated and integrated computational capabilities, including scientific consultants, software, Cascade supercomputer and a data archive, enable the following:
• Simulations that accurately mimic real molecules, solids, nanoparticles and biological systems
• Reactive chemical transport modeling for subsurface and atmospheric study
• State-of-the-art integration between theory and experiment
• Parallel and efficient computer architectures
• Computational models built on open-source framework.

Molecular Science Software Suite – Complex chemical systems at the atomic level are investigated using comprehensive, integrated tools coupled with advanced computational chemistry techniques and high-performance, massive parallel computing systems.

Graphics and Visualization Laboratory – Complex experimental and computational data sets are analyzed using high-performance graphics systems for illustration and image editing, data modeling and image analysis, scene rendering and model creation, and audio-video composition and editing.

 

Instruments

The 3.4 petaflop system's 23,000 Intel processors have 184,000 gigabytes of memory available, about four times as much memory per processor as other...
Aurora, EMSL's scientific data archive, is a dedicated computer system specifically designed for long-term storage of data collected by EMSL...
Custodian(s): Ryan Wright, Dave Cowley

Publications

Catalysis by single isolated atoms of precious metals has attracted much recent interest since it promises the ultimate economy in atom efficiency....
The photochemical properties of nitric oxide on a mixed oxide single crystal surface was examined in ultrahigh vacuum (UHV) using temperature...
We recently discovered that MgAl2O4 spinel {111} nano-facets optimally stabilize the small sizes of platinum nanoparticles even after severe high...
Coupled cluster singles and doubles (CCSD) algorithm has been optimized in NWChem software package. This modification alleviated the communication...
Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere...

Science Highlights

Posted: January 07, 2015
The Science Modeling hydrological processes in ecosystems containing both surface water and groundwater is crucial for understanding fluid flow, the...
Posted: November 20, 2014
Aluminum oxide, or alumina, has numerous industrial uses, including as a catalyst and a catalytic support. Characterizing alumina has been difficult...
Posted: November 20, 2014
The Science All eukaryotes have three essential DNA-dependent RNA polymerase enzymes. These enzymes control gene activity by constructing chains of...
Posted: November 04, 2014
The Science Projecting variations in the carbon cycle is important for predicting long-term climate changes. However, climate models used to...
Posted: September 02, 2014
The impacts of soil moisture on the carbon cycle are well known from previous research. However, interactions among soil moisture, groundwater and...

Environmental molecular research is accelerated when combined with leading-edge hardware, efficient parallel software, accurate and predictive theories and visualization capabilities. Users are encouraged to combine computation with EMSL's state-of-the-art experimental tools that make an integrated platform for scientific discovery. See a complete list of Molecular Science Computing instruments.

The Molecular Science Computing (MSC) capability supports EMSL's flagship computing resources including:

  • Cascade, a supercomputer with theoretical peak performance of 3.4 petaflops, that came online in December 2013. See announcements about the current status of Cascade
  • NWChem, a molecular modeling software developed to take full advantage of the advanced computing systems installed. NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum-mechanical descriptions of the electronic wavefunction or density.
  • GA Tools
  • Ecce, a domain encompassing problem-solving environment for molecular modeling, analysis, and simulations, and
  • Aurora, a 15.8 Petabyte HPSS data storage system

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.

Additonal Information

Influence of Adsorption Site and Wavelength on the Photodesorption of NO from the (Fe,Cr)3O4(111) Mixed Oxide Surface.

Abstract: 

The photochemical properties of nitric oxide on a mixed oxide single crystal surface was examined in ultrahigh vacuum (UHV) using temperature programmed desorption (TPD), photon stimulated desorption (PSD) and low energy electron diffraction (LEED). The mixed oxide was a 75% Fe and 25% Cr corundum (0001) oxide film prepared on an -Al2O3(0001) crystal, however its surface became terminated with a magnetite-like (111) structure after sputter/anneal cleaning, leading to a surface designated of (Fe,Cr)3O4(111). TPD of NO from the (Fe,Cr)3O4(111) surface revealed three chemisorbed states at 220, ~315 and 370 K assigned to NO binding at Fe3+, Cr3+ and Fe2+ sites, respectively. No significant thermal chemistry of NO was detected. NO photodesorption, the primary photochemical pathway in UHV, was sensitive to the adsorption site, with rates at the three adsorption sites following the trend: Fe3+ > Fe2+ > Cr3+. Multiexponential rate behavior seen in the overall NO PSD spectra was linked directly to site heterogeneity being manifested as a convolution of the individual NO photodesorption rates at the three types of surface sites. The photodesorption rate with UV light (365 nm) was ~10 times greater than that in the visible, but the per-photon rates across the visible spectrum (from 460 to 630 nm) were independent of the wavelength, which is suggestive of localized photon absorption at the adsorption site. Results in this study demonstrate that the adsorption site plays a critical role in determining photochemical rates on complex oxide surfaces. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multi-program national laboratory operated for DOE by Battelle. The research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Citation: 
Henderson MA.2014."Influence of Adsorption Site and Wavelength on the Photodesorption of NO from the (Fe,Cr)3O4(111) Mixed Oxide Surface."Journal of Physical Chemistry C 118(36):21021-21030. doi:10.1021/jp506602x
Authors: 
MA Henderson
Facility: 
Volume: 
118
Issue: 
36
Pages: 
21021-21030
Publication year: 
2014

Low-Temperature Carbon Monoxide Oxidation Catalysed by Regenerable Atomically Dispersed Palladium on Alumina.

Abstract: 

Catalysis by single isolated atoms of precious metals has attracted much recent interest since it promises the ultimate economy in atom efficiency. Previous reports have been confined to reducible oxide supports such as FeOx, TiO2 or CeO2. Here we show that isolated Pd atoms can be stabilized on industrially relevant gamma-alumina supports. At low Pd loadings (≤0.5 wt%) these catalysts contain exclusively atomically dispersed Pd species. The addition of lanthanum-oxide to the alumina, long known for its ability to improve alumina stability, is found to also help in the stabilization of isolated Pd atoms. Aberration-corrected scanning transmission electron microscopy (AC-STEM) confirms the presence of intermingled Pd and La on the gamma-alumina surface. Operando X-ray absorption spectroscopy, performed on Pd/La-alumina and Pd/gamma-alumina (0.5 wt% Pd) demonstrates the presence of catalytically active atomically dispersed ionic Pd in the Pd/La-doped gamma-alumina system. CO oxidation reactivity measurements show onset of catalytic activity at 40 ˚C, indicating that the ionic Pd species are not poisoned by CO. The reaction order in CO and O2 is positive, suggesting a reaction mechanism that is different from that on metallic Pd. The catalyst activity is lost if the Pd species are reduced to their metallic form, but the activity can be regenerated by oxidation at 700 ˚C in air. The high-temperature stability of these ionic Pd species on commercial alumina supports makes this catalyst system of potential interest for low-temperature exhaust treatment catalysts.

Citation: 
Peterson E, A DelaRiva, S Lin, RS Johnson, H Guo, J Miller, JH Kwak, CHF Peden, B Kiefer, LF Allard, F Ribeiro, and AK Datye.2014."Low-Temperature Carbon Monoxide Oxidation Catalysed by Regenerable Atomically Dispersed Palladium on Alumina."Nature Communications 5:Article No. 4885. doi:10.1038/ncomms5885
Authors: 
E Peterson
A DelaRiva
S Lin
RS Johnson
H Guo
J Miller
JH Kwak
CHF Peden
B Kiefer
LF Allard
F Ribeiro
AK Datye
Volume: 
0
Issue: 
0
Pages: 
0
Publication year: 
2014

Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures.

Abstract: 

Coupled cluster singles and doubles (CCSD) algorithm has been optimized in NWChem software package. This modification alleviated the communication bottleneck and provided from 2- to 5-fold speedup in the CCSD iteration time depending on the problem size and available memory. Sustained 0.60 petaflop/sec performance on CCSD(T) calculation has been obtained on NCSA Blue Waters. This number included all stages of the calculation from initialization till termination, iterative computation of single and double excitations, and perturbative accounting for triple excitations. In the section of perturbative triples alone, the computation maintained 1.18 petaflop/sec performance level. CCSD computations have been performed on Guanine-Cytosine deoxydinucleotide monophosphate (GC-dDMP) to probe the conformational energy difference in DNA single strand in A- and B-conformations. The computation revealed significant discrepancy between CCSD and classical force fields in prediction of relative energy of A- and B-conformations of GC-dDMP.

Citation: 
Anisimov V, GH Bauer, K Chadalavada, RM Olson, JW Glenski, WT Kramer, E Apra, and K Kowalski.2014."Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures."Journal of Chemical Theory and Computation 10(10):4307-4316. doi:10.1021/ct500404c
Authors: 
V Anisimov
GH Bauer
K Chadalavada
RM Olson
JW Glenski
WT Kramer
E Apra
K Kowalski
Volume: 
10
Issue: 
10
Pages: 
4307-4316
Publication year: 
2014

A general mechanism for stabilizing the small sizes of precious metal nanoparticles on oxide supports.

Abstract: 

We recently discovered that MgAl2O4 spinel {111} nano-facets optimally stabilize the small sizes of platinum nanoparticles even after severe high temperature aging treatments. Here we report the thermal stabilities of other precious metals with various physical and chemical properties on the MgAl2O4 spinel {111} facets, providing important new insights into the stabilization mechanisms. Besides Pt, Rh and Ir can also be successfully stabilized as small (1-3 nm) nanoparticles and even as single atomic species after extremely severe (800 °C, 1 week) oxidative aging. However, other metals either aggregate (Ru, Pd, Ag, and Au) or sublimate (Os) even during initial catalyst synthesis. On the basis of ab initio theoretical calculations and experimental observations, we rationalize that the exceptional stabilization originates from lattice matching, and the correspondingly strong attractive interactions at interfaces between the spinel {111} surface oxygens and epitaxial metals\metal oxides. On this basis, design principles for catalyst support oxide materials that are capable in stabilizing precious metals are proposed.

Citation: 
Li WZ, L Kovarik, D Mei, MH Engelhard, F Gao, J Liu, Y Wang, and CHF Peden.2014."A general mechanism for stabilizing the small sizes of precious metal nanoparticles on oxide supports."Chemistry of Materials 26(19):5475-5481. doi:10.1021/cm5013203
Authors: 
Li WZ
L Kovarik
D Mei
MH Engelhard
F Gao
J Liu
Y Wang
CHF Peden
Volume: 
26
Issue: 
19
Pages: 
5475-5481
Publication year: 
2014

Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity .

Abstract: 

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the
catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni–Fe cluster in the catalytically active Ni-C state. There are correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production.

Citation: 
Smith DMA, S Raugei, and TC Squier.2014."Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity ."Physical Chemistry Chemical Physics. PCCP 16(43):24026-24033. doi:10.1039/c4cp03518f
Authors: 
DMA Smith
S Raugei
TC Squier
Facility: 
Volume: 
16
Issue: 
43
Pages: 
24026-24033
Publication year: 
2014

Fe/SSZ-13 as an NH3-SCR Catalyst: A Reaction Kinetics and FTIR/Mössbauer Spectroscopic Study.

Abstract: 

Using a traditional aqueous solution ion-exchange method under a protecting atmosphere of N2, an Fe/SSZ-13 catalyst active in NH3-SCR was synthesized. Mössbauer and FTIR spectroscopies were used to probe the nature of the Fe sites. In the fresh sample, the majority of Fe species are extra-framework cations. The likely monomeric and dimeric ferric ions in hydrated form are [Fe(OH)2]+ and [HO-Fe-O-Fe-OH]2+, based on Mössbauer measurements. During the severe hydrothermal aging (HTA) applied in this study, a majority of cationic Fe species convert to FeAlOx and clustered FeOx species, accompanied by severe dealumination of the SSZ-13 framework. The clustered FeOx species do not give a sextet Mössbauer spectrum, indicating that these are highly disordered. However, some Fe species in cationic positions remain after aging as determined from Mössbauer measurements and CO/NO FTIR titrations. NO/NH3 oxidation reaction tests reveal that dehydrated cationic Fe are substantially more active in catalyzing oxidation reactions than the hydrated ones. For NH3-SCR, enhancement of NO oxidation under ‘dry’ conditions promotes SCR rates below ~300 C. This is due mainly to contribution from the “fast” SCR channel. Above ~300 C, enhancement of NH3 oxidation under ‘dry’ conditions, however, becomes detrimental to NOx conversions. The HTA sample loses much of the SCR activity below ~300 C; however, above ~400 C much of the activity remains. This may suggest that the FeAlOx and FeOx species become active at such elevated temperatures. Alternatively, the high-temperature activity may be maintained by the remaining extra-framework cationic species. For potential practical applications, Fe/SSZ-13 may be used as a co-catalyst for Cu/CHA as integral aftertreatment SCR catalysts on the basis of the stable high temperature activity after hydrothermal aging. The authors gratefully acknowledge the US Department of Energy (DOE), Energy Efficiency and Renewable Energy, Vehicle Technologies Office for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle.

Citation: 
Gao F, M Kollar, RK Kukkadapu, NM Washton, Y Wang, J Szanyi, and CHF Peden.2015."Fe/SSZ-13 as an NH3-SCR Catalyst: A Reaction Kinetics and FTIR/Mössbauer Spectroscopic Study."Applied Catalysis. B, Environmental 164:407-419. doi:10.1016/j.apcatb.2014.09.031
Authors: 
F Gao
M Kollar
RK Kukkadapu
NM Washton
Y Wang
J Szanyi
CHF Peden
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Fe(II)-catalyzed Recrystallization of Goethite Revisited.

Abstract: 

Results from enriched 57Fe isotope tracer experiments have shown that atom exchange can occur between structural Fe in Fe(III) oxides and aqueous Fe(II) with no formation of secondary minerals or change in particle size or shape. Here we derive a mass balance model to quantify the extent of Fe atom exchange between goethite and aqueous Fe(II) that accounts for different Fe pool sizes. We use this model to reinterpret our previous work and to quantify the influence of particle size and pH on extent of goethite exchange with aqueous Fe(II). Consistent with our previous interpretation, substantial exchange of goethite occurred at pH 7.5 (≈ 90%) and we observed little effect of particle size between nanogoethite (81 x 11 nm) and microgoethite (590 x 42 nm). Despite ≈ 90% of the bulk goethite exchanging at pH 7.5, we found no change in mineral phase, particle size, crystallinity, or reactivity after reaction with aqueous Fe(II). At a lower pH of 5.0, no net sorption of Fe(II) was observed and significantly less exchange occurred accounting for less than the estimated proportion of surface Fe atoms in the particles. Particle size appears to influence the amount of exchange at pH 5.0 and we suggest that aggregation and surface area may play a role. Results from sequential chemical extractions indicate that 57Fe accumulates in extracted Fe(III) goethite components. Isotopic compositions of the extracts indicate that a gradient of 57Fe develops within the goethite with more accumulation of 57Fe occurring in the more easily extracted Fe(III) that may be nearer to the surface. We interpret our particle size, pH, and sequential extraction findings as consistent with the mechanism of interfacial electron transfer and bulk conduction previously proposed to explain the substantial Fe atom exchange observed in goethite in contact with aqueous Fe(II).

Citation: 
Handler R, AJ Frierdich, C Johnson, KM Rosso, B Beard, CM Wang, D Latta, A Neumann, TS Pasakarnis, WAPJ Premaratne, and M Scherer.2014."Fe(II)-catalyzed Recrystallization of Goethite Revisited."Environmental Science & Technology 48(19):11302-11311. doi:10.1021/es503084u
Authors: 
R Hler
AJ Frierdich
C Johnson
KM Rosso
B Beard
CM Wang
D Latta
A Neumann
TS Pasakarnis
WAPJ Premaratne
M Scherer
Volume: 
48
Issue: 
19
Pages: 
11302-11311
Publication year: 
2014

Monitoring Long-Range Electron Transfer Pathways in Proteins by Stimulated Attosecond Broadband X-ray Raman Spectroscopy.

Abstract: 

Long-range electron transfer (ET) plays a key role in many biological energy conversion and synthesis processes. We show that nonlinear spectroscopy with attosecond X-ray pulses provides a real time movie of the evolving oxidation states and electron densities around atoms, and can probe these processes with high spatial and temporal resolution. This is demonstrated in a simulation study of the stimulated X-ray Raman (SXRS) signals in Re-modified azurin, which had long served as a benchmark for long-range ET in proteins. Nonlinear SXRS signals are sensitive to the local electronic structure and should offer a novel window for long-range ET.

Citation: 
Zhang Y, J Biggs, N Govind, and S Mukamel.2014."Monitoring Long-Range Electron Transfer Pathways in Proteins by Stimulated Attosecond Broadband X-ray Raman Spectroscopy."The Journal of Physical Chemistry Letters 5(21):3656-3661. doi:10.1021/jz501966h
Authors: 
Y Zhang
J Biggs
N Govind
S Mukamel
Volume: 
5
Issue: 
21
Pages: 
3656-3661
Publication year: 
2014

In-Situ Transmission Electron Microscopy Probing of Native Oxide and Artificial Layers on Silicon Nanoparticles for Lithium Ion

Abstract: 

Surface modification of silicon nanoparticle via molecular layer deposition (MLD) has been recently proved to be an effective way for dramatically enhancing the cyclic performance in lithium ion batteries. However, the fundamental mechanism as how this thin layer of coating function is not known, which is even complicated by the inevitable presence of native oxide of several nanometers on the silicon nanoparticle. Using in-situ TEM, we probed in detail the structural and chemical evolution of both uncoated and coated silicon particles upon cyclic lithiation/delithation. We discovered that upon initial lithiation, the native oxide layer converts to crystalline Li2O islands, which essentially increases the impedance on the particle, resulting in ineffective lithiation/delithiation, and therefore low coulombic efficiency. In contrast, the alucone MLD coated particles show extremely fast, thorough and highly reversible lithiation behaviors, which are clarified to be associated with the mechanical flexibility and fast Li+/e- conductivity of the alucone coating. Surprisingly, the alucone MLD coating process chemically changes the silicon surface, essentially removing the native oxide layer and therefore mitigates side reaction and detrimental effects of the native oxide. This study provides a vivid picture of how the MLD coating works to enhance the coulombic efficiency and preserve capacity and clarifies the role of the native oxide on silicon nanoparticles during cyclic lithiation and delithiation. More broadly, this work also demonstrated that the effect of the subtle chemical modification of the surface during the coating process may be of equal importance as the coating layer itself.

Citation: 
He Y, DM Piper, M Gu, JJ Travis, SM George, SH Lee, A Genc, L Pullan, J Liu, SX Mao, J Zhang, C Ban, and CM Wang.2014."In-Situ Transmission Electron Microscopy Probing of Native Oxide and Artificial Layers on Silicon Nanoparticles for Lithium Ion Batteries."ACS Nano 8(11):11816-11823. doi:10.1021/nn505523c
Authors: 
He Y
DM Piper
M Gu
JJ Travis
SM George
SH Lee
A Genc
L Pullan
J Liu
SX Mao
J Zhang
C Ban
CM Wang
Volume: 
8
Issue: 
11
Pages: 
11816-11823
Publication year: 
2014

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