First-Principles Modeling of Non-Covalent Interactions in Supramolecular Systems: The Role of Many-Body Effects

2012 ◽  
Vol 8 (11) ◽  
pp. 4317-4322 ◽  
Author(s):  
Alexandre Tkatchenko ◽  
Dario Alfè ◽  
Kwang S. Kim
Keyword(s):  
First Principles ◽  
Many Body ◽  
Supramolecular Systems ◽  
Non Covalent Interactions ◽  
Many Body Effects ◽  
Covalent Interactions

scholarly journals Aromatic adsorption on metals via first-principles density functional theory

2009 ◽  
Vol 465 (2110) ◽  
pp. 2949-2976 ◽  
Author(s):  
S. J. Jenkins
Keyword(s):  
First Principles ◽  
Density Functional ◽  
Functional Theory ◽  
Aromatic Molecules ◽  
Polycyclic Aromatic ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Case Basis ◽  
Electronic And Steric Effects

We review first-principles calculations relevant to the adsorption of aromatic molecules on metal surfaces. Benzene has been intensively studied on a variety of substrates, providing an opportunity to comment upon trends from one metal to another. Meanwhile, calculations elucidating the adsorption of polycyclic aromatic molecules are more sparse, but nevertheless yield important insights into the role of non-covalent interactions. Heterocyclic and substituted aromatic compounds introduce the complicating possibility of electronic and steric effects, whose relative importance can thus far only be gauged on a case-by-case basis. Finally, the coadsorption and/or reaction of aromatic molecules is discussed, highlighting an area where the predictive power of theory is likely to prove decisive in the future.

Role of non-covalent interactions in the supramolecular architectures of mercury(ii) diphenyldithiophosphates: An experimental and theoretical investigation

2021 ◽  
Vol 45 (4) ◽  
pp. 2249-2263
Author(s):  
Pretam Kumar ◽  
Snehasis Banerjee ◽  
Anu Radha ◽  
Tahira Firdoos ◽  
Subash Chandra Sahoo ◽  
...  
Keyword(s):  
Theoretical Investigation ◽  
Supramolecular Organization ◽  
Π Interactions ◽  
Supramolecular Architectures ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The H-bond, spodium bond and CH⋯π interactions playing an important role in the supramolecular organization of two mercury(ii) diphenyldithiophosphate complexes have been discussed.

The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution

2021 ◽  
Author(s):  
Sascha Jähnigen ◽  
Daniel Sebastiani ◽  
Rodolphe Vuilleumier
Keyword(s):  
Lactic Acid ◽  
Circular Dichroism ◽  
Computational Study ◽  
Bulk Water ◽  
Vibrational Circular Dichroism ◽  
Ab Initio Molecular Dynamics ◽  
Non Covalent Interactions ◽  
Circular Dichroïsm ◽  
Covalent Interactions

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss...

scholarly journals Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall

2018 ◽  
Author(s):  
Alister T. Boags ◽  
Firdaus Samsudin ◽  
Syma Khalid
Keyword(s):  
Cell Wall ◽  
Electrostatic Interactions ◽  
Cell Envelope ◽  
Binding Domain ◽  
Gram Negative Bacteria ◽  
Inner Membrane ◽  
E Coli ◽  
Non Covalent Interactions ◽  
Covalent Interactions

SUMMARYWe present a molecular modeling and simulation study of the of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. We show that non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. When OmpA is truncated to remove the peptidoglycan binding domain, TolR is able to pull the cell wall down towards the inner membrane. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.

scholarly journals Studying physisorption processes and molecular friction of cycloparaphenylene molecules on graphene nano-sized flakes: role of π⋯π and CH⋯π interactions

2017 ◽  
Vol 2 (3) ◽  
pp. 253-262 ◽  
Author(s):  
A. Pérez-Guardiola ◽  
A. J. Pérez-Jiménez ◽  
J. C. Sancho-García
Keyword(s):  
Cost Effective ◽  
Π Interactions ◽  
Graphene Flakes ◽  
Non Covalent Interactions ◽  
Molecular Friction ◽  
Covalent Interactions

We theoretically study, by means of dispersion-corrected and cost-effective methods, the strength of non-covalent interactions between cyclic organic nanorings and nano-sized graphene flakes acting as substrates.

The role of architectural engineering in macromolecular self-assemblies via non-covalent interactions: A molecular LEGO approach

2020 ◽  
Vol 103 ◽  
pp. 101230 ◽  
Author(s):  
Zebin Su ◽  
Ruimeng Zhang ◽  
Xiao-Yun Yan ◽  
Qing-Yun Guo ◽  
Jiahao Huang ◽  
...  
Keyword(s):  
Architectural Engineering ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Conformational preferences of N-acetyl-N′-methylprolineamide in different media: a 1H NMR and theoretical investigation

2019 ◽  
Vol 43 (4) ◽  
pp. 1757-1763 ◽  
Author(s):  
Carolyne B. Braga ◽  
Weslley G. D. P. Silva ◽  
Roberto Rittner
Keyword(s):  
1H Nmr ◽  
Theoretical Investigation ◽  
Conformational Preferences ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The conformational preferences and role of non-covalent interactions on the geometries of Ac–Pro–NHMe were elucidated in isolated phase and solution.

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