A mathematical formulation and solution of the CoPhMoRe inverse problem for helically wrapping polymer corona phases on cylindrical substrates

Journal of Physical Chemistry C

Volumn 119, Issue 24, 2015, Pages 13876-13886

  Bisker, Gili ^a   Ahn, Jiyoung ^a   Kruss, Sebastian ^a   Ulissi, Zachary W ^a   Salem, Daniel P ^a   Strano, Michael S ^a  

^a Massachusetts Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINS; CARBON; COPOLYMERS; DIFFERENTIAL EQUATIONS; FUNCTIONAL GROUPS; HYDROPHILICITY; MOLECULAR RECOGNITION; MOLECULES; NANOPARTICLES; POLYMERS; PROBLEM SOLVING; SINGLE-WALLED CARBON NANOTUBES (SWCN); YARN;

3-DIMENSIONAL STRUCTURES; ALTERNATIVE DESIGNS; COARSE GRAINED MODELS; COMBINATORIAL LIBRARY; CYLINDRICAL SUBSTRATE; HYDROPHOBIC-HYDROPHILIC; MATHEMATICAL FORMULATION; NANOPARTICLE SURFACE;

INVERSE PROBLEMS;

EID: 84934983330     PISSN: 19327447     EISSN: 19327455     Source Type: Journal    
DOI: 10.1021/acs.jpcc.5b01705     Document Type: Article

References (69)

1. Yalow, R. S.; Berson, S. A. Assay of Plasma Insulin in Human Subjects by Immunological Methods Nature 1959, 184 (4699) 1648-1649
2. Jayasena, S. D. Aptamers: An Emerging Class of Molecules That Rival Antibodies in Diagnostics Clin. Chem. 1999, 45 (9) 1628-1650
3. Sidhu, S. S.; Fellouse, F. A. Synthetic therapeutic antibodies Nat. Chem. Biol. 2006, 2 (12) 682-688
4. Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 1990, 249 (4968) 505-510
5. Corbett, P. T.; Leclaire, J.; Vial, L.; West, K. R.; Wietor, J.-L.; Sanders, J. K. M.; Otto, S. Dynamic Combinatorial Chemistry Chem. Rev. 2006, 106 (9) 3652-3711
6. Lehn, J.-M.; Eliseev, A. V. Dynamic Combinatorial Chemistry Science 2001, 291 (5512) 2331-2332
7. Kruss, S.; Landry, M. P.; Vander Ende, E.; Lima, B. M. A.; Reuel, N. F.; Zhang, J.; Nelson, J.; Mu, B.; Hilmer, A.; Strano, M. Neurotransmitter Detection Using Corona Phase Molecular Recognition on Fluorescent Single-Walled Carbon Nanotube Sensors J. Am. Chem. Soc. 2013, 136 (2) 713-724
8. Zhang, J.; Landry, M. P.; Barone, P. W.; Kim, J.-H.; Lin, S.; Ulissi, Z. W.; Lin, D.; Mu, B.; Boghossian, A. A.; Hilmer, A. J.; Rwei, A.; Hinckley, A. C.; Kruss, S.; Shandell, M. A.; Nair, N.; Blake, S.; Sen, F.; Sen, S.; Croy, R. G.; Li, D.; Yum, K.; Ahn, J.-H.; Jin, H.; Heller, D. A.; Essigmann, J. M.; Blankschtein, D.; Strano, M. S. Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes Nat. Nano 2013, 8 (12) 959-968
9. Mahon, C. S.; Fulton, D. A. Mimicking nature with synthetic macromolecules capable of recognition Nat. Chem. 2014, 6 (8) 665-672
10. Ye, L.; Mosbach, K. Molecular Imprinting: Synthetic Materials As Substitutes for Biological Antibodies and Receptors Chem. Mater. 2008, 20 (3) 859-868
11. Alexander, C.; Andersson, H. S.; Andersson, L. I.; Ansell, R. J.; Kirsch, N.; Nicholls, I. A.; O'Mahony, J.; Whitcombe, M. J. Molecular imprinting science and technology: a survey of the literature for the years up to and including 2003 J. Mol. Recognit. 2006, 19 (2) 106-180
12. Vlatakis, G.; Andersson, L. I.; Muller, R.; Mosbach, K. Drug assay using antibody mimics made by molecular imprinting Nature 1993, 361 (6413) 645-647
13. Hoshino, Y.; Koide, H.; Urakami, T.; Kanazawa, H.; Kodama, T.; Oku, N.; Shea, K. J. Recognition, Neutralization, and Clearance of Target Peptides in the Bloodstream of Living Mice by Molecularly Imprinted Polymer Nanoparticles: A Plastic Antibody J. Am. Chem. Soc. 2010, 132 (19) 6644-6645
14. Barone, P. W.; Baik, S.; Heller, D. A.; Strano, M. S. Near-infrared optical sensors based on single-walled carbon nanotubes Nat. Mater. 2005, 4 (1) 86-92
15. Kruss, S.; Hilmer, A. J.; Zhang, J.; Reuel, N. F.; Mu, B.; Strano, M. S. Carbon nanotubes as optical biomedical sensors Adv. Drug Delivery Rev. 2013, 65 (15) 1933-1950
16. Landry, M.; Kruss, S.; Nelson, J.; Bisker, G.; Iverson, N.; Reuel, N.; Strano, M. Experimental Tools to Study Molecular Recognition within the Nanoparticle Corona Sensors 2014, 14 (9) 16196-16211
17. Odom, T. W.; Huang, J.-L.; Kim, P.; Lieber, C. M. Atomic structure and electronic properties of single-walled carbon nanotubes Nature 1998, 391 (6662) 62-64
18. Bachilo, S. M.; Strano, M. S.; Kittrell, C.; Hauge, R. H.; Smalley, R. E.; Weisman, R. B. Structure-Assigned Optical Spectra of Single-Walled Carbon Nanotubes Science 2002, 298 (5602) 2361-2366
19. Zhang, J.; Boghossian, A. A.; Barone, P. W.; Rwei, A.; Kim, J. H.; Lin, D.; Heller, D. A.; Hilmer, A. J.; Nair, N.; Reuel, N. F.; Strano, M. S. Single Molecule Detection of Nitric Oxide Enabled by d(AT)(15) DNA Adsorbed to Near Infrared Fluorescent Single-Walled Carbon Nanotubes J. Am. Chem. Soc. 2011, 133 (3) 567-581
20. O'Connell, M. J.; Bachilo, S. M.; Huffman, C. B.; Moore, V. C.; Strano, M. S.; Haroz, E. H.; Rialon, K. L.; Boul, P. J.; Noon, W. H.; Kittrell, C.; Ma, J.; Hauge, R. H.; Weisman, R. B.; Smalley, R. E. Band Gap Fluorescence from Individual Single-Walled Carbon Nanotubes Science 2002, 297 (5581) 593-596
21. Johnson, R. R.; Johnson, A. T. C.; Klein, M. L. Probing the Structure of DNA-Carbon Nanotube Hybrids with Molecular Dynamics Nano Lett. 2007, 8 (1) 69-75
22. Zhang, J.; Kruss, S.; Hilmer, A. J.; Shimizu, S.; Schmois, Z.; De La Cruz, F.; Barone, P. W.; Reuel, N. F.; Heller, D. A.; Strano, M. S. A Rapid, Direct, Quantitative, and Label-Free Detector of Cardiac Biomarker Troponin T Using Near-Infrared Fluorescent Single-Walled Carbon Nanotube Sensors Adv. Healthcare Mater. 2014, 3 (3) 412-423
23. Moore, V. C.; Strano, M. S.; Haroz, E. H.; Hauge, R. H.; Smalley, R. E.; Schmidt, J.; Talmon, Y. Individually suspended single-walled carbon nanotubes in various surfactants Nano Lett. 2003, 3 (10) 1379-1382
24. 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. 2003, 2 (5) 338-342
25. Landry, M. P.; Vukovic, L.; Kruss, S.; Bisker, G.; Landry, A. M.; Islam, S.; Jain, R. M.; Schulten, K.; Strano, M. S. Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes J. Phys. Chem. C 2015, 119 (18) 10048-10058
26. Kruss, S.; Landry, M. P.; Vander Ende, E.; Lima, B. M.; Reuel, N. F.; Zhang, J.; Nelson, J.; Mu, B.; Hilmer, A.; Strano, M. Neurotransmitter detection using corona phase molecular recognition on fluorescent single-walled carbon nanotube sensors J. Am. Chem. Soc. 2014, 136 (2) 713-724
27. Yum, K.; Ahn, J. H.; McNicholas, T. P.; Barone, P. W.; Mu, B.; Kim, J. H.; Jain, R. M.; Strano, M. S. Boronic acid library for selective, reversible near-infrared fluorescence quenching of surfactant suspended single-walled carbon nanotubes in response to glucose ACS Nano 2012, 6 (1) 819-830
28. Reuel, N. F.; Grassbaugh, B.; Kruss, S.; Mundy, J. Z.; Opel, C.; Ogunniyi, A.; Egodage, K.; Wahl, R.; Helk, B.; Zhang, J.; Kalcioglu, Z. I.; Tvrdy, K.; Bellisario, D. O.; Mu, B.; Blake, S. S.; Van Vliet, K. J.; Love, J. C.; Wittrup, K. D.; Strano, M. S. Emergent Properties of Nanosensor Arrays: Applications for Monitoring IgG Affinity Distributions, Weakly-Affined Hypermannosylation, and Colony Selection for Biomanufacturing ACS Nano 2013, 7 (9) 7472-7482
29. Ulissi, Z. W.; Zhang, J.; Sresht, V.; Blankschtein, D.; Strano, M. S. 2D Equation-of-State Model for Corona Phase Molecular Recognition on Single-Walled Carbon Nanotube and Graphene Surfaces Langmuir 2015, 31 (1) 628-636
30. Iverson, N. M.; Barone, P. W.; Shandell, M.; Trudel, L. J.; Sen, S.; Sen, F.; Ivanov, V.; Atolia, E.; Farias, E.; McNicholas, T. P.; Reuel, N.; Parry, N. M. A.; Wogan, G. N.; Strano, M. S. In vivo biosensing via tissue-localizable near-infrared-fluorescent single-walled carbon nanotubes Nat. Nano 2013, 8 (11) 873-880
31. Bisker, G.; Iverson, N. M.; Ahn, J.; Strano, M. S. A Pharmacokinetic Model of a Tissue Implantable Insulin Sensor Adv. Healthcare Mater. 2015, 4 (1) 87-97
32. Liu, Z.; Tabakman, S.; Welsher, K.; Dai, H. Carbon nanotubes in biology and medicine: In vitro and in vivo detection, imaging and drug delivery Nano Res. 2009, 2 (2) 85-120
33. Welsher, K.; Liu, Z.; Sherlock, S. P.; Robinson, J. T.; Chen, Z.; Daranciang, D.; Dai, H. A route to brightly fluorescent carbon nanotubes for near-infrared imaging in mice Nat. Nano 2009, 4 (11) 773-780
34. Campbell, J. F.; Tessmer, I.; Thorp, H. H.; Erie, D. A. Atomic Force Microscopy Studies of DNA-Wrapped Carbon Nanotube Structure and Binding to Quantum Dots J. Am. Chem. Soc. 2008, 130 (32) 10648-10655
35. Cathcart, H.; Nicolosi, V.; Hughes, J. M.; Blau, W. J.; Kelly, J. M.; Quinn, S. J.; Coleman, J. N. Ordered DNA Wrapping Switches on Luminescence in Single-Walled Nanotube Dispersions J. Am. Chem. Soc. 2008, 130 (38) 12734-12744
36. Jin, H.; Jeng, E. S.; Heller, D. A.; Jena, P. V.; Kirmse, R.; Langowski, J.; Strano, M. S. Divalent Ion and Thermally Induced DNA Conformational Polymorphism on Single-walled Carbon Nanotubes Macromolecules 2007, 40 (18) 6731-6739
37. Yarotski, D. A.; Kilina, S. V.; Talin, A. A.; Tretiak, S.; Prezhdo, O. V.; Balatsky, A. V.; Taylor, A. J. Scanning Tunneling Microscopy of DNA-Wrapped Carbon Nanotubes Nano Lett. 2008, 9 (1) 12-17
38. Zheng, M.; Jagota, A.; Strano, M. S.; Santos, A. P.; Barone, P.; Chou, S. G.; Diner, B. A.; Dresselhaus, M. S.; McLean, R. S.; Onoa, G. B. Structure-based carbon nanotube sorting by sequence-dependent DNA assembly Science 2003, 302 (5650) 1545-1548
39. Sugio, S.; Kashima, A.; Mochizuki, S.; Noda, M.; Kobayashi, K. Crystal structure of human serum albumin at 2.5 Å resolution Protein Eng. 1999, 12 (6) 439-446
40. Bhattacharya, A. A.; Grüne, T.; Curry, S. Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin1 J. Mol. Biol. 2000, 303 (5) 721-732
41. García de la Torre, J.; Huertas, M. L.; Carrasco, B. Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure Biophys. J. 2000, 78 (2) 719-730
42. Kiselev, M. A.; Gryzunov Iu, A.; Dobretsov, G. E.; Komarova, M. N. [Size of a human serum albumin molecule in solution] Biofizika 2001, 46 (3) 423-427
43. He, X. M.; Carter, D. C. Atomic structure and chemistry of human serum albumin Nature 1992, 358 (6383) 209-215
44. O'Connell, M. J.; Boul, P.; Ericson, L. M.; Huffman, C.; Wang, Y.; Haroz, E.; Kuper, C.; Tour, J.; Ausman, K. D.; Smalley, R. E. Reversible water-solubilization of single-walled carbon nanotubes by polymer wrapping Chem. Phys. Lett. 2001, 342 (3) 265-271
45. Caddeo, C.; Melis, C.; Colombo, L.; Mattoni, A. Understanding the Helical Wrapping of Poly(3-hexylthiophene) on Carbon Nanotubes J. Phys. Chem. C 2010, 114 (49) 21109-21113
46. Kang, Y. K.; Lee, O.-S.; Deria, P.; Kim, S. H.; Park, T.-H.; Bonnell, D. A.; Saven, J. G.; Therien, M. J. Helical Wrapping of Single-Walled Carbon Nanotubes by Water Soluble Poly(p-phenyleneethynylene) Nano Lett. 2009, 9 (4) 1414-1418
47. Bachilo, S. M.; Balzano, L.; Herrera, J. E.; Pompeo, F.; Resasco, D. E.; Weisman, R. B. Narrow (n,m)-Distribution of Single-Walled Carbon Nanotubes Grown Using a Solid Supported Catalyst J. Am. Chem. Soc. 2003, 125 (37) 11186-11187
48. Tu, X.; Manohar, S.; Jagota, A.; Zheng, M. DNA sequence motifs for structure-specific recognition and separation of carbon nanotubes Nature 2009, 460, 250-253
49. Liu, H.; Nishide, D.; Tanaka, T.; Kataura, H. Large-scale single-chirality separation of single-wall carbon nanotubes by simple gel chromatography Nat. Commun. 2011, 10.1038/ncomms1313
50. Arnold, M. S.; Green, A. A.; Hulvat, J. F.; Stupp, S. I.; Hersam, M. C. Sorting carbon nanotubes by electronic structure using density differentiation Nat. Nanotechnol. 2006, 1, 60-65
51. Jain, R. M.; Tvrdy, K.; Han, R.; Ulissi, Z.; Strano, M. S. Quantitative Theory of Adsorptive Separation for the Electronic Sorting of Single-Walled Carbon Nanotubes ACS Nano 2014, 8 (4) 3367-3379
52. Heller, D. A.; Mayrhofer, R. M.; Baik, S.; Grinkova, Y. V.; Usrey, M. L.; Strano, M. S. Concomitant Length and Diameter Separation of Single-Walled Carbon Nanotubes J. Am. Chem. Soc. 2004, 126 (44) 14567-14573
53. Yum, K.; Ahn, J.-H.; McNicholas, T. P.; Barone, P. W.; Mu, B.; Kim, J.-H.; Jain, R. M.; Strano, M. S. Boronic Acid Library for Selective, Reversible Near-Infrared Fluorescence Quenching of Surfactant Suspended Single-Walled Carbon Nanotubes in Response to Glucose ACS Nano 2011, 6 (1) 819-830
54. Mu, B.; McNicholas, T. P.; Zhang, J.; Hilmer, A. J.; Jin, Z.; Reuel, N. F.; Kim, J.-H.; Yum, K.; Strano, M. S. A Structure-Function Relationship for the Optical Modulation of Phenyl Boronic Acid-Grafted, Polyethylene Glycol-Wrapped Single-Walled Carbon Nanotubes J. Am. Chem. Soc. 2012, 134 (42) 17620-17627
55. Nash, C. P.; Nelson, T. E.; Stewart, J. J. P.; Carper, W. R. Molecular structure and vibrational analysis of 2,4,6-trinitrotoluene and 2,4,6-trinitrotoluene-α-d3 Spectrochim. Acta, Part A 1989, 45 (5) 585-588
56. Foloppe, N.; MacKerell, J. A. D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 2000, 21 (2) 86-104
57. Manohar, S.; Tang, T.; Jagota, A. Structure of Homopolymer DNA-CNT Hybrids J. Phys. Chem. C 2007, 111 (48) 17835-17845
58. Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model J. Chem. Phys. 2011, 10.1063/1.3552946
59. HOOMD-blue web page. http://codeblue.umich.edu/hoomd-blue.
60. Anderson, J. A.; Lorenz, C. D.; Travesset, A. General purpose molecular dynamics simulations fully implemented on graphics processing units Journal of Computational Physics 2008, 227 (10) 5342-5359
61. Kusner, I.; Srebnik, S. Conformational behavior of semi-flexible polymers confined to a cylindrical surface Chem. Phys. Lett. 2006, 430 (1-3) 84-88
62. Gurevitch, I.; Srebnik, S. Monte Carlo simulation of polymer wrapping of nanotubes Chem. Phys. Lett. 2007, 444 (1) 96-100
63. Gurevitch, I.; Srebnik, S. Conformational behavior of polymers adsorbed on nanotubes J. Chem. Phys. 2008, 10.1063/1.2894842
64. Tallury, S. S.; Pasquinelli, M. A. Molecular Dynamics Simulations of Flexible Polymer Chains Wrapping Single-Walled Carbon Nanotubes J. Phys. Chem. B 2010, 114 (12) 4122-4129
65. Cherstvy, A. G.; Winkler, R. G. Complexation of semiflexible chains with oppositely charged cylinder J. Chem. Phys. 2004, 120 (19) 9394-9400
66. Chen, H.; Meisburger, S. P.; Pabit, S. A.; Sutton, J. L.; Webb, W. W.; Pollack, L. Ionic strength-dependent persistence lengths of single-stranded RNA and DNA Proc. Natl. Acad. Sci. U.S.A. 2012, 109 (3) 799-804
67. Tinland, B.; Pluen, A.; Sturm, J.; Weill, G. Persistence Length of Single-Stranded DNA Macromolecules 1997, 30 (19) 5763-5765
68. Sobel, E. S.; Harpst, J. A. Effects of Na+ on the persistence length and excluded volume of T7 bacteriophage DNA Biopolymers 1991, 31 (13) 1559-1564
69. Kricheldorf, H. R.; Nuyken, O.; Swift, G. Handbook of Polymer Synthesis, 2 nd ed.; Taylor & Francis: 2004.