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

Steam reforming of ethylene glycol (EG) over MgAl2O4 supported metal (15 wt.% Ni, 5 wt.% Rh, and 15 wt.% Co) catalysts were investigated using...
A combined theoretical and experimental approach is presented that uses a comprehensive mean-field microkinetic model, reaction kinetics experiments...
We report a novel non-platinum group metal (non-PGM) catalyst derived from Mn and amino- antipyrine (MnAAPyr) that shows electrochemical activity...
Conspectus Boron is an interesting element with unusual polymorphism. While three-dimensional (3D) structural motifs are prevalent in bulk boron,...
Tin oxide (SnOx) formation on tin-based electrode surfaces during CO2 electrochemical reduction can have a significant impact on the activity and...

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

Theoretical Study of the Structure, Stability and Oxygen Reduction Activity ofUltrathin Platinum Nanowires.

Abstract: 

We use density functional theory to study the difference in the structure, stability and catalytic reactivity between ultrathin, 0.5- 1.0 nm diameter, platinum nanotubes and nanowires. Model nanowires were formed by inserting an inner chain of platinum
atoms in small diameter nanotubes. In this way more stable, nonhollow structures were formed. The difference in the electronic structure of platinum nanotubes and nanowires was examined by inspecting the density of surface states and band structure. Furthermore, reactivity towards the oxygen reduction reaction of platinum nanowires was addressed by studying the change in the chemisorption energies of oxygen and hydroxyl groups, induced by inserting the inner chain of platinum atoms into the hollow nanotubes. Both ultrathin platinum nanotubes and nanowires show
distinct properties compared to bulk platinum. Nanotubes with diameters larger than 1 nm show promise for use as oxygen reduction catalysts.

Citation: 
Matanovic I, P Kent, F Garzon, and NJ Henson.2012."Theoretical Study of the Structure, Stability and Oxygen Reduction Activity ofUltrathin Platinum Nanowires."ECS Transactions 50(2):1385-1395. doi:10.1149/05002.1385ecst
Authors: 
I Matanovic
P Kent
F Garzon
NJ Henson

Density Functional Study of the Structure, Stability and Oxygen Reduction Activity of Ultrathin Platinum Nanowires.

Abstract: 

We used density functional theory to study the difference in the structure, stability and catalytic reactivity between ultrathin, 0.5–1.0 nm diameter, platinum nanotubes and nanowires. Model nanowires were formed by inserting an inner chain of platinum
atoms in small diameter nanotubes. In this way more stable, non-hollow structures were formed. The difference in the electronic structure of platinum nanotubes and nanowires was examined by inspecting the density of surface states and band structure. Furthermore, reactivity toward the oxygen reduction reaction of platinum nanowires was assessed by studying the change in the chemisorption energies of oxygen, hydroxyl, and hydroperoxyl groups, induced by converting the nanotube models to nanowires. Both ultrathin platinum nanotubes and nanowires show distinct properties compared to bulk platinum. Single-wall nanotubes and platinum nanowires with diameters larger than 1 nm show promise for use as oxygen reduction catalysts.

Citation: 
Matanovic I, P Kent, F Garzon, and NJ Henson.2013."Density Functional Study of the Structure, Stability and Oxygen Reduction Activity of Ultrathin Platinum Nanowires."Journal of the Electrochemical Society 160(6):F548-F553. doi:10.1149/2.047306jes
Authors: 
I Matanovic
P Kent
F Garzon
NJ Henson

Scanning Tunneling Microscopy and Theoretical Study of Water Adsorption on Fe3O4: Implications for Catalysis.

Abstract: 

The reduced surface of a natural Hematite single crystal a-Fe2O3(0001) sample has multiple surface domains with di!erent terminations, Fe2O3(0001), FeO(111), and Fe3O4(111). The adsorption of water on this surface was investigated via Scanning
Tunneling Microscopy (STM) and first-principle theoretical simulations. Water species are observed only on the Fe-terminated Fe3O4(111) surface at temperatures up to 235 K. Between 235 and 245 K we observed a change in the surface species from intact water molecules and hydroxyl groups bound to the surface to only hydroxyl groups atop the surface terminating FeIII cations. This indicates a low energy barrier for water dissociation on the surface of Fe3O4 that is supported by our theoretical computations. Our first principles simulations con"rm the identity of the surface species proposed from the STM images, finding that the most stable state of a water molecule is the dissociated one (OH + H), with OH atop surface terminating FeIII sites and H atop under-coordinated oxygen sites. Attempts to simulate reaction of the surface OH with coadsorbed CO fail because the only binding sites for CO are the surface FeIII atoms, which are blocked by the much more strongly bound OH. In order to promote this reaction we simulated a surface decorated with gold atoms. The Au adatoms are found to cap the under-coordinated oxygen sites and dosed CO is found to bind to the Au adatom. This newly created binding site for CO not only allows for coexistence of CO and OH on the surface of Fe3O4 but also provides colocation between the two species. These two factors are likely promoters of catalytic activity on Au/Fe3O4(111) surfaces.

Citation: 
Rim KT, D Eom, SW Chan, M Flytzani-Stephanopoulos, G Flynn, X Wen, and ER Batista.2012."Scanning Tunneling Microscopy and Theoretical Study of Water Adsorption on Fe3O4: Implications for Catalysis."Journal of the American Chemical Society 134(46):18979?18985. doi:10.1021/ja305294x
Authors: 
KT Rim
D Eom
SW Chan
M Flytzani-Stephanopoulos
G Flynn
X Wen
ER Batista

Rotational Rehybridization and the High Temperature Phase of UC2.

Abstract: 

The screened hybrid approximation (HSE) of density functional theory (DFT) is used to examine the structural, optical, and electronic properties of the high temperature phase, cubic UC(2). This phase contains C(2) units with a computed C-C distance of 1.443 Å which is in the range of a CC double bond; U is formally 4+, C(2) 4-. The closed shell paramagnetic state (NM) was found to lie lowest. Cubic UC(2) is found to be a semiconductor with a narrow gap, 0.4 eV. Interestingly, the C(2) units connecting two uranium sites can rotate freely up to an angle of 30°, indicating a hindered rotational solid. Ab-initio molecular dynamic simulations (HSE) show that the rotation of C(2) units in the low temperature phase (tetragonal UC(2)) occurs above 2000 K, in good agreement with experiment. The computed energy barrier for the phase transition from tetragonal UC(2) to cubic UC(2) is around 1.30 eV per UC(2). What is fascinating about this system is that at high temperature, the phase transformation to the cubic phase is associated with a rehybridization of the C atoms from sp to sp(3).

Citation: 
Wen X, SP Rudin, ER Batista, DL Clark, GE Scuseria, and RL Martin.2012."Rotational Rehybridization and the High Temperature Phase of UC2."Inorganic Chemistry 51(23):12650-9. doi:10.1021/ic301133m
Authors: 
X Wen
SP Rudin
ER Batista
DL Clark
GE Scuseria
RL Martin

Density Functional Theory Studies of the Electronic Structure of Solid State Actinide Oxides.

Abstract: 

The actinide oxides have been extensively studied in the context of the nuclear fuel cycle. They are also of fundamental interest as members of a class of strongly correlated materials, the Mott insulators. Their complex physical and chemical
properties make them challenging systems to characterize, both experimentally and theoretically. Chiefly, this is because actinide oxides can exhibit both electronic localization and electronic delocalization and have partially occupied f orbitals,
which can lead to multiple possibilities for ground states. Of particular concern for theoretical work is that the large number of competing states display strong correlations which are dffcult to capture with computationally tractable methods.

Citation: 
Wen X, RL Martin, TM Henderson, and GE Scuseria.2013."Density Functional Theory Studies of the Electronic Structure of Solid State Actinide Oxides."Chemical Reviews 113(2):1063?1096. doi:10.1021/cr300374y
Authors: 
X Wen
RL Martin
TM Henderson
GE Scuseria

Screened Hybrid and DFT + U Studies of the Structural, Electronic, and Optical Properties of U3O8.

Abstract: 

A systematic comparison of the structures and electronic and optical properties of U3O8 in the c2mm, P¯62m, and P21/m structures (the α, β, and γ phases, respectively) is performed using density functional theory + U (PBE + U) and the Heyd–Scuseria–Ernzerhof screened hybrid functional (HSE). The relationship between the semiconducting C2mm phase of U3O8 and the high temperature, metallic P¯62m phase is explored in more detail. Our calculated results show
that the HSE functional gives a better description of the electronic and optical properties when compared with available experimental data for the α and β phases, but neither approach does particularly well for the high pressure γ phase.

Citation: 
Wen X, RL Martin, GE Scuseria, SP Rudin, ER Batista, and AK Burrell.2012."Screened Hybrid and DFT + U Studies of the Structural, Electronic, and Optical Properties of U3O8."Journal of Physics. Condensed Matter 25:025501. doi:10.1088/0953-8984/25/2/025501
Authors: 
X Wen
RL Martin
GE Scuseria
SP Rudin
ER Batista
AK Burrell

Importance of counteranions on the hydration structure of the curium ion.

Abstract: 

Using density functional theory based ab initio molecular dynamics and metadynamics we show that counter ions can trigger noticeable changes in the hydration shell structure of the curium ion. The free energies of curium-water coordination and the solvent hydrogen bond (HB) lifetimes in the absence and presence the counter anions predict that chloride and bromide counter anions strengthen the first shell and consequently the 8-fold coordination state is dominant by at least 98%. In contrast, the perchlorate counter anions are found to weaken the coordination shell and the HB network, with the 9-fold and 8-fold states existing in an 8:1 ratio, which is in good agreement with reported 9:1 ratio seen in time resolved fluorescence spectroscopy experiments. To our knowledge this is the first time molecular simulations have shown that counter anions can directly affect the first hydration shell structure of a cation.

Citation: 
Atta Fynn R, EJ Bylaska, and WA De Jong.2013."Importance of counteranions on the hydration structure of the curium ion."Journal of Physical Chemistry Letters 4(13):2166-2170. doi:10.1021/jz400887a
Authors: 
Fynn Atta
EJ Bylaska
WA De Jong

Optical absorption and band gap reduction in (Fe1-xCrx)2O3 solid solutions: A first-principles study.

Abstract: 

We provide a detailed theoretical analysis of the character of optical transitions and band gap reduction in (Fe1-xCrx)2O3 solid solutions using extensive periodic model and embedded cluster calculations. Optical absorption bands for x = 0.0, 0.5, and 1.0 are assigned on the basis of timedependent density functional theory (TDDFT) calculations. A band-gap reduction of as much as 0.7 eV with respect to that of pure α-Fe2O3 is found. This result can be attributed to predominantly two effects: (i) the higher valence band edge for x ≈ 0.5, as compared to those in pure α-Fe2O3 and α-Cr2O3, and, (ii) the appearance of Cr  Fe d–d transitions in the solid solutions. Broadening of the valence band due to hybridization of the O 2p states with Fe and Cr 3d states also contributes to band gap reduction.

Citation: 
Wang Y, KA Lopata, SA Chambers, N Govind, and PV Sushko.2013."Optical absorption and band gap reduction in (Fe1-xCrx)2O3 solid solutions: A first-principles study."Journal of Physical Chemistry C 117(48):25504-25512. doi:10.1021/jp407496w
Authors: 
Y Wang
KA Lopata
SA Chambers
N Govind
PV Sushko

A Tetrapositive Metal Ion in the Gas Phase: Thorium(IV) Coordinated by Neutral Tridentate Ligands.

Abstract: 

ESI of 1:1 mixtures of Th(ClO₄)₄ and ligand TMOGA in acetonitrile resulted in the observation of the TMOGA supported tetracation, Th(L)₃⁴⁺, in the gas phase. Three TMOGA ligands are necessary to stabilize the tetrapositive thorium ion; no Th(L)₂⁴⁺ or Th(L)₄⁴⁺ was observed. Theoretical calculations reveal that the Th(L)₃⁴⁺ complex possesses C₃ symmetry with the thorium center coordinated by nine oxygen atoms from three ligands, which forms a twisted TPP geometry. Actinide compounds with such a geometry feature a nine-coordinate chiral actinide center. The Th-L binding energy and bond orders of Th(L)n⁴⁺ decrease as the coordination number increases, consistent with the trend of concurrently increasing Th-O distances. The Th-O bonding is mainly electrostatic in nature, but the covalent interactions are not negligible. CID of the Th(L)₃⁴⁺ complex mainly resulted in charge reduction to form Th(L)₂(L-86)³⁺oss of neutral TMOGA was not observed. The protic ligand methanol stabilized only tri- and dications of ligated thorium. The intensity of the Th(L)₃⁴⁺ peak was reduced as the percentage of water increased in the Th(ClO₄)₄/TMOGA solution.

Citation: 
Gong Y, HS Hu, G Tian, L Rao, J Li, and JK Gibson.2013."A Tetrapositive Metal Ion in the Gas Phase: Thorium(IV) Coordinated by Neutral Tridentate Ligands."Angewandte Chemie International Edition 52(27):6885-6888. doi:10.1002/anie.201302212
Authors: 
Y Gong
HS Hu
G Tian
L Rao
J Li
JK Gibson

Reliable Modeling of the Electronic Spectra of Realistic Uranium Complexes.

Abstract: 

We present an EOMCCSD (equation of motion coupled cluster with singles and doubles) study of excited states of the small [UO2]2+ and [UO2]+ model systems as well as the larger UV IO2(saldien) complex. In addition, the triples contribution within the EOMCCSDT and CR-EOMCCSD(T) (completely renormalized EOMCCSD with non-iterative triples) approaches for the [UO2]2+ and [UO2]+ systems as well as the active-space variant of the CR-EOMCCSD(T) method | CREOMCCSd(t) | for the UV IO2(saldien) molecule are investigated. The coupled cluster data was employed as benchmark to chose the "best" appropriate exchange--correlation functional for subsequent time-dependent density functional (TD-DFT) studies on the transition energies for closed-shell species. Furthermore, the influence of the saldien ligands on the electronic structure and excitation energies of the [UO2]+ molecule is discussed. The electronic excitations as well as their oscillator dipole strengths modeled with TD-DFT approach using the CAM-B3LYP exchange{correlation functional for the [UV O2(saldien)]- with explicit inclusion of two DMSOs are in good agreement with the experimental data of Takao et al. [Inorg. Chem. 49, 2349-2359, (2010)].

Citation: 
Tecmer P, N Govind, K Kowalski, WA De Jong, and L Visscher.2013."Reliable Modeling of the Electronic Spectra of Realistic Uranium Complexes."Journal of Chemical Physics 139(3):Article No. 034301. doi:10.1063/1.4812360
Authors: 
P Tecmer
N Govind
K Kowalski
WA De Jong
L Visscher

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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,...