Computer simulations give insights into how carbon dioxide reacts with a sequestering liquid

This work by Dr. Liem X. Dang and Dr. Tsun-Mei Chang is featured in an invited perspectives article in The Journal of Physical Chemistry Letters. A perspective article provides state-of-the-art research on new and emerging areas by leaders in the field. An image from the team's study graced the journal's cover.

While it might seem like an esoteric topic, useful only to those who inhabit ivory towers, understanding how gases interact with a liquid surface influences a lot, including the air we breathe and the energy we use. For example, coal-fired power plants produce large amounts of carbon dioxide. Scientists and industry leaders want to remove that dioxide and prevent its access to the environment. One option is to pump the gas through a liquid that traps only the carbon dioxide, and not other gases. But to do it, scientists must know how the gas interacts with the liquid's surface.

"If we want to optimize gas sorption, we must understand the interface, because most of the chemical and physical processes usually occur at the interface," said Dang.

When the reaction speed is measured in trillionths of a second and at scales measured in the width of atoms, scientists turn to powerful computer simulations to understand what is happening. The simulations allow them to freeze the action and gather accurate data. The researchers focused on gaseous carbon dioxide and a more hydrophobic or water-fearing room-temperature ionic liquid (see sidebar) known as [bmim][Tf2N].

The accuracy of that data depends in part on how well the molecular interactions, molecular orientation and surface tension are described. The research duo began by thoroughly examining the models, creating accurate portrayals.

Then, the team ran a series of simulations and examined how the gas and the liquid interacted. They found the solubilities of gases are critically dependent on the type of anions or negatively charged ions used to construct the ionic liquids.

"Solubilities are an active research subject in the ionic liquids field," said Dang.

The results raise questions about whether or not polarizable models are needed to simulate ionic liquids. This and questions about the influence of different charged particles in the liquid are being studied by the researchers.

More information: LX Dang and TM Chang. 2012. "Molecular Mechanism of Gas Adsorption into Ionic Liquids: A Molecular Dynamics Study." The Journal of Physical Chemistry Letters 3(2): 175-181. DOI: 10.1021/jz2011786

Provided by Pacific Northwest National Laboratory (news : web)

Computer simulations revealing how methane and hydrogen pack into gas hydrates could enlighten alternative fuel production and carbon dioxide storage

For some time, researchers have explored flammable ice for low-carbon or alternative fuel or as a place to store carbon dioxide. Now, a computer analysis of the ice and gas compound, known as a gas hydrate, reveals key details of its structure. The results show that hydrates can hold hydrogen at an optimal capacity of 5 weight-percent, a value that meets the goal of a U.S. Department of Energy standard and makes gas hydrates practical and affordable.

The analysis is the first time researchers have accurately quantified the molecular-scale interactions between the gases -- either hydrogen or methane, aka natural gas -- and the water molecules that form cages around them. A team of researchers from the Department of Energy's Pacific Northwest National Laboratory published the results in Chemical Physics Letters online December 22, 2011.

The results could also provide insight into the process of replacing methane with carbon dioxide in the naturally abundant "water-based reservoirs," according to the lead author, PNNL chemist Sotiris Xantheas.

"Current thinking is that you need large amounts of energy to push the methane out, which destroys the scaffold in the process," said Xantheas. "But the computer modeling shows that there is an alternative low energy pathway. All you need to do is break a single hydrogen bond between water molecules forming the cage -- the methane comes out, and then the hydrate reseals itself."

Cagey Ice

Gas hydrates -- especially methane hydrates, which store natural gas -- look like ice but actually hold burnable fuel. Naturally found deep in the ocean, water and gas interweave in the hydrates, but little is known about their chemical structure and processes occurring at the molecular level. They have been known to cause problems for the petroleum industry because they tend to clog pipes and can explode. A methane hydrate produced the bubble of methane gas that contributed to 2010's Gulf of Mexico oil spill.

In previous work, Xantheas and colleagues used computer algorithms and models to examine the water-based, ice-like scaffold that holds the gas. Water molecules form individual cages made with 20 or 24 molecules. Multiple cages join together in large lattices. But those scaffolds were empty in the earlier analysis.

To find out how fuels can be accommodated inside the water cages, Xantheas and PNNL colleague Soohaeng Yoo Willow built computer models of the cages with either hydrogen gas -- in which two hydrogen atoms are bound together -- or methane gas, a small molecule made with one carbon and four hydrogen atoms.

In the hydrogen hydrates, which could potentially be used as materials for hydrogen fuel storage, a small hollow cage made from 20 water molecules could hold up to a maximum of five hydrogen molecules and a larger cage made from 24 water molecules could hold up to seven.

The maximum storage capacity equates to about 10 weight-percent, or the percentage of hydrogen by mass in the chunks of ice, although packing hydrogen in that tight puts undue strain on the system. The Department of Energy's goal for hydrogen storage -- to make the fuel practical -- is above 5.5 weight-percent.

Experimentally, hydrogen storage researchers typically measure much less storage capacities. The computer model showed them why: The hydrogen molecules tended to leak out of the cages, reducing the amount of hydrogen that could be stored.

The researchers found that adding a methane molecule to the larger cages in the pure hydrogen hydrate, however, prevented the hydrogen gas from leaking out. The computer model showed the researchers that they could store the hydrogen at high pressure and practical temperatures, and release it by reducing the pressure, which melts it.

Water Gates

Understanding how the gas interacts and moves through the cages can help chemists or engineers store gas and remove it at will. Willow and Xantheas' computer simulations showed that hydrogen molecules could migrate through the cages by passing between the figurative bars of the water cages. However, the cages also had gates: Sometimes a low-energy bond between two water molecules broke, causing a water molecule to swing open and let the hydrogen molecule drift out. The "gate" closed right after the molecule passed through to reform the lattice.

With methane hydrates, some fuel producers want to remove the gas safely to use it. Others see the emptied cages as potential storage sites for carbon dioxide, which could theoretically keep it out of the atmosphere and ocean, where it warms the earth and acidifies the sea. So, Willow and Xantheas tested how methane could migrate through the cages.

The water cages were only big enough to comfortably hold one methane molecule, so the chemists stuffed two methanes inside and watched what happened. Quickly, one of the water molecules forming the cage swung open like a gate, allowing one methane molecule to escape. The gate then slammed shut as the remaining methane scooted into the middle of the cage.

"This process is important because it can happen with natural gas. It shows how methane can move in the natural world," said Xantheas. "We hope this analysis will help with the technical issues that need to be addressed with gas hydrate research and development."

Xantheas said performing computer simulations with carbon dioxide instead of methane might help determine whether it's chemically feasible to store carbon dioxide in hydrates.

This work was supported by the Department of Energy Office of Science (BES). Computer resources used were at the National Energy Research Scientific Computing Center at DOE's Lawrence Berkeley National Laboratory in Berkeley, Calif.

Story Source:

The above story is reprinted from materials provided by Pacific Northwest National Laboratory.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Soohaeng Yoo Willow, Sotiris S. Xantheas. Enhancement of hydrogen storage capacity in hydrate lattices. Chemical Physics Letters, 2011; DOI: 10.1016/j.cplett.2011.12.036

Metal oxide simulations could help green technology

The new paradigm could lead to a better understanding of corrosion and how toxic minerals leach from rocks and soil. It could also help in the development of “green” technology: new types of batteries, for example, or catalysts for splitting water to produce hydrogen fuel.

“This is a global change in how people should view these processes,” said William Casey, UC Davis professor of chemistry and co-author of the study with James Rustad, a former geology professor at UC Davis who now works as a scientist at Corning Inc. in New York.

Previously, when studying the interactions of water with clusters of metal oxides, researchers tried to pick and study individual atoms to assess their reactivity. But “none of it really made sense,” Rustad said.

Using computer simulations developed by Rustad, and comparing the resulting animations with lab experiments by Casey, the two found that the behavior of an atom on the surface of the cluster can be affected by an atom some distance away.

Instead of moving through a sequence of transitional forms, as had been assumed, metal oxides interacting with water fall into a variety of “metastable states” — short-lived intermediates, the researchers found.

For example, in one of Rustad’s animations, a water molecule approaches an oxygen atom on the surface of a cluster. The oxygen suddenly pulls away from another atom binding it into the middle of the cluster and leaps to the water molecule. Then the structure collapses back into place, ejecting a spare oxygen atom and incorporating the new one.

Provided by UC Davis (news : web)

Metal oxide simulations could help green technology

 University of California, Davis, researchers have proposed a radical new way of thinking about the chemical reactions between water and metal oxides, the most common minerals on Earth.

Their work appears in the current issue of the journal Nature Materials.

The new paradigm could lead to a better understanding of corrosion and how toxic minerals leach from rocks and soil. It could also help in the development of "green" technology: new types of batteries, for example, or catalysts for splitting water to produce hydrogen fuel.

"This is a global change in how people should view these processes," said William Casey, UC Davis professor of chemistry and co-author of the study with James Rustad, a former geology professor at UC Davis who now works as a scientist at Corning Inc. in New York.

Previously, when studying the interactions of water with clusters of metal oxides, researchers tried to pick and study individual atoms to assess their reactivity. But "none of it really made sense," Rustad said.

Using computer simulations developed by Rustad, and comparing the resulting animations with lab experiments by Casey, the two found that the behavior of an atom on the surface of the cluster can be affected by an atom some distance away.

Instead of moving through a sequence of transitional forms, as had been assumed, metal oxides interacting with water fall into a variety of "metastable states" -- short-lived intermediates, the researchers found.

For example, in one of Rustad's animations, a water molecule approaches an oxygen atom on the surface of a cluster. The oxygen suddenly pulls away from another atom binding it into the middle of the cluster and leaps to the water molecule. Then the structure collapses back into place, ejecting a spare oxygen atom and incorporating the new one.

The U.S. Department of Energy and the National Science Foundation sponsored the research.

Story Source:

The above story is reprinted from materials provided by University of California - Davis.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

James R. Rustad, William H. Casey. Metastable structures and isotope exchange reactions in polyoxometalate ions provide a molecular view of oxide dissolution. Nature Materials, 2012; DOI: 10.1038/nmat3203

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

Liquid can turn into solid under high electric field, physicists show in simulations

Physicists have demonstrated in simulations that under the influence of sufficiently high electric fields, liquid droplets of certain materials will undergo solidification, forming crystallites at temperature and pressure conditions that correspond to liquid droplets at field-free conditions. This electric-field-induced phase transformation is termed electrocrystallization.

The study, performed by scientists at the Georgia Institute of Technology, appears online and is scheduled as a feature and cover article in the 42nd issue of Volume 115 of the Journal of Physical Chemistry C.

"We show that with a strong electric field, you can induce a phase transition without altering the thermodynamic parameters," said Uzi Landman, Regents' and Institute Professor in the School of Physics, F.E. Callaway Chair and director of the Center for Computational Materials Science (CCMS) at Georgia Tech.

In these simulations, Landman and Senior Research Scientists David Luedtke and Jianping Gao at the CCMS set out first to explore a phenomenon described by Sir Geoffrey Ingram Taylor in 1964 in the course of his study of the effect of lightning on raindrops, expressed as changes in the shape of liquid drops when passing through an electric field. While liquid drops under field-free conditions are spherical, they alter their shape in response to an applied electric field to become needle-like liquid drops. Instead of the water droplets used in the almost decade-old laboratory experiments of Taylor, the Georgia Tech researchers focused their theoretical study on a 10 nanometer (nm) diameter liquid droplet of formamide, which is a material made of small polar molecules each characterized by a dipole moment that is more than twice as large as that of a water molecule.

With the use of molecular dynamics simulations developed at the CCMS, which allow scientists to track the evolution of materials systems with ultra-high resolution in space and time, the physicists explored the response of the formamide nano-droplet to an applied electric field of variable strength. Influenced by a field of less than 0.5V/nm, the spherical droplet elongated only slightly. However, when the strength of the field was raised to a critical value close to 0.5 V/nm, the simulated droplet was found to undergo a shape transition resulting in a needle-like liquid droplet with its long axis -- oriented along the direction of the applied field -- measuring about 12 times larger than the perpendicular (cross-sectional) small axis of the needle-like droplet. The value of the critical field found in the simulations agrees well with the prediction obtained almost half a decade ago by Taylor from general macroscopic considerations.

Past the shape transition further increase of the applied electric field yielded a slow, gradual increase of the aspect ratio between the long and short axes of the needle-like droplet, with the formamide molecules exhibiting liquid diffusional motions.

"Here came the Eureka moment," said Landman. "When the field strength in the simulations was ramped up even further, reaching a value close to 1.5V/nm, the liquid needle underwent a solidification phase transition, exhibited by freezing of the diffusional motion, and culminating in the formation of a formamide single crystal characterized by a structure that differs from that of the x-ray crystallographic one determined years ago under zero-field conditions. Now, who ordered that?" he added.

Further analysis has shown that the crystallization transition involved arrangement of the molecules into a particular spatial ordered lattice, which optimizes the interactions between the positive and negative ends of the dipoles of neighboring molecules, resulting in minimization of the free energy of the resulting rigid crystalline needle. When the electric field applied to the droplet was subsequently decreased, the crystalline needle remelted and at zero-field the liquid droplet reverted to a spherical shape. The field reversal process was found to exhibit a hysteresis.

Analysis of the microscopic structural changes that underlie the response of the droplet to the applied field revealed that accompanying the shape transition at 0.5 V/nm is a sharp increase in the degree of reorientation of the molecular electric dipoles, which after the transition lie preferentially along the direction of the applied electric field and coincide with the long axis of the needle-­­like liquid droplet. The directional dipole reorientation, which is essentially complete subsequent to the higher field electrocrystallization transition, breaks the symmetry and transforms the droplet into a field-induced ferroelectric state where it possesses a large net electric dipole, in contrast to its unpolarized state at zero-field conditions.

Along with the large-scale atomistic computer simulations, researchers formulated and evaluated an analytical free-energy model, which describes the balance between the polarization, interfacial tension and dielectric saturation contributions. This model was shown to yield results in agreement with the computer simulation experiments, thus providing a theoretical framework for understanding the response of dielectric droplets to applied fields.

"This investigation unveiled fascinating properties of a large group of materials under the influence of applied fields," Landman said. "Here the field-induced shape and crystallization transitions occurred because formamide, like water and many other materials, is characterized by a relatively large electric dipole moment. The study demonstrated the ability to employ external fields to direct and control the shape, the aggregation phase (that is, solid or liquid) and the properties of certain materials."

Along with the fundamental interest in understanding the microscopic origins of materials behavior, this may lead to development of applications of field-induced materials control in diverse areas, ranging from targeted drug delivery, nanoencapsulation, printing of nanostructures and surface patterning, to aerosol science, electrospray propulsion and environmental science.

This research was supported by a grant from the U.S. Air Force Office of Scientific Research.

Story Source:

The above story is reprinted (with editorial adaptations ) from materials provided by Georgia Institute of Technology.

Journal Reference:

William D. Luedtke, Jianping Gao, Uzi Landman. Dielectric Nanodroplets: Structure, Stability, Thermodynamics, Shape Transitions and Electrocrystallization in Applied Electric Fields. The Journal of Physical Chemistry C, 2011; 110901150249036 DOI: 10.1021/jp206673j

Note: If no author is given, the source is cited instead.

Catching molecular motion at just the right time: Theorists overcome loss of entropy and friction in computational simulations

 University of Oregon researchers have devised a mathematically rich analytic approach to account for often-missing thermodynamic and molecular parameters in molecular dynamic simulations.

The new approach, which returns atomistic-level data into the time frame of the macroscopic world, is detailed in a paper appearing online ahead of regular publication in the journal Physical Review E. The method is all about timing, says Marina G. Guenza, professor of theoretical physical chemistry, and may help reduce trial-and-error experimentation required in manufacturing when such information is missing.

Molecular dynamic simulations are indispensable tools -- a natural partner of experiments and theory -- that help scientists understand the properties of new materials and processes by providing a view at the resolution of atoms. Simulations expedite the development of new materials by showing how those with a specific atomistic structure behave in various conditions, for example when they are strained or frozen.

Simulations of polymers and biological systems have been used since the 1990s. That effort has focused on the short-time motion of macromolecules described in atomistic detail, which, in addition to plastics and glasses, also applies to DNA and proteins, Guenza said.

However, modelers remove critical pieces of information, such as atom-level activity, to scale back simulations to cover only generic components and access longer times in an accessible simulation run. This technique provides helpful but incomplete data about behavioral responses, Guenza said. Simulations in which atomistic information is withheld are called coarse-grained models.

"These are big molecules," she said. "They move slowly. It is difficult to set up a simulation where the atomistic definition is included and still be able to see things happen on the long time scale, which can be really important. Coarse-graining allows one to simulate macromolecules for longer time, but, because some information is eliminated, the motion measured is unrealistically fast."

Entropy -- a loss of thermodynamic energy -- and surface friction are lost in these simulations, she said. Simulations at the atomistic level depict motion occurring in femtoseconds. (A femtosecond is a millionth of a nanosecond; a nanosecond, a billionth of a second.)

To understand what happens in macroscopic systems, you have to look at movement over longer periods of time -- over seconds, says Ivan Lyubimov, a UO doctoral student in chemistry and lead author. "When you try to simulate a second's worth of information at the atomistic level, with all the details included, it might take one or two years for the computer to run the simulation, and you'd still have errors due to numerical algorithms," he said.

Guenza and Lyubimov looked at simulations where thousands of macromolecules of polyethelene are represented as interacting soft particle, i.e. a coarse-grained model, and applied an original theory that refocuses the information missing in the simulations.

Guenza -- a member of the UO's Institute of Theoretical Science, Materials Science Institute and Institute of Molecular Biology -- and Lyubimov first detailed the basics of their theoretical formula in 2010 in the Journal of Chemical Physics.

Their "first-principle" approach looks at the loss of energy, due to the change in entropy, caused by the coarse-graining of the molecule in simulations. Coarse-graining also affects the surface of molecules in simulation, so the formalism accounts for the loss of friction as well.

"We were able to show that if you run your simulation with less detail, we can correct for these factors, and you'll produce the correct motion -- the dynamics -- of the real system," Guenza said. "We have done a lot of tests with different experiments and simulations, and our method works pretty well. No one else has been able to do this with a theoretical solution."

The method, the authors wrote, is different from others currently in use, because it is analytical rather than numerical. It removes the need for separate, time-consuming atomistic simulations to account for missing information obtained from coarse-grained simulations.

"Parameters can be varied for different systems, depending on the molecule size, density and temperature," Lyubimov said. "You can make realistic predictions for the type of material you want to study, at much less expense. You don't have to know all of the details, but you do need a certain number of parameters based on the chemical structure that you want to study."

The National Science Foundation supported the research.

Story Source:

The above story is reprinted (with editorial adaptations ) from materials provided by University of Oregon.

Journal Reference:

I. Lyubimov, M. Guenza. First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids. Physical Review E, 2011; 84 (3) DOI: 10.1103/PhysRevE.84.031801

'Fingerprints' match molecular simulations with reality

A theoretical technique developed at the Department of Energy's Oak Ridge National Laboratory is bringing supercomputer simulations and experimental results closer together by identifying common "fingerprints."

ORNL's Jeremy Smith collaborated on devising a method -- dynamical fingerprints -- that reconciles the different signals between experiments and computer simulations to strengthen analyses of molecules in motion. The research will be published in the Proceedings of the National Academy of Sciences.

"Experiments tend to produce relatively simple and smooth-looking signals, as they only 'see' a molecule's motions at low resolution," said Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at the University of Tennessee. "In contrast, data from a supercomputer simulation are complex and difficult to analyze, as the atoms move around in the simulation in a multitude of jumps, wiggles and jiggles. How to reconcile these different views of the same phenomenon has been a long-standing problem."

The new method solves the problem by calculating peaks within the simulated and experimental data, creating distinct "dynamical fingerprints." The technique, conceived by Smith's former graduate student Frank Noe, now at the Free University of Berlin, can then link the two datasets.

Supercomputer simulations and modeling capabilities can add a layer of complexity missing from many types of molecular experiments.

"When we started the research, we had hoped to find a way to use computer simulation to tell us which molecular motions the experiment actually sees," Smith said. "When we were finished we got much more -- a method that could also tell us which other experiments should be done to see all the other motions present in the simulation. This method should allow major facilities like the ORNL's Spallation Neutron Source to be used more efficiently."

Combining the power of simulations and experiments will help researchers tackle scientific challenges in areas like biofuels, drug development, materials design and fundamental biological processes, which require a thorough understanding of how molecules move and interact.

"Many important things in science depend on atoms and molecules moving," Smith said. "We want to create movies of molecules in motion and check experimentally if these motions are actually happening."

"The aim is to seamlessly integrate supercomputing with the Spallation Neutron Source so as to make full use of the major facilities we have here at ORNL for bioenergy and materials science development," Smith said.

The collaborative work included researchers from L'Aquila, Italy, Wuerzburg and Bielefeld, Germany, and the University of California at Berkeley. The research was funded in part by a Scientific Discovery through Advanced Computing grant from the DOE Office of Science.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by DOE/Oak Ridge National Laboratory.