Structural Dynamics of Carbon Dots in Water and N,N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F18%3A73591461" target="_blank" >RIV/61989592:15310/18:73591461 - isvavai.cz</a>

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.7b01149" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.7b01149</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.7b01149" target="_blank" >10.1021/acs.jctc.7b01149</a>

Result language

angličtina

Original language name

Structural Dynamics of Carbon Dots in Water and N,N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations

Original language description

Carbon dots (CDs), one of the youngest members of the carbon nanostructure family, are now widely experimentally studied for their tunable fluorescence properties, bleaching resistance, and biocompatibility. Their interaction with biomolecular systems has also been explored experimentally. However, many atomistic details still remain unresolved. Molecular dynamics (MD) simulations enabling atomistic and femtosecond resolutions simultaneously are a well-established tool of computational chemistry which can provide useful insights into investigated systems. Here we present a full procedure for performing MD simulations of CDs. We developed a builder for generating CDs of a desired size and with various oxygen-containing surface functional groups. Further, we analyzed the behavior of various CDs differing in size, surface functional groups, and degrees of functionalization by MD simulations. These simulations showed that surface functionalized CDs are stable in a water environment through the formation of an extensive hydrogen bonding network. We also analyzed the internal dynamics of individual layers of CDs and evaluated the role of surface functional groups on CD stability. We observed that carboxyl groups interconnected the neighboring layers and decreased the rate of internal rotations. Further, we monitored changes in the CD shape caused by an excess of charged carboxyl groups or carbonyl groups. In addition to simulations in water, we analyzed the behavior of CDs in the organic solvent DMF, which decreased the stability of pure CDs but increased the level of interlayer hydrogen bonding. We believe that the developed protocol, builder, and parameters will facilitate future studies addressing various aspects of structural features of CDs and nanocomposites containing CDs.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10403 - Physical chemistry

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2018

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Volume of the periodical

14

Issue of the periodical within the volume

4

Country of publishing house

US - UNITED STATES

Number of pages

8

Pages from-to

2076-2083

UT code for WoS article

000430023200023

EID of the result in the Scopus database

2-s2.0-85045193301