Biomedical subjects

Kari Laasonen

Publications and source records attributed to Kari Laasonen.

6 recordsLinked to original sources

PubMed2006

Ab initio molecular dynamics study of a mixture of HF(aq) and HCl(aq).

We have studied a mixture of HF and HCl molecules in water using Car-Parrinello ab initio molecular dynamics (CPMD). We have done simulations with 1 HF and 3 HCl molecules, 3 HF and 4 HCl, 6 HF and 8 HCl (6/8 simulation), and 14 HF molecules. All simulations consist of 32 molecules, and they were 10-96 ps long. The HF dissociation probability was around 30%, and HCl's was more than 90%. The solvation of the HF molecule was much better than the solvation of HCl. The solvation environment of F, both the F- ion and the F in HF, did not depend much on the acids concentration, whereas the Cl coordination numbers were rather sensitive to the concentration. In the 6/8 simulation, all XH-Y (X, Y = F, Cl) type molecules were observed and the FH-F was the most probable. In general, the molecular structures in mixed aqueous acid systems were similar to the pure HF(aq) and HCl(aq) systems.

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PubMed2005

Computational studies of the cationic aluminium(chloro) hydroxides by quantum chemical ab initio methods.

Cationic aluminium(chloro) hydroxide complexes with two to four aluminium atoms were studied using quantum chemical methods. Complexes were studied in both gas and liquid phase. The liquid environment was modeled by using a conductor-like screening model (COSMO). COSMO calculations were carried out as a single point calculation at the optimized gas phase structures. Water (epsilon = 78.54) was used as the solvent. The minimum energy structures obtained from the gas phase studies were mostly compact cyclic structures. Aluminium preferred to be five-coordinated in oxygen rich clusters. Core oxygen preferred three-fold coordination but in the largest clusters the four-coordinated oxygen was observed. Water reacted dissociatively with hydrogen poor clusters. The COSMO calculations showed that the optimal structures of cationic aluminium(chloro) hydroxides tend to be more open in the liquid than in the gas phase.

Aluminum↗

PubMed2005

Car-Parrinello molecular dynamics study of DCl hydrate crystals.

Three DCl hydrates have been studied using Car-Parrinello (CP) molecular dynamics. The structural results at low temperatures (T<350 K) agree with experiment and previously published CP results. The monohydrate has been shown to be built from D3O+ and Cl- ions. The dihydrate is built exclusively from D5O2+ and Cl- ions. The trihydrate consists of D2O, D5O2+, and Cl- ions. Thus, the DCl hydrates are excellent systems for studying ideal D3O+ and D5O2+ ions. The data from these ideal structures can be compared to high-concentration acid-liquid simulations. [ClD...Cl]- ions were detected at amorphous and fluid conditions after melting the di- and trihydrate crystals. The experimentally observed spectral continuum can be explained by combining the Eigen and Zundel spectra, and interpolating between the shared deuterium frequencies of the latter and the stretching band of the former.

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PubMed2005

Computational study of the adsorption energetics and vibrational wavenumbers of NH3 Adsorbed on the Ni(111) Surface.

The structure and stabilities of NH(3) adsorbed on different sites of a Ni(111) surface are compared based on density functional, plane-waves calculations within a periodic framework. The surface has been modeled by 4- and 5-layer slabs with 2 x 2 and 3 x 3 unit cells. Calculated results are in good agreement with available experimental data, confirming the atop adsorption site to be the most favorable, with no preferred azimuthal orientation for the H atoms. For NH(3) adsorbed at the atop site, the one-dimensional potential energy profiles along the N-H and N-Ni bonds and the coupling between adjacent N-H bond oscillators have been calculated and fitted to an analytical expression using an accurate anharmonic potential model. Variational calculations have been performed to obtain frequencies for the N-H and N-Ni stretching vibrations and N-H stretching line widths. The model for calculating line widths has also been tested with CO adsorbed at the hcp hollow of the Ni(111) surface.

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PubMed2004

Nuclear magnetic shielding and quadrupole coupling tensors in liquid water: a combined molecular dynamics simulation and quantum chemical study.

Nuclear magnetic resonance (NMR) shielding tensors for the oxygen and hydrogen nuclei, as well as nuclear quadrupole coupling tensors for the oxygen and deuterium nuclei of water in the liquid and gaseous state, are calculated using Hartree-Fock and density functional theory methods, for snapshots sampled from Car-Parrinello molecular dynamics trajectories. Clusters representing local liquid structures and instantaneous configurations of a single molecule representing low-density gas are fed into a quantum chemical program for the calculation of the NMR tensors. The average isotropic and anisotropic tensorial properties of 400 samples in both states, averaged using a common Eckart coordinate frame, are calculated from the data. We report results for the gas-to-liquid chemical shifts of (17)O and (1)H nuclei, as well as the corresponding change in the nuclear quadrupole couplings of (17)O and (2)H. Full thermally averaged shielding and quadrupole coupling tensors are reported for the gaseous and liquid-state water, for the first time in the case of liquid. Electron correlation effects, the difference of classical vs quantum mechanical rovibrational averaging, and different methods of averaging anisotropic properties are discussed.

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PubMed2004

Molecular dynamic simulations of atom-cluster collision processes.

Monomer-cluster collisions of Lennard-Jones argon atoms have been studied using molecular dynamics simulation for target cluster sizes of 2, 3, 4, 5, 10, and 20 atoms. Capture probability of monomers by clusters and the lifetimes of the resulting clusters have been calculated as a function of impact parameter and the total energy of the target cluster. Cluster lifetime is further integrated over all impact parameters to obtain the average lifetime for each cluster size and energy. The average lifetime of the smallest aggregates is shown to be short compared to the collision time between monomers and clusters unless the vapor is highly supersaturated. The formation probability of a new cluster decreases steeply if a minimum lifetime is required for the cluster.

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