Cationic gold clusters ligated with differently substituted phosphines: effect of substitution on ligand reactivity and binding

2015 ◽  
Vol 17 (22) ◽  
pp. 14636-14646 ◽  
Author(s):  
Grant E. Johnson ◽  
Astrid Olivares ◽  
David Hill ◽  
Julia Laskin
Keyword(s):  
Ligand Binding ◽  
Lone Pair ◽  
Gold Clusters ◽  
Binding Energies ◽  
Phosphine Ligands ◽  
Strongly Correlated ◽  
P Loss ◽  
Ligand Reactivity ◽  
Cationic Gold

Loss of substituted phosphine ligands is strongly correlated with the electron donating ability of the phosphorous lone pair. The results indicate that the relative ligand binding energies increase in the order PMe3 < PPhMe2 < PPh2Me < PPh3 < PPh2Cy < PPhCy2 < PCy3.

Distinct Modulation of Wild-Type and Selective Gene Mutated Vitamin D Receptor by Essential Poly Unsaturated Fatty Acids

2021 ◽  
Vol 21 ◽  
Author(s):  
Hari Balaji ◽  
Selvaraj Ayyamperuma ◽  
Niladri Saha ◽  
Shyam Sundar Pottabathula ◽  
Jubie Selvaraj ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Vitamin D ◽  
Ligand Binding ◽  
Vitamin D Deficiency ◽  
Binding Affinity ◽  
Unsaturated Fatty Acids ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Binding Energies ◽  
Wild Type

: Vitamin-D deficiency is a global concern. Gene mutations in the vitamin D receptor’s (VDR) ligand binding domain (LBD) variously alter the ligand binding affinity, heterodimerization with retinoid X receptor (RXR) and inhibit coactivator interactions. These LBD mutations may result in partial or total hormone unresponsiveness. A plethora of evidence report that selective long chain polyunsaturated fatty acids (PUFAs) including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and arachidonic acid (AA) bind to the ligand-binding domain of VDR and lead to transcriptional activation. We therefore hypothesize that selective PUFAs would modulate the dynamics and kinetics of VDRs, irrespective bioactive of vitamin-D binding. The spatial arrangements of the selected PUFAs in VDR active site were examined by in-silico docking studies. The docking results revealed that PUFAs have fatty acid structure-specific binding affinity towards VDR. The calculated EPA, DHA & AA binding energies (Cdocker energy) were lesser compared to vitamin-D in wild type of VDR (PDB id: 2ZLC). Of note, the DHA has higher binding interactions to the mutated VDR (PDB id: 3VT7) when compared to the standard Vitamin-D. Molecular dynamic simulation was utilized to confirm the stability of potential compound binding of DHA with mutated VDR complex. These findings suggest the unique roles of PUFAs in VDR activation and may offer alternate strategy to circumvent vitamin-D deficiency.

Effect of delocalization of nonbonding electron density on the stability of the M–Ccarbene bond in main group metal-imidazol-2-ylidene complexes: a computational and structural database study

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Samuel Tetteh ◽  
Albert Ofori
Keyword(s):  
Electron Density ◽  
Lone Pair ◽  
Main Group ◽  
Binding Energies ◽  
Electrostatic Model ◽  
Group Metal ◽  
Main Group Metal ◽  
Structural Database ◽  
The Stability ◽  
Lone Pair Electrons

Abstract The M–Ccarbene bond in metal (M) complexes involving the imidazol-2-ylidene (Im) ligand has largely been described using the σ-donor only model with donation of σ electrons from the sp-hybridized orbital of the carbene carbon into vacant orbitals on the metal centre. Analyses of the M–Ccarbene bond in a series of group IA, IIA and IIIA main group metal complexes show that the M-Im interactions are mostly electrostatic with the M–Ccarbene bond distances greater than the sum of the respective covalent radii. Estimation of the binding energies of a series of metal hydride/fluoride/chloride imidazol-2-ylidene complexes revealed that the stability of the M–Ccarbene bond in these complexes is not always commensurate with the σ-only electrostatic model. Further natural bond orbital (NBO) analyses at the DFT/B3LYP level of theory revealed substantial covalency in the M–Ccarbene bond with minor delocalization of electron density from the lone pair electrons on the halide ligands into antibonding molecular orbitals on the Im ligand. Calculation of the thermodynamic stability of the M–Ccarbene bond showed that these interactions are mostly endothermic in the gas phase with reduced entropies giving an overall ΔG > 0.

Exploring the low-lying structures of Aun(CO)+ (n = 1–10): adsorption and stretching frequencies of CO on various coordination sites

RSC Advances ◽  
2016 ◽  
Vol 6 (10) ◽  
pp. 8248-8255 ◽  
Author(s):  
Jie Wang ◽  
Qing-Bo Yan ◽  
Jun Ma ◽  
Xizi Cao ◽  
Xiaopeng Xing ◽  
...  
Keyword(s):  
Gold Clusters ◽  
Adsorption Site ◽  
P Adsorption ◽  
Coordination Sites ◽  
Structural Details ◽  
Adsorption Of Co ◽  
Cationic Gold

Adsorption of CO on cationic gold clusters is insensitive to the structural details of the adsorption site.

Aggregation-Mode-Dependent Optical Properties of Cationic Gold Clusters: Formation of Ordered Assemblies in Solution and Unique Optical Responses

2020 ◽  
Vol 124 (29) ◽  
pp. 16209-16215
Author(s):  
Mizuho Sugiuchi ◽  
Mingzhe Zhang ◽  
Yusaku Hakoishi ◽  
Yukatsu Shichibu ◽  
Noriko Nishizawa Horimoto ◽  
...  
Keyword(s):  
Optical Properties ◽  
Gold Clusters ◽  
Optical Responses ◽  
Cationic Gold

A quantum mechanical approach to ligand binding — Calculation of ligand–protein binding affinities for stromelysin-1 (MMP-3) inhibitors

2009 ◽  
Vol 87 (10) ◽  
pp. 1480-1484 ◽  
Author(s):  
Jian Li ◽  
Charles. H. Reynolds
Keyword(s):  
Ligand Binding ◽  
Metal Ion ◽  
Protein Complexes ◽  
Field Method ◽  
Binding Energies ◽  
Quantum Mechanical ◽  
Binding Affinities ◽  
Bond Forming ◽  
Proton Charge ◽  
Quantum Mechanical Approach

Linear-scaling quantum mechanical method was applied to calculate binding affinities of six stromelysin-1 (MMP-3) inhibitors with two different zinc binding groups (ZBGs). The entire protein and ligand–protein complexes were calculated using PM5 Hamiltonian, which enables the treatment of metal ion coordination, bond forming/breaking, and proton/charge transfers associated with the ligand binding process by the self-consistent field method. The calculated binding energies reproduce the binding-affinity trend observed experimentally.

scholarly journals Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Igor V. Oferkin ◽  
Ekaterina V. Katkova ◽  
Alexey V. Sulimov ◽  
Danil C. Kutov ◽  
Sergey I. Sobolev ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Quantum Chemical ◽  
Target Function ◽  
Binding Energies ◽  
Low Energy ◽  
Implicit Solvent ◽  
Energy Calculation ◽  
Solvent Models ◽  
Docking Program

The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.

scholarly journals Adsorption of Ethylene on Neutral, Anionic, and Cationic Gold Clusters

2010 ◽  
Vol 114 (6) ◽  
pp. 2484-2493 ◽  
Author(s):  
Andrey Lyalin ◽  
Tetsuya Taketsugu
Keyword(s):  
Gold Clusters ◽  
Cationic Gold

The 1S0 two-nucleon T matrix and the interior wave function

1976 ◽  
Vol 54 (22) ◽  
pp. 2225-2239 ◽  
Author(s):  
R. J. W. Hodgson ◽  
J. Tan
Keyword(s):  
Wave Function ◽  
Nuclear Matter ◽  
Symmetric Function ◽  
Body Wave ◽  
Binding Energies ◽  
Strongly Correlated ◽  
Scattering Wave ◽  
T Matrix

The fully off-shell T matrix is generated from a real symmetric function σ(k,k′) which in turn can be obtained from a knowledge of the two-body wave function in the interaction interior. The resulting T matrices are employed to compute the binding energies of 16O, 40Ca, and nuclear matter. Limiting the two-body wave function to physically acceptable forms limits the allowed σ functions. A 'difference integral' is defined in terms of the two-body scattering wave function, which seems to be strongly correlated with the binding energies.

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