In general, one has to apply TD-DFT calculations with utmost caution and it is imperative to seek critical feedback from experimental data. With this provision, TD-DFT can be a useful
interpretative tool, as was recently demonstrated by Sun et al. (2007) in their study of the P700 system Selleckchem C646 found in the reaction center (Fig. 2) of photosystem I (PSI). The authors used TD-DFT in conjunction with the statistical average of different orbital potentials (SAOP) model (Gritsenko et al. 1999) to examine the excitation processes in the pair of chlorophylls that comprise P700. The detailed analysis of the individual excitations in terms of molecular orbital contributions and transition dipole moments revealed that, despite the apparent symmetric disposition of its two branches of cofactors, the P700 pair is intrinsically excited in an asymmetric fashion. On the basis of the TD-DFT results the authors were further able to establish connections with the experimentally observed asymmetric electron transfer process in PSI and propose
a charge separation mechanism for P700 (Sun et al. 2007). Fig. 2 A view of the electron-transfer chain in the reaction center of photosystem URMC-099 ic50 I. Chlorophyll pairs are arranged in two symmetric branches that diverge at P700 and reconverge at the iron–sulfur cluster. TD-DFT calculations have probed the nature of the excitation at the P700 pair X-ray absorption Thymidine kinase spectroscopy
X-ray absorption spectroscopy (XAS) is a powerful probe of the electronic and geometric structure of metal sites in inorganic and biological systems since it provides valuable information on the oxidation state, geometry, and, in some cases, spin state of the metal centre (Roe et al. 1984; Westre et al. 1997). The shape, position, and intensity of absorption peaks in the X-ray absorption near-edge structure (XANES) of the metal result from core electron excitations to valence orbitals below the ionization threshold and carry information on the oxidation state, coordination, and character of the bonding with the ligands. As with optical spectra, TD-DFT can be used for the computation of metal or ligand pre-edge features, by allowing excitations into the virtual orbital space only out of localized core-holes (Ray et al. 2007; DeBeer George et al. 2008a). Although absolute transition energies are not predicted accurately, this simple and effective protocol yields relative transition energies for a GSK458 supplier series of related complexes or for a sequence of transitions to within a few tenths of an electron volt (DeBeer George et al. 2008a; Neese 2008a).