Molecular crystals of dipeptides with a high density of uniform pores have received growing interest for gas separation. Particularly, hydrophobic dipeptides can form one-dimensional straight pores with sizes ranging from 0.37 to 0.50 nm. A molecular simulation study is reported here to investigate the membrane separation of CO2/N-2 and CO2/CH4 mixtures in eight dipeptides namely Ala-Val (AV), Val-Ala (VA), Ala-lle (AI), Ile-Ala (IA), Val-Ile (VI), Ile-Val (IV), Val-Val (VV) and Leu-Ser (LS). The gas permeation and separation performance are evaluated using a molecular dynamics simulation method with a constant-pressure difference. The pore size and helicity are revealed to be the key factors governing permeation. A higher permeability can be achieved in a dipeptide membrane with a larger pore size or a lower helicity. Among the eight, six (AV, LS, AI, VA, W and VI) surpass the Robeson upper bound for both gas mixtures. It is identified that AI and AV outperform other dipeptides for CO2/N-2 separation, while AI, VA and VV are better for CO2/CH4 separation. The permselective separation of both gas mixtures is dominated by the preferential sorption of CO2 over N-2 and CH4, respectively. This simulation study provides microscopic insights into CO2 separation in dipeptide membranes and suggests their potential use for gas separation. (C) 2020 Elsevier B.V. All rights reserved.