Contact Formation Dynamics:  Mapping Chemical Bond Formation between a Molecule and a Metallic Probe

Abstract

We present a study that maps out chemical bond formation between a Pt-inked probe and a single 1,3-cyclohexadiene (1,3-CHD) molecule on Si(100). By separating the mechanical and electronic contributions to the current during the approach to contact, we show that there are significant forces between the probe and the CdC of the molecule and we track the relaxation of the molecule, the emergence of a chemical bond feature in the LDOS, and the quenching of specific molecular vibrations during bond formation.Understanding the detailed dynamics of chemical bond formation at surfaces is essential to a wide range of technologies. For example, the prospects for future molecular electronic devices 1-13 hinge on the ability to form reproducible electrical contacts with single molecules. 2,3,14 Little is known about how individual molecules relax or how potentially important device properties such as the HOMO-LUMO gap are modified by the contacting process. Similarly, the operation of catalysts and enzymes depends on understanding how particular molecules react with surface catalytic sites. [15][16][17] The manner in which molecules engage with and ultimately dock at these surface sites is critically important. In these and related systems, numerous studies have reported on the final state properties, that is, after the contact has been assembled or the reaction completed. The actual dynamics of chemical bond formation is poorly understood and represents a serious impediment to the rational design of the materials and devices that underpin these technologies.Here we present a study that maps out chemical bond formation as a Pt-inked probe approaches and makes contact with a single 1,3-cyclohexadiene (1,3-CHD) molecule on Si-(100). By explicitly separating the mechanical and electronic contributions to the current during the approach, we show that there are significant forces 18 between the probe and Cd C region of the molecule and we track both the relaxation and rehybridization of the molecule, the emergence of a chemical bonding feature in the LDOS, and the quenching of specific molecular vibrations, all in excellent agreement with density functional theory (DFT) calculations. We envision that these methods will be useful for identifying candidate metal-molecule systems for device applications and for addressing the operation and selectivity of certain catalysts.Contact and bond formation was studied using a cryogenic STM (Createc) in which a single-crystal Pt(111) metal sample and a Si(100) substrate [n+-type As, <5 mΩ‚cm] were placed in a sample holder that allows each to be heated and prepared separately. Following characterization by LEED, both samples were simultaneously exposed at room temperature to less than 0.1% of a monolayer of 1,3-CHD, transferred into the STM, and cooled to 5 K. Tungsten STM probes were cleaned by electron bombardment and then "inked" with atoms from the Pt substrate using a method described previously 18 and which provided control over the composition of the probe. The Pt-inked prob...

Emergence and Visualization of an Interface State during Contact Formation with a Single Molecule

“…4(b). In particular the 2 level at 0:2 eV agrees well with the 0:35 eV feature in the LDOS reported previously at small probe-molecule separations [16].…”

“…In contrast to metal systems where the interaction increases the apparent corrugation, here a new state is created close to the Fermi energy (E f ) that dominates transport into the molecule-surface system. These data demonstrate that wide band-gap low-conductance molecules such as 1,3-CHD may form electrically active interface states with metals and that STM can be used to explore contact formation and to screen molecules for potential electronic applications.Previously, we showed that STM can distinguish between the reaction products of 1,3-CHD on Si(100) [13,14] and directly measures the force of the probemolecule interaction [15], including the onset of local density of states (LDOS) feature that was attributed to incipient chemical bond formation [16]. Figures 1(a)-1(e) show empty-state STM images of the five different 1,3-CHD attachment geometries in which the single remaining C --C bond appears to be the origin of the contrast FIG.…”

“…Previously, we showed that STM can distinguish between the reaction products of 1,3-CHD on Si(100) [13,14] and directly measures the force of the probemolecule interaction [15], including the onset of local density of states (LDOS) feature that was attributed to incipient chemical bond formation [16]. Figures 1(a)-1(e) show empty-state STM images of the five different 1,3-CHD attachment geometries in which the single remaining C --C bond appears to be the origin of the contrast FIG.…”

“…To resolve this discrepancy a series of 13 DFT geometry optimized calculations were performed that included the molecule-surface system and a platinum STM probe (original STM experiments were performed using cleaned W and W probes inked with Pt metal [15,16]). Our calculations were performed using the Cambridge Serial Total Energy Package (CASTEP) [19].…”

Measuring the Force of Interaction between a Metallic Probe and a Single Molecule

“…1(b)], which is known to be associated with the C --C bond region of the 1,3-CHD molecule in the intradimer [2 2] configuration [15], and the approach experiment was repeated at a sample bias of 200 meV. The low bias was chosen because within the corresponding tunneling energy window the local density of states (LDOS) was measured to be independent of the probe-molecule separation [16]. Experimentally, the approach involved applying a 0.01 nm dither at 534 Hz to the Z piezo under openloop conditions so that the current and the first and second harmonics (dI=dZ and d 2 I=dZ 2 ) are measured simultaneously using a dual-phase lock-in amplifier (SR/7265), and shown in Figs.…”