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

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...
Porous carbon nanofiber (CNF)-supported tin-antimony (SnSb) alloys is synthesized and applied as sodium ion battery anode. The chemistry and...
A fully automated titration system with infrared detection was developed for investigating interfacial chemistry at high pressures. The apparatus...

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: 

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

Structures and Stabilities of (MgO)n Nanoclusters.

Abstract: 

Global minima for (MgO)n structures were optimized using a tree growth−hybrid genetic algorithm in conjunction with MNDO/MNDO/d semiempirical molecular orbital calculations followed by density functional theory geometry optimizations with the B3LYP functional. New lowest energy isomers were found for a number of (MgO)n clusters. The most stable isomers for (MgO)n (n > 3) are 3-dimensional. For n < 20, hexagonal tubular (MgO)n structures are more favored in energy than the cubic structures. The cubic structures and their variations dominate after n = 20. For the cubic isomers, increasing the size of the cluster in any dimension improves the stability. The effectiveness of increasing the size of the cluster in a specific dimension to improve stability diminishes as the size in that dimension increases. For cubic structures of the same size, the most compact cubic structure is expected to be the more stable cubic structure. The average Mg−O bond distance and coordination number both increase as n increases. The calculated average Mg−O bond distance is 2.055 Å at n = 40, slightly smaller than the bulk value of 2.104 Å. The average coordination number is predicted to be 4.6 for the lowest energy (MgO)40 as compared to the bulk value of 6. As n increases, the normalized clustering energy ΔE(n) for the (MgO)n increases and the slope of the ΔE(n)vs n curve decreases. The value of ΔE(40) is predicted to be 150 kcal/mol, as compared to the bulk value ΔE(∞) = 176 kcal/mol. The electronic properties of the clusters are presented and the reactive sites are predicted to be at the corners.

Citation: 
Chen M, AR Felmy, and DA Dixon.2014."Structures and Stabilities of (MgO)n Nanoclusters."Journal of Physical Chemistry A 118(17):3136-3146. doi:10.1021/jp412820z
Authors: 
M Chen
AR Felmy
DA Dixon
Instruments: 
Volume: 
118
Issue: 
17
Pages: 
3136-3146
Publication year: 
2014

Automated High-Pressure Titration System with In Situ Infrared Spectroscopic Detection.

Abstract: 

A fully automated titration system with infrared detection was developed for investigating interfacial chemistry at high pressures. The apparatus consists of a high-pressure fluid generation and delivery system coupled to a high-pressure cell with infrared optics. A manifold of electronically actuated valves is used to direct pressurized fluids into the cell. Precise reagent additions to the pressurized cell are made with calibrated tubing loops that are filled with reagent and placed in-line with the cell and a syringe pump. The cell’s infrared optics facilitate both transmission and attenuated total reflection (ATR) measurements to monitor bulk-fluid composition and solid-surface phenomena such as adsorption, desorption, complexation, dissolution, and precipitation. Switching between the two measurement modes is accomplished with moveable mirrors that direct radiation from a Fourier transform infrared spectrometer into the cell along transmission or ATR light paths. The versatility of the high-pressure IR titration system is demonstrated with three case studies. First, we titrated water into supercritical CO2 (scCO2) to generate an infrared calibration curve and determine the solubility of water in CO2 at 50 °C and 90 bar. Next, we characterized the partitioning of water between a montmorillonite clay and scCO2 at 50 °C and 90 bar. Transmission-mode spectra were used to quantify changes in the clay’s sorbed water concentration as a function of scCO2 hydration, and ATR measurements provided insights into competitive residency of water and CO2 on the clay surface and in the interlayer. Finally, we demonstrated how time-dependent studies can be conducted with the system by monitoring the carbonation reaction of forsterite (Mg2SiO4) in water-bearing scCO2 at 50 °C and 90 bar. Immediately after water dissolved in the scCO2, a thin film of adsorbed water formed on the mineral surface, and the film thickness increased with time as the forsterite began to dissolve. However, after approximately 2.5 hours, the trend reversed, and a carbonate precipitate began to form on the forsterite surface, exposing dramatic chemical changes in the thin-water film. Collectively, these applications illustrate how the high-pressure IR titration system can provide molecular-level information about the interactions between variably wet scCO2 and minerals relevant to underground storage of CO2 (geologic carbon sequestration). The apparatus could also be utilized to study high-pressure interfacial chemistry in other areas such as catalysis, polymerization, food processing, and oil and gas recovery.

Citation: 
Thompson CJ, PF Martin, J Chen, P Benezeth, HT Schaef, KM Rosso, AR Felmy, and JS Loring.2014."Automated High-Pressure Titration System with In Situ Infrared Spectroscopic Detection."Review of Scientific Instruments 85(4):Article No. 044102. doi:10.1063/1.4870411
Authors: 
CJ Thompson
PF Martin
J Chen
P Benezeth
HT Schaef
KM Rosso
AR Felmy
JS Loring
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Controlling SEI Formation on SnSb-Porous Carbon Nanofibers for Improved Na Ion Storage.

Abstract: 

Porous carbon nanofiber (CNF)-supported tin-antimony (SnSb) alloys is synthesized and applied as sodium ion battery anode. The chemistry and morphology of the solid electrolyte interphase (SEI) film and its correlation with the electrode performance are studied. The addition of fluoroethylene carbonate (FEC) in electrolyte significantly reduces electrolyte decomposition and creates a very thin and uniform SEI layer on the cycled electrode surface which could promote the kinetics of Na-ion migration/transportation, leading to excellent electrochemical performance.

Citation: 
Ji L, M Gu, Y Shao, X Li, MH Engelhard, BW Arey, W Wang, Z Nie, J Xiao, CM Wang, J Zhang, and J Liu.2014."Controlling SEI Formation on SnSb-Porous Carbon Nanofibers for Improved Na Ion Storage."Advanced Materials 26(18):2901-2908. doi:10.1002/adma.201304962
Authors: 
Ji L
M Gu
Y Shao
X Li
MH Engelhard
BW Arey
W Wang
Z Nie
J Xiao
CM Wang
J Zhang
J Liu
Facility: 
Instruments: 
Volume: 
26
Issue: 
18
Pages: 
2901-2908
Publication year: 
2014

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