Biomedical subjects

David Yaron

Publications and source records attributed to David Yaron.

3 recordsLinked to original sources

PubMed2006

Modeling the effects of torsional disorder on the spectra of poly- and oligo-(p-phenyleneethynylenes).

The absorption spectra of phenyleneethynylene oligomers show an unusual change in shape with oligomer length. The unusual aspects of the spectra arise from rotation of the phenylene rings about the long axis of the oligomer. In the ground electronic state, the barrier to this rotation is low and the spectra in room temperature come from an ensemble of different structures. In the excited electronic state, the barrier to rotation is substantially higher, giving rise to strong nonlinear electron-phonon coupling. A multidimensional semiempirical model that includes these effects is developed for the photophysics of phenyleneethynylene oligomers. The ground-state energy is modeled with a molecular mechanics expression, and the excitation energy is modeled with an exciton model. Intermediate Neglect of Differential Overlap/Singles Configuration Interaction (INDO/SCI) calculations verify the exciton model and provide initial estimates of the model parameters. These parameters generate the qualitative features seen in experimental spectra. Inclusion of entropy effects from the multiple torsional coordinates is essential. Refinement of the parameters yields quantitative agreement with experiment. This agreement shows that coupling to torsional motion is a major factor in the spectroscopy and photophysics of these conjugated polymers.

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PubMed2004

Using molecular similarity to construct accurate semiempirical electronic structure theories.

Ab initio electronic structure methods give accurate results for small systems, but do not scale well to large systems. Chemical insight tells us that molecular functional groups will behave approximately the same way in all molecules, large or small. This molecular similarity is exploited in semiempirical methods, which couple simple electronic structure theories with parameters for the transferable characteristics of functional groups. We propose that high-level calculations on small molecules provide a rich source of parametrization data. In principle, we can select a functional group, generate a large amount of ab initio data on the group in various small-molecule environments, and "mine" this data to build a sophisticated model for the group's behavior in large environments. This work details such a model for electron correlation: a semiempirical, subsystem-based correlation functional that predicts a subsystem's two-electron density matrix as a functional of its one-electron density matrix. This model is demonstrated on two small systems: chains of linear, minimal-basis (H-H)(5), treated as a sum of four overlapping (H-H)(2) subsystems; and the aldehyde group of a set of HOC-R molecules. The results provide an initial demonstration of the feasibility of the approach.

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PubMed2003

Direct INDO/SCI method for excited state calculations.

Intermediate neglect of differential overlap (INDO) is the most commonly utilized semiempirical technique for performing excited state calculations on large organic systems such as organic semiconductors and fluorescent dyes. The calculations are typically done at the singles-configuration interaction (SCI) level. Direct methods provide a more efficient means of performing configuration interaction (CI) calculations, and the computational trade offs associated with various approaches to direct-CI theory have been well characterized for ab initio Hamiltonians and high-order CI. However, the INDO and SCI approximations lead to a new set of trade offs. In particular, application of the electron-electron interactions in the atomic basis leads to savings in computational time that scale as the number of atomic orbitals, which for a large organic system can be two to three orders of magnitude. These savings are largest when only a few low-lying excited states are generated and when a full SCI basis, which includes excitations between all filled and empty molecular orbitals, is used. In addition, substantial memory savings are achieved in the direct method by avoiding the evaluation of the two electron integrals in the molecular orbital basis. The method is demonstrated by calculating the absorption spectrum of a poly(paraphenylenevinylene) oligomer containing 16 phenyl rings.

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