June 16, 2008 MC-TINKERATE–version 2008 1 Manual MC-TINKERATE – version 2008/P9.1–M2008 Titus V. Albu, Oksana Tishchenko, José C. Corchado, Yongho Kim, Jordi Villà, Jianhua Xing, Hai Lin, Masahiro Higashi, and Donald G. Truhlar Department of Chemistry and Supercomputer Institute University of Minnesota, Minneapolis, Minnesota 55455 Program version: 2008/P9.1–M2008 Program version date: June 16, 2008 Manual version date: June 16, 2008 Copyright 2002−2008 Abstract: MC-TINKERATE is a computer program for carrying out calculations of chemical reaction rates of polyatomic species by using single-configuration molecular mechanics (SCMM) methods or multi-configuration molecular mechanics (MCMM) methods available in MC- TINKER to calculate the potential energy surface and by using POLYRATE for the dynamics. The interface between POLYRATE and MC-TINKER is based on the POLYRATE hooks protocol. The dynamical methods used are variational or conventional transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. Rate constants may be calculated by any of the methods available in the POLYRATE program for canonical or microcanonical ensembles or for specific vibrational states of selected modes with translational, rotational, and other vibrational modes treated thermally. MC-TINKER is based on TINKER by J. W. Ponder. In MC-TINKER both SCMM and MCMM calculations are available. In SCMM calculations, potential energies, gradients, and Hessians can be calculated by any of the well-established methods in TINKER; however, such methods are not useful for investigating processes involving bond breaking, bond making, or bond rearrangement. In MCMM calculations, the diagonal elements of the MCMM configuration interaction matrix are calculated on the fly by MC-TINKER (using TINKER routines), and the off-diagonal elements of the MCMM configuration interaction matrix are fitted to reproduce electronic structure theory data that are read from an external file. In this respect, MCMM serves as an advanced form of direct dynamics.