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Using a density matrix formalism we derive a general expression for the resonant response of an ensemble of molecular aggregates to two optical pulses. The aggregates, which can be of arbitrary geometry, are described by a Frenkel exciton Hamiltonian including exciton–exciton interactions. A hierarchy of resonant coherent transient signals is generated having wave vectors sk1+(1-s)k2, where ki is the wave vector of the ith pulse and s is an integer. General expressions for the differential pump–probe absorption spectrum D(ω;tD) (s=0) and the photon echo Iecho(tD) (s=-1) are presented for arbitrary pulse intensities. Applications are made to a linear chain of interacting Frenkel excitons with nearest neighbor exciton–exciton interaction A and exciton transfer J. Analytical expressions for D(ω;tD) and Iecho(tD) are obtained which are valid to third order in the aggregate-field interaction. The influence of the optically active red (blue) biexciton which detaches from the bottom (top) of the two-exciton band when A<-2|J| (A>=2|J|) is investigated. Biexcitons appear as extra peaks in D(ω;tD) and as oscillations in Iecho(tD). Finite size effects are responsible for quantum beat oscillations in D(ω;tD) and long time oscillations in the echo decay. Quantum beats arise predominantly from the difference between the lowest one-exciton frequencies. Our theory successfully describes the salient spectral features in the pump–probe spectra of J-aggregates. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Examines the absorption and spontaneous emission in aggregates of conjugated polymers. Relationship between the radiative decay rate of exciton and the number of polymers; Effects of intermolecular interactions on exciton sizes and energies; Implication of J-aggregate formation for the absorption and emission of polymer aggregates.

Studies spontaneous emission and absorption in an aggregate of pi-conjugated oligomers. Aggregate Hamiltonian; Aggregate-field interaction Hamiltonian; Evaluation of absorption spectra for aggregates; Radiative emission; Radiative decay in an isolated oligomer; Radiative decay in aggregates.

Studies the effects of intermacrocycle interactions on the second hyperpolaribilities of cofacial phthalocyanine dimers and trimers. Presentation of theoretical analysis based on the Frenkel exciton model for a chain of three level molecules; Identification of two mechanisms which lead to enhancements in the dimer and trimer value; Description of the first mechanism.

Proper accounting of the positional/orientational/conformational entropy loss associated with protein-ligand binding is important to obtain reliable predictions of binding affinity. Herein, we critically examine two simplified statistical mechanics-based approaches, namely a constant penalty per rotor method, and a more rigorous method, referred to here as the partition function-based scoring (PFS) method, to account for such entropy losses in high-throughput docking calculations. Our results on the estrogen receptor β and dihydrofolate reductase proteins demonstrate that, while the constant penalty method over-penalizes molecules for their conformational flexibility, the PFS method behaves in a more 'ΔG-like' manner by penalizing different rotors differently depending on their residual entropy in the bound state. Furthermore, in contrast to no entropic penalty or the constant penalty approximation, the PFS method does not exhibit any bias towards either rigid or flexible molecules in the hit list. Preliminary enrichment studies using a lead-like random molecular database suggest that an accurate representation of the 'true' energy landscape of the protein-ligand complex is critical for reliable predictions of relative binding affinities by the PFS method. Proteins 2007. © 2006 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]