Browse
Submit Data
Databases
API
Help

Dataset Information

72 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Realization of a four-step molecular switch in scanning tunneling microscope manipulation of single chlorophyll-a molecules.

ABSTRACT: Single chlorophyll-a molecules, a vital resource for the sustenance of life on Earth, have been investigated by using scanning tunneling microscope manipulation and spectroscopy on a gold substrate at 4.6 K. Chlorophyll-a binds on Au(111) via its porphyrin unit while the phytyl-chain is elevated from the surface by the support of four CH(3) groups. By injecting tunneling electrons from the scanning tunneling microscope tip, we are able to bend the phytyl-chain, which enables the switching of four molecular conformations in a controlled manner. Statistical analyses and structural calculations reveal that all reversible switching mechanisms are initiated by a single tunneling-electron energy-transfer process, which induces bond rotation within the phytyl-chain.

SUBMITTER: Iancu V

PROVIDER: S-EPMC1560088 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Realization of a four-step molecular switch in scanning tunneling microscope manipulation of single chlorophyll-a molecules.

Iancu Violeta V Hla Saw-Wai SW

Proceedings of the National Academy of Sciences of the United States of America 20060905 37

Single chlorophyll-a molecules, a vital resource for the sustenance of life on Earth, have been investigated by using scanning tunneling microscope manipulation and spectroscopy on a gold substrate at 4.6 K. Chlorophyll-a binds on Au(111) via its porphyrin unit while the phytyl-chain is elevated from the surface by the support of four CH(3) groups. By injecting tunneling electrons from the scanning tunneling microscope tip, we are able to bend the phytyl-chain, which enables the switching of fou ...[more]

PMID: 16954201

Similar Datasets

Near-Field Manipulation in a Scanning Tunneling Microscope Junction with Plasmonic Fabry-Perot Tips.

Project description:Near-field manipulation in plasmonic nanocavities can provide various applications in nanoscale science and technology. In particular, a gap plasmon in a scanning tunneling microscope (STM) junction is of key interest to nanoscale imaging and spectroscopy. Here we show that spectral features of a plasmonic STM junction can be manipulated by nanofabrication of Au tips using focused ion beam. An exemplary Fabry-Pérot type resonator of surface plasmons is demonstrated by producing the tip with a single groove on its shaft. Scanning tunneling luminescence spectra of the Fabry-Pérot tips exhibit spectral modulation resulting from interference between localized and propagating surface plasmon modes. In addition, the quality factor of the plasmonic Fabry-Pérot interference can be improved by optimizing the overall tip shape. Our approach paves the way for near-field imaging and spectroscopy with a high degree of accuracy.

| S-EPMC6750903 | biostudies-literature

Computational scanning tunneling microscope image database.

Project description:We introduce the systematic database of scanning tunneling microscope (STM) images obtained using density functional theory (DFT) for two-dimensional (2D) materials, calculated using the Tersoff-Hamann method. It currently contains data for 716 exfoliable 2D materials. Examples of the five possible Bravais lattice types for 2D materials and their Fourier-transforms are discussed. All the computational STM images generated in this work are made available on the JARVIS-STM website ( https://jarvis.nist.gov/jarvisstm ). We find excellent qualitative agreement between the computational and experimental STM images for selected materials. As a first example application of this database, we train a convolution neural network model to identify the Bravais lattice from the STM images. We believe the model can aid high-throughput experimental data analysis. These computational STM images can directly aid the identification of phases, analyzing defects and lattice-distortions in experimental STM images, as well as be incorporated in the autonomous experiment workflows.

| S-EPMC7878481 | biostudies-literature

Longitudinal and transverse electron paramagnetic resonance in a scanning tunneling microscope.

Project description:Electron paramagnetic resonance (EPR) spectroscopy is widely used to characterize paramagnetic complexes. Recently, EPR combined with scanning tunneling microscopy (STM) achieved single-spin sensitivity with sub-angstrom spatial resolution. The excitation mechanism of EPR in STM, however, is broadly debated, raising concerns about widespread application of this technique. We present an extensive experimental study and modeling of EPR-STM of Fe and hydrogenated Ti atoms on a MgO surface. Our results support a piezoelectric coupling mechanism, in which the EPR species oscillate adiabatically in the inhomogeneous magnetic field of the STM tip. An analysis based on Bloch equations combined with atomic-multiplet calculations identifies different EPR driving forces. Specifically, transverse magnetic field gradients drive the spin-1/2 hydrogenated Ti, whereas longitudinal magnetic field gradients drive the spin-2 Fe. Also, our results highlight the potential of piezoelectric coupling to induce electric dipole moments, thereby broadening the scope of EPR-STM to nonpolar species and nonlinear excitation schemes.

| S-EPMC7527223 | biostudies-literature

Upgrade of a variable temperature scanning tunneling microscope for nanometer-scale spectromicroscopy.

Project description:Tip-enhanced Raman spectroscopy (TERS), tip-enhanced photoluminescence (TEPL), and scanning tunneling microscope-induced luminescence (STML) combine the high spatial resolution of probe microscopies with the spectroscopic capabilities of optical techniques. Here, we describe the upgrade of an ultrahigh vacuum (UHV) variable-temperature scanning probe microscope (VT-SPM) to perform tip-enhanced spectromicroscopy experiments at cryogenic temperatures. The home-made design includes a portable focusing lens (NA=0.45) that allows the simultaneous collection and injection of light from the tip-sample junction while assuring easy tip and sample transfers. We demonstrate the capabilities of our upgrade to resolve electroluminescence (EL), Raman, and TERS spectra using plasmonically active probes (Ag and Au tips) on various surfaces. We are able to observe the vibrational levels of C60 deposited on Ag(111) with a lateral resolution of ∼2 nanometers. Moreover, we use the tunability of the gap plasmon distribution to observe intense anti-Stokes signals of C60, highlighting the spectral sensitivity of the system. This upgrade opens new possibilities for studying surface chemistry, catalysis, and molecular electronics at state-of-the-art spatial and spectral resolutions using accessible SPM systems.•Portable lens holder•In-situ adjustable position•Nanometer-scale vibrational spectroscopy.

| S-EPMC11787449 | biostudies-literature

Open STM: A low-cost scanning tunneling microscope with a fast approach method.

Project description:In this study, we have developed an low-cost scanning tunneling microscope (STM) cost of 300 USD or 2000 CNY. The microscope is suitable for educational purposes and low-demand research imaging at the nanometer level. The microscope's motion components and scanner are controlled using piezoelectric materials, avoiding the thermal drift associated with traditional motor control. Our tip approach algorithm, which considers the capacitance and friction characteristics during piezoelectric slider movement, has reduced the time required for sample loading to establish tunneling current to approximately 1 min. The physical dimensions of the microscope body are 45 × 45 × 31.5 mm (W × L × H), and the control voltage does not exceed 15 V, ensuring the safety of operators, particularly those with limited experience. During performance verification, we conducted a scanning tunneling scan on a Highly Oriented Pyrolytic Graphite (HOPG) sample, utilizing bias voltages of 50 mV and 60 mV, resulting in clear observations of the atomic features of HOPG within the STM pattern.

| S-EPMC10825635 | biostudies-literature

Current-voltage characterization of individual as-grown nanowires using a scanning tunneling microscope.

Project description:Utilizing semiconductor nanowires for (opto)electronics requires exact knowledge of their current-voltage properties. We report accurate on-top imaging and I-V characterization of individual as-grown nanowires, using a subnanometer resolution scanning tunneling microscope with no need for additional microscopy tools, thus allowing versatile application. We form Ohmic contacts to InP and InAs nanowires without any sample processing, followed by quantitative measurements of diameter dependent I-V properties with a very small spread in measured values compared to standard techniques.

| S-EPMC3834301 | biostudies-literature

Phase-Resolved Detection of Ultrabroadband THz Pulses inside a Scanning Tunneling Microscope Junction.

Project description:Coupling phase-stable single-cycle terahertz (THz) pulses to scanning tunneling microscope (STM) junctions enables spatiotemporal imaging with femtosecond temporal and Ångstrom spatial resolution. The time resolution achieved in such THz-gated STM is ultimately limited by the subcycle temporal variation of the tip-enhanced THz field acting as an ultrafast voltage pulse, and hence by the ability to feed high-frequency, broadband THz pulses into the junction. Here, we report on the coupling of ultrabroadband (1-30 THz) single-cycle THz pulses from a spintronic THz emitter (STE) into a metallic STM junction. We demonstrate broadband phase-resolved detection of the THz voltage transient directly in the STM junction via THz-field-induced modulation of ultrafast photocurrents. Comparison to the unperturbed far-field THz waveform reveals the antenna response of the STM tip. Despite tip-induced low-pass filtering, frequencies up to 15 THz can be detected in the tip-enhanced near-field, resulting in THz transients with a half-cycle period of 115 fs. We further demonstrate simple polarity control of the THz bias via the STE magnetization and show that up to 2 V THz bias at 1 MHz repetition rate can be achieved in the current setup. Finally, we find a nearly constant THz voltage and waveform over a wide range of tip-sample distances, which by comparison to numerical simulations confirms the quasi-static nature of the THz pulses. Our results demonstrate the suitability of spintronic THz emitters for ultrafast THz-STM with unprecedented bandwidth of the THz bias and provide insight into the femtosecond response of defined nanoscale junctions.

| S-EPMC7441495 | biostudies-literature

Manipulation of nanoparticles of different shapes inside a scanning electron microscope.

Project description:In this work polyhedron-like gold and sphere-like silver nanoparticles (NPs) were manipulated on an oxidized Si substrate to study the dependence of the static friction and the contact area on the particle geometry. Measurements were performed inside a scanning electron microscope (SEM) that was equipped with a high-precision XYZ-nanomanipulator. To register the occurring forces a quartz tuning fork (QTF) with a glued sharp probe was used. Contact areas and static friction forces were calculated by using different models and compared with the experimentally measured force. The effect of NP morphology on the nanoscale friction is discussed.

| S-EPMC3943919 | biostudies-literature

Control of Surface Plasmon Propagation and Terahertz Near-Field Waveforms in a Scanning Tunneling Microscope.

Project description:Coupling subcycle THz pulses to a scanning tunneling microscope (STM) enables ultrafast spectroscopy at the atomic scale. This technique critically depends on the shape of the THz near-field waveform in the tunnel junction. We characterize the THz electric field waveform in the STM junction by electro-optic sampling of tip-scattered THz light (s-EOS) and pulse correlation using the THz-induced current. Combined with full-wave simulations, we identify THz spectral distortions and reflections arising from THz surface plasmon propagation along the tip wire and cavity modes at the tip apex. By optimizing the tip shape, tip holder geometry and materials, we achieve a drastically flattened THz near-field waveform. This optimization ensures point-like coupling to the far-field and, thus, allows precise Gouy phase control at the STM tip. The improved THz waveforms facilitate atomically-resolved THz time-domain spectroscopy in the STM with high dynamic range for investigating local electron and phonon dynamics on surfaces.

| S-EPMC11622368 | biostudies-literature

Near-Field Spectral Response of Optically Excited Scanning Tunneling Microscope Junctions Probed by Single-Molecule Action Spectroscopy.

Project description:The near-field spectral response of metallic nanocavities is a key characteristic in plasmon-assisted photophysical and photochemical processes. Here, we show that the near-field spectral response of an optically excited plasmonic scanning tunneling microscope (STM) junction can be probed by single-molecule reactions that serve as a nanoscale sensor detecting the local field intensity. Near-field action spectroscopy for the cis ↔ cis tautomerization of porphycene on a Cu(110) surface reveals that the field enhancement in the STM junction largely depends on microscopic structures not only on the tip apex, but also on its shaft. Using nanofabrication of Au tips with focused ion beam, we show that the spectral response is strongly modulated through the interference between the localized surface plasmon in the junction and propagating surface plasmon polariton generated on the shaft. Furthermore, it is demonstrated that the near-field spectral response can be manipulated by precisely shaping the tip shaft.

| S-EPMC6727595 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data