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.

scholarly journals Characterization of Cisplatin/Membrane Interactions by QM/MM Energy Decomposition Analysis

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

scholarly journals Characterization of Cisplatin/Membrane Interactions by QM/MM Energy Decomposition Analysis

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

scholarly journals Characterization of Cisplatin/Membrane Interactions by QM/MM Energy Decomposition Analysis

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

Characterization of fluorine-centred `F...O' σ-hole interactions in the solid state

2017 ◽  
Vol 73 (2) ◽  
pp. 140-152 ◽  
Author(s):  
Abhishek Sirohiwal ◽  
Venkatesha R. Hathwar ◽  
Dhananjay Dey ◽  
Roshni Regunathan ◽  
Deepak Chopra
Keyword(s):  
Solid State ◽  
Crystal Packing ◽  
Interaction Analysis ◽  
Decomposition Analysis ◽  
Atoms In Molecules ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Topological Features ◽  
Atomic Polarizability

In the current study, the crystal structure of 1-(3-nitrophenyl)-2,2,2-trifluoroethanone (A1) and (E)-4-((4-fluorophenyl) diazenyl)phenol (A2) has been analyzed for the characterization of the presence of a `unique' and `rare' intermolecular C(sp3/sp2)—F...O contact, which has been observed to play a significant role in the crystal packing. Theoretical charge-density calculations have been performed to study the nature and strength associated with the existence of this intermolecular F...O contact, wherein the F atom is attached to ansp3-hybridized C atom in the case of A1 and to ansp2hybridized carbon in the case of A2. The crystal packing of the former contains two `electronically different' Csp3—F...O contacts which are present across and in between the layers of molecules. In the latter case, it is characterized by the presence of a very `short' (2.708 Å) and `highly directional' (168° at ∠C4—F1...O1 and 174° at ∠C10—O1...F1) Csp2—F...O contact. According to the Cambridge Structural Database (CSD) study, it is a rare example in molecular crystals. Topological features of F...O contacts in the solid state were compared with the gas-phase models. The two-dimensional and three-dimensional static deformation density obtained from theoretical multipole modeling confirm the presence of a charge depleted region on the F atoms. Minimization of the electrostatic repulsion between like charges are observed through subtle arrangements in the electronic environment in two of the short intermolecular F...O contacts. These contacts were investigated using inputs from pair energy decomposition analysis, Bader's quantum theory of atoms in molecules (QTAIM), Hirshfeld surface analysis, delocalization index, reduced density gradient (RDG) plot, electrostatic potential surface and distributed atomic polarizability. The intermolecular energy decomposition (PIXEL) and RDG–NCI (non-covalent interaction) analysis of the F...O contacts establish the interaction to be dispersive in nature. The mutual polarization of an O atom by fluorine andviceversaprovides real physical insights into the role of atomic polarizability in interacting atoms in molecules in crystals.

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.

scholarly journals Water Complexes of Cytochrome P450: Insights from Energy Decomposition Analysis

Molecules ◽  
2013 ◽  
Vol 18 (6) ◽  
pp. 6782-6791 ◽  
Author(s):  
Nandun Thellamurege ◽  
Hajime Hirao
Keyword(s):  
Cytochrome P450 ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition

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
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