The difficulty in simulating a large number of large molecules lies in the enormous difference in time scale between translational and intramolecular motions. If a molecular dynamics simulation is to model an event of microsecond duration, a computation time step on the order of a femtosecond is still required, making the simulation virtually impossible. One approach is to ignore intramolecular interactions (i.e., a hard spheres or rigid molecule model; see, for example, Chushak, Y. G.; Bartell, L. S. J. Phys. Chem. B 1999, 103, 11196), which may be adequate if the energy stored inside a molecule is unaltered. This excludes a number of important applications, such as MALDI and laser desorption/ionization of organic particles, which are based on the ability of molecules to absorb energy. Another approach is to combine all molecular motions into a single degree of freedom with a time scale that is chosen based on the phonon spectrum of the particle (Zhigilei, L. V.; Kodali, P. B. S.; Garrison, B. J. J. Phys. Chem. B 1997, 101, 2028). This approach has been used to model MALDI (Zhigilei, L. V.; Yingling, Y. G.; Itina, T. E.; Schoolcraft, T. A.; Garrison, B. J. Int. J. Mass Spectrom. 2003, 226, 85) and laser ablation of nanosized (Zhigilei, L. V.; Garrison, B. J. Appl. Surf. Sci. 1998, 129, 142) and micrometer-sized (Schoolcraft, T. A.; Constable, G. S.; Zhigilei, L. V.; Garrison, B. J. Anal. Chem. 2000, 72, 5143) particles, although the incorporation of chemical reactions is quite challenging in this approach due to the difficulty in enforcing energy conservation. We propose an alternative molecular dynamics model (based on the notion of dissipative particle dynamics with energy conservation, developed by Avalos and Mackie; see, Avalos, J. B.; Mackie, A. D. J. Chem. Phys. 1999, 111, 5267; Avalos, J. B.; Mackie, A. D Europhys. Lett. 1997, 40, 141) that uses concepts of statistical mechanics and thermodynamics of irreversible processes to describe the intramolecular energy. This is manifested in the definition of an internal molecular temperature, which describes the stored energy and governs the energy transfer into and out of the molecule. This model allows for the incorporation of some quantum statistical phenomena of the internal interactions and satisfies irreversibility of collision processes, while remaining computationally inexpensive. In this approach, criteria for chemical reactions to take place can be easily stated in terms of internal molecular temperatures and proximity of approach. Also energy conservation can be implemented in a computationally efficient manner. We apply the model to the laser ablation of chlorobenzene nanoparticles, a system similar to that studied by Yingling et al. (Yingling, Y. G.; Zhigilei, L. V.; Garrison, B. J. Nucl. Instrum. Methods Phys. Res., Sect. B 2001, 180, 171).