Skip to main content
Top
Published in: Adsorption 1/2018

27-11-2017

Interaction of photosynthetic pigments with single-walled carbon nanotube (15, 15): a molecular dynamics study

Authors: Majid Ghasemi-Kooch, Maryam Dehestani

Published in: Adsorption | Issue 1/2018

Log in

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

In this study, adsorption of photosynthetic pigments on the inner and outer surfaces of single-walled carbon nanotube (15, 15) has been investigated using molecular dynamics simulation. The binding free energy is calculated by using the linear interaction energy algorithm, that its value indicates the adsorption of all pigments is desirable in both positions. Also, despite the high similarity between each category of these pigments, their interaction with the nanotube is different, that this result can be useful to separate these pigments from one another. According to Lennard–Jones potential energy between the pigments and carbon nanotube, the interaction on the inner surface is stronger than that on the outer surface for all pigments. The chlorophylls phytol tail interacts more strongly with the nanotube compared with the porphyrin ring of chlorophylls. The ability of carotenoids to institute π–π stacking is attributed to conjugated system. Furthermore, xanthophylls due to hydrogen bonded to oxygen atom form semi-hydrogen bonds with carbon nanotube.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Literature
go back to reference Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., Lindahl, E.: GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25 (2015)CrossRef Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., Lindahl, E.: GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25 (2015)CrossRef
go back to reference Åqvist, J., Medina, C., Samuelsson, J.-E.: A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7(3), 385–391 (1994)CrossRef Åqvist, J., Medina, C., Samuelsson, J.-E.: A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7(3), 385–391 (1994)CrossRef
go back to reference Az’hari, S., Ghayeb, Y.: Effect of chirality, length and diameter of carbon nanotubes on the adsorption of 20 amino acids: a molecular dynamics simulation study. Mol. Simul. 40(5), 392–398 (2014)CrossRef Az’hari, S., Ghayeb, Y.: Effect of chirality, length and diameter of carbon nanotubes on the adsorption of 20 amino acids: a molecular dynamics simulation study. Mol. Simul. 40(5), 392–398 (2014)CrossRef
go back to reference Breneman, C.M., Wiberg, K.B.: Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 11(3), 361–373 (1990)CrossRef Breneman, C.M., Wiberg, K.B.: Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 11(3), 361–373 (1990)CrossRef
go back to reference Bussi, G., Donadio, D., Parrinello, M.: Canonical sampling through velocity rescaling. J. Chem. Phys. 126(1), 014101 (2007)CrossRef Bussi, G., Donadio, D., Parrinello, M.: Canonical sampling through velocity rescaling. J. Chem. Phys. 126(1), 014101 (2007)CrossRef
go back to reference Chai, J.D., Head-Gordon, M.: Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys. Chem. Chem. Phys. 10(44), 6615–6620 (2008)CrossRef Chai, J.D., Head-Gordon, M.: Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys. Chem. Chem. Phys. 10(44), 6615–6620 (2008)CrossRef
go back to reference Che, J., Cagin, T., Goddard, W.A. III: Thermal conductivity of carbon nanotubes. Nanotechnology. 11(2), 65 (2000)CrossRef Che, J., Cagin, T., Goddard, W.A. III: Thermal conductivity of carbon nanotubes. Nanotechnology. 11(2), 65 (2000)CrossRef
go back to reference da Silva, A.W.S., Vranken, W.F.: ACPYPE-Antechamber python parser interface. BMC Res. Notes 5(1), 1 (2012) da Silva, A.W.S., Vranken, W.F.: ACPYPE-Antechamber python parser interface. BMC Res. Notes 5(1), 1 (2012)
go back to reference DeLano, W.L.: The PyMOL molecular graphics system. (2002) DeLano, W.L.: The PyMOL molecular graphics system. (2002)
go back to reference Ditchfield, R., Hehre, W.J., Pople J.A.: Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules J. Chem. Phys. 54, 724–728 (1971)CrossRef Ditchfield, R., Hehre, W.J., Pople J.A.: Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules J. Chem. Phys. 54, 724–728 (1971)CrossRef
go back to reference Donhowe, E.G., Kong, F.: Beta-carotene: digestion, microencapsulation, and in vitro bioavailability. Food Bioprocess. Technol. 7(2), 338–354 (2014)CrossRef Donhowe, E.G., Kong, F.: Beta-carotene: digestion, microencapsulation, and in vitro bioavailability. Food Bioprocess. Technol. 7(2), 338–354 (2014)CrossRef
go back to reference Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T.: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24(16), 1999–2012 (2003)CrossRef Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T.: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24(16), 1999–2012 (2003)CrossRef
go back to reference Fischer, J.E., Johnson, A.T.: Electronic properties of carbon nanotubes. Curr. Opin. Solid State Mater. Sci. 4(1), 28–33 (1999)CrossRef Fischer, J.E., Johnson, A.T.: Electronic properties of carbon nanotubes. Curr. Opin. Solid State Mater. Sci. 4(1), 28–33 (1999)CrossRef
go back to reference Frisch, M., Trucks, G., Schlegel, H., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.: Gaussian 09, revision D. 01. Gaussian Inc., Wallingford (2009) Frisch, M., Trucks, G., Schlegel, H., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.: Gaussian 09, revision D. 01. Gaussian Inc., Wallingford (2009)
go back to reference Garcia, G., Ciofini, I., Fernandez-Gomez, M., Adamo, C.: Confinement effects on UV–visible absorption spectra: β-carotene inside carbon nanotube as a test case. J Phys. Chem. Lett. 4(8), 1239–1243 (2013)CrossRef Garcia, G., Ciofini, I., Fernandez-Gomez, M., Adamo, C.: Confinement effects on UV–visible absorption spectra: β-carotene inside carbon nanotube as a test case. J Phys. Chem. Lett. 4(8), 1239–1243 (2013)CrossRef
go back to reference Ghasemi-Kooch, M., Dehestani, M., Housaindokht, M.R., Bozorgmehr, M.R.: Oleuropein interactions with inner and outer surface of different types of carbon nanotubes: Insights from molecular dynamic simulation. J. Mol. Liq. 241, 367–373 (2017)CrossRef Ghasemi-Kooch, M., Dehestani, M., Housaindokht, M.R., Bozorgmehr, M.R.: Oleuropein interactions with inner and outer surface of different types of carbon nanotubes: Insights from molecular dynamic simulation. J. Mol. Liq. 241, 367–373 (2017)CrossRef
go back to reference Gupta, V.K., Kumar, R., Nayak, A., Saleh, T.A., Barakat, M.: Adsorptive removal of dyes from aqueous solution onto carbon nanotubes: a review. Adv. Coll. Interface. Sci. 193, 24–34 (2013)CrossRef Gupta, V.K., Kumar, R., Nayak, A., Saleh, T.A., Barakat, M.: Adsorptive removal of dyes from aqueous solution onto carbon nanotubes: a review. Adv. Coll. Interface. Sci. 193, 24–34 (2013)CrossRef
go back to reference Jakubus, A., Paszkiewicz, M., Stepnowski, P.: Carbon nanotubes application in the extraction techniques of pesticides: a review. Crit. Rev. Anal. Chem. 47(1), 76–91 (2017)CrossRef Jakubus, A., Paszkiewicz, M., Stepnowski, P.: Carbon nanotubes application in the extraction techniques of pesticides: a review. Crit. Rev. Anal. Chem. 47(1), 76–91 (2017)CrossRef
go back to reference Jung, C., Son, A., Her, N., Zoh, K.-D., Cho, J., Yoon, Y.: Removal of endocrine disrupting compounds, pharmaceuticals, and personal care products in water using carbon nanotubes: a review. J. Ind. Eng. Chem. 27, 1–11 (2015)CrossRef Jung, C., Son, A., Her, N., Zoh, K.-D., Cho, J., Yoon, Y.: Removal of endocrine disrupting compounds, pharmaceuticals, and personal care products in water using carbon nanotubes: a review. J. Ind. Eng. Chem. 27, 1–11 (2015)CrossRef
go back to reference Karki, K., Roccatano, D.: Molecular dynamics simulation study of chlorophyll a in different organic solvents. J. Chem. Theor. Comput. 7(4), 1131–1140 (2011)CrossRef Karki, K., Roccatano, D.: Molecular dynamics simulation study of chlorophyll a in different organic solvents. J. Chem. Theor. Comput. 7(4), 1131–1140 (2011)CrossRef
go back to reference Kataura, H., Kumazawa, Y., Maniwa, Y., Umezu, I., Suzuki, S., Ohtsuka, Y., Achiba, Y.: Optical properties of single-wall carbon nanotubes. Synth. Metals 103(1–3), 2555–2558 (1999)CrossRef Kataura, H., Kumazawa, Y., Maniwa, Y., Umezu, I., Suzuki, S., Ohtsuka, Y., Achiba, Y.: Optical properties of single-wall carbon nanotubes. Synth. Metals 103(1–3), 2555–2558 (1999)CrossRef
go back to reference Kostarelos, K., Lacerda, L., Pastorin, G., Wu, W., Wieckowski, S., Luangsivilay, J., Godefroy, S., Pantarotto, D., Briand, J.-P., Muller, S.: Cellular uptake of functionalized carbon nanotubes is independent of functional group and cell type. Nat. Nanotechnol. 2(2), 108–113 (2007)CrossRef Kostarelos, K., Lacerda, L., Pastorin, G., Wu, W., Wieckowski, S., Luangsivilay, J., Godefroy, S., Pantarotto, D., Briand, J.-P., Muller, S.: Cellular uptake of functionalized carbon nanotubes is independent of functional group and cell type. Nat. Nanotechnol. 2(2), 108–113 (2007)CrossRef
go back to reference Krawczyk, T., Marian, K., Pawlyta, M.: Linear polymer separation using carbon-nanotube-modified centrifugal filter units. J. Sep. Sci. 39(4), 725–731 (2016)CrossRef Krawczyk, T., Marian, K., Pawlyta, M.: Linear polymer separation using carbon-nanotube-modified centrifugal filter units. J. Sep. Sci. 39(4), 725–731 (2016)CrossRef
go back to reference Levitt, M., Perutz, M.F.: Aromatic rings act as hydrogen bond acceptors. J. Mol. Biol. 201(4), 751–754 (1988)CrossRef Levitt, M., Perutz, M.F.: Aromatic rings act as hydrogen bond acceptors. J. Mol. Biol. 201(4), 751–754 (1988)CrossRef
go back to reference Matorin, D., Karateyeva, A., Osipov, V., Lukashev, E., Seifullina, N.K., Rubin, A.: Influence of carbon nanotubes on chlorophyll fluorescence parameters of green algae Chlamydomonas reinhardtii. Nanotechnol. Russ. 5(5–6), 320–327 (2010)CrossRef Matorin, D., Karateyeva, A., Osipov, V., Lukashev, E., Seifullina, N.K., Rubin, A.: Influence of carbon nanotubes on chlorophyll fluorescence parameters of green algae Chlamydomonas reinhardtii. Nanotechnol. Russ. 5(5–6), 320–327 (2010)CrossRef
go back to reference Shioi, Y., Brotosudarmo, T.H.P., Limantara, L.: Separation of photosynthetic pigments by high-performance liquid chromatography: comparison of column performance, mobile phase, and temperature. Proced. Chem. 14, 202–210 (2015)CrossRef Shioi, Y., Brotosudarmo, T.H.P., Limantara, L.: Separation of photosynthetic pigments by high-performance liquid chromatography: comparison of column performance, mobile phase, and temperature. Proced. Chem. 14, 202–210 (2015)CrossRef
go back to reference Srivatsan, A., Pera, P., Joshi, P., Wang, Y., Missert, J.R., Tracy, E.C., Tabaczynski, W.A., Yao, R., Sajjad, M., Baumann, H.: Effect of chirality on cellular uptake, imaging and photodynamic therapy of photosensitizers derived from chlorophyll-a. Bioorg. Med. Chem. 23(13), 3603–3617 (2015)CrossRef Srivatsan, A., Pera, P., Joshi, P., Wang, Y., Missert, J.R., Tracy, E.C., Tabaczynski, W.A., Yao, R., Sajjad, M., Baumann, H.: Effect of chirality on cellular uptake, imaging and photodynamic therapy of photosensitizers derived from chlorophyll-a. Bioorg. Med. Chem. 23(13), 3603–3617 (2015)CrossRef
go back to reference Wang, W., Wang, J., Kollman, P.A.: What determines the van der waals coefficient β in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins 34(3), 395–402 (1999)CrossRef Wang, W., Wang, J., Kollman, P.A.: What determines the van der waals coefficient β in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins 34(3), 395–402 (1999)CrossRef
go back to reference Wesołowski, R.P., Furmaniak, S., Terzyk, A.P., Gauden, P.A.: Simulating the effect of carbon nanotube curvature on adsorption of polycyclic aromatic hydrocarbons. Adsorption. 17(1), 1–4 (2011)CrossRef Wesołowski, R.P., Furmaniak, S., Terzyk, A.P., Gauden, P.A.: Simulating the effect of carbon nanotube curvature on adsorption of polycyclic aromatic hydrocarbons. Adsorption. 17(1), 1–4 (2011)CrossRef
go back to reference Wong, B.S., Yoong, S.L., Jagusiak, A., Panczyk, T., Ho, H.K., Ang, W.H., Pastorin, G.: Carbon nanotubes for delivery of small molecule drugs. Adv. Drug Del. Rev. 65(15), 1964–2015 (2013)CrossRef Wong, B.S., Yoong, S.L., Jagusiak, A., Panczyk, T., Ho, H.K., Ang, W.H., Pastorin, G.: Carbon nanotubes for delivery of small molecule drugs. Adv. Drug Del. Rev. 65(15), 1964–2015 (2013)CrossRef
go back to reference Xie, J., Xue, Q., Zheng, Q., Chen, H.: Investigation of the interactions between molecules of β-carotene, vitamin A and CNTs by MD simulations. Mater. Lett. 63(2), 319–321 (2009)CrossRef Xie, J., Xue, Q., Zheng, Q., Chen, H.: Investigation of the interactions between molecules of β-carotene, vitamin A and CNTs by MD simulations. Mater. Lett. 63(2), 319–321 (2009)CrossRef
go back to reference Xu, Z., Yang, X., Yang, Z.: A molecular simulation probing of structure and interaction for supramolecular sodium dodecyl sulfate/single-wall carbon nanotube assemblies. Nano Lett. 10(3), 985–991 (2010)CrossRef Xu, Z., Yang, X., Yang, Z.: A molecular simulation probing of structure and interaction for supramolecular sodium dodecyl sulfate/single-wall carbon nanotube assemblies. Nano Lett. 10(3), 985–991 (2010)CrossRef
go back to reference Yakobson, B.I., Avouris, P.: Mechanical properties of carbon nanotubes. In: Dresselhaus M.S., Dresselhaus G., Avouris P. (eds) Carbon Nanotubes, pp. 287–327. Springer, New York (2001)CrossRef Yakobson, B.I., Avouris, P.: Mechanical properties of carbon nanotubes. In: Dresselhaus M.S., Dresselhaus G., Avouris P. (eds) Carbon Nanotubes, pp. 287–327. Springer, New York (2001)CrossRef
go back to reference Zhang, L., Silva, D.A., Yan, Y., Huang, X.: Force field development for cofactors in the photosystem II. J. Comput. Chem. 33(25), 1969–1980 (2012)CrossRef Zhang, L., Silva, D.A., Yan, Y., Huang, X.: Force field development for cofactors in the photosystem II. J. Comput. Chem. 33(25), 1969–1980 (2012)CrossRef
go back to reference Zheng, M., Jagota, A., Semke, E.D., Diner, B.A., McLean, R.S., Lustig, S.R., Richardson, R.E., Tassi, N.G.: DNA-assisted dispersion and separation of carbon nanotubes. Nat. Mater. 2(5), 338–342 (2003)CrossRef Zheng, M., Jagota, A., Semke, E.D., Diner, B.A., McLean, R.S., Lustig, S.R., Richardson, R.E., Tassi, N.G.: DNA-assisted dispersion and separation of carbon nanotubes. Nat. Mater. 2(5), 338–342 (2003)CrossRef
Metadata
Title
Interaction of photosynthetic pigments with single-walled carbon nanotube (15, 15): a molecular dynamics study
Authors
Majid Ghasemi-Kooch
Maryam Dehestani
Publication date
27-11-2017
Publisher
Springer US
Published in
Adsorption / Issue 1/2018
Print ISSN: 0929-5607
Electronic ISSN: 1572-8757
DOI
https://doi.org/10.1007/s10450-017-9920-3

Other articles of this Issue 1/2018

Adsorption 1/2018 Go to the issue

Premium Partners