Conditioning of biomass hydrolysates prior to fermentation is essential in the production of bioethanol. The removal of acetic acid, furfural and 5-hydroxymethylfurfural by membrane extraction has been investigated. Removal of these compounds is essential in order to maximize ethanol yields. The organic phase consisted of Alamine 336 in octanol. Ab initio calculations, coupled with the implicit continuum solvation method were performed in order to determine the free energies associated with extraction of acetic acid, furfural and 5-hydroxymethylfurfural from an aqueous to organic phase in the presence and absence of a tertiary amine. Due to complexation between amines and acetic acid, furfural and 5-hydroxymethylfurfural, extraction from an aqueous to organic phase becomes favorable. The formation of acetic acid dimers in octanol also appears to be favorable. Experimentally, layer by layer deposition of polyelectrolytes onto flat sheet polypropylene membranes has been conducted in order to improve the extraction performance during biomass conditioning. The resulting membranes have one hydrophilic surface while the other surface remains hydrophobic. The results obtained here indicate the importance of choosing an appropriate solvent and membrane surface chemistry that maximizes extraction of compounds that are toxic to the micro-organisms during fermentation. Finally the advantages of using amphiphilic polymeric membranes are discussed. (c) 2012 Elsevier B.V. All rights reserved.