Depolarized light scattering and terahertz absorption of protein solutions

similar procedure and the same type of interaction model were used for glucose solutions. Specifically, MD simulation was carried out using the DL_POLY2.0 package. The MD trajectories were generated using the SPC/E potential model for water and the optimized potential for liquid simulation (OPLS) all-atom force field for carbohydrates, developed by Jorgensen and co-workers, for both trehalose and glucose. The SPC/E model treats the molecules as nonpolarizable, rigid bodies, interacting via a pairwise sum of site−site interactions involving electrostatic terms between fixed partial charges and Lennard-Jones (LJ) interactions, with a single LJ site on the oxygen atom. Within the all-atom OPLS model, trehalose and glucose are represented by 45 and 23 interaction sites, respectively, and modeled as a fully flexible molecules. Bonded interactions include stretching, bending and torsional potentials. The nonbonded interactions include Coulombic and LJ potentials between atoms separated by at least three bonds within the same carbohydrate molecule and between atoms on different molecules. For atoms separated by three bonds within a glucose or a trehalose molecule, the nonbonded interaction is decreased by a factor of 2. The OPLS model was chosen for this study because it is a relatively simple, pairwise-additive, potential that has been shown to be accurate for the properties of monoand disaccharide aqueous solutions relevant to the present application. Interatomic distances within water molecules were kept fixed by using the SHAKE iterative procedure. This constraint method was used to integrate the equations of motion of the rigid molecules, in combination with the velocity Verlet algorithm, with a time step of 1 fs. We have considered, in addition to the pure water, aqueous mixtures having trehalose mole fractions of XTRE = 0.004, 0.009, 0.02, and 0.04 and glucose mole fractions of XGLU = 0.004, 0.01, 0.019, 0.03, 0.039, 0.04, 0.06, and 0.078. The simulations were performed in the microcanonical ensemble with a total number of N = 200−250 molecules placed in a cubic box with periodic boundary conditions. Short-ranged intermolecular interactions were cut off at half the box length, while standard Ewald sums with conducting boundaries were used to handle long-range Coulombic forces. Preliminary trajectories of 200 ps in the NPT ensemble were first run in order to equilibrate the system at 27 °C K and 1 atm. Production runs of 2 ns each were then generated in the microcanonical ensemble.