Molecular Isomers

Charge transport through alkane and benzene molecules is extensively investigated because they have a simple structure and are considered a basis unit for molecular circuits.[9, 12, 13, 57] Alkanedithiol (ADT), as a saturated molecule, is one of the most appropriate candidates to study these properties and can adopt the usual trans conformation as well as a gauche (or defect) conformation (see Fig. 2.22), which is predicted to give rise to alterations of the charge tunneling.[27, 39, 40, 73] As illustrated in Fig. 2.21, the alkane molecule shows trans and gauche conformations. In each conformation, the potential energy is different and influences the molecular conductance by a factor of ~ 10.[27] The 1,4-benzenedithiol (BDT) molecule, as a conjugated molecule with one aromatic ring, varies orientation between electrodes, including tilting of the ring plane with respect to the electrodes varying conductance ranging from ~ 0.5 G0 to ~ 10^-4 G0, when the molecular junction is stretched or compressed.[32, 47-50] In Fig. 2.22, the transmission as a function of tilt angle is well presented theoretically. These properties make both ADT and BDT very promising candidates for studying fundamental aspects of quantum transport– provided that the configuration can be controlled – and also for manifold applications in molecular electronics devices.

Figure 2.21. (a) The trans conformation is the usual one, having lower potential energy, in which the H atoms attached to neighboring C atoms are positioned opposite to each other.

(b) The carbon chain has a zig-zag shape all over the molecule. If one gauche defect is present, the H atoms attached to the two neighboring C atoms are rotated along the long axis of the molecule such that they enclose an angle of roughly 120 degrees, having higher potential energy. The image shows a gauche defect between the C atoms labeled 1 and 2.

31

Figure 2.22. (a) Graphics of the different stages of the evolution of BDT on gold of different junction distances. The initial configuration is that of a flat BDT molecule on the surface. L is the leads separation at each stage. (b) GGA (generalized gradient approximation) and ASIC (approximate self-interaction correction scheme) transmission coefficient at the Fermi level calculated for BDT in the flat initial configuration as a function of the lead-lead separation. (Reproduced from Ref. [49])

Figure 2.23. (a) Structures of a subset of the biphenyl series studied, shown in order of   increasing twist angle or decreasing conjugation. (b) Conductance histograms obtained from measurements using molecule 2 (purple; constructed from 15,000 traces and scaled by 1/15), 4 (cyan; constructed from 7,000 traces and scaled by 1/7), 6 (pink; constructed from 11,000 traces and scaled by 1/11) and 8 (blue; constructed from 5,000 traces and scaled by 1/5).

Also shown is the control histogram obtained from measurements without molecules between the contacts (yellow; constructed from 6,000 traces and scaled by 1/6). Arrows point to the peak conductance values obtained from Lorentzian fits (solid black curves). All data were taken at a bias voltage of 25 mV. (c) Position of the peaks for all the molecules studied plotted against cos²θ, where θ is the calculated twist angle for each molecule. Error bars are determined from the standard deviation of the peak locations determined from the fits to histograms of 1,000 traces. (Reproduced from Ref. [14])

32

Finally, we present another interesting example under the influence of the molecular conformation onto the conductance. This study addresses the role of the conjugation of aromatic molecules for the conductance. The investigated molecules contain two aromatic rings that can be tilted with respect to each other and thereby continuously suppressing the conjugation changing the entire set of molecular orbitals. The conductance of a series of molecules with carrying torsion angle has been studied and shown to follow a cos²φ law.

[14, 68, 86] While the torsion angle varies from 0˚ to 90˚ between two phenyl rings, the conductance decreases linearly as shown in Fig. 2.23. For these studies, the molecules are engineered such that the phenyl rings include a certain angle intrinsically. Another experiment was carried out while controlling the torsion angle stressing a bipyridine molecule using a external mechanical stress.[63]

The photochromic switching molecules, as shown in Figs. 2.24 and 2.25, isomerize and change their energy states, refractive index, dielectric constant, and redox potential under external stimuli such as light irradiations. Basically, under UV and visible (Vis) light irradiation, the photochromic molecules switch between two isomers.[10, 58, 87-89] In a conjugated molecule, when electrons in a ground state absorb certain energy, double bonding becomes a single bonding, and the electrons are excited. Then the orbitals rotate and vibrate until they are relaxed in another ground state (see Fig. 2.26). Therefore, the bonding sequence can be changed under light irradiation. This switching behavior is easily examined by UV/Vis spectroscopy as shown in Fig. 2.25.

Figure 2.24. Several types of switching molecules and their switching reaction under UV/Vis light. (a) Sketches of open (left) and closed (right) forms of diarylethene molecules.

(b) Sketches of trans (up) and cis (down) forms of helix molecules. (c) Sketches of trans (up) and cis (down) forms of azobenzene molecules. (d) Sketches of closed (up) and open (down) forms of spiropyran molecules.

33

Figure 2.25. UV/Visible spectroscopy of photochromic molecules. (These molecules are synthesized by D. Sysoiev. Related work will be presented in Chapter 8 and Ref.[65]) (a) Absorption spectra of YnPhT diarylethene molecules under UV irradiation from 0 to 150 sec. (b) Absorption spectra of azobenzene derivative molecules (AzoATM) under UV irradiation from 0 to 1800 sec. The longest-wavelength absorption edge is indicative for the possible optical excitation with lowest energy. A variation in the absorption band thus signals a variation of the HOMO-LUMO gap of the molecules.

Figure 2.26. (illustration by Prof. Ulrich E. Steiner) Potential energy of a diarylethene molecule. S₀ and S₁ indicate ground state and excited state, respectively. A and B are the ground state of closed and open form. When electrons on B state absorb certain energy by UV light, the electrons excite and jump to S1 state. Then along the reaction coordinate, electrons relax to A state. The reverse reaction is vice versa. Depending on the position of low energy point C along the reaction coordinate, the excited electrons from B state can relax back to B state, again. In the ring opening process, there could be a potential barrier D, which hinders the relaxation of excited electrons. This energy coordinate is different for every type of molecules.

34