DOI 10.1140/epje/i2005-10043-5 Eur. Phys. J. E 18, 201–206 (2005) T HE EUROPEAN P HYSICAL JOURNAL E Combined experimental and theoretical DFT study of molecular nanowires negative differential resistance and interaction with gold clusters S.Z´aliˇ s 1 , I. Kratochvilova 2, a , A. Zambova 3 , J. Mbindyo 3 , T.E. Mallouk 3 , and T.S. Mayer 3 1 J. Heyrovsk´ y Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejˇ skova 3, 18223 Praha 8, Czech Republic 2 Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Praha 8, Czech Republic 3 Department of Electrical Engineering and Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA Received 31 March 2005 and Received in final form 9 August 2005 / Published online: 21 October 2005 – c  EDP Sciences / Societ` a Italiana di Fisica / Springer-Verlag 2005 Abstract. Electric-field–assisted assembly has been used to place rod-shaped metal nanowires containing 4-[[2-nitro-4-(phenylethynyl) phenyl] ethynyl] benzenthiol molecules onto lithographically defined metal pads. These junctions exhibited negative differential resistance. The quantum chemical approach was used to compare the properties of Au-bonded 4-[[2-nitro-4-(phenylethynyl) phenyl] ethynyl] benzenthiol molecule and a molecule that does not exhibit the negative differential resistance, Au-bonded 4-[[4-(phenylethynyl) phenyl] ethynyl] benzenthiol. The influence of the static electric field and charge variation were modelled for both systems. PACS. 85.35.-p Nanoelectronic devices – 73.63.-b Electronic transport in nanoscale materials and struc- tures – 31.15.-p Calculations and mathematical techniques in atomic and molecular physics (excluding electron correlation calculations) 1 Introduction Molecular conductors represent the ultimate goal in de- vice miniaturization, with the added advantages of spon- taneous self-assembly, mechanical flexibility and chemical tenability. Recently, remarkable progress has been made in iden- tifying candidate molecules with interesting electronic properties such as molecular conduction, rectification, negative differential resistance (i.e. increased resistance with increasing voltage) and configurable switching [1– 10]. We observed large negative differential resistance behaviour at room temperature in an electronic de- vice that utilizes organic molecules as active compo- nents. We worked with nanowires containing 4-[[2-nitro- 4-(phenylethynyl) phenyl] ethynyl] benzenthiol (below re- ferred to as NDR molecules) integrated into a matrix of N- mercaptohexadecanoic acid molecules of the composition HS(CH 2 ) 15 COOH (below referred to as C 16 molecules) with Au contacts (see Fig. 1a). A detailed description of the formation of nanowires (containing metal top contact C 16 SAM as active region, and a metal bottom contact) has been already published [2,3]. a e-mail: hruba@fzu.cz The molecules in a nanopore were self-assembled on a gold surface, and sulphur atoms served as alligator clips to make the connection of the molecules to the gold terminal. The other terminal is built by gold vapour deposition to the H-terminated molecules. The exact nature of bonding to the gold terminals, especially the vapour-deposited side, has not been characterized experimentally. In earlier the- oretical and experimental reports, it was shown that one group of these molecules could act as molecular resonant diodes, presenting negative differential resistance [1–10]. Understanding the correlation between the chem- ical and electric properties of various types of the molecules is a first step towards developing a bottom-up molecule-based technology. The electronic transport through molecules has been previously described using several theoretical approaches —quantum chemical com- putation and Landauer-B¨ uttiker–type theory, hopping models, tight-binding model, etc. [11–15]. The system dif- fers from conventional solid-state devices where conduc- tion is understood in terms of alignment of a band struc- ture. In contrast to conventional chemistry, the molecule is not an isolated unit in equilibrium. Coupling with metal- lic contacts makes the system an open one, capable of freely exchanging a fractional amount of charge to and