Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Jan 11;11(1):435.
doi: 10.1038/s41598-020-80161-z.

Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation

Ghazaleh Hashemkhani Shahnazari  1 , Masoud Darvish Ganji  2
Affiliations

Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation

Ghazaleh Hashemkhani Shahnazari et al. Sci Rep. .

Abstract

The characterization of the complexes of biomolecules and nanostructures is highly interesting and benefits the rational development and design of nano-materials and nano-devices in nano-biotechnology. In this work, we have used dispersion corrected density functional theory (DFT-D) as well as DFT based molecular dynamics simulations to provide an atomistic understanding of interaction properties of DNA nucleobases and Au13 nanocluster. Various active sites of interacting molecules considering their relative orientation and distance are explored. Our goal is to stimulate the binding characteristics between two entities and evaluate this through the interaction energy, the charge transfer, the electronic structure, and the specific role of the molecular properties of the nucleobase-Au13 system. The primary outcomes of this comprehensive research illuminated that nucleic bases have potent affinity for binding to the Au cluster being chemisorption type and following the trend: Adenine > Cytosine > Guanine > Thymine. The AIM analysis indicated that the binding nature of the interacting species was predominantly partial covalent and high polar. We discuss the bearing of our findings in view of gene-nanocarrier, biosensing applications as well as nanodevices for sequencing of DNA.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Optimized structures of (a) Au13 cluster, (b) adenine, (c) cytosine, (d) guanine, and (e) thymine bases with DFT-D3/TZVP.
Figure 2
Figure 2
Representation of potential active sites for (a) Au13 cluster and (b) adenine. Optimized structures of (c) adenine/Au13, (d) cytosine/Au13, (e) guanine/Au13, and (f) thymine/Au13 complexes with DFT-D3/TZVP and implicit solvent media.
Figure 3
Figure 3
Calculated total electronics charge for (a) adenine/Au13 and (b) cytosine/Au13 systems with DFT-D3/TZVP (iso-value was set to 0.07). (c) Calculated bonding critical points (BCPs) for adenine/Au13 system with DFT‒D3/TZVP.
Figure 4
Figure 4
Schematic representation of (a) initial configuration and (b) snapshots of configurations during the optimization procedure for cytosine-Au13/25H2O system with DFT‒D3/TZVP.
Figure 5
Figure 5
Representation of (a) initial model of cytosine/Au13/70H2O system considered for DFT-MD simulation. Calculated plots of (b) temperature and (c) total energy obtained during the DFT‒MD simulation procedure for cytosine-Au13/70H2O system. Snapshot of the molecular structure of cytosine-Au13/70H2O at 12 ps representing bond distances between water molecules and (d) NH2 and (e) O groups. Bonding distances between (f) C, (g) N, and (h) O atoms and nearest Au atom during the 8.5 ps of simulation times.
Figure 5
Figure 5
Representation of (a) initial model of cytosine/Au13/70H2O system considered for DFT-MD simulation. Calculated plots of (b) temperature and (c) total energy obtained during the DFT‒MD simulation procedure for cytosine-Au13/70H2O system. Snapshot of the molecular structure of cytosine-Au13/70H2O at 12 ps representing bond distances between water molecules and (d) NH2 and (e) O groups. Bonding distances between (f) C, (g) N, and (h) O atoms and nearest Au atom during the 8.5 ps of simulation times.
See this image and copyright information in PMC

References

    1. Wagner V, Dullaart A, Bock A-K, Zweck A. The emerging nanomedicine landscape. Nat. Biotechnol. 2006;24:1211–1217. doi: 10.1038/nbt1006-1211. - DOI - PubMed
    1. Duncan R, Gaspar R. Nanomedicine (s) under the microscope. Mol. Pharm. 2011;8:2101–2141. doi: 10.1021/mp200394t. - DOI - PubMed
    1. Farokhzad OC, Langer R. Nanomedicine: Developing smarter therapeutic and diagnostic modalities. Adv. Drug Deliv. Rev. 2006;58:1456–1459. doi: 10.1016/j.addr.2006.09.011. - DOI - PubMed
    1. Mout R, Moyano DF, Rana S, Rotello VM. Surface functionalization of nanoparticles for nanomedicine. Chem. Soc. Rev. 2012;41:2539–2544. doi: 10.1039/c2cs15294k. - DOI - PMC - PubMed
    1. Chen F, Hableel G, Zhao ER, Jokerst JV. Multifunctional nanomedicine with silica: Role of silica in nanoparticles for theranostic, imaging, and drug monitoring. J. Colloid Interface Sci. 2018;521:261–279. doi: 10.1016/j.jcis.2018.02.053. - DOI - PMC - PubMed

LinkOut - more resources