A recent study using differential scanning calorimetry (DSC) showed that the thermotropic phase behavior of 1,2-dipalmitoyl-sn-glycero-3-thiophosphocholine (DPPsC) is sensitive to the configuration at phosphorus and that the Rp isomer displayed only a broad transition at 45.6 degrees C [Wisner, D. A., Rosario-Jansen, T., & Tsai, M.-D. (1986) J. Am. Chem. Soc. 108, 8064-8068]. We have employed X-ray diffraction, 31P NMR, and Fourier transform infrared (FT-IR) spectroscopy to characterize various phases of the isomers of DPPsC, to compare the structural differences between 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and isomers of DPPsC, and to identify structural factors responsible for the unique behavior of the RP isomer. The results from all three techniques support the previous proposal based on DSC studies that (SP)- and (RP + SP)-DPPsC undergo a subtransition, a pretransition, and a main transition analogous to those of DPPC, while (RP)-DPPsC is quite stable at the subgel phase and undergoes a direct subgel----liquid-crystalline transition at 46 degrees C. Quantitative differences between DPPC and DPPsC (i.e., the effect of sulfur substitution rather than the configurational effect) in the subgel phase have also been observed in the chain spacing, the motional averaging, and the factor group splitting (revealed by X-ray diffraction, 31P NMR, and FT-IR, respectively). In particular, DPPsC isomers are motionally rigid and show enhanced factor group splitting in the subgel phase. These results suggest that DPPsC is packed in different subcells relative to DPPC in the subgel phase.(ABSTRACT TRUNCATED AT 250 WORDS)