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    A mechanistic rationalization of the degradation of caffeine in homogeneous and heterogeneous media
    (Elsevier, 2026) Ozerdem, Zekihan; Ergen, Yigit; Savun, Basak; Cinar, Sesil Agopcan; Ince, Nilsun; Aviyente, Viktorya
    The current study complements the experimental findings of Ziylan-Yavas et al. on the degradability of the emerging water contaminant caffeine through homogeneous and heterogeneous Advanced Oxidation Processes (AOPs). Density Functional Theory (DFT) and Plane-Wave Self-Consistent Field (PWSCF) were employed to propose plausible reaction mechanisms consistent with the experimental data. The study also involves modeling and discussion in detail of the radical adduct formation (RAF), hydrogen atom transfer (HAT), demethylation reactions (DEMET), byproduct formation, and the role of TiO2surface on the degradation process. The discussion is based on free energy barriers, reaction free energies, and the electronic energies of adsorption. The peak corresponding to the strongest binding to the TiO2surface (P1, MW = 228) aligns closely with the LC-MS signals observed for the byproducts with MW = 58 and 102. This correlation underscores the predictive power of the computational model and lays the groundwork for future mechanistic investigations.
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    Computational insights into substrate-assisted citrullination mechanisms of PAD2 isozyme: A comparative analysis of reaction pathways
    (Elsevier Science Inc, 2025) Cicek, Erdem; Munar, Ipek; Cinar, Sesil Agopcan; Basceken, Sinan; Monard, Gerald; Aviyente, Viktorya; Sungur, Fethiye Aylin
    Citrullination, catalyzed by protein arginine deiminase enzymes, involves the conversion of peptidyl-arginine to peptidyl-citrulline, disrupting protein interactions and leading to functional alterations. Despite the experimental studies on PAD2 indicating calcium dependence and substrate specificity, the catalytic mechanism remains contentious, with conflicting evidence regarding the roles of active site residues such as Cys647 and His471. The present study is an expansion of prior molecular dynamics simulations that investigated the dynamics of the enzyme PAD2, which indicated that Asp473 may function as a general acid/base, thereby challenging the experimentally proposed pathways. To further elucidate this controversial issue, quantum mechanical methods were employed to examine the protonation states of key residues and their roles in catalysis. Herein, three different pathways have been studied for the substrate-assisted citrullination mechanism of PAD2 isozyme using a model structure that includes the active site residues Asp351, His471, Val472, Asp473, and Cys647 and a water molecule. The highest barriers for two of the designed mechanisms, RM1 and RM3 are comparable: the choice of a single mechanism is not possible since the differences in barriers fall within the error margins in DFT calculations. These findings offer insights into PAD2's enzymatic activity, thereby advancing our understanding of its biological significance.
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    How substitution tunes the electronic and transport properties of oligothiophenes, oligoselenophenes and oligotellurophenes
    (Elsevier Science Sa, 2015) Erbay, Tugce Gulsen; Aviyente, Viktorya; Salman, Seyhan
    The geometrical, electronic and charge-transport properties of a series of unsubstituted and dicyanovinyl (DCV)-substituted oligothiophenes (nT), oligoselenophenes (nS) and oligotellurophenes (nTe) where n = 3-5 are investigated by means of Density Functional Theory (DFT) and Time-Dependent DFT calculations. The intramolecular reorganization energy is found to decrease upon dicyanovinyl substitution, with a larger decrease for holes than electrons. The ground state HOMO and LUMO energies along with the Time-Dependent DFT calculations show smaller HOMO-LUMO gaps for the DCV-substituted oligomers. Calculations of the intermolecular charge transfer integrals in the crystals have been performed to understand the role of substitution on the charge-transport rate. DCV-substitution changes the packing motifs in the crystal and results in larger transfer integrals for holes along the pi-stacldng direction, calculated as -63 and -88 meV for DCV4T and DCV4S respectively. These results suggest that DCV-substituted oligomers studied here are more promising charge transporting materials than their unsubstituted analogues. (C) 2015 Elsevier B.V. All rights reserved.