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.

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

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
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...

Publications

Supported early transition metal oxides have important applications in numerous catalytic reactions. In this article we review preparation and...
The reactions of deuterated methanol, ethanol, 1-propanol, 1-butanol, 2-propanol, 2-butanol and t-butanol over cyclic (MO3)3 (M = Mo, W) clusters...
The syntheses of the new 1,5-diphenyl-3,7-di(isopropyl)-1,5-diaza-3,7-diphosphacyclooctane ligand, PiPr2NPh2, is reported. The two equivalents of the...
We establish a new estimate for the interaction energy between two benzene molecules in the parallel displaced (PD) conformation by systematically...
Grand Canonical Monte Carlo (GCMC) simulations were carried out to study the equilibrium adsorption concentration of methanol and water in all-silica...

Science Highlights

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...
Posted: September 02, 2014
The impacts of soil moisture on the carbon cycle are well known from previous research. However, interactions among soil moisture, groundwater and...
Posted: August 21, 2014
While trying to understand the chemistry that turns plant material into biofuel, researchers discovered water in the conversion process forms an...

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.

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

Attachments: 

Oxidation, Reduction, and Condensation of Alcohols over (MO3)3 (M=Mo, W) Nanoclusters .

Abstract: 

The reactions of deuterated methanol, ethanol, 1-propanol, 1-butanol, 2-propanol, 2-butanol and t-butanol over cyclic (MO3)3 (M = Mo, W) clusters were studied experimentally with temperature programmed desorption (TPD) and theoretically with coupled cluster CCSD(T) theory and density functional theory. The reactions of two alcohols per M3O9 cluster are required to provide agreement with experiment for D2O release, dehydrogenation and dehydration. The reaction begins with the elimination of water by proton transfers and forms an intermediate dialkoxy species which can undergo further reaction. Dehydration proceeds by a β hydrogen transfer to a terminal M=O. Dehydrogenation takes place via an α hydrogen transfer to an adjacent MoVI = O atom or a WVI metal center with redox involved for M = Mo and no redox for M = W. The two channels have comparable activation energies. H/D exchange to produce alcohols can take place after olefin is released or via the dialkoxy species depending on the alcohol and the cluster. The Lewis acidity of the metal center with WVI being larger than MoVI results in the increased reactivity of W3O9 over Mo3O9 for dehydrogenation and dehydration.

Citation: 
Fang Z, Z Li, MS Kelley, BD Kay, S Li, JM Hennigan, RJ Rousseau, Z Dohnalek, and DA Dixon.2014."Oxidation, Reduction, and Condensation of Alcohols over (MO3)3 (M=Mo, W) Nanoclusters ."Journal of Physical Chemistry C 118(39):22620-22634. doi:10.1021/jp5072132
Authors: 
Z Fang
Z Li
MS Kelley
BD Kay
S Li
JM Hennigan
RJ Rousseau
Z Dohnalek
DA Dixon
Instruments: 
Volume: 
118
Issue: 
39
Pages: 
22620-22634
Publication year: 
2014

Dehydration, Dehydrogenation, and Condensation of Alcohols on Supported Oxide Catalysts Based on Cyclic (WO3)3 and (MoO3)3

Abstract: 

Supported early transition metal oxides have important applications in numerous catalytic reactions. In this article we review preparation and activity of well-defined model WO3 and MoO3 catalysts prepared via deposition of cyclic gas-phase (WO3)3 and (MoO3)3 clusters generated by sublimation of WO3 and MoO3 powders. Conversion of small aliphatic alcohols to alkenes, aldehydes/ketons, and ethers is employed to probe the structure-activity relationships on model WO3 and MoO3 catalysts ranging from unsupported (WO3)3 and (MoO3)3 clusters embedded in alcohol matrices, to (WO3)3 clusters supported on surfaces of other oxides, and epitaxial and nanoporous WO3 films. Detailed theoretical calculations reveal the underlying reaction mechanisms and provide insight into the origin of the differences in the WO3 and MoO3 reactivity. For the range of interrogated (WO3)3 they further shed light into the role structure and binding of (WO3)3 clusters with the support play in determining their catalytic activity.

Citation: 
Rousseau RJ, DA Dixon, BD Kay, and Z Dohnalek.2014."Dehydration, Dehydrogenation, and Condensation of Alcohols on Supported Oxide Catalysts Based on Cyclic (WO3)3 and (MoO3)3 Clusters."Chemical Society Reviews 43(22):7664-7680. doi:10.1039/c3cs60445d
Authors: 
RJ Rousseau
DA Dixon
BD Kay
Z Dohnalek
Instruments: 
Volume: 
43
Issue: 
22
Pages: 
7664-7680
Publication year: 
2014

A Ni(II) Bis(diphosphine)-Hydride Complex Containing Proton Relays - Structural Characterization and Electrocatalytic Studies.

Abstract: 

The syntheses of the new 1,5-diphenyl-3,7-di(isopropyl)-1,5-diaza-3,7-diphosphacyclooctane ligand, PiPr2NPh2, is reported. The two equivalents of the ligand react with [Ni(CH3CN)6](BF4)2 to form the bis-diphosphine Ni(II)-complex [Ni(PiPr2NPh2)2](BF4)2, which acts as a proton reduction electrocatalyst. In addition to [Ni(PiPr2NPh2)2]2+, we report the syntheses and structural characterization of the Ni(0)-complex Ni(PiPr2NPh2)2, and the Ni(II)-hydride complex [HNi(PiPr2NPh2)2]BF4. The [HNi(PiPr2NPh2)2]BF4 complex represents the first Ni(II)-hydride in the [Ni(PR2NR'2)2]2+ family of compounds to be isolated and structurally characterized. In addition to the experimental data, the mechanism of electrocatalysis facilitated by [Ni(PiPr2NPh2)2]2+ is analyzed using linear free energy relationships recently established for the [Ni(PR2NR'2)2]2+ family. We thank Dr. Aaron Appel, Dr. Simone Raugei and Dr. Eric Wiedner for helpful discussions. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Mass spectrometry was provided at W. R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s office of Biological and Environmental Research located at Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

Citation: 
Das PP, RM Stolley, EF Van Der Eide, and ML Helm.2014."A Ni(II) Bis(diphosphine)-Hydride Complex Containing Proton Relays - Structural Characterization and Electrocatalytic Studies."European Journal of Inorganic Chemistry 27:4611-4618. doi:10.1002/ejic.201402250
Authors: 
PP Das
RM Stolley
EF Van Der Eide
ML Helm
Facility: 
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Benchmark Theoretical Study of the π–π Binding Energy in the Benzene Dimer.

Abstract: 

We establish a new estimate for the interaction energy between two benzene molecules in the parallel displaced (PD) conformation by systematically converging (i) the intra- and intermolecular geometry at the minimum geometry, (ii) the expansion of the orbital basis set and (iii) the level of electron correlation. The calculations were performed at the second order Møller - Plesset perturbation (MP2) and the Coupled Cluster including Singles, Doubles and a perturbative estimate of Triples replacements [CCSD(T)] levels of electronic structure theory. At both levels of theory, by including results corrected for Basis Set Superposition Error (BSSE), we have estimated the Complete Basis Set (CBS) limit by employing the family of Dunning’s correlation consistent polarized valence basis sets. The largest MP2 calculation was performed with the cc-pV6Z basis set (2,772 basis functions), whereas the largest CCSD(T) calculation with the cc-pV5Z basis set (1,752 basis functions). The cluster geometries were optimized with basis sets up to quadruple-ζ quality, observing that both its intra- and inter-molecular parts have practically converged with the triple-ζ quality sets. The use of converged geometries was found to play an important role for obtaining accurate estimates for the CBS limits. Our results demonstrate that the binding energies with the families of the plain (cc-pVnZ) and augmented (aug-cc-pVnZ) sets converge [to within < 0.01 kcal/mol for MP2 and < 0.15 kcal/mol for CCSD(T)] to the same CBS limit. In addition, the average of the uncorrected and BSSEcorrected binding energies was found to converge to the same CBS limit must faster than either of the two constituents (uncorrected or BSSE-corrected binding energies). Due to the fact that the family of augmented basis sets (especially for the larger sets) causes serious linear dependency problems, the plain basis sets (for which no linear dependencies were found) are deemed as a more efficient and straightforward path for obtaining an accurate CBS limit. We considered extrapolations of the uncorrected (Δ��) and BSSE-corrected (Δ��!") binding energies, their average value (Δ��!"#) as well as the average of the latter over the plain and augmented sets (Δ��!"#) with the cardinal number of the basis set n. Our best estimate of the CCSD(T)/CBS limit for the π-π interaction energy in the PD benzene dimer is De = 2.65 ± 0.02 kcal/mol. The best CCSD(T)/cc-pV5Z calculated value is 2.62 kcal/mol, just 0.03 kcal/mol away from the CBS limit. For comparison, the MP2/CBS limit estimate is 5.00 ± 0.01 kcal/mol, demonstrating a 90% overbinding with respect to CCSD(T). The Spin-Component-Scaled (SCS) MP2 variant was found to closely reproduce the CCSD(T) results for each basis set, while Scaled-Opposite-Spin (SOS) yielded results that are too low when compared to CCSD(T).

Citation: 
Miliordos E, E Apra, and SS Xantheas.2014."Benchmark Theoretical Study of the ?–? Binding Energy in the Benzene Dimer."Journal of Physical Chemistry A 118(35):7568-7578. doi:10.1021/jp5024235
Authors: 
E Miliordos
E Apra
SS Xantheas
Instruments: 
Volume: 
118
Issue: 
35
Pages: 
7568-7578
Publication year: 
2014

A Comparative Study of the Adsorption of Water and Methanol in Zeolite BEA: A Molecular Simulation Study.

Abstract: 

Grand Canonical Monte Carlo (GCMC) simulations were carried out to study the equilibrium adsorption concentration of methanol and water in all-silica zeolite BEA over the wide temperature and pressure ranges. For both water and methanol, their adsorptive capacity increases with increasing pressure and decreasing temperature. The onset of methanol adsorption occurs at much lower pressures than water adsorption at all temperatures. Our GCMC simulation results also indicate that the adsorption isotherms of methanol exhibit a gradual change with pressure while water adsorption shows a sharp first-order phase transition at low temperatures. To explore the effects of Si/Al ratio on adsorption, a series of GCMC simulations of water and methanol adsorption in zeolites HBEA with Si/Al=7, 15, 31, 63 were performed. As the Si/Al ratio decreases, the onsets of both water and methanol adsorption dramatically shift to lower pressures. The type V isotherm obtained for water adsorption in hydrophobic BEA progressively changes to type I isotherm with decreasing Si/Al ratio in hydrophilic HBEA. This work was 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.

Citation: 
Nguyen VT, PT Nguyen, LX Dang, D Mei, CD Wick, and DD Do.2014."A Comparative Study of the Adsorption of Water and Methanol in Zeolite BEA: A Molecular Simulation Study."Molecular Simulation 40(14):1113-1124. doi:10.1080/08927022.2013.848280
Authors: 
VT Nguyen
PT Nguyen
LX Dang
D Mei
CD Wick
DD Do
Instruments: 
Volume: 
40
Issue: 
14
Pages: 
1113-1124
Publication year: 
2014

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