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

This paper describes and demonstrates two methods of providing a-priori information to a surface-based time-lapse three-dimensional electrical...
We report low-temperature photoelectron spectra of isolated gas-phase complexes of the hexachloroplatinate dianion bound to the nucleobases uracil,...
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...

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

First-principles Study of Phenol Hydrogenation on Pt and Ni Catalysts in Aqueous Phase.

Abstract: 

The effects of aqueous phase on the reactivity of phenol hydrogenation over Pt and Ni catalysts were investigated using density functional theory based ab initio molecular dynamics (AIMD) calculations. The adsorption of phenol and the first hydrogenation steps via three carbon positions (ortho, meta and para) with respect to the phenolic OH group were studied in both vacuum and liquid phase conditions. To gain insight into how the aqueous phase affects the metal catalyst surface, increasing water environments including singly adsorbed water molecule, mono- (9 water molecules), double layers (24 water molecules), and the bulk liquid water which (52 water molecules) on the Pt(111) and the Ni(111) surfaces were modeled. Compared to the vacuum/metal interfaces, AIMD simulation results suggest that the aqueous Pt(111) and Ni(111) interfaces have a lower metal work function in the order of 0.8 - 0.9 eV, thus, making the metals in aqueous phase stronger reducing agents and poorer oxidizing agents. Phenol adsorption from the aqueous phase is found to be slightly weaker that from the vapor phase. The first hydrogenation step of phenol at the ortho position of the phenolic ring is slightly favored over the other two positions. The polarization induced by the surrounding water molecules and the solvation effect play important roles in stabilizing the transition states associated with phenol hydrogenation by lowering the barriers of 0.1 - 0.4 eV. The detailed discussion on the basis of the interfacial electrostatics from the current study is very useful to understand the nature of a broader class of metal catalyzed reactions in liquid solution phase. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences and Office of Energy Efficiency and Renewable Energy. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.

Citation: 
Yoon Y, RJ Rousseau, RS Weber, D Mei, and JA Lercher.2014."First-principles Study of Phenol Hydrogenation on Pt and Ni Catalysts in Aqueous Phase."Journal of the American Chemical Society 136(29):10287-10298. doi:10.1021/ja501592y
Authors: 
Y Yoon
RJ Rousseau
RS Weber
D Mei
JA Lercher

Near quantitative agreement of model free DFT- MD predictions with XAFS observations of the hydration structure of highly

Abstract: 

DFT-MD simulations (PBE96 and PBE0) with MD-XAFS scattering calculations (FEFF9) show near quantitative agreement with new and existing XAFS measurements for a comprehensive series of transition metal ions which interact with their hydration shells via complex mechanisms (high spin, covalency, charge transfer, etc.). This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the U.S. DOE by Battelle. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the U.S. DOE's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Citation: 
Fulton JL, EJ Bylaska, SA Bogatko, M Balasubramanian, EL Cauet, GK Schenter, and JH Weare.2012."Near quantitative agreement of model free DFT- MD predictions with XAFS observations of the hydration structure of highly charged transition metal ions."The Journal of Physical Chemistry Letters 3(18):2588-2593. doi:10.1021/jz3008497
Authors: 
JL Fulton
EJ Bylaska
SA Bogatko
M Balasubramanian
EL Cauet
GK Schenter
JH Weare

A Radar-like Iron based Nanohybrid as an Efficient and Stable Electrocatalyst for Oxygen Reduction.

Abstract: 

The present study shows a design concept for fabricating Fe-PyNG hybrid via strong coupling between FePc and pyridine-N. The prominent features of the Fe-PyNG hybrid include high electrocatalytic activity, superior durability, and better performance than Pt/C toward ORR in alkaline media. These features potentially make Fe-PyNG an outstanding nonprecious metal cathode catalyst for fuel cells. The incorporation of Fe ion and pyridine-N afforded effective bonding and synergetic coupling effects, which lead to significant electrocatalytic performance. DFT calculations indicate that N-modified Fe is a superior site for OOH adsorption and ORR reaction. Meanwhile, the strong chemical bonding between FePc and pyridyne in PyNG leads to its superior stability. We believe that our present synthetic strategy can be further extended to develop other metal complexes/N-doped carbon materials for broad applications in the field of catalysts, batteries, and supercapacitors. This work was supported by National Basic Research Program of China (973 Program) (2013CB733501), the National Natural Science Foundation of China (NSFC-21306169, 21176221, 21136001 and 21101137), Zhejiang Provincial Natural Science Foundation of China (ZJNSF-R4110345) and the New Century Excellent Talents in University Program (NCET-10-0979). We thank Prof. Youqun Zhu for Instruments support. D. Mei is 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 multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.

Citation: 
Zhong XY, L Liu, X Wang, H Yu, G Zhuang, D Mei, X Li, and J Wang.2014."A Radar-like Iron based Nanohybrid as an Efficient and Stable Electrocatalyst for Oxygen Reduction."Journal of Materials Chemistry A 2(19):6703-6707. doi:10.1039/C4TA00647J
Authors: 
XY Zhong
L Liu
X Wang
H Yu
G Zhuang
D Mei
X Li
J Wang

Effect Of Preparation Methods On The Performance Of Co/Al2O3 Catalysts For Dry Reforming Of Methane.

Abstract: 

Two methods, dry impregnation (DI) and controlled adsorption (CA), are used for the preparation of Co/ Al2O3 catalysts for methane dry reforming reactions. Point of zero charge (PZC) measurements, pH-precipitation studies, and adsorption isotherms are used to develop a synthesis procedure in which deposition of Co2+ takes place in a more controlled manner than metal deposition during drying in synthesis by dry impregnation. The possible adsorption phenomena that occur during preparation of Co/Al2O3 catalysts by controlled adsorption are discussed. H2 chemisorption and TEM show that catalysts prepared by CA have smaller average particle sizes and higher dispersions. TPR studies show that for the sample prepared by CA a higher amount of cobalt is reduced to its metallic state and that more CoAl2O4 spinel species are present relative to DI samples. The catalyst prepared by CA shows higher activity and slower deactivation for methane dry reforming than the catalyst prepared by DI. XPS and C, H, N analysis on spent catalysts confirm two types of carbonaceous deposits are formed depending on the preparation method.

Citation: 
Ewbank JL, L Kovarik, CC Kenvin, and C Sievers.2014."Effect Of Preparation Methods On The Performance Of Co/Al2O3 Catalysts For Dry Reforming Of Methane."Green Chemistry 16(2):885-896. doi:10.1039/c3gc41782d
Authors: 
JL Ewbank
L Kovarik
CC Kenvin
C Sievers
Facility: 

Inverse-Micelle-Encapsulated Water-Enabled Bond Breaking ofDialkyl Diselenide/Disulfide: A Critical Step for Synthesizing High

Abstract: 

Inverse-micelle-encapsulated water formed in the two-phase Brust−Schiffrin
method (BSM) synthesis of Au nanoparticles (NPs) is identified as essential for dialkyl diselenide/disulfide to react with the Au(III) complex in which the Se−Se/S−S bond is broken, leading to formation of higher-quality Au NPs.

Citation: 
Zaluzhna O, Y Li, TC Allison, and YJ Tong.2012."Inverse-Micelle-Encapsulated Water-Enabled Bond Breaking ofDialkyl Diselenide/Disulfide: A Critical Step for Synthesizing High-Quality Gold Nanoparticles."Journal of the American Chemical Society 134(43):17991-17996. doi:10.1021/ja3068758
Authors: 
O Zaluzhna
Y Li
TC Allison
YJ Tong

Electro-Reduction of Nitrogen on Molybdenum Nitride: Structure, Energetics, and Vibrational Spectra from DFT.

Abstract: 

We used density functional theory to study the electrochemical conversion of nitrogen to ammonia on the (001), (100/010), (101), and (111) surfaces of g-Mo2N. Based on the calculated free energy profiles for the reduction of nitrogen by the associative and dissociative mechanisms, reactivity was found to decrease in the order (111) > (101) > (100/010) E (001). Namely, the cell potentials needed to drive the reduction to ammonia increase in the following order: *0.7 V on (111), *1.2 V on (101), and *1.4 V on (100/010) and (001) surfaces. The (111) surface was found to be the most reactive for nitrogen due to (i) its ability to adsorb the N2 in the side-on position which activates N–N bonding and (ii) its high affinity for N-adatoms which also prevents accumulation of H-adatoms on the catalytic surface at low cell potentials. We have also calculated vibrational frequencies of different NxHy species adsorbed on various g-Mo2N surfaces. The frequencies are found to depend strongly on the type of the binding sites available on the crystal facets. A comparison of the calculated frequencies with the frequencies of the corresponding species in transition metal complexes and other metal surfaces shows that the frequencies of several signature modes fall in a similar region and might be used to assign the spectra of hydrogen and nitrogen containing surface species on different metal surfaces.

Citation: 
Matanovic I, F Garzon, and NJ Henson.2014."Electro-Reduction of Nitrogen on Molybdenum Nitride: Structure, Energetics, and Vibrational Spectra from DFT."Physical Chemistry Chemical Physics. PCCP 16(7):3014-3026. doi:10.1039/c3cp54559h
Authors: 
I Matanovic
F Garzon
NJ Henson

Pages

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,...