The full potential of biomass as a resource for transportation fuels, fine chemicals or syngas can only be reached through improved understanding of the underlying conversion chemistry. This in turn means the development of predictive models, which will support the process design and optimization of a conversion process. Given the complexity of biomass, highly detailed model predictions will be impossible in the foreseeable future.

Another serious problem for fast pyrolysis processing is the high acid number of the bio-oils, which will cause corrosion in standard refinery units. Although the bio-oils can probably be processed using 317 stainless steel cladding, this material is not standard in refinery units making it difficult to introduce bio-oil into the existing refinery infrastructure. Therefore pyrolysis bio-oils require pre-processing to reduce the acid number before processing in typical refinery units. Research is needed to understand how to accomplish this pre-processing in an efficient manner.

Due to the complexity of the biomass pyrolysis  reaction system, the underlying chemistry is not well understood. Therefore, the correlations that  have been developed between bio-oil composition  and pyrolysis and condensation conditions are  empirical. The lack of basic understanding of the  reaction system limits the ability to draw general  relationships between biomass composition, pyrolysis  conditions, condensation conditions, and bio-oil  composition.

The complex and ill-defined issues related to biomass  conversion pose a huge challenge to the production  and widespread use of biofuels.

As biomass is routed through various liquid phase  processing steps, the degree of compositional complexity may increase, primarily due to the  complex chemistry of oxygen functional groups. Often this complexity may prohibit a detailed  analysis of what occurs during a reaction step. One way to address this issue is to use a model  compound, such as purified sugar, polyol, or a process intermediate, as a feedstock to a given  reaction step. Even in these cases, the products emanating from a reaction step may not be able to be fully characterized due to non-specific reactions.

Another major obstacle is to understand whether  and how the liquid phase affects reactions, for which there are known examples. There is yet no well-established methodology for describing reactions across the liquid-solid interface under the influence of the dynamics of the liquid, with quantum chemical accuracy. Ad-hoc or highly simplified models can be found in the literature that attempt to capture the effect of water on adsorption and reaction. Some of them may well be effective to some degree and can possibly be used beneficially, but no calibration of results is yet available, and better theoretical development is very much needed.