We probe the single molecule-polymer interactions for two types of carbocyanine dyes having the same conjugated core but different side chains. Several conformers of the conjugated core were observed and could be assigned owing to quantum chemistry and molecular dynamics simulations. The relative population of the various conformers is different for the two types of probe molecules in (non) annealed films. The presented results and discussion, of high interest from a fundamental point of view, might also be of primordial importance for the understanding of the plasticizing effect in polymers on a very local scale. (C) 2009 Elsevier B. V. All rights reserved.