Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.     

Formation of photochemical π-cation radicals

We have monitored the spectra and kinetics of μ-oxo iron (III) tetraphenyl porphyrin. The spectral changes between 460 nm and 770 nm were observed after excitation with 25 ps fwhm, 355 nm pulse. Kinetic studies from — 100 ps to 4 ns suggest that after the immediate formation of the excited states a transient species is formed which we assign to the π-caion radical-ferrous porphyrin pair. This pair decays with a time constant of 600 ps ± 100 ps leaving a small amount of disproportionation reaction photoproducts. The spectra and kinetics of the transients, were not altered by concentration (0.15 OD – 1.0 OD at 571 nm), solvent or addition of oxygen.     

Distributed data parallel coupled-cluster algorithm: Application to the 2-hydroxypyridine/2-pyridone tautomerism

The recently developed parallel coupled-cluster algorithm of Rendell, Lee, and Lindh [Chem. Phys. Lett., 194 , 84 (1992)] is extended to allow four-indexed quantities containing one or two indices in the virtual orbital space to be stored across the global memory of distributed-memory parallel processors. Quantities such as the double-excitation amplitudes can now be distributed over multiple nodes, with blocks of data retrieved from remote nodes by the use of interrupt handlers. As an application of the new code, we have investigated the potential energy surface of the 2-hydroxypyridine/2-pyridone tautomers. Using large basis sets, the structure of each tautomer and the transition state connecting the two minima has been determined at the SCF level. The relative energy difference and the activation energy were then redetermined using the MP2, CCSD, and CCSD(T) methods. All calculations have been performed on Intel distributed-memory supercomputers. The largest coupled-cluster calculations contained over 2 million double-excitation amplitudes. © John Wiley & Sons, Inc.