Molecular logic and computing

Nature Nanotechnology

Volumn 2, Issue 7, 2007, Pages 399-410

  De Silva, A Prasanna ^a   Uchiyama, Seiichi ^b  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL OPERATIONS; COMPUTATION THEORY; OBJECT RECOGNITION;

APPLICATION AREA; COMPUTATIONAL DEVICES; COMPUTING INDUSTRY; INFORMATION HANDLING; INTELLIGENT DIAGNOSTICS; LOGIC OPERATIONS; LOGICAL OPERATORS; MOLECULAR SUBSTRATES;

COMPUTER CIRCUITS;

ARITHMETIC; BIOMEDICINE; BIOSENSOR; CHEMICAL INDUSTRY; CHEMICAL PHENOMENA; CHEMICAL REACTION; DEVICE; ELECTRON TRANSPORT; INFORMATION PROCESSING; INTEGRATION; LOGIC; MATHEMATICAL COMPUTING; MOLECULAR COMPUTER; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NANOTECHNOLOGY; PARTICLE SIZE; PRIORITY JOURNAL; REVIEW; SEMICONDUCTOR; SIGNAL TRANSDUCTION;

EID: 34447275457     PISSN: 17483387     EISSN: 17483395     Source Type: Journal    
DOI: 10.1038/nnano.2007.188     Document Type: Review

References (103)

1. Raymo, F. M. Digital processing and communication with molecular switches. Adv. Mater. 14, 401-414 (2002).
2. Margulies, D. Felder, C. E., Melman, G. & Shanzer, A. A molecular keypad lock: a photochemical device capable of authorizing password entries. J. Am. Chem. Soc. 129, 347-354 (2007).
3. Boole, G. An Investigation of the Laws of Thought (Dover, New York, 1958).
4. Malvino, A. P. & Brown, J. A. Digital Computer Electronics 3rd edn (Glencoe, New York, 1993).
5. Bray, D. Protein molecules as computational elements in living cells. Nature 376, 307-312 (1995).
6. Williams, K. A. Three-dimensional structure of the ion-coupled transport protein NhaA. Nature 403, 112-115 (2000).
7. Lehn, J.-M. Supramolecular Chemistry (VCH, Weinheim, 1995).
8. Collier, C. P. et al. Electronically configurable molecular-based logic gates. Science 285, 391-394 (1999).
9. Amir, R. J., Popkov, M., Lerner, R. A., Barbas III, C. F. & Shabat, D. Prodrug activation gated by a molecular "OR" logic trigger. Angew. Chem. Int. Edn 44, 4378-4381 (2005).
10. 2+ indicators with greatly improved fluorescence properties. J. Biol. Chem. 260, 3440-3450 (1985).
11. Holman, M. W. & Adams, D. M. Using single-molecule fluorescence spectroscopy to study electron transfer. ChemPhysChem 5, 1831-1836 (2004).
12. Uchiyama, S., McClean, G. D., Iwai, K. & de Silva, A. P. Membrane media create small nanospaces for molecular computation. J. Am. Chem. Soc. 127, 8920-8921 (2005).
13. Drexler, K. E. Engines of Creation (Anchor Press, New York, 1986).
14. de Silva, A. P., Gunaratne, H. Q. N. & McCoy, C. P. A molecular photoionic AND gate based on fluorescent signalling. Nature 364, 42-44 (1993).
15. Bissell, R. A. et al. Fluorescent PET (photoinduced electron transfer) sensors. Top. Curr. Chem. 168, 223-264 (1993).
16. Komura, T., Niu, G. Y., Yamaguchi, T. & Asano, M. Redox and ionic-binding switched fluorescence of phenosafranine and thionine included in Nafion® films. Electrochim. Acta 48, 631-639 (2003).
17. Szaciłowski, K., Macyk, W. & Stochel, G. Light-driven OR and XOR programmable chemical logic gates. J. Am. Chem. Soc. 128, 4550-4551 (2006).
18. Biancardo, M., Bignozzi, C., Doyle, H. & Redmond, G. A potential and ion switched molecular photonic logic gate. Chem. Commun. 3918-3920 (2005).
19. Matsui, J., Mitsuishi, M., Aoki, A. & Miyashita, T. Molecular optical gating devices based on polymer nanosheets assemblies. J. Am. Chem. Soc. 126, 3708-3709 (2004).
20. Yurke, B., Mills Jr., A. P. & Cheng, S. L. DNA implementation of addition in which the input strands are separate from the operator strands. Biosystems 52, 165-174 (1999).
21. Schneider, H.-J., Tianjun, L., Lomadze, N. & Palm, B. Cooperativity in a chemomechanical polymer: a chemically induced macroscopic logic gate. Adv. Mater. 16, 613-615 (2004).
22. Okamoto, A., Tanaka, K. & Saito, I. DNA logic gates. J. Am. Chem. Soc. 126, 9458-9463 (2004).
23. Ashkenasy, G. & Ghadiri, M. R. Boolean logic functions of a synthetic peptide network. J. Am. Chem. Soc. 126, 11140-11141 (2004).
24. Blittersdorf, R., Müller, J. & Schneider, F. W. Chemical visualization of Boolean functions: a simple chemical computer. J. Chem. Educ. 72, 760-763 (1995).
25. Raymo, F. M. & Giordani, S. All-optical processing with molecular switches. Proc. Natl. Acad. Sci. USA 99, 4941-4944 (2002).
26. Szaciłowski, K. Molecular logic gates based on pentacyanoferrate complexes: from simple gates to three-dimensional logic systems. Chem. Eur. J. 10, 2520-2528 (2004).
27. de Silva, A. P. et al. Signaling recognition events with fluorescent sensors and switches. Chem. Rev. 97, 1515-1566 (1997).
28. Balzani, V., Credi, A. & Venturi, M. Molecular Devices and Machines (Wiley-VCH, Weinheim, 2003).
29. de Silva, A. P. & McClenaghan, N. D. Molecular-scale logic gates. Chem. Eur. J. 10, 574-586 (2004).
30. de Silva, A. P. & McClenaghan, N. D. Simultaneously multiply-configurable or superposed molecular logic systems composed of ICT (internal charge transfer) chromophores and fluorophores integrated with one- or two-ion receptors. Chem. Eur. J. 8, 4935-4945 (2002).
31. de Silva, A. P. & McClenaghan, N. D. Proof-of-principle of molecular-scale arithmetic. J. Am. Chem. Soc. 122, 3965-3966 (2000).
32. Zhou, Y., Zhang, D., Zhang, Y., Tang, Y. & Zhu, D. Tuning the CD spectrum and optical rotation value of a new binaphthalene molecule with two spiropyran units: mimicking the function of a molecular "AND" logic gate and a new chiral molecular switch. J. Org. Chem. 70, 6164-6170 (2005).
33. Tamaki, T. & Ichimura, K. Photochromic chelating spironaphthoxazines. J. Chem. Soc., Chem. Commun. 1477-1479 (1989).
34. Gobbi, L., Seiler, P. & Diederich, F. A novel three-way chromophoric molecular switch: pH and light controllable switching cycles. Angew. Chem. Int. Edn 38, 674-678 (1999).
35. Wojtyk, J. T. C., Kazmaier, P. M. & Buncel, E. Effects of metal ion complexation on the spiropyran-merocyanine interconversion: development of a thermally stable photo-switch. Chem. Commun. 1703-1704 (1998).
36. Raymo, F. M. & Giordani, S. Multichannel digital transmission in an optical network of communicating molecules. J. Am. Chem. Soc. 124, 2004-2007 (2002).
37. Baron, R., Lioubashevski, O., Katz, E., Niazov, T. & Willner, I. Two coupled enzymes perform in parallel the 'AND' and 'InhibAND' logic gate operations. Org. Biomol. Chem. 4, 989-991 (2006).
38. Baron, R., Lioubashevski, O., Katz, E., Niazov, T. & Willner, I. Elementary arithmetic operations by enzymes: a model for metabolic pathway based computing. Angew. Chem. Int. Edn 45, 1572-1576 (2006).
39. Zauner, K.-P. & Conrad, M. Enzymatic Computing. Biotechnol. Prog. 17, 553-559 (2001).
40. Deonarine, A. S., Clark, S. M. & Konermann, L. Implementation of a multifunctional logic gate based on folding/unfolding transitions of a protein. Future Gener. Comp. Sy. 19, 87-97 (2003).
41. Sivan, S., Tuchman, S. & Lotan, N. A biochemical logic gate using an enzyme and its inhibitor. Part II: The logic gate. BioSystems 70, 21-33 (2003).
42. Adleman, L. M. Molecular computation of solutions to combinatorial problems. Science 266, 1021-1024 (1994).
43. Stojanovic, M. N., Mitchell, T. E. & Stefanovic, D. Deoxyribozyme-based logic gates. J. Am. Chem. Soc. 124, 3555-3561 (2002).
44. Hod, O., Baer, R. & Rabani, E. A parallel electromagnetic molecular logic gate. J. Am. Chem. Soc. 127, 1648-1649 (2005).
45. Tour, J. M. in Stimulating Concepts in Chemistry (eds. Vögtle, F. Stoddart, J. F. & Shibasaki, M.) 237-253 (Wiley-VCH, Weinheim, 2000).
46. Kele, P., Orbulescu, J., Gawley, R. E. & Leblanc, R. M. Spectroscopic detection of saxitoxin: An alternative to mouse bioassay. Chem. Commun. 1494-1496 (2006).
47. 2 chelated azadipyrromethene platform. Org. Biomol. Chem. 4, 776-780 (2006).
48. 2+ . J. Am. Chem. Soc. 127, 10107-10111 (2005).
49. Yoon, S., Albers, A. E., Wong, A. P. & Chang, C. J. Screening mercury levels in fish with a selective fluorescent chemosensor. J. Am. Chem. Soc. 127, 16030-16031 (2005).
50. Banthia, S. & Samanta, A. A two-dimensional chromogenic sensor as well as fluorescence inverter: selective detection of copper(II) in aqueous medium. New J. Chem. 29, 1007-1010 (2005).
51. Dale, T. J. & Rebek Jr., J. Fluorescent sensors for organophosphorus nerve agent mimics. J. Am. Chem. Soc. 128, 4500-4501 (2006).
52. Bencic-Nagale, S., Sternfeld, T. & Walt, D. R. Microbead chemical switches: An approach to detection of reactive organophosphate chemical warfare agent vapors. J. Am. Chem. Soc. 128, 5041-5048 (2006).
53. de Silva, A. P., Gunaratne, H. Q. N. & Gunnlaugsson, T. Fluorescent PET (photoinduced electron transfer) reagents for thiols. Tetrahedron Lett. 39, 5077-5080 (1998).
54. Cooper, C. R. & James, T. D. Selective D-glucosamine hydrochloride fluorescence signalling based on ammonium cation and diol recognition. Chem. Commun. 1419-1420 (1997).
55. Fages, F. et al. Synthesis and fluorescence emission properties of a bis-anthracenyl macrotricyclic ditopic receptor. Crystal structure of its dinuclear rubidium cryptate. J. Chem. Soc., Chem. Commun. 655-658 (1990).
56. de Silva, A. P. & Sandanayake, K. R. A. S. Fluorescence "off -on" signalling upon linear recognition and binding of α,ω- alkanediyldiammonium ions by 9,10-bis{(1-aza-4,7,10,13,16-pentaoxacycloocta decyl)methyl}anthracene. Angew. Chem. Int. Edn Engl. 29, 1173-1175 (1990).
57. Misumi, S. Recognitory coloration of cations with chromoacerands. Top. Curr. Chem. 165, 163-192 (1993).
58. Secor, K., Plante, J., Avetta, C. & Glass, T. Fluorescent sensors for diamines. J. Mater. Chem. 15, 4073-4077 (2005).
59. Zhao, J., Fyles, T. M. & James, T. D. Chiral binol-bisboronic acid as fluorescence sensor for sugar acids. Angew. Chem. Int. Edn 43, 3461-3464 (2004).
60. James, T. D., Sandanayake, K. R. A. S. & Shinkai, S. Chiral discrimination of monosaccharides using a fluorescent molecular sensor. Nature 374, 345-347 (1995).
61. Gray Jr., C. W. & Houston, T. A. Boronic acid receptors for α-hydroxycarboxylates: high affinity of Shinkai's glucose receptor for tartrate. J. Org. Chem. 67, 5426-5428 (2002).
62. He, J. X. et al. Metal-free silicon-molecule-nanotube testbed and memory device. Nature Mater. 5, 63-68 (2006).
63. de Silva, A. P. et al. Integration of logic functions and sequential operation of gates at the molecular-scale. J. Am. Chem. Soc. 121, 1393-1394 (1999).
64. Mu, L. X., Wang, Y., Zhang, Z. & Jin, W. J. Room temperature phosphorescence pH switch based on photo-induced electron transfer. Chinese Chem. Lett. 15, 1131-1134 (2004).
65. de Sousa, M., de Castro, B., Abad, S., Miranda, M. A. & Pischel, U. A molecular tool kit for the variable design of logic operations (NOR, INH, EnNOR). Chem. Commun. 2051-2053 (2006).
66. Cheng, P.-N., Chiang, P.-T. & Chiu, S.-H. A switchable macrocycle-clip complex that functions as a NOR logic gate. Chem. Commun. 1285-1287 (2005).
67. Giordani, S., Cejas, M. A. & Raymo, F. M. Photoinduced proton exchange between molecular switches. Tetrahedron 60, 10973-10981 (2004).
68. Margulies, D., Melman, G. & Shanzer, A. Fluorescein as a model molecular calculator with reset capability. Nature Mater. 4, 768-771 (2005).
69. Shiraishi, Y., Tokitoh, Y. & Hirai, T. A fluorescent molecular logic gate with multiply-configurable dual outputs. Chem. Commun. 5316-5318 (2005).
70. Alves, S. et. al. Open-chain polyamine ligands bearing an anthracene unit-chemosensors for logic operations at the molecular level. Eur. J. Inorg. Chem. 405-412 (2001).
71. 2+ -driven AND logic operations. Chem. Commun. 2048-2049 (2004).
72. Qu, D.-H., Wang, Q.-C. & Tian, H. A half adder based on a photochemically driven [2]rotaxane. Angew. Chem. Int. Edn 44, 5296-5299 (2005).
73. Andréasson, J. et al. Molecule-based photonically switched half-adder. J. Am. Chem. Soc. 126, 15926-15927 (2004).
74. Lederman, H., Macdonald, J., Stefanovic, D. & Stojanovic, M. N. Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Biochemistry 45, 1194-1199 (2006).
75. Guo, X., Zhang, D., Zhang, G. & Zhu, D. Monomolecular logic: "half-adder" based on multistate/multifunctional photochromic spiropyrans. J. Phys. Chem. B 108, 11942-11945 (2004).
76. Stojanovic, M. N. & Stefanovic, D. A deoxyribozyme-based molecular automaton. Nature Biotechnol. 21, 1069-1074 (2003).
77. Wild, U. P., Bernet, S., Kohler, B. & Renn, A. From supramolecular photochemistry to the molecular computer. Pure Appl. Chem. 64, 1335-1342 (1992).
78. Margulies, D., Melman, G. & Shanzer, A. A molecular full-adder and full-subtractor, an additional step toward a moleculator. J. Am. Chem. Soc. 128, 4865-4871 (2006).
79. Tour, J. M. Molecular electronics. Synthesis and testing of components. Acc. Chem. Res. 33, 791-804 (2000).
80. Williams, R. S., quoted in Ball, P. Chemistry meets computing. Nature 406, 118-120 (2000).
81. Cox, J. C., Cohen, D. S. & Ellington, A. D. The complexities of DNA computation. Trends Biotechnol. 17, 151-154 (1999).
82. Lam, K. S. et al. A new type of synthetic peptide library for identifying ligand-binding activity. Nature 354, 82-84 (1991).
83. Furka, Á., Sebestyén, F., Asgedom, M. & Dibó, G. General-method for rapid synthesis of multicomponent peptide mixtures. Int. J. Pept. Prot. Res. 37, 487-493 (1991).
84. Shepard, S. RFID: Radio Frequency Identification (McGraw-Hill, New York, 2005).
85. Nicolaou, K. C., Xiao, X.-Y., Parandoosh, Z., Senyei, A. & Nova, M. P. Radiofrequency encoded combinatorial chemistry. Angew. Chem. Int. Edn Engl. 34, 2289-2291 (1995).
86. Moran, E. J. et al. Radio frequency tag encoded combinatorial library method for discovery of tripeptide-substituted cinnamic acid inhibitors of the protein tyrosine phosphatase PTP1B. J. Am. Chem. Soc. 117, 10787-10788 (1995).
87. Walt, D. R. Bead-based fiber-optic arrays. Science 287, 451-452 (2000).
88. Battersby, B. J., Lawrie, G. A., Johnston, A. P. R. & Trau, M. Optical barcoding of colloidal suspensions: applications in genomics, proteomics and drug discovery. Chem. Commun. 1435-1441 (2002).
89. de Silva, A. P., James, M. R., McKinney, B. O. F., Pears, P. A. & Weir, S. M. Molecular computational elements encode large populations of small objects. Nature Mater. 5, 787-790 (2006).
90. Hayes, B. Third base. Am. Scientist 89, 490-494 (2001).
91. Callan, J. F., de Silva, A. P., Ferguson, J., Huxley, A. J. M. & O'Brien, A. M. Fluorescent photoionic devices with two receptors and two switching mechanisms: applications to pH sensors and implications for metal ion detection. Tetrahedron 60, 11125-11131 (2004).
92. Magri, D. C., Brown, G. J., McClean, G. D. & de Silva, A. P. Communicating chemical congregation: a molecular AND logic gate with three chemical inputs as a "lab-on-a-molecule" prototype. J. Am. Chem. Soc. 128, 4950-4951 (2006).
93. Gunnlaugsson, T., Lee, T. C. & Parkesh, R. A highly selective and sensitive fluorescent PET (photoinduced electron transfer) chemosensor for Zn(II). Org. Biomol. Chem. 1, 3265-3267 (2003).
94. Lankshear, M. D., Cowley, A. R. & Beer, P. D. Cooperative AND receptor for ion-pairs. Chem. Commun. 612-614 (2006).
95. Koskela, S. J. M., Fyles, T. M. & James, T. D. A ditopic fluorescent sensor for potassium fluoride. Chem. Commun. 945-947 (2005).
96. Saghatelian, A., Völcker, N. H., Guckian, K. M., Lin, V. S.-Y. & Ghadiri, M. R. DNA-based photonic logic gates: AND, NAND, and INHIBIT. J. Am. Chem. Soc. 125, 346-347 (2003).
97. Gust, D., Moore, T. A. & Moore, A. L. Molecular switches controlled by light. Chem. Commun. 1169-1178 (2006).
98. Pina, F. et al. Multistate/multifunctional molecular-level systems: light and pH switching between the various forms of a synthetic flavylium salt. Chem. Eur. J. 4, 1184-1191 (1998).
99. Uchiyama, S., Kawai, N., de Silva, A. P. & Iwai, K. Fluorescent polymeric AND logic gate with temperature and pH as inputs. J. Am. Chem. Soc. 126, 3032-3033 (2004).
100. Leigh, D. A. et al. Patterning through controlled submolecular motion: rotaxane-based switches and logic gates that function in solution and polymer films. Angew. Chem. Int. Edn 44, 3062-3067 (2005).
101. Penchovsky, R. & Breaker, R. R. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nature Biotechnol. 23, 1424-1433 (2005).
102. Remacle, F., Speiser, S. & Levine, R. D. Intermolecular and intramolecular logic gates. J. Phys. Chem. B 105, 5589-5591 (2001).
103. Remacle, F., Weinkauf, R. & Levine, R. D. Molecule-based photonically switched half and full adder. J. Phys. Chem. A 110, 177-184 (2006).