Many methods are currently available for estimating physicochemical properties of atmospherically relevant compounds. Though a substantial body of literature has focused on the development and intercomparison of methods based on molecular structure, there has been an increasing focus on methods based only on molecular formula. However, prior work has not quantified the extent to which isomers of the same formula may differ in their properties or, relatedly, the extent to which lacking or ignoring molecular structure degrades estimates of parameters. Such an evaluation is complicated by the fact that structure-based methods bear significant uncertainty and are typically not well constrained for atmospherically relevant molecules. Using species produced in the modeled atmospheric oxidation of three representative atmospheric hydrocarbons, we demonstrate here that estimated differences between isomers are greater than differences between three widely used estimation methods. Specifically, isomers tend to differ in their estimated vapor pressures and Henry's law constants by a half to a full order of magnitude greater than differences between estimation methods, and they differ in their rate constant for reaction with OH radicals (k.sub.OH) by a factor of 2. Formula-based estimation of these parameters, using certain methods, is shown to agree with structure-based estimates with little bias and approximately normally distributed error. Specifically, vapor pressure can be estimated using a combination of two existing methods, Henry's law constants can be estimated based on vapor pressure, and k.sub.OH can be approximated as a constant for all formulas containing a given set of elements. Formula-based estimation is, therefore, reasonable when applied to a mixture of isomers but creates uncertainty commensurate with the lack of structural information.