| Abstract
| - The Qy absorption spectrum of Photosystem-I from Thermosynecochoccus elongatus (formerly Synecochoccuselongatus) is calculated using the CAM-B3LYP density functional and INDO schemes based on a quantum-mechanically refined structure for the entire photosystem obtained using the PW91 density functional. Thesemethods present a priori predictions of the absorption and linear dichroism spectra and include proteinelectrostatic effects, short range inductive effects, long-range and short-range exciton couplings, andsuperexchange effects involving aromatic residues and carotenes. CAM-B3LYP is used as it is the only knowndensity functional that correctly describes the Q bands of chlorophylls, all other methods contaminating themwith erroneous charge-transfer excitations. A critical feature is found to be the use of fully optimized heavy-atom coordinates, with those obtained from just X-ray crystallography providing a poor description of theelectronic properties of the chromophores. The result is a realistic first-principles prediction of the observedabsorption band that identifies the nature of the red-shifted chlorophylls as well as the energies of the reaction-center chlorophylls and the exciton couplings acting between them. The “special pair” appears more like adimer of dimers than a self-contained functional unit, with the exciton couplings between its members andthe accessory chlorophylls exceeding the internal coupling.
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