Biomedical subjects

Spiridoula Matsika

Publications and source records attributed to Spiridoula Matsika.

7 recordsLinked to original sources

PubMed2006

Combined multireference configuration interaction/ molecular dynamics approach for calculating solvatochromic shifts: application to the n(O) --> pi* electronic transition of formaldehyde.

A combined quantum mechanics/molecular mechanics method is described here for considering the solvatochromic shift of excited states in solution. The quantum mechanical solute is described using high level multireference configuration interaction methods (MRCI), while molecular dynamics is used for obtaining the structure of the solvent around the solute. The electrostatic effect of the solvent is included in the quantum description of the solute in an averaged way. This method is used to study solvent effects on the n(O) --> pi* electronic transition of formaldehyde in aqueous solution. The effects of solute polarization, basis sets, and dynamical correlation on the solvatochromic shift, and on dipole moments, have been investigated.

Journal Article↗

PubMed2005

Excited electronic states of the cyclic isomers of O2 and SO2.

The low-lying electronic states of O3 and SO2 in their bent and cyclic isomers up to about 10 eV are calculated using the multireference configuration interaction (MRCI) method with a standard Gaussian correlation consistent polarized triple-zeta (cc-pVTZ) basis set. The vertical excitation energies, electron configurations, and oscillator strengths of these states are reported. The molecular orbital structures and excited states of the cyclic isomers are discussed in relation to the bent ones. Coherent anti-Stokes Raman spectroscopy (CARS) schemes for detecting the synthesis of the cyclic isomers are suggested.

Journal Article↗

PubMed2005

Three-state conical intersections in nucleic acid bases.

The involvement of three-state conical intersections in the photophysics and radiationless decay processes of the nucleobases has been investigated using multireference configuration interaction methods. Three-state conical intersections have been located for the pyrimidine base, uracil, and the purine base, adenine. In uracil, a three-state degeneracy between the S(0), S(1), and S(2) states has been located at 6.2 eV above the ground-state minimum energy. This energy is 0.4 eV higher than vertical excitation to S(2) and at least 1.3 eV higher than the two-state conical intersections found previously. In adenine, two different three-state degeneracies between the S(1), S(2), and S(3) states have been located at energies close to the vertical excitation energies. The energetics of these three-state conical intersections suggest they can play a role in a radiationless decay pathway present in adenine. The existence of two different seams of three-state conical intersections indicates that these features are common and complicate the potential energy surfaces of adenine and possibly many other aromatic molecules.

Adenine↗

PubMed2004

Quantitative detection of singlet O2 by cavity-enhanced absorption.

A method for the practical determination of the absolute concentration of single (a1delta(g)) oxygen is discussed. The method is based on sensitive off-axis integrated-cavity-output spectroscopy (ICOS). Off-axis ICOS allows narrowband, continuous-wave lasers to be used in conjunction with optical cavities to record sensitive absorption measurements. The details of the method as well as spectroscopic data confirming the first observation of the (1, 0) band of the b1sigma(g)(+) - a1delta(g) Noxon system are presented. The absolute transition probabilities for the b1sigma(g)(+) - a1delta(g) Noxon system, which are not known precisely from experiments, are determined by quantum chemistry theory.

Journal Article↗

PubMed2003

Conical intersections of three electronic states affect the ground state of radical species with little or no symmetry: pyrazolyl.

Conical intersections of three states of the same symmetry are located in the pyrazolyl radical using wave functions of approximately 40 million configuration state functions. The three-state intersection is found to be only approximately 3400 cm-1 above the minimum energy structure on the ground electronic state. It is suggested that many organic radicals may also exhibit this feature.

Journal Article↗

PubMed2003

Beyond two-state conical intersections. Three-state conical intersections in low symmetry molecules: the allyl radical.

Using multireference configuration interaction expansions comprised of over 7 million configuration state functions, three-state conical intersections are reported for the closely spaced, spectroscopically observed (tilde)B(2A1), (tilde)C(2B1), and (tilde)D(2B2) states (in C(2v) symmetry) of the allyl radical. These conical intersections of states which were previously assigned as the 3,4,5(2)A states and are here reassigned as the 4,5,6(2)A states, are expected to be accessible using optical probes. This conclusion is obtained from the structure of the minimum energy point on the 4,5,6(2)A three-state conical intersection seam which is similar to the equilibrium structure of the ground (tilde)X(2A2) state and only 1.1 eV above the (tilde)D(2B2) state at its equilibrium geometry. The seam of three-state degeneracies joins two two-state seams of conical intersection, the 4,5(2)A and 5,6(2)A conical intersection seams. The energy of the minimum energy point on the 4,5(2)A two-state seam is only 0.15 eV above that of the (tilde)D(2B2) state at its equilibrium structure. Three-state intersections are also reported for the 3,4,5(2)A states.

Journal Article↗

PubMedDate not supplied

The fluorescence mechanism of 5-methyl-2-pyrimidinone: an ab initio study of a fluorescent pyrimidine analog.

The photophysically important potential energy surfaces of the fluorescent pyrimidine analog 5-methyl-2-pyrimidinone have been explored using multireference configuration-interaction ab initio methods at three levels of dynamical correlation, all of which support a fluorescence mechanism. At vertical excitation S1 (dark, n(N)pi*) and S2 (bright, pipi*) are almost degenerate at 4.4 eV, with S3 (dark, n(O)pi*) at 5.1 eV. The excited system can follow the S1-S2 seam of conical intersections, accessible from the Franck-Condon region, to its minimum and then evolve from this conical intersection on the S1 (pipi*) surface to a global minimum. At lower levels of correlation, the S1 surface shows two minima separated by a barrier of up to 0.18 eV. The secondary minimum found at the lower levels of correlation becomes the global minimum with higher correlation. The S1 population at this minimum can be trapped from accessing the lowest energy S0-S1 (pipi*/gs) conical intersection by an energy gap at least 0.3-0.4 eV higher than the S1 minimum. The calculated emission energy from this minimum is 2.80 eV. Gradient pathways connecting important S1 geometries are presented, as well as other excited state conical intersections.

Fluorescence↗