Biomedical subjects

John S Tse

Publications and source records attributed to John S Tse.

7 recordsLinked to original sources

PubMed2003

Thermodynamic stability of hydrogen clathrates.

The stability of the recently characterized type II hydrogen clathrate [Mao, W. L., Mao, H.-K., Goncharov, A. F., Struzhkin, V. V., Guo, Q., et al. (2002) Science 297, 2247-2249] with respect to hydrogen occupancy is examined with a statistical mechanical model in conjunction with first-principles quantum chemistry calculations. It is found that the stability of the clathrate is mainly caused by dispersive interactions between H2 molecules and the water forming the cage walls. Theoretical analysis shows that both individual hydrogen molecules and nH2 guest clusters undergo essentially free rotations inside the clathrate cages. Calculations at the experimental conditions--2,000 bar (1 bar = 100 kPa) and 250 K confirm multiple occupancy of the clathrate cages with average occupations of 2.00 and 3.96 H2 molecules per D-5(12) (small) and H-5(12)6(4) (large) cage, respectively. The H2-H2O interactions also are responsible for the experimentally observed softening of the H[bond]H stretching modes. The clathrate is found to be thermodynamically stable at 25 bar and 150 K.

Biophysical Phenomena↗

PubMed2002

Structural stability and phase transitions in K8Si46 clathrate under high pressure.

The structural stability of type-I K8Si46 clathrate has been investigated at high pressure by synchrotron x-ray diffraction. In contrast to that observed in the Na-doped structure-II analogue [A. San-Miguel, Phys. Rev. Lett. 83, 5290 (1999)]], no phase separation into the beta-Sn Si structure was identified at 11 GPa. Instead, K8Si46 is found to undergo a transition to an isostructural positional disordered phase at around 15 GPa. Ab initio phonon band structure calculations reveal a novel phenomenon of phonon instabilities of K atoms in the large cavities is responsible for this transition. Above 32 GPa, the new structure transforms into an amorphous phase.

Journal Article↗

PubMed2002

Doming modes and dynamics of model heme compounds.

Synchrotron far-IR spectroscopy and density-functional calculations are used to characterize the low-frequency dynamics of model heme FeCO compounds. The "doming" vibrational mode in which the iron atom moves out of the porphyrin plane while the periphery of this ring moves in the opposite direction determines the reactivity of oxygen with this type of molecule in biological systems. Calculations of frequencies and absorption intensities and the measured pressure dependence of vibrational modes in the model compounds are used to identify the doming and related normal modes.

Animals↗

PubMed2002

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction.

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.

Journal Article↗

PubMed2002

Structure and phase stability of binary zintl-phase compounds: lithium-group 13 intermetallics and metal-doped group 14 clathrate compounds.

The structure/bonding relationship in a series of intermetallic phases of Li with Al, Ga, and In was investigated by density functional theory and complemented by a model based on tight-binding theory and the method of moments. The combination of these two approaches provides a simple scheme which allows for both a comprehensive understanding of structural trends and the ability to predict low-energy structures for a given composition. This analysis gives a straightforward picture of phase stability in terms of local geometric features such as triangular, square, and hexagonal arrangements of atoms. The approach was extended to examine the structural properties of metal-doped clathrate compounds of C, Si, Ge, and Sn. Clathrate-type phases based on the frameworks Si172, Ge172, Si40, and Ge40 are not only likely to be energetically favorable but may also exhibit high thermoelectric efficiency.

Journal Article↗

PubMed2002

Spontaneous assembly of perfectly ordered identical-size nanocluster arrays.

A method, by which periodic two-dimensional arrays of identical metal clusters of nanometer size and spacing could be spontaneously obtained by taking advantage of surface mediated clustering, is reported. The versatility of the method is demonstrated for a broad range of metals on Si(111)-(7 x 7) substrates. In situ scanning tunneling microscopy analysis of In clusters, combined with first-principles total energy calculations, unveils unique initial-stage atomic structures of the surface-supported clusters and the vital steps that lead to the success of this method. A strong interaction between the clusters and the surface holds the key to the observed cluster sizes.

Journal Article↗

PubMed2001

Ab initio molecular dynamics with density functional theory.

Recent applications of density functional theory base ab initio molecular dynamics in chemical relevant systems are reviewed. The emphasis is on the dynamical aspect in the study of structures, reaction mechanisms, and electronic properties in both the molecular and condensed phases. Examples were chosen from fluxional molecules, solution reactions, and biological systems to illustrate the broad potential applications and unique information that can be obtained from ab initio molecular dynamics calculations. Recent advances in the development of efficient numerical algorithms for the prediction of spectroscopic properties are highlighted.

Electrons↗