This study deals with the participation of 10 upper secondary chemistry students, aged 16-17, and their chemistry teacher in a pharmacochemistry research community on anti-allergy medicines at VU University, Amsterdam, The Netherlands. Participation of students in scientific research raises the question of how to bridge the gap between an upper secondary school inquiry practice and a scientific research practice. To bridge this gap, a design based on 6 principles derived from an educational model of a community of learners was proposed. The study first aimed at revealing whether the proposed principles were necessary according to the students, their teacher and three pharmacochemistry researchers for successful participation of the students in the research community. Second, the study examined whether the students' understanding of discipline-specific content knowledge, interest in scientific research and knowledge about the nature of science changed during the course of the study. Data were obtained from questionnaires, interviews and video tapes. The results indicated that according to the teacher all 6 principles were necessary to bridge the gap, whereas according to the students 1 principle and according to the pharmacochemistry researchers 2 principles were necessary but difficult to achieve. Furthermore, all students gained discipline-specific content knowledge. Their interest in scientific research exhibited a positive change and their knowledge about the nature of science increased. The implications for further research and practice are discussed. © 2013 Copyright Taylor and Francis Group, LLC.