Theor Chem Account (2008) 121:247–255 DOI 10.1007/s00214-008-0470-3 REGULAR ARTICLE Metal induced molecular nano-extraction Aned de Leon · Abraham F. Jalbout Received: 28 May 2008 / Accepted: 17 July 2008 / Published online: 18 September 2008 © Springer-Verlag 2008 Abstract We have previously devised a “scorpion” like system which is composed of a zigzag (8,0) single walled carbon nanotube attached to a 20 ringed graphene sheet by a glycine dimer species. Theoretical density functional the- ory calculations on a potential mechanism driven by a metal induced charge transfer process has been proposed for the extraction of molecules from nanotubes. Keywords Polar molecules · Metals · SWNT · Carbon sheet · DFT-BLYP 1 Introduction The study of single walled nanotubes (SWNT) [1, 2] has many important implications in the field of material science as well as catalysis [3–5]. The unique structural features of these materials permit for interesting elucidations and reac- tive mechanisms to be undertaken. Additionally, the mechan- ical and chemical stability of SWNT materials allows for functionalizations [6, 7] to be performed. Multiple investiga- tions suggest contribute to their ability to distribute peptides, DNA fragments in vivo. The nanosystems under consideration present certain dis- advantages that should be addressed. Their hydrophilicity leads to toxicity in biological systems which limit A. de Leon · A. F. Jalbout Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510 Mexico D.F., Mexico A. F. Jalbout (B ) Departamento de Investigacion en Fisica, Universidad de Sonora Hermosillo, Sonora, Mexico e-mail: ajalbout@u.arizona.edu applications in drug design and discovery. Typically, carbon based systems are functionalized in order to resolve this prob- lem and enhance polar molecular and aqueous interactions. These processes are local transformations that do not lead to problematic structural situations without modification of their physical properties. The lack of specificity associated with SWNT materials is another issue of difficulty in performing chemical modifi- cations on their surfaces. This is intrinsically related to the nature of the carbon atoms in the nanotubes which are similar. To alleviate this matter novel complexes have synthesized to promote chemical differentiation. Theoretical calculations performed by our group suggest that nanotube systems can localize charge on their exterior as a result of charge transfer systems with endohedral met- als. The effect that is related to this issue is correlated to studies of ion transfer mechanisms on molecular surfaces. Small polar molecules have been demonstrated to interact on the interior cavity of SWNT systems [8] and on the exterior [9]. Amino acids can favorably interact with biomolecules [10–12] as well as with nanostructures [13] to form pep- tide interconnected species. The tips of the SWNT molecules can be modified with organic groups [13] to form interesting frameworks that posses variable properties [14–18]. In the present work we have exploited the ability of polar molecules to be stabilized on the surface of graphene sheets to develop a molecular extraction nano-device. Recently, we localized polar species on localized regions of extended lin- ear sheets [19] as well as to the interior of SWNT mole- cules [8]. While gold surfaces usually mediate connections of amino acids to SWNT structures [20] as a consequence of computational difficulties such models cannot be used. To compensate we designed a “scorpion” shaped (based on its interesting structural features) that is composed of a zigzag (8,0) SWNT connected to a 20 ring carbon sheet [21]. 123