Microscopic mechanism of electron transfer through the hydrogen bonds between carboxylated alkanethiol molecules connected to gold electrodes

Abstract

The atomic structure and the electron transfer properties of hydrogen bonds formed between two carboxylated alkanethiol molecules connected to gold electrodes are investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Three types of molecular junctions are constructed, in which one carboxyl alkanethiol molecule contains two methylene, -CH2, groups and the other one is composed of one, two, or three -CH2 groups. Our calculations show that, similarly to the cases of isolated carboxylic acid dimers, in these molecular junctions the two carboxyl, -COOH, groups form two H-bonds resulting in a cyclic structure. When self-interaction corrections are explicitly considered, the calculated transmission coefficients of these three H-bonded molecular junctions at the Fermi level are in good agreement with the experimental values. The analysis of the projected density of states confirms that the covalent Au-S bonds localized at the molecule-electrode interfaces and the electronic coupling between -COOH and S dominate the low-bias junction conductance. Following the increase of the number of the -CH2 groups, the coupling between -COOH and S decreases deeply. As a result, the junction conductance decays rapidly as the length of the H-bonded molecules increases. These findings not only provide an explanation to the observed distance dependence of the electron transfer properties of H-bonds, but also help the design of molecular devices constructed through H-bonds.

Electron Transport through a Coordination Junction Formed by Carboxy Thiophenols and Bivalent Metal Ions

“…As can be seen from Table , the dihedral angle and the Mulliken charge have obvious changes as compared to other geometric parameters. For CTP-H without metal ions, the dihedral angle, ϕ, is 179.8°, displaying a coplanar cyclic configuration, the same as that reported previously . However, the coordination structure might be changed, while a bivalent metal ion is applied to replace the two protons.…”

“…Recently, many studies focus on the electronic properties as well as the transportation behavior of systems with noncovalent interactions, including hydrogen bond (H-bond), π–π stacking, and electrostatic interactions. − Since the H-bond is ubiquitous in both biological and self-assembling materials, electron transportation of H-bond-mediated systems has gained great attention. − Nishino et al have studied experimentally the electron transport behavior of H-bonds formed in two carboxylated alkanethiol molecules (SC n COOH//HOOCC n S) and found that it conducts electrons better than a covalent σ-bond at a short range; however, the conductance decays rapidly with the increase of molecular length. , Hou et al have studied the conductance of carboxylated alkanethiol molecules by first-principles calculations, and they attributed the high conductance of H-bonded systems to the presence of resonance in the transmission near Fermi energy . The inclusion of this observation is essential in understanding the electron transport behavior of H-bond-mediated systems .…”

“…21,22 Hou et al have studied the conductance of carboxylated alkanethiol molecules by first-principles calculations, and they attributed the high conductance of Hbonded systems to the presence of resonance in the transmission near Fermi energy. 25 The inclusion of this observation is essential in understanding the electron transport behavior of H-bond-mediated systems. 23 Moreover, due to the directional characteristic of H-bonds, multiple H-bonds are favorable for maintaining the planarity of H-bond-mediated systems, 23 under some conditions, the existence of H-bonds in a molecular junction largely affects the transport behavior.…”

Adsorption, Stretching, and Breaking Processes in Single‐Molecule Conductance of para‐Benzenedimethanethiol in Gold Nanogaps: A DFT‐NEGF Theoretical Study**

“…We first contracted the molecular junctions by the AuÀ S bond distance until about 2.30-2.40 Å, corresponding to the sulfur atom binding at the top site. [37,[42][43][44][45] Following contraction, we pulled them apart gradually, until the bond fission occurred. In the stretching process, we obtained a series of optimized structures at given distances, as shown in Supporting Information, and built the relationship between the distance and total electronic energy, stretching force, and molecular conductance.…”

Single-Molecule Conductance through Hydrogen Bonds: The Role of Resonances

“…An alternative theoretical explanation to this finding was given by Li et al, who took into account an explicit self-energy correction in their calculations. 13 In a more general context, our results are also relevant for the issue of understanding the role of the chemical bond in electron transfer and transport processes. In this connection, high-level calculations are required to account both for the electronic structure of weakly bonded systems and transport properties.…”