Biomedical subjects

Alexandra Simperler

Publications and source records attributed to Alexandra Simperler.

6 recordsLinked to original sources

PubMed2006

Glass transition temperature of glucose, sucrose, and trehalose: an experimental and in silico study.

Isothermal-isobaric molecular dynamics simulations are used to calculate the specific volume of models of different amorphous carbohydrates (glucose, sucrose, and trehalose) as a function of temperature. Plots of specific volume vs temperature exhibit a characteristic change in slope when the amorphous systems change from the glassy to the rubbery state. The intersection of the regression lines of data below (glassy state) and above (rubbery state) the change in slope provides the glass transition temperature (T(g)). These predicted glass transition temperatures are compared to experimental T(g) values as obtained from differential scanning calorimetry measurements. As expected, the predicted values are systematically higher than the experimental ones (about 12-34 K) as the cooling rates of the modeling methods are about a factor of 10(12) faster. Nevertheless, the calculated trend of T(g) values agrees exactly with the experimental trend: T(g)(glucose) < T(g)(sucrose) < T(g)(trehalose). Furthermore, the relative differences between the glass transition temperatures were also computed precisely, implying that atomistic molecular dynamics simulations can reproduce trends of T(g) values in amorphous carbohydrates with high quality.

Biophysics↗

PubMed2006

Adsorption of methanol on zeolites X and Y. An atomistic and quantum chemical study.

The adsorption of methanol on basic zeolites X and Y was investigated with both atomistic and quantum chemical methods. The Monte Carlo docking method was used to localize preferred adsorption sites within the framework. Sites were found adjacent to the interstitial alkali cations in the sites SI, SII, and SIII. We investigated the influence on adsorption behavior of all possible interstitial alkali metal cations, i.e., Li(+), Na(+), K(+), Rb(+), and Cs(+), and in the case of site SII also the influence of varying the Si/Al ratio and distribution. Clusters were cut from the periodic framework in a way that the topological character of the different sites was preserved. DFT calculations yielded geometries and energetic data, which are analyzed with respect to the nature of the cation and to the Si/Al ratio. Adsorption of the methanol molecule is influenced mainly by the identity of the alkali metal cation. Other factors, including Si/Al ratio, are of secondary importance, though there is evidence of weak hydrogen bonding between methanol hydrogen and framework. Cation positions are displaced only slightly by interaction with methanol, although somewhat more at the SIII sites than the SII. We propose that the SIII sites may be a more likely location for methanol activation, particularly in the reaction with toluene, which favors the SII site.

Journal Article↗

PubMed2005

Tetrahedral distortion and energetic packing penalty in "zeolite" frameworks: linked phenomena?

We report a computational study on the distortion of SiO4 tetrahedra in zeolite frameworks. For all previously observed frameworks, the tetrahedral mismatch was found to span a narrow range (1.0 x 10(-3) to 2.5 x 10(-2) angstroms2) of values, in contrast to the hypothetical frameworks, which were calculated to have a much wider range of mismatch values. The energy of the frameworks was not found to be a function of the tetrahedral distortion for the previously observed and moderately distorted (tetrahedral mismatch <2.5 x 10(-2) angstroms2) hypothetical frameworks. In contrast, the energy of the bulk of the hypothetical frameworks was shown to be a strong function of the tetrahedral distortion. The fact that the framework energies of some hypothetical frameworks lie much higher than both those of the observed frameworks and the values we would expect from our previously developed topological method (the so-called energetic packing penalty) is explained in terms of the tetrahedral distortion contribution to the framework energy which is negligible for the observed frameworks. Finally, it is hypothesized that the absence of tetrahedral distortion is pivotal for a framework to be experimentally realized, in which case a large fraction of hypothetical frameworks are unrealizable and will forever remain in the realms of the abstract.

Letter↗

PubMed2005

Hypothetical binodal zeolitic frameworks.

Hypothetical binodal zeolitic structures (structures containing two kinds of tetrahedral sites) were systematically enumerated using tiling theory and characterized by computational chemistry methods. Each of the 109 refineable topologies based on "simple tilings" was converted into a silica polymorph and its energy minimized using the GULP program with the Sanders-Catlow silica potential. Optimized structural parameters, framework energies relative to alpha-quartz and volumes accessible to sorption have been calculated. Eleven of the 30 known binodal topologies listed in the Atlas of Zeolite Framework Types were found, leaving 98 topologies that were unknown previously. The chemical feasibility of each structure as a zeolite was evaluated by means of a feasibility factor derived from the correlation between lattice energy and framework density. Structures are divided into 15 families, based on common structural features. Many "feasible" structures contain only small pores. Several very open structures were also enumerated, although they contain three-membered rings which are thermodynamically disfavoured and not found in conventional zeolites. We believe that such topologies may be realizable as framework materials, but with different elemental compositions to those normally associated with zeolites.

Computing Methodologies↗

PubMed2004

Evidence for heterodimers of 2,4,5-trichlorophenol on planar lipid layers. A FTIR-ATR investigation.

Trichlorophenols are weak acids of high hydrophobicity and are able to transport protons across the mitochondrial membrane. Thus the proton motive force is dissipated and the ATP production decreased. In situ Fourier Transform Infrared-Attenuated Total Reflection (FTIR-ATR) experiments with 2,4,5-trichlorophenol (TCP) adsorbed to model membranes resulted in good evidence for the formation of the TCP-heterodimer. Two surfaces were examined: a dipalmitoyl phosphatidic acid (DPPA) monolayer and a planar DPPA/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. TCP was adsorbed from 1 to 3 mM solutions at pH 6.0 to the lipid layers leading to surface layers at the water/lipid interface. Difference spectra showed an effect on DPPA acyl chains even when it was covered with POPC. Time-resolved measurements revealed two distinct adsorption processes, which were assigned to TCP and its deprotonated anion (phenoxide), respectively. For DPPA/POPC bilayers, the adsorption of TCP was faster than that of its phenoxide, whereas adsorption of both species to DPPA monolayers proceeded with similar velocity. In both cases, phenoxide formation at the membrane was found to be delayed with respect to phenol adsorption. Phenoxide and phenol were retained after replacing the TCP solution with buffer. For the retained species, we estimated a phenol/phenoxide molar ratio of 1 at pH 6.0 (pKa=6.94 for TCP), demonstrating strong evidence for heterodimer formation.

Adsorption↗

PubMed2004

Chemically feasible hypothetical crystalline networks.

Our systematic enumeration of 4-connected crystalline networks (that is, networks in which each atom is connected to exactly four neighbours) used recent advances in tiling theory to evolve over 900 topologies. The results are relevant to the structures of zeolites and other silicates, aluminophosphates (AlPOs), oxides, nitrides, chalcogenides, halides, carbon networks, and even to polyhedral bubbles in foams. Given their importance as molecular sieves, ion exchangers, catalysts and catalyst supports, we have applied the results to microporous aluminosilicates and aluminophosphates (zeolites). Zeolite chemistry has to date produced 152 distinct types of structure. However, it was always clear that although many further structures can be synthesised, only a fraction of the mathematically generated networks would be chemically feasible (many are 'strained' frameworks requiring unrealistic bond lengths and bond angles), and that an effective 'filtering' process is needed to identify the most plausible frameworks. Here, we describe the use of computational chemistry methods to calculate optimized structural parameters, framework energies relative to alpha-quartz, volumes accessible to sorption, and X-ray diffraction patterns for systematically enumerated hypothetical 4-connected crystalline frameworks. Structures were treated as silica polymorphs with the empirical formula SiO(2), and their energies were minimized.

Crystallization↗