Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices

Hughes, Zak E.; Walsh, Tiffany R.

doi:10.1039/c6cp02323a

Cited by 26 publications

(24 citation statements)

References 91 publications

(179 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In vacuo plane-wave density functional theory (PW-DFT) calculations have shown that imidazole adsorbs more strongly to the edge and vertex sites of Au NPs than to the planar Au(111) surface. 76 In contrast, this same study found benzene (the closest analogue to Tyr; phenol was not investigated in this study) to adsorb more weakly to Au NPs at both the low-coordinate Au atom sites and both facets, compared with the infinite planar surfaces.…”

Section: 38mentioning

confidence: 71%

Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation

2017

Self Cite

View full text Add to dashboard Cite

The adsorption of three homo-tri-peptides, HHH, YYY and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations.We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tri-peptide binding affinities at aqueous Au (111) In a separate set of simulations, we predict the structures of the adsorbed tri-peptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data.

show abstract

Section: 38mentioning

confidence: 71%

Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation

2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…[33][34][35] The vdW-DF approaches use an explicit nonlocal correlation term to describe the dispersion interactions and have been applied to a wide range of systems. 30,[36][37][38][39][40] Previously-reported lane wave density functional theory (PW-DFT) calculations using the revPBE-vdW-DF functional of the ad-sorption energies of non-covalently adsorbed molecules to noble metal interfaces have shown good agreement with experiment. [40][41][42][43][44][45][46][47] The adsorption energy of the trans isomer of AB (tAB) to Ag(111) has previously been reported, involving calculations using the revPBE-vdW-DF functional.…”

Section: Introductionmentioning

confidence: 79%

Halo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties

et al. 2017

Self Cite

View full text Add to dashboard Cite

The adsorption of azobenzene (AB), ortho fluoro-azobenzene (FAB) and ortho chlor-azobenzol (ClAB), in both the cis and trans isomers, at the Au(111) and Ag(111) surfaces is investigated using plane wave density functional (PW-DFT) calculations with the revPBE-vdW-DF functional. The resulting adsorption energies and internal structures of AB adsorbed to both metal surfaces are in broad agreement with available experimental data. In the gas phase, FAB and ClAB feature a significant reduction in the energy difference between the two isomeric states, compared with AB. This relative reduction in the energy difference is still significant for the adsorbed form of FAB but is only weakly apparent for ClAB. The absorption spectra of the molecules have also been calculated, with the halogen substituents generating significant changes in the gas phase, but only a modest difference for the adsorbed molecules.

show abstract

“…CYP is a group of isozymes containing the metabolism of drugs, steroids, fatty acids, bile acids, and carcinogens. The results indicate that these studied compounds are nonsubstrate and noninhibitor of CYP enzymes [ 34 ]. In terms of AMES toxicity, all the studied compounds were observed to be nontoxic.…”

Section: Resultsmentioning

confidence: 99%

Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination therapy

et al. 2020

View full text Add to dashboard Cite

Presently, the SARS-CoV-2 (COVID-19) pandemic has been spreading throughout the world. Some drugs such as lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir have been recommended for COVID-19 treatment by some researchers, but these drugs were not effective enough against this virus. This study based on in silico approaches was aimed to increase the anti-COVID-19 activities of these drugs by using caulerpin and its derivatives as an adjunct drug against SARS-CoV-2 receptor proteins: the SARS-CoV-2 main protease and the SARS-CoV-2 spike protein. Caulerpin exhibited antiviral activities against chikungunya virus and herpes simplex virus type 1. Caulerpin and some of its derivatives showed inhibitory activity against Alzheimer’s disease. The web server ANCHOR revealed higher protein stability for the two receptors with disordered score (< 0.6). Molecular docking analysis showed that the binding energies of most of the caulerpin derivatives were higher than all the suggested drugs for the two receptors. Also, we deduced that inserting NH 2 , halogen, and vinyl groups can increase the binding affinity of caulerpin toward 6VYB and 6LU7, while inserting an alkyl group decreases the binding affinity of caulerpin toward 6VYB and 6LU7. So, we can modify the inhibitory effect of caulerpin against 6VYB and 6LU7 by inserting NH 2 , halogen, and vinyl groups. Based on the protein disordered results, the SARS-CoV-2 main protease and SARS-CoV-2 spike protein domain are highly stable proteins, so it is quite difficult to unstabilize their integrity by using individual drugs. Also, molecular dynamics (MD) simulation indicates that binding of the combination therapy of simeprevir and the candidate studied compounds to the receptors was stable and had no major effect on the flexibility of the protein throughout the simulations and provided a suitable basis for our study. So, this study suggested that caulerpin and its derivatives could be used as a combination therapy along with lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir for disrupting the stability of SARS-CoV2 receptor proteins to increase the antiviral activity of these drugs.

show abstract

Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices

Abstract: First-principles calculations on nanoscale-sized noble metal nanoparticles demonstrate that planes, edges and vertices show different noncovalent adsorption propensities depending on the adsorbate functional group.

Cited by 26 publications

References 91 publications

Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation

Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation

Halo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties

Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination therapy

Contact Info

Product

Resources

About