This paper studies security engineering of distributed systems when following the chemical-programming paradigm, represented here by the High-Order Chemical Language (HOCL). We have analysed how to model secure systems using HOCL. Emphasis is on modularity, hence we advocate for the use of aspect-oriented techniques, where security is seen as a cross-cutting concern impacting the whole system. We show how HOCL can be used to model Virtua  Organisations (VOs), exemplified by a VO system for the generation of digital products. We also develop security patterns for HOCL, including patterns for security properties such as authorisation, integrity and secure logs. The patterns are applied to HOCL programs following an aspectoriented approach, where aspects are modelled as transformation functions that add to a program a cross-cutting concern.