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We report a path integral molecular dynamics (PIMD) study of the temperature dependence of the spatial distribution of two and four H2molecules inside the large cage of the structure II clathrate hydrate. The PIMD calculations were performed at five temperatures ranging from 25 to 200 K. Their results were combined with those from an earlier diffusion Monte Carlo (DMC) study of this system at T= 0 K [Sebastianelli, F.; Xu, M.; Bačić, Z. J. Chem. Phys.2008, 129, 244706]. The spatial distribution of the confined H2molecules at each of the temperatures considered was characterized with the help of several one-dimensional (1D) and three-dimensional (3D) distribution functions of suitably chosen intermolecular coordinates, generated by the PIMD and DMC calculations. The 1D distribution that proved to be the most strongly temperature dependent, and also the most revealing about the structural properties of the system as a function of temperature, involves the H2−cage center−H2angle. In the case of four caged H2molecules, this angular distribution provides clear evidence that between 50 and ∼100 K the system undergoes a qualitative change. At 50 K and below, the system is fully localized in the global minimum of the intermolecular potential, corresponding to a tetrahedral configuration of H2molecules with a unique orientation relative to the cage frame. At temperatures of 75−100 K and higher, nearly degenerate local minima ∼200 cm−1above the global minimum become accessible and are increasingly sampled by the system. The 3D spatial distributions also show this growing delocalization above 75−100 K. Our findings are in accord with the localization−delocalization transition observed experimentally to occur at 50 K for four D2molecules in the large cage [Lokshin, K. A.; Zhao, Y.; He, D.; Mao, W. L.; Mao, H. K.; Hemley, R. J.; Lobanov, M. V.; Greenblatt, M. Phys. Rev. Lett.2004, 93, 125503].

When only equilibrium thermodynamics or averages of position-dependent functions in classical molecular dynamics calculations are sought, the choice of the atomic masses in the Hamiltonian becomes irrelevant. Consequently, the masses can be used as free parameters to help improve conformational sampling efficiency in the spirit of Bennett’s mass-tensor dynamics (Bennett, C. H.J. Comput. Phys.1975, 19, 267.). Here we report on the effect of reducing side-chain and solvent masses on the folding behavior of a 9-residue hairpin-forming peptide in solution. A physical motivation for reducing the solvent mass is an effective reduction in solvent viscosity. Side-chain mass scaling is motivated by the idea of solvent potentials of mean force which are employed in select coarse-grained protein models. In the limit of very large mass differences, the mass reduction effectively creates an adiabatic decoupling between solvent, side-chain, and backbone motions, so that both the backbone and side chains move on the instantaneous solvent potential of mean force (PMF) surface, and the backbone additionally moves on the side-chain PMF. Because of the arbitrariness in the choice of masses, this limit only needs to be reached approximately in practice. In particular, we show that a 10-fold reduction in solvent masses and a side-chain mass scale that is intermediate between the scaled solvent and the backbone lead to a quantitative enhancement in conformational sampling.