Characterisation of the hydrophobic collapse of polystyrene in water using free energy techniques

Molecular Simulation

Volumn 43, Issue 3, 2017, Pages 234-241

  Drenscko, Mihaela ^a,b   Loverde, Sharon M ^a,b  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

hydrophobic collapse; metadynamics; molecular dynamics; Polystyrene; solvent accessible surface area

Indexed keywords

CHAIN LENGTH; FREE ENERGY; HYDROPHOBICITY; POLYSTYRENES; SOLVENTS;

HYDROPHOBIC COLLAPSE; METADYNAMICS; MINIMUM ENERGY CONFIGURATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; POTENTIAL OF MEAN FORCE; RADIUS OF GYRATION; SOLVENT ACCESSIBLE SURFACE AREAS;

MOLECULAR DYNAMICS;

EID: 84996555449     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2016.1253840     Document Type: Article

References (49)

1. Rubinstein M, Colby R., Polymer physics. 1st ed. New York(NY):Oxford University Press; 2003.
2. Breitenbach J. Melt extrusion:from process to drug delivery technology. Eur J Pharm Biopharm. 2002;54:107–117.10.1016/S0939-6411(02)00061-9
3. Madhusoodanan KN, Varghese S., Technological and processing properties of natural rubber layered silicate-nanocomposites by melt intercalation process. J Appl Polym Sci. 2006;102:2537–2543.10.1002/(ISSN)1097-4628
4. Ramakrishna S, Mayer J, Wintermantel E, et al. Biomedical applications of polymer-composite materials:a review. Compos Sci Technol. 2001;61:1189–1224.10.1016/S0266-3538(00)00241-4
5. Bates FS, Hillmyer MA, Lodge TP, et al. Multiblock polymers:panacea or pandora’s box? Science. 2012;336:434–440.10.1126/science.1215368
6. Discher DE, Eisenberg A. Polymer vesicles. Science. 2002;297:967–973.10.1126/science.1074972
7. Geng Y, Dalhaimer P, Cai SS, et al. Shape effects of filaments versus spherical particles in flow and drug delivery. Nat Nanotechnol. 2007;2:249–255.10.1038/nnano.2007.70
8. Mai YY, Xiao L, Eisenberg A., Morphological control in aggregates of amphiphilic cylindrical metal-polymer “brushes”. Macromolecules. 2013;46:3183–3189.
9. Wilson DA, Nolte RJM, Van Hest JCM. Autonomous movement of platinum-loaded stomatocytes. Nat Chem. 2012;4:268–274.10.1038/nchem.1281
10. Fava D, Nie Z, Winnik MA. Evolution of self-assembled structures of polymer-terminated gold nanorods in selective solvents. Adv Mater. 2008;20:4318–4322.10.1002/adma.v20:22
11. Harmandaris VA, Adhikari NP, Van der Vegt NFA, et al. Hierarchical modeling of polystyrene:from atomistic to coarse-grained simulations. Macromolecules. 2006;39:6708–6719.10.1021/ma0606399
12. Varnik F, Baschnagel J, Binder K., Reduction of the glass transition temperature in polymer films:a molecular-dynamics study. Phys Rev E; 2002;65:021507.
13. Yoshimoto K, Jain TS, Workum KV, et al. Mechanical heterogeneities in model polymer glasses at small length scales. Phys Rev Lett. 2004;93:175501.
14. Milano G, Muller-Plathe F. Mapping atomistic simulations to mesoscopic models:a systematic coarse-graining procedure for vinyl polymer chains. J Phys Chem B. 2005;109:18609–18619.10.1021/jp0523571
15. Harimi-Varzaneh HA, Van der Vegt NFA, Mueller Plathe F, et al. How good are coarse-grained polymer models? A comparison for atactic polystyrene. Chem Phys Chem. 2012;13:3428–3439. doi:10.1002/cphc.201200111.
16. Rossi G, Monticelli L, Puisto SR, et al. Coarse-graining polymers with the MARTINI force-field:polystyrene as a benchmark case. Soft Matter. 2011;7:698–708.10.1039/C0SM00481B
17. Periole X, Marrink S., The martini coarse-grained force field. In:Salonen L, editor. Biomolecular simulations:methods and protocols. 294. New York (NY):Springer; 2013. p. 533–565.
18. Lee H, De Vries AH, Marrink SJ, et al. A coarse-grained model for polyethylene oxide and polyethylene glycol:conformation and hydrodynamics. J Phys Chem B. 2009;113:13186–13194.10.1021/jp9058966
19. Shinoda W, DeVane R, Klein ML., Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants molecular simulation. 2007;33:27–36.
20. Shinoda W, DeVane R, Klein ML., Zwitterionic lipid assemblies:molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. J Phys Chem B. 2010;114:6836–6849.10.1021/jp9107206
21. DeVane R, Shinoda W, Moore PB, et al. A transferable coarse grain non-bonded interaction model for amino acids. J Chem Theory Comput. 2009;5:2115–2124.10.1021/ct800441u
22. Shinoda W, DeVane R, Klein ML., Self-assembly of surfactants in bulk phases and at interfaces using coarse-grain models. In:Voth GA, editor. Coarse-graining of condensed phase and biomolecular systems. Boca Raton (FL):CRC Press; 2008. p. 329–342.
23. Loverde SM, Klein ML, Discher DE., Nanoparticle shape improves delivery:rational coarse grain molecular dynamics (rCG-MD) of taxol in worm-like PEG-PCL micelles. Adv Mater. 2012;24:3823–3830.10.1002/adma.v24.28
24. Groot RD., Applications of dissipative particle dynamics. Lect Notes Phys. 2004;640:5–38.10.1007/b95265
25. Groot RD, Warren PB., Dissipative particle dynamics:bridging the gap between atomistic and mesoscopic simulation. J Chem Phys. 1997;107:4423–4435.10.1063/1.474784
26. Loverde SM, Ortiz V, Kamien RD, et al. Curvature-driven molecular demixing in the budding and breakup of mixed component worm-like micelles. Soft Matter. 2010;6:1419–1425.10.1039/b919581e
27. Ortiz V, Nielsen SO, Discher DE, et al. Dissipative particle dynamics simulations of polymersomes. J Phys Chem. 2005;109:17708–17714.10.1021/jp0512762
28. Laio A, Parrinello M., Escaping free-energy minima. Proc Natl Acad Sci USA. 2002;99:12562–12566.10.1073/pnas.202427399
29. Bussi G, Gervasio FL, Laio A, Parrinello M., Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc. 2006;128:13435–13441.10.1021/ja062463w
30. Ensing B, De Vivo M, Liu ZW, et al. Metadynamics as a tool for exploring free energy landscapes of chemical reactions. Acc Chem Res. 2006;39:73–81.10.1021/ar040198i
31. Torrie GM, Valleau JP. Non-physical sampling distributions in monte-carlo free-energy estimation–umbrella sampling. J Comput Phys. 1977;23:187–199.10.1016/0021-9991(77)90121-8
32. Athawale MV, Goel G, Ghosh T, et al. Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water. Proc Natl Acad Sci USA. 2007;104:733–738.10.1073/pnas.0605139104
33. Ten Wolde PR, Chandler D. Drying-induced hydrophobic polymer collapse. Proc Natl Acad Sci USA. 2002;99:6539–6543.10.1073/pnas.052153299
34. Vanommeslaeghe K, Hatcher E, Acharya C, et al. CHARMM general force field:a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010;31:671–690.
35. Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–1802.10.1002/(ISSN)1096-987X
36. Kale L., Skeel R, Bhandarkar M. NAMD2:greater scalability for parallel molecular dynamics. J Comput Phys. 1999;151:283–312.10.1006/jcph.1999.6201
37. Fiorin G, Klein ML, Hénin J, et al. Using collective variables to drive molecular dynamics simulations. Mol Phys. 2013;111:3345–3362.10.1080/00268976.2013.813594
38. Plimpton S., Fast parallel algorithms for short-range molecular-dynamics. J Comput Phys. 1995;117:1–19.10.1006/jcph.1995.1039
39. Hoover WG., Canonical dynamics:equilibrium phase-space distributions. Phys Rev A. 1985;31:1695–1697.10.1103/PhysRevA.31.1695
40. Deserno M, Holm C., How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. J Chem Phys. 1998;109:7678–7693.10.1063/1.477414
41. Fiorin G, Hénin J, Kohlmeyer A., Collective variables module reference manual for LAMMPS; Albuquerque:Sandia National Laboratories; 2013.
42. Khokhlov A, Grosberg A, Pande V., Statistical physics of macromolecules:polymers and complex materials. New York(NY):AIP Press; 2002.
43. Lee B, Richards FM, Interpretation of protein structures–estimation of static accesibilty. J Mol Biol. 1971;55:379–400.10.1016/0022-2836(71)90324-X
44. Miller S, Lesk AM, Janin J, et al. The accessible surface area and stability of oligomeric proteins. Nature. 1987;328:834–836.10.1038/328834a0
45. Moret MA., Self-organized critical model for protein folding. Physica A. 2011;390:3055–3059.10.1016/j.physa.2011.04.008
46. Harano Y, Kinoshita M., Translational-entropy gain of solvent upon protein folding. Biophys J. 2005;89:2701–2710.10.1529/biophysj.104.057604
47. Graziano G., On the signature of the hydrophobic effect at a single molecule level. PCCP. 2013;15:7389–7395.10.1039/c3cp50616a
48. Graziano G., On the mechanism of cold denaturation. PCCP. 2014;16:21755–21767.10.1039/C4CP02729A
49. Pica A, Graziano G., On the effect of sodium salts on the coil-to-globule transition of poly (N-isopropylacrylamide). PCCP. 2015;17:27750–27757.10.1039/C5CP04094A