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What will happen if I incubate a clean gold surface in un-deprotected ($\ce{oligo-C6-S-SH}$) thiolated oligonucleotide solution instead of deprotected ($\ce{oligo-C6-SH}$) solution. I have read clean gold surface can cleave disulfide bond.

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    $\begingroup$ I don't have references at the ready, but I would expect the disulfide would cleave and you'd end up with oligo-$\ce{C6}$-S-Au on your surface $\endgroup$ – Geoff Hutchison Jul 13 '15 at 22:43
  • $\begingroup$ How stable are those hydrodisulfides? Wouldn't they be prone to disproportionation to things like oligo-S-S-oligo, oligo-S-S-S-oligo, and oligo-SH? $\endgroup$ – Curt F. Jul 13 '15 at 23:44
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What actually happens in sulfur-gold bonding is not very well known. There have been many proposals and studies done, well-summarized here. There is some evidence, including computational studies, that suggest that dissociation into two thiolates is energetically favourable. Bridging across protruding bits of gold (we often draw gold surfaces as straight lines, but they're seldom that flat) may also be involved. This case, where you only have a chain on one of the two sulfurs, may be less interesting and I haven't found many studies of terminal disulfides so the exact process might be different.

To answer the practical question, Can I stick a disulfide-functionalized molecule onto gold?, yes you can, and they will stick very well.

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