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Dynamic behavior and selective adsorption of a methanol/water mixture inside a cyclic peptide nanotube

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Abstract

Present molecular dynamics simulations indicate that the methanol component in a methanol/water mixture is more likely to be trapped in a cyclic peptide nanotube (CPNT), while water molecules tend to be present at the channel mouths as transient guests. Channel water resides mainly between methanol and the CPNT wall, resulting in a distinct decrease in the H-bond number per channel methanol. Six designed CPNTs with different channel diameters and outer surface characteristics all possess distinct selectivity to methanol over water. Of these, the amphipathic 8 × (AQ)4-CPNT exhibits the best performance. Results in this study provide basic information for the application of a CPNT to enrich methanol from a methanol/water mixture.

Typical overview of water and methanol molecular distribution in cyclic peptide nanotubes

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References

  1. Remy T, Cousin Saint Remi J, Singh R, Webley PA, Baron GV, Denayer JFM (2011) Adsorption and separation of C1−C8 alcohols on SAPO-34. J Phys Chem C 115:8117–8125

    Article  CAS  Google Scholar 

  2. Kaewkannetra P, Chutinate N, Moonamart S, Kamsan T, Chiu TY (2011) Separation of ethanol from ethanol–water mixture and fermented sweet sorghum juice using pervaporation membrane reactor. Desalination 271:88–91

    Article  CAS  Google Scholar 

  3. Sunitha K, Satyanarayana SV, Sridhar S (2012) Phosphorylated chitosan membranes for the separation of ethanol–water mixtures by pervaporation. Carbohydr Polym 87:1569–1574

    Article  CAS  Google Scholar 

  4. Qureshi N, Hughes S, Maddox IS, Cotta MA (2005) Energy-efficient recovery of butanol from model solutions and fermentation broth by adsorption. Bioprocess Biosyst Eng 27:215–222

    Article  CAS  PubMed  Google Scholar 

  5. Nimcevic D, Gapes JR (2000) The acetone-butanol fermentation in pilot plant and pre-industrial scale. J Mol Microbiol Biotechnol 2:15–20

    CAS  PubMed  Google Scholar 

  6. Zang J, Konduri S, Nair S, Sholl DS (2009) Self-diffusion of water and simple alcohols in single-walled aluminosilicate nanotubes. ACS Nano 3:1548–1556

    Article  CAS  PubMed  Google Scholar 

  7. Farhadian N (2011) Transport of a liquid water-methanol mixture in a single wall carbon nanotube. Int J Nanosci Nanotechnol 7:173–182

    Google Scholar 

  8. Zheng J, Lennon EM, Tsao HK, Sheng YJ, Jiang S (2005) Transport of a liquid water and methanol mixture through carbon nanotubes under a chemical potential gradient. J Chem Phys 122:214702

    Article  CAS  PubMed  Google Scholar 

  9. Liu Y, Consta S, Goddard WA (2010) Nanoimmiscibility: selective sbsorption of liquid methanol-water mixtures in carbon nanotubes. J Nanosci Nanotechnol 10:3834–3843

    Article  CAS  PubMed  Google Scholar 

  10. Zhao WH, Shang B, Du SP, Yuan LF, Yang J, Zeng XC (2012) Highly selective adsorption of methanol in carbon nanotubes immersed in methanol-water solution. J Chem Phys 137:034501

    Article  CAS  PubMed  Google Scholar 

  11. Winarto W, Takaiwa D, Yamamoto E, Yasuoka K (2015) Water–methanol separation with carbon nanotubes and electric fields. Nanoscale 7:12659–12665

    Article  CAS  PubMed  Google Scholar 

  12. Winarto, Takaiwa D, Yamamoto E, Yasuoka K (2016) Structures of water molecules in carbon nanotubes induced with electric fields and its application for water-methanol separation. Appl Mech Mater 842:453–456

    Article  Google Scholar 

  13. Wang H, Shi J, Liu G, Zhang Y, Zhang J, Li S (2017) Investigation of transport properties of water−methanol solution through a CNT with oscillating electric field. J Phys Chem B 121:1041–1053

    Article  CAS  PubMed  Google Scholar 

  14. Ghadiri MR, Granja JR, Milligan RA, Mcree DE (1993) Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature 266:324–327

    Article  Google Scholar 

  15. Khazanovich N, Granja JR, Mcree DE, Milligan RA, Ghadiri MR (1994) Nanoscale tubular ensembles with specified internal diameters. Design of a self-assembled nanotube with a 13-.ANG. Pore. J Am Chem Soc 116:6011–6012

    Article  CAS  Google Scholar 

  16. Granja JR, Ghadiri MR (1994) Channel-mediated transport of glucose across lipid bilayers. J Am Chem Soc 116:10785–10786

    Article  CAS  Google Scholar 

  17. Okamoto H, Nakanishi T, Nagai Y, Maki Kasahara A, Kyozaburo T (2003) Variety of the molecular conformation in peptide nanorings and nanotubes. J Am Chem Soc 125:2756–2769

    Article  CAS  PubMed  Google Scholar 

  18. Ghadiri MR, Granja JR, Buehler LK (1994) Artificial transmembrane ion channels from self-assembling peptide nanotubes. Nature 369:301–304

    Article  CAS  PubMed  Google Scholar 

  19. Xu J, Fan JF, Zhang MM, Weng PP, Lin HF (2016) Transport properties of simple organic molecules in a transmembrane cyclic peptide nanotube. J Mol Model 22:107

    Article  CAS  PubMed  Google Scholar 

  20. Li R, Fan J, Li H, Yan X, Yu Y (2015) Dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes. J Chem Phys 143:015101

    Article  CAS  PubMed  Google Scholar 

  21. Liu J, Fan J, Tang M, Cen M, Yan J (2010) Water diffusion behaviors and transportation properties in transmembrane cyclic hexa-, octa- and decapeptide nanotubes. J Phys Chem B 114:12183–12192

    Article  CAS  PubMed  Google Scholar 

  22. Yan X, Fan J, Yu Y, Xu J, Zhang M (2015) Transport behavior of a single Ca2+, K+, and Na+ in a water-filled transmembrane cyclic peptide nanotube. J Chem Inf Model 55:998–1011

    Article  CAS  PubMed  Google Scholar 

  23. Li R, Fan J, Li H, Yan X, Yu Y (2013) Exploring the dynamic behaviors and transport properties of gas molecules in a transmembrane cyclic peptide nanotube. J Phys Chem B 117:14916–14927

    Article  CAS  PubMed  Google Scholar 

  24. Liu J, Fan J, Tang M, Zhou W (2010) Molecular dynamics simulation for the structure of the water chain in a transmembrane peptide nanotube. J Phys Chem A 114:2376–2383

    Article  CAS  PubMed  Google Scholar 

  25. Engels M, Bashford D, Ghadiri MR (1995) Structure and dynamics of self-assembling peptide nanotubes and the channel-mediated water organization and self-diffusion. A molecular dynamics study. J Am Chem Soc 117:9151–9158

    Article  CAS  Google Scholar 

  26. Vijayaraj R, Van Damme S, Bultinck P, Subramanian V (2012) Structure and stability of cyclic peptide based nanotubes: a molecular dynamics study of the influence of amino acid composition. Phys Chem Chem Phys 14:15135–15144

    Article  CAS  PubMed  Google Scholar 

  27. Vijayaraj R, Sundar RS, Mahesh KR, Subramanian V (2010) Studies on the structure and stability of cyclic peptide based nanotubes using oligomeric approach: a computational chemistry investigation. J Phys Chem B 114:16574–16583

    Article  CAS  PubMed  Google Scholar 

  28. Granja JR, Ghadiri MR (1996) Self-assembling peptide nanotubes. J Am Chem Soc 118:43–50

    Article  Google Scholar 

  29. Wensink EJW, Hoffmann AC, van Maaren PJ, van der Spoel D (2003) Dynamic properties of water/alcohol mixtures studied by computer simulation. J Chem Phys 119:7308–7317

    Article  CAS  Google Scholar 

  30. González B, Calvar N, Gómez E, Domínguez Á (2007) Density, dynamic viscosity, and derived properties of binary mixtures of methanol or ethanol with water, ethyl acetate, and methyl acetate at T= (293.15, 298.15, and 303.15) K. J Chem Thermodyn 39:1578–1588

    Article  CAS  Google Scholar 

  31. Mikhail SZ, Kimel WR (1961) Densities and viscosities of methanol-water mixtures. J Chem Eng Data 6:533–537

    Article  CAS  Google Scholar 

  32. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217

    Article  CAS  Google Scholar 

  34. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  35. Hwang H, And GCS, Ratner MA (2016) Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube. J Phys Chem B 110:26448–26460

    Article  CAS  Google Scholar 

  36. Comer J, Dehez F, Cai W, Chipot C (2013) Water conduction through a peptide nanotube. J Phys Chem C 117:26797–26803

    Article  CAS  Google Scholar 

  37. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33

    Article  CAS  PubMed  Google Scholar 

  38. Pastor RW, Brooks BR, Szabo A (2006) An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol Phys 65:1409–1419

    Article  Google Scholar 

  39. Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101:4177–4189

    Article  CAS  Google Scholar 

  40. Darden T, York D, Pedersen L (1993) An N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  41. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n -alkanes. J Comput Phys 23:327–341

    Article  CAS  Google Scholar 

  42. Darve E, Pohorille A (2001) Calculating free energies using average force. J Chem Phys 115:9169–9183

    Article  CAS  Google Scholar 

  43. Darve E, Rodriguez-Gomez D, Pohorille A (2008) Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys 128:144120

    Article  CAS  PubMed  Google Scholar 

  44. Mas EM, Bukowski R, Szalewicz K (2003) Ab initio three-body interactions for water. II. Effects on structure and energetics of liquid. J Chem Phys 118:4404–4413

    Article  CAS  Google Scholar 

  45. Kuo IF, Mundy CJ (2004) An ab initio molecular dynamics study of the aqueous liquid-vapor interface. Science 303:658–660

    Article  CAS  PubMed  Google Scholar 

  46. Soper AK, Bruni F, Ricci MA (1997) Site–site pair correlation functions of water from 25 to 400 °C: revised analysis of new and old diffraction data. J Chem Phys 106:247–254

    Article  CAS  Google Scholar 

  47. Haughney M, Ferrario M, Mcdonald IR (1987) Molecular-dynamics simulation of liquid methanol. J Phys Chem 91:4934–4940

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work has been supported by the priority academic program development of Jiangsu higher education institutions and the project of scientific and technologic infrastructure of Suzhou (SZ 201708). It was further supported by the national basic research program of China (973 program, Grant No. 2012CBB25803). The authors are grateful to Dr. Jian Liu and Miss Yi Yu for their insightful suggestions.

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Authors and Affiliations

  1. College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, People’s Republic of China

    Xialan Si, Jianfen Fan, Jian Xu, Xin Zhao, Lingling Zhang & Mengnan Qu

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  1. Xialan Si
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Correspondence to Jianfen Fan.

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Si, X., Fan, J., Xu, J. et al. Dynamic behavior and selective adsorption of a methanol/water mixture inside a cyclic peptide nanotube. J Mol Model 24, 184 (2018). https://doi.org/10.1007/s00894-018-3712-x

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