Optimized structures for the redox species of the diiron active site in [Fe]-hydrogenase as observed by FTIR and for species in the catalytic cycle for the reversible H(2) oxidation have been determined by density-functional calculations on the active site model, [(L)(CO)(CN)Fe(mu-PDT)(mu-CO)Fe(CO)(CN)(L')](q)(L = H(2)O, CO, H(2), H(-); PDT = SCH(2)CH(2)CH(2)S, L' = CH(3)S(-), CH(3)SH; q = 0, 1-, 2-, 3-). Analytical DFT frequencies on model complexes (mu-PDT)Fe(2)(CO)(6) and [(mu-PDT)Fe(2)(CO)(4)(CN)(2)](2)(-) are used to calibrate the calculated CN(-) and CO frequencies against the measured FTIR bands in these model compounds. By comparing the predicted CN(-) and CO frequencies from DFT frequency calculations on the active site model with the observed bands of D. vulgaris [Fe]-hydrogenase under various conditions, the oxidation states and structures for the diiron active site are proposed. The fully oxidized, EPR-silent form is an Fe(II)-Fe(II) species. Coordination of H(2)O to the empty site in the enzyme's diiron active center results in an oxidized inactive form (H(2)O)Fe(II)-Fe(II). The calculations show that reduction of this inactive form releases the H(2)O to provide an open coordination site for H(2). The partially oxidized active state, which has an S = (1)/(2) EPR signal, is an Fe(I)-Fe(II) species. Fe(I)-Fe(I) species with and without bridging CO account for the fully reduced, EPR-silent state. For this fully reduced state, the species without the bridging CO is slightly more stable than the structure with the bridging CO. The correlation coefficient between the predicted CN(-) and CO frequencies for the proposed model species and the measured CN(-) and CO frequencies in the enzyme is 0.964. The proposed species are also consistent with the EPR, ENDOR, and Mössbauer spectroscopies for the enzyme states. Our results preclude the presence of Fe(III)-Fe(II) or Fe(III)-Fe(III) states among those observed by FTIR. A proposed reaction mechanism (catalytic cycle) based on the DFT calculations shows that heterolytic cleavage of H(2) can occur from (eta(2)-H(2))Fe(II)-Fe(II) via a proton transfer to "spectator" ligands. Proton transfer to a CN(-) ligand is thermodynamically favored but kinetically unfavorable over proton transfer to the bridging S of the PDT. Proton migration from a metal hydride to a base (S, CN, or basic protein site) results in a two-electron reduction at the metals and explains in part the active site's dimetal requirement and ligand framework which supports low-oxidation-state metals. The calculations also suggest that species with a protonated Fe-Fe bond could be involved if the protein could accommodate such species.

The acid-catalyzed hydrolysis of formamide in aqueous solutions was investigated by ab initio calculations. Solvent effects on the hydrolysis reaction were reasonably considered by the cluster-continuum model with explicit water molecules in the first solvation shell, and the selection of hydration cluster plays an important role in reliable estimation of thermodynamic values for the hydrolysis reaction. Possible concerted and stepwise mechanisms of the O-protonated and N-protonated pathways were investigated by extensive calculations. On the basis of unbiased theoretical treatments on all plausible pathways, the O-protonated stepwise pathway was shown to be the favored mechanism, and the predicted activation free energies for the rate-determining step and the breaking of the C-N bond are 21.8 and 9.4 kcal/mol by B3LYP, respectively. The present results show good agreement with experiment and provide a complete description of the acid-catalyzed hydrolysis of formamide.

Structures and properties of the low-lying states in 4-(dicyanomethylene)-2-methyl-6(p-dimethylaminostyryl)-4H-pyran (DCM) have been investigated theoretically. Calculations show that the dimethylamino and dimethylanilino twisted conformations of DCM on the potential energy surface of the first excited state (S-1) have relatively high stabilities and remarkable intramolecular charge transfers (ICT). Both structures can serve as candidates for the red-shifted emissive state in polar solvent. In particular, the dimethylanilino twisted ICT state has been predicted to have a dipole moment increment of 20 Debye with respect to the ground state by CASSCF calculations, in good agreement with the suggested experimental values. The optimized geometry of the S-1 state exhibits a long central CC bond of 1.458 angstrom, which makes the trans-cis isomerization quite facile through intramolecular rotation around the central CC bond on the S-1 potential surface. The S-1 state is a precursor to the formation of the ICT emissive state and photoinduced trans cis isomerization. The S-1/S-0 crossing in polar solvent and avoid-crossing in the gas phase as well as in non-polar solvent are involved in the trans-cis isomerization process. The presence of an early S-1/S-0 crossing in the strong polar solvent reduces the isomerization efficiency.Research Grants Council of Hong Kong SAR [CityU 103106]; National Science Foundation [20173042, 20473062, 20233020, 20021002]; Ministry of Science and Technology [2004CB719902, 001CB1089]; Ministry of Educatio

The vibrationally resolved spectral method and quantum chemical calculations are employed to reveal the structural and spectral properties of Coumarin 343 (C343), an ideal candidate for organic dye photosensitizers, in vacuum and solution. The results manifest that the ground-state energies are dominantly determined by different placements of hydrogen atom in carboxylic group of C343 conformations. Compared to those in vacuum, the electronic absorption spectra in methanol solvent show a hyperchromic property together with the redshift and blueshift for the neutral C343 isomers and their deprotonated anions, respectively. From the absorption, emission, and resonance Raman spectra, it is found that the maximal absorption and emission come from low-frequency modes whereas the high-frequency modes have high Raman activities. The detailed spectra are further analyzed for the identification of the conformers and understanding the potential charge transfer mechanism in their photovoltaic applications.

Singlet and triplet low-lying states of the 4-dimethylaminobenzonitrile and its derivatives have been studied by the density functional theory and ab initio methodologies. Calculations reveal that the existence of the methyl groups in the phenyl ring and the amino twisting significantly modify properties of their excited states. A twisted singlet intramolecular charge-transfer state can be accessed through decay of the second planar singlet excited state with charge-transfer character along the amino twisting coordinate or by an intramolecular charge-transfer reaction involved with a locally first excited singlet state. Plausible charge-transfer triplet states and intersystem crossing processes among singlet and triplet states have been explored by spin-orbit coupling calculations. The intersystem crossing process was predicted to be the dominant deactivation channel of the photoexcited 4-dimethylaminobenzonitrile.

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Mechanisms and reactivity differences for the cycloaddition of anhydride to alkyne catalyzed by the palladium and nickel catalysts have been investigated by extensive density functional theory (DFT) calculations. The predicted free energy profiles for the Pd- and Ni-catalyzed reactions have been used to evaluate possible mechanisms for the formation of different products. Calculations show that the formation of isocoumarin via the decarbonylative addition of anhydride to alkyne is kinetically more favorable than the channel to indenone in the Ni-catalyzed reaction. On the contrary, the preparation of naphthalene through sequential liberation of CO2 and CO is kinetically more favorable than that the formation of indenone in the Pd-catalyzed process. The bonding differences between Pd-C and Ni-C bonds, arising from the relativistic effect of late transition metals, play an important role in regulating their catalytic activity. The calculation results show good agreement with the experiments.

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