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We use X-ray morphological measurements and the scatter of clusters about observed and simulated scaling relations to examine the impact of merging and core-related phenomena on the structure of galaxy clusters. We use a range of X-ray and near-infrared (near-IR) scaling relations; all observed scaling relations constructed from emission-weighted mean temperature and intracluster medium mass, X-ray luminosity, isophotal size, and near-IR luminosity show a separation between clusters identified as cool core (CC) and those identified as non-cool core (NCC). We attribute this partially to a simple temperature bias in CC clusters and partially to other cool core-related structural changes. Scaling relations constructed from observables that are largely independent of core structure show smaller separation between CC and NCC populations. We attempt to minimize CC-related separation in scaling relations via two methods: by applying a uniform scale factor to CC cluster temperatures and determining the scale factor for each relation that minimizes the separation between CC and NCC populations, and by introducing cluster central surface brightness as a third parameter in observable-temperature scaling relations. We find an average temperature bias factor of 1.07 +/- 0.02 between the CC and NCC populations; the three-parameter approach reduces scatter in scaling relations more than a simple CC temperature scaling. We examine the scatter about the best-fit observable-temperature-brightness scaling relations and compare the intrinsic scatter within subsamples split by CC/NCC and four different morphological merger indicators. CC clusters and clusters with less substructure generally exhibit higher scatter about scaling relations. The larger structural variations in CC clusters are present well outside the core, suggesting that a process more global than core radiative instability is at work. Simulations without cooling mechanisms also show no correlation between substructure and larger scatter about scaling relations, indicating that any merger-related scatter increases are subtle. Taken together, the observational and simulation results indicate that cool core-related phenomena-not merging processes-are the primary contributor to scatter in scaling relations. Our analysis does not appear to support the scenario in which clusters evolve cool cores over time unless they experience major mergers

Effects of Mergers and Core Structure on the Bulk Properties of Nearby Galaxy Clusters