scholarly journals Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

2020 ◽  
Author(s):  
Thomas Fellowes ◽  
JONATHAN WHITE
Keyword(s):  
Decomposition Analysis ◽  
Md Simulations ◽  
Accurate Method ◽  
Energy Decomposition Analysis ◽  
Selenium Atom ◽  
Biological Macromolecules ◽  
Energy Decomposition ◽  
Amber Force Field ◽  
Sigma Hole ◽  
Positively Charged

The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19, however<br>efforts to model ebselen in silico have been hampered by the lack of a efficient and accurate method to assess<br>its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which<br>incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to<br>simulate the sigma?-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach<br>is justified using an energy decomposition analysis of a number DFT optimised structures, which shows that the<br>?sigma-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting MD simulations<br>on a number of simple complexes, as well the clinically relevant SOD1, which is known to bind to ebselen.

scholarly journals Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

2020 ◽  
Author(s):  
Thomas Fellowes ◽  
JONATHAN WHITE
Keyword(s):  
Decomposition Analysis ◽  
Md Simulations ◽  
Accurate Method ◽  
Energy Decomposition Analysis ◽  
Selenium Atom ◽  
Biological Macromolecules ◽  
Energy Decomposition ◽  
Amber Force Field ◽  
Sigma Hole ◽  
Positively Charged

The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19, however<br>efforts to model ebselen in silico have been hampered by the lack of a efficient and accurate method to assess<br>its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which<br>incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to<br>simulate the sigma?-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach<br>is justified using an energy decomposition analysis of a number DFT optimised structures, which shows that the<br>?sigma-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting MD simulations<br>on a number of simple complexes, as well the clinically relevant SOD1, which is known to bind to ebselen.

scholarly journals Direct estimate of the internal π-donation to the carbene centre within N-heterocyclic carbenes and related molecules

2015 ◽  
Vol 11 ◽  
pp. 2727-2736 ◽  
Author(s):  
Diego M Andrada ◽  
Nicole Holzmann ◽  
Thomas Hamadi ◽  
Gernot Frenking
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Heterocyclic Carbenes ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Direct Estimate ◽  
Functional Theory ◽  
Bonding Analysis

Fifteen cyclic and acylic carbenes have been calculated with density functional theory at the BP86/def2-TZVPP level. The strength of the internal X→p(π) π-donation of heteroatoms and carbon which are bonded to the C(II) atom is estimated with the help of NBO calculations and with an energy decomposition analysis. The investigated molecules include N-heterocyclic carbenes (NHCs), the cyclic alkyl(amino)carbene (cAAC), mesoionic carbenes and ylide-stabilized carbenes. The bonding analysis suggests that the carbene centre in cAAC and in diamidocarbene have the weakest X→p(π) π-donation while mesoionic carbenes possess the strongest π-donation.

Characterization of cisplatin/membrane interactions by QM/MM energy decomposition analysis

2021 ◽  
Vol 23 (36) ◽  
pp. 20533-20540
Author(s):  
Gustavo Cárdenas ◽  
Álvaro Pérez-Barcia ◽  
Marcos Mandado ◽  
Juan J. Nogueira
Keyword(s):  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Membrane Interactions

The interactions that control the permeation of cisplatin through a DOPC bilayer are unveiled by a QM/MM EDA scheme.

XEDA , a fast and multipurpose energy decomposition analysis program

2021 ◽  
Author(s):  
Zhen Tang ◽  
Yanlin Song ◽  
Shu Zhang ◽  
Wei Wang ◽  
Yuan Xu ◽  
...  
Keyword(s):  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Analysis Program ◽  
Energy Decomposition

scholarly journals Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns

2015 ◽  
Vol 44 (10) ◽  
pp. 3177-3211 ◽  
Author(s):  
Maximillian J. S. Phipps ◽  
Thomas Fox ◽  
Christofer S. Tautermann ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Interaction ◽  
Charge Transfer ◽  
Interaction Energy ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Chemical Components ◽  
Protein Drug ◽  
Interaction Patterns ◽  
Energy Decomposition

The partitioning of the interaction energy into chemical components such as electrostatics, polarization, and charge transfer is possible with energy decomposition analysis approaches. We review and evaluate these for biomolecular applications.

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