Generally, there are three options.
Option 1 is to work on the FTE-basis (full time equivalent). In case of process development or synthesis of novel compounds, this is the preferable option for us. Our FTE includes work of one chemist, basic chemicals and basic analysis (HPLC, NMR). Cost for basic chemicals and basic analysis should not exceed 5% of FTE cost. FTE cost does not cover any special chemicals (which are sometimes quite expensive) or any additional analyses (AAS, elemental analysis etc).
Option 2 is the fixed price per compound. The conditions may vary case by case. Normally we offer the fixed price only if already know the synthesis or we do not consider the risk too high.
Option 3 is a combination of short feasibility study (offered at fixed price) and estimation of the production costs. After the feasibility study is carried out and we are sure the synthetic route actually works, we will recalculate the production costs.