Research
Bridging Dimensions: Computational Chemistry Across Scales and Systems
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Research Overview
Research Overview
The research activities of the BD Computational Chemistry Research Group focus on the application of quantum chemical methods and molecular simulations to understand chemical reactivity, molecular function, and structure–property relationships across scales and systems. Our work spans a wide range of chemical domains, including organic and organometallic reactions and organocatalysis, multiscale modeling of biomolecular systems, noncovalent interactions governing molecular assembly, and the development of functional molecular materials with optical, electronic, sensing, and energy-relevant properties.
By bridging dimensions from molecular-level mechanisms to complex biological and material systems, our research provides mechanistic and kinetic insight that not only complements experimental studies but also actively guides experimental design through close interdisciplinary collaboration.
Main Research Themes
Reaction Mechanisms & Organocatalysis
Reaction Mechanisms & Organocatalysis
Elucidation of reaction mechanisms, stereoselectivity, and kinetic control in organic and organometallic chemistry through quantum chemical approaches, with particular emphasis on organocatalysis.
Selected Publications:
Avcı, O.N.; Catak, S.; Dereli, B.; Aviyente, V.; Dedeoglu, B.* Elucidation of the Mechanism of Silver-Catalyzed Inverse Electron-Demand Diels-Alder (IEDDA) Reaction of 1,2-Diazines and Siloxy Alkynes. ChemCatChem (2020).
Tanriver, G.; Dedeoglu, B.; et al. Computational Studies on Cinchona Alkaloid-Catalyzed Asymmetric Organic Reactions. Accounts of Chemical Research (2016).
Dedeoglu, B.; Catak, S.; et al. Cinchona Alkaloid Catalyzed Asymmetric Desymmetrization of meso-Cyclic Anhydrides: The Origins of Stereoselectivity. ChemCatChem (2015).
Multiscale Modeling of Biomolecular Systems
Multiscale Modeling of Biomolecular Systems
Multiscale computational investigation of biomolecular systems, integrating quantum chemical methods and molecular simulations to understand binding, activation, and molecular function in biological environments.
Selected Publications:
Majeed, S.R.; Dedeoglu, B.; et al. 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).
Cetin, E.; Dedeoglu, B.* et al. Kinetic Barrier to Enzyme Inhibition is Manipulated by Dynamical Local Interactions in E. coli DHFR. Journal of Chemical Information and Modeling (2023).
Emirik, Ö.F.; Dedeoglu, B.* et al. Theoretical investigation of the hydrolysis and DNA binding of platinum (II) complexes of imidazolidine dioximes. Molecular Physics (2023).
Koca Fındık, B.; Dedeoglu, B.* et al. Computational Assessment of Iron Release from the N- and C- Lobes of Human Serum Transferrin. Organic & Biomolecular Chemistry (2022).
Noncovalent Interactions & Molecular Assembly
Noncovalent Interactions & Molecular Assembly
Theoretical investigation of noncovalent interactions—such as halogen and tetrel bonding—that govern molecular recognition, self-assembly, and functional supramolecular architectures.
Selected Publications:
Dedeoglu, B.; Gürek, A.G.; Zorlu, Y.; Ayhan, M.M. Engineering supramolecular helical assemblies via interplay between carbon (sp) tetrel and halogen bonding interactions. Physical Chemistry Chemical Physics (2023).
Gümüşgöz, G.; Dedeoglu, B.; et al. Enhancing supramolecular assembly in BODIPY derivatives: Harnessing halogen bonding for cocrystal design. Crystal Growth & Design (2023).
Ayhan, M.M.; Dedeoglu, B.; et al. Halogen-Bonded BODIPY Frameworks with Tunable Optical Features. Chemistry – A European Journal (2021).
Functional Molecular Materials
Functional Molecular Materials
Quantum chemical modeling of organic and organometallic materials with tailored optical, electronic, sensing, optoelectronic properties and energy conversion properties, , in close synergy with experiments.
Selected Publications:
Özer, Z.; Dedeoglu, B.; et al. Heating Effect on the Liquid-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).
Tunç, G.; Dedeoglu, B.; et al. p-Phenyleneethynylene unit-conjugated dimeric zinc-phthalocyanines in bulk heterojunction solar cell: A comparative experimental and theoretical study. New Journal of Chemistry (2025).
Haghmoradi, N.; Dedeoglu, B.; et al. Co2+, Fe2+, and Ni2+: Modifiers for Photocatalytic Deposition of Highly Active Pt on Graphene-based Supports. ACS Applied Energy Materials (2022).
Dedeoglu, B.; Monari, A.; et al. Detection of Nitroaromatic Explosives Based on Fluorescence Quenching of Silafluorene- and Silole-Containing Polymers: A Time Dependent-Density Functional Theory Study. Journal of Physical Chemistry C (2014).
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