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In-cylinder engine modeling is a necessary aspect of combustion research. In particular, simulating heat release connects variable combustion behavior to fuel properties through the 1st Law of Thermodynamics. One extension of such models is to evaluate changes to in-cylinder behavior using the Second Law of Thermodynamics in order to identify the peak period of availability for work extraction. Thus, Second Law models are a useful tool to augment research into alternative fuel usage and optimization. These models also help identify internal irreversibilities that are separate from heat transfer and exhaust gas losses. This study utilizes a multi-zone 1st and 2nd Law Heat Release model to characterize the changes in combustion behavior of a number of neat fuels used in a single-cylinder compression ignition (CI) engine.