Information gathering and processing with fluorescent molecules

Brian DALY, Jue LING, A. Prasanna de SILVA

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PDF(329 KB)
Front. Chem. Sci. Eng. ›› 2014, Vol. 8 ›› Issue (2) : 240-251. DOI: 10.1007/s11705-014-1432-z
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Information gathering and processing with fluorescent molecules

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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.

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Keywords

molecular logic / molecular computation / molecular sensor / fluorescent molecular device / fluorescent sensor

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Brian DALY, Jue LING, A. Prasanna de SILVA. Information gathering and processing with fluorescent molecules. Front. Chem. Sci. Eng., 2014, 8(2): 240‒251 https://doi.org/10.1007/s11705-014-1432-z

Brian Daly, born and bred in Belfast, Northern Ireland, enjoys running, cycling, swimming and bringing up his two daughters. He is in the first year of his PhD research on switchable receptors. Jue Ling is a second-year PhD researcher in fluorescent molecular logic. He was born in Zhenjiang, Jiangsu province, P.R. China, and counts playing basketball and cooking among his interests. AP de Silva was born in Colombo, Sri Lanka, and plays percussion in an Irish traditional band. He pioneered molecular logic and fluorescent PET (photoinduced electron transfer) sensors. He wrote the book ‘Molecular-logic based Computation’. His collaboration with Roche Diagnostics led to the Optimedical OPTI analyzer for blood electrolytes, the chemistry module of which has sales of 110M $ so far.

References

[1]
de Silva A P, Gunaratne H Q N, McCoy C P. A molecular photoionic AND gate based on fluorescent signalling. Nature, 1993, 364(6432): 42–44
[2]
Balzani V, Venturi M, Credi A. Molecular Devices and Machines. 2nd ed. Weinheim: Wiley-VCH, 2008
[3]
Katz E. Molecular and Supramolecular Information Processing: from Molecular Switches to Logic Systems. Weinheim: Wiley-VCH, 2012
[4]
Katz E. Biomolecular Information Processing: from Logic Systems to Smart Sensors and Actuators. Weinheim: Wiley-VCH, 2012
[5]
Szacilowski K. Infochemistry: Information Processing at the Nanoscale. Chichester: Wiley, 2012
[6]
Feringa B, Browne W S. Molecular Switches. 2nd ed. Wiley-VCH, Weinheim, 2012
[7]
de Silva A P. Molecular Logic-based Computation. Cambridge: Royal Society of Chemistry, 2012
[8]
de Silva A P, McClenaghan N D, McCoy C P. Logic gates. In: Balzani V, ed. Electron Transfer in Chemistry, Vol 5. Weinheim: Wiley-VCH, 2001, 156
[9]
Raymo F M. Digital processing and communication with molecular switches. Advanced Materials, 2002, 14(6): 401–414
[10]
de Silva A P, McClenaghan N D. Molecular-scale logic gates. Chemistry, 2004, 10(3): 574–586
[11]
de Silva A P, Leydet Y, Lincheneau C, McClenaghan N D. Chemical approaches to nanometre-scale logic gates. Journal of Physics Condensed Matter, 2006, 18(33): S1847–S1872
[12]
de Silva A P, Uchiyama S. Molecular logic and computing. Nature Nanotechnology, 2007, 2(7): 399–410
[13]
Benenson Y. Biocomputers: from test tubes to live cells. Molecular BioSystems, 2009, 5(7): 675–685
[14]
Katz E, Privman V. Enzyme-based logic systems for information processing. Chemical Society Reviews, 2010, 39(5): 1835–1857
[15]
Tian H. Data processing on a unimolecular platform. Angewandte Chemie International Edition, 2010, 49(28): 4710–4712
[16]
Pischel U, Andréasson J, Gust D, Pais V F. Information processing with molecules — Quo vadis? ChemPhysChem, 2013, 14(1): 28–46
[17]
Bissell R A, de Silva A P. 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]
Bryan A J, de Silva A P, de Silva S A, Rupasinghe R A D, Sandanayake K R A. Photo-induced electron transfer as a general design logic for fluorescent molecular sensors for cations. Biosensors, 1989, 4(3): 169–179
[19]
Gell C, Brockwell D, Smith A. Handbook of Single Molecule Fluorescence Spectroscopy. New York: Oxford University Press, 2006
[20]
Gregg J. Ones and Zeros: Understanding Boolean Algebra, Digital Circuits, and the Logic of Sets. Wiley-IEEE Press, 1998
[21]
Malvino A P, Brown J A. Digital Computer Electronics, Glencoe. 3rd ed. Lake Forest, 1993
[22]
Maxfield C. Bebop to the Boolean Boogie: An Unconventional Guide to Electronics. Massachusetts: Newnes, 2008
[23]
Ben-Ari M. Mathematical Logic for Computer Science. Hemel Hempstead: Prentice-Hall, 1993
[24]
Hughes E. Electrical Technology. 6th ed. Burnt Mill: Longman, 1990
[25]
Keirstead A E, Bridgewater J W, Terazono Y, Kodis G, Straight S, Liddell P A, Moore A L, Moore T A, Gust D. Photochemical “triode” molecular signal transducer. Journal of the American Chemical Society, 2010, 132(18): 6588–6595
[26]
Copley G, Moore T A, Moore A L, Gust D. Analog applications of photochemical switches. Advanced Materials, 2013, 25(3): 456–461
[27]
Irie M. Diarylethenes for memories and switches. Chemical Reviews, 2000, 100(5): 1685–1716
[28]
Huxley A J M, Schroeder M, Gunaratne H Q N, de Silva A P. Modification of fluorescent photoinduced electron transfer (PET) sensors/switches to produce molecular photoionic triode action. Angewandte Chemie, 2014, 126(14): 3696–3699
[29]
Callan J F, de Silva A P, Ferguson J, Huxley A J, 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, 2004, 60(49): 11125–11131
[30]
de Silva A P, Gunaratne H Q N, Sandanayake K R A S. A new benzo-annelated cryptand and a derivative with alkali cation-sensitive fluorescence. Tetrahedron Letters, 1990, 31(36): 5193–5196
[31]
de Silva A P, Gunaratne H Q, Gunnlaugsson T, Huxley A J, McCoy C P, Rademacher J T, Rice T E. Signaling recognition events with fluorescent sensors and switches. Chemical Reviews, 1997, 97(5): 1515–1566
[32]
Bishop E. Indicators. Oxford: Pergamon, 1972
[33]
de Silva A P, Gunaratne H Q N, Lynch P L M, Patty A J, Spence G L. 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]
de Silva A P, Vance T P, West M E S, Wright G D. Bright molecules with sense, logic, numeracy and utility. Organic & Biomolecular Chemistry, 2008, 6(14): 2468–2480
[35]
Avouris P, Chen Z, Perebeinos V. Carbon-based electronics. Nature Nanotechnology, 2007, 2(10): 605–615
[36]
Bachtold A, Hadley P, Nakanishi T, Dekker C. Logic circuits with carbon nanotube transistors. Science, 2001, 294(5545): 1317–1320
[37]
Wang B, Anslyn E V. Chemosensors: Principles, Strategies, and Applications. John Wiley & Sons, 2011
[38]
Ast S, Schwarze T, Müller H, Sukhanov A, Michaelis S, Wegener J, Wolfbeis O S, Körzdörfer T, Dürkop A, Holdt H J. 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]
Schultz R A, White B D, Dishong D M, Arnold K A, Gokel G W. 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]
Zheng S, Lynch P L M, Rice T E, Moody T S, Gunaratne H Q, de Silva A P. Structural effects on the pH-dependent fluorescence of naphthalenic derivatives and consequences for sensing/switching. Photochemical & Photobiological Sciences, 2012, 11(11): 1675–1681
[41]
Grabowski Z R, Dobkowski J. Twisted intramolecular charge transfer (TICT) excited states: Energy and molecular structure. Pure and Applied Chemistry, 1983, 55(2): 245–252
[42]
Batat P, Vives G, Bofinger R, Chang R W, Kauffmann B, Oda R, Jonusauskas G, McClenaghan N D. Dynamics of ion-regulated photoinduced electron transfer in BODIPY-BAPTA conjugates. Photochemical & Photobiological Sciences, 2012, 11(11): 1666–1674
[43]
He H, Mortellaro M A, Leiner M J P, Young S T, Fraatz R J, Tusa J K. A fluorescent chemosensor for sodium based on photoinduced electron transfer. Analytical Chemistry, 2003, 75(3): 549–555
[44]
He H, Mortellaro M A, Leiner M J P, Fraatz R J, Tusa J K. A fluorescent sensor with high selectivity and sensitivity for potassium in water. Journal of the American Chemical Society, 2003, 125(6): 1468–1469
[45]
Tusa J K, He H. Critical care analyzer with fluorescent optical chemosensors for blood analytes. Journal of Materials Chemistry, 2005, 15(27–28): 2640–2647
[46]
He H, Jenkins K, Lin C. A fluorescent chemosensor for calcium with excellent storage stability in water. Analytica Chimica Acta, 2008, 611(2): 197–204
[47]
de Silva A P, Gunaratne H Q N, Habib-Jiwan J L, McCoy C P, Rice T E, Soumillion J P. 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]
de Silva A P, Gunaratne H Q N, Gunnlaugsson T. Fluorescent PET (photoinduced electron transfer) reagents for thiols. Tetrahedron Letters, 1998, 39(28): 5077–5080
[50]
Kojima H, Nagano T. Fluorescent indicators for nitric oxide. Advanced Materials, 2000, 12(10): 763–765
[51]
Plater M J, Greig I, Helfrich M H, Ralston S H. 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]
James T D, Phillips M D, Shinkai S. Boronic Acids in Saccharide Recognition. Royal Society of Chemistry, 2006
[53]
Bissell R A, Bryan A J, de Silva A P, McCoy C P. Fluorescent PET 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]
Uchiyama S, Iwai K, de Silva A P. Multiplexing sensory molecules map protons near micellar membranes. Angewandte Chemie International Edition, 2008, 47(25): 4667–4669
[55]
Harold F M. The Vital Force: A Study of Bioenergetics. New York: WH Freeman, 1986
[56]
Bhardwaj V K, Hundal M S, Hundal G. A tripodal receptor bearing catechol groups for the chromogenic sensing of F ions via frozen proton transfer. Tetrahedron, 2009, 65(41): 8556–8562
[57]
Winstanley K J, Sayer A M, Smith D K. Anion binding by catechols — an NMR, optical and electrochemical study. Organic & Biomolecular Chemistry, 2006, 4(9): 1760–1767
[58]
de Silva A P, McClean G D, Pagliari S. Direct detection of ion pairs by fluorescence enhancement. Chemical Communications, 2003, (16): 2010–2011
[59]
Koskela S J M, Fyles T M, James T D. A ditopic fluorescent sensor for potassium fluoride. Chemical Communications, 2005, (7): 945–947
[60]
Alfonso M, Espinosa A, Tárraga A, Molina P. 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]
Moro A J, Cywinski P J, Körsten S, Mohr G J. 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]
de Silva A P, Gunaratne H Q N, McVeigh C, Maguire G E M, Maxwell P R S, O’Hanlon E. Fluorescent signalling of the brain neurotransmitter γ-aminobutyric acid and related amino acid zwitterions. Chemical Communications, 1996, (18): 2191–2192
[63]
Karak D, Das S, Lohar S, Banerjee A, Sahana A, Hauli I, Mukhopadhyay S K, Safin D A, Babashkina M G, Bolte M, Garcia Y, Das D. 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]
Farrugia T J, Magri D C. ‘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]
Magri D C. A fluorescent and logic gate driven by electrons and protons. New Journal of Chemistry, 2009, 33(3): 457–461
[66]
Pourbaix M. Atlas of Electrochemical Equilibria in Aqueous Solutions. Oxford: Pergamon Press, 1966
[67]
Bu J H, Zheng Q Y, Chen C F, Huang Z T. New fluorescence-quenching process through resumption of PET process induced by complexation of alkali metal ion. Organic Letters, 2004, 6(19): 3301–3303
[68]
Nishimura G, Ishizumi K, Shiraishi Y, Hirai T. 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]
Montenegro J M, Perez-Inestrosa E, Collado D, Vida Y, Suau R. A natural-product-inspired photonic logic gate based on photoinduced electron-transfer-generated dual-channel fluorescence. Organic Letters, 2004, 6(14): 2353–2355
[70]
Banthia S, Samanta A. 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]
Gunnlaugsson T, Mac Dónaill D A, Parker D. Lanthanide macrocyclic quinolyl conjugates as luminescent molecular-level devices. Journal of the American Chemical Society, 2001, 123(51): 12866–12876
[72]
de Sousa M, Kluciar M, Abad S, Miranda M A, de Castro B, Pischel U. An inhibit (INH) molecular logic gate based on 1,8-naphthalimide-sensitised europium luminescence. Photochemical & Photobiological Sciences, 2004, 3(7): 639–642
[73]
Park J S, Karnas E, Ohkubo K, Chen P, Kadish K M, Fukuzumi S, Bielawski C W, Hudnall T W, Lynch V M, Sessler J L. Ion-mediated electron transfer in a supramolecular donor-acceptor ensemble. Science, 2010, 329(5997): 1324–1327
[74]
Kaur K, Bhardwaj V K, Kaur N, Singh N. 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]
Kloppfer W. Intramolecular proton transfer in electronically excited molecules. In: Pitts J N, Hammond G S, Gollnick K, eds. Advances in Photochemistry, Volume 10. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2007, 311–358
[76]
Lieu V T, Handy C A. The in situ fluorometric determination of alkaline earth metal ions resolved on paper. Analytical Letters, 1974, 7(4): 267–278
[77]
Kilby J S C. Turning potential into realities: the invention of the integrated circuit (Nobel lecture). ChemPhysChem, 2001, 2(8–9): 482–489
[78]
Guliyev R, Ozturk S, Kostereli Z, Akkaya E U. From virtual to physical: integration of chemical logic gates. Angewandte Chemie International Edition, 2011, 50(42): 9826–9831
[79]
de Silva A P. Molecular logic gate arrays. Chemistry, an Asian Journal, 2011, 6(3): 750–766
[80]
Erbas-Cakmak S, Akkaya E U. Cascading of molecular logic gates for advanced functions: a self-reporting, activatable photosensitizer. Angewandte Chemie International Edition, 2013, 52(43): 11364–11368
[81]
McDonnell S O, Hall M J, Allen L T, Byrne A, Gallagher W M, O’Shea D F. Supramolecular photonic therapeutic agents. Journal of the American Chemical Society, 2005, 127(47): 16360–16361
[82]
Ozlem S, Akkaya E U. 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]
Raymo F M, Giordani S. Signal communication between molecular switches. Organic Letters, 2001, 3(22): 3475–3478
[84]
Raymo F M, Giordani S. Digital communication through intermolecular fluorescence modulation. Organic Letters, 2001, 3(12): 1833–1836
[85]
de Silva A P, Dixon I M, Gunaratne H Q N, Gunnlaugsson T, Maxwell P R, Rice T E. 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]
Wang L, Li B, Zhang L, Luo Y. 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]
Rurack K. 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]
Magri D C, Fava M C, Mallia C J. 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]
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. Journal of the American Chemical Society, 2006, 128(15): 4950–4951
[90]
Rout B, Unger L, Armony G, Iron M A, Margulies D. Medication detection by a combinatorial fluorescent molecular sensor. Angewandte Chemie, 2012, 124(50): 12645–12649
[91]
Wright A T, Anslyn E V. Differential receptor arrays and assays for solution-based molecular recognition. Chemical Society Reviews, 2006, 35(1): 14–28
[92]
Sharaf M A, Illman D L, Kowalski B R. Chemometrics. New York: Wiley, 1986
[93]
Rout B, Milko P, Iron M A, Motiei L, Margulies D. Authorizing multiple chemical passwords by a combinatorial molecular keypad lock. Journal of the American Chemical Society, 2013, 135(41): 15330–15333
[94]
Chen S, Guo Z, Zhu S, Shi W E, Zhu W. 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]
Rout B, Motiei L, Margulies D.Combinatorial fluorescent molecular sensors: The road to differential sensing at the molecular level. Synlett, 2014, 25: A–E
[96]
Margulies D, Felder C E, Melman G, Shanzer A. A molecular keypad lock: a photochemical device capable of authorizing password entries. Journal of the American Chemical Society, 2007, 129(2): 347–354
[97]
de Silva A P, Gunaratne H Q N, McCoy C P. Direct visual indication of pH windows: ‘off-on-off’ fluorescent PET (photoinduced electron transfer) sensors/switches. Chemical Communications, 1996, (21): 2399–2400
[98]
de Silva S A, Zavaleta A, Baron D E, Allam O, Isidor E V, Kashimura N, Percarpio J M. A fluorescent photoinduced electron transfer sensor for cations with an off-on-off proton switch. Tetrahedron Letters, 1997, 38(13): 2237–2240
[99]
Pais V F, Lineros M, López-Rodríguez R, El-Sheshtawy H S, Fernández R, Lassaletta J M, Ros A, Pischel U. Preparation and pH-switching of fluorescent borylated arylisoquinolines for multilevel molecular logic. The Journal of Organic Chemistry, 2013, 78(16): 7949–7961
[100]
Callan J F, de Silva A P, Ferguson J, Huxley A J, 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, 2004, 60(49): 11125–11131
[101]
Morawetz H. Difficulties in the emergence of the polymer concept — an essay. Angewandte Chemie International Edition, 1987, 26(2): 93–97
[102]
Ratner T, Reany O, Keinan E. Encoding and processing of alphanumeric information by chemical mixtures. ChemPhysChem, 2009, 10(18): 3303–3309
[103]
Wu Y, Xie Y, Zhang Q, Tian H, Zhu W, Li A D Q. Quantitative photoswitching in bis(dithiazole) ethene enables modulation of light for encoding optical signals. Angewandte Chemie International Edition, 2014, 53(8): 2090–2094

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