scholarly journals Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 506 ◽  
Author(s):  
Carlos Romero-Muñiz ◽  
María Ortega ◽  
J. G. Vilhena ◽  
Ismael Diéz-Pérez ◽  
Juan Carlos Cuevas ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Structural Changes ◽  
Gold Surface ◽  
Scanning Tunneling ◽  
Total Density ◽  
Tunneling Microscopy ◽  
Functional Theory ◽  
Blue Copper ◽  
Total Density Of States

Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of the formation and electronic structure of a metal-protein-metal junction based on the blue-copper azurin from pseudomonas aeruginosa. We focus on the case in which the protein is adsorbed on a gold surface and is contacted, at the opposite side, to an STM (Scanning Tunneling Microscopy) tip by spontaneous attachment. This has been simulated through a combination of molecular dynamics and density functional theory. We find that the attachment to the tip induces structural changes in the protein which, however, do not affect the overall electronic properties of the protein. Indeed, only changes in certain residues are observed, whereas the electronic structure of the Cu-centered complex remains unaltered, as does the total density of states of the whole protein.

scholarly journals Binary supramolecular networks of bridged triphenylamines with different substituents and identical scaffolds

2018 ◽  
Vol 54 (82) ◽  
pp. 11554-11557 ◽  
Author(s):  
Christian Steiner ◽  
Zechao Yang ◽  
Bettina D. Gliemann ◽  
Ute Meinhardt ◽  
Martin Gurrath ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Scanning Tunneling Microscopy ◽  
Density Functional ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Functional Theory ◽  
Supramolecular Networks

Based on scanning tunneling microscopy experiments combined with density functional theory, we report the formation and the electronic structure of porous binary supramolecular networks on Au(111).

scholarly journals Self-assembly of N-heterocyclic carbenes on Au(111)

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alex Inayeh ◽  
Ryan R. K. Groome ◽  
Ishwar Singh ◽  
Alex J. Veinot ◽  
Felipe Crasto de Lima ◽  
...  
Keyword(s):  
Self Assembly ◽  
Density Functional ◽  
Surface Coverage ◽  
High Mobility ◽  
Heterocyclic Carbenes ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Surface Geometry ◽  
Functional Theory ◽  
Interesting Alternative

AbstractAlthough the self-assembly of organic ligands on gold has been dominated by sulfur-based ligands for decades, a new ligand class, N-heterocyclic carbenes (NHCs), has appeared as an interesting alternative. However, fundamental questions surrounding self-assembly of this new ligand remain unanswered. Herein, we describe the effect of NHC structure, surface coverage, and substrate temperature on mobility, thermal stability, NHC surface geometry, and self-assembly. Analysis of NHC adsorption and self-assembly by scanning tunneling microscopy and density functional theory have revealed the importance of NHC-surface interactions and attractive NHC-NHC interactions on NHC monolayer structures. A remarkable way these interactions manifest is the need for a threshold NHC surface coverage to produce upright, adatom-mediated adsorption motifs with low surface diffusion. NHC wingtip structure is also critical, with primary substituents leading to the formation of flat-lying NHC2Au complexes, which have high mobility when isolated, but self-assemble into stable ordered lattices at higher surface concentrations. These and other studies of NHC surface chemistry will be crucial for the success of these next-generation monolayers.

scholarly journals Lithium incorporation into a silica thin film: Scanning tunneling microscopy and density functional theory

2009 ◽  
Vol 80 (24) ◽  
Author(s):  
Jan Frederik Jerratsch ◽  
Niklas Nilius ◽  
Hans-Joachim Freund ◽  
Umberto Martinez ◽  
Livia Giordano ◽  
...  
Keyword(s):  
Thin Film ◽  
Density Functional Theory ◽  
Scanning Tunneling Microscopy ◽  
Density Functional ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Functional Theory ◽  
Silica Thin Film ◽  
Lithium Incorporation

scholarly journals Exact location of dopants below the Si(001):H surface from scanning tunneling microscopy and density functional theory

2017 ◽  
Vol 95 (7) ◽  
Author(s):  
Veronika Brázdová ◽  
David R. Bowler ◽  
Kitiphat Sinthiptharakoon ◽  
Philipp Studer ◽  
Adam Rahnejat ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Scanning Tunneling Microscopy ◽  
Density Functional ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Functional Theory ◽  
Exact Location

Understanding molecular self-assembly of a diol compound by considering competitive interactions

2016 ◽  
Vol 18 (39) ◽  
pp. 27390-27395 ◽  
Author(s):  
Oscar Díaz Arado ◽  
Maike Luft ◽  
Harry Mönig ◽  
Philipp Alexander Held ◽  
Armido Studer ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Scanning Tunneling Microscopy ◽  
Self Assembly ◽  
Density Functional ◽  
Competitive Interactions ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Functional Theory ◽  
Chemical Groups

With a combination of scanning tunneling microscopy and density functional theory, effects on molecular self-assembly involving two distinct chemical groups were investigated.

Subsurface cation vacancy stabilization of the magnetite (001) surface

Science ◽  
2014 ◽  
Vol 346 (6214) ◽  
pp. 1215-1218 ◽  
Author(s):  
R. Bliem ◽  
E. McDermott ◽  
P. Ferstl ◽  
M. Setvin ◽  
O. Gamba ◽  
...  
Keyword(s):  
Iron Oxides ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Atomic Scale ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Material Interface ◽  
Functional Theory ◽  
Ordered Array ◽  
Low Energy Electron

Iron oxides play an increasingly prominent role in heterogeneous catalysis, hydrogen production, spintronics, and drug delivery. The surface or material interface can be performance-limiting in these applications, so it is vital to determine accurate atomic-scale structures for iron oxides and understand why they form. Using a combination of quantitative low-energy electron diffraction, scanning tunneling microscopy, and density functional theory calculations, we show that an ordered array of subsurface iron vacancies and interstitials underlies the well-known (2×2)R45° reconstruction of Fe3O4(001). This hitherto unobserved stabilization mechanism occurs because the iron oxides prefer to redistribute cations in the lattice in response to oxidizing or reducing environments. Many other metal oxides also achieve stoichiometry variation in this way, so such surface structures are likely commonplace.

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