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Molecules 2010, 15, 8641-8688; doi:10.3390/molecule OPEN ACCESS molecules ISSN 1420-3049 /journal/molecules Review Supramolecular Self-Assembled Chaos: Polyphenolic Lignin’s Barrier to Cost-Effective Lignocellulosic Biofuels Komandoor Elayavalli Achyuthan 1,2,*, Ann Mary Achyuthan 3, Paul David Adams 1,4, Shawn Matthew Dirk 2, Jason Carl Harper 2, Blake Alexander Simmons 1,5 and Anup Kumar Singh 1,5 1 Joint BioEnergy Institute (JBEI), Emeryville, CA 94550, USA 2 Sandia National Laboratories, Albuquerque, NM 87185, USA; E-Mails: smdirk@ (S.M.D.); jcharpe@ (J.C.H.) 3 Biology Department, Northern New Mexico College, Espanola, NM 87532, USA; E-Mail: annachyuthan@ (A.M.A.) 4 Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; E-Mail: pdadams@ 5 Sandia National Laboratories, Livermore, CA 94550, USA; E-Mails: basimmo@ (B.A.S.); aksingh@ (A.K.S.) * Author to whom correspondence should be addressed; E-Mail: kachyut@; Tel.: +1-505-284-8979; Fax: +1-505-844-1198. Received: 15 October 2010; in revised form: 22 November 2010 / Accepted: 25 November 2010 / Published: 29 November 2010 Abstract: Phenylpropanoid metabolism yields a mixture of monolignols that undergo chaotic, non-enzymatic reactions such as free radical polymerization and spontaneous self- assembly in order to form the polyphenolic lignin which is a barrier to cost-effective lignocellulosic biofuels. Post-synthesis lignin integration into the plant cell wall is unclear, including how the hydrophobic lignin incorporate