Here is a selection of online journals that contain organic chemistry:
Accounts of Chemical Research
Advanced Synthesis & Catalysis
Angewandte Chemie International Edition
ARKIVOC
Beilstein Journal of Organic Chemistry
Bioorganic & Medicinal Chemistry
Bioorganic & Medicinal Chemistry Letters
Chemical Communications
Chemical & Pharmaceutical Bulletin
Chemical Reviews
Chemical Society Reviews
Chemistry - A European Journal
Chemistry - An Asian Journal
Chemistry Letters
Current Organic Chemistry
Current Organic Synthesis
European Journal of Organic Chemistry
Helvetica Chimica Acta
Heterocycles
Journal of Antibiotics
Journal of the American Chemical Society
Journal of Chemical Research
Journal of the Chemical Society, Perkin Transactions 1 or 2
Journal of Medicinal Chemistry
Journal of Natural Products
Journal of Organic Chemistry
Journal of Organometallic Chemistry
Letters in Organic Chemistry
Natural Product Reports
Organic & Biomolecular Chemistry
Organic Letters
Organic Process Research & Development
Organometallics
Synthetic Communications
Tetrahedron
Tetrahedron: Asymmetry
Tetrahedron Letters
Thieme-connect for Synthesis and Synlett
For other electronic journals, see All Electronic Journals
For hard copy journals, search the journal name on the University library database: Star