Joint Space-Time Coherent Vibration Driven Conformational Transitions in a Single Molecule

Shaowei Li (李绍巍), Siyu Chen (陈思宇), Jie Li, Ruqian Wu, and W. Ho

Phys. Rev. Lett. 119, 176002 – Published 26 October 2017

Abstract

We report single-molecule conformational transitions with joint angstrom-femtosecond resolution by irradiating the junction of a scanning tunneling microscope with femtosecond laser pulses. An isolated pyrrolidine molecule adsorbed on a Cu(001) surface undergoes reversible transitions between two conformational states. The transition rate decays in time and exhibits sinusoidal oscillations with periods of specific molecular vibrations. The dynamics of this transition depends sensitively on the molecular environment, as exemplified by the effects of another molecule in proximity.

Received 24 July 2017

DOI:https://doi.org/10.1103/PhysRevLett.119.176002

Physics Subject Headings (PhySH)

Chemical Physics & Physical Chemistry Chemical bonding Chemical kinetics, dynamics & catalysis Optical & microwave phenomena Surface & interfacial phenomena

Interdisciplinary PhysicsCondensed Matter, Materials & Applied Physics

Authors & Affiliations

Shaowei Li (李绍巍)¹, Siyu Chen (陈思宇)¹, Jie Li², Ruqian Wu^1,2,†, and W. Ho^1,3,*

¹Department of Physics and Astronomy, University of California, Irvine, California 92697-4575, USA
²State Key Laboratory of Surface Physics and Key Laboratory of Computational Physical Sciences, Fudan University, Shanghai, China 200433
³Department of Chemistry, University of California, Irvine, California 92697-2025, USA

^*To whom all correspondence should be addressed. wilsonho@uci.edu
^†wur@uci.edu

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Issue

Vol. 119, Iss. 17 — 27 October 2017

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Images

Figure 1
(a) Schematic diagram of the STM junction illuminated by pairs of phase-correlated femtosecond laser pulses. (b) Reversible transitions between two structural states I and II for pyrrolidine on Cu(001). (c) Topographic images revealing the two states. (d) Vertical line cut across state I of the upper molecule [red dashed lines in (c) and (d)]; vertical line cut (black dashed line of state II) and horizontal line cut [blue solid lines in (c) and (d) showing I to II and II to I transitions] across the lower molecule. (e) Topographic images and corresponding time traces of changes in the tunneling gap ( $Δ z$ ) recorded over positions marked by a circular symbol, from top to bottom: isolated pyrrolidine molecule without light; isolated pyrrolidine irradiated by a laser; lower molecule in the dimer irradiated by a laser; center of the dimer with a laser. Tunneling gap set at 30 mV sample bias, 50 pA tunneling current, and with the feedback on. A transition cycle consists of I to II and back to I. (f) Topographic image showing the 17 locations where the transition rate was measured. (g) Transition rate obtained from $Δ z$ trace recorded for 300 s for the 17 locations.
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Figure 2
(a) Delay scan (red dots, $- 3500$ to $+ 3500 fs$ in 2 fs steps) over the center of a monomer. The sign of the delay reflects the temporal order of the two pulses. The transition rate is determined from the sum of five passes, each pass with $Δ z$ trace recorded for 12 s at every delay, except one pass of 60 s at each delay for $| τ | \leq 100 fs$ . The black dashed line is the fit using Eq. (1). The two insets above (blue dots) show delay scans from the sum of ten passes; the same fit is shown. The green dots are the transition rate vs delay of the control measurement at the same total power of 1.5 mW of cw light at 820 nm (laser not mode locked). The black dots are for the transition rate in the dark vs delay, another control measurement. (b) Fourier transform of the data presented in (a), showing a dominant peak ( $145 \pm 4 fs$ , $6.9 \pm 0.2 THz$ , or $28.5 \pm 0.7 meV$ ) and a weak peak ( $365 \pm 44 fs$ , $2.7 \pm 0.3 THz$ , or $11.3 \pm 1.4 meV$ ). The uncertainty of the 6.9 THz peak is obtained from fitting the delay scan to only the dominant sinusoidal function at 6.9 THz. The uncertainty of the 2.7 THz peak is the step size in the FFT spectrum. The inset shows the topographic image of the molecule for all the data in this figure. (c) Topographic image taken in the dark with the gap set at 3 mV, 7 nA, and with molecular hydrogen in the background and trapped in the STM junction to enhance spatial resolution.
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Figure 3
(a)-(h) DFT calculations of the eight vibrations of a single pyrrolidine adsorbed as state I on the Cu(001) surface with energies smaller than 50 meV (11.85, 12.91, 13.36, 13.57, 17.32, 18.85, 27.24, and 46.51 meV). Green arrows show the directions and amplitudes of atom motions for each eigenmode. Mode $a$ (11.85 meV) and mode $g$ (27.24 meV) are assigned to the two peaks in Fig. 2. (i) Energetics pathway for structural transition and the optimized structures for conformations I and II and the transition state between them.
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Figure 4
(a) Delay scan over the center of the lower pyrrolidine molecule separated by 7.21 Å from the upper molecule (red dots), taken under the same conditions as Fig. 2. The black dashed line is the fit using Eq. (1). The insets are delay scans taken under the same conditions as the insets in Fig. 2. The horizontal dashed line indicates the transition rate vs delay recorded in the dark, as a control measurement, over the same molecule in the dimer, showing a background count rate of $\sim 51 counts \min^{- 1}$ driven by tunneling electrons. (b) Fourier transform of time domain data in (a), revealing one peak at $6.0 \pm 0.2 THz$ ( $167 \pm 4 fs$ or $24.8 \pm 0.6 meV$ ; uncertainty obtained from the sinusoidal fit to the delay scan). The insets are a topographic image (left) and an atom-resolved topographic image with a superimposed schematic of substrate surface atoms (right). (c) Atom-resolved topographic image. The smaller white solid circles in a square arrangement are copper atoms of the Cu(001) surface.
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