PubMed Health⌕ Search

Biomedical subjects

R A van Santen

Publications and source records attributed to R A van Santen.

13 recordsLinked to original sources
PubMed2006

Vesicle shapes from molecular dynamics simulations.

Lipid bilayer membranes are known to form various structures such as large sheets or vesicles. When the two leaflets of the bilayer have an equal composition, the membrane preferentially forms a flat sheet or a spherical vesicle. However, a difference in the composition of the two leaflets may result in a curved bilayer or in a wide variety of vesicle shapes. Vesicles with different shapes have already been shown in experiments and diverse vesicle shapes have been predicted theoretically from energy minimization of continuous curves. Here we present a molecular dynamics study of the effect of small changes in the phospholipid headgroups on the spontaneous curvature of the bilayer and on the resulting vesicle shape transformations. Small asymmetries in the bilayers already result in high spontaneous curvature and large vesicle deformations. Vesicle shapes that are formed include ellipsoids, discoids, pear-shaped vesicles, cup-shaped vesicles, as well as budded vesicles. Comparison of these vesicles with theoretically derived vesicle shapes shows both resemblances and differences.

Algorithms↗
PubMed2005

Lateral interactions and multi-isotherms: nitrogen recombination from Rh(111).

Lateral adsorbate-adsorbate interactions result in variation of the desorption rate constants with coverage. This effect can be studied in great detail from the shape of a multi-isotherm. To produce the multi-isotherm, the temperature is increased in a (semi)stepwise fashion to some temperature, followed by maintaining this temperature for a prolonged time. Then, the temperature is stepped to a higher value and held constant at this new temperature. This cycle is continued until all of the adsorbates have desorbed. Using a detailed kinetic Monte Carlo model and an optimization algorithm based on Evolutionary Strategy, we are able to reproduce the shape of the experimentally measured multi-isotherm of nitrogen on Rh(111) and obtain the lateral interactions between the nitrogen atoms.

Journal Article↗
PubMed2005

On two alternative mechanisms of ethane activation over ZSM-5 zeolite modified by Zn2+ and Ga1+ cations.

The activation of ethane over zinc- and gallium-modified HZSM-5 dehydrogenation catalysts was studied by diffuse reflectance infrared spectroscopy. Hydrocarbon activation on HZSM-5 modified by bivalent Zn and univalent Ga cations proceeds via two distinctly different mechanisms. The stronger molecular adsorption of ethane by the acid-base pairs formed by distantly separated cationic Zn2+ and basic oxygen sites results already at room temperature in strong polarizability of adsorbed ethane and subsequent heterolytic dissociative adsorption at moderate temperatures. In contrast, molecular adsorption of ethane on Ga+ cations is weak. At high temperatures dissociative hydrocarbon adsorption takes place, resulting in the formation of ethyl and hydride fragments coordinating to the cationic gallium species. Whereas in the zinc case a Brønsted acid proton is formed upon ethane dissociation, decomposition of the ethyl fragment on gallium results in gallium dihydride species and does not lead to Brønsted acid protons. This difference in alkane activation has direct consequences for hydrocarbon conversions involving dehydrogenation.

Adsorption↗
PubMed2005

A periodic density functional theory study of cumene formation catalyzed by H-mordenite.

A periodic density functional theory study of the alkylation of benzene with propene in proton-exchanged mordenite has been achieved. The two different reaction routes that are usually proposed for this reaction, namely the direct and the step-by-step reaction pathways, have been investigated. The explicit consideration of the zeolite catalyst framework allows a better level of description of the interactions between the catalyst framework and the reaction than what is obtained with the cluster approach method. The direct reaction route is found to be the preferred one. It is observed that the cluster approach method, which does not describe the zeolite framework, is unable to qualitatively described the trend in activation energies. This is owing to the greater stabilization of larger transition state by the mordenite zeolite framework compared with smaller ones.

Journal Article↗
PubMed2004

Quantum chemical calculation of infrared spectra of acidic groups in chabazite in the presence of water.

The changes in the spectra of the acidic group in chabazite are studied by quantum chemical calculations. The zeolite is modeled by two clusters consisting of eight tetrahedral atoms arranged in a ring and seven tetrahedral atoms coordinated around the zeolite OH group. The potential energy and dipole surfaces were constructed from the zeolite OH stretch, in-plane and out-of-plane bending coordinates, and the intermolecular stretch coordinate that corresponds to a movement of the water molecule as a whole. Both the anharmonicities of the potential energy and dipole were taken into account by calculation of the frequencies and intensities. The matrix elements of the vibrational Hamiltonian were calculated within the discrete variable representation basis set. We have assigned the experimentally observed frequencies at approximately 2900, approximately 2400, and approximately 1700 cm(-1) to the strongly perturbed zeolite OH vibrations caused by the hydrogen bonding with the water molecule. The ABC triplet is a Fermi resonance of the zeolite OH stretch mode with the overtone of the in-plane bending (the A band) and the overtone of the out-of-plane bending (the C band). In the B band the stretch is also coupled with the second overtone of the out-of-plane bending. The frequencies at approximately 3700 and approximately 3550 cm(-1) we have assigned to the OH stretch frequencies of a slightly perturbed water molecule.

Journal Article↗
PubMed2002

Production of chemically pure gaseous [13N]NH3 pulses for PEP studies using a modified DeVarda reduction.

A fast and reproducible production method for pure gaseous [13N]NH3 pulses has been developed. 13N was produced by irradiation of water with 500 nA of 16 MeV protons via the 16O(p,alpha)13N reaction. A mixture of DeVarda's alloy and NaOH was used to convert the produced nitrate/nitrite to ammonia. Pre-treatment of this mixture with water increased the concentrated production of gaseous [13N]NH3. Separation and further purification of ammonia were performed with GC, leading to 5s pulses (1.1 ml STP) with 3.5 +/- 0.5 MBq [13N]NH3 with a high chemical and radiochemical purity suited for positron emission profiling (PEP).

Journal Article↗
PubMed2001

A periodic DFT study of intramolecular isomerization reactions of toluene and xylenes catalyzed by acidic mordenite.

A periodic density functional theory (DFT) study of the isomerization reactions of toluene and xylene catalyzed by acidic mordenite is reported. Monomolecular isomerization reactions have been considered and analyzed. The different reaction pathways have been discussed in detail. The use of periodic structure calculations allows consideration and analysis of zeolite electrostatic contributions and steric constraints that occur within zeolite micropores. Major differences in the details of protonation reaction pathways are found when periodic structures are used rather than small cluster models of the Brønsted acidic site. Complex relationships are found between zeolite topology and reaction pathways.

Journal Article↗
PubMed2001

Synthesis, structural characterization, and transmetalation reactions of a tetranuclear magnesium silsesquioxane complex.

The reaction of a silsesquioxane trisilanol with methylmagnesium chloride leads to an unprecedented tetranuclear magnesium silsesquioxane complex 1 in high yield. The crystal structure shows an unusually short Mg-Cl bond, indicative of an electron-deficient magnesium atom; 1 has been used as transmetalation agent for the synthesis of metal silsesquioxane complexes. Transmetalation activity was low, but can easily be followed by multinuclear NMR. Crystal data for 1: C(78)H(142)Cl(2)Mg(4)O(26)Si(14).6(C(4)H(8)O), a = 15.744(1) A, b = 26.526(2) A, c = 16.917(1) A, beta = 113.229(2) degrees, monoclinic, P2(1)/n, Z = 2.

Journal Article↗
PubMed2001

Stability of Zn(II) cations in chabazite studied by periodical density functional theory.

The location of the Zn(2+) cation in Zn-exchanged chabazite has been studied by the periodical density functional method. Chabazite was chosen as a zeolite model, because it contains three different types of rings commonly found in the zeolite structures: four-, six-, and eight-membered rings. Two aluminum atoms have been employed to substitute the silicon atoms in the same D6R unit cell of the zeolite framework. This leads to different arrangements for the Brønsted site pair and the Zn(II) cation. The two Brønsted sites are found to be more stable when placed in the small ring (4T ring) than in the other rings. This suggests that the most reactive Brønsted sites are located in the large rings. Two Brønsted sites are most stable when the O(H)-Al-O-Si-O(H)-Al sequence is followed in the same ring instead of being located in two different rings. This resembles the aluminum distribution in the small four-membered ring and agrees with bond order conservation rules. The cation stability is markedly influenced by the distortions of the framework. Other factors that also contribute to the stabilization are the aluminum content near the cation and the stability of the original Brønsted sites. The Zn(2+) cation is more stable in the large rings than in the small ones, the six-membered one being the most stable configuration. In the small rings, the cation is, therefore, more reactive. Two different probe molecules have been used to study the interaction with the Zn(II) cation: water and methane. These probe molecules can extract the active center from its original position. For the water molecule, this effect is large and leads to a high framework relaxation. The value of the binding energy of this molecule to the active sites is influenced by these framework relaxations as well as by the cationic position environment. For weakly interacting methane, these effects are significantly less.

Journal Article↗
PubMed2001

A theoretical study of the alkylation reaction of toluene with methanol catalyzed by acidic mordenite.

A theoretical study of the alkylation reaction of toluene with methanol catalyzed by the acidic Mordenite (Si/Al = 23) is reported. Cluster DFT as well as periodical structure DFT calculations have been performed. Full reaction energy diagrams of the elementary reaction steps that lead to the formation of the three xylene isomers are given. The use of periodical structure calculations allows one to account for zeolite framework electrostatic contributions and steric constraints that take place in zeolitic catalysts. Especially the steric constraint energy contribution has a significant effect on the energies and bond formation paths. The activation energy barrier of p-xylene formation is found to be approximately 20 kJ/mol lower than the corresponding values for the formation of its isomers. Computed host-guest binding energies according to the DFT method need a correction due to the absence of the dispersive interaction with the zeolite wall. Apparent activation energies obtained with this correction are in good agreement with experimental data.

Journal Article↗
PubMed1997

27Al quadrupole interaction in zeolites loaded with probe molecules--a quantum-chemical study of trends in electric field gradients and chemical bonds in clusters.

The electric field gradient (EFG) has been calculated in zeolite clusters at the aluminium site surrounded by four SiO4 tetrahedra. Density functional theory (DFT) with the 6-31G** basis set has been employed. Formation of a Brønsted acid site by protonation of one oxygen atom of the AlO4 tetrahedron perturbs the coordination of aluminium, i.e., the corresponding Al-O bond is considerably weaker than in the unprotonated case. This leads to a large EFG, and the calculated quadrupole coupling constant (QCC) for 27Al is 18.2 MHz. Different probe molecules were adsorbed on the Brønsted site. The hydrogen bond formed between the acid proton and the probe molecule weakened the zeolitic O-H bond. For conservation of the overall bond order of the oxygen atom, its bonds to the neighboring tetrahedral atoms (Si, Al) become stronger. As a consequence, the perturbation of the AlO4 tetrahedron and the EFG at the aluminium position decrease depending on the strength of the hydrogen bond. Perturbation of an oxygen atom of the AlO4 tetrahedron by accepting a hydrogen bond from the base molecule also affects the corresponding Al-O bond order. A linear correlation is found between the calculated QCC constants for 27Al and the Al-O bond orders of the oxygen atoms which are perturbed by protonation or by hydrogen bonds. A geometrical shear strain parameter and a simple electrostatic point charge model are less successful at predicting the trends in EFG which clearly shows the importance of the chemical bonds.

Aluminum↗