Publications
Bridging Dimensions: Computational Chemistry Across Scales and Systems
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HeatingEffectontheLiquid-Crystalline Octakis(hexylthio)zinc(II) Phthalocyanine Thin Film Sensor for the Detection of Chlorinated Hydrocarbon Vapors and Interaction Mechanism Analysis Using Density Functional Theory.
HeatingEffectontheLiquid-Crystalline Octakis(hexylthio)zinc(II) Phthalocyanine Thin Film Sensor for the Detection of Chlorinated Hydrocarbon Vapors and Interaction Mechanism Analysis Using Density Functional Theory.
ACS Omega, 2026, 11, 2034-2045.
Özer, Z.; Gümüşgüz, G.; Capan, I.; Dedeoglu, B.; Gürek, A.G.; Capan, R.
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Synthesis, characterization, ADME, molecular docking, in silico structural and mechanistic studies and biological activities of Pt(IV) complexes based on diamine derivatives.
Synthesis, characterization, ADME, molecular docking, in silico structural and mechanistic studies and biological activities of Pt(IV) complexes based on diamine derivatives.
Applied Organometallic Chemistry, 2025, 39:e70323.
Majeed, S.R.; Amin, M.A.; Goren, H.Y.; Dedeoglu, B.; Attaby, F.F.; Soliman, A.A.
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Enthalpy of Formation of Polycyclic Aromatic Hydrocarbons and Heterocyclic Aromatic Compounds.
Enthalpy of Formation of Polycyclic Aromatic Hydrocarbons and Heterocyclic Aromatic Compounds.
ACS Omega, 2025, 10 (22), 23433-23439.
Cilesiz, U.; Sincer, E.Y.; Dedeoglu, B.; Aviyente, V.
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p-Phenyleneethynylene unit-conjugated dimeric zinc-phthalocyanines in bulk heterojunction solar cell: A comparative experimental and theoretical study.
p-Phenyleneethynylene unit-conjugated dimeric zinc-phthalocyanines in bulk heterojunction solar cell: A comparative experimental and theoretical study.
New Journal of Chemistry, 2025, 49, 8102-8113.
Tunç, G.; Gumusgoz Celik, G.; Canımkurbey, B.; Dedeoglu, B.; Gurek, A.G.
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Design, synthesis and in vitro evaluations of new cyclotriphosphazenes as safe drug candidates.
Design, synthesis and in vitro evaluations of new cyclotriphosphazenes as safe drug candidates.
RSC Medicinal Chemistry, 2025, 16, 2061-2077.
Gül, E.Y.; Tiryaki, B.; Köse, B.; Öztürk, N.; Okutan, E.; Dedeoglu, B.; Tanrıverdi Eçik, E.
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Computational assessment of the platinum (II) complex of imidazolidine dioximes substituted with methoxydiglycol units: from activation to DNA binding.
Computational assessment of the platinum (II) complex of imidazolidine dioximes substituted with methoxydiglycol units: from activation to DNA binding.
BAUN J. Inst. Sci. Technol., 2025, 27(1), 218-227.
Dedeoglu, B.
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Kinetic Barrier to Enzyme Inhibition is Manipulated by Dynamical Local Interactions in E. coli DHFR.
Kinetic Barrier to Enzyme Inhibition is Manipulated by Dynamical Local Interactions in E. coli DHFR.
J. Chem. Inf. Model., 2023, 63, 4839-4849.
Cetin, E.; Guclu, T.F.; Kantarcioglu, I.; Gaszek, I.K.; Toprak, E.; Atilgan, A.R.; Dedeoglu, B.;* Atilgan, C.*
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Enhancing supramolecular assembly in BODIPY derivatives: Harnessing halogen bonding for cocrystal design.
Enhancing supramolecular assembly in BODIPY derivatives: Harnessing halogen bonding for cocrystal design.
Crsytal Growth and Design, 2023, 23 (10), 7285-7294.
Gümüşgöz, G.; Dedeoglu, B.; Gül, A.G.; Zorlu, Y.; Ayhan, M.M.
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Theoretical investigation of the hydrolysis and DNA binding of platinum (II) complexes of imidazolidine dioximes.
Theoretical investigation of the hydrolysis and DNA binding of platinum (II) complexes of imidazolidine dioximes.
Mol. Phys., 2023, 121 (22), e2236244.
Emirik, Ö.F.; Şanlı, C.; Ahsen, V.; Gürek, A.G.; Dedeoglu, B.*
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Engineering supramolecular helical assemblies via interplay between carbon (sp) tetrel and halogen bonding interactions.
Engineering supramolecular helical assemblies via interplay between carbon (sp) tetrel and halogen bonding interactions.
Phys. Chem. Chem. Phys., 2023, 25 (16), 11493-11500.
Dedeoglu, B.; Gürek, A.G.; Zorlu, Y.; Ayhan, M.M.;
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The chemical and electrochemical stimuli viologen substituted phtalocyanine with tunable optical properties.
The chemical and electrochemical stimuli viologen substituted phtalocyanine with tunable optical properties.
Turkish Journal of Chemistry, 2023, 47 (5), 1149-1159.
Ates, Ö.D.; Tunç, G.; Şenocak, A.;Dedeoglu, B.; Ayhan, M.M.; Gürek, A.G.
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Computational Assessment of Iron Release from the N- and C- Lobes of Human Serum Transferrin.
Computational Assessment of Iron Release from the N- and C- Lobes of Human Serum Transferrin.
OBC, 2022, 20, 8766-8774.
Koca Fındık, B.; Çilesiz, U.; Bali, S.K.; Atılgan, C.; Aviyente, V.; Dedeoglu, B.*;
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Co2+, Fe2+, and Ni2+: Modifiers for Photocatalytic Deposition of Highly Active Pt on Graphene-based Supports.
Co2+, Fe2+, and Ni2+: Modifiers for Photocatalytic Deposition of Highly Active Pt on Graphene-based Supports.
ACS Appl. Energy Mater. 2022, 5, 11, 13939–13951.
Haghmoradi, N.; Sarı, Z.T.; Kırlıoğlu, A.C.; Yarar Kaplan, B.; Dedeoglu, B.; Zahedimaram, P.; Abdolhosseinzadeh, S.; Alkan Gürsel, S.
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Theoretical Investigation of the Biogenetic Pathway for Formation of Antibacterial Indole Alkaloids from Voacanga Africana.
Theoretical Investigation of the Biogenetic Pathway for Formation of Antibacterial Indole Alkaloids from Voacanga Africana.
ACS Omega, 2022, 7, 31591−31596.
Soysal, E.N.; Findik, V.; Dedeoglu, B.; Aviyente, V.; Tantillo, D.J.
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Exploring Halogen···Halogen Interactions in Supramolecular Self-Assembly of BODIPY Networks.
Exploring Halogen···Halogen Interactions in Supramolecular Self-Assembly of BODIPY Networks.
CrystEngComm, 2022, 24, 5630-5641.
Topaloğlu-Aksoy, B.; Dedeoglu, B.; Zorlu, Y.; Ayhan, M.M.; Çoşut, B.
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Synthesis, Crystal Structure and Electronic Applications of Monocarboxylic Acid Substituted Phthalonitrile Derivatives Combined with DFT studies.
Synthesis, Crystal Structure and Electronic Applications of Monocarboxylic Acid Substituted Phthalonitrile Derivatives Combined with DFT studies.
Journal of Molecular Structure, 1240, 130545.
Tunç, G.; Canımkurbey, B.; Dedeoglu, B.; Zorlu, Y.; Eryılmaz, S.; Gürek, A.G.
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Carbon (sp 3) tetrel bonding mediated BODIPY supramolecular assembly via unprecedented synergy of C sp3⋯ N and C sp3⋯ F pair interactions.
Carbon (sp 3) tetrel bonding mediated BODIPY supramolecular assembly via unprecedented synergy of C sp3⋯ N and C sp3⋯ F pair interactions.
CrystEngComm, 2021, 23, 268-272.
Ayhan, M.M.; Özcan, E.; Dedeoglu, B.; Chumakov, Y.; Zorlu, Y.; Çoşut, B.
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Modulation of supramolecular self-assembly of BODIPY tectons via halogen bonding.
Modulation of supramolecular self-assembly of BODIPY tectons via halogen bonding.
CrystEngComm, 2021, 23, 6365-6375.
Özcan, E.; Dedeoglu, B.; Chumakov, Y.; Zorlu, Y.; Çoşut, B.; Ayhan, M.M.
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Halogen‐Bonded BODIPY Frameworks with Tunable Optical Features.
Halogen‐Bonded BODIPY Frameworks with Tunable Optical Features.
Chemistry–A European Journal, 2021, 27, 1603-1608.
Ayhan, M.M.; Özcan, E.; Dedeoglu, B.; Chumakov, Y.; Gürek, A.G.; Zorlu, Y.; Çoşut, B.
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Elucidation of the Mechanism of Silver-Catalyzed Inverse Electron-Demand Diels-Alder (IEDDA) Reaction of 1,2-Diazines and Siloxy Alkynes.
Elucidation of the Mechanism of Silver-Catalyzed Inverse Electron-Demand Diels-Alder (IEDDA) Reaction of 1,2-Diazines and Siloxy Alkynes.
ChemCatChem, 2020, 12, 366– 372.
Avcı, O.N.; Catak, S.; Dereli, B.; Aviyente, V.; Dedeoglu, B.*
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Influence of odd– even effect and intermolecular interactions in 2D molecular layers of bisamide organogelators.
Influence of odd– even effect and intermolecular interactions in 2D molecular layers of bisamide organogelators.
RSC Advances, 2018, 8, 35195.
Kocasoy, V.; Dedeoglu, B.*; Demir-Ordu, Oznur; Aviyente, V.
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Computational approaches for deciphering equilibrium and kinetic properties of iron transport proteins.
Computational approaches for deciphering equilibrium and kinetic properties of iron transport proteins.
Metallomics, 2017, 9, 1513-1533.
Abdizadeh, H.; Atilgan, A.R.; Atilgan, C.; Dedeoglu, B.
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1,3-Dipolar Cycloaddition Reactions of Low-Valent Rhodium and Iridium Carboranyl and Cyclopentadienyl Complexes with Arylnitrile N-Oxides.
1,3-Dipolar Cycloaddition Reactions of Low-Valent Rhodium and Iridium Carboranyl and Cyclopentadienyl Complexes with Arylnitrile N-Oxides.
Journal of Organic Chemistry, 2017, 82, 5096–5101.
Ugur, I.; Agopcan Cinar, S.; Dedeoglu, B.; Aviyente, V.; Hawthorne, M. F.; Liu, P.; Liu, F.; Houk, K.N.; Jiménez-Osése, G.
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Structure-Reactivity Relationships of Novel Monomeric Photoinitiators.
Structure-Reactivity Relationships of Novel Monomeric Photoinitiators.
Journal of Photochemistry and Photobiology A: Chemistry, 2016, 329, 77-87.
Agopcan Cinar, S.; Guven, M. N.; Eren, T. N.; Cesur, B.; Aleksanyan, M.; Dedeoglu, B.; Okte, N.; Aviyente, V.; Morlet-Savary, F.; Lalevee, J.
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Computational Studies on Cinchona Alkaloid-Catalyzed Asymmetric Organic Reactions.
Computational Studies on Cinchona Alkaloid-Catalyzed Asymmetric Organic Reactions.
Accounts of Chemical Research 2016, 49, 1250 – 1262.
Tanriver, G.; Dedeoglu, B.; Catak, S.; Aviyente, V.
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Cinchona Alkaloid Catalyzed Asymmetric Desymmetrization of meso-Cyclic Anhydrides: The Origins of Stereoselectivity.
Cinchona Alkaloid Catalyzed Asymmetric Desymmetrization of meso-Cyclic Anhydrides: The Origins of Stereoselectivity.
ChemCatChem 2015, 7, 4173 – 4179.
Dedeoglu, B.; Catak, S.; Yildirim, A.; Bolm, C.; Aviyente, V.
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Rhenium(V) Complexes Containing Mono- and Tridentate Imido Ligands: Crystal Structures, Spectroscopic Results and DFT Optimization.
Rhenium(V) Complexes Containing Mono- and Tridentate Imido Ligands: Crystal Structures, Spectroscopic Results and DFT Optimization.
S. Afr. J. Chem., 2014, 67, 189–197.
Schmitt, B.; Sabanci, N.; Dedeoglu, B.; Aviyente, V.; Hosten, E.; Gerber, T.I.A.; Habarurema, G.
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Detection of Nitroaromatic Explosives Based on Fluorescence Quenching of Silafluorene- and Silole-Containing Polymers: A Time Dependent-Density Functional Theory Study.
Detection of Nitroaromatic Explosives Based on Fluorescence Quenching of Silafluorene- and Silole-Containing Polymers: A Time Dependent-Density Functional Theory Study.
J. Phys. Chem. C, 2014, 118, 23946 - 23953.
Dedeoglu, B.; Monari, A.; Etienne, T.; Aviyente, V.; Özen, A.S.
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Computational Insight into the Explosive Detection Mechanisms in Silafluorene- and Silole-Containing Photoluminescent Polymers.
Computational Insight into the Explosive Detection Mechanisms in Silafluorene- and Silole-Containing Photoluminescent Polymers.
J. Phys. Chem. C, 2014, 118, 6385−6397.
Dedeoglu, B.; Aviyente, V.; Özen, A.S.
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First RAFT polymerization of captodative 2-acetamidoacrylic acid (AAA) monomer: An experimental and theoretical study.
First RAFT polymerization of captodative 2-acetamidoacrylic acid (AAA) monomer: An experimental and theoretical study.
Polymer, 2013, 54, 5122-5132.
Dedeoglu B., Ugur I., Degirmenci I, Aviyente V., Barcin B., Cayli G., Acar H.
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Peptide nanotube formation: a crystal growth process.
Peptide nanotube formation: a crystal growth process.
Soft Matter, 2012, 8, 7463-7470.
Cenker, Ç. C.; Bomans, P. H. H.; Friedrich, H.; Dedeoglu, B.; Aviyente, V.; Olsson, U.; Sommerdijk, N.A.J.M.; Bucak, S.
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Selectivity in the aggregates of the chiral organolithium N-Boc-2-lithiopiperidine with a chiral ligand: A DFT study.
Selectivity in the aggregates of the chiral organolithium N-Boc-2-lithiopiperidine with a chiral ligand: A DFT study.
Molecular Physics 2012, 110, 353–359.
Ince, H.H.; Dedeoglu, B.; Gul, S.; Aviyente, V.; Coldham, I.
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Theoretical Study of the Mechanism of the Desymmetrization of Cyclic meso-Anhydrides by Chiral Amino Alcohols.
Theoretical Study of the Mechanism of the Desymmetrization of Cyclic meso-Anhydrides by Chiral Amino Alcohols.
ChemCatChem, 2010, 2, 1122–1129.
Dedeoglu, B.; Catak, S.; Houk, K.N.; Aviyente, V. A
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