Name: probing the structure and dynamics of interfacial water with scanning tunneling microscopy and spectroscopy
Uploaded: 2018-05-27T13:00:00
Description: Watch this Scientific Journal Video about Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy at JoVE.com

This work is funded by the National Key R&amp;D Program under Grant No. 2016YFA0300901 2016YFA0300903 and 2017YFA0205003, the National Natural Science Foundation of China under Grant No. 11634001, 11290162/A040106. Y.J. acknowledges support by National Science Fund for Distinguished Young Scholars and Cheung Kong Young Scholar Program. J. G. acknowledges support from the National Postdoctoral Program for Innovative Talents.

NOTE: The experiments are performed on water molecules adsorbed on the Au-supported NaCl(001) film (Figure 1a) at 5 K with an ultrahigh-vacuum (UHV) cryogenic STM equipped with Nanonis electronic controller.
1. Fabrication of Experimental Sample
<ol>
	<li>Clean the Au(111) single crystal
	<ol>
		<li>Pump the gas line to the pressure of ~10-7 mbar and then flush the gas line with Ar gas. Put through the pump/flush cycl...

<ol>
	<li>Thiel, P. A., Madey, T. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+interaction+of+water+with+solid+surfaces:+Fundamental+aspects.">The interaction of water with solid surfaces: Fundamental aspects.</a> Surf. Sci. Rep. 7 (6-8), 211-385 (1987).</li><li>Henderson, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+interaction+of+water+with+solid+surfaces:+fundamental+aspects+revisited.">The interaction of water with solid surfaces: fundamental aspects revisited.</a> Surf. Sci. Rep. 46 (1-8), 1-308 (2002).</li><li>Hodgson, A., Haq, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Water+adsorption+and+the+wetting+of+metal+surfaces.">Water adsorption and the wetting of metal surfaces.</a> Surf. Sci. Rep. 64 (9), 381-451 (2009).</li><li>Brougham, D. F., Caciuffo, R., Horsewill, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coordinated+proton+tunnelling+in+a+cyclic+network+of+four+hydrogen+bonds+in+the+solid+state.">Coordinated proton tunnelling in a cyclic network of four hydrogen bonds in the solid state.</a> Nature. 397 (6716), 241-243 (1999).</li><li>Andreani, C., Colognesi, D., Mayers, J., Reiter, G. F., Senesi, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+momentum+distribution+of+light+atoms+and+molecules+in+condensed+matter+systems+using+inelastic+neutron+scattering.">Measurement of momentum distribution of light atoms and molecules in condensed matter systems using inelastic neutron scattering.</a> Adv. Phys. 54 (5), 377-469 (2005).</li><li>Shen, Y. R., Ostroverkhov, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sum-frequency+vibrational+spectroscopy+on+water+interfaces:+Polar+orientation+of+water+molecules+at+interfaces.">Sum-frequency vibrational spectroscopy on water interfaces: Polar orientation of water molecules at interfaces.</a> Chem. Rev. 106 (4), 1140-1154 (2006).</li><li>Soper, A. K., Benmore, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantum+differences+between+heavy+and+light+water.">Quantum differences between heavy and light water.</a> Phys. Rev. Lett. 101 (6), 065502 (2008).</li><li>Kimmel, G. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polarization-+and+azimuth-resolved+infrared+spectroscopy+of+water+on+TiO2(110):+Anisotropy+and+the+hydrogen-bonding+network.">Polarization- and azimuth-resolved infrared spectroscopy of water on TiO2(110): Anisotropy and the hydrogen-bonding network.</a> J. Phys. Chem. Lett. 3 (6), 778-784 (2012).</li><li>Eigler, D. M., Schweizer, E. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Positioning+single+atoms+with+as+a+scanning+tunneling+microscope.">Positioning single atoms with as a scanning tunneling microscope.</a> Nature. 344 (6266), 524-526 (1990).</li><li>Stroscio, J. A., Eigler, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+and+molecular+manipulation+with+the+scanning+tunneling+microscope.">Atomic and molecular manipulation with the scanning tunneling microscope.</a> Science. 254 (5036), 1319-1326 (1991).</li><li>Stipe, B. C., Rezaei, M. A., Ho, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-molecule+vibrational+spectroscopy+and+microscopy.">Single-molecule vibrational spectroscopy and microscopy.</a> Science. 280 (5370), 1732-1735 (1998).</li><li>Ho, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-molecule+chemistry.">Single-molecule chemistry.</a> J. Chem. Phys. 117 (24), 11033-11061 (2002).</li><li>Repp, J., Meyer, G., Stojkovic, S. M., Gourdon, A., Joachim, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecules+on+insulating+films:+Scanning-tunneling+microscopy+imaging+of+individual+molecular+orbitals.">Molecules on insulating films: Scanning-tunneling microscopy imaging of individual molecular orbitals.</a> Phys. Rev. Lett. 94 (2), 026803 (2005).</li><li>Weiss, C., Wagner, C., Temirov, R., Tautz, F. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+imaging+of+intermolecular+bonds+in+scanning+tunneling+microscopy.">Direct imaging of intermolecular bonds in scanning tunneling microscopy.</a> J. Am. Chem. Soc. 132 (34), 11864-11865 (2010).</li><li>Verdaguer, A., Sacha, G. M., Bluhm, H., Salmeron, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+structure+of+water+at+interfaces:+Wetting+at+the+nanometer+scale.">Molecular structure of water at interfaces: Wetting at the nanometer scale.</a> Chem. Rev. 106 (4), 1478-1510 (2006).</li><li>Michaelides, A., Morgenstern, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ice+nanoclusters+at+hydrophobic+metal+surfaces.">Ice nanoclusters at hydrophobic metal surfaces.</a> Nat. Mater. 6 (8), 597-601 (2007).</li><li>Feibelman, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+first+wetting+layer+on+a+solid.">The first wetting layer on a solid.</a> Phys. Today. 63 (2), 34-39 (2010).</li><li>Carrasco, J., Hodgson, A., Michaelides, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+molecular+perspective+of+water+at+metal+interfaces.">A molecular perspective of water at metal interfaces.</a> Nat. Mater. 11 (8), 667-674 (2012).</li><li>Kumagai, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+observation+and+control+of+hydrogen-bond+dynamics+using+low-temperature+scanning+tunneling+microscopy.">Direct observation and control of hydrogen-bond dynamics using low-temperature scanning tunneling microscopy.</a> Prog. Surf. Sci. 90 (3), 239-291 (2015).</li><li>Maier, S., Salmeron, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+does+water+wet+a+surface.">How does water wet a surface.</a> Acc. Chem. Res. 48 (10), 2783-2790 (2015).</li><li>JoVE Science Education Database. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.+Essentials+of+Organic+Chemistry.+Degassing+Liquids+with+Freeze-Pump-Thaw+Cycling.">. Essentials of Organic Chemistry. Degassing Liquids with Freeze-Pump-Thaw Cycling.</a> JoVE. , (2017).</li><li>Guo, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-space+imaging+of+interfacial+water+with+submolecular+resolution.">Real-space imaging of interfacial water with submolecular resolution.</a> Nat. Mater. 13 (2), 184-189 (2014).</li><li>Guo, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+quantum+effects+of+hydrogen+bonds+probed+by+tip-enhanced+inelastic+electron+tunneling.">Nuclear quantum effects of hydrogen bonds probed by tip-enhanced inelastic electron tunneling.</a> Science. 352 (6283), 321-325 (2016).</li><li>Meng, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+visualization+of+concerted+proton+tunnelling+in+a+water+nanocluster.">Direct visualization of concerted proton tunnelling in a water nanocluster.</a> Nat. Phys. 11 (3), 235-239 (2015).</li><li>Thuermer, K., Nie, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Formation+of+hexagonal+and+cubic+ice+during+low-temperature+growth.">Formation of hexagonal and cubic ice during low-temperature growth.</a> Proc. Natl. Acad. Sci. U.S.A. 110 (29), 11757-11762 (2013).</li><li>Shiotari, A., Sugimoto, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrahigh-resolution+imaging+of+water+networks+by+atomic+force+microscopy.">Ultrahigh-resolution imaging of water networks by atomic force microscopy.</a> Nat. Commun. 8, (2017).</li><li>Terada, Y., Yoshida, S., Takeuchi, O., Shigekawa, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-space+imaging+of+transient+carrier+dynamics+by+nanoscale+pump-probe+microscopy.">Real-space imaging of transient carrier dynamics by nanoscale pump-probe microscopy.</a> Nat. Photonics. 4 (12), 869-874 (2010).</li><li>Yoshida, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+ultrafast+spin+dynamics+with+optical+pump-probe+scanning+tunnelling+microscopy.">Probing ultrafast spin dynamics with optical pump-probe scanning tunnelling microscopy.</a> Nat. Nanotechnol. 9 (8), 588-593 (2014).</li><li>Mamin, H. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanoscale+nuclear+magnetic+resonance+with+a+nitrogen-vacancy+spin+sensor.">Nanoscale nuclear magnetic resonance with a nitrogen-vacancy spin sensor.</a> Science. 339 (6119), 557-560 (2013).</li><li>Staudacher, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+magnetic+resonance+spectroscopy+on+a+(5-nanometer)3+sample+volume.">Nuclear magnetic resonance spectroscopy on a (5-nanometer)3 sample volume.</a> Science. 339 (6119), 561-563 (2013).</li><li>Aslam, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanoscale+nuclear+magnetic+resonance+with+chemical+resolution.">Nanoscale nuclear magnetic resonance with chemical resolution.</a> Science. 357 (6346), 67-71 (2017).</li></ol>

To probe the internal structure, dynamics, and vibrational spectroscopy of water molecules adsorbed on the solid surfaces, paying particular attention to the degrees of freedom of hydrogen, some experimental steps are of crucial importance, which will be discussed in the following paragraphs.
The orbital imaging of water molecules is achieved based on two key steps. First, the insulating NaCl films decouple the water electronically from the Au substrate, second the orbital gating effect of the...

The interactions of water with the surfaces of solid materials are involved in various surface reaction processes, such as heterogeneous catalysis, photoconversion, electrochemistry, corrosion and lubrication et al.1,2,3 In general, to investigate interfacial water, spectroscopic and diffraction techniques are commonly used, such as infrared and Raman spectroscopy, sum-frequency generation (SFG), X-ray diffraction (XRD), nuclear magnetic resonance (NMR), neutron scattering4,5,6,7,8. However, these methods suffer from the limitation of spatial resolution, spectral broadening, and averaging effects.
STM is a promising technique to overcome these limitations, which combines the sub-&#197;ngstr&#246;m spatial resolution, atomic manipulation, and single-bond vibrational sensitivity9,10,11,12,13,14. Since the beginning of this century, STM has been extensively applied to investigate the structure and dynamics of water on solid surfaces3,15,16,17,18,19,20. Additionally, vibrational spectroscopy based on STM could be obtained from the second-derivative differential tunneling conductance (d2I/dV2), also known as inelastic electron tunneling spectroscopy (IETS). However, resolving the internal structure, i.e. the H-bond directionality, and acquiring reliable vibrational spectroscopy of water are still challenging. The main difficulty lies in that water is a close shell molecule, whose frontier orbitals are far away from the EF, thus the electrons from the STM tip can hardly tunnel into the molecular resonance states of water, leading to the poor signal-to-noise ratio of molecular imaging and vibrational spectroscopy.
Water adsorbed on the Au-supported NaCl(001) films provides an ideal system for atomic-scale investigation by STM with a Cl-terminated tip (Figure 1a), which is performed at 5 K in the ultrahigh-vacuum (UHV) environment with a base pressure better than 8&#215;10-11 mbar. On one hand, the insulating NaCl films decouple water molecules electronically from the Au substrate so the native frontier orbitals of water are preserved and the lifetime of the electrons residing in the molecular resonant state is prolonged. On the other hand, the STM tip could effectively tune the frontier orbital of water toward the EF via tip-water coupling, especially when the tip is functionalized with a Cl atom. These key steps enable high-resolution orbital imaging and vibrational spectroscopy of water monomers and clusters. In addition, water molecules could be manipulated in a well-controlled manner, due to the strong electrostatic interaction between the negatively charged Cl-tip and water.
In this report, the preparation procedures of the sample and the Cl-terminated tip for STM investigation are outlined in detail in section 1 and 2, respectively. In section 3, we describe the orbital imaging technique, by which the O-H directionality of water monomer and tetramer are resolved. The tip-enhanced IETS is introduced in section 4, which allows the detection of vibrational modes of water molecules at single-bond limit, and determination of the H-bonding strength with high accuracy from the red shift in the oxygen-hydrogen stretching frequency of water. In section 5, we show how the water tetramer can be constructed and switched by controlled tip manipulation. Based on the orbital imaging, spectroscopy, and manipulation techniques, isotopic substitution experiments can be performed to probe the quantum nature of protons in interfacial water, such as quantum tunneling and zero-point motion.

<table border="0" cellpadding="0" cellspacing="0" style="width:632px;" width="633">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Au(111) single crystal</td>
			<td style="width:131px;">MaTeck</td>
			<td style="width:119px;">NA</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">NaCl</td>
			<td style="width:131px;">Sigma Aldrich</td>
			<td align="right">450006</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Water, deuterium-depleted&#160;</td>
			<td style="width:131px;">Sigma Aldrich</td>
			<td align="right">195294</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Deuterium oxide&#160;</td>
			<td style="width:131px;">Sigma Aldrich</td>
			<td align="right" style="width:119px;">364312</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Sealed-off glass-UHV adapters</td>
			<td style="width:131px;">MDC vacuum products</td>
			<td align="right" style="width:119px;">46300</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Diaphragm-sealed valve</td>
			<td style="width:131px;">any</td>
			<td style="width:119px;">NA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Bellows-sealed valve</td>
			<td style="width:131px;">any</td>
			<td style="width:119px;">NA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Leak valve</td>
			<td style="width:131px;">Kurt J. Lesker&#160;</td>
			<td style="width:119px;">NA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Scanning tunneling microscopy</td>
			<td style="width:131px;">CreaTec</td>
			<td style="width:119px;">NA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Electronic controller.</td>
			<td style="width:131px;">Nanonis&#160;</td>
			<td style="width:119px;">NA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Tungsten wire</td>
			<td style="width:131px;">any</td>
			<td style="width:119px;"></td>
			<td>diameter:0.3 mm; purity: 99.95%</td>
		</tr>
	</tbody>
</table>

probing the structure and dynamics of interfacial water with scanning tunneling microscopy and spectroscopy

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal structure and probing the hydrogen-bond (H-bond) dynamics of the water molecules adsorbed on solid surfaces are fundamental issues of water science, which remains a great challenge owing to the light mass and small size of hydrogen. Scanning tunneling microscopy (STM) is a promising tool for attacking these problems, thanks to its capabilities of sub-&#197;ngstr&#246;m spatial resolution, single-bond vibrational sensitivity, and atomic/molecular manipulation. The designed experimental system consists of a Cl-terminated tip and a sample fabricated by dosing water molecules in situ onto the Au(111)-supported NaCl(001) surfaces. The insulating NaCl films electronically decouple the water from the metal substrates, so the intrinsic frontier orbitals of water molecules are preserved. The Cl-tip facilitates the manipulation of the single water molecules, as well as gating the orbitals of water to the proximity of Fermi level (EF) via tip-water coupling. This paper outlines the detailed methods of submolecular resolution imaging, molecular/atomic manipulation, and single-bond vibrational spectroscopy of interfacial water. These studies open up a new route for investigating the H-bonded systems at the atomic scale.

Figure 1a illustrates the schematic of the STM experimental setup. First, Au(111) substrate is cleaned by sputtering and annealing cycles in the UHV chamber. The clean Au(111) sample shows 22&#215;&#8730;3 reconstructed surface, where the atoms of the surface layer occupy both the hcp and the fcc sites forming herringbone structures (Inset of Figure 1b). The NaCl is evaporated on the Au(111) subs...

Watch this Scientific Journal Video about Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy at JoVE.com

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy

Here, we present a protocol to investigate the structure and dynamics of interfacial water at the atomic scale, in terms of submolecular resolution imaging, molecular manipulation, and single-bond vibrational spectroscopy.

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal ...

The overall goal of this experiment is to probe the structure and dynamics of interfacial water at the atomic scale using submolecular resolution imaging, molecular manipulation and single bond vibrational spectroscopy. This method can help answer fundamental issues about water science such as identifying the hydrogen bond and directionality of water and probing the hydrogen bond dynamics and vibrational spectroscopy of water molecules as shown on solid surfaces. The main advantage of this technique is that STM combines the capability of sub-angstrom Spatial resolution, atomic manipulation, and single bond vibrational sensitivity.Except for providing insight into the structure, dynamics, and nuclear quantum effects of surface water, it can also be applied to more complex and realistic hydrogen bond system such as confined water, buck eyes, multilayer water, and water hydrogen systems. To begin, follow along with the accompanying text protocol to clean the gold 111 single crystal using cycles of argon ion sputtering and subsequent annealing. Deposit sodium chloride onto the surface of the gold crystal and then transfer it to the scanning stage of an STM set up.Using standard STM techniques, check the coverage and size of the bi-layer sodium chloride 001 eye lens on the gold 111 substrateaight. The results should look similar to those shown here. Next purify water using freeze, pump, thaw cycles to remove any remaining impurities.Pump the gas line to 10 to the minus five pascals and then freeze the liquid water with liquid nitrogen. Now close the bellows sealed valve and leave the gas line under vacuum. Then open the diaphragm sealed valve and let the water vapor fill in the gas line.Then decrease the temperature of the sample to five kelvin. Open the leak valve slowly to make the pressure of the ultra high vacuum STM chamber increase to two times 10 to the minus 10th millibar. Next open the shutter.Dose the water molecules onto the gold supported sodium chloride surface for one minute. Then close the shutter and the leak valve. At this point, check the coverage of water molecules on the surface using standard STM techniques.Expect to see isolated water monomers on the sample surface. To begin, fabricate an electrochemically etched tungsten tip, etch it in three molar sodium hydroxide and then clean it using distilled water and ethanol as described in the accompanying text protocol. Next apply voltage pulses and controlled crashing procedures on the STM tip until the atomic chlorine atoms of the sodium chloride surface are resolved.Then position the STM tip over the center of one of the chlorine atoms and bring the bare tip close to the sodium chloride surface in proximity with the set point. Next retract the tip to the original set point and scan the same area. Check that a chlorine atom has attached to the tip by visualizing both the improved resolution and the missing chlorine atom in the STM image.To begin, set up the biospectroscopy module. Select the current, the differential conductance, the derivative of the differential conductance channels. Then adjust the setting time to 50 milliseconds and integration time as 300 milliseconds.The spectro tunneling spectroscopy and the inelastic electro tunneling spectroscopy are acquired simultaneously using a lock in amplifier by modulating the first and second harmonics of the tunneling current respectively. Increase the integration time and sweep times as needed to obtain smooth spectra. Then tune the Z offset to take the biospectroscopy at different tip heights.Next open lock in, modulate the bias, and demodulate the current. Set the modulation frequency as a few hundred hertz and the modulation amplitude as five to seven millivolts. After setting the modulation frequency, make sure there is no mechanical and electronic noise at the set point frequency and the corresponding second harmonic frequency.To set the first harmonic phase, start by switching to the Z-Controller module. Set the tip lift to 10 nanometers and turn off the feedback, then switch to the lock in module and turn on the lock in button. Click on the first harmonic auto phase and record the phase.Repeat the auto phase at least five times and take the average. Then subtract 90 degrees from the averaged phase to get the phase of the junction. Next set the second harmonic phase.To accomplish this, position the STM tip on the gold substrate and start the biospectroscopy sweep from minus one volts to one volt. Then select the differential conductance channel LI X 1, and the function dY/dX which together show the derivative of DI over DV spectrum. Find a prominent peak feature in the spectrum and set the corresponding energy as the bias.Next turn on the lock in and keep the STM system in tunneling mode. Click the second harmonic auto phase at least five times and take the average. To begin, scan the water monomer with the chlorine atom tip.Then position the tip on the sodium chloride surface and take the biospectroscopy as the background signal. Next position the tip on the water monomer and start the biospectroscopy sweep. If the dI/dV and second derivative spectra of water are featureless, simply follow the background sodium chloride coated surface, then decrease the tip height by tuning the Z offset until the vibrational features emerge in the spectra.To begin the construction of a water tetramer, first scan for an area containing four water monomers and position the chlorine tip on top of a monomer at the set point of V equals 100 millivolts and I equals 50 picoamperes. Decrease the height so the voltage is 10 millivolts and the current is 150 picoamperes. This will enhance the tip water interaction.Next move the chlorine atom tip along the predesigned trajectories. Then retract the tip to its initial set point and rescan the same area to check that the water dimer is formed. Repeat this process until a water trimer and eventually tetramer are formed.The tetramer contains two degenerate chiral states. Anti clockwise, and clockwise H bonded loops. As the chlorine atom terminated tip is lowered, the representative current bounces around as the tetramer changes between the clockwise and anticlockwise states.When retracting the tip to the original height, the tetramer shown here is left in the anti clockwise state. The switching rates between clockwise and anti clockwise can be extracted from the current versus time trace to show the lifetime distribution of a tetramer. The clockwise tetramer can be fitted by an exponential decay.To explore the mechanism of the proton transfer in the tetramer, the effect of full and partial isotopic substitution on the chirality switching is described here. Strikingly the chirality switching rate of the four water tetramer is substantially reduced by replacing a single water molecule with deuterium oxide. Almost to the same level of the four deuterium oxide tetramer.While performing the procedure for manipulation and vibrational spectroscopy, it is important to remember to functionalize the STM tip with a single chlorine atom. This technology provides surface signs an ingenious method to explore the detailed topology of hydrogen bond network and the quantum motions of protons in water clusters at an atomic scale. After watching this video you should have a good understanding of how to identify the hydrogen bond directionality via opto imaging.You should also understand how to push the vibrational spectroscopy down to a single bond limit and how to manipulate water molecules in a controlled manner.

probing-structure-dynamics-interfacial-water-with-scanning-tunneling

Research

Education

JoVE Journal

JoVE Core

Chemistry

Chemical Bonding: Molecular Geometry and Bonding Theories

SCIENTISTS IN ACTION

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy.
NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. Due to difficulty in crystallization to provide single crystals suitable for X-ray crystallography, the NMR technique is extremely valuable, especially as it provides information on the solution state rather than the solid state. Herein we describe all steps that are required for full three-dimensional structure determinations by NMR. The protocol includes sample preparation in an NMR tube, 1D and 2D data collection and processing, peak assignment and integration, molecular mechanics calculations, and structure analysis. Importantly, the analysis was first conducted without any preset metal-ligand bonds, to assure a reliable structure determination in an unbiased manner.

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

The NMR-solution structure of a metallochaperone model peptide with Cu (I) was determined, and a detailed protocol from sample preparation and 1D and 2D data collection to a three-dimensional structure is described.

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox ...

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

Here we present a protocol to measure the force of interactions between a well-defined inorganic surface and either peptides or amino acids by single-molecule force spectroscopy measurements using an atomic force microscope (AFM). The information obtained from the measurement is important to better understand the peptide-inorganic material interphase.

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals ...

Synthesis and Structure Determination of &#181;-Conotoxin PIIIA Isomers with Different Disulfide Connectivities

Peptides with a high number of cysteines are usually influenced regarding the three-dimensional structure by their disulfide connectivity. It is thus highly important to avoid undesired disulfide bond formation during peptide synthesis, because it may result in a completely different peptide structure, and consequently altered bioactivity. However, the correct formation of multiple disulfide bonds in a peptide is difficult to obtain by using standard self-folding methods such as conventional buffer oxidation protocols, because several disulfide connectivities can be formed. This protocol represents an advanced strategy required for the targeted synthesis of multiple disulfide-bridged peptides which cannot be synthesized via buffer oxidation in high quality and quantity. The study demonstrates the application of a distinct protecting group strategy for the synthesis of all possible 3-disulfide-bonded peptide isomers of &#181;-conotoxin PIIIA in a targeted way. The peptides are prepared by Fmoc-based solid phase peptide synthesis using a protecting group strategy for defined disulfide bond formation. The respective pairs of cysteines are protected with trityl (Trt), acetamidomethyl (Acm), and tert-butyl (tBu) protecting groups to make sure that during every oxidation step only the required cysteines are deprotected and linked. In addition to the targeted synthesis, a combination of several analytical methods is used to clarify the correct folding and generation of the desired peptide structures. The comparison of the different 3-disulfide-bonded isomers indicates the importance of accurate determination and knowledge of the disulfide connectivity for the calculation of the three-dimensional structure and for interpretation of the biological activity of the peptide isomers. The analytical characterization includes the exact disulfide bond elucidation via tandem mass spectrometry (MS/MS) analysis which is performed with partially reduced and alkylated derivatives of the intact peptide isomer produced by an adapted protocol. Furthermore, the peptide structures are determined using 2D nuclear magnetic resonance (NMR) experiments and the knowledge obtained from MS/MS analysis.

Synthesis and Structure Determination of &amp;#181;-Conotoxin PIIIA Isomers with Different Disulfide Connectivities

Cysteine-rich peptides fold into distinct three-dimensional structures depending on their disulfide connectivity. Targeted synthesis of individual disulfide isomers is required when buffer oxidation does not lead to the desired disulfide connectivity. The protocol deals with the selective synthesis of 3-disulfide-bonded peptides and their structural analysis using NMR and MS/MS studies.

Peptides with a high number of cysteines are usually influenced regarding the three-dimensional structure by their disulfide connectivity. It is thus ...

Synthesis of Soft Polysiloxane-urea Elastomers for Intraocular Lens Application

This study discusses a synthesis route for soft polysiloxane-based urea (PSU) elastomers for their applications as accommodating intraocular lenses (a-IOLs). Aminopropyl-terminated polydimethylsiloxanes (PDMS) were previously prepared via the ring-chain equilibration of the cyclic siloxane octamethylcyclotetrasiloxane (D4) and 1,3-bis(3-aminopropyl)-tetramethyldisiloxane (APTMDS). Phenyl groups were introduced into the siloxane backbone via the copolymerization of D4 and 2,4,6,8-tetramethyl-2,4,6,8-tetraphenyl-cyclotetrasiloxane (D4Me,Ph). These polydimethyl-methyl-phenyl-siloxane-block copolymers were synthesized for increasing the refractive indices of polysiloxanes. For applications as an a-IOL, the refractive index of the polysiloxanes must be equivalent to that of a young human eye lens. The polysiloxane molecular weight is controlled by the ratio of the cyclic siloxane to the endblocker APTMDS. The transparency of the PSU elastomers is examined by the transmittance measurement of films between 200 and 750 nm, using a UV-Vis spectrophotometer. Transmittance values at 750 nm (upper end of the visible spectrum) are plotted against the PDMS molecular weight, and &#62; 90% of the transmittance is observed until a molecular weight of 18,000 g&#183;mol&#8722;1. Mechanical properties of the PSU elastomers are investigated using stress-strain tests on die-cut dog-bone-shaped specimens. For evaluating mechanical stability, mechanical hysteresis is measured by repeatedly stretching (10x) the specimens to 5% and 100% elongation. Hysteresis considerably decreases with the increase in the PDMS molecular weight. In vitro cytotoxicity of some selected PSU elastomers is evaluated using an MTS cell viability assay. The methods described herein permit the synthesis of a soft, transparent, and noncytotoxic PSU elastomer with a refractive index approximately equal to that of a young human eye lens.

This study describes synthetic routes for aminopropyl-terminated polydimethylsiloxanes and polydimethyl-methyl-phenyl-siloxane-block copolymers and for soft polysiloxane-based urea (PSU) elastomers. It presents the application of PSUs as accommodating an intraocular lens. An evaluation method for in vitro cytotoxicity is also described.

This study discusses a synthesis route for soft polysiloxane-based urea (PSU) elastomers for their applications as accommodating intraocular lenses ...

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

A significant number of heterogeneously-catalyzed chemical processes occur under liquid conditions, but simulating catalyst function under such conditions is challenging when it is necessary to include the solvent molecules. The bond breaking and forming processes modeled in these systems necessitate the use of quantum chemical methods. Since molecules in the liquid phase are under constant thermal motion, simulations must also include configurational sampling. This means that multiple configurations of liquid molecules must be simulated for each catalytic species of interest. The goal of the protocol presented here is to generate and sample trajectories of configurations of liquid water molecules around catalytic species on flat transition metal surfaces in a way that balances chemical accuracy with computational expense. Specifically, force field molecular dynamics (FFMD) simulations are used to generate configurations of liquid molecules that can subsequently be used in quantum mechanics-based methods such as density functional theory or ab initio molecular dynamics. To illustrate this, in this manuscript, the protocol is used for catalytic intermediates that could be involved in the pathway for the decomposition of glycerol (C3H8O3). The structures that are generated using FFMD are modeled in DFT in order to estimate the enthalpies of solvation of the catalytic species and to identify how H2O molecules participate in catalytic decompositions.

The goal of the protocol presented here is to generate and sample trajectories of configurations of liquid water molecules around catalytic species on a flat transition metal surface. The sampled configurations can be used as starting structures in quantum mechanics-based methods.

A significant number of heterogeneously-catalyzed chemical processes occur under liquid conditions, but simulating catalyst function under such conditions ...

Performing Spectroscopy on Plasmonic Nanoparticles with Transmission-Based Nomarski-Type Differential Interference Contrast Microscopy

Differential interference contrast (DIC) microscopy is a powerful imaging tool that is most commonly employed for imaging microscale objects using visible-range light. The purpose of this protocol is to detail a proven method for preparing plasmonic nanoparticle samples and performing single particle spectroscopy on them with DIC microscopy. Several important steps must be followed carefully in order to perform repeatable spectroscopy experiments. First, landmarks can be etched into the sample substrate, which aids in locating the sample surface and in tracking the region of interest during experiments. Next, the substrate must be properly cleaned of debris and contaminants that can otherwise hinder or obscure examination of the sample. Once a sample is properly prepared, the optical path of the microscope must be aligned, using Kohler Illumination. With a standard Nomarski style DIC microscope, rotation of the sample may be necessary, particularly when the plasmonic nanoparticles exhibit orientation-dependent optical properties. Because DIC microscopy has two inherent orthogonal polarization fields, the wavelength-dependent DIC contrast pattern reveals the orientation of rod-shaped plasmonic nanoparticles. Finally, data acquisition and data analyses must be carefully performed. It is common to represent DIC-based spectroscopy data as a contrast value, but it is also possible to present it as intensity data. In this demonstration of DIC for single particle spectroscopy, the focus is on spherical and rod-shaped gold nanoparticles.

The goal of this protocol is to detail a proven approach for the preparation of plasmonic nanoparticle samples and for performing single particle spectroscopy on them with differential interference contrast (DIC) microscopy.

Differential interference contrast (DIC) microscopy is a powerful imaging tool that is most commonly employed for imaging microscale objects using ...

Probing Surface Electrochemical Activity of Nanomaterials using a Hybrid Atomic Force Microscope-Scanning Electrochemical Microscope (AFM-SECM)

Scanning electrochemical microscopy (SECM) is used to measure the local electrochemical behavior of liquid/solid, liquid/gas and liquid/liquid interfaces. Atomic force microscopy (AFM) is a versatile tool to characterize micro- and nanostructure in terms of topography and mechanical properties. However, conventional SECM or AFM provides limited laterally resolved information on electrical or electrochemical properties at nanoscale. For instance, the activity of a nanomaterial surface at crystal facet levels is difficult to resolve by conventional electrochemistry methods. This paper reports the application of a combination of AFM and SECM, namely, AFM-SECM, to probe nanoscale surface electrochemical activity while acquiring high-resolution topographical data. Such measurements are critical to understanding the relationship between nanostructure and reaction activity, which is relevant to a wide range of applications in material science, life science and chemical processes. The versatility of the combined AFM-SECM is demonstrated by mapping topographical and electrochemical properties of faceted nanoparticles (NPs) and nanobubbles (NBs), respectively. Compared to previously reported SECM imaging of nanostructures, this AFM-SECM enables quantitative assessment of local surface activity or reactivity with higher resolution of surface mapping.

Probing Surface Electrochemical Activity of Nanomaterials using a Hybrid Atomic Force Microscope-Scanning Electrochemical Microscope AFM-SECM

Atomic force microscopy (AFM) combined with scanning electrochemical microscopy (SECM), namely, AFM-SECM, can be used to simultaneously acquire high-resolution topographical and electrochemical information on material surfaces at nanoscale. Such information is critical to understanding heterogeneous properties (e.g., reactivity, defects, and reaction sites) on local surfaces of nanomaterials, electrodes and biomaterials.

Scanning electrochemical microscopy (SECM) is used to measure the local electrochemical behavior of liquid/solid, liquid/gas and liquid/liquid interfaces. ...

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

We have developed a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts, water-based fluids, and various supercritical fluids. The package is a collection of Python scripts that include two major libraries dealing with file formats and with crystallography. All the scripts are run at the command line. We propose a simplified format to store the atomic trajectories and relevant thermodynamic information of the simulations, which is saved in UMD files, standing for Universal Molecular Dynamics. The UMD package allows the computation of a series of structural, transport and thermodynamic properties. Starting with the pair-distribution function it defines bond lengths, builds an interatomic connectivity matrix, and eventually determines the chemical speciation. Determining the lifetime of the chemical species allows running a full statistical analysis. Then dedicated scripts compute the mean-square displacements for the atoms as well as for the chemical species. The implemented self-correlation analysis of the atomic velocities yields the diffusion coefficients and the vibrational spectrum. The same analysis applied on the stresses yields the viscosity. The package is available via the GitHub website and via its own dedicated page of the ERC IMPACT project as open-access package.

Melts and fluids are ubiquitous vectors of mass transport in natural systems. We have developed an open-source package to analyze ab initio molecular-dynamics simulations of such systems. We compute structural (bonding, clusterization, chemical speciation), transport (diffusion, viscosity) and thermodynamic properties (vibrational spectrum).

We have developed a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package ...

Atomic Force Microscopy Combined with Infrared Spectroscopy as a Tool to Probe Single Bacterium Chemistry

Atomic Force Microscopy-Infrared Spectroscopy (AFM-IR) is a novel combinatory technique, enabling simultaneous characterization of physical properties and chemical composition of sample with nanoscale resolution. By combining AFM with IR, the spatial resolution limitation of conventional IR is overcome, enabling a resolution of 20&#8211;100 nm to be achieved. This opens the door for a broad array of new applications of IR toward probing samples smaller than several micrometers, previously unachievable by means of conventional IR microscopy. AFM-IR is eminently suited for bacterial research, providing both spectral and spatial information at the single cell and intracellular level. The increasing global health concerns and unfavorable future prediction regarding bacterial infections, and especially, rapid development of antimicrobial resistance, has created an urgent need for a research tool capable of phenotypic probing at the single cell and subcellular level. AFM-IR offers the potential to address this need, by enabling detail characterization of chemical composition of a single bacterium. Here, we provide a complete protocol for sample preparation and data acquisition of single spectra and mapping modality, for the application of AFM-IR toward bacterial studies.

Atomic Force Microscopy-Infrared Spectroscopy (AFM-IR) provides a powerful platform for bacterial studies, enabling to achieve nanoscale resolution. Both, mapping of subcellular changes (e.g., upon cell division) as well as comparative studies of chemical composition (e.g., arising from drug resistance) can be conducted at a single cell level in bacteria.

Atomic Force Microscopy-Infrared Spectroscopy (AFM-IR) is a novel combinatory technique, enabling simultaneous characterization of physical properties and ...

Preparation of Nanoparticles for ToF-SIMS and XPS Analysis

Nanoparticles have gained increasing attention in recent years due to their potential and application in different fields including medicine, cosmetics, chemistry, and their potential to enable advanced materials. To effectively understand and regulate the physico-chemical properties and potential adverse effects of nanoparticles, validated measurement procedures for the various properties of nanoparticles need to be developed. While procedures for measuring nanoparticle size and size distribution are already established, standardized methods for analysis of their surface chemistry are not yet in place, although the influence of the surface chemistry on nanoparticle properties is undisputed. In particular, storage and preparation of nanoparticles for surface analysis strongly influences the analytical results from various methods, and in order to obtain consistent results, sample preparation must be both optimized and standardized. In this contribution, we present, in detail, some standard procedures for preparing nanoparticles for surface analytics. In principle, nanoparticles can be deposited on a suitable substrate from suspension or as a powder. Silicon (Si) wafers are commonly used as substrate, however, their cleaning is critical to the process. For sample preparation from suspension, we will discuss drop-casting and spin-coating, where not only the cleanliness of the substrate and purity of the suspension but also its concentration play important roles for the success of the preparation methodology. For nanoparticles with sensitive ligand shells or coatings, deposition as powders is more suitable, although this method requires particular care in fixing the sample.

A number of different procedures for preparing nanoparticles for surface analysis are presented (drop casting, spin coating, deposition from powders, and cryofixation). We discuss the challenges, opportunities, and possible applications of each method, particularly regarding the changes in the surface properties caused by the different preparation methods.

Nanoparticles have gained increasing attention in recent years due to their potential and application in different fields including medicine, cosmetics, ...