scholarly journals Identify Similarities in Diverse Polycyclic Aromatic Hydrocarbons of Asphaltenes and Heavy Oils Revealed by Noncontact Atomic Force Microscopy: Aromaticity, Bonding, and Implications in Reactivity

2019 ◽  
Author(s):  
Yunlong Zhang
Keyword(s):  
Atomic Force Microscopy ◽  
Aromatic Hydrocarbons ◽  
Molecular Structures ◽  
Polynuclear Aromatic Hydrocarbons ◽  
Heavy Oils ◽  
Diverse Range ◽  
Force Microscopy ◽  
Chemical Structures ◽  
Atomic Force ◽  
Polycyclic Aromatic

Heavy oils are enriched with polycyclic (or polynuclear) aromatic hydrocarbons (PAH or PNA), but characterization of their chemical structures has been a great challenge due to their tremendous diversity. Recently, with the advent of molecular imaging with noncontact Atomic Force Microscopy (nc-AFM), molecular structures of petroleum has been imaged and a diverse range of novel PAH structures was revealed. Understanding these structures will help to understand their chemical reactivities and the mechanisms of their formation or conversion. Studies on aromaticity and bonding provide means to recognize their intrinsic structural patterns which is crucial to reconcile a small number of structures from AFM and to predict infinite number of diverse molecules in bulk. Four types of PAH structures can be categorized according to their relative stability and reactivity, and it was found that the most and least stable types are rarely observed in AFM, with most molecules as intermediate types in a subtle balance of kinetic reactivity and thermodynamic stability. Local aromaticity was found maximized when possible for both alternant and nonalternant PAHs revealed by the aromaticity index NICS (Nucleus-Independent Chemical Shift) values. The unique role of five-membered rings in disrupting the electron distribution was recognized. Especially, the presence of partial double bonds in most petroleum PAHs was identified and their implications in the structure and reactivity of petroleum are discussed.

scholarly journals Identify Similarities in Diverse Polycyclic Aromatic Hydrocarbons of Asphaltenes and Heavy Oils Revealed by Noncontact Atomic Force Microscopy: Aromaticity, Bonding, and Implications in Reactivity

2019 ◽  
Author(s):  
Yunlong Zhang
Keyword(s):  
Atomic Force Microscopy ◽  
Aromatic Hydrocarbons ◽  
Molecular Structures ◽  
Polynuclear Aromatic Hydrocarbons ◽  
Heavy Oils ◽  
Diverse Range ◽  
Force Microscopy ◽  
Chemical Structures ◽  
Atomic Force ◽  
Polycyclic Aromatic

Heavy oils are enriched with polycyclic (or polynuclear) aromatic hydrocarbons (PAH or PNA), but characterization of their chemical structures has been a great challenge due to their tremendous diversity. Recently, with the advent of molecular imaging with noncontact Atomic Force Microscopy (nc-AFM), molecular structures of petroleum has been imaged and a diverse range of novel PAH structures was revealed. Understanding these structures will help to understand their chemical reactivities and the mechanisms of their formation or conversion. Studies on aromaticity and bonding provide means to recognize their intrinsic structural patterns which is crucial to reconcile a small number of structures from AFM and to predict infinite number of diverse molecules in bulk. Four types of PAH structures can be categorized according to their relative stability and reactivity, and it was found that the most and least stable types are rarely observed in AFM, with most molecules as intermediate types in a subtle balance of kinetic reactivity and thermodynamic stability. Local aromaticity was found maximized when possible for both alternant and nonalternant PAHs revealed by the aromaticity index NICS (Nucleus-Independent Chemical Shift) values. The unique role of five-membered rings in disrupting the electron distribution was recognized. Especially, the presence of partial double bonds in most petroleum PAHs was identified and their implications in the structure and reactivity of petroleum are discussed.

scholarly journals Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure

2021 ◽  
Vol 17 (7) ◽  
pp. e1009215
Author(s):  
Toru Niina ◽  
Yasuhiro Matsunaga ◽  
Shoji Takada
Keyword(s):  
Atomic Force Microscopy ◽  
Rigid Body ◽  
Correlation Coefficient ◽  
High Speed ◽  
Similarity Score ◽  
Molecular Structures ◽  
Cosine Similarity ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dynamics Simulations

Atomic force microscopy (AFM) can visualize functional biomolecules near the physiological condition, but the observed data are limited to the surface height of specimens. Since the AFM images highly depend on the probe tip shape, for successful inference of molecular structures from the measurement, the knowledge of the probe shape is required, but is often missing. Here, we developed a method of the rigid-body fitting to AFM images, which simultaneously finds the shape of the probe tip and the placement of the molecular structure via an exhaustive search. First, we examined four similarity scores via twin-experiments for four test proteins, finding that the cosine similarity score generally worked best, whereas the pixel-RMSD and the correlation coefficient were also useful. We then applied the method to two experimental high-speed-AFM images inferring the probe shape and the molecular placement. The results suggest that the appropriate similarity score can differ between target systems. For an actin filament image, the cosine similarity apparently worked best. For an image of the flagellar protein FlhAC, we found the correlation coefficient gave better results. This difference may partly be attributed to the flexibility in the target molecule, ignored in the rigid-body fitting. The inferred tip shape and placement results can be further refined by other methods, such as the flexible fitting molecular dynamics simulations. The developed software is publicly available.

scholarly journals Simulation atomic force microscopy to predict correlated conformational dynamics in proteins from topographic imaging

2021 ◽  
Author(s):  
Holger Flechsig
Keyword(s):  
Atomic Force Microscopy ◽  
Conformational Dynamics ◽  
Molecular Structures ◽  
Molecular Surface ◽  
Membrane Transporter ◽  
Force Microscopy ◽  
Atomic Force ◽  
Afm Imaging ◽  
Topographic Imaging ◽  
Alternating Access

Atomic force microscopy (AFM) of proteins can detect only changes within the scanned molecular surface, missing all motions in other regions and thus information about functionally relevant conformational couplings. We show that simulation AFM can overcome this drawback by reconstruction of 3D molecular structures from topographic AFM images. A proof of principle demonstration is provided for an in-silico AFM experiment visualizing the conformational dynamics of a membrane transporter. The application shows that the alternating access mechanism underlying its operation can be retrieved from only AFM imaging of one membrane side. Simulation AFM is implemented in the freely available BioAFMviewer software platform, providing the convenient applicability to better understand experimental AFM observations.

Understanding the Effects of Sample Preparation on the Chemical Structures of Petroleum Imaged with Noncontact Atomic Force Microscopy

2018 ◽  
Vol 57 (46) ◽  
pp. 15935-15941 ◽  
Author(s):  
Yunlong Zhang ◽  
Bruno Schuler ◽  
Shadi Fatayer ◽  
Leo Gross ◽  
Michael R. Harper ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Sample Preparation ◽  
Force Microscopy ◽  
Chemical Structures ◽  
Atomic Force

Pushing, pulling, dragging, and vibrating renal epithelia by using atomic force microscopy

2000 ◽  
Vol 278 (5) ◽  
pp. F689-F701 ◽  
Author(s):  
Robert M. Henderson ◽  
Hans Oberleithner
Keyword(s):  
Atomic Force Microscopy ◽  
Molecular Level ◽  
Molecular Structures ◽  
Biologically Active ◽  
Renal Physiology ◽  
Intact Cells ◽  
Force Microscopy ◽  
Physiological Conditions ◽  
Atomic Force ◽  
Near Future

Renal physiologists focus on events that take place on and around the surfaces of cells. Various techniques have been developed that follow transport functions at the molecular level, but until recently none of these techniques has been capable of making the behavior of molecular structures visible under physiological conditions. This apparent gap may be filled in the future by the application of atomic force microscopy. This technique produces an image not by optical means, but by “feeling” its way across a surface. Atomic force microscopy can, however, be modified in a number of ways, which means that besides producing a high-resolution image, it is possible to obtain several types of data on the interactions between the ultrastructural components of cell membranes (such as proteins) and other biologically active molecules (such as ATP). In this review we describe the recent use of the atomic force microscope in renal physiology, ranging from experiments in intact cells to those in isolated renal transport protein molecules, include examples of these extended applications of the technique, and point to uses that the microscope has recently found in other areas of biology that should prove fruitful in renal physiology in the near future.

Unraveling the Molecular Structures of Asphaltenes by Atomic Force Microscopy

2015 ◽  
Vol 137 (31) ◽  
pp. 9870-9876 ◽  
Author(s):  
Bruno Schuler ◽  
Gerhard Meyer ◽  
Diego Peña ◽  
Oliver C. Mullins ◽  
Leo Gross
Keyword(s):  
Atomic Force Microscopy ◽  
Molecular Structures ◽  
Force Microscopy ◽  
Atomic Force
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