Interaction of graphene-on-Al(111) composite with d -glucopyranose and its application in biodetection

Journal of Physical Chemistry C

Volumn 117, Issue 16, 2013, Pages 8475-8480

  Yang, Jun Wei ^a   Chen, Xiang Rong ^a   Song, Bo ^b  

^a SICHUAN UNIVERSITY   (China)

^b SHANGHAI INSTITUTE OF APPLIED PHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIODETECTION; D-GLUCOPYRANOSE; GLUCOPYRANOSE; HIGH-ACCURACY; ITS APPLICATIONS; POLAR GROUPS; STABLE ADSORPTION; STM TECHNIQUE;

ALUMINUM; BIOSENSORS; CARBOHYDRATES; CONFORMATIONS; MOLECULAR BIOLOGY; NANOSTRUCTURED MATERIALS; SCANNING TUNNELING MICROSCOPY;

GRAPHENE;

EID: 84876850221     PISSN: 19327447     EISSN: 19327455     Source Type: Journal    
DOI: 10.1021/jp311959g     Document Type: Article

References (51)

1. Lehmann, J. and Haines, A. H. Carbohydrates: Structure and Biology; Wiley-VCH: Weinheim, Germany, 2002.
2. Rao, V. S. R., Qasba, P. K., Balaji, P. V., and Chandrasekaran, R. Conformation of Carbohydrates; Harwood Academic Publishers: Amsterdam, The Netherlands, 1998.
3. Ionescu, A. R.; Berces, A.; Zgierski, M. Z.; Whitfield, D. M.; Nukada, T. Conformational Pathways of Saturated Six-Membered Rings. A Static and Dynamical Density Functional Study J. Phys. Chem. A 2005, 109, 8096-8105
4. Jebber, K. A.; Zhang, K.; Cassady, C. J.; ChungPhillips, A. Ab Initio and Experimental Studies on the Protonation of Glucose in the Gas Phase J. Am. Chem. Soc. 1996, 118, 10515-10524
5. Biarnes, X.; Ardevol, A.; Planas, A.; Rovira, C.; Laio, A.; Parrinello, M. The Conformational Free Energy Landscape of β- d -Glucopyranose. Implications for Substrate Preactivation in β -Glucoside Hydrolases J. Am. Chem. Soc. 2007, 129, 10686-10693
6. Dwek, R. A.; Edge, C. J.; Harvey, D. J.; Wormald, M. R.; Parekh, R. B. Analysis of Glycoprotein-Associated Oligosaccharides Annu. Rev. Biochem. 1993, 62, 65-100
7. Rice, K. G.; Wu, P. G.; Brand, L.; Lee, Y. C. Experimental-Determination of Oligosaccharide 3-Dimensional Structure Curr. Opin. Struct. Biol. 1993, 3, 669-674
8. Dwek, R. A. Glycobiology: Toward Understanding the Function of Sugars Chem. Rev. 1996, 96, 683-720
9. Davis, A. P.; Wareham, R. S. Carbohydrate Recognition through Noncovalent Interactions: A Challenge for Biomimetic and Supramolecular Chemistry Angew. Chem., Int. Ed. 1999, 38, 2978-2996
10. Rudiger, H.; Siebert, H. C.; Solis, D.; Jimenez-Barbero, J.; Romero, A.; Von der Lieth, C. W.; Diaz-Maurino, T.; Gabius, H. J. Medicinal Chemistry Based on the Sugar Code: Fundamentals of Lectinology and Experimental Strategies with Lectins as Targets Curr. Med. Chem. 2000, 7, 389-416
11. Wormald, M. R.; Petrescu, A. J.; Pao, Y. L.; Glithero, A.; Elliott, T.; Dwek, R. A. Conformational Studies of Oligosaccharides and Glycopeptides: Complementarity of NMR, X-Ray Crystallography, and Molecular Modelling Chem. Rev. 2002, 102, 371-386
12. Lowe, J. B.; Marth, J. D. A Genetic Approach to Mammalian Glycan Function Annu. Rev. Biochem. 2003, 72, 643-691
13. Tunnacliffe, A.; Lapinski, J. Resurrecting Van Leeuwenhoek's Rotifers: A Reappraisal of the Role of Disaccharides in Anhydrobiosis Philos. Trans. R. Soc. London, Ser. B 2003, 358, 1755-1771
14. Gabius, H. J.; Andre, S.; Kaltner, H.; Siebert, H. C. The Sugar Code: Functional Lectinomics Biochim. Biophys. Acta, Gen. Subj. 2002, 1572, 165-177
15. Hricovini, M. Structural Aspects of Carbohydrates and the Relation with Their Biological Properties Curr. Med. Chem. 2004, 11, 2565-2583
16. Gabius, H. J.; Siebert, H. C.; Andre, S.; Jimenez-Barbero, J.; Rudiger, H. Chemical Biology of the Sugar Code ChemBioChem 2004, 5, 740-764
17. Jimenez-Barbero, J.; Asensio, J. L.; Cuevas, G.; Canales, A.; Fernandez-Alonso, M. C.; Canada, F. J. Conformational Insights on the Molecular Recognition Processes of Carbohydrate Molecules by Proteins and Enzymes: A 3D View by Using NMR Biocatal. Biotransform. 2006, 24, 13-22
18. Ramesh, H. P.; Tharanathan, R. N. Carbohydrates-The Renewable Raw Materials of High Biotechnological Value Crit. Rev. Biotechnol. 2003, 23, 149-173
19. Mason, P. E.; Neilson, G. W.; Enderby, J. E.; Saboungi, M. L.; Cuello, G.; Brady, J. W. Neutron Diffraction and Simulation Studies of the Exocyclic Hydroxymethyl Conformation of Glucose J. Chem. Phys. 2006, 125, 224505
20. Da Costa, R. F.; Bettega, M. H. F.; Varella, M. T. D.; Lima, M. A. P. Electron Collisions with α- d -Glucose and β- d -Glucose Monomers J. Chem. Phys. 2010, 132, 124309
21. Stenger, J.; Cowman, M.; Eggers, F.; Eyring, E. M.; Kaatze, U.; Petrucci, S. Molecular Dynamics and Kinetics of Monosaccharides in Solution. A Broadband Ultrasonic Relaxation Study J. Phys. Chem. B 2000, 104, 4782-4790
22. CH Spin-Spin Coupling Constants J. Org. Chem. 2002, 67, 949-958
23. Rundlof, T.; Venable, R. M.; Pastor, R. W.; Kowalewski, J.; Widmalm, G. Distinguishing Anisotropy and Flexibility of the Pentasaccharide LNF-1 in Solution by Carbon-13 NMR Relaxation and Hydrodynamic Modeling J. Am. Chem. Soc. 1999, 121, 11847-11854
24. CCCCH as Probes of Exocyclic Hydroxymethyl Group Conformation in Saccharides J. Org. Chem. 2005, 70, 7542-7549
25. 13C NMR J -Couplings J. Am. Chem. Soc. 2004, 126, 15668-15685
26. 3,O Boats, and Skew-Boat Conformations Carbohydr. Res. 2004, 339, 537-551
27. Lins, R. D.; Hunenberger, P. H. A New GROMOS Force Field for Hexopyranose-Based Carbohydrates J. Comput. Chem. 2005, 26, 1400-1412
28. Hansen, H. S.; Hunenberger, P. H. A Reoptimized GROMOS Force Field for Hexopyranose-Based Carbohydrates Accounting for the Relative Free Energies of Ring Conformers, Anomers, Epimers, Hydroxymethyl Rotamers, and Glycosidic Linkage Conformers J. Comput. Chem. 2011, 32, 998-1032
29. Krautler, V.; Muller, M.; Hunenberger, P. H. Conformation, Dynamics, Solvation and Relative Stabilities of Selected β-Hexopyranoses in Water: A Molecular Dynamics Study with the GROMOs 45A4 Force Field Carbohydr. Res. 2007, 342, 2097-2124
30. Song, B.; Cuniberti, G.; Sanvito, S.; Fang, H. P. Nucleobase Adsorbed at Graphene Devices: Enhance Bio-sensorics Appl. Phys. Lett. 2012, 100, 063101
31. Artiles, M. S.; Rout, C. S.; Fisher, T. S. Graphene-Based Hybrid Materials and Devices For Biosensing Adv. Drug Delivery Rev. 2011, 63, 1352-1360
32. Reed, J. C.; Zhu, H.; Zhu, A. Y.; Li, C.; Cubukcu, E. Graphene-Enabled Silver Nanoantenna Sensors Nano Lett. 2012, 12, 4090-4094
33. Ge, C. C.; Du, J. F.; Zhao, L. H.; Wang, L. M.; Liu, Y.; Li, D. H.; Yang, Y. L.; Zhou, R. H.; Zhao, Y. L.; Chai, Z. F. Binding of Blood Proteins to Carbon Nanotubes Reduces Cytotoxicity Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 16968-16973
34. 22 and Its Implication for De Novo Design of Nanomedicine Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 15431-15436
35. Song, B.; Li, D.; Qi, W. P.; Elstner, M.; Fan, C. H.; Fang, H. P. Graphene on Au(111): A Highly Conductive Material with Excellent Adsorption Properties for High-Resolution Bio/Nanodetection and Identification ChemPhysChem 2010, 11, 585-589
36. Wu, L.; Chu, H. S.; Koh, W. S.; Li, E. P. Highly Sensitive Graphene Biosensors Based on Surface Plasmon Resonance Opt. Express 2010, 18, 14395-14400
37. Soler, J. M.; Artacho, E.; Gale, J. D.; Garcia, A.; Junquera, J.; Ordejon, P.; Sanchez-Portal, D. The SIESTA Method for Ab Initio Order-N Materials Simulation J. Phys.: Condens. Matter 2002, 14, 2745-2779
38. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868
39. Troullier, N.; Martins, J. L. Efficient Pseudopotentials for Plane-Wave Calculations Phys. Rev. B 1991, 43, 1993-2006
40. Kleinman, L.; Bylander, D. M. Efficacious Form for Model Pseudopotentials Phys. Rev. Lett. 1982, 48, 1425-1428
41. Sánchez-Portal, D.; Ordejon, P.; Artacho, E.; Soler, J. M. Density-Functional Method for Very Large Systems with LCAO Basis Sets Int. J. Quantum Chem. 1997, 65, 453-461
42. Hestenes, M. R.; Stiefel, E. Methods of Conjugate Gradients for Solving Linear Systems J. Res. Natl. Bur. Stand. 1952, 49, 409-436
43. Tougait, O.; Noel, H. Stoichiometry of UAl4 Intermetallics 2004, 12, 219-223
44. Shallenberger, R. S. Advanced Sugar Chemistry: Principles of Sugar Stereochemistry; AVI: Westport, CT, 1982.
45. Stoddart, J. F. Stereochemistry of Carbohydrates; Wiley-Interscience: New York, 1971.
46. Joshi, N. V.; Rao, V. S. R. Flexibility of the Pyranose Ring in α- d -Glucose and β- d -Glucose Biopolymers 1979, 18, 2993-3004
47. Machado Charry, F. E. First Principles Calculations of Surfaces and Layered Materials; Universitat Autònoma de Barcelona: Bellaterra, Spain, 2007.
48. Paz, O.; Soler, J. M. Efficient and Reliable Method for the Simulation of Scanning Tunneling Images and Spectra with Local Basis Sets Phys. Status Solidi B 2006, 243, 1080-1094
49. Tersoff, J.; Hamann, D. R. Theory and Application for the Scanning Tunneling Microscope Phys. Rev. Lett. 1983, 50, 1998-2001
50. Tersoff, J.; Hamann, D. R. Theory of the Scanning Tunneling Microscope Phys. Rev. B 1985, 31, 805-813
51. Bai, C. Scanning Tunneling Microscopy and Its Application; Springer Verlag: New York, 2000.