Comparison of classical reaction paths and tunneling paths studied with the semiclassical instanton theory.

Atom tunneling in the hydrogen atom transfer reaction of the 2,4,6-tri-tert-butylphenyl radical to 3,5-di-tert-butylneophyl, which has a short but strongly curved reaction path, was investigated using instanton theory. We found the tunneling path to deviate qualitatively from the classical intrinsic reaction coordinate, the steepest-descent path in mass-weighted Cartesian coordinates. To perform that comparison, we implemented a new variant of the predictor-corrector algorithm for the calculation of the intrinsic reaction coordinate. We used the reaction force analysis method as a means to decompose the reaction barrier into structural and electronic components. Due to the narrow energy barrier, atom tunneling is important in the abovementioned reaction, even above room temperature. Our calculated rate constants between 350 K and 100 K agree well with experimental values. We found a H/D kinetic isotope effect of almost 106 at 100 K. Tunneling dominates the protium transfer below 400 K and the deuterium transfer below 300 K. We compared the lengths of the tunneling path and the classical path for the hydrogen atom transfer in the reaction HCl + Cl and quantified the corner cutting in this reaction. At low temperature, the tunneling path is about 40% shorter than the classical path.

Nudged-elastic band used to find reaction coordinates based on the free energy.

Transition paths characterize chemical reaction mechanisms. In this paper, we present a new method to find mean reaction paths based on the free energy. A nudged elastic band (NEB) is optimized using gradients and Hessians of the free energy, which are obtained from umbrella integration. The transition state can be refined by a Newton-Raphson search starting from the highest point of the NEB path. All optimizations are done using Cartesian coordinates. Independent molecular dynamics (MD) runs are performed at each image used to discretize the path. This makes the method intrinsically parallel. In contrast to other free energy methods, the algorithm does not become more expensive when including more degrees of freedom in the active space. The method is applied to the alanine-dipeptide as a test case and compared to pathways that have been derived from metadynamics and forward flux sampling.

A Quadratically-Converging Nudged Elastic Band Optimizer.

Nudged elastic band (NEB) is a well established chain-of-states method to locate the minimum energy path in configuration space. Unfortunately, existing search algorithms suffer from slow convergence. We provide an analytic derivative of the nudged elastic band force, enabling a full Newton-Raphson optimization. For molecular systems, the components of the step belonging to translations and rotations are removed with an efficient algorithm. Minimization of the NEB force is ensured by reversing components for which the Newton-Raphson step would increase the force. We achieve quadratic convergence of this optimizer when applied to simple test cases where analytic Hessians are available: one analytic two-dimensional potential and a system of Lennard-Jones particles.

An algorithm to find minimum free-energy paths using umbrella integration.

The calculation of free-energy barriers by umbrella sampling and many other methods is hampered by the necessity for an a priori choice of the reaction coordinate along which to sample. We avoid this problem by providing a method to search for saddle points on the free-energy surface in many coordinates. The necessary gradients and Hessians of the free energy are obtained by multidimensional umbrella integration. We construct the minimum free-energy path by following the gradient down to minima on the free-energy surface. The change of free energy along the path is obtained by integrating out all coordinates orthogonal to the path. While we expect the method to be applicable to large systems, we test it on the alanine dipeptide in vacuum. The minima, transition states, and free-energy barriers agree well with those obtained previously with other methods.