Please wait a minute...
Frontiers of Chemical Science and Engineering

ISSN 2095-0179

ISSN 2095-0187(Online)

CN 11-5981/TQ

Postal Subscription Code 80-969

2018 Impact Factor: 2.809

Front. Chem. Sci. Eng.    2014, Vol. 8 Issue (2) : 240-251    https://doi.org/10.1007/s11705-014-1432-z
REVIEW ARTICLE
Information gathering and processing with fluorescent molecules
Brian DALY, Jue LING, A. Prasanna de SILVA()
School of Chemistry and Chemical Engineering, Queen’s University, Belfast BT9 5AG, Northern Ireland
 Download: PDF(329 KB)   HTML
 Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks
Abstract

Molecular information gathering and processing — a young field of applied chemistry — is undergoing good growth. The progress is occurring both in terms of conceptual development and in terms of the strengthening of older concepts with new examples. This review critically surveys these two broad avenues. We consider some cases where molecules emulate one of the building blocks of electronic logic gates. We then examine molecular emulation of various Boolean logic gates carrying one, two or three inputs. Some single-input gates are popular information gathering devices. Special systems, such as ‘lab-on-a-molecule’ and molecular keypad locks, also receive attention. A situation deviating from the Boolean blueprint is also discussed. Some pointers are offered for maintaining the upward curve of the field.

Keywords molecular logic      molecular computation      molecular sensor      fluorescent molecular device      fluorescent sensor     
Corresponding Author(s): A. Prasanna de SILVA   
Issue Date: 22 May 2014
 Cite this article:   
Brian DALY,Jue LING,A. Prasanna de SILVA. Information gathering and processing with fluorescent molecules[J]. Front. Chem. Sci. Eng., 2014, 8(2): 240-251.
 URL:  
https://academic.hep.com.cn/fcse/EN/10.1007/s11705-014-1432-z
https://academic.hep.com.cn/fcse/EN/Y2014/V8/I2/240
Fig.1  Molecular structure of compounds 1 and 2
Fig.2  Molecular structure of compounds 3, 4, and 5
Fig.3  Molecular structure of compounds 6, 7, and 8
Fig.4  Molecular structure of compounds 9 and 10
Fig.5  Molecular structure of compounds 11, 12, and 13
Fig.6  Molecular structure of compound 14
Fig.7  Molecular structure of compound 15
  Photo: (from left) Brian Daly, Jue Ling and AP de Silva
1 A P de Silva, H Q N Gunaratne, C P McCoy. A molecular photoionic AND gate based on fluorescent signalling. Nature, 1993, 364(6432): 42–44
2 V Balzani, M Venturi, A Credi. Molecular Devices and Machines. 2nd ed. Weinheim: Wiley-VCH, 2008
3 E Katz. Molecular and Supramolecular Information Processing: from Molecular Switches to Logic Systems. Weinheim: Wiley-VCH, 2012
4 E Katz. Biomolecular Information Processing: from Logic Systems to Smart Sensors and Actuators. Weinheim: Wiley-VCH, 2012
5 K Szacilowski. Infochemistry: Information Processing at the Nanoscale. Chichester: Wiley, 2012
6 B Feringa, W S Browne. Molecular Switches. 2nd ed. Wiley-VCH, Weinheim, 2012
7 A P de Silva. Molecular Logic-based Computation. Cambridge: Royal Society of Chemistry, 2012
8 A P de Silva, N D McClenaghan, C P McCoy. Logic gates. In: V Balzani, ed. Electron Transfer in Chemistry, Vol 5. Weinheim: Wiley-VCH, 2001, 156
9 F M Raymo. Digital processing and communication with molecular switches. Advanced Materials, 2002, 14(6): 401–414
10 A P de Silva, N D McClenaghan. Molecular-scale logic gates. Chemistry, 2004, 10(3): 574–586
11 A P de Silva, Y Leydet, C Lincheneau, N D McClenaghan. Chemical approaches to nanometre-scale logic gates. Journal of Physics Condensed Matter, 2006, 18(33): S1847–S1872
12 A P de Silva, S Uchiyama. Molecular logic and computing. Nature Nanotechnology, 2007, 2(7): 399–410
13 Y Benenson. Biocomputers: from test tubes to live cells. Molecular BioSystems, 2009, 5(7): 675–685
14 E Katz, V Privman. Enzyme-based logic systems for information processing. Chemical Society Reviews, 2010, 39(5): 1835–1857
15 H Tian. Data processing on a unimolecular platform. Angewandte Chemie International Edition, 2010, 49(28): 4710–4712
16 U Pischel, J Andréasson, D Gust, V F Pais. Information processing with molecules — Quo vadis? ChemPhysChem, 2013, 14(1): 28–46
17 R A Bissell, A P de Silva. Phosphorescent PET (photoinduced electron transfer) sensors: Prototypical examples for proton monitoring and a ‘message in a bottle’ enhancement strategy with cyclodextrins. Journal of the Chemical Society: Chemical Communications, 1991, 17(17): 1148–1150
18 A J Bryan, A P de Silva, S A de Silva, R A D Rupasinghe, K R A Sandanayake. Photo-induced electron transfer as a general design logic for fluorescent molecular sensors for cations. Biosensors, 1989, 4(3): 169–179
19 C Gell, D Brockwell, A Smith. Handbook of Single Molecule Fluorescence Spectroscopy. New York: Oxford University Press, 2006
20 J Gregg. Ones and Zeros: Understanding Boolean Algebra, Digital Circuits, and the Logic of Sets. Wiley-IEEE Press, 1998
21 A P Malvino, J A Brown. Digital Computer Electronics, Glencoe. 3rd ed. Lake Forest, 1993
22 C Maxfield. Bebop to the Boolean Boogie: An Unconventional Guide to Electronics. Massachusetts: Newnes, 2008
23 M Ben-Ari. Mathematical Logic for Computer Science. Hemel Hempstead: Prentice-Hall, 1993
24 E Hughes. Electrical Technology. 6th ed. Burnt Mill: Longman, 1990
25 A E Keirstead, J W Bridgewater, Y Terazono, G Kodis, S Straight, P A Liddell, A L Moore, T A Moore, D Gust. Photochemical “triode” molecular signal transducer. Journal of the American Chemical Society, 2010, 132(18): 6588–6595
26 G Copley, T A Moore, A L Moore, D Gust. Analog applications of photochemical switches. Advanced Materials, 2013, 25(3): 456–461
27 M Irie. Diarylethenes for memories and switches. Chemical Reviews, 2000, 100(5): 1685–1716
28 A J M Huxley, M Schroeder, H Q N Gunaratne, A P de Silva. Modification of fluorescent photoinduced electron transfer (PET) sensors/switches to produce molecular photoionic triode action. Angewandte Chemie, 2014, 126(14): 3696–3699
29 J F Callan, A P de Silva, J Ferguson, A J Huxley, A M O'Brien. Fluorescent photoionic devices with two receptors and two switching mechanisms: Applications to pH sensors and implications for metal ion detection. Tetrahedron, 2004, 60(49): 11125–11131
30 A P de Silva, H Q N Gunaratne, K R A S Sandanayake. A new benzo-annelated cryptand and a derivative with alkali cation-sensitive fluorescence. Tetrahedron Letters, 1990, 31(36): 5193–5196
31 A P de Silva, H Q Gunaratne, T Gunnlaugsson, A J Huxley, C P McCoy, J T Rademacher, T E Rice. Signaling recognition events with fluorescent sensors and switches. Chemical Reviews, 1997, 97(5): 1515–1566
32 E Bishop. Indicators. Oxford: Pergamon, 1972
33 A P de Silva, H Q N Gunaratne, P L M Lynch, A J Patty, G L Spence. Luminescence and charge transfer. Part 3. The use of chromophores with ICT (internal charge transfer) excited states in the construction of fluorescent PET (photoinduced electron transfer) pH sensors and related absorption pH sensors with aminoalkyl side chains. Journal of the Chemical Society, Perkin Transactions 2: Physical Organic Chemistry, 1993, (9): 1611–1616
34 A P de Silva, T P Vance, M E S West, G D Wright. Bright molecules with sense, logic, numeracy and utility. Organic & Biomolecular Chemistry, 2008, 6(14): 2468–2480
35 P Avouris, Z Chen, V Perebeinos. Carbon-based electronics. Nature Nanotechnology, 2007, 2(10): 605–615
36 A Bachtold, P Hadley, T Nakanishi, C Dekker. Logic circuits with carbon nanotube transistors. Science, 2001, 294(5545): 1317–1320
37 B Wang, E V Anslyn. Chemosensors: Principles, Strategies, and Applications. John Wiley & Sons, 2011
38 S Ast, T Schwarze, H Müller, A Sukhanov, S Michaelis, J Wegener, O S Wolfbeis, T Körzdörfer, A Dürkop, H J Holdt. A highly K+-selective phenylaza-[18] crown-6-lariat-ether-based fluoroionophore and its application in the sensing of K+ ions with an optical sensor film and in cells. Chemistry, 2013, 19(44): 14911–14917
39 R A Schultz, B D White, D M Dishong, K A Arnold, G W Gokel. 12-, 15-, and 18-Membered-ring nitrogen-pivot lariat ethers: Syntheses, properties, and sodium and ammonium cation binding properties. Journal of the American Chemical Society, 1985, 107(23): 6659–6668
40 S Zheng, P L M Lynch, T E Rice, T S Moody, H Q Gunaratne, A P de Silva. Structural effects on the pH-dependent fluorescence of naphthalenic derivatives and consequences for sensing/switching. Photochemical & Photobiological Sciences, 2012, 11(11): 1675–1681
41 Z R Grabowski, J Dobkowski. Twisted intramolecular charge transfer (TICT) excited states: Energy and molecular structure. Pure and Applied Chemistry, 1983, 55(2): 245–252
42 P Batat, G Vives, R Bofinger, R W Chang, B Kauffmann, R Oda, G Jonusauskas, N D McClenaghan. Dynamics of ion-regulated photoinduced electron transfer in BODIPY-BAPTA conjugates. Photochemical & Photobiological Sciences, 2012, 11(11): 1666–1674
43 H He, M A Mortellaro, M J P Leiner, S T Young, R J Fraatz, J K Tusa. A fluorescent chemosensor for sodium based on photoinduced electron transfer. Analytical Chemistry, 2003, 75(3): 549–555
44 H He, M A Mortellaro, M J P Leiner, R J Fraatz, J K Tusa. A fluorescent sensor with high selectivity and sensitivity for potassium in water. Journal of the American Chemical Society, 2003, 125(6): 1468–1469
45 J K Tusa, H He. Critical care analyzer with fluorescent optical chemosensors for blood analytes. Journal of Materials Chemistry, 2005, 15(27–28): 2640–2647
46 H He, K Jenkins, C Lin. A fluorescent chemosensor for calcium with excellent storage stability in water. Analytica Chimica Acta, 2008, 611(2): 197–204
47 A P de Silva, H Q N Gunaratne, J L Habib-Jiwan, C P McCoy, T E Rice, J P Soumillion. New fluorescent model compounds for the study of photoinduced electron transfer: the influence of a molecular electric field in the excited state. Angewandte Chemie International Edition, 1995, 34(16): 1728–1731
48 The opitimedical website
49 A P de Silva, H Q N Gunaratne, T Gunnlaugsson. Fluorescent PET (photoinduced electron transfer) reagents for thiols. Tetrahedron Letters, 1998, 39(28): 5077–5080
50 H Kojima, T Nagano. Fluorescent indicators for nitric oxide. Advanced Materials, 2000, 12(10): 763–765
51 M J Plater, I Greig, M H Helfrich, S H Ralston. The synthesis and evaluation of o-phenylenediamine derivatives as fluorescent probes for nitric oxide detection. Journal of the Chemical Society, Perkin Transactions 1: Organic and Bio-Organic Chemistry, 2001, (20): 2553–2559
52 T D James, M D Phillips, S Shinkai. Boronic Acids in Saccharide Recognition. Royal Society of Chemistry, 2006
53 R A Bissell, A J Bryan, A P de Silva, C P McCoy. PET Fluorescent sensors with targeting/anchoring modules as molecular versions of submarine periscopes for mapping membrane-bounded protons. Journal of the Chemical Society: Chemical Communications, 1994, (4): 405–407
54 S Uchiyama, K Iwai, A P de Silva. Multiplexing sensory molecules map protons near micellar membranes. Angewandte Chemie International Edition, 2008, 47(25): 4667–4669
55 F M Harold. The Vital Force: A Study of Bioenergetics. New York: WH Freeman, 1986
56 V K Bhardwaj, M S Hundal, G Hundal. A tripodal receptor bearing catechol groups for the chromogenic sensing of F– ions via frozen proton transfer. Tetrahedron, 2009, 65(41): 8556–8562
57 K J Winstanley, A M Sayer, D K Smith. Anion binding by catechols — an NMR, optical and electrochemical study. Organic & Biomolecular Chemistry, 2006, 4(9): 1760–1767
58 A P de Silva, G D McClean, S Pagliari. Direct detection of ion pairs by fluorescence enhancement. Chemical Communications, 2003, (16): 2010–2011
59 S J M Koskela, T M Fyles, T D James. A ditopic fluorescent sensor for potassium fluoride. Chemical Communications, 2005, (7): 945–947
60 M Alfonso, A Espinosa, A Tárraga, P Molina. A simple but effective dual redox and fluorescent ion pair receptor based on a ferrocene-imidazopyrene dyad. Organic Letters, 2011, 13(8): 2078–2081
61 A J Moro, P J Cywinski, S Körsten, G J Mohr. An ATP fluorescent chemosensor based on a Zn(II)-complexed dipicolylamine receptor coupled with a naphthalimide chromophore. Chemical Communications, 2010, 46(7): 1085–1087
62 A P de Silva, H Q N Gunaratne, C McVeigh, G E M Maguire, P R S Maxwell, E O’Hanlon. Fluorescent signalling of the brain neurotransmitter γ-aminobutyric acid and related amino acid zwitterions. Chemical Communications, 1996, (18): 2191–2192
63 D Karak, S Das, S Lohar, A Banerjee, A Sahana, I Hauli, S K Mukhopadhyay, D A Safin, M G Babashkina, M Bolte, Y Garcia, D Das. A naphthalene-thiophene hybrid molecule as a fluorescent AND logic gate with Zn2+ and OAc- ions as inputs: cell imaging and computational studies. Dalton Transactions, 2013, 42(19): 6708–6715
64 T J Farrugia, D C Magri. ‘Pourbaix sensors’: A new class of fluorescent pE–pH molecular AND logic gates based on photoinduced electron transfer. New Journal of Chemistry, 2012, 37(1): 148–151
65 D C Magri. A fluorescent and logic gate driven by electrons and protons. New Journal of Chemistry, 2009, 33(3): 457–461
66 M Pourbaix. Atlas of Electrochemical Equilibria in Aqueous Solutions. Oxford: Pergamon Press, 1966
67 J H Bu, Q Y Zheng, C F Chen, Z T Huang. New fluorescence-quenching process through resumption of PET process induced by complexation of alkali metal ion. Organic Letters, 2004, 6(19): 3301–3303
68 G Nishimura, K Ishizumi, Y Shiraishi, T Hirai. A triethylenetetramine bearing anthracene and benzophenone as a fluorescent molecular logic gate with either-or switchable dual logic functions. The Journal of Physical Chemistry B, 2006, 110(43): 21596–21602
69 J M Montenegro, E Perez-Inestrosa, D Collado, Y Vida, R Suau. A natural-product-inspired photonic logic gate based on photoinduced electron-transfer-generated dual-channel fluorescence. Organic Letters, 2004, 6(14): 2353–2355
70 S Banthia, A Samanta. Multiple logical access with a single fluorophore-spacer-receptor system: Realization of inhibit (INH) logic function. European Journal of Organic Chemistry, 2005, 2005(23): 4967–4970
71 T Gunnlaugsson, D A Mac Dónaill, D Parker. Lanthanide macrocyclic quinolyl conjugates as luminescent molecular-level devices. Journal of the American Chemical Society, 2001, 123(51): 12866–12876
72 M de Sousa, M Kluciar, S Abad, M A Miranda, B de Castro, U Pischel. An inhibit (INH) molecular logic gate based on 1,8-naphthalimide-sensitised europium luminescence. Photochemical & Photobiological Sciences, 2004, 3(7): 639–642
73 J S Park, E Karnas, K Ohkubo, P Chen, K M Kadish, S Fukuzumi, C W Bielawski, T W Hudnall, V M Lynch, J L Sessler. Ion-mediated electron transfer in a supramolecular donor-acceptor ensemble. Science, 2010, 329(5997): 1324–1327
74 K Kaur, V K Bhardwaj, N Kaur, N Singh. Fluorescent primary sensor for zinc and resultant complex as secondary sensor towards phosphorylated biomolecules: INHIBIT logic gate. Inorganica Chimica Acta, 2013, 399: 1–5
75 W Kloppfer. Intramolecular proton transfer in electronically excited molecules. In: J N Pitts, G S Hammond, K Gollnick, eds. Advances in Photochemistry, Volume 10. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2007, 311–358
76 V T Lieu, C A Handy. The in situ fluorometric determination of alkaline earth metal ions resolved on paper. Analytical Letters, 1974, 7(4): 267–278
77 J S C Kilby. Turning potential into realities: the invention of the integrated circuit (Nobel lecture). ChemPhysChem, 2001, 2(8–9): 482–489
78 R Guliyev, S Ozturk, Z Kostereli, E U Akkaya. From virtual to physical: integration of chemical logic gates. Angewandte Chemie International Edition, 2011, 50(42): 9826–9831
79 A P de Silva. Molecular logic gate arrays. Chemistry, an Asian Journal, 2011, 6(3): 750–766
80 S Erbas-Cakmak, E U Akkaya. Cascading of molecular logic gates for advanced functions: a self-reporting, activatable photosensitizer. Angewandte Chemie International Edition, 2013, 52(43): 11364–11368
81 S O McDonnell, M J Hall, L T Allen, A Byrne, W M Gallagher, D F O’Shea. Supramolecular photonic therapeutic agents. Journal of the American Chemical Society, 2005, 127(47): 16360–16361
82 S Ozlem, E U Akkaya. Thinking outside the silicon box: molecular and logic as an additional layer of selectivity in singlet oxygen generation for photodynamic therapy. Journal of the American Chemical Society, 2009, 131(1): 48–49
83 F M Raymo, S Giordani. Signal communication between molecular switches. Organic Letters, 2001, 3(22): 3475–3478
84 F M Raymo, S Giordani. Digital communication through intermolecular fluorescence modulation. Organic Letters, 2001, 3(12): 1833–1836
85 A P de Silva, I M Dixon, H Q N Gunaratne, T Gunnlaugsson, P R Maxwell, T E Rice. Integration of logic functions and sequential operation of gates at the molecular-scale. Journal of the American Chemical Society, 1999, 121(6): 1393–1394
86 L Wang, B Li, L Zhang, Y Luo. Three-input-three-output logic operations based on absorption and fluorescence dual-mode from a thiourea compound. Dalton Transactions, 2013, 42(2): 459–465
87 K Rurack. Flipping the light switch ‘on’ — the design of sensor molecules that show cation-induced fluorescence enhancement with heavy and transition metal ions. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2001, 57(11): 2161–2195
88 D C Magri, M C Fava, C J Mallia. A sodium-enabled ‘Pourbaix sensor’: a three-input AND logic gate as a ‘lab-on-a-molecule’ for monitoring Na+, pH and pE. Chemical Communications, 2014, 50(8): 1009–1011
89 D C Magri, G J Brown, G D McClean, A P de Silva. Communicating chemical congregation: a molecular AND logic gate with three chemical inputs as a “lab-on-a-molecule” prototype. Journal of the American Chemical Society, 2006, 128(15): 4950–4951
90 B Rout, L Unger, G Armony, M A Iron, D Margulies. Medication detection by a combinatorial fluorescent molecular sensor. Angewandte Chemie, 2012, 124(50): 12645–12649
91 A T Wright, E V Anslyn. Differential receptor arrays and assays for solution-based molecular recognition. Chemical Society Reviews, 2006, 35(1): 14–28
92 M A Sharaf, D L Illman, B R Kowalski. Chemometrics. New York: Wiley, 1986
93 B Rout, P Milko, M A Iron, L Motiei, D Margulies. Authorizing multiple chemical passwords by a combinatorial molecular keypad lock. Journal of the American Chemical Society, 2013, 135(41): 15330–15333
94 S Chen, Z Guo, S Zhu, W E Shi, W Zhu. A multiaddressable photochromic bisthienylethene with sequence-dependent responses: construction of an INHIBIT logic gate and a keypad lock. ACS Applied Materials & Interfaces, 2013, 5(12): 5623–5629
95 B Rout, L Motiei, D. MarguliesCombinatorial fluorescent molecular sensors: The road to differential sensing at the molecular level. Synlett, 2014, 25: A–E
96 D Margulies, C E Felder, G Melman, A Shanzer. A molecular keypad lock: a photochemical device capable of authorizing password entries. Journal of the American Chemical Society, 2007, 129(2): 347–354
97 A P de Silva, H Q N Gunaratne, C P McCoy. Direct visual indication of pH windows: ‘off-on-off’ fluorescent PET (photoinduced electron transfer) sensors/switches. Chemical Communications, 1996, (21): 2399–2400
98 S A de Silva, A Zavaleta, D E Baron, O Allam, E V Isidor, N Kashimura, J M Percarpio. A fluorescent photoinduced electron transfer sensor for cations with an off-on-off proton switch. Tetrahedron Letters, 1997, 38(13): 2237–2240
99 V F Pais, M Lineros, R López-Rodríguez, H S El-Sheshtawy, R Fernández, J M Lassaletta, A Ros, U Pischel. Preparation and pH-switching of fluorescent borylated arylisoquinolines for multilevel molecular logic. The Journal of Organic Chemistry, 2013, 78(16): 7949–7961
100 J F Callan, A P de Silva, J Ferguson, A J Huxley, A M O'Brien. Fluorescent photoionic devices with two receptors and two switching mechanisms: applications to pH sensors and implications for metal ion detection. Tetrahedron, 2004, 60(49): 11125–11131
101 H Morawetz. Difficulties in the emergence of the polymer concept — an essay. Angewandte Chemie International Edition, 1987, 26(2): 93–97
102 T Ratner, O Reany, E Keinan. Encoding and processing of alphanumeric information by chemical mixtures. ChemPhysChem, 2009, 10(18): 3303–3309
103 Y Wu, Y Xie, Q Zhang, H Tian, W Zhu, A D Q Li. Quantitative photoswitching in bis(dithiazole) ethene enables modulation of light for encoding optical signals. Angewandte Chemie International Edition, 2014, 53(8): 2090–2094
[1] Maria L. Odyniec, Jordan E. Gardiner, Adam C. Sedgwick, Xiao-Peng He, Steven D. Bull, Tony D. James. Dual enzyme activated fluorescein based fluorescent probe[J]. Front. Chem. Sci. Eng., 2020, 14(1): 117-121.
[2] Harrison D. Root, Gregory Thiabaud, Jonathan L. Sessler. Reduced texaphyrin: A ratiometric optical sensor for heavy metals in aqueous solution[J]. Front. Chem. Sci. Eng., 2020, 14(1): 19-27.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed