Real-Space Imaging of a Single-Molecule Monoradical Reaction

2020 ◽  
Vol 142 (31) ◽  
pp. 13550-13557 ◽  
Author(s):  
Shaotang Song ◽  
Na Guo ◽  
Xinzhe Li ◽  
Guangwu Li ◽  
Yohei Haketa ◽  
...  
Keyword(s):  
Single Molecule ◽  
Real Space

scholarly journals Probing intramolecular vibronic coupling through vibronic-state imaging

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fan-Fang Kong ◽  
Xiao-Jun Tian ◽  
Yang Zhang ◽  
Yun-Jie Yu ◽  
Shi-Hao Jing ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Spectroscopy ◽  
Transition Density ◽  
Real Space ◽  
Vibronic Coupling ◽  
Vibronic State ◽  
Dipole Orientation ◽  
Transition Dipole ◽  
Franck Condon ◽  
Strong Dynamic

AbstractVibronic coupling is a central issue in molecular spectroscopy. Here we investigate vibronic coupling within a single pentacene molecule in real space by imaging the spatial distribution of single-molecule electroluminescence via highly localized excitation of tunneling electrons in a controlled plasmonic junction. The observed two-spot orientation for certain vibronic-state imaging is found to be evidently different from the purely electronic 0–0 transition, rotated by 90°, which reflects the change in the transition dipole orientation from along the molecular short axis to the long axis. Such a change reveals the occurrence of strong vibronic coupling associated with a large Herzberg–Teller contribution, going beyond the conventional Franck–Condon picture. The emergence of large vibration-induced transition charges oscillating along the long axis is found to originate from the strong dynamic perturbation of the anti-symmetric vibration on those carbon atoms with large transition density populations during electronic transitions.

scholarly journals Single-Molecule van der Waals Compass

2020 ◽  
Author(s):  
Xiao Chen ◽  
Boyuan Shen ◽  
Huiqiu Wang ◽  
Hao Xiong ◽  
Weizhong Qian ◽  
...  
Keyword(s):  
Single Molecule ◽  
Potential Field ◽  
Van Der Waals ◽  
Real Space ◽  
Channel Structure ◽  
Transmission Electron ◽  
Imaging Results ◽  
Scanning Transmission ◽  
Para Xylene ◽  
Temporal Dimensions

Abstract Imaging the single molecules is always challenging under the diverse microscopes, but highly demanded for investigating the intermolecular interactions at the molecular level1-6. The van der Waals (vdW) interactions at sub-nanometer scale will deeply influence various molecular behaviors under the confinement conditions7-11. Here, inspired by the traditional compass12, we introduce a classical strategy using a vertical para-xylene (PX) molecule as a rotating pointer to detect the vdW potential field in a MFI straight channel. Based on the integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM)13-17, we achieve the real-space imaging of single PX molecule pointer in each channel with a certain orientation. The solid relation between the pointer orientation and atomic channel structure in this vdW compass is established by combining the calculations and imaging results. Thus, these PX orientations help us identify the varied vdW potential field related to the channel geometry both in the spatial and temporal dimensions. This work not only provides a visible and sensitive pointer to investigate the host-guest vdW interactions in porous materials at the molecular level, but also promotes the further imaging and study of other single-molecule behaviors by the iDPC-STEM.

Real-space and real-time observation of a plasmon-induced chemical reaction of a single molecule

Science ◽  
2018 ◽  
Vol 360 (6388) ◽  
pp. 521-526 ◽  
Author(s):  
Emiko Kazuma ◽  
Jaehoon Jung ◽  
Hiromu Ueba ◽  
Michael Trenary ◽  
Yousoo Kim
Keyword(s):  
Real Time ◽  
Chemical Reaction ◽  
Single Molecule ◽  
Real Space ◽  
Time Observation ◽  
Real Time Observation

scholarly journals Single-molecule observation of nucleotide induced conformational changes in basal SecA-ATP hydrolysis

2018 ◽  
Vol 4 (10) ◽  
pp. eaat8797 ◽  
Author(s):  
Nagaraju Chada ◽  
Kanokporn Chattrakun ◽  
Brendan P. Marsh ◽  
Chunfeng Mao ◽  
Priya Bariya ◽  
...  
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Conformational Dynamics ◽  
Real Space ◽  
Biochemical Activity ◽  
Force Microscopy ◽  
Atomic Force ◽  
Reversible Transitions ◽  
Space Measurement

SecA is the critical adenosine triphosphatase that drives preprotein transport through the translocon, SecYEG, in Escherichia coli. This process is thought to be regulated by conformational changes of specific domains of SecA, but real-time, real-space measurement of these changes is lacking. We use single-molecule atomic force microscopy (AFM) to visualize nucleotide-dependent conformations and conformational dynamics of SecA. Distinct topographical populations were observed in the presence of specific nucleotides. AFM investigations during basal adenosine triphosphate (ATP) hydrolysis revealed rapid, reversible transitions between a compact and an extended state at the ~100-ms time scale. A SecA mutant lacking the precursor-binding domain (PBD) aided interpretation. Further, the biochemical activity of SecA prepared for AFM was confirmed by tracking inorganic phosphate release. We conclude that ATP-driven dynamics are largely due to PBD motion but that other segments of SecA contribute to this motion during the transition state of the ATP hydrolysis cycle.

scholarly journals Real-space characterization of hydroxyphenyl porphyrin derivatives designed for single-molecule devices

RSC Advances ◽  
2015 ◽  
Vol 5 (96) ◽  
pp. 79152-79156 ◽  
Author(s):  
Akitoshi Shiotari ◽  
Yusuke Ozaki ◽  
Shoichi Naruse ◽  
Hiroshi Okuyama ◽  
Shinichiro Hatta ◽  
...  
Keyword(s):  
Transport Properties ◽  
Single Molecule ◽  
Electronic States ◽  
Real Space ◽  
Porphyrin Derivatives ◽  
Molecular Rectifier ◽  
Space Characterization

Using STM, we image the hydroxyphenyl porphyrin unit and its array which are synthesized as the basis of a molecular rectifier, and characterize the electronic states associated with the transport properties through the molecule.

scholarly journals Visually constructing the chemical structure of a single molecule by scanning Raman picoscopy

2019 ◽  
Vol 6 (6) ◽  
pp. 1169-1175 ◽  
Author(s):  
Yao Zhang ◽  
Ben Yang ◽  
Atif Ghafoor ◽  
Yang Zhang ◽  
Yu-Fan Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Chemical Structure ◽  
Vibrational Mode ◽  
Real Space ◽  
Vibrational Modes ◽  
Spatial Confinement ◽  
Ultrahigh Resolution ◽  
Building Process ◽  
Structural Details ◽  
Fingerprint Database

Abstract The strong spatial confinement of a nanocavity plasmonic field has made it possible to visualize the inner structure of a single molecule and even to distinguish its vibrational modes in real space. With such ever-improved spatial resolution, it is anticipated that full vibrational imaging of a molecule could be achieved to reveal molecular structural details. Here we demonstrate full Raman images of individual vibrational modes at the ångström level for a single Mg-porphine molecule, revealing distinct characteristics of each vibrational mode in real space. Furthermore, by exploiting the underlying interference effect and Raman fingerprint database, we propose a new methodology for structural determination, which we have called ‘scanning Raman picoscopy’, to show how such ultrahigh-resolution spectromicroscopic vibrational images can be used to visually assemble the chemical structure of a single molecule through a simple Lego-like building process.

scholarly journals Characterization of the structure of polydisperse human low-density lipoprotein by neutron scattering

1995 ◽  
Vol 310 (2) ◽  
pp. 407-415 ◽  
Author(s):  
D F Meyer ◽  
A S Nealis ◽  
K R Bruckdorfer ◽  
S J Perkins
Keyword(s):  
Neutron Scattering ◽  
Single Molecule ◽  
Structural Changes ◽  
Density Lipoprotein ◽  
Real Space ◽  
Scattering Data ◽  
Ldl Oxidation ◽  
Radius Of Gyration ◽  
Low Density ◽  
Spherical Structure

Low-density lipoproteins (LDL) in plasma are constructed from a single molecule of apolipoprotein B-100 (M(r) 512000) in association with lipid (approximate M(r) 2-3 x 10(6)). The gross structure was studied using an updated pulsed-neutron camera LOQ with an area detector to establish the basis for the interpretation of structural changes seen during dynamic studies of LDL oxidation. Neutron-scattering data for LDL in 100% 2H2O buffers emphasize their external appearance. Guinier analysis on a continuous-flux neutron camera D17 revealed pronounced concentration-dependences in the radius of gyration, RG, and the intensity of forward scattering, I(0) (equivalent to the M(r) of LDL) between 0.5 and 11 mg of LDL protein/ml. LDL preparations from different donors gave different RG values. When extrapolated to zero concentration, RG values ranged between 8.3 and 10.6 nm and were linearly correlated with M(r), which is consistent with a spherical structure. The distance-distribution function P(r) in real space showed a single maximum at 9.1-10.9 nm, which is just under half the observed maximum dimension of 23.1 +/- 1.2 nm expected for a spherical structure. The neutron radial-density function p(r) exhibited a plateau of high and featureless density at the centre of LDL. LDL can be modelled by a polydisperse assembly of spheres with two internal densities and a mean radius close to 10.0 nm in a normal distribution of radii with a standard deviation of 2.0 nm. The data are consistent with recent electron-microscopy and ultracentrifugation data.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Real-space observation of spin-split molecular orbitals of adsorbed single-molecule magnets

2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Jörg Schwöbel ◽  
Yingshuang Fu ◽  
Jens Brede ◽  
Andrew Dilullo ◽  
Germar Hoffmann ◽  
...  
Keyword(s):  
Single Molecule ◽  
Real Space ◽  
Molecular Orbitals ◽  
Single Molecule Magnets

High-resolution structure determination by ALCHEMI

1983 ◽  
Vol 41 ◽  
pp. 178-181 ◽  
Author(s):  
Peter G. Self ◽  
Peter R. Buseck
Keyword(s):  
Site Occupancy ◽  
Real Space ◽  
Unit Cell ◽  
Bragg Angle ◽  
Electron Current ◽  
High Resolution Structure ◽  
Beam Incident ◽  
Crystallographic Planes ◽  
Electron Beam Incident ◽  
Resolution Structure

ALCHEMI (Atom Location by CHanneling Enhanced Microanalysis) enables the site occupancy of atoms in single crystals to be determined. In this article the fundamentals of the method for both EDS and EELS will be discussed. Unlike HRTEM, ALCHEMI does not place stringent resolution requirements on the microscope and, because EDS clearly distinguishes between elements of similar atomic number, it can offer some advantages over HRTEM. It does however, place certain constraints on the crystal. These constraints are: a) the sites of interest must lie on alternate crystallographic planes, b) the projected charge density on the alternate planes must be significantly different, and c) there must be at least one atomic species that lies solely on one of the planes.An electron beam incident on a crystal undergoes elastic scattering; in reciprocal space this is seen as a diffraction pattern and in real space this is a modulation of the electron current across the unit cell. When diffraction is strong (i.e., when the crystal is oriented near to the Bragg angle of a low-order reflection) the electron current at one point in the unit cell will differ significantly from that at another point.

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