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...
Custodian(s): Doug Baxter
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

The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and...
We have studied the reactions of 1,2-propylene glycol (1,2-PG), DOCH(CH3)CH2OD, on partially reduced, hydroxylated and oxidized TiO2(110) surfaces...
Oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in...
Rigid tricyclic locked in all axial 1,3,5-cyclohexanetriol derivatives with 0–3 trifluoromethyl groups were synthesized and photoelectron...
Reduction of transition metal oxides can greatly change their physical and chemical properties. Using deposition of WO3 as a case study, we...

Science Highlights

Posted: February 23, 2015
To reduce emissions from coal-fired power plants, scientists want to transform the carbon dioxide into minerals that last for thousands of years....
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...

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

Conversion of 1,2-Propylene Glycol on Rutile TiO2(110).

Abstract: 

We have studied the reactions of 1,2-propylene glycol (1,2-PG), DOCH(CH3)CH2OD, on partially reduced, hydroxylated and oxidized TiO2(110) surfaces using temperature programmed desorption. On reduced TiO2(110), propylene, propanal, and acetone are identified as primary carbon-containing products. While the propylene formation channel dominates at low 1,2-PG coverages, all of the above-mentioned products are observed at high coverages. The carbon-containing products are accompanied by the formation of D2O and D2. The observation of only deuterated products shows that the source of hydrogen (D) is from the 1,2-PG hydroxyls. The role of bridging oxygen vacancy (VO) sites was further investigated by titrating them via hydroxylation and oxidation. The results show that hydroxylation does not change the reactivity because the VO sites are regenerated at 500 K, which is a temperature lower than the 1,2-PG product formation temperature. In contrast, surface oxidation causes significant changes in the product distribution, with increased acetone and propanal formation and decreased propylene formation. Additionally D2 is completely eliminated as an observed product at the expense of D2O formation.

Citation: 
Chen L, Z Li, RS Smith, BD Kay, and Z Dohnalek.2014."Conversion of 1,2-Propylene Glycol on Rutile TiO2(110)."Journal of Physical Chemistry C 118(28):15339-15347. doi:10.1021/jp504770f
Authors: 
L Chen
Z Li
RS Smith
BD Kay
Z Dohnalek
Facility: 
Volume: 
118
Issue: 
28
Pages: 
15339-15347
Publication year: 
2014

Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations.

Abstract: 

The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and chemically, sandwiched between two distinct boundaries - pristine glass surface at the inner most interface and aqueous solution at the outer most. The physico-chemical processes that control the development of this region have a significant impact on the long-term glass-water reaction. Computational models, spanning different length and time-scales, are currently being developed to improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include Geochemical Reaction Path simulations, Glass Reactivity in Allowance for Alteration Layer simulations, Monte Carlo simulations, and Molecular Dynamics methods. Discussed in this manuscript are the advances and limitations of each modeling approach placed in the context of the glass water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers; thus providing the fundamental data needed to develop pore-scale equations that enable more accurate predictions of nuclear waste glass corrosion in a geologic repository.

Citation: 
Pierce EM, P Frugier, LJ Criscenti, KD Kwon, and SN Kerisit.2014."Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations."International Journal of Applied Glass Science 5(4):421-435. doi:10.1111/ijag.12077
Authors: 
EM Pierce
P Frugier
LJ Criscenti
KD Kwon
SN Kerisit
Volume: 
5
Issue: 
4
Pages: 
421-435
Publication year: 
2014

Reflection High-Energy Electron Diffraction Beam-Induced Structural and Property Changes on WO3 Thin Films.

Abstract: 

Reduction of transition metal oxides can greatly change their physical and chemical properties. Using deposition of WO3 as a case study, we demonstrate that reflection high-energy electron diffraction (RHEED), a surface-sensitive tool widely used to monitor thin-film deposition processes, can significantly affect the cation valence and physical properties of the films through electron-beam induced sample reduction. The RHEED beam is found to increase film smoothness during epitaxial growth of WO3, as well as change the electronic properties of the film through preferential removal of surface oxygen.

Citation: 
Du Y, H Zhang, T Varga, and SA Chambers.2014."Reflection High-Energy Electron Diffraction Beam-Induced Structural and Property Changes on WO3 Thin Films."Applied Physics Letters 105(5):051606. doi:10.1063/1.4892810
Authors: 
Du Y
H Zhang
T Varga
SA Chambers
Volume: 
Issue: 
Pages: 
Publication year: 
2014

A Preorganized Hydrogen Bond Network and Its Effect on Anion Stability.

Abstract: 

Rigid tricyclic locked in all axial 1,3,5-cyclohexanetriol derivatives with 0–3 trifluoromethyl groups were synthesized and photoelectron spectra of their conjugate bases and chloride anion clusters are reported along with density functional computations. The resulting vertical and adiabatic detachment energies provide measures of the anion stabilization due to the hydrogen bond network and inductive effects. The latter mechanism is found to be transmitted through space via hydrogen bonds

Citation: 
Samet M, XB Wang, and SR Kass.2014."A Preorganized Hydrogen Bond Network and Its Effect on Anion Stability."Journal of Physical Chemistry A 118(31):5989-5993. doi:10.1021/jp505308v
Authors: 
M Samet
XB Wang
SR Kass
Volume: 
118
Issue: 
31
Pages: 
5989-5993
Publication year: 
2014

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes.

Abstract: 

Oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified marine waters. Currently OMZs are expanding due to global climate change. This expansion alters marine ecosystem function and the productivity of fisheries due to habitat compression and changes in biogeochemical cycling leading to fixed nitrogen loss and greenhouse gas production. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally anoxic fjord, Saanich Inlet to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification and inorganic carbon fixation predominantly co-varied with abundance and distribution patterns of Thaumarchaeota, Nitrospira, Planctomycetes and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Within these groups, pathways mediating inorganic carbon fixation and nitrogen and sulfur transformations were differentially expressed across the redoxcline. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters and denitrification, sulfur-oxidation and inorganic carbon fixation pathways affiliated with SUP05 dominated suboxic and anoxic waters. Nitrite-oxidation and anammox pathways affiliated with Nitrospina and Planctomycetes respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The differential expression of these pathways under changing water column redox conditions has quantitative implications for coupled biogeochemical cycling linking different modes of inorganic carbon fixation with distributed nitrogen and sulfur-based energy metabolism extensible to coastal and open ocean OMZs.

Citation: 
Hawley AK, HM Brewer, AD Norbeck, L Pasa-Tolic, and SJ Hallam.2014."Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes."Proceedings of the National Academy of Sciences of the United States of America 111(31):11395-11400. doi:10.1073/pnas.1322132111
Authors: 
AK Hawley
HM Brewer
AD Norbeck
L Pasa-Tolic
SJ Hallam
Volume: 
111
Issue: 
31
Pages: 
11395-11400
Publication year: 
2014

Excited States and Luminescent Properties of UO2F2 and Its Solvated Complexes in Aqueous Solution.

Abstract: 

The electronic absorption and emission spectra of free UO2F2 and its water solvated complexes below 32,000 cm1 are investigated at the levels of ab initio CASPT2 and CCSD(T) with inclusion of scalar relativistic and spin-orbit coupling effects. The influence of the water coordination on the electronic spectra of UO2F2 is explored by investigating the excited states of solvated complexes (H2O)nUO2F2 (n = 13). In these uranyl-complexes, water coordination is found to have appreciable influence on the 3 ( = 1g) character of the luminescent state and on the electronic spectral shape. The simulated luminescence spectral curves based on the calculated spectral parameters of (H2O)nUO2F2 from CCSD(T) approach agree well with experimental spectra in aqueous solution at both near liquid helium temperature and room temperature. The possible luminescence spectra of free UO2F2 in gas phase are predicted based on CASPT2 and CCSD(T) results, respectively, by considering three symmetric vibration modes. The effect of competition between spin-orbital coupling and ligand field repulsion on the luminescent state properties is discussed.

Citation: 
Su J, Z Wang, D Pan, and J Li.2014."Excited States and Luminescent Properties of UO2F2 and Its Solvated Complexes in Aqueous Solution."Inorganic Chemistry 53(14):7340-7350. doi:10.1021/ic5006852
Authors: 
Su J
Z Wang
D Pan
J Li
Volume: 
53
Issue: 
14
Pages: 
7340-7350
Publication year: 
2014

Reversible nano-structuring of SrCrO3-δ through oxidization and reduction at low temperatures.

Abstract: 

Oxygen vacancies are often present in complex oxides as point defects and their effect on the electronic properties of the oxides is typically uniform and isotropic. Exploiting oxygen deficiency in order to generate controllably, novel structures and functional properties remains a challenging goal. We show that epitaxial strontium chromite films can be transformed, reversibly and at low temperature, from the cubic metallic perovskite SrCrO3-δ to the rhombohedral semiconducting SrCrO2.8. Oxygen vacancies aggregate and give rise to ordered arrays of {111}-oriented SrO2 planes interleaved between layers of tetrahedrally-coordinated Cr4+ and separated by ~1 nm. First-principle calculations provide insight into the origin of the stability of such nanostructures and, consistent with the experimental data, predict that the barrier for oxide ion diffusion along these quasi-2D nanostructures is ~5 times lower than that in the cubic SrCrO3-δ – a property of considerable importance in, for example, solid oxide fuel cells.

Citation: 
Zhang H, P Sushko, RJ Colby, Y Du, ME Bowden, and SA Chambers.2014."Reversible nano-structuring of SrCrO3-? through oxidization and reduction at low temperatures."Nature Communications 5:Artcle No. 4669. doi:10.1038/ncomms5669
Authors: 
H Zhang
P Sushko
RJ Colby
Y Du
ME Bowden
SA Chambers
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Synthesis and Evaluation of Cu/SAPO-34 Catalysts for NH3-SCR 2: Solid-state Ion Exchange and One-pot Synthesis.

Abstract: 

Cu-SAPO-34 catalysts are synthesized using two methods: solid-state ion exchange (SSIE) and one-pot synthesis. SSIE is conducted by calcining SAPO-34/CuO mixtures at elevated temperatures. For the one-pot synthesis method, Cu-containing chemicals (CuO and CuSO4) are added during gel preparation. A high-temperature calcination step is also needed for this method. Catalysts are characterized with surface area/pore volume measurements, temperature programmed reduction (TPR), electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopies, and scanning electron microscopy (SEM). Catalytic properties are examined using standard ammonia selective catalytic reduction (NH3-SCR) and ammonia oxidation reactions. In Cu-SAPO-34 samples formed using SSIE, Cu presents both as isolated Cu2+ ions and unreacted CuO. The former is highly active and selective in NH3-SCR, while the latter catalyzes a side reaction; notably, the non-selective oxidation of NH3 above 350 ºC. Using the one-pot method followed by a high-temperature aging treatment, it is possible to form Cu SAPO-34 samples with predominately isolated Cu2+ ions at low Cu loadings. However at much higher Cu loadings, isolated Cu2+ ions that bind weakly with the CHA framework and CuO clusters also form. These Cu moieties are very active in catalyzing non-selective NH3 oxidation above 350 ºC. Low-temperature reaction kinetics indicate that Cu-SAPO-34 samples formed using SSIE have core-shell structures where Cu is enriched in the shell layers; while Cu is more evenly distributed within the one-pot samples. Reaction kinetics also suggest that at low temperatures, the local environment next to Cu2+ ion centers plays little role on the overall catalytic properties. 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 under contract number DE-AC05-76RL01830. The authors also thank Shari Li (PNNL) for surface area/pore volume measurements, and Bruce W. Arey (PNNL) for SEM measurements. Discussions with Drs. A. Yezerets, K. Kamasamudram, J.H. Li, N. Currier and J.Y. Luo from Cummins, Inc. and H.Y. Chen and H. Hess from Johnson-Matthey are greatly appreciated.

Citation: 
Gao F, ED Walter, NM Washton, J Szanyi, and CHF Peden.2015."Synthesis and Evaluation of Cu/SAPO-34 Catalysts for NH3-SCR 2: Solid-state Ion Exchange and One-pot Synthesis."Applied Catalysis. B, Environmental 162:501-514. doi:10.1016/j.apcatb.2014.07.029
Authors: 
F Gao
ED Walter
NM Washton
J Szanyi
CHF Peden
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Strain Accommodation By Facile WO6 Octahedral Distortion and Tilting During WO3 Heteroepitaxy on SrTiO3(001).

Abstract: 

In this paper, we show that compared to other BO6 octahedra in ABO3 structured perovskite oxides, the WO6 octahedra in tungsten trioxide (WO3) can withstand a much larger degree of distortion and tilting to accommodate interfacial strain, which in turn strongly impact the nucleation, structure, and defect formation during the epitaxial growth of WO3 on SrTiO3(001). A meta-stable tetragonal phase can be stabilized by epitaxy and a thickness dependent phase transition (tetragonal to monoclinic) is observed. In contrast to misfit dislocations to accommodate the interfacial stain, the facial WO6 octahedral distortion and tilting give rise to three types of planar defects that affect more than 15 monolayers from the interface. These atomically resolved, unusual interfacial defects may significantly alter the electronic, electrochromic, and mechanical properties of the epitaxial films.

Citation: 
Du Y, M Gu, T Varga, CM Wang, ME Bowden, and SA Chambers.2014."Strain Accommodation By Facile WO6 Octahedral Distortion and Tilting During WO3 Heteroepitaxy on SrTiO3(001)."ACS Applied Materials & Interfaces 6(16):14253-14258. doi:10.1021/am5035686
Authors: 
Du Y
M Gu
T Varga
CM Wang
ME Bowden
SA Chambers
Volume: 
6
Issue: 
16
Pages: 
14253-14258
Publication year: 
2014

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