Gaussian molecular simulation

Shan YB, Klepeis JL, Eastwood MP, Dror RO, Shaw DE (2005) Gaussian split Ewald A fast Ewald mesh method for molecular simulation. J Chem Phys 122 054101... 

Rambusch, T. Hollmann-Gloe, K. Gloe, K. J. Prakt. Chem. 1999, 341, 202. Cerius Version 3.5 Molecular Simulations Inc., San Diego, CA. GAUSSIAN 98 Revision A.5, Gaussian Inc., Pittsburgh, PA, 1998. 

INDO/S Kotzian M, RoschN, Zemer MC (1992) Theor Chim Acta 81 201 (b) ZINDO/S is a version of INDO/S with some modifications, plus the ability to handle transition metals. The Z comes from the name of the late Professor Michael C. Zemer, whose group developed the suite of (mostly semiempirical) programs called ZINDO, which includes ZINDO/S. ZINDO is available from, e.g., Molecular Simulations Inc., San Diego, CA, and CAChe Scientific, Beaverton, OR. INDO and ZINDO are available in some program suites, e.g. Gaussian [55]... 

Figure 3 Comparison of PSDs obtained using the Dubinin-Stoeckli (DS), Horvalh-Kawazoe (HK), and density fitnctional theory (DFT) methods to interpret an isotherm generated from molecular simulation of nitrogen adsorption in a model carbon that has an Gaussian distribution of slit pore widths (18]. Results are shown for mean pore widths of 8.9 A (left) and 16.9 A (right).

This chapter is organized as follows. Section 18.2 describes the theoretical foundation of Marcus theory, formulated in a molecular rather than dielectric continuum solvent framework. Its non-Gaussian extension is presented in section 18.3 and its implications for rate calculations are discussed in section 18.4. The theory is then confronted to various molecular simulation results in section 18.5 and a conclusion is proposed in section 18.6. 

It should be noted, however, that the quantity AE, is not an experimental observable but it can be tested by molecular simulations this is done in section 18.5. We turn below to possible experimental evidences of the breakdown of Marcus Gaussian solvation theory, namely the study of reaction rate/free energy relationships. 

Molecular. simulators (e.g., Gaussian) are used to make predictions of the activation energy. 

The following are programs created specifically for force field based simulations. There are also molecular mechanics programs bundled with the Spartan, Gaussian, and Hyperchem products discussed previously in this appendix. 

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