Large-Scale Normal Coordinate Analysis of Macromolecular Systems: Thermal Properties of Polymer Particles and Crystals†

Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150 K

An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about approximately 2-2.5 meV, originates from approximately 10(2) collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.

Direct INDO/SCI method for excited state calculations

Intermediate neglect of differential overlap (INDO) is the most commonly utilized semiempirical technique for performing excited state calculations on large organic systems such as organic semiconductors and fluorescent dyes. The calculations are typically done at the singles-configuration interaction (SCI) level. Direct methods provide a more efficient means of performing configuration interaction (CI) calculations, and the computational trade offs associated with various approaches to direct-CI theory have been well characterized for ab initio Hamiltonians and high-order CI. However, the INDO and SCI approximations lead to a new set of trade offs. In particular, application of the electron-electron interactions in the atomic basis leads to savings in computational time that scale as the number of atomic orbitals, which for a large organic system can be two to three orders of magnitude. These savings are largest when only a few low-lying excited states are generated and when a full SCI basis, which includes excitations between all filled and empty molecular orbitals, is used. In addition, substantial memory savings are achieved in the direct method by avoiding the evaluation of the two electron integrals in the molecular orbital basis. The method is demonstrated by calculating the absorption spectrum of a poly(paraphenylenevinylene) oligomer containing 16 phenyl rings.