2D-FFCASP—A New Approach for 2D Structure Prediction Applied to Self-Assemblies of DNA Bases

Gözde İniş Demir, Samet Demir, Adem Tekin*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

Biomolecular self-assembly on surfaces is an emerging and exciting field for the fabrication of 2D nanostructures that are being used in a wide range of applications. Self-assembly of the nucleic acid bases, which are mostly stabilized by hydrogen bonding, in both solution and solid have been well characterized by various experimental techniques such as nuclear magnetic resonance (NMR) and scanning tunneling microscopy (STM). Especially for the surface based self assemblies, the resolution of STM images is quite insufficient to reveal the dominating intermolecular interactions which lead to the formation of self-assembled DNA bases. Moreover, it is also possible to form crystalline order self assemblies by finding suitable experimental conditions. This fact allows the application of crystal structure prediction (CSP) tools for the discovery of ordered self assemblies. In this regard, the existing CSP method called FFCASP has been extended with a new implementation allowing the prediction of 1D or 2D periodic and nonperiodic structures. The new approach, 2D-FFCASP, has been applied to four DNA bases and the best resulting structures have been further evaluated by dispersion-corrected density functional theory (DFT-D) and cluster in a molecule local correlation approach at the second-order Møller–Plesset perturbation (CIM-RI-MP2). 2D-FFCASP successfully reproduced the known self-assemblies of DNA bases in addition to many newly found isoenergetic structures.

Original languageEnglish
Article number2200308
JournalAdvanced Theory and Simulations
Volume5
Issue number10
DOIs
Publication statusPublished - Oct 2022

Bibliographical note

Publisher Copyright:
© 2022 Wiley-VCH GmbH.

Funding

The authors acknowledge that the results of this research have been achieved using the DECI resource (Cartesius and Snellius) based in The Netherlands at SURFsara with support from the PRACE aisbl. Computing resources were also provided by the National Center for High Performance Computing of Turkey (UHeM), under the Grant Number 1002132012, and Informatics Institute of Istanbul Technical University. This work was financially supported by Research Fund of the Istanbul Technical University. Project Number: TDK‐2019‐42142 and TDK‐2020‐42437. The authors acknowledge that the results of this research have been achieved using the DECI resource (Cartesius and Snellius) based in The Netherlands at SURFsara with support from the PRACE aisbl. Computing resources were also provided by the National Center for High Performance Computing of Turkey (UHeM), under the Grant Number 1002132012, and Informatics Institute of Istanbul Technical University. This work was financially supported by Research Fund of the Istanbul Technical University. Project Number: TDK-2019-42142 and TDK-2020-42437.

FundersFunder number
National Center for High Performance Computing of Turkey
Ulusal Yüksek Başarımlı Hesaplama Merkezi, Istanbul Teknik Üniversitesi1002132012
Partnership for Advanced Computing in Europe AISBL
Istanbul Teknik ÜniversitesiTDK-2019-42142, TDK-2020-42437

    Keywords

    • 2D-nanostructures
    • crystal structure prediction
    • DNA bases
    • FFCASP
    • self-assembly

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