Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts

ACS Nano

Volumn 9, Issue 5, 2015, Pages 5082-5092

  Bedford, Nicholas M ^a,b,g   Ramezani Dakhel, Hadi ^c   Slocik, Joseph M ^a   Briggs, Beverly D ^b   Ren, Yang ^d   Frenkel, Anatoly I ^e   Petkov, Valeri ^f   Heinz, Hendrik ^c   Naik, Rajesh R ^a   Knecht, Marc R ^b  

^a AIR FORCE RESEARCH LABORATORY   (United States)

^b University of Miami   (United States)

^c University of Akron   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

^e YESHIVA UNIVERSITY   (United States)

^f CENTRAL MICHIGAN UNIVERSITY   (United States)

^g NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

atomic pair distribution function; biotemplating; catalysis; molecular dynamics simulations; peptides

Indexed keywords

AMINO ACIDS; BIOINFORMATICS; CATALYSIS; CATALYST ACTIVITY; DISTRIBUTION FUNCTIONS; LIGANDS; MOLECULAR DYNAMICS; MONTE CARLO METHODS; PALLADIUM; REACTION KINETICS; REACTION RATES;

ATOMIC PAIR DISTRIBUTION FUNCTIONS; BIO-TEMPLATING; MOLECULAR DYNAMICS SIMULATIONS; REVERSE MONTE CARLO METHOD; STRUCTURE/FUNCTION RELATIONSHIPS; SYNCHROTRON X-RAY TECHNIQUE; THERMODYNAMICALLY STABLE; TRIAL-AND-ERROR APPROACH;

PEPTIDES;

ALKENE; BIOMIMETIC MATERIAL; METAL NANOPARTICLE; OLIGOPEPTIDE; PALLADIUM;

AMINO ACID SEQUENCE; CATALYSIS; CHEMISTRY; HYDROGENATION; MOLECULAR DYNAMICS; NANOTECHNOLOGY; PROCEDURES; PROTEIN CONFORMATION; SURFACE PROPERTY;

ALKENES; AMINO ACID SEQUENCE; BIOMIMETIC MATERIALS; CATALYSIS; HYDROGENATION; METAL NANOPARTICLES; MOLECULAR DYNAMICS SIMULATION; NANOTECHNOLOGY; OLIGOPEPTIDES; PALLADIUM; PROTEIN CONFORMATION; SURFACE PROPERTIES;

EID: 84930226681     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/acsnano.5b00168     Document Type: Article

References (58)

1. Dickerson, M. B.; Sandhage, K. H.; Naik, R. R. Protein- and Peptide-Directed Syntheses of Inorganic Materials Chem. Rev. 2008, 108, 4935-4978
2. Sarikaya, M.; Tamerler, C.; Jen, A. K. Y.; Schulten, K.; Baneyx, F. Molecular Biomimetics: Nanotechnology through Biology Nat. Mater. 2003, 2, 577-585
3. Briggs, B. D.; Knecht, M. R. Nanotechnology Meets Biology: Peptide-based Methods for the Fabrication of Functional Materials J. Phys. Chem. Lett. 2012, 3, 405-418
4. Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. A DNA-Based Method for Rationally Assembling Nanoparticles into Macroscopic Materials Nature 1996, 382, 607-609
5. Schreiber, R.; Do, J.; Roller, E. M.; Zhang, T.; Schuller, V. J.; Nickels, P. C.; Feldmann, J.; Liedl, T. Hierarchical Assembly of Metal Nanoparticles, Quantum Dots and Organic Dyes Using DNA Origami Scaffolds Nat. Nanotechnol. 2014, 9, 74-78
6. Kharlampieva, E.; Slocik, J. M.; Singamaneni, S.; Poulsen, N.; Kroger, N.; Naik, R. R.; Tsukruk, V. V. Protein-Enabled Synthesis of Monodisperse Titania Nanoparticles On and Within Polyelectrolyte Matrices Adv. Funct. Mater. 2009, 19, 2303-2311
7. Nam, K. T.; Kim, D. W.; Yoo, P. J.; Chiang, C. Y.; Meethong, N.; Hammond, P. T.; Chiang, Y. M.; Belcher, A. M. Virus-Enabled Synthesis and Assembly of Nanowires for Lithium Ion Battery Electrodes Science 2006, 312, 885-888
8. Coppage, R.; Slocik, J. M.; Ramezani-Dakhel, H.; Bedford, N. M.; Heinz, H.; Naik, R. R.; Knecht, M. R. Exploiting Localized Surface Binding Effects to Enhance the Catalytic Reactivity of Peptide-Capped Nanoparticles J. Am. Chem. Soc. 2013, 135, 11048-11054
9. Coppage, R.; Slocik, J. M.; Sethi, M.; Pacardo, D. B.; Naik, R. R.; Knecht, M. R. Elucidation of Peptide Effects that Control the Activity of Nanoparticles Angew. Chem., Int. Ed. 2010, 49, 3767-3770
10. So, C. R.; Hayamizu, Y.; Yazici, H.; Gresswell, C.; Khatayevich, D.; Tamerler, C.; Sarikaya, M. Controlling Self-Assembly of Engineered Peptides on Graphite by Rational Mutation ACS Nano 2012, 6, 1648-1656
11. Seferos, D. S.; Giljohann, D. A.; Hill, H. D.; Prigodich, A. E.; Mirkin, C. A. Nano-Flares: Probes for Transfection and mRNA Detection in Living Cells J. Am. Chem. Soc. 2007, 129, 15477-15479
12. Reynolds, R. A.; Mirkin, C. A.; Letsinger, R. L. Homogeneous, Nanoparticle-Based Quantitative Colorimetric Detection of Oligonucleotides J. Am. Chem. Soc. 2000, 122, 3795-3796
13. Brown, S. Metal-Recognition by Repeating Polypeptides Nat. Biotechnol. 1997, 15, 269-272
14. Naik, R. R.; Stringer, S. J.; Agarwal, G.; Jones, S. E.; Stone, M. O. Biomimetic Synthesis and Patterning of Silver Nanoparticles Nat. Mater. 2002, 1, 169-172
15. Chiu, C. Y.; Li, Y. J.; Ruan, L. Y.; Ye, X. C.; Murray, C. B.; Huang, Y. Platinum Nanocrystals Selectively Shaped Using Facet-Specific Peptide Sequences Nat. Chem. 2011, 3, 393-399
16. Pacardo, D. B.; Sethi, M.; Jones, S. E.; Naik, R. R.; Knecht, M. R. Biomimetic Synthesis of Pd Nanocatalysts for the Stille Coupling Reaction ACS Nano 2009, 3, 1288-1296
17. Dickerson, M. B.; Jones, S. E.; Cai, Y.; Ahmad, G.; Naik, R. R.; Kröger, N.; Sandhage, K. H. Identification and Design of Peptides for the Rapid, High-Yield Formation of Nanoparticulate TiO2 from Aqueous Solutions at Room Temperature Chem. Mater. 2008, 20, 1578-1584
18. Whaley, S. R.; English, D. S.; Hu, E. L.; Barbara, P. F.; Belcher, A. M. Selection of Peptides with Semiconductor Binding Specificity for Directed Nanocrystal Assembly Nature 2000, 405, 665-668
19. Puddu, V.; Perry, C. C. Peptide Adsorption on Silica Nanoparticles: Evidence of Hydrophobic Interactions ACS Nano 2012, 6, 6356-6363
20. Li, Y.; Tang, Z.; Prasad, P. N.; Knecht, M. R.; Swihart, M. T. Peptide-Mediated Synthesis of Gold Nanoparticles: Effects of Peptide Sequence and Nature of Binding on Physicochemical Properties Nanoscale 2014, 6, 3165-3172
21. Tamerler, C.; Oren, E. E.; Duman, M.; Venkatasubramanian, E.; Sarikaya, M. Adsorption Kinetics of an Engineered Gold Binding Peptide by Surface Plasmon Resonance Spectroscopy and a Quartz Crystal Microbalance Langmuir 2006, 22, 7712-7718
22. Hnilova, M.; Oren, E. E.; Seker, U. O. S.; Wilson, B. R.; Collino, S.; Evans, J. S.; Tamerler, C.; Sarikaya, M. Effect of Molecular Conformations on the Adsorption Behavior of Gold-Binding Peptides Langmuir 2008, 24, 12440-12445
23. Skelton, A. A.; Liang, T. N.; Walsh, T. R. Interplay of Sequence, Conformation, and Binding at the Peptide-Titania Interface as Mediated by Water ACS Appl. Mater. Interfaces 2009, 1, 1482-1491
24. Heinz, H.; Farmer, B. L.; Pandey, R. B.; Slocik, J. M.; Patnaik, S. S.; Pachter, R.; Naik, R. R. Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd-Au Bimetal Surfaces in Aqueous Solution J. Am. Chem. Soc. 2009, 131, 9704-9714
25. Coppage, R.; Slocik, J. M.; Briggs, B. D.; Frenkel, A. I.; Heinz, H.; Naik, R. R.; Knecht, M. R. Crystallographic Recognition Controls Peptide Binding for Bio-Based Nanomaterials J. Am. Chem. Soc. 2011, 133, 12346-12349
26. Mirau, P. A.; Naik, R. R.; Gehring, P. Structure of Peptides on Metal Oxide Surfaces Probed by NMR J. Am. Chem. Soc. 2011, 133, 18243-18248
27. Patwardhan, S. V.; Emami, F. S.; Berry, R. J.; Jones, S. E.; Naik, R. R.; Deschaume, O.; Heinz, H.; Perry, C. C. Chemistry of Aqueous Silica Nanoparticle Surfaces and the Mechanism of Selective Peptide Adsorption J. Am. Chem. Soc. 2012, 134, 6244-6256
28. Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100) J. Chem. Theory Comput. 2013, 9, 1616-1630
29. Ruan, L. Y.; Ramezani-Dakhel, H.; Chiu, C. Y.; Zhu, E. B.; Li, Y. J.; Heinz, H.; Huang, Y. Tailoring Molecular Specificity Toward a Crystal Facet: A Lesson From Biorecognition Toward Pt{111} Nano Lett. 2013, 13, 840-846
30. Emami, F. S.; Puddu, V.; Berry, R. J.; Varshney, V.; Patwardhan, S. V.; Perry, C. C.; Heinz, H. Prediction of Specific Biomolecule Adsorption on Silica Surfaces as a Function of pH and Particle Size Chem. Mater. 2014, 26, 5725-5734
31. Ramezani-Dakhel, H.; Mirau, P. A.; Naik, R. R.; Knecht, M. R.; Heinz, H. Stability, Surface Features, and Atom Leaching of Palladium Nanoparticles: Toward Prediction of Catalytic Functionality Phys. Chem. Chem. Phys. 2013, 15, 5488-5492
32. Pandey, R. B.; Heinz, H.; Feng, J.; Farmer, B. L.; Slocik, J. M.; Drummy, L. F.; Naik, R. R. Adsorption of Peptides (A3, Flg, Pd2, Pd4) on Gold and Palladium Surfaces by a Coarse-Grained Monte Carlo Simulation Phys. Chem. Chem. Phys. 2009, 11, 1989-2001
33. Coppage, R.; Slocik, J. M.; Briggs, B. D.; Frenkel, A. I.; Naik, R. R.; Knecht, M. R. Determining Peptide Sequence Effects That Control the Size, Structure, and Function of Nanoparticles ACS Nano 2012, 6, 1625-1636
34. Teranishi, T.; Miyake, M. Size Control of Palladium Nanoparticles and Their Crystal Structures Chem. Mater. 1998, 10, 594-600
35. Yancey, D. F.; Chill, S. T.; Zhang, L.; Frenkel, A. I.; Henkelman, G.; Crooks, R. M. A Theoretical and Experimental Examination of Systematic Ligand-Induced Disorder in Au Dendrimer-Encapsulated Nanoparticles Chem. Sci. 2013, 4, 2912-2921
36. Bedford, N.; Dablemont, C.; Viau, G.; Chupas, P.; Petkov, V. 3-D Structure of Nanosized Catalysts by High-Energy X-ray Diffraction and Reverse Monte Carlo Simulations: Study of Ru J. Phys. Chem. C 2007, 111, 18214-18219
37. Chakroune, N.; Viau, G.; Ammar, S.; Poul, L.; Veautier, D.; Chehimi, M. M.; Mangeney, C.; Villain, F.; Fievet, F. Acetate- and Thiol-Capped Monodisperse Ruthenium Nanoparticles: XPS, XAS, and HRTEM Studies Langmuir 2005, 21, 6788-6796
38. MacDonald, M. A.; Zhang, P.; Qian, H. F.; Jin, R. C. Site-Specific and Size-Dependent Bonding of Compositionally Precise Gold-Thiolate Nanoparticles from X-ray Spectroscopy J. Phys. Chem. Lett. 2010, 1, 1821-1825
39. Jadzinsky, P. D.; Calero, G.; Ackerson, C. J.; Bushnell, D. A.; Kornberg, R. D. Structure of a Thiol Monolayer-Protected Gold Nanoparticle at 1.1 Angstrom Resolution Science 2007, 318, 430-433
40. Keen, D. A.; Mcgreevy, R. L. Structural Modeling of Glasses Using Reverse Monte-Carlo Simulation Nature 1990, 344, 423-425
41. Heinz, H. Computational Screening of Biomolecular Adsorption and Self-Assembly on Nanoscale Surfaces J. Comput. Chem. 2010, 31, 1564-1568
42. Feng, J.; Slocik, J. M.; Sarikaya, M.; Naik, R. R.; Farmer, B. L.; Heinz, H. Influence of the Shape of Nanostructured Metal Surfaces on Adsorption of Single Peptide Molecules in Aqueous Solution Small 2012, 8, 1049-1059
43. Heinz, H.; Lin, T.-J.; Mishra, R. K.; Emami, F. S. Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field Langmuir 2013, 29, 1754-1765
44. Heinz, H.; Vaia, R. A.; Farmer, B. L.; Naik, R. R. Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6 Lennard-Jones Potentials J. Phys. Chem. C 2008, 112, 17281-17290
45. Cremer, P. S.; Somorjai, G. A. Surface Science and Catalysis of Ethylene Hydrogenation J. Chem. Soc., Faraday Trans. 1995, 91, 3671-3677
46. Horiuti, I.; Polanyi, M. Exchange Reactions of Hydrogen on Metallic Catalysts Trans. Faraday Soc. 1934, 30, 1164-1172
47. Mattson, B.; Foster, W.; Greimann, J.; Hoette, T.; Le, N.; Mirich, A.; Wankum, S.; Cabri, A.; Reichenbacher, C.; Schwanke, E. Heterogeneous. Catalysis: The Horiuti-Polanyi Mechanism and Alkene Hydrogenation J. Chem. Educ. 2013, 90, 613-619
48. Newville, M. IFEFFIT: Interactive XAFS Analysis and FEFF Fitting J. Synchrotron Radiat. 2001, 8, 322-324
49. Moore, W. J.; Pauling, L. The Crystal Structures of the Tetragonal Monoxides of Lead, Tin, Palladium, and Platinum J. Am. Chem. Soc. 1941, 63, 1392-1394
50. Gaskell, T. F. The Structure of Braggite and Palladium Sulphide Z. Kristallogr. 1937, 96, 203-213
51. Wyckoff, R. W. G. Cystal Structures, 2 nd ed.; Wiley Interscience: New York, 1963; Vol. 1, pp 7-83.
52. Petkov, V. RAD, a Program for Analysis of X-Ray-Diffraction Data from Amorphous Materials for Personal Computers J. Appl. Crystallogr. 1989, 22, 387-389
53. Petkov, V. Nanostructure by High-Energy X-ray Diffraction Mater. Today 2008, 11, 28-38
54. Billinge, S. J. L.; Kanatzidis, M. G. beyond Crystallography: The Study of Disorder, Nanocrystallinity and Crystallographically Challenged Materials with Pair Distribution Functions Chem. Commun. 2004, 749-760
55. Petkov, V.; Ren, Y.; Kabekkodu, S.; Murphy, D. Atomic Pair Distribution Functions Analysis of Disordered Low-Z Materials Phys. Chem. Chem. Phys. 2013, 15, 8544-8554
56. Benmore, C. J.; Izdebski, T.; Yarger, J. L. Total X-ray Scattering of Spider Dragline Silk Phys. Rev. Lett. 2012, 108, 178102-178105
57. Gereben, O.; Jovari, P.; Temleitner, L.; Pusztai, L. A New Version of the RMC++ Reverse Monte Carlo Programme, Aimed at Investigating the Structure of Covalent Glasses J. Optoelectron. Adv. Mater. 2007, 9, 3021-3027
58. Bedford, N. M.; Bhandari, R.; Slocik, J. M.; Seifert, S.; Naik, R. R.; Knecht, M. R. Peptide-Modified Dendrimers as Templates for the Production of Highly Reactive Catalytic Nanomaterials Chem. Mater. 2014, 26, 4082-4091