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A molecular dynamics study on the diffusion and imprint ability of spectinomycin under different sizes of aniline oligomers

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Abstract

Molecularly imprinted polymers (MIP) are the polymers created by molecular imprinting techniques that leave cavities for the specific interactions with a template molecule and have been applied in molecular selectivity tasks. In this study, the molecular dynamics (MD) simulation technique was used to demonstrate that aniline oligomer could be developed as a potential MIP for detection and separation of the spectinomycin drug molecule for gonorrhea treatment. MD simulations were performed for the systems of a spectinomycin within aniline oligomers of different sizes. The mean square displacement (MSD) and the diffusivity calculated from MD simulations showed that the diffusion coefficient was significantly dropped when the length of aniline oligomer was greater than two. The diffusion coefficient of spectinomycin became the lowest within aniline trimers, corresponded to the highest atomic distribution of MIP around the template. Then, the specific cavity in MIP systems with and without spectinomycin was calculated to assess the stability of the cavity created by the template. The volume of a cavity created within the trimer system was closest to the spectinomycin volume and therefore became the optimal oligomer size for further development of MIP.

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The authors confirm that the data supporting the findings of this study are available within the article and its supplementary material.

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Funding

The authors are grateful for the research funding provided by the Department of Physics and the Center of Excellence in Theoretical and Computational Science (TaCS), KMUTT.

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Authors and Affiliations

  1. Theoretical and Computational Physics Group, Department of Physics, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand

    Chanadan Douykhumklaw & Thana Sutthibutpong

  2. Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok, 10140, Thailand

    Chanadan Douykhumklaw & Thana Sutthibutpong

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  1. Chanadan Douykhumklaw
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  2. Thana Sutthibutpong
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Contributions

Chanadan Douykhumklaw performed all the simulations and the drafts of the manuscript under the supervision of Thana Sutthibutpong.

Corresponding author

Correspondence to Thana Sutthibutpong.

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All authors have participated in (a) conception and design or analysis and interpretation of the data, (b) drafting the article or revising it critically for important intellectual content, and (c) approval of the final version. This manuscript has not been submitted to, nor is under review at, another journal or other publishing venue. The authors have no affiliation with any organization with a direct or indirect financial interest in the subject matter discussed in the manuscript. The authors declare no competing interests.

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Douykhumklaw, C., Sutthibutpong, T. A molecular dynamics study on the diffusion and imprint ability of spectinomycin under different sizes of aniline oligomers. J Mol Model 28, 387 (2022). https://doi.org/10.1007/s00894-022-05371-w

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  • DOI: https://doi.org/10.1007/s00894-022-05371-w

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