Biomedical subjects

Stanley I Sandler

Publications and source records attributed to Stanley I Sandler.

At least 19 recordsLinked to original sources

PubMed2007

Storage and separation of CO2 and CH4 in silicalite, C168 schwarzite, and IRMOF-1: a comparative study from Monte Carlo simulation.

Storage of pure CO2 and CH4 and separation of their binary mixture in three different classes of nanostructured adsorbents--silicalite, C168 schwarzite, and IRMOF-1--have been compared at room temperature using atomistic simulation. CH4 is represented as a spherical Lennard-Jones molecule, and CO2 is represented as a rigid linear molecule with a quadrupole moment. For pure component adsorption, CO2 is preferentially adsorbed than CH4 in all the three adsorbents over the pressure range under this study, except in C168 schwarzite at high pressures. The simulated adsorption isotherms and isosteric heats match closely with available experimental data. A dual-site Langmuir-Freundlich equation is used to fit the isotherms satisfactorily. Compared to silicalite and C168 schwarzite, the gravimetric adsorption capacity of pure CH4 and CO2 separately in IRMOF-1 is substantially larger. This implies that IRMOF-1 might be a potential storage medium for CH4 and CO2. For adsorption from an equimolar binary mixture, CO2 is preferentially adsorbed in all three adsorbents. Predictions of mixture adsorption with the ideal-adsorbed solution theory on the basis of only pure component adsorption agree well with simulation results. Though IRMOF-1 has a significantly higher adsorption capacity than silicalite and C168 schwarzite, the adsorption selectivity of CO2 over CH4 is found to be similar in all three adsorbents.

Journal Article↗

PubMed2006

Capillary phase transitions of linear and branched alkanes in carbon nanotubes from molecular simulation.

Capillary phase transitions of linear (from C(1) to C(12)) and branched (C(5) isomers) alkanes in single-walled carbon nanotubes have been investigated using the gauge-cell Monte Carlo simulation. The isotherm at a supercritical temperature increases monotonically with chemical potential and coincides with that from the traditional grand canonical Monte Carlo simulation, whereas the isotherm at a subcritical temperature exhibits a sigmoid van der Waals loop including stable, metastable, and unstable regions. Along this loop, the coexisting phases are determined using an Maxwell equal-area construction. A generic confinement effect is found that reduces the saturation chemical potential, lowers the critical temperature, increases the critical density, and shrinks the phase envelope. The effect is greater in a smaller diameter nanotube and is greater in a nanotube than in a nanoslit.

Journal Article↗

PubMed2006

Free energy of the solid C60 fullerene orientational order-disorder transition.

The free energies of the orientationally ordered crystal phase of C60 at low temperatures and the disordered crystal phase at high temperatures are calculated to an accuracy of +/-0.05 kJ/mol using the expanded ensemble Monte Carlo method with the potential model of Sprik et al. [J. Phys. Chem. 96, 2027 (1992)]. The order-disorder transition temperature at zero pressure is determined directly from these free energies, and is found to be consistent with the abrupt changes in configurational energy and unit cell size also found in simulation. A modification of the potential results in predictions of the transition temperature of 257 K and the entropy change of 18.1 J/mol K at this transition, which are in good agreement with the experimental values of 260 K and 19 J/mol K, respectively. The orientational distinguishability in the ordered phase and the indistinguishability in the disordered phase lead to a contribution to the entropy difference of k ln 60, with 60 being the symmetry number of C60. This quantum mechanical correction is important for the accurate prediction of the phase transition properties of the C60 crystals.

Journal Article↗

PubMed2006

Monte Carlo simulation for the adsorption and separation of linear and branched alkanes in IRMOF-1.

The adsorption and separation of linear and branched alkanes in the isoreticular metal-organic framework IRMOF-1 have been investigated using Monte Carlo simulation. For pure linear alkanes (C1-nC5), the limiting adsorption properties exhibit linear behavior with the alkane carbon number; the long alkane is preferentially adsorbed over the short alkane at low fugacities, whereas the reverse is found at high fugacities. For pure branched alkanes (C5 isomers), the linear isomer adsorbs more than its branched analogue. The adsorbed amounts of pure alkanes in IRMOF-1 are substantially greater than in a carbon nanotube bundle and in silicalite. For a five-component mixture of C1 to nC5 linear alkanes, the long alkane adsorption first increases and then decreases with increasing fugacity, whereas short alkane adsorption continually increases and progressively replaces the long alkane at high fugacity due to the size entropy effect. For a three-component mixture of C5 isomers, the adsorption of each isomer increases with increasing fugacity until saturation, though there is less adsorption of the branched isomer due to the configurational entropy effect. The adsorption selectivity among the alkanes in IRMOF-1 is smaller than in a carbon nanotube bundle and in silicalite.

Journal Article↗

PubMed2006

Mass transport of O2 and N2 in nanoporous carbon (C168 schwarzite) using a quantum mechanical force field and molecular dynamics simulations.

A hierarchical approach is used to calculate the single-component fluxes of N2 and O2 in nanoporous carbon molecular sieves (represented by C168 schwarzite) over a wide range of pressures and pressure drops. The self- and corrected diffusivities are calculated using equilibrium molecular dynamics simulations with force fields for the gas-carbon interactions obtained from quantum mechanical calculations. These results are combined with previously reported adsorption isotherms of N2 and O2 in C168 to obtain transport diffusivities and, by use of the Fick's equation of mass transport, to obtain single-component fluxes across the membrane. The diffusion coefficients and fluxes are also calculated using an empirical potential, which has been obtained by fitting low coverage adsorption data of N2 and O2 on a planar graphite sheet. By analyzing the diffusivities calculated with the ab initio potential in the limit of infinite dilution over the temperature range from 80 to 450 K, it is observed that the N2/O2 separation is energetically driven and a high selectivity of O2 over N2 can be obtained at low temperatures. However, with the empirical potential both the energetic and entropic contributions to selectivity were found to be close to unity. Similarly, by calculating single-component fluxes and ideal selectivities at 300 K and finite pressures it is found that the ab initio potential better explains the large O2/N2 selectivities of similarly sized molecules that have been observed experimentally. An interesting reversal in ideal selectivity is observed by adjusting the pressure at the two ends of the membrane. As a consequence, we predict that a highly selective kinetic separation in favor of either nitrogen or oxygen could be obtained with the same membrane depending on the operating conditions.

Journal Article↗

PubMed2006

Kinetics and equilibria of lysozyme precipitation and crystallization in concentrated ammonium sulfate solutions.

The kinetics and thermodynamics of lysozyme precipitation in ammonium sulfate solutions at pH 4 and 8 and room temperature were studied. X-ray powder diffraction (XRD) was used to characterize the structure of lysozyme precipitates. It was found that, if sufficient time was allowed, microcrystals developed following an induction period after initial lysozyme precipitation, even up to ionic strengths of 8 m and at acidic pH, where lysozyme is refractory to crystallization in ammonium sulfate. The full set of precipitation and crystallization data allowed construction of a phase diagram of lysozyme, showing the ammonium sulfate dependence. It suggests that precipitation may reflect a frustrated metastable liquid-liquid phase separation, which would allow this process to be understood within the framework of the generic phase diagram for proteins. The results also demonstrate that XRD, more frequently used for characterizing inorganic and organic polycrystalline materials, is useful both in characterizing the presence of crystals in the dense phase and in verifying the crystal form of proteins.

Ammonium Sulfate↗

PubMed2006

Air separation by single wall carbon nanotubes: Mass transport and kinetic selectivity.

Mass transport of pure nitrogen, pure oxygen, and their mixture (air) has been studied at 100 K in a single wall carbon nanotube of 12.53 A diameter. Phenomenological coefficients, and self- and corrected diffusivities are calculated using molecular-dynamics simulations, and transport diffusivities are obtained by combining these results with thermodynamic factors obtained from previous grand canonical Monte Carlo simulations [G. Arora and S. I. Sandler, J. Chem. Phys. 123, 044705 (2005)]. For mixtures, cross-term diffusion coefficients are found to be of similar order of magnitude as main-term diffusion coefficients over the entire range of pressure studied. These results are then combined with a continuum description of mass transport to determine the ideal and kinetic separation factors for a nanotube membrane. High permeances are observed for both pure components and the mixture inside the nanotubes. The concentration profiles, diffusivity profiles, and membrane fluxes are calculated, and it is demonstrated that by carefully adjusting the upstream and downstream pressures, a good kinetic selectivity can be achieved for air separation using single wall carbon nanotubes.

Journal Article↗

PubMed2006

Shape versus inverse-shape selective adsorption of alkane isomers in carbon nanotubes.

Simulation results are reported for the adsorption of pure pentane (C5) isomers and their ternary mixture in a series of open-ended armchair-type (m,m) single-walled carbon nanotubes (SWNTs). Inverse-shape selective adsorption occurs in the order of nC5 or=iC5>neoC5 as a result of the configurational entropy effect. In smaller SWNTs, depending on the diameter, only nC5 adsorbs, or no adsorption at all occurs. The entropy effects are found to lead to a large adsorptive separation among the C5 isomers from their mixture. Using the ideal-adsorbed-solution theory with data on the adsorption of only the pure isomers, we predict mixture adsorption. The agreement between predictions and simulations deteriorates with decreasing diameter of the SWNT.

Journal Article↗

PubMed2005

Effects of conformational distributions on sigma profiles in COSMO theories.

The charge density or sigma profile of a solute molecule is an essential component in COSMO (conductor-like screen model) based solvation theories, and its generation depends on the molecular conformation used. The usual procedure is to determine the conformation of an isolated molecule, and assume that this is unchanged when the molecule is placed in solution. In this paper, the conformations of 1-hexanol and 2-methoxy-ethanol in both the liquid and vapor phases obtained from Gibbs ensemble simulation and from an isolated-molecule quantum DFT optimization are used to determine the effect of realistic conformation differences on COSMO-based properties predictions. In particular, the vapor pressure at the normal boiling temperature and the binary mixture VLE (vapor-liquid equilibrium) predictions obtained using different conformations are investigated. The results show that the sigma profile for 1-hexanol varies only slightly using the different conformations, while the sigma profile of 2-methoxy-ethanol shows a significant difference between the liquid and vapor phases. Consequently, the vapor pressure predictions for 1-hexanol are similar regardless of the manner in which the conformation population was obtained, while there is a larger difference for 2-methoxy-ethanol depending on whether the liquid or vapor conformations from simulation or the DFT-optimized structure is used. These differences in predictions are seen to be largely due to differences in the ideal solvation energy term. In mixture VLE calculations involving 1-hexanol, we again see that there is little difference in the phase equilibrium predictions among the different conformations, while for the mixture with 2-methoxy-ethanol, the differences in the sigma profiles lead to a more noticeable, though not significant, difference in the phase equilibrium predictions.

Journal Article↗

PubMed2005

The combined simulation approach of atomistic and continuum models for the thermodynamics of lysozyme crystals.

We have studied the thermodynamic properties of hen egg white lysozyme crystals using a novel simulation method combining atomistic Monte Carlo simulation to calculate van der Waals interactions and the boundary element method to solve the Poisson-Boltzmann equation for the electrostatic interactions. For computational simplicity, we treat the protein as a rigid body, using the crystallographic coordinates of all non-hydrogen atoms of the protein to describe the detailed shape. NVT Monte Carlo simulations are carried out for tetragonal and orthorhombic crystals to obtain the van der Waals energy, incorporating an implicit solvation effect. For crystal phases, an optimally linearized Poisson-Boltzmann equation is used to include the effect of the Donnan equilibrium of the salt ions. The Helmholtz energy is obtained from expanded ensemble Monte Carlo simulations. By using the force field parameters that had previously been tuned for the solution properties, reasonable agreement with experiment is found for the crystallization energy of the tetragonal form. The prediction of the entropy is also reasonable with a slight underestimation suggesting the release of a few water molecules per protein during the crystallization. However, the predictions of the properties of the orthorhombic crystal are poor, probably due to differences in the solvation structure as indicated by experiments, and also as a result of the approximate force field used.

Algorithms↗

PubMed2005

A comparative study of nitrogen physisorption on different C70 crystal structures using an ab initio based potential.

Quantum mechanical calculations are performed using the recently developed hybrid method for interaction energies to determine atom site Lennard-Jones potential parameters for the interactions of molecular nitrogen with C(70) molecules. This ab initio based potential is used in grand canonical Monte Carlo simulations to predict surface adsorption properties of N(2) on five known C(70) structures: rhombohedral, fcc, ideal hcp, deformed hcp, and monoclinic crystals. Because of the presence of five-membered carbon rings and the surface curvature of C(70) molecule, the Lennard-Jones potential parameters for nitrogen-carbon interactions obtained from ab initio based calculations are found to be different from that with planar graphite. The simulation results obtained from these two sets of force fields are compared and shown to differ, particularly at low coverage, where the nitrogen-carbon interactions are more important than the nitrogen-nitrogen interactions. The surface area, monolayer capacity, and isosteric heat of adsorption are calculated for various C(70) crystals and found to change appreciably as a result of the shear-induced phase transformation from hcp to rhombohedral lattice.

Crystallography, X-Ray↗

PubMed2005

Separation of CO2 and N2 by adsorption in C168 schwarzite: a combination of quantum mechanics and molecular simulation study.

Using a hierarchical multiscale approach combining quantum mechanics and molecular simulation, we have investigated the adsorption of pure CO(2) and N(2) and their mixture at room temperature in C(168) schwarzite, as a model for nanoporous carbons. First, the adsorbate-adsorbent interaction potential is determined using ab initio quantum mechanics computations, and then the adsorption is predicted using full atomistic Monte Carlo simulations. The extents of adsorption, adsorption energies, and isosteric heats of pure CO(2) and N(2) simulated with the ab initio potential are found to be higher than those with the empirical Steele potential that had been developed from gas adsorption on planar graphite. The inclusion of the electric quadrupole moment of adsorbate in simulation has no discernible effect on N(2) adsorption but results in a larger extent of CO(2) adsorption at high coverages. The selectivity of CO(2) over N(2) in the C(168) schwarzite from a model flue gas is predicted to be significantly larger with the ab initio potential than with the Steele potential. This illustrates the importance of an accurate adsorbate-adsorbent interaction potential in determining gas adsorption and suggests that nanoporous carbons might be useful for the separation of flue gases. As a comparison, the adsorption and selectivity of CO(2) and N(2) in ZSM-5 zeolites are also simulated with the experimentally validated potential parameters. The selectivity in the C(168) schwarzite predicted with the ab initio or Steele potential is found to be larger than the selectivity in all-silica ZSM-5, but less than that in Na-exchanged ZSM-5 zeolites.

Journal Article↗

PubMed2005

A potential from quantum chemistry for thermodynamic property predictions for methanethiol.

An ab initio potential for methanethiol is determined by computing quantum-chemical interaction energies for a range of orientations and center-of-mass separation distances. These energies are initially fitted to a pairwise-additive, site-site Morse-C6 intermolecular potential. Additional interaction energies were then calculated at separation distances determined to be important from the angle-averaged Mayer f function calculated with the initial potential. This expanded set of interaction energies is then fitted using Boltzmann-type weighting to obtain the final intermolecular potential. Although there are some discrepancies in the fit for a particular type of orientation, the phase behavior calculated from Gibbs ensemble Monte Carlo simulations using this final potential is in very good agreement with experimental data. The prescription used here for obtaining the optimum potential from quantum-chemical methods should be applicable to other systems.

Journal Article↗

PubMed2005

Air separation by single wall carbon nanotubes: thermodynamics and adsorptive selectivity.

Separation of a nitrogen-oxygen mixture (air) by single wall carbon nanotubes has been studied using grand canonical Monte Carlo simulations at a range of nanotube diameters, temperatures, and pressures. It is demonstrated that depending on these operating parameters, the extent of adsorptive selectivity can vary significantly. Detailed calculations are also presented for the adsorption isotherms, energies, and isosteric heats of pure nitrogen, oxygen, and their mixture at 100 K in a carbon nanotube of 12.53-A diameter. In single-component simulations, it is found that near saturation loading nitrogen forms only an annular layer close to the nanotube wall, while smaller-sized oxygen also occupies the region near the center of the nanotube. In mixture adsorption, the energetically favored nitrogen is preferentially adsorbed at low loadings. However, at high loadings oxygen replaces nitrogen due to the dominant entropic effects, and therefore a high selectivity towards oxygen is observed close to the saturation loading. The effect of the entropic change on mixture adsorption is evident from the calculated isosteric heats of adsorption. The mixture isotherms obtained from simulations are found to be in good agreement with the predictions based only on the pure component simulation results.

Journal Article↗

PubMed2005

Hierarchical modeling N2 adsorption on the surface of and within a C60 crystal: from quantum mechanics to molecular simulation.

The adsorption of N(2) on the surface of, and within, a C(60) face-centered cubic crystal has been studied using a hierarchical approach. First, an ab initio potential between N(2) and C(60) is obtained from a recently developed quantum mechanical hybrid method, and then the adsorption behavior is predicted using Monte Carlo simulation. On the crystal surface, N(2) adsorption isotherm at 77.3 K is of type II. The adsorption simulated with the ab initio potential is slightly greater than that with the empirical Steele potential derived from experimental N(2) adsorption on planar graphite, and both are in fairly good agreement with measured results. With increasing pressure, N(2) molecules are found to sequentially occupy three favorable sites: the octahedral sites, the tetrahedral sites, and the top of C(60) molecules. Finally multiple layers form and wetting occurs as the bulk N(2) saturation pressure is reached. The isosteric heat of adsorption exhibits two maxima and finally approaches the enthalpy of vaporization of bulk N(2). Within the crystal, the N(2) adsorption isotherm at 77.3 K is of type I, and the use of ab initio potential leads to significantly greater adsorption than the Steele potential. N(2) molecules are observed to intercalate only the octahedral sites, and the isosteric heat of adsorption is nearly a constant. As in our previous work of N(2) and O(2) adsorption in the C(168) schwarzite (Jiang et al. J. Phys. Chem. B 2004, 108, 9852), this work demonstrates the importance of an accurate adsorbate-adsorbent interaction potential in the determination of gas adsorption behavior.

Journal Article↗

PubMed2004

Nitrogen and oxygen mixture adsorption on carbon nanotube bundles from molecular simulation.

The adsorption of a nitrogen and oxygen mixture (air) on two types of single-walled carbon nanotube bundles at both sub- and supercritical temperatures is studied using grand canonical Monte Carlo molecular simulation. On an infinite periodic hexagonal bundle without an external surface, adsorption at a subcritical temperature is of type I. With increasing pressure, nitrogen adsorption first increases and then decreases until saturation; oxygen adsorption continues increasing, displacing nitrogen, until saturation. Both nitrogen and oxygen first form annuli inside the nanotubes, then with increased coverage they occupy the nanotube centers, and at the highest coverage some oxygen also adsorbs in the interstitial channels between the nanotubes. The selectivity of nitrogen over oxygen decreases with increasing pressure and reaches a constant near saturation. Adsorption at a supercritical temperature is also of type I, with both nitrogen and oxygen adsorption increasing with increasing pressure, though the selectivity of nitrogen to oxygen first increases slightly and then decreases with increasing pressure. On a small isolated hexagonal bundle with an external surface, adsorption at a subcritical temperature is of type II. With increasing pressure, nitrogen adsorption first increases, then decreases, and finally increases again due to wetting by liquid air, while oxygen adsorption increases continually. Both nitrogen and oxygen adsorb first at the internal annuli and at the grooves, and with increasing pressure, they then adsorb at the ridges and at the nanotube centers; at higher pressures, only oxygen adsorbs in the interstitial channels, and multilayer adsorption and wetting occur on the external surface as the bulk phase approaches saturation. The selectivity, like that of subcritical temperature adsorption on the infinite periodic bundle, decreases with increasing pressure and reaches a constant upon wetting. Adsorption at a supercritical temperature is of type I, with both nitrogen and oxygen adsorption increasing with increasing pressure. The selectivity of nitrogen to oxygen, like that of supercritical temperature adsorption on the infinite periodic bundle, first increases slightly and then decreases with increasing pressure. These results indicate that the adsorption selectivity strongly depends on temperature but only weakly depends on the type of the bundle and that a nitrogen--oxygen mixture (air) might be separated by competitive adsorption on the carbon nanotube bundles.

Adsorption↗

PubMed2004

Interatomic Lennard-Jones potentials of linear and branched alkanes calibrated by Gibbs ensemble simulations for vapor-liquid equilibria.

We propose Lennard-Jones potential parameters for interatomic interactions of linear and branched alkanes based on matching the results of Gibbs ensemble simulations of vapor-liquid equilibria to experimental data. The alkane model is similar as in the OPLS-AA, but multiple atom types for carbon based on the number of covalently bonded hydrogen atoms are necessary to accurately reproduce liquid densities and enthalpies of vaporization with the errors of 2.1% and 3.3%, respectively, for hydrocarbons of various chain lengths and structures. We find that the attraction energies of the carbon atoms are almost proportional to the number of covalent hydrogen atoms with each increasing the carbon energy parameter by approximately 0.033 kcal/mol. Though the present force field outperforms the OPLS-AA force field for alkanes we studied, systematic deviations for vapor pressures are still observed with errors of 15%-30%, and critical temperatures are slightly underestimated. We think that these shortcomings are probably due to the inadequacy of the two-parameter Lennard-Jones potential, and especially its behavior at short distances.

Journal Article↗

PubMed2004

Correlation of diafiltration sieving behavior of lysozyme-BSA mixtures with osmotic second virial cross-coefficients.

The role of protein-protein interactions in membrane separations of protein mixtures remains incompletely understood, largely due to the difficulty of characterizing protein self- and, especially, cross-association. Recently, a novel technique, cross-interaction chromatography, has been developed to measure weak protein cross-association in terms of the osmotic second virial cross-coefficient. In this work the relationship between protein cross-association and the sieving behavior of lysozyme in the presence of BSA has been investigated. Sieving coefficients were measured using a stirred diafiltration cell over a range of pH and ionic strength, and a striking correlation between the lysozyme sieving and second virial cross-coefficients for BSA/lysozyme mixtures has been found: when the protein cross-interactions are most attractive (negative second virial cross-coefficient), the lysozyme sieving coefficients are lowest, and vice versa. The correlation between the sieving and second virial cross-coefficients may be due to the physically similar environments in the chromatography and filtration experiments since one protein is passed through a concentrated region of the second protein either immobilized on the column or accumulated at the membrane surface, and the migration rate of the mobile protein in both cases is influenced by protein cross-association. This study represents the first time that molecular interactions in binary mixtures have been related directly to filtration behavior, and may provide a useful approach to optimize the separation of other binary protein mixtures.

Complex Mixtures↗