PubMed Health⌕ Search

Biomedical subjects

David S Sholl

Publications and source records attributed to David S Sholl.

At least 19 recordsLinked to original sources
PubMed2006

Molecular dynamics simulations of mass transfer resistance in grain boundaries of twinned zeolite membranes.

The net mass transfer resistance for gas molecules permeating through zeolite membranes includes contributions from intracrystalline diffusion and contributions from interfacial effects. These interfacial effects can arise either from gas-zeolite interfaces or from interfaces that exist within zeolite crystals due to grain boundaries. We present the first atomically detailed simulations that examine interfacial mass transfer resistance due to internal grain boundaries in zeolites that are relevant for membrane applications. Our calculations examine twinned silicalite crystals in crystallographic configurations that have been identified in previous experiments. We used the dual control volume grand canonical molecular dynamics method to simulate the permeance of CH(4) and CF(4) through thin twinned silicalite crystals. The magnitudes of the grain boundary resistances are quite substantial, at least for the thin crystals that are accessible in our simulations.

Journal Article↗
PubMed2006

Structures of dense glycine and alanine adlayers on chiral Cu(3,1,17) surfaces.

Density Functional Theory calculations have been used to predict the structures of dense glycine and alanine adlayers on Cu(3,1,17)(S). Facets of this chiral Cu surface result from adsorbate-induced surface reconstruction when glycine or alanine are adsorbed and annealed on Cu(100). We have calculated the surface energy changes associated with this surface reconstruction. Our results allow the enantiospecificity of this reconstruction following adsorption of enantiopure or racemic alanine on Cu(100) to be discussed. The overall stability of glycine and alanine adlayers on Cu(3,1,17)(S) arises from an interplay between the formation of chemical bonds with the Cu surface, deformations in the adsorbed molecules during adsorption, and intermolecular hydrogen bonds within the adlayer; none of these factors individually dominates.

Alanine↗
PubMed2006

Identification of destabilized metal hydrides for hydrogen storage using first principles calculations.

Hydrides of period 2 and 3 elements are promising candidates for hydrogen storage but typically have heats of reaction that are too high to be of use for fuel cell vehicles. Recent experimental work has focused on destabilizing metal hydrides through alloying with other elements. A very large number of possible destabilized metal hydride reaction schemes exist. The thermodynamic data required to assess the enthalpies of these reactions, however, are not available in many cases. We have used first principles density functional theory calculations to predict the reaction enthalpies for more than 100 destabilization reactions that have not previously been reported. Many of these reactions are predicted not be useful for reversible hydrogen storage, having calculated reaction enthalpies that are either too high or too low. More importantly, our calculations identify five promising reaction schemes that merit experimental study: 3LiNH(2) + 2LiH + Si --> Li(5)N(3)Si + 4H(2), 4LiBH(4) + MgH(2) --> 4LiH + MgB(4) + 7H(2), 7LiBH(4) + MgH(2) --> 7LiH + MgB(7) + 11.5H(2), CaH(2) + 6LiBH(4) --> CaB(6) + 6LiH + 10H(2), and LiNH(2) + MgH(2) --> LiMgN + 2H(2).

Journal Article↗
PubMed2006

Testing predictions of macroscopic binary diffusion coefficients using lattice models with site heterogeneity.

Quantitatively predicting mass transport rates for chemical mixtures in porous materials is important in applications of materials such as adsorbents, membranes, and catalysts. Because directly assessing mixture transport experimentally is challenging, theoretical models that can predict mixture diffusion coefficients using only single-component information would have many uses. One such model was proposed by Skoulidas, Sholl, and Krishna (Langmuir, 2003, 19, 7977), and applications of this model to a variety of chemical mixtures in nanoporous materials have yielded promising results. In this paper, the accuracy of this model for predicting mixture diffusion coefficients in materials that exhibit a heterogeneous distribution of local binding energies is examined. To examine this issue, single-component and binary mixture diffusion coefficients are computed using kinetic Monte Carlo for a two-dimensional lattice model over a wide range of lattice occupancies and compositions. The approach suggested by Skoulidas, Sholl, and Krishna is found to be accurate in situations where the spatial distribution of binding site energies is relatively homogeneous, but is considerably less accurate for strongly heterogeneous energy distributions.

Journal Article↗
PubMed2006

First-principles studies of chiral step reconstructions of Cu(100) by adsorbed glycine and alanine.

Adsorption of amino acids on Cu(100) is known experimentally to induce surface reconstructions featuring intrinsically chiral Cu(3,1,17) facets, but no information about the geometry of the molecules on these chiral facets is available. We present density-functional theory calculations for the structure of glycine and alanine at moderate coverages on Cu(3,1,17). As might be expected, molecules prefer to bind at the step edges on this surface rather than on the surface's (100)-oriented terraces. The adsorption of enantiopure alanine on Cu(3,1,17) is predicted to be weakly enantiospecific, with S-alanine being more stable on Cu(3,1,17)(S) than R-alanine. By comparing the surface energies of Cu(100) and Cu(3,1,17) in the presence of adsorbed glycine or alanine, our calculations provide insight into the driving force for chiral reconstructions of Cu(100) by amino acids.

Absorption↗
PubMed2006

Transport diffusion of gases is rapid in flexible carbon nanotubes.

Molecular dynamics simulations of rigid, defect-free single-walled carbon nanotubes have previously suggested that the transport diffusivity of gases adsorbed in these materials can be orders of magnitude higher than any other nanoporous material (A. I. Skoulidas et al., Phys. Rev. Lett. 2002, 89, 185901). These simulations must overestimate the molecular diffusion coefficients because they neglect energy exchange between the diffusing molecules and the nanotube. Recently, Jakobtorweihen et al. have reported careful simulations of molecular self-diffusion that allow nanotube flexibility (Phys. Rev. Lett. 2005, 95, 044501). We have used the efficient thermostat developed by Jakobtorweihen et al. to examine the influence of nanotube flexibility on the transport diffusion of CH4 in (20,0) and (15,0) nanotubes. The inclusion of nanotube flexibility reduces the transport diffusion relative to the rigid nanotube by roughly an order of magnitude close to zero pressure, but at pressures above about 1 bar the transport diffusivities for flexible and rigid nanotubes are very similar, differing by less than a factor or two on average. Hence, the transport diffusivities are still extremely large compared to other known materials when flexibility is taken into account.

Journal Article↗
PubMed2006

Adsorption and diffusion of carbon dioxide and nitrogen through single-walled carbon nanotube membranes.

We have used atomically detailed simulations to examine the adsorption and transport diffusion of CO2 and N2 in single-walled carbon nanotubes at room temperature as a function of nanotube diameter. Linear and spherical models for CO2 are compared, showing that representing this species as spherical has only a slight impact in the computed diffusion coefficients. Our results support previous predictions that transport diffusivities of molecules inside carbon nanotubes are extremely rapid when compared with other porous materials. By examining carbon nanotubes as large as the (40,40) nanotube, we are able to compare the transport rates predicted by our calculations with recent experimental measurements. The predicted transport rates are in reasonable agreement with experimental observations.

Journal Article↗
PubMed2006

First principles study of adsorption and dissociation of CO on W(111).

The adsorption and dissociation of carbon monoxide on the W(111) surface is studied with density functional theory. The CO molecule is found to adsorb in end-on configurations (alpha states) and inclined configurations (beta states). The dissociation of the most strongly bound beta state CO is found to have an activation energy of about 0.8 eV, which is lower than the energy required to desorb CO molecularly from the surface. The diffusion of CO and O on W(111) is predicted to be facile at room temperature, whereas C atoms are virtually immobile up to approximately 600 K, according to our calculations. Preadsorbed carbon atoms are shown to prevent the dissociation of CO by blocking the most strongly bound beta state adsorption site and by blocking the dissociation pathway. We predict that dissociation of CO on W(111) is a self-poisoning process.

Journal Article↗
PubMed2006

Efficient simulation of binary adsorption isotherms using transition matrix Monte Carlo.

Molecular simulations of binary adsorption in porous materials are a useful complement to experimental studies of mixture adsorption. Most molecular simulations of binary adsorption are performed using grand canonical Monte Carlo (GCMC) to independently examine a range of state points of interest. A disadvantage of this approach is that it only yields information at a discrete set of state points; therefore, if a complete isotherm is required for arbitrary conditions, some type of data fitting or interpolation must be used in combination with the GCMC data. We show that the transition matrix Monte Carlo (TMMC) method of Shen and Errington (Shen, V. K.; Errington, J. R. J. Chem.Phys. 2005, 122, 064508) is well-suited to simulation of binary adsorption in porous materials. At the completion of a TMMC simulation, the adsorption isotherm for all possible bulk phase compositions and pressures is available without data fitting or interpolation. It is also straightforward to use results from TMMC to compute derivatives of the isotherm such as the mixture thermodynamic correction factors, partial differential ln f(i)/partial differential ln c(j), again without data fitting or interpolation. This approach should be useful in contexts where information on the full adsorption isotherm is needed, such as the design of adsorption- or membrane-based separations.

Journal Article↗
PubMed2006

Understanding macroscopic diffusion of adsorbed molecules in crystalline nanoporous materials via atomistic simulations.

The diffusion rates of molecules inside nanoporous materials lie at the heart of many large-scale industrial applications of these materials. Quantitatively describing this diffusion, particularly diffusion of chemical mixtures in situations leading to net mass transport, remains challenging. Molecular dynamics (MD) simulations can play an important complementary role to experiments in this area. This Account describes applications of MD to diffusion in nanoporous materials with a particular focus on macroscopic diffusion, that is, diffusion involving mass transport. These methods have made useful contributions to developing mixing theories for predicting multicomponent diffusion from single-component data and to screening new classes of materials for practical applications.

Journal Article↗
PubMed2006

Influences of interfacial resistances on gas transport through carbon nanotube membranes.

Carbon nanotubes have significant promise as gas separation membranes. Gas permeation through nanopores involves mass transfer resistances from molecules entering and leaving pores (so-called surface resistances) and diffusion within the pores. We use molecular simulations to give the first estimates of surface resistances for gas transport through nanotubes. For CH4 transport through (20,0) carbon nanotubes at 300 K, surface resistances are small for nanotubes 5-10 mum in length but can be significant for shorter nanotubes.

Computer Simulation↗
PubMed2005

Structures of glycine, enantiopure alanine, and racemic alanine adlayers on Cu(110) and Cu(100) surfaces.

We have determined the structures of dense adlayers of glycine and alanine on the Cu(110) and Cu(100) surfaces using plane wave density functional theory. These calculations resolve several experimental controversies regarding these structures. Glycine exists on Cu(110) as a single adlayer structure, while on Cu(100) two distinct glycine adlayers coexist. The glycine structures serve as useful starting points for constructing alanine adlayer structures. We considered separately the adsorption of enantiopure alanine and racemic alanine on each surface. Adlayers of enantiopure alanine are found to be closely related to the adlayers observed for glycine. Racemic alanine adlayers on Cu(110) are structurally analogous to those observed for glycine on this surface and adopt a pseudo-racemate ordering. On Cu(100), in contrast to glycine, racemic alanine is found to adopt a single adlayer structure that is an ordered racemate. Spontaneous segregation of molecular enantiomers does not occur in racemic adsorbed mixtures on either surface. Consideration of the orientationally distinct domains that may exist for each adlayer on these surfaces provides important information for the interpretation of the adlayer domain boundaries that are commonly observed in scanning tunneling microscopy images of amino acid adlayers. Examining this set of amino acid adlayers provides useful insight into the range of subtle behaviors that can arise in these and related systems where chiral molecules form ordered adlayers on flat metal surfaces.

Journal Article↗
PubMed2005

Self-diffusion and transport diffusion of light gases in metal-organic framework materials assessed using molecular dynamics simulations.

Metal-organic framework (MOF) materials pose an interesting alternative to more traditional nanoporous materials for a variety of separation processes. Separation processes involving nanoporous materials can be controlled by either adsorption equilibrium, diffusive transport rates, or a combination of these factors. Adsorption equilibrium has been studied for a variety of gases in MOFs, but almost nothing is currently known about molecular diffusion rates in MOFs. We have used equilibrium molecular dynamics (MD) to probe the self-diffusion and transport diffusion of a number of small gas species in several MOFs as a function of pore loading at room temperature. Specifically, we have studied Ar, CH4, CO2, N2, and H2 diffusion in MOF-5. The diffusion of Ar in MOF-2, MOF-3, and Cu-BTC has been assessed in a similar manner. Our results greatly expand the range of MOFs for which data describing molecular diffusion is available. We discuss the prospects for exploiting molecular transport properties in MOFs in practical separation processes and the future role of MD simulations in screening families of MOFs for these processes.

Journal Article↗
PubMed2005

Chemisorption and diffusion of hydrogen on surface and subsurface sites of flat and stepped nickel surfaces.

Plane-wave density functional theory calculations were performed to investigate the binding and diffusion of hydrogen on three flat Ni surfaces, Ni(100), Ni(110), and Ni(111), and two stepped Ni surfaces, Ni(210) and Ni(531). On each surface, the favored adsorption sites were identified by considering the energy and stability of various binding sites and zero-point energy corrections were computed. Binding energies are compared with experimental and theoretical results from the literature. Good agreement with experimental and previous theoretical data is found. At surface coverages where adsorbate-adsorbate interactions are relatively weak, the binding energy of H is similar on the five Ni surfaces studied. Favorable binding energies are observed for stable surface sites, while subsurface sites have unfavorable values relative to the gas phase molecular hydrogen. Minimum energy paths for hydrogen diffusion on Ni surfaces and into subsurface sites were constructed.

Journal Article↗
PubMed2005

Predictive assessment of surface resistances in zeolite membranes using atomically detailed models.

The diffusive transport of molecules through nanoporous membranes is determined by both intracrystalline diffusion and mass transport resistances associated with entering and leaving the membrane material. We compare two methods for assessing the relative importance of these resistances based on atomically detailed descriptions of the membrane material. For extremely thin membranes, net transport can be assessed using dual control volume grand canonical molecular dynamics (DCV-GCMD). We show that previous implementations of this technique may have been influenced by nonisothermal effects in interfacial regions and suggest a simple remedy to this situation. We also introduce an approximate method that uses information only from equilibrium MD simulations, which avoids the significant computational expense associated with DCV-GCMD. This approximate method can be used to rapidly assess the importance of interface-related resistances to mass transport over broad ranges of membrane operating conditions. This method will be useful in allowing a rapid determination of whether these interface resistances are significant in practical experimental situations. These two methods are compared by considering the transport of CH(4) and CF(4) through defect-free silicalite membranes.

Journal Article↗
PubMed2005

TCE dechlorination rates, pathways, and efficiency of nanoscale iron particles with different properties.

Nanoscale Fe0 particles are a promising technology for in situ remediation of trichloroethene (TCE) plumes and TCE-DNAPL source areas, butthe physical and chemical properties controlling their reactivity are not yet understood. Here, the TCE reaction rates, pathways, and efficiency of two nanoscale Fe0 particles are measured in batch reactors: particles synthesized from sodium borohydride reduction of ferrous iron (Fe/B) and commercially available particles (RNIP). Reactivity was determined under iron-limited (high [TCE]) and excess iron (low [TCE]) conditions and with and without added H2. Particle efficiency, defined as the fraction of the Fe0 in the particles that is used to dechlorinate TCE, was determined under iron-limited conditions. Both particles had a core/shell structure and similar specific surface areas (approximately 30 m2/g). Using excess iron, Fe/B transformed TCE into ethane (80%) and C3-C6 coupling products (20%). The measured surface area normalized pseudo-first-order rate constant for Fe/B (1.4 x 10(-)2 L.h(-1).m(-2) is approximately 4-fold higher than for RNIP (3.1 x 10-(3) L.h(-1).m(-2). All the Fe0 in Fe/B was accessible for TCE dechlorination, and 92 +/- 0.7% of the Fe0 was used to reduce TCE. For Fe/B, H2 evolved from reduction of water (H+) was subsequently used for TCE dechlorination, and adding H2 to the reactor increased both the dechlorination rate and the mass of TCE reduced, indicating that a catalytic pathway exists. RNIP yielded unsaturated products (acetylene and ethene). Nearly half (46%) of the Fe0 in RNIP was unavailable for TCE dechlorination over the course of the experiment and remained in the particles. Adding H2 did not change the reaction rate or efficiency of RNIP. Despite this, the mass of TCE dechlorinated per mass of Fe0 added was similar for both particles due to the less saturated products formed from RNIP. The oxide shell composition and the boron content are the most likely causes for the differences between the particle types.

Catalysis↗