Publications

52. Khan, S. A.; Surme, S.; Eren, G. O.; Almammadov, T.; Pehlivan, Ç.; Kaya, L.; Hassnain, M.; Onal, A.; Balamur, R.; Şahin, A.; Vanalakar, S.; Kolemen, S.; Alkan, F.; Kavakli, I. H.; Nizamoglu S.* “Sulfide-Capped InP/ZnS Quantum Dot Nanoassemblies for a Photoactive Antibacterial Surface” ACS Appl. Nano Mater., 2024, 10.1021/acsanm.3c05640

51. Dirak, M.; Yenici, C.; Kolemen, S.* “Recent advances in organelle-targeted organic photosensitizers for efficient photodynamic therapy” Coord. Chem. Rev., 2024, 10.1016/j.ccr.2024.215710

50. Bosson, J.*; Dirak, M.; Knysh, I.; Jacquemin, D.*; Kolemen, S.* “A rapid access to activity-based and mitochondria targeting rhodol-like chromenoxanthene dyes for selective bioimaging” Dyes Pigm., 2024, 10.1016/j.dyepig.2024.111952

49. Dirak, M.; Chan, J.; Kolemen, S.* “Optical imaging probes for selective detection of butyrylcholinesterase” J. Mater. Chem. B, 2024, 10.1039/D3TB02468G

48. Khan, S. U.; Eren, G. O.; Atac, N; Onal, A; Qureshi, M. H.; Cooper, F. K.; Almammadov, T.; Kolemen, S.;  Sahin M.; Can F.; Nizamoglu S. “Antibacterial type-II InP/ZnO quantum dots via multimodal reactive oxygen species” Chem. Eng. J., 2024, 10.1016/j.cej.2023.148140

47. Almammadov, T.*; Dirak, M.; Saymaz, A.; Acari, A.; Kolemen, S.* “A hydrogen sulfide and tyrosinase responsive dual-locked fluorophore for selective imaging of melanoma cells” Chem. Commun., 2023, 10.1039/D3CC02676K

46. Gunduz, H.; Almammadov T.; Dirak M.; Acari, A.; Bozkurt B.; Kolemen S.* “A mitochondria-targeted chemiluminescent probe for detection of hydrogen sulfide in cancer cells, human serum and in vivo” RSC Chem. Biol., 2023, 10.1039/d3cb00070b

45. Acari, A.; Almammadov, T.; Dirak, M.; Gulsoy, G.; Kolemen, S.* “Real-time visualization of butyrylcholinesterase activity using a highly selective and sensitive chemiluminescent probe” J. Mater. Chem. B, 2023, 10.1039/d3tb01022h

44. Dirak, M.; Turan, S. E.; Kolemen, S.* “Hydrogen Sulfide Responsive Phototherapy Agents: Design Strategies and Biological Applications” ACS Bio Med Chem Au, 2023, 10.1021/acsbiomedchemau.3c00028

43. Celikbas, E.; Saymaz, A.; Gunduz, H.; Koc, I.; Cakir, E.; Sennaroglu, A.; Kolemen, S.*; Yagci Acar, H.*; Onbasli, K.*  “Image-Guided Enhanced PDT/PTT Combination Therapy Using Brominated Hemicyanine-Loaded Folate Receptor-Targeting Ag2S Quantum Dots” BioconjugateChem., 2023, 10.1021/acs.bioconjchem.3c00096
42. Kilic, E.; Dirak, M.; Kolemen, S.* “Activatable Photodynamic Photosensitizers for Cancer Treatment” in Fluorescent Chemosensors, ed. by Tony D. James, Luling Wu, Adam C. Sedgewick and Xiao-Peng He, Royal Society of Chemistry (RSC), 2023, 345-377, 10.1039/9781839167324-00345

41. Gunduz, H.; Acari, A.; Cetin, S.; Almammadov, T.; Pinarbasi-Degirmenci, N.; Dirak, M.; Cingoz, A.; Kilic, E.; Bagci-Onder, T.; Kolemen, S.* “Directing chemiluminescent dioxetanes to mitochondria: A cationic luminophore enables in vitro and in vivo detection of cancer cells upon enzymatic activation”Sens. Actuators B Chem.,2023, 10.1016/j.snb.2023.133574

40. Dirak, M.; Kepil, D.; Almammadov, T.; Elmaoglu, Z.; Cetin, S.; Ozogul, N.; Gunbas, G.*; Kolemen, S.* “Selective monitoring and treatment of neuroblastoma cells with hydrogen sulfide activatable phototheranostic agent”Dyes Pigm.,2023, 10.1016/j.dyepig.2022.111011

39. Ozsan, C.; Kailass, K.; Digby, E. M.;Almammadov, T.; Beharry, A. A.;*Kolemen, S.*“Selective detection of carboxylesterase 2 activity in cancer cells using an activity-based chemiluminescent probe”Chem. Commun.,2022, 10.1039/D2CC03309G

38. Ozketen, A. C.; Karaman, O.; Ozdemir, A.; Soysal, I.; Kizilenis; C.; Ntelichatzioglou, A.; Cicek, Y. A.;Kolemen, S.; Gunbas, G. “Selenophene Modified BODIPY-Based Photosensitizers Exhibit Photodynamic Inhibition on Broad Range of Bacteria”ACS Omega,2022, 10.1021/acsomega.2c02868

37. Almammadov, T.; Elmazoglu, Z.; Atakan, G.;Kepil, D.; Aykent, G.;Kolemen, S.;* Gunbas, G.*“Locked and loaded: β-galactosidase activated photodynamic therapy agent enables selective imaging and targeted treatment of glioblastoma multiforme cancer cells”ACS Appl. Biomater.2022,10.1021/acsabm.2c00484 (Highlighted on theCover)

36. Sertcelik Ozvural, K. N; Karaman, O.; Almammadov, T.; Gunbas, G.;* Kolemen, S.;* Yagci Acar, H.;* Bilici, K.* “Selective on the outside deadly on the inside: Superior photodynamic therapy of EGFR positive colon cancer cells by selenophene-BODIPY loaded SPIONs” ChemPhotoChem, 2022, 10.1002/cptc.202200104

35. Yabaş, E.; Kölemen, S.; Biçer, E.; Almammadov, T.; Başer, P.; Kul, M. “Organo-soluble dendritic zinc phthalocyanine: photoluminescence and fluorescence properties” Inorg. Nano-Met. Chem., 2022, 10.1080/24701556.2022.2078360

34. Xiang, C.; Dirak, M.; Luo, Y.; Peng, Y.; Cai, L.; Gong, P.*; Zhang, P.*; Kolemen, S.* “A responsive AIE-active fluorescent probe for visualization of acetylcholinesterase activity in vitro and in vivo” Mater. Chem. Front., 2022, 10.1039/D2QM00239F

33. Kilic, E.; Elmazoglu, Z.; Almammadov, T.; Kepil, D.; Etienne, T.; Marion, A.; Gunbas, G.*; Kolemen, S.* “Activity-Based Photosensitizers with Optimized Triplet State Characteristics Toward Cancer Cell Selective and Image Guided Photodynamic Therapy” ACS Appl. Bio Mater., 2022, 10.1021/acsabm.2c00202.

32. Savani, S.; Onbasli, K.; Gunduz, H.; Aydındogan, E.; Erkısa, M.; Muti, A.; Khan, M.; Sennaroglu, A.; Ulukaya, E.; Yagci Acar, H.*; Kolemen, S.* “Development of a cysteine responsive chlorinated hemicyanine for image-guided dual phototherapy” Bioorg. Chem., 2022, 122, 105725.

31. Xiang, C.; Li, C.; Xiang, J.;  Luo, Y.;  Peng, J.; Deng, G.; Wang, J.; Kolemen, S.; Li, H.; Zhang, P.; Gong P.; Cai, L. “An Easily Available Lysosomal-targeted Ratiometric Fluorescent Probe with Aggregation Induced Emission Characteristics for Hydrogen Polysulfide Visualization in Acute Ulcerative Colitis”Mater. Chem. Front., 2021, 5, 7638-7644

30. Arslan, B.; Bilici, K.;* Durmaz, G.; Almammadov, T.; Khan, M.; Sennaroglu, A.; Yagci Acar, H.; Kolemen, S.* “A Leucine Aminopeptidase Activatable Photosensitizer for Cancer Cell Selective Photodynamic Therapy Action” Dyes Pigm., 2021, 195, 109735.

29. Kolemen, S.* “A Near-infrared Benzothiazole-based Chemodosimeter for Rapid and Selective Detection of Hydrogen Sulfide”JOTCSA, 2021, 8, 567-578.

28. Bilici K, Cetin S, Aydındogan E,Yagci Acar H.* and Kolemen S.*  Recent Advances in Cyanine-Based Phototherapy Agents. Front. Chem., 2021, 9, 707876.

27. Almammadov, T.; Kolemen, S.*. “A hydrogen peroxide responsive resorufin-based phototheranostic agent for selective treatment of cancer cells” Dyes Pigm., 2021, 193, 109499.

26. Gunduz, H.; Bilici, K.; Cetin, S.; Muti, A.; Sennaroglu, A.*; Acar, H. Y.*; Kolemen, S.*. “Dual Laser Activatable Brominated Hemicyanine as a Highly Efficient and Photostable Multimodal Phototherapy Agent” J. Photochem. Photobiol. B: Biology, 2021, 217, 112171.

25. Cetin, S.; Elmazoglu, Z.; Karaman, O.; Gunduz, H.; Gunbas, G.*; Kolemen, S.*. “Balanced Intersystem Crossing in Iodinated Silicon-Fluoresceins Allows New Class of Red Emissive Theranostic Agents” ACS Med. Chem. Lett.2021, 12, 5, 752–757.

24. Gunduz, H.; Kolemen, S.*; Akkaya, E. U.*. “Singlet oxygen probes: Diversity in signal generation mechanisms yields a larger color palette” Coord. Chem. Rev., 2021, 429, 213641.

23. Almammadov, T.; Atakan, G.; Leylek, O.; Ozcan, G.*; Gunbas, G.*; Kolemen, S.*. “Resorufin Enters the Photodynamic Therapy Arena: A Monoamine Oxidase Activatable Agent for Selective Cytotoxicity” ACS Med. Chem. Lett. 2020, 11, 2491-2496

22. Kalay, E.; Cetin, S.; Kolemen, S.*; Metin, Ö*. ” A facile synthesis of mesoporous graphitic carbon nitride supported palladium nanoparticles as highly effective and reusable catalysts for Stille coupling reactions under mild conditions” New J. Chem., 2020, 44, 6714-6723

21. Karaman, O.; Almammadov, T.; Gedik, M. E.; Gunaydin, G.*; Kolemen, S.*; Gunbas, G.* “Mitochondria‐Targeting Selenophene‐Modified BODIPY‐Based Photosensitizers for the Treatment of Hypoxic Cancer Cells” ChemMedChem, 2019, 14, 1879-1886

20. Erbas-Cakmak, S.; Kolemen, S.; Sedgwick, A. C.; Gunnlaugsson, T.; James, T. D.; Yoon, J.; Akkaya, E. U. “Molecular logic gates: the past, present and future” Chem Soc. Rev., 2018, 47, 2228-2248.

19. Kolemen, S*.; Akkaya, E. U. “Reaction-Based BODIPY Probes for Selective Bio- Imaging” Coord. Chem. Rev., 2018, 354, 121-134.

18. Jia, S.; Ramos-Torres, K. M.; Kolemen, S.; Ackerman, C. M.; Chang, C. J. “‘Tuning the Color Palette of Fluorescent Copper Sensors through Systematic Heteroatom Substitution at Rhodol Cores” ACS Chem. Biol., 2018, 13, 7, 1844-1852.

Before Koc University

17. Ozdemir, T.; Lu, Y.-C.; Kolemen, S.; Tanriverdi-Ecik, E.; Akkaya, E. U. “Generation of Singlet Oxygen by ex situ Sensitized Persistent Luminescent Nanoparticles-Photosensitizer Conjugates: A proof of Principle for PDT without Light” ChemPhotoChem, 2017, 1, 183-187.

16. Li, X.; Kolemen, S.; Akkaya, E. U.; Yoon, J.; “Activatable Photosensitizers: Agents for Selective Photodynamic Therapy” Adv. Funct. Mater., 2017, 27, 1604053.

15. Ramos-Torres, K. M.; Kolemen, S.; Chang, C. J. “Thioether Receptors for Selective Copper   Detection by Fluorescence and MRI” Isr. J. Chem, 2016, 56, 9-10, 724-737.

14. Kolemen, S.; Ozdemir, T.; Lee, D.; Kim, G.M.; Karatas, T.; Yoon, J.; Akkaya, E. U. “Remote Controlled Release of Singlet Oxygen via Plasmonic Heating of Gold Nanorods: Towards a Paradigm Change in Photodynamic Therapy” Angew. Chem. Int. Ed., 2016, 55, 3606-3610.

13. Cakmak, Y.; Kolemen, S.; Buyuktemiz, M.; Dede, Y.; Erten-Ela, S. “Synthesis and dye sensitized solar cell applications of Bodipy derivatives with bis-dimethylfluorenyl amine donor groups” New. J. Chem., 2015, 39, 4086-4092.

12. Kolemen, S.; Isik, M.; Kim, G. M.; Kim, D.; Geng, H.; Buyuktemiz, M.; Zhang, X. F.; Dede, Y.; Yoon, J.; Akkaya, E. U. “Intracellular Modulation of Excited States Dynamics in a Chromophore Dyad: Differential Enhancement of Photocytotoxicity Targeting Cancer Cells” Angew. Chem. Int. Ed., 2015, 54, 5340-5344. Highlighted on the Front Cover.

11. Sozmen, F.; Kolemen, S.; Kumada, H. O.; Ono, M.; Saji, H.; Akkaya, E. U. “Designing Bodipy-Based Probes for Fluorescence Imaging of β-amyloid Plaques” RSC Advances, 2014, 4, 51032-51037.

10. Isik, M.; Guliyev, R.; Kolemen, S.; Altay, Y.; Senturk, B.; Tekinay, T.; Akkaya, E. U. “Designing a Glutathione Selective Fluorescent Sensor: “The Use of Multiple Modulators in Signal Transduction” Org. Lett., 2014, 16, 3260-3263.

9. Kolemen, S.; Cakmak, Y.; Ozdemir, T.; Erten-Ela, S.; Buyuktemiz, M.; Dede, Y.; Akkaya, E. U. “Design and Characterization of Bodipy Derivatives for Bulk Heterojunction Solar Cells” Tetrahedron, 2014, 70, 6229-6234.  

8. Kolemen, S.; Cakmak, Y.; Kostereli, Z.; Akkaya, E. U. “Atropisomeric Dyes: “Axial Chirality in Orthogonal BODIPY Oligomers” Org. Lett., 2014, 16, 660-663.

7. Isik, M.; Ozdemir, T.; Turan Simsek, I.; Kolemen, S.; Akkaya, E. U. “Chromogenic and Fluorogenic Sensing of Biological Thiols in Aqueous Solutions Using BODIPY-Based Reagents” Org. Lett., 2013, 15, 216-219.  

6. Duman S.; Cakmak, Y.; Kolemen, S.; Akkaya, E. U.; Dede, Y. “Heavy Atom Free Singlet Oxygen Generation: Doubly Substituted Configurations Dominate S-1 States of Bis-BODIPYs” J. Org. Chem., 2012, 77, 4516-4527.

5. Cakmak, Y.; Kolemen, S.; Duman, S.; Dede, Y.; Dolen, Y.; Kilic, B.; Kostereli, Z.; Yildirim, L. T.; Dogan, A. L.; Guc, D.; Akkaya, E. U. “Designing Excited States: Theory-Guided Access to Efficient Photosensitizers for Photodynamic Action” Angew. Chem. Int. Ed., 2011, 50, 11937-11941.

4. Kolemen, S.; Bozdemir, O. A.; Cakmak, Y.; Barin, G.; Erten-Ela, S.; Marszalek, M.; Jun, J.-H.; Zakeeruddin, S. M.; Nazeeruddin, M. K.; Gratzel, M.; Akkaya, E. U. “Optimization of distyryl-Bodipy chromophores for efficient panchromatic sensitization in dye sensitized solar cells” Chem. Sci., 2011, 2, 949-954.

3. Kolemen, S.; Cakmak, Y.; Erten-Ela, S.; Altay, Y.; Brendel, J.; Thelakkat, M.; Akkaya, E. U. “Solid-State Dye-Sensitized Solar Cells Using Red and Near-IR Absorbing Bodipy Sensitizers” Org. Lett., 2010, 12, 3812-3815.

2. Bozdemir, O.A.; Guliyev, R.; Buyukcakir, O.; Selcuk, S.; Kolemen, S.; Gulseren, G.; Nalbantoglu, T.; Boyaci, H.; Akkaya, E.U. “Selective Manipulation of ICT and PET Processes in Styryl-Bodipy Derivatives: Applications in Molecular Logic and Fluorescence Sensing of Metal Ions” J. Am. Chem. Soc., 2010, 132, 8029-8036. Highlighted on the Front Cover.

1. Buyukcakir, O.; Bozdemir, O. A.; Kolemen, S.; Erbas, S.; Akkaya, E. U. “Tetrastyryl-Bodipy Dyes: Convenient Synthesis and Characterization of Elusive Near IR Fluorophores” Org. Lett., 2009, 11, 4644-4647.