Person: ERDEM, SAFİYE
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ERDEM
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SAFİYE
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Publication Metadata only A DFT Study on the Mechanism of the Annulation Reaction of Trichloronitroethylene with Aniline in the Synthesis of Quinoxalinone-N-oxides(AMER CHEMICAL SOC, 2009) ERDEM, SAFİYE; Ozpinar, Gul A.; Erdem, Safiye S.; Meyer, Christian; Kaufmann, Dieter E.The new annulation reaction of trichloronitroethylene with aniline results in the formation of a quinoxalinone-N-oxide derivative. The mechanism of this one-pot annulation reaction between trichloronitroethylene (TCNiE) and anilines has been extensively investigated with B3LYP/6-31+G** methodology. Five different paths (1-5) were proposed and modeled by using this method. These paths were compared in terms of the activation energies of their rate-determining steps and in regard to the experimental findings. Paths 3 and 5, proceeding via four-membered heterocyclic rings, were found to be the most plausible paths with activation energies of 32 and 29 kcal/mol for the rate-determining steps, respectively. The effects of substituent, solvent, temperature, and computational method on these steps were also investigated. The results showed that path 5 is the most plausible mechanism for the annulation reaction of trichloronitroethylene with aniline.Publication Metadata only A computational study on heterodimerization of charged porphyrins(JOHN WILEY & SONS LTD, 2001) ERDEM, SAFİYE; Erdem, SSThe structures of the charged porphyrins and their dimers have been investigated with computational methods. Dimers have been formed based on electrostatic attraction of the opposite charges on two different porphyrin monomers, tetra ammonium porphyrin (TAP) and tetra carboxy porphyrin (TCP). Semi-empirical quantum mechanical calculations have been employed to explore the most stable ground-state structures of TCP, TAP and their hetero-dimers. Dimeric structures analyzed are all in face-to-face fashion indicating the strong electrostatic attraction between the two porphyrin rings. Calculations have also predicted that the protons transfer from -NH3+; groups to -COO- groups when the interplanar separation is shorter than 3.7 Angstrom. Copyright (C) 2001 John Wiley & Sons, Ltd.Publication Metadata only QSPR analysis of the toxicity of aromatic compounds to the algae (Scenedesmus obliquus)(PERGAMON-ELSEVIER SCIENCE LTD, 2007) ERDEM, SAFİYE; Sacan, Melek Turker; Ozkul, Mustafa; Erdem, Safiye SagThe quantitative structure-property relationship (QSPR) model was developed for the 50% effective inhibition concentration (48 h - EC50) of 36 selected substituted benzenes for the algae Scenedesmus obliquus by the application of the Characteristic Root Index (CRI) model. To increase the predictive power of the CRI-based model, the following semi-empirical molecular descriptors calculated by the quantum chemical PM3 method were included: the energy of the highest occupied molecular orbital (E-HOMO), the energy of the lowest unoccupied molecular orbital (E-LUMO), and the dipole moment (mu). A two-descriptor model with a correlation coefficient of r = 0.926 was developed without the outliers from multiple regression analysis [-log EC50 = 0.494 (+/- 0.072) CRI - 0.798 (+/- 0.063) E-LUMO + 1.985 (+/- 0.169)]. E-LUMO was the most important parameter, followed by the CRI. E-LUMO reflects electronic properties, whereas the CRI reflects hydrophobicity, molecular size, and branching. The statistical robustness of the developed model was validated by the modified jackknife test. The predictive accuracy of the proposed model was compared with the recently published study in which a toxicity model was developed for the same algae. Because of its high statistical significance, the validated model has been used to predict -log EC50 values of compounds for which there are no experimental measurements. (C) 2007 Elsevier Ltd. All rights reserved.Publication Metadata only Investigation on the aromaticity of 1,3,4-thiadiazole-2-thione and its oxygen analogs including their tautomeric forms(ELSEVIER SCIENCE BV, 2005) ERDEM, SAFİYE; Erdem, SS; Ozpinar, GA; Sacan, MTThe aromaticity of 1,3,4-thiadiazole-2-thione and its oxygen analogs including their tautomeric forms, and 1,3,4-thiadiazole, 1,3,4-oxadiazole, furan, thiophene, cyclopentadiene, the cyclopentadienyl anion and the cyclopentadienyl cation has been examined by harmonic oscillator measure of aromaticity (HOMA), aromatic stabilization energy (ASE), differential heat of hydrogenation (Delta Delta HH), and nucleus independent chemical shifts (NICS (0)), calculated at the HF/6-31G**, B3LYP/6-31G**, B3LYP/6-311G**, and B3LYP/6-311 + +G** levels. A principal component analysis (PCA) of the data set generated from these aromaticity results has been presented and compared with similar analyses in the recent literature. It has been shown that aromaticity is at least a two-dimensional phenomenon, independent of the level of the computational method employed. We observed that the sulfur-containing heterocyclic compounds are more aromatic than their oxygen analogs according to geometrical aromaticity measurements. In addition, our calculations of the energies of the tautomeric forms showed that the carbonyl and thiocarbonyl tautomers are more stable than the hydroxy and mercapto forms, which is in good agreement with the experimental findings in the literature. (c) 2005 Elsevier B.V. All rights reserved.Publication Metadata only QSPR study on the bioconcentration factors of nonionic organic compounds in fish by characteristic root index and semiempirical molecular descriptors(AMER CHEMICAL SOC, 2004) ERDEM, SAFİYE; Sacan, MT; Erdem, SS; Ozpinar, GA; Balcioglu, IAThe characteristic root index (CRI) was modeled together with four semiempirical molecular descriptors, namely-energies of the highest occupied and the lowest unoccupied molecular orbital (E-HOMO and E-LUMO), heat of formation (DeltaH(f)), and dipole moment (mu)-to predict the fish bioconcentration factor (BCF) of 122 nonionic organic compounds. The best fit equation found by forward multiple linear regression showed that the topology based CRI was the most important parameter. The addition of quantum chemical descriptors made only a slight improvement in the predictive capability of the Quantitative Structure-Property Relationship (QSPR) model. The CRI was followed by EHOMO. A two-parameter equation with a correlation coefficient of r = 0.921 was obtained for a diverse set of nonionic organic chemicals. Statistical robustness of the developed model was validated by modified jackknife tests where random deletion of a class of compounds and specific deletion of a set of compounds were both performed. The predictive accuracy of the proposed model was compared with the commonly used K-ow model and recently published studies in which BCF models were developed. Particular emphasis has been made to clearly define the boundaries for the application of the alternative developed model as well as the quality of estimates.Publication Metadata only A computational study on the amine-oxidation mechanism of monoamine oxidase: Insight into the polar nucleophilic mechanism(ROYAL SOC CHEMISTRY, 2006) ERDEM, SAFİYE; Erdem, SS; Karahan, O; Yildiz, I; Yelekci, KThe proposed polar nucleophilic mechanism of MAO was investigated using quantum chemical calculations employing the semi-empirical PM3 method. In order to mimic the reaction at the enzyme's active site, the reactions between the flavin and the p-substituted benzylamine substrate analogs were modeled. Activation energies and rate constants of all the reactions were calculated and compared with the published experimental data. The results showed that electron-withdrawing groups at the para position of benzylamine increase the reaction rate. A good correlation between the log of the calculated rate constants and the electronic parameter (sigma) of the substituent was obtained. These results agree with the previous kinetic experiments on the effect of p-substituents on the reduction of MAO-A by benzylamine analogs. In addition, the calculated rate constants showed a correlation with the rate of reduction of the flavin in MAO-A. In order to verify the results obtained from the PM3 method single-point B3LYP/6-31G*//PM3 calculations were performed. These results demonstrated a strong reduction in the activation energy for the reaction of benzylamine derivatives having electron-withdrawing substituents, which is in agreement with the PM3 calculations and the previous experimental QSAR study. PM3 and B3LYP/6-31G* energy surfaces were obtained for the overall reaction of benzylamine with flavin. Results suggest that PM3 is a reasonable method for studying this kind of reaction. These theoretical findings support the proposed polar nucleophilic mechanism for MAO-A.Publication Metadata only Thermal rearrangement of 2-acetoxy-2,6,6-trimethylbicyclo[3.1.0]hexane: Theoretical elucidation of the mechanism(ELSEVIER SCIENCE BV, 2007) ERDEM, SAFİYE; Erdem, Safiye Sag; Uyar, Fahriye; Karahan, Ozlem; Yelekci, KemalBicyclohexenes are believed to be the immediate precursors of aromatic compounds. As a part of the exploratory study of thermal aromatization reactions, 2,6,6-trimethylbicyclo[3.1.0]hexan-2-ol and its ester derivative 2-acetoxy-2,6,6-trimethylbicyclo[3.1.0]hexane were synthesized. Pyrolysis of 2-acetoxy-2,6,6-trimethylbicyclo[3.1.0]hexane at 350 degrees C gave 1,3,3-trimethyl-1,4-cyclohexadiene instead of the expected product, 2,6,6-trimethylbicyclo[3.1.0]hex-2-ene. Computational methods such as PM3, 31G]* were employed in order to elucidate the mechanism of this reaction. The Gibbs free energy of activation and the reaction energy were calculated for the proposed polar and biradical mechanisms. The results showed that a two-step mechanism is plausible at 350 degrees C in which the expected product 2,6,6-trimetliylbicyclo[3.1.0]hex2-ene is the intermediate. The first step is the 1,2-elimination of the ester, leading to 2,6,6-trimethylbicyclo [3. 1. 0]hex-2-ene. The second step is the sigmatropic rearrangement of 2,6,6-trimethylbicyclo[3.1.0]hex-2-ene via concerted homodienyl 1,5-hydrogen shift, which is also the rate-determining step. UB3LYP/6-31G* calculations reveal that the cyclopropyl moiety of bicyclo[3.1.0]hex-2-ene can undergo homolytic bond cleavage to give an allylically stabilized biradical intermediate. However, the formation of 1,4-cyclohexadiene from such an intermediate through a biradical transition state involving 1,2-hydrogen migration does not seem to be plausible. (c) 2007 Elsevier B.V. All rights reserved.Publication Metadata only Physico-chemical properties of PCDD/PCDFs and phthalate esters(TAYLOR & FRANCIS LTD, 2005) ERDEM, SAFİYE; Sacan, MT; Ozkul, M; Erdem, SSQSPR models for water solubility (S), n-octanol/ water partition coefficient (K-OW), and Henry's law constant (H) for polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzo-p-furans (PCDFs) and phthalates have been established based on two different sets of parameters. Those parameters were topology based characteristic root index (CRI) and three semi-empirical molecular descriptors, namely - energies of the highest occupied and the lowest unoccupied molecular orbital (E-HOMO and E-LUMO), and dipole moment (mu). The best fit equation found by 'forward multiple linear regression' showed that the topology based CRI was the most important parameter for the modelling of solubility and n-octanol/ water partition coefficient. For n-octanol/ water partition coefficient a two-parameter equation including the CRI and E-HOMO with a correlation coefficient of r = 0.992 was obtained whereas a three-parameter equation for solubility and Henry's law constant including the CRI, E-LUMO and mu with a correlation coefficient of r = 0.986 and r = 0.933 was obtained, respectively. E-HOMO and mu didn't appear in the same model because of the collinearity. The results of modified jackknife tests indicated that the three models were statistically robust. Mean deviation of calculated values from experimental data amounted to 0.27, 0.17, and 0.28 log units for the three properties mentioned. The developed models have been used to predict the S, KOW and H of compounds not included in the training sets.Publication Metadata only The aromatic cage in the active site of monoamine oxidase B: effect on the structural and electronic properties of bound benzylamine and p-nitrobenzylamine(SPRINGER WIEN, 2007) ERDEM, SAFİYE; Akyuz, M. A.; Erdem, S. S.; Edmondson, D. E.Computational studies using the ONIOM methods have been performed to probe the catalytic roles of tyrosine residues 398 and 435 which constitute the '' aromatic cage '' in the active site of MAO-B. The results presented here provide additional new insights into the interactions that take place on activation of the amine substrate by the aromatic cage residues in MAO-B catalysis and have relevance to the MAO-A catalytic mechanism.