Some years back, after a conversation with Fr. David Coffey here at Marquette University, I put together a one-page handout containing locations in Thomas's writings where he seemed to me to speak in earnest about what we call 'pure nature'—though the Thomist in me is always leery of denominating anything 'pure.'

Certainly the list can be longer than the one found here. If you have passages that strike you as touching upon this topic, please share them in the comments. Here's the list, followed by a link to a PDF of the file. 

Loca de natura pura tractantia

• In II Sent., d. 31, a. 1, a. 2, ad 3.
• Quodlibetum I, q. 4, a. 3.
• In II Sent., d. 29, q. 1, a. 2, in corp.
• Summa theologiae, I, q. 62, a. 3, in corp.
• Summa theologiae, I, q. 95, a. 1, in corp.
• In II Sent., d. 29, a. 1, a. 2, in corp.
• Summa theologiae, I, q. 57, a. 5, in corp.
• Summa theologiae, III, q. 2, a. 10, in corp.
• Summa theologiae, III, a. 1, a. 3, in corp.
• De veritate, q. 14, a. 10, ad 1 et 2.
• De veritate, q. 6, a. 2, in corp.
• Summa theologiae, I, q. 58, a. 5, in corp.
• De malo, q. 5, a. 3, ad 1; a. 1, ad 15; q. 4, a. 1, ad 14.
• In II Sent., d. 29, q. 1, a. 1, ad 4; d. 30, q. 1, a. 1, in corp.
• De malo, q. 5, a. 2, in corp.
• Vide et. Caietanum, in Summa theologiae, I, q. 82, a. 1, no. 7. 

You can grab a PDF of the file here.