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

Systematic theoretical and experimental investigations have been performed to understand the periodicity and electronic structures of trivalent-gold...
To account for thermal and entropic effects caused by the dynamics of the motion of the reaction intermediates, ethanol adsorption on the Brønsted...
Microkinetic models, combined with experimentally measured reaction rates and orders, play a key role in elucidating detailed reaction mechanisms in...
The photophysics of Green Fluorescent Protein (GFP) chromophore is critically dependent on its local structure and on its environment. Despite...
Liquid phase dehydration of 1-octdecanol, which is intermediately formed during the hydrodeoxygenation of microalgae oil, has been explored in a...

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

Band Formation in a Molecular Quantum Well via 2D Superatom Orbital Interactions.

Abstract: 

By scanning tunneling microscopy and spectroscopy, we study nearly free electron band formation of the σ*lowest unoccupied molecular orbital of C₆F₆ on a Cu(111) surface. In fractal islands, the lowest unoccupied molecular orbital energy systematically stabilizes with the number of interacting near-neighbor C₆F₆ molecules. Density functional theory calculations reveal the origin of effective intermo- lecular orbital overlap in the previously unrecognized superatom character of the σ*orbital of ₆F₆ molecules. The discovery of superatom orbitals in planar molecules offers a new universal principle for effective band formation, which can be exploited in designing organic semiconductors with nearly free electron properties

Citation: 
Dougherty DB, M Feng, H Petek, JT Yates, JR, and J Zhao.2012."Band Formation in a Molecular Quantum Well via 2D Superatom Orbital Interactions."Physical Review Letters 109(26):266802 (5 pages). doi:10.1103/PhysRevLett.109.266802
Authors: 
DB Dougherty
M Feng
H Petek
JT Yates
JR
J Zhao

Ultra-low contact resistance at an epitaxial metal/oxide heterojunction through interstitial site doping.

Abstract: 

The ability to form reliable, low-resistance Ohmic contacts is of critical importance to the ongoing development of oxide electronics. Most metals form Schottky barriers when deposited on oxide surfaces. Ohmic contacts rarely occur, and the associated contact resistances are not particularly low. Little is known at an atomistic level about what leads to a good Ohmic contact on a wide-gap oxide. Here we describe the structure of a simple, yet exceptionally low-contact resistance Ohmic metal on an important oxide semiconductor -- epitaxial Cr on Nb-doped SrTiO3(001). Heteroepitaxial growth is accompanied by Cr diffusion into the STO and occupation of interstitial sites within the first few atomic planes. Interstitial Cr is ionized and the resulting electrons occupy the STO conduction band, resulting in effective metallization near the interface.

Citation: 
Chambers SA, M Gu, PV Sushko, H Yang, CM Wang, and ND Browning.2013."Ultra-low contact resistance at an epitaxial metal/oxide heterojunction through interstitial site doping."Advanced Materials 25(29):4001–4005. doi:10.1002/adma.201301030
Authors: 
SA Chambers
M Gu
PV Sushko
H Yang
CM Wang
ND Browning

Density Functional Theory Study of Oxygen Reduction Activity on Ultrathin Platinum Nanotubes.

Abstract: 

The structure, stability, and catalytic activity of a number of single- and double-wall platinum (n,m) nanotubes ranging in diameter from 0.3 to 2.0 nm were studied using plane-wave based density functional theory in the gas phase and water environment. The change in the catalytic activity toward the oxygen reduction reaction (ORR) with the size and chirality of the nanotube was studied by calculating equilibrium adsorption potentials for ORR intermediates and by constructing free energy diagrams in the ORR dissociative mechanism network. In addition, the stability of the platinum nanotubes is investigated in terms of electrochemical dissolution potentials and by determining the most stable state of the material as a function of pH and
potential, as represented in Pourbaix diagrams. Our results show that the catalytic activity and the stability toward electrochemical dissolution depend greatly on the diameter and chirality of the nanotube. On the basis of the estimated overpotentials for ORR, we conclude that smaller, approximately 0.5 nm in diameter single-wall platinum nanotubes consistently show a huge, up to 400 mV larger overpotential than platinum, indicating very poor catalytic activity toward ORR. This is the
result of substantial structural changes induced by the adsorption of any chemical species on these tubes. Single-wall n = m platinum nanotubes with a diameter larger than 1 nm have smaller ORR overpotentials than bulk platinum for up to 180 mV and
thus show improved catalytic activity relative to bulk. We also predict that these nanotubes can endure the highest cell potentials but dissolution potentials are still for 110 mV lower than for the bulk, indicating a possible corrosion problem.

Citation: 
Matanovic I, P Kent, F Garzon, and NJ Henson.2012."Density Functional Theory Study of Oxygen Reduction Activity on Ultrathin Platinum Nanotubes."Journal of Physical Chemistry C 116(31):16499-16510. doi:10.1021/jp3035456
Authors: 
I Matanovic
P Kent
F Garzon
NJ Henson

Spectroscopic Characterization of a Multiband Complex Oxide: Insulating and Conducting Cement 12CaO·7AlO.

Abstract: 

Natural 12CaO·7Al₂O₃ (C12A7) is a wide band gap insulator, but conductivity can be realized by introducing oxygen deficiency. Currently, there are two competing models explaining conductivity in oxygen-deficient C12A7, one involving the electron transfer via a “cage conduction band” inside the nominal band gap, the other involving electron hopping along framework lattice sites. To help resolve this debate, we probe insulating and conducting C12A7 with x-ray emission, x-ray absorption, and x-ray photoemission spectroscopy, which provide a full picture of both the valence and conduction band edges in these materials. Thesemeasurements suggest the existence of a narrow conduction band between themain conduction and valence bands common in both conducting and insulating C12A7 and support the theory that free electrons in oxygen-deficient C12A7 occupy the low-energy states of this narrow band. Our measurements are corroborated with density functional theory calculations.

Citation: 
McLeod JA, A Buling, EZ Kurmaev, PV Sushko, N Neumann, LD Finkelstein, SW Kim, H Hosono, and A Moewes.2012."Spectroscopic Characterization of a Multiband Complex Oxide: Insulating and Conducting Cement 12CaO·7Al?O?."Physical Review. B, Condensed Matter and Materials Physics 85(4):045204 - 045212. doi:10.1103/PhysRevB.85.045204
Authors: 
JA McLeod
A Buling
EZ Kurmaev
PV Sushko
N Neumann
LD Finkelstein
SW Kim
H Hosono
A Moewes

Selective Response of Mesoporous Silicon to Adsorbants with Nitro Groups.

Abstract: 

We demonstrate that the electronic structure of mesoporous silicon is affected by adsorption of nitrobased explosive molecules in a compound-selective manner. This selective response is demonstrated by probing the adsorption of two nitro-based molecular explosives (trinitrotoluene and cyclotrimethylenetrinitramine) and a
nonexplosive nitro-based aromatic molecule (nitrotoluene) on mesoporous silicon using soft X-ray spectroscopy. The Si atoms strongly interact with adsorbed molecules to form Si-O and Si-N bonds, as evident from the large shifts in emission energy present in the Si L2,3 X-ray emission spectroscopy (XES) measurements. Furthermore, we find that the energy gap (band gap) of mesoporous silicon changes depending on the adsorbant, as estimated from the Si L2,3 XES and 2p X-ray absorption spectroscopy (XAS) measurements. Our ab initio molecular dynamics calculations of model compounds suggest that these changes are due to
spontaneous breaking of the nitro groups upon contacting surface Si atoms. This compound-selective change in electronic structure may provide a powerful tool for the detection and identification of trace quantities of airborne explosive molecules.

Citation: 
McLeod JA, EZ Kurmaev, PV Sushko, TD Boyko, IA Levitsky, and A Moewes.2012."Selective Response of Mesoporous Silicon to Adsorbants with Nitro Groups."Chemistry - A European Journal 18(10):2912-2922. doi:10.1002/chem.201102084
Authors: 
JA McLeod
EZ Kurmaev
PV Sushko
TD Boyko
IA Levitsky
A Moewes

Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes.

Abstract: 

Combined collision-induced dissociation mass-spectrometry experiments and DFT calculations were employed to elucidate the molecular structure of "hypercoordinated" species and the energetics of water-elimination reactions of uranyl acetone complexes observed in earlier work (Rios, D.; Rutkowski, P. X.; Van Stipdonk, M. J.; Gibson, J. K. Inorg. Chem. 2011, 50, 4781). It is shown that the "hypercoordinated" species contain diacetone alcohol ligands bonded in either bidentate or monodentate fashion, which are indistinguishable from (acetone)2 in mass spectrometry. Calculations confirm that four diacetone ligands can form stable complexes, but that the effective number of atoms coordinating with uranium in the equatorial plane does not exceed five. Diacetone alcohol ligands are shown to form mesityl oxide ligands and alkoxide species through the elimination of water, providing an explanation for the observed water-elimination reactions.

Citation: 
Rios D, GE Schoendorff, MJ Van Stipdonk, MS Gordon, TL Windus, JK Gibson, and WA De Jong.2012."Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes."Inorganic Chemistry 51(23):12768-12775.
Authors: 
D Rios
GE Schoendorff
MJ Van Stipdonk
MS Gordon
TL Windus
JK Gibson
WA De Jong

Sensitivity of the Properties of Ruthenium Blue Dimer” to Method, Basis Set, and Continuum Model.

Abstract: 

The ruthenium “blue dimer” [(bpy)2RuIIIOH2]2O4+ is best known as the first well-defined molecular catalyst for water oxidation. It has been subject to numerous computational studies primarily employing density functional theory. However, those studies have been limited in the functionals, basis sets, and continuum models employed. The controversy in the calculated electronic structure and the reaction energetics of this catalyst highlights the necessity of benchmark calculations that explore the role of density functionals, basis sets, and continuum models upon the essential features of blue-dimer reactivity. In this paper, we report Kohn-Sham complete basis set (KS-CBS) limit extrapolations of the electronic structure of “blue dimer” using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.

Citation: 
Ozkanlar A, and AE Clark.2012."Sensitivity of the Properties of Ruthenium “Blue Dimer” to Method, Basis Set, and Continuum Model."Journal of Chemical Physics 136(20):204104. doi:10.1063/1.4719937
Authors: 
A Ozkanlar
AE Clark

Tomography and High-Resolution Electron Microscopy Study of Surfaces and Porosity in a Plate-Like γ-Al2O3.

Abstract: 

Morphological and surface characteristics of gamma-Al2O3 are topics of high relevance in the field of catalysis. Using tomography and high-resolution S/TEM imaging, we have studied the surface characteristics of a model gamma-Al2O3 synthesized in the shape of platelets and macroscopically defined by (110)Al2O3 and (111)Al2O3 surface facets. We show that the dominant (110)Al2O3 surface of the synthesized gamma-Al2O3 is not atomically flat but undergoes a significant reconstruction, forming nanoscale (111)Al2O3 terraces. In addition to high resolution imaging, tomographic analysis was carried out, enabling an examination of the pores/voids, which were found to be mostly enclosed within the bulk and inaccessible to gasses or metals. Tomographic analysis shows that the surfaces of the pores are defined exclusively by (100)Al2O3 and (111)Al2O3 facets. The importance of these findings is discussed in the context of relative surface energies of low index surfaces and ethanol desorption characteristics.

Citation: 
Kovarik L, A Genc, CM Wang, A Qiu, CHF Peden, J Szanyi, and JH Kwak.2013."Tomography and High-Resolution Electron Microscopy Study of Surfaces and Porosity in a Plate-Like ?-Al2O3."Journal of Physical Chemistry C 117(1):179?186. doi:10.1021/jp306800h
Authors: 
L Kovarik
A Genc
CM Wang
A Qiu
CHF Peden
J Szanyi
JH Kwak
Facility: 

The surface structure of α-uranophane and its interaction with Eu(III) – An integrated computational and fluorescence

Abstract: 

Uranophane is a rare U(VI) secondary silicate mineral formed in nature by the oxidation of the primary mineral uraninite. It is also relevant to the long-term geochemistry of nuclear waste repositories, where it can be formed under oxidizing conditions and has the potential to act as a secondary barrier to the migration of radionuclides through mineral sorption reactions. A combination of classical molecular dynamics and ab-initio density functional theory (DFT) has been employed to investigate the uranophane|water interface as well as the interfacial reactivity of the U(VI) silicate toward acidic conditions and radionuclide ion sorption. The sorption simulations have been complemented by experimental sorption studies and laser induced fluorescence spectroscopy to help identify the molecular structure of the surface sorbed species. Experimental distances and essential coordination numbers are properly captured by the simulation results within bulk uranophane, while interfacial water is found to orient primarily with the hydrogen-atoms directed towards the negatively charged surface. Sorption sites for water are observed to belong to 3 different groups: (1) those involving uranyl oxygen, (2) involving uranyl and silica hydroxyl oxygen atoms, and (3) involving hydroxyl hydrogen. The pKa of the surface -OH groups have been calculated using a variety of models, including a bond valence approach and utilization of the energetics of deprotonation within DFT. Under basic conditions, deprotonation of the Si-OH groups is likely responsible for uranophane dissolution. Finally, the stability and structure of surface sorbed Eu3+ has been examined, with a stable inner-sphere species being observed.

Citation: 
Kuta J, Z Wang, K Wisuri, MCF Wander, N Wall, and AE Clark.2013."The surface structure of ?-uranophane and its interaction with Eu(III) – An integrated computational and fluorescence spectroscopy study."Geochimica et Cosmochimica Acta 103:184-196. doi:10.1016/j.gca.2012.10.056
Authors: 
J Kuta
Z Wang
K Wisuri
MCF Wer
N Wall
AE Clark
Facility: 

Mechanistic Insights on One-phase vs.Two-phase Brustrin MethodSynthesis of Au Nanoparticles with Dioctyl-diselenides.

Abstract: 

Metal precursors in the one-phase (1p) and two-phase (2p) Brust–Schiffrin method (BSM) synthesis of Au nanoparticles (NPs) using dioctyl-diselenides were identified. A single dominant type of metal precursor was found in the 1p synthesis as compared to multiple ones in the 2p synthesis, which was proposed as the key reason why the former is better than the latter.

Citation: 
Zaluzhna O, Y Li, CD Zangmeister, TC Allison, and YJ Tong.2012."Mechanistic Insights on One-phase vs.Two-phase Brust–Schi?rin MethodSynthesis of Au Nanoparticles with Dioctyl-diselenides."Chemical Communications 48(3):362-364. doi:10.1039/C1CC15955K
Authors: 
O Zaluzhna
Y Li
CD Zangmeister
TC Allison
YJ Tong

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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,...