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

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...

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Autores principales:	Ghazaleh Hashemkhani Shahnazari, Masoud Darvish Ganji
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8d0c92550add4e48970b569f4279d0d2
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spelling	oai:doaj.org-article:8d0c92550add4e48970b569f4279d0d22021-12-02T14:12:10ZUnderstanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation10.1038/s41598-020-80161-z2045-2322https://doaj.org/article/8d0c92550add4e48970b569f4279d0d22021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80161-zhttps://doaj.org/toc/2045-2322Abstract 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.Ghazaleh Hashemkhani ShahnazariMasoud Darvish GanjiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ghazaleh Hashemkhani Shahnazari Masoud Darvish Ganji Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation
description	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.
format	article
author	Ghazaleh Hashemkhani Shahnazari Masoud Darvish Ganji
author_facet	Ghazaleh Hashemkhani Shahnazari Masoud Darvish Ganji
author_sort	Ghazaleh Hashemkhani Shahnazari
title	Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation
title_short	Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation
title_full	Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation
title_fullStr	Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation
title_full_unstemmed	Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation
title_sort	understanding structural and molecular properties of complexes of nucleobases and au13 golden nanocluster by dft calculations and dft-md simulation
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8d0c92550add4e48970b569f4279d0d2
work_keys_str_mv	AT ghazalehhashemkhanishahnazari understandingstructuralandmolecularpropertiesofcomplexesofnucleobasesandau13goldennanoclusterbydftcalculationsanddftmdsimulation AT masouddarvishganji understandingstructuralandmolecularpropertiesofcomplexesofnucleobasesandau13goldennanoclusterbydftcalculationsanddftmdsimulation
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Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation

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