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We present an ab initio based, scaled quantum mechanical oligomer force field (SQMOFF) method for modeling the structure and vibrational spectra of doped poly(p-phenylene). By integrating this theoretical method and Raman spectroscopic technique, we are able to investigate quantitatively the structural evolution of poly(p-phenylene) upon doping. On the basis of our periodic quinonoid model and the observed inter-ring stretching frequency, we find heavily doped PPP to have only about 30% quinonoid character on the average. Accordingly, the average inter-ring C-C bond length decreases from 1.501 to 1.45(2) Á upon doping. This structural information, available for the first time, is fundamental in understanding the effects of doping. Additionally, we find that the corresponding force constant increases from 4.573 to 5.475 mdyn/A upon doping. The intensity ratios of the four Ag modes are predicted by the SQMOFF method to be primarily dependent on the quinonoid structure of the doped polymer. The role of charge transfer in this context is primarily to increase the quinonoid character of the structure. A discussion on intensity ratios with respect to the effective conjugation coordinates theory is also presented.

A continuum model is provided of the free energy terms that contribute to the molecular association of ricin A-chain (RTA) with the rRNA substrate and several small ligands. The model for RTA interactions with the RNA was taken from a previously proposed complex containing a 29-mer oligonucleotide hairpin (. Proteins 27:80-95), and models for the ligands were constructed from x-ray crystallographic structures. The calculated absolute free energies of complex formation for the RTA-RNA assembly and several single-residue substitutions are in good agreement with experimental data, given the approximations of evaluating the strain energy and conformational entropy. The free energy terms were found to resemble those of protein-protein complexes, with the net unfavorable electrostatic contribution offset by the favorable nonspecific hydrophobic effect. Decomposition of the RTA-RNA binding free energy into individual contributions revealed the electrostatic "hot" spots arising from charge-charge complementarity of the interfacial arginines with the RNA phosphate backbone. Base interactions of the GAGA loop structure dominate the hydrophobic complementarity. A linear-scaling model was parametrized for evaluating the binding of small ligands against the rRNA substrate and illustrates the free energy determinant required for designing specific RTA inhibitors.

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By combining vibrational spectra and ab initio calculations, we obtained a consistent description of the IR and nonresonant Raman spectra, including intensities, of four thiophene based polymers—undoped and heavily doped poly(thiophene) (PTh), undoped poly(thieno[3,4-b]benzene) (PITN), and poly(thieno[3,4-b]pyrazine) (PThP) for the first time. Predicted spectra for poly(thiophene) agree with experiment very well. Based on the calculated force constants and Badger’s rule, we also estimated the average inter-ring bond lengths of undoped and doped PTh to be 1.47 and 1.42 Å, respectively. The latter leads to an estimated 33% quinonoid character on average for heavily doped PTh. The average inter-ring bond lengths of undoped PITN and PThP, that are consistent with their vibrational spectra, are estimated to be 1.41, and 1.42 Å, respectively. These values showed that undoped PITN and PThP have quinonoid character close to that of heavily doped PTh. Further, we also estimated that, upon doping the average bond lengths of PTh changed by −0.01, 0.11, and −0.05 Å for intra-ring Cβ–Cβ, Cα–Cβ, and inter-ring bonds, respectively. These bond length changes are significantly different from those of Hartree–Fock-type calculations, reflecting significant correlation contributions and are also in conflict with earlier empirical fits of the vibrational spectrum of the highly doped phase of PTh. However, our results are more in line with the generally accepted picture of an aromatic to quinonoid “transition” of the doping process. Furthermore, the counterintuitive downward frequency shifts in the vibrational spectra of PTh upon doping can be explained by the structural change from an essentially aromatic to a partially quinonoid form.