K. K. Liang

Bonding interaction, low-lying states and excited charge-transfer states of pyridine–metal clusters: Pyridine–Mn (M=Cu, Ag, Au; n=2–4)

The binding interactions between the pyridine and small coinage metal clusters such as copper, silver and gold in different sizes (n=2–4) have been investigated by a density function theory approach. We obtain the binding energies of these pyridine–metal cluster complexes and analyze the nature of the binding interactions in terms of the metal cluster-dependent molecular orbital properties and binding orientations. The calculated binding energies show a good agreement with the experimental values of the pyridine adsorbed on the metal surfaces. We find that the order in the binding energies between pyridine and then metals clusters is Cu–Au>Ag and the interaction between pyridine and the silver is the weakest among these three metals. The donation of the lone-pair electrons on the nitrogen atom of the pyridine molecule is the major contribution to the binding interaction between pyridine and each metal cluster. The back-donation interaction from the metal atoms to the π-type anti-bonding orbital is very we...

A modified Ising model for the thermodynamic properties of local and global protein folding- unfolding observed by circular dichroism and small-angle X-ray scattering

Based on the mean-field approximation, we have applied a modified Ising model to describe general protein unfolding behavior at thermodynamic equilibrium with the free energy contributed by the subgroup units (amino acids or peptide bonds) of the protein. With the thermodynamic properties of the protein, this model can associate the stepwise change of an unfolding fraction ratio profile with the local and global conformation unfolding. Taking cytochrome c (cyt c) as a model protein, we have observed, using small-angle X-ray scattering and circular dichroism (CD), the global and local structure changes for the protein in three kinds of denaturant environments: acid, urea and guanidine hydrochloride. The small-angle X-ray scattering and CD results are mapped to the unfolding fractions as a function of the pH value or denaturant concentration, from which we have extracted local and global unfolding free energies of cyt c in different denaturant environments using a modified Ising model. Based on the characteristics of the thermodynamic properties deduced from the local and global protein folding–unfolding, we discuss the thermodynamic stabilities of the protein in the three denaturant environments, and the possible correlation between the global conformation change of the protein and the local unfolding activities of the S—Fe bond in the Met80-heme and the α-helices.

Application of the density matrix method to spectroscopy and dynamics of photosynthetic reaction centers

The density matrix method is well known for being useful to theoretically treat complicated phenomena. In this work, this method will be applied to study the ultrafast energy and electron transfers in photosynthetic reaction centers. We present a microscopic model to describe the spectroscopy and dynamics for photosynthetic bacterial reaction centers (RCs). In this model, we propose eight vibrational modes and their Huang–Rhys factors for different electronic states, and the couplings between the electronic states. As applications, we have constructed steady-state and ultrafast time-resolved spectra for the wild-type RC of Rhodobacter (Rb.) sphaeroides.

Chapter 5 Density Matrix Treatments of Ultrafast Radiationless Transitions

In this chapter, the ultrafast radiationless transition processes are treated theoretically. The method employed is based on the density matrix method, and specifically, a generalized linear response theory is developed by applying the projection operator technique on the Liouville equation so that non-equilibrium cases can be handled properly. The ultrafast molecular processes are often monitored experimentally by transient spectroscopic techniques. In order to directly interpret these experimental observations, the susceptibility method is combined with the density matrix method so that linear/non-linear transient spectra of the system under consideration can be calculated. As an example, the interfacial photo-induced electron transfer process in dye-sensitized solar cell system, whose kinetics is often examined by the ultrafast spectroscopic techniques, is studied quantitatively with our methods.