Biomedical subjects

Ivana Adamovic

Publications and source records attributed to Ivana Adamovic.

6 recordsLinked to original sources

PubMed2006

Methanol-water mixtures: a microsolvation study using the effective fragment potential method.

The formation process of methanol-water mixtures, (MeOH/H2O)n, n = 2, 3,..., 8 is studied at the molecular level using the general effective fragment potential (EFP2) method and second-order perturbation theory (MP2). Extensive Monte Carlo/simulated annealing global optimizations were used to locate global minimum structures for each n, for both homo and hetero clusters. Mixing at the microscopic level was investigated, and some general conclusions about the microsolvation behavior of these mixtures are presented. For all of these clusters, incomplete mixing is observed at the molecular level. Low-energy (MeOH/H2O)n clusters retain much of their initial structure in the global minima of the mixed clusters.

Computer Simulation↗

PubMed2006

Modeling styrene-styrene interactions.

This study is the first step in the systematic investigation of substituted (carboxyl) polystyrene nanoparticles. Understanding the fundamental interactions between the p-carboxyl styrene monomers, where an ethyl group is used instead of a vinyl group (referenced, for convenience, as "p-carboxyl styrene"), provides the basic information needed to construct potentials for nanoparticles composed of these monomers. In this work, low-energy isomers of p-carboxyl styrene dimer were studied. The dimer structures and their relative and binding energies were determined using both Møller-Plesset second-order perturbation theory (MP2) and the general effective fragment potential (EFP2) method. Sections of the intermolecular potential energy surface (PES) of the p-carboxylated styrene dimer in its global minimum orientation were also determined. As expected, double hydrogen bonding between the two carboxylic groups provides the strongest interaction in this system, followed by isomers with a single H-bond and strong benzene ring-benzene ring (pi-pi) type interactions. Generally, the EFP2 method reproduces the MP2 geometries and relative energies with good accuracy, so it appears to be an efficient alternative to the correlated ab initio methods, which are too computationally demanding to be routinely used in the study of the more-complex polymeric systems of interest.

Journal Article↗

PubMed2005

Potential energy surfaces of SimOn cluster formation and isomerization.

The reaction paths for formation and isomerization of a set of silica SimOn (m = 2,3, n = 1-5) nanoclusters have been investigated using second-order perturbation theory (MP2) with the 6-31G(d) basis set. The MP2/6-31G(d) calculations have predicted singlet ground states for all clusters excluding Si3O2. The total energies of the most important points on the potential energy surfaces (PES) have been determined using the completely renormalized (CR) singles and doubles coupled cluster method including perturbative triples, CR-CCSD(T) with the cc-pVTZ basis set. Although transition states have been located for many isomerization reactions, only for Si3O3 and Si3O4 have some transition states been found for the formation of a cluster from the separated reactants. In all other cases, the process of formation of SimOn clusters appears to proceed without potential energy barriers.

Journal Article↗

PubMed2005

Time-resolved gas-phase kinetic and quantum chemical studies of the reaction of silylene with oxygen.

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reaction with O(2). The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF(6) bath gas, at five temperatures in the range 297-600 K. The second order rate constants at 10 Torr were fitted to the Arrhenius equation: [see text] The decrease in rate constant values with increasing temperature, although systematic is very small. The rate constants showed slight increases in value with pressure at each temperature, but this was scarcely beyond experimental uncertainty. From estimates of Lennard-Jones collision rates, this reaction is occurring at ca. 1 in 20 collisions, almost independent of pressure and temperature. Ab initio calculations at the G3 level backed further by multi-configurational (MC) SCF calculations, augmented by second order perturbation theory (MRMP2), support a mechanism in which the initial adduct, H(2)SiOO, formed in the triplet state (T), undergoes intersystem crossing to the more stable singlet state (S) prior to further low energy isomerisation processes leading, via a sequence of steps, ultimately to dissociation products of which the lowest energy pair are H2O+SiO. The decomposition of the intermediate cyclo-siladioxirane, via O-O bond fission, plays an important role in the overall process. The bottleneck for the overall process appears to be the T-->S process in H2SiOO. This process has a small spin-orbit coupling matrix element, consistent with an estimate of its rate constant of 1x10(9) s-1 obtained with the aid of RRKM theory. This interpretation preserves the idea that, as in its reactions in general, SiH2 initially reacts at the encounter rate with O2. The low values for the secondary reaction barriers on the potential energy surface account for the lack of an observed pressure dependence. Some comparisons are drawn with the reactions of CH2+O2 and SiCl2+O2.

Algorithms↗

PubMed2005

Solvent effects on the S(N)2 reaction: Application of the density functional theory-based effective fragment potential method.

The performance of the density functional theory (DFT)-based effective fragment potential (EFP) method is assessed using the S(N)2 reaction: Cl- + nH2O + CH3Br = CH3Cl + Br- + nH2O. The effect of the systematic addition of water molecules on the structures and relative energies of all species involved in the reaction has been studied. The EFP1 method is compared with second-order perturbation theory (MP2) and DFT results for n = 1, 2, and 3, and EFP1 results are also presented for four water molecules. The incremental hydration effects on the barrier height are the same for all methods. However, only full MP2 or MP2 with EFP1 solvent molecules are able to provide an accurate treatment of the transition state (TS) and hence the central barriers. Full DFT and DFT with EFP1 solvent molecules both predict central barriers that are too small. The results illustrate that the EFP1-based DFT method gives reliable results when combined with an accurate quantum mechanical (QM) method, so it may be used as an efficient alternative to fully QM methods in the treatment of larger microsolvated systems.

Journal Article↗

PubMed2005

Multireference second-order perturbation theory: how size consistent is "almost size consistent".

A systematic study of the deviation from size consistency of the multireference second-order Moller-Plesset perturbation theory (MRMP2) method is presented. The size-consistency error is shown to depend on the number of monomers in a supermolecule calculation, size of basis set, number of correlated valence electrons, and size of active space. HF, F(2), and N(2) are used as test cases, with stretched bonds, to include simple, well-defined multireference character. This is essential in ensuring that MRMP2 is being tested as a multireference method. It is concluded that the MRMP2 and other multireference perturbation theory methods can exhibit significant size-consistency errors, and that the size of the error depends on the manner in which the perturbation theory is implemented.

Journal Article↗