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Processes to produce biofuels from biomass is provided where the biomass is contacted with an aqueous media to form a extracted biomass and at least a portion of an aqueous liquor separated from the extracted biomass containing soluble carbohydrate is treated with a purification substrate to form a

Processes to produce biofuels from biomass is provided where the biomass is contacted with an aqueous media to form a extracted biomass and at least a portion of an aqueous liquor separated from the extracted biomass containing soluble carbohydrate is treated with a purification substrate to form a treated carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content, based on the untreated aqueous liquor stream prior to contact with a hydrogenolysis catalyst to form a plurality of oxygenated intermediates that can be further processed to form a liquid fuel. An extracted biomass solids stream is also separated from the extracted biomass which is contacted with a first digestive solvent to form a pretreated biomass and then a second digestive solvent to form a solubilized pulp comprising soluble carbohydrates.

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1. A method comprising: (i) providing a biomass containing celluloses, hemicelluloses and lignin;(ii) contacting the biomass with an aqueous media to form a extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin;(iii) separating at least a portion of an aqueous liq

1. A method comprising: (i) providing a biomass containing celluloses, hemicelluloses and lignin;(ii) contacting the biomass with an aqueous media to form a extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin;(iii) separating at least a portion of an aqueous liquor from the extracted biomass thereby providing the aqueous liquor stream comprising soluble carbohydrates and a pretreated biomass solids stream comprising celluloses, hemicelluloses, and lignin;(iv) contacting said extracted biomass solids stream with a first digestive solvent to form a pretreated biomass comprising celluloses, residual hemicelluloses and lignin;(v) contacting said pretreated biomass with a second digestive solvent to form a solubilized pulp comprising soluble carbohydrates;(vi) contacting the aqueous liquor stream with a purification substrate effective to remove sulfur compounds and nitrogen compounds thereby producing a treated carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content based on the untreated aqueous liquor stream;(vii) contacting the treated carbohydrate stream and the solubilized pulp stream directly with hydrogen in the presence of a hydrogenolysis catalyst to form a plurality of oxygenated intermediates wherein a first portion of the oxygenated intermediates are recycled to form the second digestive solvent; and(viii) processing at least a second portion of the oxygenated intermediates to form a liquid fuel. 2. The method of claim 1 wherein the purification substrate is selected from the group consisting of activated carbons, aluminas, silicas, silica-aluminas, clay minerals, diatomatious earth, zirconia, titania, polymeric adsorbents, and ion-exchange resins. 3. The method of claim 2 wherein the purification substrate is an ion exchange resin. 4. The method of claim 1 wherein the oxygenated intermediates is subjected to condensation to produce a liquid fuel. 5. The method of claim 1 wherein the oxygenated intermediates is subjected to dehydration and alkylation to produce a liquid fuel. 6. A method comprising: (i) providing a biomass containing celluloses, hemicelluloses and lignin;(ii) contacting the biomass with an aqueous media to form an extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin;(iii) separating at least a portion of an aqueous liquor from the extracted biomass thereby providing the aqueous liquor stream comprising soluble carbohydrates and a pretreated biomass solids stream comprising celluloses, hemicelluloses, and lignin;(iv) contacting said extracted biomass solids stream with a first digestive solvent to form a pretreated biomass comprising celluloses, and residual hemicelluloses and lignin;(v) contacting said pretreated biomass with a second digestive solvent to form a solubilized pulp comprising soluble carbohydrates wherein at least a portion of the solubilized pulp is provided to the aqueous liquor stream;(vi) contacting the aqueous liquor stream with a purification substrate effective to remove sulfur compounds and nitrogen compounds thereby producing a treated carbohydrate stream having less than 35% of the sulfur content and less than 35% nitrogen content based on the untreated aqueous liquor stream;(vii) contacting the treated carbohydrate stream directly with hydrogen in the presence of a hydrogenolysis catalyst to form a plurality of oxygenated intermediates wherein a first portion of the oxygenated intermediates are recycled to form the second digestive solvent; and(viii) processing at least a second portion of the oxygenated intermediates to form a liquid fuel. 7. The method of claim 6 wherein the purification substrate is selected from the group consisting of activated carbons, aluminas, silicas, silica-aluminas, clay minerals, diatomatious earth, zirconia, titania, polymeric adsorbents, and ion-exchange resins. 8. The method of claim 7 wherein the purification substrate is an ion exchange resin. 9. The method of claim 6 wherein the oxygenated intermediates is subjected to condensation to produce a liquid fuel. 10. The method of claim 6 wherein the oxygenated intermediates is subjected to dehydration and alkylation to produce a liquid fuel. 11. The method of claim 1 wherein the pretreated biomass and the second digestive solvent is operated counter-currently and the countercurrent solvent is provided to the aqueous medium counter-currently to the biomass stream. 12. A method comprising (i) providing a biomass containing celluloses, hemicelluloses and lignin; (ii) contacting the biomass with an aqueous media to form a extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin; (iii) separating at least a portion of an aqueous liquor from the extracted biomass thereby providing the aqueous liquor stream comprising soluble carbohydrates, and a extracted biomass solids stream comprising celluloses, hemicelluloses, and lignin; (iv) contacting said extracted biomass solids stream with a first digestive solvent to form a pretreated biomass comprising celluloses, and residual hemicelluloses; (v) contacting said pretreated biomass with a second digestive solvent to form a solubilized pulp comprising soluble carbohydrates wherein at least a portion of the solubilized pulp is provided to the aqueous media; (vi) contacting the aqueous liquor stream with a purification substrate effective to remove sulfur compounds and nitrogen compounds thereby producing a treated carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content, based on untreated aqueous liquor stream thereby producing a treated aqueous liquor carbohydrate stream; (vii) contacting the treated carbohydrate stream directly with hydrogen in the presence of a hydrogenolysis catalyst to form a plurality of oxygenated intermediates wherein the a first portion of the oxygenated intermediates are recycled to form the second digestive solvent; and (viii) processing at least a second portion of the oxygenated intermediates to form a liquid fuel. 13. The method of claim 12 wherein the purification substrate is selected from the group consisting of activated carbons, aluminas, silicas, silica-aluminas, clay minerals, diatomatious earth, zirconia, titania, polymeric adsorbents, and ion-exchange resins. 14. The method of claim 13 wherein the purification substrate is an ion exchange resin. 15. The method of claim 12 wherein the oxygenated intermediates is subjected to condensation to produce a liquid fuel. 16. The method of claim 12 wherein the oxygenated intermediates is subjected to dehydration and alkylation to produce a liquid fuel. 17. A system comprising: a system comprises: a vessel that receives a biomass feedstock and an aqueous media operating under conditions effective to produce a extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin and discharges an aqueous liquor stream comprising soluble carbohydrates; a digester that receives the extracted biomass and a first digestive solvent operating under conditions effective to produce a pretreated biomass comprising celluloses, and residual hemicelluloses and lignin; a vessel that receives the pretreated biomass and a second digestive solvent operating under conditions effective to produce a solubilized pulp comprising soluble carbohydrates; an aqueous liquor treater comprising a purification substrate that receives the aqueous liquor and discharges a treated carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content, based on the untreated aqueous liquor stream; a hydrogenolysis reactor comprising a hydrogenolysis catalyst that receives hydrogen and the treated carbohydrate stream and the solubilized pulp and discharges an oxygenated intermediate stream, wherein a first portion of the oxygenated intermediate stream is recycled as the second digestive solvent to the vessel that receives the pretreated biomass to form the solubilized pulp; a first fuels processing reactor comprising a dehydrogenation catalyst that receives a second portion of the oxygenated intermediate stream and discharges an olefin-containing stream; and a second fuels processing reactor comprising an alkylation catalyst that receives the olefin-containing stream and discharges a liquid fuel. 18. A system comprising: a vessel that receives a biomass feedstock and an aqueous media operating under conditions effective to produce a extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin and discharges an aqueous liquor stream comprising soluble carbohydrates; a digester that receives the extracted biomass and a first digestive solvent operating under conditions effective to produce a pretreated biomass comprising celluloses, residual hemicelluloses and lignin; a vessel that receives the pretreated biomass and a second digestive solvent operating under conditions effective to produce a solubilized pulp comprising soluble carbohydrates; an aqueous liquor treater comprising a purification substrate that receives the aqueous liquor and the solubilized pulp and discharges a treated carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content based on the untreated aqueous liquor stream; a hydrogenolysis reactor comprising a hydrogenolysis catalyst that receives hydrogen and the treated carbohydrate stream and discharges an oxygenated intermediate stream, wherein a first portion of the oxygenated intermediate stream is recycled to the vessel that receives the pretreated biomass to form the solubilized pulp; and a fuels processing reactor comprising a condensation catalyst that receives a second portion of the oxygenated intermediate stream and discharges a liquid fuel. 19. A system comprising: a vessel that receives a biomass feedstock and an aqueous media operating under conditions effective to produce a extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin and discharges an aqueous liquor stream comprising soluble carbohydrates; a digester that receives the extracted biomass and a first digestive solvent operating under conditions effective to produce a pretreated biomass comprising celluloses, residual hemicelluloses and lignin; a vessel that receives the pretreated biomass and a second digestive solvent operating under conditions effective to produce a solubilized pulp comprising soluble carbohydrates; an aqueous liquor treater comprising a purification substrate that receives the aqueous liquor and discharges a treated aqueous liquor carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content based on the untreated aqueous liquor stream; a hydrogenolysis reactor comprising a hydrogenolysis catalyst that receives hydrogen and the treated aqueous liquor carbohydrate stream and discharges an oxygenated intermediate stream, wherein a first portion of the oxygenated intermediate stream is recycled as the second digestive solvent to the vessel that receives the pretreated biomass to form the solubilized pulp; and at least a portion of the solubilized pulp is recycled to the vessel that receives the biomass feedstock to comprise at least a portion of the aqueous media, and a fuels processing reactor comprising a condensation catalyst that receives a second portion of the oxygenated intermediate stream and discharges a liquid fuel. 20. A system comprising: a vessel that receives a biomass feedstock and an aqueous media operating under conditions effective to produce a extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin and discharges an aqueous liquor stream comprising soluble carbohydrates; a digester that receives the extracted biomass and a first digestive solvent operating under conditions effective to produce a pretreated biomass comprising celluloses, residual hemicelluloses and lignin; a vessel that receives the pretreated biomass and a second digestive solvent operating under conditions effective to produce a solubilized pulp comprising soluble carbohydrates; an aqueous liquor treater comprising a purification substrate that receives the aqueous liquor and discharges a treated aqueous liquor carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content based on the untreated aqueous liquor stream; a hydrogenolysis reactor comprising a hydrogenolysis catalyst that receives hydrogen and the treated aqueous liquor carbohydrate stream and discharges an oxygenated intermediate stream, wherein a first portion of the oxygenated intermediate stream is recycled as the second digestive solvent to the vessel that receives the pretreated biomass to form the solubilized pulp; and at least a portion of the solubilized pulp is recycled to the vessel that receives the biomass feedstock to comprise at least a portion of the aqueous media; a first fuels processing reactor comprising a dehydrogenation catalyst that receives a second portion of the oxygenated intermediate stream and discharges an olefin-containing stream; and a second fuels processing reactor comprising an alkylation catalyst that receives the olefin-containing stream and discharges a liquid fuel.