Smart molecules at work-mimicking advanced logic operations

Molecular logic is an interdisciplinary research field, which has captured worldwide interest. This tutorial review gives a brief introduction into molecular logic and Boolean algebra. This serves as the basis for a discussion of the state-of-the-art and future challenges in the field. Representative examples from the most recent literature including adders/subtractors, multiplexers/demultiplexers, encoders/decoders, and sequential logic devices (keypad locks) are highlighted. Other horizons, such as the utility of molecular logic in bio-related applications, are discussed as well

Molecules for security measures: From keypad locks to advanced communication protocols

The idea of using molecules in the context of information security has sparked the interest of researchers from many scientific disciplines. This is clearly manifested in the diversity of the molecular platforms and the analytical techniques used for this purpose, some of which we highlight in this Tutorial Review. Moreover, those molecular systems can be used to emulate a broad spectrum of security measures. For a long time, molecular keypad locks enjoyed a clear preference and the review starts off with a description of how these devices developed. In the last few years, however, the field has evolved into something larger. Examples include more complex authentication protocols (multi-factor authentication and one-time passwords), the recognition of erroneous procedures in data transmission (parity devices), as well as steganographic and cryptographic protection

An acido- and photochromic molecular device that mimics triode action

© The Royal Society of Chemistry 2016. The photo-controlled shift of pH titration curves, describing the acidochromic behaviour of a spiropyran switch network, was harnessed for the realisation of a molecular triode. The intricate network can be correctly interpreted with respect to the pH dependence of the main involved species

Molecular Logic: From Single Logic Gates to Sophisticated Logic Circuits, from Fundamental Science to Practical Applications

[No abstract available

Site-selective installation of BASHY fluorescent dyes to Annexin V for targeted detection of apoptotic cells

Fluorophores are indispensable for imaging biological processes. We report the design and synthesis of azide-tagged boronic acid salicylidenehydrazone (BASHY) dyes and their use for site-selective labelling of Annexin V. The Annexin V-BASHY conjugate maintained function and fluorescence as demonstrated by the targeted detection of apoptotic cells.We thank FCT Portugal (Doctoral Fellowship, SFRH/BD/94779/2013 to F. M. F. S., Postdoctoral Fellowship, SFRH/BPD/103172/2014 to P. M. S. D. C.; projects PTDC/QUI-QUI/118315/2010 and PTDC/BBB BQB/0506/2012; PTDC/QEQ-QOR/1434/2014: PTDC/SAUFAR/119389/2010; FCT Investigator to G. J. L. B. and P. M. P. G.; iMed.ULisboa grant UID/DTP/04138/2013), EU (Marie-Curie CIG to G. J. L. B.; Marie-Sklodowska Curie ITN ProteinConjugates to G. J. L. B. and P. M. P. G.), DFG (SI 2117/1-1 to F. S.), CNPq Brazil (fellowship 200456/2015-6 to J. B. B.); Ministerio de Economía y Competitividad, Madrid, Spain (grant CTQ2014-54729-C2-1-P), Junta de Andalucía (grant P12-FQM-2140) and the EPSRC (G. J. L. B.) for financial support. G. J. L. B. is a Royal Society University Research Fellow and the recipient of a European Research Council Starting Grant (TagIt)

All-Photonic Multifunctional Molecular Logic Device

Photochromes are photoswitchable, bistable chromophores which, like transistors, can implement binary logic operations. When several photochromes are combined in one molecule, interactions between them such as energy and electron transfer allow design of simple Boolean logic gates and more complex logic devices with all-photonic inputs and outputs. Selective isomerization of individual photochromes can be achieved using light of different wavelengths, and logic outputs can employ absorption and emission properties at different wavelengths, thus allowing a single molecular species to perform several different functions, even simultaneously. Here, we report a molecule consisting of three linked photochromes that can be configured as AND, XOR, INH, half-adder, half-subtractor, multiplexer, demultiplexer, encoder, decoder, keypad lock, and logically reversible transfer gate logic devices, all with a common initial state. The system demonstrates the advantages of light-responsive molecules as multifunctional, reconfigurable nanoscale logic devices that represent an approach to true molecular information processing units

OFF-ON-OFF Fluorescence Switch with T-Latch Function

A novel molecular system with characteristics of an OFF-ON-OFF fluorescence switch was designed to integrate the function of a T-latch. In detail, a receptor(1)-fluorophore-receptor(2) architecture was adopted to achieve fluorescence switching upon addition of protons

An All-Photonic Molecule-Based D Flip-Flop

The photochromic fluorescence switching of a fulgimide derivative was used to implement the first molecule-based D (delay) flip-flop device, which works based on the principles of sequential logic. The device operates exclusively with photonic signals and can be conveniently switched in repeated cycles. \ua9 2011 American Chemical Society

Spin chemistry investigation of peculiarities of photoinduced electron transfer in donor-acceptor linked system

Photoinduced intramolecular electron transfer in linked systems, (R,S)- and (S,S)-naproxen-N-methylpyrrolidine dyads, has been studied by means of spin chemistry methods [magnetic field effect and chemically induced dynamic nuclear polarization (CIDNP)]. The relative yield of the triplet state of the dyads in different magnetic field has been measured, and dependences of the high-field CIDNP of the N-methylpyrrolidine fragment on solvent polarity have been investigated. However, both (S,S)- and (R,S)-enantiomers demonstrate almost identical CIDNP effects for the entire range of polarity. It has been demonstrated that the main peculiarities of photoprocesses in this linked system are connected with the participation of singlet exciplex alongside with photoinduced intramolecular electron transfer in chromophore excited state quenching.This work was supported by the grants 08-03-00372 and 11-03-01104 of the Russian Foundation for Basic Research, and the grant of Priority Programs of the Russian Academy of Sciences, nr. 5.1.5.Magin, I.; Polyakov, N.; Khramtsova, E.; Kruppa, A.; Stepanov, A.; Purtov, P.; Leshina, T.... (2011). Spin chemistry investigation of peculiarities of photoinduced electron transfer in donor-acceptor linked system. Applied Magnetic Resonance. 41(2-4):205-220. https://doi.org/10.1007/s00723-011-0288-3S205220412-4J.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, Science 329, 1324–1327 (2010)S.Y. Reece, D.G. Nocera, Annu. Rev. Biochem. 78, 673–699 (2009)M.S. Afanasyeva, M.B. Taraban, P.A. Purtov, T.V. Leshina, C.B. Grissom, J. Am. Chem. Soc. 128, 8651–8658 (2006)M.A. Fox, M. Chanon, in Photoinduced Electron Transfer. C: Photoinduced Electron Transfer Reactions: Organic Substrates (Elsevier, New York, 1988), p. 754P.J. Hayball, R.L. Nation, F. Bochner, Chirality 4, 484–487 (1992)N. Suesa, M.F. Fernandez, M. Gutierrez, M.J. Rufat, E. Rotllan, L. Calvo, D. Mauleon, G. Carganico, Chirality 5, 589–595 (1993)A.M. Evans, J. Clin. Pharmacol. 36, 7–15 (1996)Y. Inoue, T. Wada, S. Asaoka, H. Sato, J.-P. Pete, Chem Commun. 4, 251–259 (2000)T. Yorozu, K. Hayashi, M. Irie, J. Am. Chem. Soc. 103, 5480–5548 (1981)N.J. Turro, in Modern Molecular Photochemistry (Benjamin/Cummings, San Francisco, 1978)K.M. Salikhov, Y.N. Molin, R.Z. Sagdeev, A.L. Buchachenko, in Spin Polarization and Magnetic Field Effects in Radical Reactions (Akademiai Kiado, Budapest, 1984), p. 419E.A. Weiss, M.A. Ratner, M.R. Wasielewski, J. Phys. Chem. A 107, 3639–3647 (2003)A.S. Lukas, P.J. Bushard, E.A. Weiss, M.R. Wasielewski, J. Am. Chem. Soc. 125, 3921–3930 (2003)R. Nakagaki, K. Mutai, M. Hiramatsu, H. Tukada, S. Nakakura, Can. J. Chem. 66, 1989–1996 (1988)M.C. Jim′enez, U. Pischel, M.A. Miranda, J. Photochem. Photobiol. C Photochem. Rev. 8, 128–142 (2007)S. Abad, U. Pischel, M.A. Miranda, Photochem. Photobiol. Sci. 4, 69–74 (2005)U. Pischel, S. Abad, L.R. Domingo, F. Bosca, M.A. Miranda, Angew. Chem. Int. Ed. 42, 2531–2534 (2003)G.L. Closs, R.J. Miller, J. Am. Chem. Soc. 101, 1639–1641 (1979)G.L. Closs, R.J. Miller, J. Am. Chem. Soc. 103, 3586–3588 (1981)M. Goez, Chem. Phys. Lett. 188, 451–456 (1992)I.F. Molokov, Y.P. Tsentalovich, A.V. Yurkovskaya, R.Z. Sagdeev, J. Photochem. Photobiol. A 110, 159–165 (1997)U. Pischel, S. Abad, M.A. Miranda, Chem. Commun. 9, 1088–1089 (2003)H. Hayashi, S. Nagakura, Bull. Chem. Soc. Jpn. 57, 322–328 (1984)Y. Sakaguchi, H. Hayashi, S. Nagakura, Bull. Chem. Soc. Jpn. 53, 39–42 (1980)H. Yonemura, H. Nakamura, T. Matsuo, Chem. Phys. Lett. 155, 157–161 (1989)N. Hata, M. Hokawa, Chem. Lett. 10, 507–510 (1981)M. Shiotani, L. Sjoeqvist, A. Lund, S. Lunell, L. Eriksson, M.B. Huang, J. Phys. Chem. 94, 8081–8090 (1990)E. Schaffner, H. Fischer, J. Phys. Chem. 100, 1657–1665 (1996)Y. Mori, Y. Sakaguchi, H. Hayashi, Chem. Phys. Lett. 286, 446–451 (1998)I.M. Magin, A.I. Kruppa, P.A. Purtov, Chem. Phys. 365, 80–84 (2009)K.K. Barnes, Electrochemical Reactions in Nonaqueous Systems (M. Dekker, New York, 1970), p. 560J. Bargon, J. Am. Chem. Soc. 99, 8350–8351 (1977)M. Goez, I. Frisch, J. Phys. Chem. A 106, 8079–8084 (2002)A.K. Chibisov, Russ. Chem. Rev. 50, 615–629 (1981)J. Goodman, K. Peters, J. Am. Chem. Soc. 107, 1441–1442 (1985)H. Cao, Y. Fujiwara, T. Haino, Y. Fukazawa, C.-H. Tung, Y. Tanimoto, Bull. Chem. Soc. Jpn. 69, 2801–2813 (1996)P.A. Purtov, A.B. Doktorov, Chem. Phys. 178, 47–65 (1993)A.I. Kruppa, O.I. Mikhailovskaya, T.V. Leshina, Chem. Phys. Lett. 147, 65–71 (1988)M.E. Michel-Beyerle, R. Haberkorn, W. Bube, E. Steffens, H. Schröder, H.J. Neusser, E.W. Schlag, H. Seidlitz, Chem. Phys. 17, 139–145 (1976)K. Schulten, H. Staerk, A. Weller, H.-J. Werner, B. Nickel, Z. Phys. Chem. 101, 371–390 (1976)K. Gnadig, K.B. Eisenthal, Chem. Phys. Lett. 46, 339–342 (1977)T. Nishimura, N. Nakashima, N. Mataga, Chem. Phys. Lett. 46, 334–338 (1977)M.G. Kuzmin, I.V. Soboleva, E.V. Dolotova, D.N. Dogadkin, High Eng. Chem. 39, 86–96 (2005

Network Analysis of Biochemical Logic for Noise Reduction and Stability: A System of Three Coupled Enzymatic AND Gates

We develop an approach aimed at optimizing the parameters of a network of biochemical logic gates for reduction of the "analog" noise buildup. Experiments for three coupled enzymatic AND gates are reported, illustrating our procedure. Specifically, starch - one of the controlled network inputs - is converted to maltose by beta-amylase. With the use of phosphate (another controlled input), maltose phosphorylase then produces glucose. Finally, nicotinamide adenine dinucleotide (NAD+) - the third controlled input - is reduced under the action of glucose dehydrogenase to yield the optically detected signal. Network functioning is analyzed by varying selective inputs and fitting standardized few-parameters "response-surface" functions assumed for each gate. This allows a certain probe of the individual gate quality, but primarily yields information on the relative contribution of the gates to noise amplification. The derived information is then used to modify our experimental system to put it in a regime of a less noisy operation.Comment: 31 pages, PD