Various chemicals are being explored for catalyzing efficient lignocellulose deconstruction. In particular, when liquid ammonia is used to convert the naturally occurring cellulose crystalline phase I(beta), to cellulose Mb the rearrangement of the hydrogen bond network in cellulose III(I) results in enhanced hydrolysis yields. We use molecular dynamics simulations to analyze the interaction between a cellulose I(beta) fibril and ammonia. Our simulations reveal that early structural changes in the fibril are driven by the rapid formation of an extended hydrogen bond network between the solvent-exposed surface chains and ammonia that precedes ammonia penetration into the fibril. The emergence of this hydrogen bond network causes relative shifting of the cellulose layers within the fibril that in turn leads to the formation of channels orthogonal to the (100) and (-100) fibril surfaces. The channels allow ammonia molecules to penetrate into the cellulose fibril. These findings provide avenues for improving existing chemical pretreatments to make them more effective and economical.