In Silico Modeling of Indigo and Tyrian Purple Single-Electron Nano-Transistors Using Density Functional Theory Approach
© The Author(s). 2017
Received: 24 April 2017
Accepted: 8 June 2017
Published: 5 July 2017
The purpose of this study was to develop and implement an in silico model of indigoid-based single-electron transistor (SET) nanodevices, which consist of indigoid molecules from natural dye weakly coupled to gold electrodes that function in a Coulomb blockade regime. The electronic properties of the indigoid molecules were investigated using the optimized density-functional theory (DFT) with a continuum model. Higher electron transport characteristics were determined for Tyrian purple, consistent with experimentally derived data. Overall, these results can be used to correctly predict and emphasize the electron transport functions of organic SETs, demonstrating their potential for sustainable nanoelectronics comprising the biodegradable and biocompatible materials.
The development of organic semiconductors that are capable of both hole and electron transport is of pivotal importance in designing new organic field-effect transistors (OFET) and optoelectronic nanodevices [1, 2]. Recently, the use of indigoids has been widely explored in such devices with a view to the creation of natural and sustainable semiconductors [3–5]. These botanical substances were derived from the plants Indigofera tinctoria and Isatis tintora and have been employed as organic dyes for the textile industry .
Indigoids, including indigo and its derivative, Tyrian purple, are insoluble agents with a very high melting point, a property which is explained by the presence of inter- and intramolecular stabilizing hydrogen bonds (H-bonds). On the other hand, the existence of π-skeleton intermolecular interactions also strongly influences the charge transport within indigo thin films . Both materials are stable in terms of degradation within aerated conditions  and tend to form tiny and highly crystalline films upon evaporation, which exhibit promising charge transport properties . Recent studies have also reported the development of indigo-based OLEDs (organic light-emitting diodes) and OFET devices due to the visible and near-infrared absorption spectra and electron transport characteristics of indigoid molecules [8, 9]. In particular, indigo and Tyrian purple show high and almost perfectly balanced electron and hole charge transport in OFET, owing to their reversible two-electron reduction and oxidation . Another example of OLED devices contained a metal of 5-hydroxy-quinoxaline as a host component and indigo-based electroluminescent layer as a dopant material, comprising of a bisphenyl-squarilium compound .
Various computational approaches have been adapted and successfully implemented in the modeling of coherent transport in different types of molecular junctions, including density-functional theory (DFT), in combination with non-equilibrium Green’s functions or semi-empirical methods [11–14]. However, none of these in silico methods are applicable in the case of molecular single-electron transistors (SET) with incoherent electron transport . Therefore, Kaasbjerg and Flensberg have devised a novel methodology, where they introduced a semi-empirical model for simulating the properties of molecular SETs, including a renormalization of the molecular charge states due to the environment polarization . However, the possibility of indigoid integration within SET nanodevices remains to be investigated.
In the present work, to improve the performance of organic semiconductors, we modeled indigoid-based molecular SETs, which consist of the natural dye molecule weakly coupled to gold electrodes using the optimized DFT approach. These SET systems operate in the incoherent transport regime, and the electron transport is described by sequential tunneling of single electrons and a sequential transport mechanism, such as Coulomb blockade, rather than coherent, ballistic tunneling. The proposed in silico approach has the potential to correctly predict experimentally determined parameters and to explore the electronic properties of indigoids as bio-inspired materials for the development of novel organic semiconductors.
where K is the initial number of electrons in the drain electrode.
where W is the work function of the electrode and the V applied bias.
where ΔE island (N) = E island (N + 1) − E island (N) is the charging energy of the island.
Results and Discussion
The configuration of modeled organic SETs was adjusted where the “indigoid” island only weakly coupled to the metal electrodes, tunneling the electrons from the source to the gate in a time-dependent manner. Therefore, to model this situation correctly, the DFT with LDA and a double-ζ-polarized basis set were applied . The subsequent tunneling process from the island to the drain electrode could be in this regard referred to a transport mechanism, which is independent of the tunneling process into the island . One of the prerequisites for indigoid molecules to be exploited in SET nanodevices is the presence of many alternating double and single bonds because such patterns delocalize the molecular orbitals, making it possible for electrons to move freely over the conjugated area .
Charging energy E N–1 –E N of different charge states of indigo and Tyrian purple molecules in the gas phase
Charging energy (eV)
It is clear from Fig. 3 that the conductance is directly related to the number of energy levels inside the bias window. In this regard, for any given value of V SD (source-drain bias voltage) and V G , the calculated number of charge states in the bias window corresponded to the charge stability diagrams for indigo (Fig. 3a) and Tyrian purple (Fig. 3b). If the charging energy of the “indigoid” island in the gas phase is modified by an electrostatic gate through a tuning of the V G parameter, the energy levels of SET are moved in and out of the bias window.
The relationship between E(q, V G ) and V G is non-linear because the atoms closest to the dielectric region screen V G for the rest of the molecule, decreasing the gate coupling. A difference in the charges on different atoms in the indigoid molecule alters a molecular dipole, which in turn contributes to E(q, V G ).
In the regions starting from 0 to 5 gate voltage, the minimal E(q, V G ) states were detected for Tyrian purple due to the bromination of this molecule (Fig. 5b). Since, the polarizability of a halogen atom increases in the order of F < Cl < Br, bromine shows large polarizability between the halogen atoms . These data also reflected the experimentally determined relative permittivity values of 4.3 for indigo and 6.2 for Tyrian purple calculated from the geometric capacitance at high frequency (>1.0 MHz) . Moreover, the indigoid-based nanodevices exhibited ambipolar operation with the electron (μ e ) and hole (μ h ) mobilities from 10−2 to 0.2 cm2(V × s)−1. In a more recent study, higher mobilities in Tyrian purple were also reported with the μ e and μ h values of 0.4 cm2(V × s)−1 . However, the analyzed SET nanodevices are different from any conventional OFET, which only controls the charge density between the electrodes but on the single-electron transport through the energy modifications of molecular orbitals [32, 33].
Charging energy E N–1 –E N of different charge states of indigo and Tyrian purple molecules in the SET environment
Charging energy (eV)
From these diagrams, it is clear that the non-linear dependence of E(q, V G ) on V G is not detectable because the diagrams only depend on the ΔE values between the charge states. The excitation energy for indigo is greater than for Tyrian purple, but this energy term of the second electron is smaller than for the first one in both modeled systems. Overall, in terms of stability, mobility, low operating voltage, and ON/OFF ratio, the indigoid OFET nanodevices are among the best reported in the literature .
SETs have been proposed as a future alternative to modern Si-based electronics. The use of single molecules, or nanoscale collections of single molecules, as electronic components is the ultimate goal for conventional electronics in order to minimize electrical circuits, replacing bulk materials. Some SETs were successfully realized within individual carbon nanotubes, organic molecules, and self-assembled gold nanoparticles in an experiment [35–37]. The other example of promising SETs based on graphene is being heavily investigated in research labs, because this material promises a band gap tunable by electrostatic gates . For this reason, we have developed the in silico model of the indigoid-based SET nanodevices using the optimized DFT methodology. This theoretical approach was able to correctly predict the main electronic properties of the natural dye molecules weakly coupled to gold electrodes. The improved electron transport characteristics were determined for Tyrian purple SET system, operating in the incoherent transport regime and describing by sequential tunneling of single electrons and sequential transport mechanism, such as Coulomb blockade, rather than coherent, ballistic tunneling. As the best available organic semiconductors, indigoids demonstrate the potential for sustainable electronics based on the biodegradable and biocompatible materials. Concerning the aforementioned experimental data, our simulation results inspire confidence that indigoid-based SET devices will work and be competitive to normal transistors soon or more in the far future.
The authors are grateful to the BMBF (Bundesministerium für Bildung und Forschung) for their partial support of this work by providing the BMBF01 grant to Jens-Albert Broscheit. This publication was funded by the German Research Foundation (DFG) and the University of Wuerzburg in the funding program Open Access Publishing.
SS conceived of the study, participated in its design and coordination, performed the DFT calculations and analysis of results, and drafted the manuscript. NR, CF, and JB conceived of the study and participated in its design and coordination, and analysis of results. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
- Zaumseil J, Sirringhaus H (2007) Electron and ambipolar transport in organic field-effect transistors. Chem Rev 107(4):1296–1323View ArticleGoogle Scholar
- Bisri SZ, Piliego C, Gao J, Loi MA (2014) Outlook and emerging semiconducting materials for ambipolar transistors. Adv Mater 26(8):1176–1199View ArticleGoogle Scholar
- Irimia-Vladu M, Sariciftci NS, Bauer S (2011) Exotic materials for bio-organic electronics. J Mater Chem 21(5):1350–1361View ArticleGoogle Scholar
- Glowacki ED, Voss G, Leonat L, Irimia-Vladu M, Bauer S, Sariciftci NS (2012) Indigo and Tyrian purple—from ancient natural dyes to modern organic semiconductors. Isr J Chem 52(6):540–551View ArticleGoogle Scholar
- Pitayatanakul O, Higashino T, Kadoya T, Tanaka M, Kojima H, Ashizawa M, Kawamoto T, Matsumoto H, Ishikawa K, Mori T (2014) High performance ambipolar organic field-effect transistors based on indigo derivatives. J Mater Chem C 2(43):9311–9317View ArticleGoogle Scholar
- Comlekcioglu N, Efe L, Karaman S (2015) Extraction of indigo from some Isatis species and dyeing standardization using low-technology methods. Braz Arch Biol Technol 58(1):96–102View ArticleGoogle Scholar
- Irimia-Vladu M, Glowacki ED, Troshin PA, Schwabegger G, Leonat L, Susarova DK, Krystal O, Ullah M, Kanbur Y, Bodea MA, Razumov VF, Sitter H, Bauer S, Sariciftci NS (2012) Indigo—a natural pigment for high performance ambipolar organic field effect transistors and circuits. Adv Mater 24(3):375-+View ArticleGoogle Scholar
- Irimia-Vladu M (2014) “Green“ electronics: biodegradable and biocompatible materials and devices for sustainable future. Chem Soc Rev 43(2):588–610View ArticleGoogle Scholar
- Joshi A, Ramachandran CN (2016) Charge transport and optical properties of the complexes of indigo wrapped over carbon nanotubes. Phys Chem Chem Phys 18(20):14040–14045View ArticleGoogle Scholar
- Thompson ME, Forrest SR, Burrows PE, You Y, Shoustikov A (1999) The Trustees Of Princeton University and The University of Southern California. Organic light emitting devices containing a metal complex of 5-hydroxy-quinoxaline as a host material. U.S. Patent 5,861,219Google Scholar
- Corbel S, Cerda J, Sautet P (1999) Ab initio calculations of scanning tunneling microscopy images within a scattering formalism. Phys Rev B 60(3):1989–1999View ArticleGoogle Scholar
- Taylor J, Guo H, Wang J, (2001) Ab initio modeling of quantum transport properties of molecular electronic devices. Phys Rev B 63 (24).Google Scholar
- Zahid F, Paulsson M, Polizzi E, Ghosh AW, Siddiqui L, Datta S (2005) A self-consistent transport model for molecular conduction based on extended Huckel theory with full three-dimensional electrostatics. J Chem Phys 123(6):64707View ArticleGoogle Scholar
- Kienle D, Bevan KH, Liang GC, Siddiqui L, Cerda JI, Ghosh AW (2006) Extended Huckel theory for band structure, chemistry, and transport. II. Silicon. J Appl Phys 100 (4).Google Scholar
- Kubatkin S, Danilov A, Hjort M, Cornil J, Bredas JL, Stuhr-Hansen N, Hedegard P, Bjornholm T (2003) Single-electron transistor of a single organic molecule with access to several redox states. Nature 425(6959):698–701View ArticleGoogle Scholar
- Kaasbjerg K, Flensberg K (2008) Strong polarization-induced reduction of addition energies in single-molecule nanojunctions. Nano Lett 8(11):3809–3814View ArticleGoogle Scholar
- Li Q, Cheng T, Wang Y, Bryant SH (2010) PubChem as a public resource for drug discovery. Drug Discov Today 15(23-24):1052–7View ArticleGoogle Scholar
- Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR (2012) Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminformatics 4Google Scholar
- Pirok G, Mate N, Varga J, Szegezdi J, Vargyas M, Dorant S, Csizmadia F (2006) Making “real” molecules in virtual space. J Chem Inf Model 46(2):563–568View ArticleGoogle Scholar
- Brandbyge M, Mozos JL, Ordejon P, Taylor J, Stokbro K (2002) Density-functional method for nonequilibrium electron transport. Phys Rev B 65(16).Google Scholar
- Vosko SH, Wilk L (1980) Influence of an improved local-spin-density correlation-energy functional on the cohesive energy of alkali-metals. Phys Rev B 22(8):3812–3815View ArticleGoogle Scholar
- Latajka Z, Scheiner S (1984) Improvement of polarized double-zeta basis-sets for molecular-interactions—complexes of Nh3, Oh2, and Fh with H+ and Li+. Chem Phys Lett 105(4):435–439View ArticleGoogle Scholar
- Savaikar MA, Banyai D, Bergstrom PL, Jaszczak JA (2013) Simulation of charge transport in multi-island tunneling devices: Application to disordered one-dimensional systems at low and high biases. J Appl Phys 114(11).Google Scholar
- Sun L, Diaz-Fernandez YA, Gschneidtner TA, Westerlund F, Lara-Avila S, Moth-Poulsen K (2014) Single-molecule electronics: from chemical design to functional devices. Chem Soc Rev 43(21):7378–7411View ArticleGoogle Scholar
- Anthopoulos TD, Anyfantis GC, Papavassiliou GC, de Leeuw DM (2007) Air-stable ambipolar organic transistors. Appl Phys Lett 90 (12).Google Scholar
- Riviere JC (1966) Work function of gold—(5.28 +-002 contact potential difference method vacuum 10-10 torr surface contamination ion vs Hg pumps E). Appl Phys Lett 8(7):172View ArticleGoogle Scholar
- Perrin ML, Verzijl CJO, Martin CA, Shaikh AJ, Eelkema R, van Esch JH, van Ruitenbeek JM, Thijssen JM, van der Zant HSJ, Dulic D (2013) Large tunable image-charge effects in single-molecule junctions. Nat Nanotechnol 8(4):282–287View ArticleGoogle Scholar
- Irimia-Vladu M, Glowacki ED, Schwabegger G, Leonat L, Akpinar HZ, Sitter H, Bauer S, Sariciftci NS (2013) Natural resin shellac as a substrate and a dielectric layer for organic field-effect transistors. Green Chem 15(6):1473–1476View ArticleGoogle Scholar
- Stokbro K (2010) First-principles modeling of molecular single-electron transistors. J Phys Chem C 114(48):20461–20465View ArticleGoogle Scholar
- Duarte DJR, Sosa GL, Peruchena NM, Alkorta I (2016) Halogen bonding. The role of the polarizability of the electron-pair donor. Phys Chem Chem Phys 18(10):7300–7309View ArticleGoogle Scholar
- Kanbur Y, Irimia-Vladu M, Glowacki ED, Voss G, Baumgartner M, Schwabegger G, Leonat L, Ullah M, Sarica H, Erten-Ela S, Schwodiauer R, Sitter H, Kucukyavuz Z, Bauer S, Sariciftci NS (2012) Vacuum-processed polyethylene as a dielectric for low operating voltage organic field effect transistors. Org Electron 13(5):919–924View ArticleGoogle Scholar
- Oehzelt M, Koch N, Heimel G (2014) Organic semiconductor density of states controls the energy level alignment at electrode interfaces. Nat Commun 5Google Scholar
- Frolova LA, Rezvanova AA, Lukyanov BS, Sanina NA, Troshin PA, Aldoshin SM (2015) Design of rewritable and read-only non-volatile optical memory elements using photochromic spiropyran-based salts as light-sensitive materials. J Mater Chem C 3(44):11675–11680View ArticleGoogle Scholar
- Klauk H, Zschieschang U, Pflaum J, Halik M (2007) Ultralow-power organic complementary circuits. Nature 445(7129):745–748View ArticleGoogle Scholar
- Postma HW, Teepen T, Yao Z, Grifoni M, Dekker C (2001) Carbon nanotube single-electron transistors at room temperature. Science 293(5527):76–9View ArticleGoogle Scholar
- Martinez-Blanco J, Nacci C, Erwin SC, Kanisawa K, Locane E, Thomas M, von Oppen F, Brouwer PW, Folsch S (2015) Gating a single-molecule transistor with individual atoms. Nat Phys 11(8):640View ArticleGoogle Scholar
- Wang F, Fang JY, Chang SL, Qin SQ, Zhang XA, Xu H (2017) Room temperature Coulomb blockade mediated field emission via self-assembled gold nanoparticles. Phys Lett A 381(5):476–480View ArticleGoogle Scholar
- Zhang Y, Tang T-T, Girit C, Hao Z, Martin MC, Zettl A, Crommie MF, Shen YR, Wang F (2009) Direct observation of a widely tunable bandgap in bilayer graphene. Nature 459(7248):820–3View ArticleGoogle Scholar