Engin U. Akkaya

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Organization: Bilkent University
Department: UNAM-National Nanotechnology Research Center and Department of Chemistry
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Co-reporter:O. Altan Bozdemir, Ruslan Guliyev, Onur Buyukcakir, Sencer Selcuk, Safacan Kolemen, Gulcihan Gulseren, Tugrul Nalbantoglu, Hande Boyaci and Engin U. Akkaya
Journal of the American Chemical Society June 16, 2010 Volume 132(Issue 23) pp:8029-8036
Publication Date(Web):March 18, 2010
DOI:10.1021/ja1008163
Remarkably versatile chemistry of Bodipy dyes allows the design and straightforward synthesis of multivalent-multitopic derivatives, which, with judicious selection of metal ion−ligand pairs based on known affinities, affords control and manipulation of photoinduced electron transfer and internal charge transfer processes as desired. We have demonstrated that metal ions acting as modulators (or inputs, in digital design parlance) can generate absorbance changes in accordance with the operation of a half-adder. In addition, an AND logic gate in the emission mode was delivered using a different binucleating arrangement of ligands. A molecular equivalent of a three-input AND logic gate was also obtained exploiting differential binding affinities of metal ions for different ligands. The results suggest that different metal ions can be used as nonannihilating inputs, selectively targeting various ligands incorporated within a single fluorophore, and with careful design, diverse photophysical processes can be selectively modulated, resulting in a range of signals, useful in molecular logic design, and offering an enticing potential for multianalyte chemosensors.
Co-reporter:Ilke S. Turan, Ozlem Seven, Seylan Ayan, and Engin U. Akkaya
ACS Omega July 2017? Volume 2(Issue 7) pp:3291-3291
Publication Date(Web):July 7, 2017
DOI:10.1021/acsomega.7b00537
Bringing together the concepts of self-immolative linkers and chemiluminogen dioxetane modules, a chemiluminescence-based sensor for fluoride with signal amplification is presented. Signal amplification is obtained by triggering two chemiluminescence events for each reacting fluoride ion that in turn releases two fluoride ions for each ion. As expected, the chemiluminescence signal starts to rise following an induction period. In addition to the analytical potential, this chemical system is also of interest as a demonstration of positive feedback loop character.Topics: Luminescence; Luminescence;
Co-reporter:Nisa Yesilgul, T. Bilal Uyar, Ozlem Seven, and Engin U. Akkaya
ACS Omega April 2017? Volume 2(Issue 4) pp:1367-1367
Publication Date(Web):April 17, 2017
DOI:10.1021/acsomega.7b00228
Chemical generation of singlet oxygen under biologically relevant conditions is very important, considering the role played by singlet oxygen in cancer therapeutics. We now demonstrate that a luminol derivative can be chemically excited and transfer the excitation energy to the covalently attached photosensitizer derived from erythrosin. A photosensitizer module, when excited in this manner, can generate singlet oxygen in solution. As hydrogen peroxide is present in a relatively high concentration in cancer cells, singlet oxygen generation through chemical excitation may evolve into an important therapeutic approach.
Co-reporter:Di Wu;Adam C. Sedgwick;Thorfinnur Gunnlaugsson;Juyoung Yoon;Tony D. James
Chemical Society Reviews 2017 vol. 46(Issue 23) pp:7105-7123
Publication Date(Web):2017/11/27
DOI:10.1039/C7CS00240H
Fluorescent chemosensors for ions and neutral analytes have been widely applied in many diverse fields such as biology, physiology, pharmacology, and environmental sciences. The field of fluorescent chemosensors has been in existence for about 150 years. In this time, a large range of fluorescent chemosensors have been established for the detection of biologically and/or environmentally important species. Despite the progress made in this field, several problems and challenges still exist. This tutorial review introduces the history and provides a general overview of the development in the research of fluorescent sensors, often referred to as chemosensors. This will be achieved by highlighting some pioneering and representative works from about 40 groups in the world that have made substantial contributions to this field. The basic principles involved in the design of chemosensors for specific analytes, problems and challenges in the field as well as possible future research directions are covered. The application of chemosensors in various established and emerging biotechnologies, is very bright.
Co-reporter:Tugba Ozdemir, Jose Luis Bila, Fazli Sozmen, Leyla T. Yildirim, and Engin U. Akkaya
Organic Letters 2016 Volume 18(Issue 19) pp:4821-4823
Publication Date(Web):September 15, 2016
DOI:10.1021/acs.orglett.6b02418
Orthogonally linked BODIPY units show exceptional intersystem crossing efficiencies. We now report orthogonal BODIPY trimers with strong absorption in the visible region and high singlet oxygen generation capability. The X-ray diffraction structure confirms that the two peripheral BODIPY units are at a perpendicular angle to the core structure.
Co-reporter:Bilal Kilic, Nisa Yesilgul, Veli Polat, Zuhal Gercek, Engin U. Akkaya
Tetrahedron Letters 2016 Volume 57(Issue 12) pp:1317-1320
Publication Date(Web):23 March 2016
DOI:10.1016/j.tetlet.2016.02.033
Bodipy dyes with n-decyloxyphenyl-(4, 5) and pentadecyl-(8) meso substituents can easily embed themselves into micellar structures formed from Cremophor-EL. In micelles of approximately 20 nm median size, heavy-atom substituted dyes show remarkable photosensitization properties as evidenced by the rate of reaction with an anthracene-based selective singlet oxygen trap in buffered aqueous solutions. Considering the ease of Bodipy derivatization and the advantages of Cremophor-EL carried therapeutic agents, these photosensitizing agents may offer novel targeting opportunities and enhanced chemical and photophysical stability.
Co-reporter:Dr. Ilke Simsek Turan;Deniz Yildiz;Abdurrahman Turksoy;Dr. Gurcan Gunaydin;Dr. Engin U. Akkaya
Angewandte Chemie 2016 Volume 128( Issue 8) pp:2925-2928
Publication Date(Web):
DOI:10.1002/ange.201511345

Abstract

The photosensitized generation of singlet oxygen within tumor tissues during photodynamic therapy (PDT) is self-limiting, as the already low oxygen concentrations within tumors is further diminished during the process. In certain applications, to minimize photoinduced hypoxia the light is introduced intermittently (fractional PDT) to allow time for the replenishment of cellular oxygen. This condition extends the time required for effective therapy. Herein, we demonstrated that a photosensitizer with an additional 2-pyridone module for trapping singlet oxygen would be useful in fractional PDT. Thus, in the light cycle, the endoperoxide of 2-pyridone is generated along with singlet oxygen. In the dark cycle, the endoperoxide undergoes thermal cycloreversion to produce singlet oxygen, regenerating the 2-pyridone module. As a result, the photodynamic process can continue in the dark as well as in the light cycles. Cell-culture studies validated this working principle in vitro.

Co-reporter:Dr. Ilke Simsek Turan;Deniz Yildiz;Abdurrahman Turksoy;Dr. Gurcan Gunaydin;Dr. Engin U. Akkaya
Angewandte Chemie International Edition 2016 Volume 55( Issue 8) pp:2875-2878
Publication Date(Web):
DOI:10.1002/anie.201511345

Abstract

The photosensitized generation of singlet oxygen within tumor tissues during photodynamic therapy (PDT) is self-limiting, as the already low oxygen concentrations within tumors is further diminished during the process. In certain applications, to minimize photoinduced hypoxia the light is introduced intermittently (fractional PDT) to allow time for the replenishment of cellular oxygen. This condition extends the time required for effective therapy. Herein, we demonstrated that a photosensitizer with an additional 2-pyridone module for trapping singlet oxygen would be useful in fractional PDT. Thus, in the light cycle, the endoperoxide of 2-pyridone is generated along with singlet oxygen. In the dark cycle, the endoperoxide undergoes thermal cycloreversion to produce singlet oxygen, regenerating the 2-pyridone module. As a result, the photodynamic process can continue in the dark as well as in the light cycles. Cell-culture studies validated this working principle in vitro.

Co-reporter:Sundus Erbas-Cakmak, Fatma Pir Cakmak, Seda Demirel Topel, Taha Bilal Uyar and Engin U. Akkaya  
Chemical Communications 2015 vol. 51(Issue 61) pp:12258-12261
Publication Date(Web):22 Jun 2015
DOI:10.1039/C5CC01261A
A series of pH and GSH responsive photosensitizers were designed and synthesized. pKa values were optimized by adjusting the inductive contribution of substituents to reach a pH range (6.0–7.4) relevant to the tumour microenvironment. pH-Activatable behaviour and redox mediated release of the quencher from the PS by GSH allow the construction of an AND logic operator for selective photodynamic action in aqueous solutions.
Co-reporter:Ilke Simsek Turan, Ozge Yilmaz, Betul Karatas and Engin U. Akkaya  
RSC Advances 2015 vol. 5(Issue 44) pp:34535-34540
Publication Date(Web):08 Apr 2015
DOI:10.1039/C5RA01551K
Palladium triggered removal of a propargyl group leads to the cleavage of the 1,2-dioxetane ring, leading to bright chemiluminescence. The reaction of the probe is highly specific for the Pd species, thus the probe described here has considerable potential for practical utility.
Co-reporter:Seda Demirel Topel, Gunseli Turgut Cin and Engin U. Akkaya  
Chemical Communications 2014 vol. 50(Issue 64) pp:8896-8899
Publication Date(Web):16 Jun 2014
DOI:10.1039/C4CC03387F
Orthogonal dimers of Bodipy were recently shown to be efficient generators of singlet oxygen. However, these dyes require green light for excitation, which would be very quickly attenuated inside the mammalian tissues. We now demonstrate that when these dyes are covalently attached to UCNPs, near IR irradiation results in very efficient generation of singlet oxygen.
Co-reporter:Safacan Kolemen, Yusuf Cakmak, Ziya Kostereli, and Engin U. Akkaya
Organic Letters 2014 Volume 16(Issue 3) pp:660-663
Publication Date(Web):January 13, 2014
DOI:10.1021/ol403193f
A dissymmetrically substituted orthogonal BODIPY dimer and an orthogonal BODIPY trimer exist as two stable conformers, which are in fact atropisomeric enantiomers. The racemic mixture can be separated by HPLC using a chiral stationary phase. These enantiomeric derivatives hold great potential as chiral agents in asymmetric synthesis, fluorogenic/chromogenic sensing, and biological applications.
Co-reporter:Sundus Erbas-Cakmak and Engin U. Akkaya
Organic Letters 2014 Volume 16(Issue 11) pp:2946-2949
Publication Date(Web):May 21, 2014
DOI:10.1021/ol501084n
A Bodipy-based energy transfer cassette with a singlet oxygen reactive linker between the donor and acceptor modules has an interesting emergent property, if the acceptor module is also a photosensitizer. Singlet oxygen produced by the photosensitizer reacts rapidly with the molecule itself to liberate the energy donor, resulting in an enhanced fluorescence emission. The result is a self-reporting photosensitizer providing an assessment of the singlet oxygen production rate under the operational conditions.
Co-reporter:Ilke Simsek Turan and Engin U. Akkaya
Organic Letters 2014 Volume 16(Issue 6) pp:1680-1683
Publication Date(Web):March 7, 2014
DOI:10.1021/ol5003412
An enhanced chemiluminescence signal is obtained when electronically triggered dioxetane cleavage is initiated by fluoride-mediated deprotection of the silyl-protecting group, followed by self-immolation via 1,4-quinone–methide rearrangement. The reaction takes place even when the probe is trapped within a PMMA layer on top of a glass plate. In that arrangement, fluoride in aqueous solutions can be detected selectively at low micromolar concentrations.
Co-reporter:Murat Işık, Ruslan Guliyev, Safacan Kolemen, Yigit Altay, Berna Senturk, Turgay Tekinay, and Engin U. Akkaya
Organic Letters 2014 Volume 16(Issue 12) pp:3260-3263
Publication Date(Web):June 2, 2014
DOI:10.1021/ol501272z
A selective probe for glutathione was designed and synthesized. The design incorporates spatial and photophysical constraints for the maximal emission signal. Thus, pHs, as well as the intracellular thiol concentrations, determine the emission signal intensity through a tight control of charge-transfer and PeT processes. The probe works satisfactorily inside the human breast adenocarcinoma cells, highlighting GSH distribution in the cytosol.
Co-reporter:Esra Tanriverdi Ecik, Ahmet Atilgan, Ruslan Guliyev, T. Bilal Uyar, Aysegul Gumus and Engin U. Akkaya  
Dalton Transactions 2014 vol. 43(Issue 1) pp:67-70
Publication Date(Web):30 Sep 2013
DOI:10.1039/C3DT52375F
Systematic cascading of molecular logic gates is an important issue to be addressed for advancing research in this field. We have demonstrated that photochemically triggered metal ion signals can be utilized towards that goal. Thus, independent logic gates were shown to work together while keeping their identity in more complex logic designs. Communication through the intermediacy of ion signals is clearly inspired from biological processes modulated by such signals, and implemented here with ion responsive molecules.
Co-reporter:Tugba Ozdemir, Ziya Kostereli, Ruslan Guliyev, Soydan Yalcin, Yavuz Dede and Engin U. Akkaya  
RSC Advances 2014 vol. 4(Issue 29) pp:14915-14918
Publication Date(Web):13 Mar 2014
DOI:10.1039/C4RA00989D
Tetrastyryl-substituted BODIPY dyes are likely to evolve into a new class of near IR fluorophores. In this work we demonstrate that 1,7 and 3,5-positions show marked differences in charge transfer characteristics. Using a Hg(II) selective ligand, the signal transduction potentials were explored: one isomer shows a large blue shift in electronic absorption spectrum, while the other just shows an intensity increase in the emission spectrum. Electronic structure calculations were undertaken to elucidate the reasons for different signals on metal ion binding in relation to core BODIPY properties.
Co-reporter:Fazli Sozmen, Safacan Kolemen, Henri-Obadja Kumada, Masahiro Ono, Hideo Saji and Engin U. Akkaya  
RSC Advances 2014 vol. 4(Issue 92) pp:51032-51037
Publication Date(Web):04 Sep 2014
DOI:10.1039/C4RA07754G
Styryl-congutated BODIPY dyes which are structurally similar to known Aβ peptide binding dyes, were designed and synthesized. The binding is accompanied by a large increase in the emission intensity in all cases, suggesting a high potential for use in the fluorescence imaging of Aβ plaques.
Co-reporter:Yusuf Cakmak, Tugrul Nalbantoglu, Tugce Durgut, Engin U. Akkaya
Tetrahedron Letters 2014 Volume 55(Issue 2) pp:538-540
Publication Date(Web):8 January 2014
DOI:10.1016/j.tetlet.2013.11.083
Heavy atom substituted Bodipy compounds, unlike the parent chromophore, undergo rapid intersystem crossing to generate singlet oxygen, which is the primary cytotoxic agent exploited in PDT. In this work, we show that an organic soluble calix[4]arene can be functionalized by Knoevenagel reaction and then converted into an amphiphilic photosensitizer in a few steps. In addition to generating a potentially useful photosensitizer, the sequence of reactions is the first use of a Bodipy dye as a chromophoric/fluorogenic label without the typical reactive functional groups.
Co-reporter:Safacan Kolemen, Yusuf Cakmak, Tugba Ozdemir, Sule Erten-Ela, Muhammed Buyuktemiz, Yavuz Dede, Engin U. Akkaya
Tetrahedron 2014 70(36) pp: 6229-6234
Publication Date(Web):
DOI:10.1016/j.tet.2014.03.049
Co-reporter:Ilke Simsek Turan;Fatma Pir Cakmak;Deniz Cansen Yildirim;Rengul Cetin-Atalay;Dr. Engin U. Akkaya
Chemistry - A European Journal 2014 Volume 20( Issue 49) pp:16088-16092
Publication Date(Web):
DOI:10.1002/chem.201405450

Abstract

Enhanced spatiotemporal selectivity in photonic sensitization of dissolved molecular oxygen is an important target for improving the potential and the practical applications of photodynamic therapy. Considering the high intracellular glutathione concentrations within cancer cells, a series of BODIPY-based sensitizers that can generate cytotoxic singlet oxygen only after glutathione-mediated cleavage of the electron-sink module were designed and synthesized. Cell culture studies not only validate our design, but also suggest an additional role for the relatively hydrophobic quencher module in the internalization of the photosensitizer.

Co-reporter:Ahmet Atilgan;Dr. Esra TanriverdiEçik;Dr. Ruslan Guliyev;T. Bilal Uyar;Dr. Sundus Erbas-Cakmak;Dr. Engin U. Akkaya
Angewandte Chemie International Edition 2014 Volume 53( Issue 40) pp:10678-10681
Publication Date(Web):
DOI:10.1002/anie.201405462

Abstract

A ligand incorporating a dithioethenyl moiety is cleaved into fragments which have a lower metal-ion affinity upon irradiation with low-energy red/near-IR light. The cleavage is a result of singlet oxygen generation which occurs on excitation of the photosensitizer modules. The method has many tunable factors that could make it a satisfactory caging strategy for metal ions.

Co-reporter:Ahmet Atilgan;Dr. Esra TanriverdiEçik;Dr. Ruslan Guliyev;T. Bilal Uyar;Dr. Sundus Erbas-Cakmak;Dr. Engin U. Akkaya
Angewandte Chemie 2014 Volume 126( Issue 40) pp:10854-10857
Publication Date(Web):
DOI:10.1002/ange.201405462

Abstract

A ligand incorporating a dithioethenyl moiety is cleaved into fragments which have a lower metal-ion affinity upon irradiation with low-energy red/near-IR light. The cleavage is a result of singlet oxygen generation which occurs on excitation of the photosensitizer modules. The method has many tunable factors that could make it a satisfactory caging strategy for metal ions.

Co-reporter:Sundus Erbas-Cakmak, O. Altan Bozdemir, Yusuf Cakmak and Engin U. Akkaya  
Chemical Science 2013 vol. 4(Issue 2) pp:858-862
Publication Date(Web):16 Oct 2012
DOI:10.1039/C2SC21499G
Guided by the digital design concepts, we synthesized a two-module molecular demultiplexer (DEMUX) where the output is switched between emission at near IR, and cytotoxic singlet oxygen, with light at 625 nm as the input (I), and acid as the control (c). In the neutral form, the compound fluoresces brightly under excitation at 625 nm, however, acid addition moves the absorption bands of the two modules in opposite directions, resulting in an effective reversal of excitation energy transfer direction, with a concomitant upsurge of singlet oxygen generation and decrease in emission intensity.
Co-reporter:Murat Isik, Tugba Ozdemir, Ilke Simsek Turan, Safacan Kolemen, and Engin U. Akkaya
Organic Letters 2013 Volume 15(Issue 1) pp:216-219
Publication Date(Web):December 20, 2012
DOI:10.1021/ol303306s
Judicious design of BODIPY dyes carrying nitroethenyl substituents in conjugation with the BODIPY core yields dyes that respond to biological thiols by both absorbance and emission changes. Incorporation of solubilizing ethyleneglycol units ensures water solubility. The result is bright signaling of biologically relevant thiols in the longer wavelength region of the visible spectrum and in aqueous solutions.
Co-reporter:Onur Buyukcakir, F.Tuba Yasar, O. Altan Bozdemir, Burcak Icli, and Engin U. Akkaya
Organic Letters 2013 Volume 15(Issue 5) pp:1012-1015
Publication Date(Web):February 11, 2013
DOI:10.1021/ol303495n
A bipyridinium dication-substituted Bodipy fluorophore, with a terminal carboxylic acid function, provides two alternative stations for cucurbit[7]uril. Changing pH from basic to acidic results in shuttling of the cucurbit[7]uril from one station to another. In addition, this shuttling is accompanied by a change in the emissive properties of the Bodipy dye, which is only observed in the presence of cucurbit[7]uril. More striking, is a demonstration of autonomous shuttling of the pseudorotaxane system in an oscillating pH system.
Co-reporter:Dr. Sundus Erbas-Cakmak;Dr. Engin U. Akkaya
Angewandte Chemie 2013 Volume 125( Issue 43) pp:11574-11578
Publication Date(Web):
DOI:10.1002/ange.201306177
Co-reporter:Dr. Sundus Erbas-Cakmak;Dr. Engin U. Akkaya
Angewandte Chemie International Edition 2013 Volume 52( Issue 43) pp:11364-11368
Publication Date(Web):
DOI:10.1002/anie.201306177
Co-reporter:Ruslan Guliyev, Seyma Ozturk, Ertan Sahin, and Engin U. Akkaya
Organic Letters 2012 Volume 14(Issue 6) pp:1528-1531
Publication Date(Web):February 29, 2012
DOI:10.1021/ol300260q
Oxalyl-tethered pyrroles can be doubly bridged with two difluoroboron chelating units to yield bright orange dyes. Interestingly, in polar organic solvents, the addition of fluoride and cyanide result in reversible detachment of the otherwise stable difluoroboron bridges, resulting in sharp changes in color. Thus, this novel compound behaves as a highly selective chromogenic sensor for fluoride and cyanide ions.
Co-reporter:Fazli Sozmen, Birsen S. Oksal, O. Altan Bozdemir, Onur Buyukcakir, and Engin U. Akkaya
Organic Letters 2012 Volume 14(Issue 20) pp:5286-5289
Publication Date(Web):October 10, 2012
DOI:10.1021/ol302451r
Bodipy dyes with integral phenanthroline and terpyridine units heteroleptically assemble in the presence of zinc(II) ions to form energy transfer cassettes. These discrete complexes exhibit an approach to modularly designed efficient energy transfer and light harvesting systems through metal ion coordination.
Co-reporter:Selin Duman, Yusuf Cakmak, Safacan Kolemen, Engin U. Akkaya, and Yavuz Dede
The Journal of Organic Chemistry 2012 Volume 77(Issue 10) pp:4516-4527
Publication Date(Web):April 24, 2012
DOI:10.1021/jo300051v
S0, S1, and T1 states of various orthogonal 8,8′ and 8,2′-bis-boradiaza-s-indacene (BODIPY) dyes, recently (Angew. Chem., Int. Ed.2011, 50, 11937) proposed as heavy atom free photosensitizers for O2(1Δg) generation, were studied by multireference quantum chemical approaches. S0→S1 excitation characteristics of certain bis-BODIPYs are shown to be drastically different than the parent BODIPY chromophore. Whereas a simple HOMO→LUMO-type single substitution perfectly accounts for the BODIPY core, S1 states of certain orthogonal bis-BODIPYs are described as linear combinations of doubly substituted (DS) configurations which overall yield four electrons in four singly occupied orbitals. Computed DS character of S1, strongly correlated with facile 1O2 production, was presumed to occur via S1→T1 intersystem crossing (ISC) of the sensitizer. Further confirmation of this relation was provided by newly synthesized BODIPY derivatives and comparison of spectroscopic properties of their dimers and monomers. Near-IR absorption, desired for potential photodynamic therapy applications, was not pursuable for bis-chromophores by the standard strategy of π-extension, as DS singlet states are destabilized. Decreased exchange coupling in π-extended cases appears to be responsible for this destabilization. Comparisons with iodine incorporated bis-BODIPYs suggest that the dynamics of 1O2 generation via DS S1 states are qualitatively different from that via ISC originating from heavy atom spin–orbit coupling. Although red-shifting the absorption wavelength to enter the therapeutic window does not seem attainable for orthogonal bis-BODIPYs with DS S1 states, modifications in the chromophore cores are shown to be promising in fine-tuning the excitation characteristics.
Co-reporter:Safacan Kolemen, O. Altan Bozdemir, Yusuf Cakmak, Gokhan Barin, Sule Erten-Ela, Magdalena Marszalek, Jun-Ho Yum, Shaik M. Zakeeruddin, Mohammad K. Nazeeruddin, Michael Grätzel and Engin U. Akkaya  
Chemical Science 2011 vol. 2(Issue 5) pp:949-954
Publication Date(Web):01 Mar 2011
DOI:10.1039/C0SC00649A
Versatility of Bodipy (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes was further expanded in recent dye-sensitized solar cell applications. Here we report a series of derivatives designed to address earlier problems in Bodipy sensitized solar cells. In the best case example, an overall efficiency of a modest 2.46% was achieved, but panchromatic nature of the dyes is quite impressive. This is the best reported efficiency in liquid electrolyte solar cells with Bodipy dyes as photosensitizers.
Co-reporter:Yusuf Cakmak;Safacan Kolemen;Selin Duman;Dr. Yavuz Dede;Yusuf Dolen;Bilal Kilic;Ziya Kostereli;Dr. Leyla Tatar Yildirim;Dr. A. Lale Dogan;Dr. Dicle Guc;Dr. Engin U. Akkaya
Angewandte Chemie 2011 Volume 123( Issue 50) pp:12143-12147
Publication Date(Web):
DOI:10.1002/ange.201105736
Co-reporter:Yusuf Cakmak;Safacan Kolemen;Selin Duman;Dr. Yavuz Dede;Yusuf Dolen;Bilal Kilic;Ziya Kostereli;Dr. Leyla Tatar Yildirim;Dr. A. Lale Dogan;Dr. Dicle Guc;Dr. Engin U. Akkaya
Angewandte Chemie International Edition 2011 Volume 50( Issue 50) pp:11937-11941
Publication Date(Web):
DOI:10.1002/anie.201105736
Co-reporter:Ruslan Guliyev;Seyma Ozturk;Ziya Kostereli;Dr. Engin U. Akkaya
Angewandte Chemie International Edition 2011 Volume 50( Issue 42) pp:9826-9831
Publication Date(Web):
DOI:10.1002/anie.201104228
Co-reporter:Dr. O. AltanBozdemir;Sundus Erbas-Cakmak;O. Oner Ekiz;Dr. Aykutlu Dana;Dr. Engin U. Akkaya
Angewandte Chemie 2011 Volume 123( Issue 46) pp:11099-11104
Publication Date(Web):
DOI:10.1002/ange.201104846
Co-reporter:Dr. O. AltanBozdemir;Sundus Erbas-Cakmak;O. Oner Ekiz;Dr. Aykutlu Dana;Dr. Engin U. Akkaya
Angewandte Chemie International Edition 2011 Volume 50( Issue 46) pp:10907-10912
Publication Date(Web):
DOI:10.1002/anie.201104846
Co-reporter:Ruslan Guliyev;Seyma Ozturk;Ziya Kostereli;Dr. Engin U. Akkaya
Angewandte Chemie 2011 Volume 123( Issue 42) pp:10000-10005
Publication Date(Web):
DOI:10.1002/ange.201104228
Co-reporter:Safacan Kolemen, Yusuf Cakmak, Sule Erten-Ela, Yigit Altay, Johannes Brendel, Mukundan Thelakkat and Engin U. Akkaya
Organic Letters 2010 Volume 12(Issue 17) pp:3812-3815
Publication Date(Web):August 12, 2010
DOI:10.1021/ol1014762
Boron-dipyrrin dyes, through rational design, yield promising new materials. With strong electron-donor functionalities and anchoring groups for attachment to nanocrystalline TiO2, these dyes proved useful as sensitizers in dye-sensitized solar cells. Their applicability in a solid-state electrolyte regime offers additional opportunities for practical applications.
Co-reporter:O. Altan Bozdemir, Fazli Sozmen, Onur Buyukcakir, Ruslan Guliyev, Yusuf Cakmak and Engin U. Akkaya
Organic Letters 2010 Volume 12(Issue 7) pp:1400-1403
Publication Date(Web):March 11, 2010
DOI:10.1021/ol100172w
Two Bodipy derivatives with silyl-protected phenolic functionalities signal fluoride concentrations both in solution and in a poly(methyl methacrylate) matrix. The exact location of the “nascent” phenolate group is important. If it is at the meso position, photoinduced electron transfer is triggered; however, if it is in full conjugation via a styryl moiety to the Bodipy core, strong intramolecular charge transfer is triggered, resulting in a large red shift in the absorbance peak. In either case, a selective methodology for fluoride sensing is the invariable result.
Co-reporter:Serdar Atilgan, Tugba Ozdemir, and Engin U. Akkaya
Organic Letters 2010 Volume 12(Issue 21) pp:4792-4795
Publication Date(Web):October 11, 2010
DOI:10.1021/ol1019426
Versatile chemistry of the Bodipy chromophore allows modular assembly of an excitation energy donor, acceptor, and a cation selective ligand in just a couple of steps. The new approach should be applicable in other designs which target molecular sensors with large Stokes shifts and red to near IR emission.
Co-reporter:O. Altan Bozdemir, M. Deniz Yilmaz, Onur Buyukcakir, Aleksander Siemiarczuk, Mehmet Tutas and Engin U. Akkaya  
New Journal of Chemistry 2010 vol. 34(Issue 1) pp:151-155
Publication Date(Web):03 Nov 2009
DOI:10.1039/B9NJ00380K
A convergent synthesis methodology, together with “click-chemistry” between azides and terminal alkynes, allows straighforward access to dendritic light harvesting systems. The novel dendrimer reported in this study has eight boradiazaindacene (BODIPY) units at the periphery and a perylenediimide (PDI) dye at the core. We have demonstrated that visible light is effectively collected as a result of the large absorption cross section of the dendrimer and efficiently channeled to the core PDI unit, resulting in a significant antenna effect. While being one of the very few energy transfer systems with a BODIPY and PDI chromophore pair, this novel dendritic molecule is one of the most efficient in light harvesting. The factors that may play important roles as the generation number increases also become apparent when emission characteristics were analyzed in comparison with a lower generation dendrimer.
Co-reporter:O.Altan Bozdemir Dr.;Yusuf Cakmak;Fazli Sozmen;Tugba Ozdemir;Alekser Siemiarczuk Dr.;EnginU. Akkaya Dr.
Chemistry - A European Journal 2010 Volume 16( Issue 21) pp:6346-6351
Publication Date(Web):
DOI:10.1002/chem.200903449

Abstract

Multichromophoric boron-dipyrromethene (Bodipy) dyes synthesized on phenylene-ethynylene platforms have been be converted to energy transfer cassettes in a one-step chemical transformation. Excitation energy transfer processes in these highly symmetrical derivatives were studied in detail, including time-resolved fluorescence spectroscopy techniques. Excitation spectra and the emission lifetimes suggest efficient energy transfer between the donor and acceptor chromophore. These novel energy transfer cassettes, while highlighting a short-cut approach to similar energy transfer systems, could be useful as large pseudo-Stokes shift multichromophoric dyes with potential applications in diverse applications.

Fenilenetilen platformu üzerinde sentezlenen multikromoforik Bodipy boyarmaddeleri, tek basamaklı bir kimyasal transformasyonla enerji transferi kasetlerine dönüştürülmüştür. Zaman ayrımlı floresans spektroskopisi tekniklerinin de içinde bulunduğu yöntemlerle, yüksek simetri öğeleri bulunduran bu türevlerdeki eksitasyon enerjisi transferi süreçleri ayrıntılı olarak çalışılmıştır. Eksitasyon spektrumları ve emisyon ömürlerindeki değişim, donör ve akseptör kromoforları arasında etkin bir enerji transferi olduğunu düşündürmektedir. Bu yeni enerji transfer kasetleri, benzer enerji transfer sistemlerine kolay bir geçiş yolu göstermekle birlikte, pek çok farklı alanda potansiyel uygulamaları olabilecek, büyük pseudo-Stokes kayması değerlerine sahip multikromoforik boyarmaddeler olarak da yararlı olabilirler.

Co-reporter:Onur Buyukcakir, O. Altan Bozdemir, Safacan Kolemen, Sundus Erbas and Engin U. Akkaya
Organic Letters 2009 Volume 11(Issue 20) pp:4644-4647
Publication Date(Web):September 16, 2009
DOI:10.1021/ol9019056
1,3,5,7-Tetramethyl-Bodipy derivatives undergo Knoevenagel-type condensations with aromatic aldehydes to ultimately yield tetrastyryl-Bodipy derivatives. The resulting dyes absorb and emit strongly in the near IR. As the versatility of the Bodipy dyes are fully appreciated, these new tetrastyryl dyes are likely to be featured in a variety of functional supramolecular systems.
Co-reporter:Tugba Ozdemir, Serdar Atilgan, Ilker Kutuk, Leyla T. Yildirim, Abdullah Tulek, Mehmet Bayindir and Engin U. Akkaya
Organic Letters 2009 Volume 11(Issue 10) pp:2105-2107
Publication Date(Web):April 20, 2009
DOI:10.1021/ol9005568
Bright fluorescence of the BODIPY dyes, just like most other fluorophores, is quenched in the solid state due to reabsorption and self-quenching. However, introduction of bulky tert-butyl substituents on the meso-phenyl groups result in more spaced packing in the solid state, resulting in highly luminescent powders and films.
Co-reporter:Sundus Erbas, Asli Gorgulu, Merve Kocakusakogullari and Engin U. Akkaya  
Chemical Communications 2009 (Issue 33) pp:4956-4958
Publication Date(Web):21 Jul 2009
DOI:10.1039/B908485A
Pyrenyl-functionalized distyryl-Bodipy sensitizer attached non-covalently to SWNTs was shown to generate singlet oxygen when excited at 660 nm with a red LED array; this work emphasizes the potential of SWNT as a viable alternative carrier of bioactive agents, including photodynamic therapy sensitizers.
Co-reporter:Gokhan Barin, M. Deniz Yilmaz, Engin U. Akkaya
Tetrahedron Letters 2009 50(15) pp: 1738-1740
Publication Date(Web):
DOI:10.1016/j.tetlet.2009.01.141
Co-reporter:Ö. Altan Bozdemir Dr.;Onur Büyükcakir;EnginU. Akkaya Dr.
Chemistry - A European Journal 2009 Volume 15( Issue 15) pp:3830-3838
Publication Date(Web):
DOI:10.1002/chem.200802538
Co-reporter:O. Altan Bozdemir ; Ruslan Guliyev ; Onur Buyukcakir ; Sencer Selcuk ; Safacan Kolemen ; Gulcihan Gulseren ; Tugrul Nalbantoglu ; Hande Boyaci
Journal of the American Chemical Society () pp:
Publication Date(Web):March 18, 2010
DOI:10.1021/ja1008163
Remarkably versatile chemistry of Bodipy dyes allows the design and straightforward synthesis of multivalent-multitopic derivatives, which, with judicious selection of metal ion−ligand pairs based on known affinities, affords control and manipulation of photoinduced electron transfer and internal charge transfer processes as desired. We have demonstrated that metal ions acting as modulators (or inputs, in digital design parlance) can generate absorbance changes in accordance with the operation of a half-adder. In addition, an AND logic gate in the emission mode was delivered using a different binucleating arrangement of ligands. A molecular equivalent of a three-input AND logic gate was also obtained exploiting differential binding affinities of metal ions for different ligands. The results suggest that different metal ions can be used as nonannihilating inputs, selectively targeting various ligands incorporated within a single fluorophore, and with careful design, diverse photophysical processes can be selectively modulated, resulting in a range of signals, useful in molecular logic design, and offering an enticing potential for multianalyte chemosensors.
Co-reporter:Safacan Kolemen, O. Altan Bozdemir, Yusuf Cakmak, Gokhan Barin, Sule Erten-Ela, Magdalena Marszalek, Jun-Ho Yum, Shaik M. Zakeeruddin, Mohammad K. Nazeeruddin, Michael Grätzel and Engin U. Akkaya
Chemical Science (2010-Present) 2011 - vol. 2(Issue 5) pp:NaN954-954
Publication Date(Web):2011/03/01
DOI:10.1039/C0SC00649A
Versatility of Bodipy (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes was further expanded in recent dye-sensitized solar cell applications. Here we report a series of derivatives designed to address earlier problems in Bodipy sensitized solar cells. In the best case example, an overall efficiency of a modest 2.46% was achieved, but panchromatic nature of the dyes is quite impressive. This is the best reported efficiency in liquid electrolyte solar cells with Bodipy dyes as photosensitizers.
Co-reporter:Sundus Erbas, Asli Gorgulu, Merve Kocakusakogullari and Engin U. Akkaya
Chemical Communications 2009(Issue 33) pp:NaN4958-4958
Publication Date(Web):2009/07/21
DOI:10.1039/B908485A
Pyrenyl-functionalized distyryl-Bodipy sensitizer attached non-covalently to SWNTs was shown to generate singlet oxygen when excited at 660 nm with a red LED array; this work emphasizes the potential of SWNT as a viable alternative carrier of bioactive agents, including photodynamic therapy sensitizers.
Co-reporter:Esra Tanriverdi Ecik, Ahmet Atilgan, Ruslan Guliyev, T. Bilal Uyar, Aysegul Gumus and Engin U. Akkaya
Dalton Transactions 2014 - vol. 43(Issue 1) pp:NaN70-70
Publication Date(Web):2013/09/30
DOI:10.1039/C3DT52375F
Systematic cascading of molecular logic gates is an important issue to be addressed for advancing research in this field. We have demonstrated that photochemically triggered metal ion signals can be utilized towards that goal. Thus, independent logic gates were shown to work together while keeping their identity in more complex logic designs. Communication through the intermediacy of ion signals is clearly inspired from biological processes modulated by such signals, and implemented here with ion responsive molecules.
Co-reporter:Seda Demirel Topel, Gunseli Turgut Cin and Engin U. Akkaya
Chemical Communications 2014 - vol. 50(Issue 64) pp:NaN8899-8899
Publication Date(Web):2014/06/16
DOI:10.1039/C4CC03387F
Orthogonal dimers of Bodipy were recently shown to be efficient generators of singlet oxygen. However, these dyes require green light for excitation, which would be very quickly attenuated inside the mammalian tissues. We now demonstrate that when these dyes are covalently attached to UCNPs, near IR irradiation results in very efficient generation of singlet oxygen.
Co-reporter:Sundus Erbas-Cakmak;O. Altan Bozdemir;Yusuf Cakmak
Chemical Science (2010-Present) 2013 - vol. 4(Issue 2) pp:
Publication Date(Web):2013/01/02
DOI:10.1039/C2SC21499G
Guided by the digital design concepts, we synthesized a two-module molecular demultiplexer (DEMUX) where the output is switched between emission at near IR, and cytotoxic singlet oxygen, with light at 625 nm as the input (I), and acid as the control (c). In the neutral form, the compound fluoresces brightly under excitation at 625 nm, however, acid addition moves the absorption bands of the two modules in opposite directions, resulting in an effective reversal of excitation energy transfer direction, with a concomitant upsurge of singlet oxygen generation and decrease in emission intensity.
Co-reporter:Sundus Erbas-Cakmak, Fatma Pir Cakmak, Seda Demirel Topel, Taha Bilal Uyar and Engin U. Akkaya
Chemical Communications 2015 - vol. 51(Issue 61) pp:NaN12261-12261
Publication Date(Web):2015/06/22
DOI:10.1039/C5CC01261A
A series of pH and GSH responsive photosensitizers were designed and synthesized. pKa values were optimized by adjusting the inductive contribution of substituents to reach a pH range (6.0–7.4) relevant to the tumour microenvironment. pH-Activatable behaviour and redox mediated release of the quencher from the PS by GSH allow the construction of an AND logic operator for selective photodynamic action in aqueous solutions.