Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating
Abstract
:1. Introduction
2. Simulation Models and Methods
2.1. Models
- ZnS (110) Slabs
- ZnS Nanoparticles
- Biomolecules
- Coating
2.2. Force Fields
2.3. Methods
2.3.1. Free Energy Calculations
2.3.2. Simulation Protocols
3. Results and Discussion
3.1. Binding Preferences of Biomolecules to Pristine ZnS Nanosurfaces
3.2. Potential of Mean Force and Binding Configurations of Biomolecules at Pristine ZnS (110) Surface and Nanoparticle
3.3. Binding Preferences of Biomolecules to PMMA-Coated ZnS (110) Slab and ZnS Nanoparticle
3.4. Influence of Solvation Shell on Binding Preferences of Biomolecules to ZnS (110) Slab and ZnS Nanoparticle
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
CV | Collective variable |
MD | Molecular dynamics |
MetaD | Metadynamics |
PMMA | poly-methylmethacrylate |
PMF | Potential of mean force |
RDF | Radial distribution function |
QD | Quantum dot |
SSD | Surface separation distance |
References
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Bond potential | kb (kJ/mol) | r0 (Å) | |
Zn–S | 92,000 | 1.6 | |
Angular potential | (kJ/mol) | () | |
S–Zn–S | 274.022 | 109.47 | |
Zn–S–Zn | 274.022 | 109.47 | |
Non-bonded | Charge (e) | σ (Å) | ε (kJ/mol) |
Zn | 2.0 | 3.816 | 0.022 |
S | −2.0 | 4.27 | 1.087 |
Special LJ parameters | |||
Zn *-O | 1.75 | 86.00 | |
S *-O | 5.80 | 0.01 |
Adsorbate | Code | NS-Pristine | NS-Coated | NP-Pristine | NP-Coated |
---|---|---|---|---|---|
SCA of alanine | ALA | 0.2 | −2.1 ± 0.6 | 0.7 | – |
SCA of arginine | ARG | 0.1 ± 0.1 | −0.3 ± 0.2 | 0.8 | – |
SCA of aspargine | ASN | 0.0 ± 0.1 | −0.2 ± 0.4 | 0.7 | – |
SCA of aspartic acid | ASP | −2.9 ± 0.2 | 0.3 ± 0.2 | −30.3 ± 2.3 | −0.4 ± 0.4 |
SCA of cysteine ion | CYM | −3.7 ± 0.7 | 0.4 ± 0.1 | −31.1 ± 7.4 | 0.2 |
SCA of cysteine | CYS | 0.0 | −3.2 ± 0.6 | 0.6 | – |
SCA of glutamine | GLN | 0.1 | −1.0 ± 0.4 | 0.7 ± 0.1 | – |
SCA of glutamic acid | GLU | −2.5 ± 0.1 | −0.5 ± 0.2 | −39.1 ± 4.8 | −1.0 ± 4.6 |
SCA of histidine | HID | 0.0 ± 0.1 | −2.8 ± 0.3 | 0.6 | – |
SCA of histidine | HIE | 0.0 ± 0.1 | −3.0 ± 0.5 | 0.5 | – |
SCA of histidine | HIP | 0.1 ± 0.1 | 0.2 ± 0.1 | 0.8 | – |
SCA of isoleucine | ILE | 0.0 | −7.4 ± 0.9 | 0.7 | – |
SCA of leucine | LEU | 0.2 | −7.7 ± 0.1 | 0.6 | – |
SCA of lysine | LYS | 0.3 | 0.4 ± 0.1 | 0.8 | – |
SCA of methionine | MET | 0.1 | −5.9 ± 0.7 | 0.6 | – |
SCA of phenylalanine | PHE | 0.2 | −6.6 ± 0.7 | 0.6 | – |
SCA of serine | SER | 0.3 | −0.4 ± 0.5 | 0.7 | – |
SCA of threonine | THR | 0.2 | −1.3 ± 0.4 | 0.7 | – |
SCA of tryptophan | TRP | 0.0 | −6.6 ± 0.8 | 0.5 ± 0.1 | – |
SCA of tyrosine | TYR | 0.3 ± 0.1 | −8.7 ± 1.1 | 0.6 | – |
SCA of valine | VAL | 0.0 | −4.7 ± 0.8 | 0.6 | – |
SCA glutamic acid (neutral) | GAN | 0.0 ± 0.1 | −1.9 ± 0.4 | 0.5 | – |
SCA of glycine (amino acid) | GLY | −0.8 ± 0.1 | −0.3 ± 0.1 | 0.2 | – |
proline (amino acid) | PRO | 0.1 ± 0.1 | −2.5 ± 0.4 | 0.3 ± 0.1 | – |
choline group of lipid | CHL | 0.0 ± 0.1 | 0.4 ± 0.1 | 0.9 | – |
phosphate group of lipid | PHO | −1.1 ± 0.2 | 0.0 ± 0.2 | −1.5 ± 0.2 | −0.4 |
etanolamine group of lipid | ETA | 0.2 ± 0.3 | 0.4 ± 0.1 | 1.3 ± 0.2 | – |
ester group of lipid | EST | 0.0 | −2.6 ± 0.4 | 0.5 ± 0.1 | – |
D-glucose | DGL | −1.7 ± 0.2 | −2.0 ± 0.5 | 0.2 ± 0.1 | – |
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Rahmani, R.; Lyubartsev, A.P. Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating. Nanomaterials 2023, 13, 2239. https://doi.org/10.3390/nano13152239
Rahmani R, Lyubartsev AP. Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating. Nanomaterials. 2023; 13(15):2239. https://doi.org/10.3390/nano13152239
Chicago/Turabian StyleRahmani, Roja, and Alexander P. Lyubartsev. 2023. "Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating" Nanomaterials 13, no. 15: 2239. https://doi.org/10.3390/nano13152239