This paper studies the development of autonomic and secure Virtual Organisations (VOs) when following the chemical programming paradigm. We have selected the Higher-Order Chemical Language (HOCL) as the representative of the chemical paradigm, due mainly to its generality, its implicit autonomic property, and its potential application to emerging computing paragidms such as Grid computing and service computing. We have advocated the use of aspect-oriented techniques, where autonomicity and security can be seen as cross-cutting concerns impacting the whole system. We show how HOCL can be used to model VOs, exemplified by a VO system for the generation of digital products. We develop patterns for HOCL, including patterns for traditional security properties such as authorisation and secure logs, as well as autonomic properties such as self-protection and self-healing. The patterns are applied to HOCL programs following an aspect-oriented approach, where aspects are modelled as transformation functions that add to a program a cross-cutting concern.