Environmental Molecular Sciences Laboratory

A DOE Office of Science User Facility

This page lives in the old site. Check out our new site here.

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

Different Mechanisms Govern the Two-Phase Brust−SchiffrinDialkylditelluride Syntheses of Ag and Au Nanoparticles.

Abstract: 

Here we report the first unambiguous identification of the chemical structures of the precursor species involving metal (Au and Ag) ions and Tecontaining ligands in the Brust−Schiffrin syntheses of the respective metal nanoparticles, through which the different reaction pathways involved are delineated.

Citation: 
Li Y, O Zaluzhna, CD Zangmeister, TC Allison, and YJ Tong.2012."Different Mechanisms Govern the Two-Phase Brust?SchiffrinDialkylditelluride Syntheses of Ag and Au Nanoparticles."Journal of the American Chemical Society 134(4):1990-1992. doi:10.1021/ja210359r
Authors: 
Li Y
O Zaluzhna
CD Zangmeister
TC Allison
YJ Tong

Multiband Optical Absorption Controlled by Lattice Strain in Thin-Film LaCrO3.

Abstract: 

Experimental measurements and ab initio modeling of the optical transitions in strained G-type antiferromagnetic LaCrO3 resolve two decades of debate regarding the magnitude of the optical band gap and the character of the corresponding transitions in this material. Using time-dependent density functional theory and accounting for thermal disorder effects, we demonstrate that the fourmost prominent low-energy absorption features are due to intra-Cr t2g {eg (2.4, 3.6 eV), inter-Crt2g {t2g (4.4 eV), and inter-ion O 2p { Cr 3d (from ˘5 eV) transitions and show that the excitation energies of the latter type can be strongly affected by the lattice strain.

Citation: 
Sushko P, L Qiao, ME Bowden, T Varga, GJ Exarhos, FK Urban, III, D Barton, and SA Chambers.2013."Multiband Optical Absorption Controlled by Lattice Strain in Thin-Film LaCrO3."Physical Review Letters 110(7):077401. doi:10.1103/PhysRevLett.110.077401
Authors: 
P Sushko
L Qiao
ME Bowden
T Varga
GJ Exarhos
FK Urban
III
D Barton
SA Chambers

Covalent Hydration” Reactions in Model Monomeric Ru 2,2'-Bipyridine Complexes: Thermodynamic Favorability as a Function of Metal

Abstract: 

Density functional theory (DFT) has been used to investigate the plausibility of water addition to the simple mononuclear ruthenium complexes, [(NH3)3(bpy)RudO]2+/3+
and [(NH3)3(bpy)RuOH]3+, in which theOHfragment adds to the 2,20-bipyridine (bpy) ligand. Activation of bpy toward water addition has frequently been postulated within the literature, although there exists little definitive experimental evidence for this type of “covalent hydration”. In this study, we examine the energetic dependence of the reaction upon metal oxidation state, overall spin state of the complex, as well as selectivity for various positions on the bipyridine ring. The thermodynamic favorability is found to be highly dependent upon all three parameters, with free energies of reaction that span favorable and unfavorable regimes. Aqueous addition to [(NH3)3(bpy)RudO]3+ was found to be highly favorable for the S = 1/2 state, while reduction of the formal oxidation state on the metal center makes the reaction highly
unfavorable. Examination of both facial and meridional isomers reveals that when bipyridine occupies the position trans to the ruthenyl oxo atom, reactivity toward OH addition decreases and the site preferences are altered. The electronic structure and
spectroscopic signatures (EPR parameters and simulated spectra) have been determined to aid in recognition of “covalent hydration” in experimental systems. EPR parameters are found to uniquely characterize the position of theOHaddition to the bpy as well as the overall spin state of the system.

Citation: 
Ozkanlar A, JL Cape, JK Hurst, and AE Clark.2011."“Covalent Hydration” Reactions in Model Monomeric Ru 2,2'-Bipyridine Complexes: Thermodynamic Favorability as a Function of Metal Oxidation and Overall Spin States."Inorganic Chemistry 50(17):8177-8187. doi:10.1021/ic200646h
Authors: 
A Ozkanlar
JL Cape
JK Hurst
AE Clark

Structure and Hydrolysis of the U(IV), U(V), and U(VI) Aqua Ions from Ab Initio Molecular Simulations.

Abstract: 

Ab initio molecular dynamics simulations at 300 K based on density functional theory have been used to study the hydration shell geometries, solvent dipole, and first hydrolysis of the Uranium(IV) (U4+) and Uranyl(V) (UO2+) ions in aqueous solution. The solvent dipole and first of hydrolysis of aqueous Uranium(VI) (UO22+) has also been probed. The first shell of U4+ is coordinated by 8-9 water ligands with an average U−O distance of 2.42 Å. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 Å respectively. The simulated EXAFS spectra of U4+ matched well with recent experimental data. The first shell of UO2+ is coordinated by 5 water ligands in the equatorial plane, with the average U=Oax and U−O distances being 1.85 Å and 2.54 Å respectively. Overall, the hydration shell structure of UO2+ matches closely with that of UO22+ except for small expansions in the average U=Oax and U−O distances. Each ion strongly polarizes their respective first shell water ligands. The computed acidity constant (pKa) of U4+ and UO22+ are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24 respectively. The predicted pKa of UO2+ is 8.5.

Citation: 
Atta-Fynn R, DF Johnson, EJ Bylaska, ES Ilton, GK Schenter, and WA De Jong.2012."Structure and Hydrolysis of the U(IV), U(V), and U(VI) Aqua Ions from Ab Initio Molecular Simulations."Inorganic Chemistry 51(5):3016-3024. doi:10.1021/ic202338z
Authors: 
R Atta-Fynn
DF Johnson
EJ Bylaska
ES Ilton
GK Schenter
WA De Jong

Evaluation of Methods to Predict Reactivity of Gold Nanoparticles.

Abstract: 

Several methods have appeared in the literature for predicting reactivity on metallic surfaces and on the surface of metallic nanoparticles. All of these methods have some relationship to the concept of frontier molecular orbital theory. The d-band theory of Hammer and Nørskov is perhaps the most widely used predictor of reactivity on metallic surfaces, and it has been successfully applied in many cases. Use of the Fukui function and the condensed Fukui function is well established in organic chemistry, but has not been so widely applied in predicting the reactivity of metallic nanoclusters. In this article, we will evaluate the usefulness of the condensed
Fukui function in predicting the reactivity of a family of cubo-octahedral gold nanoparticles and make comparison with the d-band method.

Citation: 
Allison TC, and YJ Tong.2011."Evaluation of Methods to Predict Reactivity of Gold Nanoparticles."Physical Chemistry Chemical Physics. PCCP 13(28):12858–12864. doi:10.1039/c1cp20376b
Authors: 
TC Allison
YJ Tong

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,...