Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model.

The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.

Dynamics of acrylodan-labeled bovine and human serum albumin entrapped in a sol-gel-derived biogel.

We investigate acrylodan-labeled bovine and human serum albumin (BSA-Ac and HSA-Ac) entrapped within a tetramethylorthosilane-derived biogel composite. The effects of biogel aging and drying were studied by following the acrylodan steady-state and time-resolved emission, the decay of anisotropy, and the dipolar relaxation kinetics as a function of ambient storage time. The results indicate that there is a substantial amount of nanosecond and subnanosecond dipolar relaxation within the local environment surrounding cysteine-34 in both proteins, even when they are fully encapsulated in a dry biogel. Time-resolved anisotropy experiments show that the acrylodan residue and the protein are able to undergo nanosecond motion within the biogel. The semiangle through which the acrylodan can process is the same for a freshly formed biogel and the native protein in buffer. However, once the biogel begins to dry, the semiangle increases (approximately 20 degrees and 10 degrees for BSA-Ac and HSA-Ac, respectively). This suggests that the "pocket" hosting the acrylodan reporter group opens as the biogel dries.