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Experimental studies have reported that glycine is adsorbed on the Cu(110) and Cu(100) surfaces in its deprotonated form at room temperature, but in its zwitterionic form on Pd(111) and Pt(111). In contrast, recent density functional theory (DFT) calculations indicated that the deprotonated molecules are thermodynamically favored on Cu(110), Cu(100), and Pd(111). To explore the source of this disagreement, we have tested three possible hypotheses. Using DFT calculations, we first show that the kinetic barrier for the deprotonation reaction of glycine on Pd(111) is larger than on Cu(110) or Cu(100). We then report that the presence of excess hydrogen would have little influence on the experimentally observed results, especially for Pd(111). Lastly, we perform Monte Carlo simulations to demonstrate that the aggregates of zwitterionic species on Pt(111) are energetically preferred to those of neutral species. Our results strongly suggest that the formation of aggregates with relatively large numbers of adsorbed molecules is favored under experimentally relevant conditions and that the adsorbate-adsorbate interactions in these aggregates stabilize the zwitterionic species. [ABSTRACT FROM AUTHOR]

Osmotic framework adsorbed solution theory is a useful molecular simulation method to predict the evolution of structural transitions upon adsorption of guest molecules in flexible nanoporous solids. One challenge with previous uses of this approach has been the estimation of free energy differences between the solid phases of interest in the absence of adsorbed molecules. Here we demonstrate that these free energy differences can be calculated without reference to experimental data via the vibrational density of states of each phase, a quantity that can be obtained from molecular dynamics simulations. We show the applicability of this method through case studies of the swelling behaviors of two representative systems in which swelling upon adsorption of water is of importance: single-walled aluminosilicate nanotube bundles and cesium montmorillonite. The resulting predictions show that the aluminosilicate nanotube bundles swell significantly with increasing interstitial adsorption and that the layer spacing of cesium montmorillonite expands up to about 12.5 Å, giving good agreement with experiments. The method is applicable to a wide range of flexible nanoporous materials, such as zeolites, metal-organic frameworks, and layered oxide materials, when candidate structures can be defined and a force field to describe the material is available. [ABSTRACT FROM AUTHOR]

Chemical interactions of H2O, CO, NO, pyridine, C2H2, H2S, and NH3 with open metal sites in the metal-organic framework (MOF) Cu3(benzenetricarboxylate)2 are examined using plane wave periodic density functional theory (DFT). In the case of single molecule adsorption on a Cu dimer, NH3 and pyridine have the strongest binding, while NO binds weakly. Binding of pairs of molecules on a Cu dimer shows significant interaction energies, that is, the binding energy of the pair of molecules is not a simple summation of the binding energies of each molecule. The effect of molecular adsorption on the magnetic moments of Cu atoms in the MOF is also examined. Using the binding energies from DFT calculations, the effects of the pressure and temperature on the chemisorbed species are investigated. Finally the effect of water adsorption on the elastic behavior of Cu3(BTC)2 is described. [ABSTRACT FROM AUTHOR]

Diffusion of interstitial hydrogen plays a key role in potential uses for amorphous metals as membranes for hydrogen purification. We show how first principles-based methods can be used to characterize diffusion of interstitial H in amorphous metals using amorphous Fe3B as an example. Net transport of interstitial H is governed by the transport diffusion coefficient that appears in Fick’s law. This diffusion coefficient is strongly dependent on the interstitial concentration, and is not equal to the self-diffusion coefficient except at dilute interstitial concentrations. Under conditions of practical interest, the concentrations of interstitial H in amorphous metals are nondilute so methods to determine the transport diffusion coefficient must be used if net mass transport is to be described. We show how kinetic Monte Carlo simulations of interstitial H diffusion that use rates derived from first-principles calculations can be used to assess both self- and transport diffusion coefficients of H in amorphous metals. These methods will be helpful in efforts to screen amorphous metal alloys as potential membranes for hydrogen purification. [ABSTRACT FROM AUTHOR]

Highly stepped metal surfaces can define intrinsically chiral structures and these chiral surfaces can potentially be used to separate chiral molecules. The decoration of steps on these surfaces with additional metal atoms is one potential avenue for improving the enantiospecificity of these surfaces. For a successful step decoration, the additional metal atoms should ideally remain at the kinked step sites on the surface. We performed density functional theory (DFT) calculations to identify pairs of metal adatoms and metal surfaces where this kind of step decoration could be thermodynamically stable. These calculations have identified multiple stable examples of step decoration. Using our DFT results, we developed a model to predict surface segregation on a wide range of stepped metal surfaces. With this model, we have estimated the stability of step decoration without further DFT calculations for surface segregation for all combinations of the 3d, 4d, and 5d metals. [ABSTRACT FROM AUTHOR]

First-principles calculations offer a useful complement to experimental approaches for characterizing hydrogen permeance through dense metal membranes. A challenge in applying these methods to disordered alloys is to make quantitative predictions for the net solubility and diffusivity of interstitial H based on the spatially local information that can be obtained from first-principles calculations. In this study, we used a combination of density functional theory calculations and a cluster expansion method to describe interstitial H in alloys of composition Pd96M4, where M=Ag, Cu, and Rh. The cluster expansion approach highlights the shortcomings of simple lattice models that have been used in the past to study similar systems. We use Sieverts’ law to calculate H solubility and a kinetic Monte Carlo scheme to find the diffusivity of H in PdAg, PdCu, and PdRh alloys at a temperature range of 400≤=T≤=1200 K. From these results, we are able to predict the permeability of hydrogen through membranes made from these Pd-based binary alloys. [ABSTRACT FROM AUTHOR]

Surfaces of simple fcc metals such as Cu with nonzero and unequal Miller indices are intrinsically chiral. Density functional theory (DFT) calculations are a useful way to study the enantiospecific adsorption of small chiral molecules on these chiral metal surfaces. We report DFT calculations of seven chiral molecules on several structurally distinct chiral Cu surfaces. These surfaces include two surfaces with (111)-oriented terraces and one with (100)-oriented terraces. Calculations are also described on a surface that was modified to mimic the surface structures that typically appear on real metal surfaces following thermally driven fluctuations in step edges. Our results provide initial information on how variation in the surface structure of intrinsically chiral metal surfaces can affect the enantiospecific adsorption of small molecules on these surfaces. [ABSTRACT FROM AUTHOR]

Plane wave density functional theory calculations have been used to characterize the transition states for β-hydride elimination of ethyl on Cu(100), Cu(110), Cu(111), and Cu(221). The reaction rates predicted by these calculations have been compared to experiments by including tunneling corrections within harmonic transition state theory. Tunneling corrections are found to be important in describing the peak temperatures observed using temperature programed desorption experiments on Cu(110), Cu(111), and Cu(221). Once these corrections are included, the effective activation energies obtained from our calculations are in good agreement with previous experimental studies of this reaction on these four Cu surfaces. The transition states determined in our calculations are used to examine two general hypotheses that have been suggested to describe structure sensitivity in metal-catalyzed surface reactions. [ABSTRACT FROM AUTHOR]

Optimization of enantioselectivity in heterogeneous catalysis and chiral chromatography is a challenging task for the production of enantiopure chemicals. Enantioselective adsorbents usually consist of a surface with chiral receptors being either chiral molecules linked to the surface or chiral pockets formed by molecular templating of the surface. In both cases, the enantioselectivity is controlled mainly by the strength of the receptor-enantiomer interaction, such that one-to-one correspondence is usually preserved. The authors use Monte Carlo calculations to show that this steric requirement is not a necessary condition for the effective separation of chiral molecules. In particular, they propose a way in which a chiral surface can be constructed by a suitable spatial distribution of active sites for which the classical concept of a chiral receptor is no longer useful. Their calculations indicate that the effectiveness of the separation is affected mainly by the difference in shape of the adsorption energy distribution functions corresponding to the enantiomers. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The adsorption of atomic oxygen and carbon was studied with plane wave density functional theory on four Ni surfaces, Ni(110), Ni(111), Ni(210), and Ni(531). Various adsorption sites on these surfaces are examined in order to identify the most favorable adsorption site for each atomic species. The dependence of surface bonding on adsorbate coverage is also investigated. Adsorption energies and structural information are obtained and compared with existing experimental results for Ni(110) and Ni(111). In addition, activation barriers to CO dissociation have been determined on Ni(111) and Ni(531) by locating the transition states for these processes. Our results indicate that the binding energies of C are comparatively stronger on stepped surfaces than on flat surfaces, and the energy barriers associated with CO dissociation strongly favor reactions occurring near surface steps. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We use density functional theory to investigate Pt growth on SrTiO[sub 3](100) surfaces. We have determined the favored monolayer arrangement for Pt on both terminations of SrTiO[sub 3](100). The work of separation as a function of the number of monolayers of Pt has been determined for Pt films of up to 5 monolayers. To examine which surface growth mode will dominate Pt film growth on this substrate, we have also examined isolated Pt clusters on each termination of SrTiO[sub 3](100). Our results indicate that the TiO[sub 2]-terminated surface is more favorable for epitaxial growth of (100) oriented Pt films than the SrO-terminated surface. [ABSTRACT FROM AUTHOR]

Adsorption isotherms of hydrogen isotopes from molecular simulations in carbon nanotubes and interstices are presented. The adsorption of pure isotopes follows Henry’s law up to moderate coverages. A modified path integral grand canonical Monte Carlo (PI-GCMC) technique for mixture adsorption is presented and applied to adsorption of isotope mixtures in carbon nanotubes. Adsorption isotherms of H[sub 2]–T[sub 2] mixtures in nanotubes and interstices are determined at 20 and 77 K. Selectivities for T[sub 2] over H[sub 2] are calculated over a range of pressures. Selectivity in the nanotubes and interstices increases with pressure until the nanotube is saturated. Comparison of simulation results with predictions based on ideal adsorbed solution theory (IAST) shows good agreement up to moderate loadings. At higher loadings, selectivities determined from multicomponent simulations remain roughly constant, whereas IAST predicts continued increase in selectivities. Isotherms for H[sub 2]–D[sub 2] and the selectivities of D[sub 2] over H[sub 2] are determined for adsorption in (10,10) nanotubes and in the interstitial channels of closed (10,10) nanotubes. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A study was conducted to demonstrate the application of an efficient computational models to evaluate large numbers of metal-organic frameworks (MOFs) for kinetic separations of light gases based on finding materials with large differences between the diffusion coefficients of adsorbed gas species. The study identified a significant number of materials that are predicted to have extraordinary properties for separation of gases such as C[O.sub.2], C[H.sub.4], and [H.sub.2].

Molecular simulations are used for describing the diffusion of C[O.sub.2] and C[H.sub.4] inside the silica zeolite DDR pores. The studies have shown that DDR membranes are favorable for C[O.sub.2]/C[H.sub.4] separations and also similar properties are present for other 8MR zeolites.

Applications of molecular dynamics (MD) were described to diffusion in nanoporous materials with a particular focus on macroscopic diffusion. It was found that these methods made useful contributions to developing mixing theories for predicting multicomponent diffusion from single-component data and to screening new classes of material for practical applications.

A study was carried out to determine the diffusive transport of molecules through nanoporous membranes by both intracrystalline diffusion and mass transport resistances associated with entering and leaving the membrane material. This study introduces an approximate method that uses information only from equilibrium MD simulations, which avoids the significant computational expense associated with dual control volume grand canonical molecular dynamics (DCV-GCMD).