Abstract
We have designed a novel nanobiosensor for in silico detecting proteins based on leucine/Pd-loaded single-walled carbon nanotube matrix. Density functional theory at the B3LYP/6-31G (d) level of theory was realized to analyze the geometrical and electronic structure of the proposed nanobiosensor. The solvent effects were investigated using the Tomasi’s polarized continuum model. Atoms-in-molecules theory was used to study the nature of interactions by calculating the electron density ρ(r) and Laplacian at the bond critical points. Natural bond orbital analysis was performed to achieve a deep understanding of the nature of the interactions. The biosensor has potential application for high sensitive and rapid response to protein due to the chemical adsorption of l-leucine amino acid onto Pd-loaded single-walled carbon nanotube and reactive functional groups that can incorporate in hydrogen binding, hydrophobic interactions and van der Waals forces with the protein surface in detection process.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bader RF (1998) A bond path: a universal indicator of bonded interactions. J Phys Chem A 102(37):7314–7323
Balasubramanian K, Burghard M (2006) Biosensors based on carbon nanotubes. Anal Bioanal Chem 385(3):452–468
Barone V, Cossi M, Tomasi J (1997) A new definition of cavities for the computation of solvation free energies by the polarizable continuum model. J Chem Phys 107(8):3210–3221
Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648
Cao Q, S-j Han, Tulevski GS, Zhu Y, Lu DD, Haensch W (2013) Arrays of single-walled carbon nanotubes with full surface coverage for high-performance electronics. Nat Nanotechnol 8(3):180–186
Clark LC, Lyons C (1962) Electrode systems for continuous monitoring in cardiovascular surgery. Ann N Y Acad Sci 102(1):29–45
Etminan N, Yoosefian M, Raissi H, Hakimi M (2016) Solvent effects on the stability and the electronic properties of histidine/Pd-doped single-walled carbon nanotube biosensor. J Mol Liq 214:313–318
Frisch M, Trucks G, Schlegel H, Scuseria G, Robb M, Cheeseman J, Scalmani G, Barone V, Mennucci B, Petersson G (2010) Gaussian 09, Rev B 01. Gaussian Inc, Wallingford
Iijima S (1991) Helical microtubules of graphitic carbon. Nature 354(6348):56–58
Jianrong C, Yuqing M, Nongyue H, Xiaohua W, Sijiao L (2004) Nanotechnology and biosensors. Biotechnol Adv 22(7):505–518
Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37(2):785–789
Liu Z, Liang X-J (2012) Nano-carbons as theranostics. Theranostics 2(3):235–237
Liu P, Wei Y, Liu K, Liu L, Jiang K, Fan S (2012) New-type planar field emission display with superaligned carbon nanotube yarn emitter. Nano Lett 12(5):2391–2396
Mammino L, Kabanda MM (2009) A computational study of the effects of different solvents on the characteristics of the intramolecular hydrogen bond in acylphloroglucinols. J Phys Chem A 113:15064–15077
Nambiar S, Yeow JT (2011) Conductive polymer-based sensors for biomedical applications. Biosens Bioelectron 26(5):1825–1832
Parr RG, Lv Szentpaly, Liu S (1999) Electrophilicity index. J Am Chem Soc 121(9):1922–1924
Pearson RG (1988) Absolute electronegativity and hardness: application to inorganic chemistry. Inorg Chem 27(4):734–740
Raissi H, Yoosefian M, Moshfeghi E, Farzad F (2012) Theoretical study on β-aminoacroleine; density functional theory, atoms in molecules theory and natural bond orbitals studies. J Chem Sci 124(3):731–739
Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88(6):899–926
Ye Y, Ju H (2005) Rapid detection of ssDNA and RNA using multi-walled carbon nanotubes modified screen-printed carbon electrode. Biosens Bioelectron 21(5):735–741
Yoosefian M (2017) Powerful greenhouse gas nitrous oxide adsorption onto intrinsic and Pd doped Single walled carbon nanotube. Appl Surf Sci 392:225–230
Yoosefian M, Etminan N (2016a) Density functional theory (DFT) study of a new novel bionanosensor hybrid; tryptophan/Pd doped single walled carbon nanotube. Physica E 81:116–121
Yoosefian M, Etminan N (2016b) The role of solvent polarity in the electronic properties, stability and reactivity trend of a tryptophane/Pd doped SWCNT novel nanobiosensor from polar protic to non-polar solvents. RSC Adv 6(69):64818–64825
Yoosefian M, Mola A (2015) Solvent effects on binding energy, stability order and hydrogen bonding of guanine–cytosine base pair. J Mol Liq 209:526–530
Yoosefian M, Ansarinik Z, Etminan N (2016) Density functional theory computational study on solvent effect, molecular conformations, energies and intramolecular hydrogen bond strength in different possible nano-conformers of acetaminophen. J Mol Liq 213:115–121
Acknowledgements
The authors wish to thank Graduate University of Advanced Technology, Kerman, Iran, for their support.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Informed consent
Informed consent was obtained from all individual participants included in the study.
Ethical approval
All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.
Additional information
Handling Editor: H. S. Sharma.
Rights and permissions
About this article
Cite this article
Yoosefian, M., Etminan, N. Leucine/Pd-loaded (5,5) single-walled carbon nanotube matrix as a novel nanobiosensors for in silico detection of protein. Amino Acids 50, 653–661 (2018). https://doi.org/10.1007/s00726-018-2552-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00726-018-2552-4