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 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.

TOPOLOGICAL INDICES – WHY AND HOW

2021 ◽  
Author(s):  
Ivan Gutman ◽  
Keyword(s):  
Single Molecule ◽  
Chemical Structure ◽  
Chemical Reactivity ◽  
Chemical Species ◽  
Chemical Compounds ◽  
Simple Calculation ◽  
Topological Indices ◽  
High Level ◽  
Complex Phenomena ◽  
Real World Problems

By means of presently available high-level computational methods, based on quantum theory, it is possible to determine (predict) the main structural, electronic, energetic, geometric, and thermodynamic properties of a particular chemical species (usually a molecule), as well as the ways in which it changes in chemical reactions. When one needs to estimate such properties of thousands or millions of chemical species, such high-level calculations are no more feasible. Then simpler, but less accurate, approaches are necessary. One such approach utilized so-called “topological indices”. According to IUPAC ‘s definition [Pure Appl. Chem. 69 (1997) 1137]: A topological index is a numerical value associated with chemical constitution for correlation of chemical structure with various physical properties, chemical reactivity or biological activity. In the first part of the lecture, we show that „numerical values“are associated with many other complex phenomena, encountered in various areas of human activity, implying that „topological indices“ are used far beyond chemistry. Next, we discuss the number of possible chemical compounds. Simple calculation shows that the number of possible compounds zillion times exceeds the number of those that have been experimentally characterized. Even worse, in the entire Universe, there is not enough matter to make at least a single molecule of each possible compound. In the second part of the lecture, a few most popular topological indices will be presented, as well as the way in which these can be (and are being) applied in treating real-world problems.

Proanthocyanidin Structural Details Revealed by Ultrahigh Resolution FT-ICR MALDI-Mass Spectrometry, 1H–13C HSQC NMR, and Thiolysis-HPLC–DAD

2020 ◽  
Vol 68 (47) ◽  
pp. 14038-14048
Author(s):  
Savanah G. Reeves ◽  
Arpad Somogyi ◽  
Wayne E. Zeller ◽  
Theresa A. Ramelot ◽  
Kelly C. Wrighton ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Maldi Mass Spectrometry ◽  
Ultrahigh Resolution ◽  
Structural Details ◽  
Ft Icr

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

Synchrotron spectroscopy of the CSH-bending and CH3-rocking bands of methyl mercaptan

2020 ◽  
Vol 98 (6) ◽  
pp. 519-529
Author(s):  
R.M. Lees ◽  
E.M Reid ◽  
Li-Hong Xu ◽  
B.E. Billinghurst
Keyword(s):  
Ground State ◽  
Vibrational Mode ◽  
Good Representation ◽  
Methyl Mercaptan ◽  
Vibrational Modes ◽  
Oscillatory Structure ◽  
Out Of Plane ◽  
Type Character ◽  
Fourier Transform Spectra ◽  
Synchrotron Spectroscopy

The CSH-bending and CH3-rocking infrared bands of CH3SH have been investigated in Fourier transform spectra recorded at 0.001 cm−1 resolution employing synchrotron radiation at the Canadian Light Source in Saskatoon. The relative band strengths and structures are quite different from those of the CH3OH methanol analogue, with the CSH bend being very weak and both the in-plane and out-of-plane CH3 rocks being strong with intensities greater than the C–S stretch. The CSH bend has parallel a-type character with no detectable b-type component. The out-of-plane CH3 rock is a purely c-type perpendicular band, whereas the in-plane rock is of mixed a/b character. Sub-bands have been assigned for A and E torsional species up to about K = 10 for each vibrational mode, providing upper-state term values from which K-reduced substate origins were determined. For the CSH bend, the origins follow the customary oscillatory torsional pattern as a function of K with a sharply reduced amplitude of 0.362 cm−1 compared to the 0.653 cm−1 for the ground state. The torsional energy curves for the out-of-plane rock are also well-behaved but have inverted ordering of the A–E torsional splitting components and a larger amplitude of 1.33 cm−1. In contrast, the substate origins for the in-plane rock are scattered over a range of about 2 cm−1 without clear oscillatory structure. Several instances of coupling among the lower modes and the ground state via resonances between accidentally near-degenerate levels have been observed and characterized. Ab initio calculations are found to give a good representation of the frequency and relative intensity patterns for the lower vibrational modes.

scholarly journals Bacterial flagellar motor

2008 ◽  
Vol 41 (2) ◽  
pp. 103-132 ◽  
Author(s):  
Yoshiyuki Sowa ◽  
Richard M. Berry
Keyword(s):  
Single Molecule ◽  
Cell Envelope ◽  
Molecular Motor ◽  
Motive Force ◽  
Flagellar Motor ◽  
Large Size ◽  
Structural Details ◽  
Bacterial Flagellar Motor ◽  
And Function ◽  
Rotary Motor

AbstractThe bacterial flagellar motor is a reversible rotary nano-machine, about 45 nm in diameter, embedded in the bacterial cell envelope. It is powered by the flux of H+or Na+ions across the cytoplasmic membrane driven by an electrochemical gradient, the proton-motive force or the sodium-motive force. Each motor rotates a helical filament at several hundreds of revolutions per second (hertz). In many species, the motor switches direction stochastically, with the switching rates controlled by a network of sensory and signalling proteins. The bacterial flagellar motor was confirmed as a rotary motor in the early 1970s, the first direct observation of the function of a single molecular motor. However, because of the large size and complexity of the motor, much remains to be discovered, in particular, the structural details of the torque-generating mechanism. This review outlines what has been learned about the structure and function of the motor using a combination of genetics, single-molecule and biophysical techniques, with a focus on recent results and single-molecule techniques.

scholarly journals Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Kota Iwata ◽  
Shiro Yamazaki ◽  
Pingo Mutombo ◽  
Prokop Hapala ◽  
Martin Ondráček ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Chemical Structure ◽  
Room Temperature ◽  
Force Microscopy ◽  
Atomic Force

An Analysis of Infrared Spectroscopic Geometries

1997 ◽  
Vol 477 ◽  
Author(s):  
Gregory T. Merklin ◽  
Huihong Luo ◽  
Christopher E. D. Chidsey
Keyword(s):  
Vibrational Mode ◽  
Signal To Noise Ratio ◽  
Signal Strength ◽  
Internal Reflection ◽  
Infrared Spectrometry ◽  
Vibrational Modes ◽  
Signal To Noise ◽  
Transmission Spectroscopy ◽  
Infrared Spectroscopic ◽  
Experimental Geometry

ABSTRACTThe influence of experimental geometry on the signal strength and signal-to-noise ratio of infrared spectrometry has been investigated. In general, it was found that the choice of optimum experimental geometry depended on the orientation of the vibrational mode being investigated. In particular, it has been calculated that internal reflection spectrometry is relatively insensitive to vibrational modes perpendicular to the surface relative to transmission spectroscopy at Brewster's angle, and this has been confirmed by experiment.

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