Showing papers by "Adrian E. Roitberg published in 2005"
TL;DR: A novel technique for computing free energy profiles in enzymatic reactions using the multiple steering molecular dynamics approach in the context of an efficient QM-MM density functional scheme is presented.
Abstract: A novel technique for computing free energy profiles in enzymatic reactions using the multiple steering molecular dynamics approach in the context of an efficient QM−MM density functional scheme is presented. The conversion reaction of chorismate to prephenate catalyzed by the Bacillus subtilis enzyme chorismate mutase has been chosen as an illustrative example.
107 citations
TL;DR: The rate constants obtained with the TDC are extremely sensitive to the phenyl group rotation, whereas the constants computed with the Förster model and the IDA are not, and the temperature dependence of the rate constant for energy transfer is predicted.
Abstract: We present a theoretical investigation of energy transfer in the phenylene ethynelene dendrimer known as the nanostar. Data from extensive molecular dynamics simulations are used to model the dynamical effects caused by torsional motion of the phenyl groups. We compare rate constants for energy transfer between the two-ring chromophore and the three-ring chromophore obtained via the Forster model, the ideal dipole approximation (IDA), and the transition density cube (TDC) method, which has as its limit an exact representation of the Coulombic coupling. We find that the rate constants obtained with the TDC are extremely sensitive to the phenyl group rotation, whereas the constants computed with the Forster model and the IDA are not. The implications of these results for the interpretation of recent pump-probe experiments on the nanostar are discussed in detail. Finally, we predict the temperature dependence of the rate constant for energy transfer.
52 citations
TL;DR: In this article, the authors focus on nonequilibrium approaches to free energy calculations, and propose the Jarzynski relationship (JR) which takes the exponentially weighted average of the work distribution.
Abstract: Publisher Summary This chapter focuses on nonequilibrium approaches to free energy calculations. Free energies are central quantities to both thermodynamics and kinetics, relating to experimentally determined properties, such as equilibrium constants and reaction rates. Even though proper computation of enthalpies is relatively simple at particular molecular conformations, the estimates of entropic factors require sampling over large numbers of conformations. Under quasi-static (QS) conditions, the distribution of work values is very nearly a delta function. Under any transformation rate larger than zero, two things happen at the same time: the average work gets larger as the rate increases, while the width of the work distribution also increases. The Jarzynski relationship (JR) takes the exponentially weighted average of this distribution. The net effect of this nonlinear averaging is to pick, from the work distribution, trajectories that are low in work values. The number of these trajectories decreases drastically with an increase of the transformation rate, and hence the effort required to converge the nonexponential average increases quickly.
7 citations