ACADEMIC STAFF PROFILEAçıklama: D:\Resimler_2013\ben\iyiler\IMG_1834_kesik.jpg

POSITION: Prof. Dr.

NAME, SURNAME: Safiye, (Sağ) ERDEM

BIRTHPLACE AND DATE: Bolu /  25.5.1961

ADDRESS: Marmara Üniversitesi, Fen Edebiyat Fakültesi, Kimya Bölümü, Göztepe Kampüsü, 34722, Göztepe, Istanbul.                              (Marmara University, Faculty of Arts and Sciences, Chemistry Department)

TEL: +90 216 3479641 extension 1377  

FAX: +90 216 3478783

 E-MAIL: erdem@marmara.edu.tr

 

 

ACADEMIC CAREER:

 

BSc: 1980-1985  Boğaziçi University, Chemistry Department

 

MSc : 1986-1988  Villanova University, ABD, Chemistry Department

 

PhD: 1990-1995  Boğaziçi University, Chemistry Department

(Superviser: Prof. Dr. Tereza Varnalı Co-superviser: Prof. Dr. Viktorya Aviyente)

 

ASSISTANT PROF: 1999-2002  Marmara University, Chemistry Department

 

ASSOCIATE PROF: 2002-2008  Marmara University, Chemistry Department

 

 PROF: 2008-         Marmara University, Chemistry Department     

 

 

 

RESEARCH INTEREST:

Computational Chemistry, Physical Organic Chemistry, Organic Reaction Mechanisms, Aromaticity, Bio-Organic Chemistry, Modeling of Enzyme Catalysis and Inhibition (Monoamine Oxidases), Modeling Assymetric Catalysis Mechanisms, QSAR, QSPR, Computer-aided Drug Design.

 

 

 

RESEARCH ARTICLES

 

1.     K. Cakir, S. Sag-Erdem, V. Enisoglu-Atalay, ONIOM calculations on serotonin degradation by monoamine oxidase B: insight into the oxidation mechanism and covalent reversible inhibition, Organic & Biomolecular Chemistry, 2016, 14, 9239-9252. DOI: 10.1039/c6ob01175f

2.     S. E. Gunal, G. S. Gurses, S. S. Erdem, I. Dogan, Synthesis of stable tetrahedral intermediates (hemiaminals) and kinetics of their conversion to thiazol-2-imines, Tetrahedron, 2016, 72, 17, 2122–2131. DOI: 10.1016/j.tet.2016.03.003 

3.     P. Erzincan,  M. Türker-Saçan, B. Yüce-Dursun, Ö. Danış, S. Demir, S. Sağ-Erdem, A. Ogan,  QSAR models for antioxidant activity of new coumarin derivatives, SAR and QSAR in Environmental Research, 2015, 26 (7-9): 721-737.  DOI: 10.1080/1062936X.2015.1088571

4.     Ş. G, Küçükgüzel, D. Koç, P. Çıkla-Süzgün, D. Özsavcı,  Ö. Bingöl-Özakpınar, P. Mega-Tiber, O. Orun, P. Erzincan, S. Sağ-Erdem, F. Şahin, Synthesis of Tolmetin Hydrazide–Hydrazones and Discovery of a Potent Apoptosis Inducer in Colon Cancer Cells. Archiv der Pharmazie, 2015, 348: 730–742. DOI: 10.1002/ardp.201500178   

  1. Ö. Sari, S. S. Erdem, D. E. Kaufmann, Mechanisms of the Reaction between Polyhalogenated Nitrobutadienes and Electron-Deficient Anilines: Computational Modeling. Journal of Organic Chemistry. 2014, 79, 2123-2138. Doi: 10.1021/jo402858j
  2. S. S. Erdem. , G. A. Özpınar & Ü. Boz , Quantum chemical modelling of the inhibition mechanism of monoamine oxidase by oxazolidinone and analogous heterocyclic compounds. Journal of Enzyme Inhibition and Medicinal Chemistry, 2014, 29, 81-86. Doi: 10.3109 / 14756366.2012.75388.
  3. V. E. Atalay, S. S. Erdem, A Comparative Computational Investigation on the Proton and Hydride Transfer Mechanism of Monoamine Oxidase Using Model Molecules, Computational Biology and Chemistry, 2013, 47, 181-191. doi: 10.1016/j.compbiolchem.2013.08.007.
  4. S. S. Erdem, S.Türkkan, K. Yelekçi & Gökhan- N. Kelekçi , Insights into the Binding Mode of New N-substituted Pyrazoline Derivatives to MAO-A: Docking and Quantum Chemical Calculations. Journal of Neural Transmission, 2013, 120 , 859-862.
  5. M.A. Akyüz & S. S. Erdem., Computational modeling of the direct hydride transfer mechanism for the MAO catalyzed oxidation of phenethylamine and benzylamine: ONIOM (QM/QM) calculations. Journal of Neural Transmission, 2013, 120 ,  937-945.
  6. N. Mengeş, Ö. Sarı,  Y. Abdullayev, S. S. Erdem & M. Balcı , Design and Synthesis of Pyrrolotriazepine Derivatives: An Experimental and Computational Study. Journal of Organic Chemistry, 2013, 78 , 5184-5195.
  7. S. S. Erdem & B. Büyükmenekşe , Computational investigation on the structure-activity relationship of the biradical mechanism for. Journal of Neural Transmission, 2011, 118 , 1021-1029.
  8. S. S. Erdem, G. A. Özpınar & A. Güngör , Diizosiyanatların Polimerleşme Aktivitelerinin Hesapsal Yöntemlerle İncelenmesi. Marmara Üniversitesi Fen Bilimleri Dergisi, 2011, 23 , 33-45.

 

  1. G. A. Özpınar, S. S. Erdem, C. Meyer, D. E. Kaufmann, A DFT Study on the Mechanism of the Annulation Reaction of Trichloronitroethylene with Aniline in the Synthesis of Quinoxalinone-N-oxides, Journal of Organic Chemistry , 2009, 74, 4727-4739.

 

  1. M. Akyüz, S. S. Erdem, D. E. Edmondson, Aromatic Cage in the Active Site of Monoamine Oxidase B: Effect on the Structural and Electronic Properties of Bound Benzylamine and p-Nitrobenzylamine, Journal of Neural Transmission 2007, 114, 693-698.

 

  1. S. S. Erdem, F. Uyar, Ö. Karahan, K. Yelekçi, Thermal rearrangement of 2-acetoxy-2,6,6-trimethylbicyclo[3.1.0]hexane: Theoretical elucidation of the mechanism, Journal of Molecular Structure (Theochem) 2007, 814, 61-73.

 

16.  M. T. Saçan, M. Özkul, S. S. Erdem, QSPR analysis of the toxicity of aromatic compounds to the algae (Scenedesmus obliquus), Chemosphere, 2007, 68, 695-702.

 

  1. S. S. Erdem, Ö. Karahan, İ. Yıldız, K. Yelekçi, A Computational Study on the Amine-Oxidation Mechanism of Monoamine Oxidase: Insight into the Polar Nucleophilic Mechanism, Organic and Biomolecular Chemistry, 2006, 4, 646-658.

 

  1. S. S. Erdem, G. A. Özpınar, M. T. Saçan, Investigation on the Aromaticity of 1,3,4-thiodiazole-2-thione and Its Oxygen Analogs Including Their Tautomeric Forms, Journal of Molecular Structure (Theochem), 2005, 726, 233-243.

 

  1. M. T. Saçan, M. Özkul, S. S. Erdem, Physico-chemical Properties of PCDD/PCDFs and Phthalate Esters, SAR and QASR in Environmental Research, 2005, 16, 443-459.

 

  1. M. T. Saçan, S. S. Erdem, G. A. Özpınar, I. A. Balcıoğlu, QSPR Study on the Bioconcentration Factors of Nonionic Organic Compounds in Fish by Characteristic Root Index and Semiempirical Molecular Descriptor, Journal of Chemical Information and Computer Sciences, 2004, 44, 985-992.

 

21.  F. Aydoğan, Z. Turgut, N. Öcal, S. S. Erdem, Synthesis and Electronic Structure of New Aryl- and Alkyl-Substituted 1,3,4-Oxadiazole-2-thione Derivatives, Turkish Journal of Chemistry, 2002, 26, 159-169.

 

22.  S. S. Erdem, K. Yelekçi, Computer Modeling of Oxygen Containing Heptylamines As Monoamine Oxidase Inactivators, Journal of Molecular Structure (Theochem), 2001, 572, 97-106.

 

23.  S. S. Erdem, A Computational Study on Heterodimerization of Charged Porphyrins, Journal of Porphyrins and Phthalocyanines, 2001, 5, 512-522.

 

24.  A. Akın, S. S. Erdem, T. Nugay, V. Aviyente, H. Reşat, A ComputationalStudy of the Reactivity of Diethenylnaphthalines Towards Anionic Polymerization, J. Chem. Soc., Perkin Trans. 1999, 2, 5-13.

 

25.  A. S. Özen, S. S. Erdem, V. Aviyente, A Computational Study of the Wallach Rearrangement, Structural Chemistry, 1998, 9, 15-25.

 

26.  S. S. Erdem, Spectral Evidence for Heterodimerization of Water Soluble Metalloporphyrins, Journal of Porphyrins and Phthalocyanines, 1998, 2, 61-68.

 

27.  S. S. Erdem, T. Varnalı, V. Aviyente, Ab Initio Study on the Conformational Behaviour of Ethane-1,1-diol and Ethane-1,1,2-triol in Solution, Journal of Physical Organic Chemistry, 1997, 10, 196-206.

 

  1. S. S. Erdem, T. Varnalı, V. Aviyente, A Computational Study on the Conformational Behaviour of 1,1,2-Trihydroxyethane in Solution, Turkish Journal of Chemistry, 1997, 21, 50-58.

 

  1. S. S. Erdem, T. Varnalı, V. Aviyente, M. F. Ruiz-Lopez, Solvent Effect on the Conformational Behaviour of Substituted Spiro[4.5]decanes and Spiro[5.5]undecanes, Canadian Journal of Chemistry, 1995, 73, 703-709.

 

  1. S. S. Erdem, T. Varnalı, V. Aviyente, M. F. Ruiz-Lopez, Solvent Effect on the Conformational Equilibria of 2-Methyl and 2-Halo Cyclohexanone Ethylene Ketals, in “Turkish VIIIth National Symposium on Chemistry and Chemical Engineering”,  Marmara University Publication, 1992, 169-174.

 

CITATIONS TO RESEARCH ARTICLES 

Over 300 citations according to Science Citation Index.

 

 

PROJECTS (Completed)

(Project name, grand organization and number, starting year)

 

1.     Monoamin Oksidaz A ve B Enzimlerinin Nörotransmitter Aminleri (Serotonin/Dopamin) Oksitlemesi Aynı Mekanizmayla mı Farklı Mekanizmalarla mı Gerçekleşir? TUBITAK-1001, 113Z616, 2014 (Project Director).

2.     Çift etkiye sahip potansiyel antioksidan ve anti-Parkinson ilaç aktif maddelerin in siliko tasarımı, FEN-C-YLP-130515-0186, 2015 (Project Director).

3.     2-Arilimino-3-Ariltiyazolidin İzomerlerinin Aksiyel Kiralitesinin Hesapsal Modellenmesi, FEN-C-YLP-090414-0095, 2014 (Project Director).

4.     Investigation on the Inhibition of Human Monoamine Oxidase A and B Enzymes by 3-Aryl Cumarins, BAPKO, FEN-A-110913-0376, 2013 (Researcher)

5.     Computational Modeling of the Proposed Hydride Transfer Mechanism for Monoamine Oxidases Inside the Active Site, BAPKO, FEN-C-DRP-031210-0289, 2010 (Project Director).

6.     QSAR Modeling Of Toxicity Based On Measured Aquatic Algae Toxicity, TUBITAK-ARRS (Turkey-Slovenia Joint Research), 2009 (Researcher)

7.     Design and Synthesis of New Pyrazolines as MAO Inhibitors Using Molecular Modeling Methods and Determination of Inhibition Kinetics Using Computational and Experimental Methods, TUBITAK, 108T232, 2008 (Researcher)

8.     Modeling the Active Site of MAO-A Enzyme Using ONIOM Method, Marmara Univ. BAPKO, FEN-C-DRP-181208-0279, 2008 (Project Director)

  1. Theoretical Modeling of the Radical Mechanism Proposed for Monoamine Oxidase Enzyme, Marmara Univ. BAPKO, FEN-BGS-270306-0049, 2006 (Project Director)
  2. Computational Modeling of the Reaction Mechanisms Related with the Synthesis of Quinoxalinone-N-Oxides, Marmara Univ. BAPKO, FEN-DKR-041206-0258, 2006 (Project Director)
  3. Multi-species Tool For Modeling Acute Toxicity of Substituted Aromatic Compounds in Aquatic Systems, Boğaziçi Univ. Scientific Research Project, 06HY101, 2006 (Researcher)
  4. Conversion of Heterocyclic Metylthioamines to Imminium Ions Via Beta-Elimination Reactions, Marmara Univ. BAPKO, BSE-087/051201, 2001 (Project Director)
  5. Thermal Pyrolysis Mechanism of 2-Acetoxy-2,6,6-trimethylbicyclo[3.1.0] hexane, Marmara Univ. BAPKO, BSE-086/051201, 2001 (Project Director)
  6. Investigation on the Aromaticity of 1,3,4-Oxadiazole-2-thione Ring, Marmara Univ. BAPKO, BSE-DYD-035\020701, 2001 (Project Director)
  7. Chemical Modeling of the Inactivation of Monoamine Oxidase, Marmara Univ. BAPKO, Fen Bilimleri/2000/FE-2, 2000. (Project Director)
  8. Computational Analysis on the Structures of Porphyrine Dimers, Bogazici Univ. Scientific Research Project, 97HB504, 1997. (Project Director)

 

PROJECTS (On-going)

17.  A New Catalyst for Assymmetric Aldol Reactions: Modelling the Assymmetric Catalyst Effect of Homoboroproline. BAPKO, FEN-B-100615-0269, 2015 (Project Director).

18.  In silico models for environmentally and biologically relevant endpoints, TÜBİTAK-ARRS (Turkey-Slovenia Joint Research),   (Researcher), 2015

 

POSTGRADUATE THESIS SUPERVISED (Completed)

 

 (Student Name, Thesis Name, Institute, Year of Completion)

PhD. Thesis:     

  1. M. Ali Akyüz, Modeling of the Hydride Mechanism Proposed for Monoamine Oxidase in the Enzyme Active Site, M.U. Institute of Pure and Applied Sciences, 2014.

2.     Mustafa Köktürk, QSAR Analysis of MAO Inhibitors for Rational Drug Design, M.U. Institute of Pure and Applied Sciences, 2013.

3.     Vildan Enisoğlu, Modelling of the Active Site of MAO A Enzyme by ONIOM method, M.U. Institute of Pure and Applied Sciences, 2010.

4.     Gül Altınbaş Özpınar, Computational Modeling of Reaction Mechanisms Related to Synthesis of Quinoxalinone-N-oxides, M.U. Institute of Pure and Applied Sciences, 2008.

 

MS. Thesis:

 

1.     Lalehan Özalp, Investigation of Phthalocyanine – DNA Binding with in silico Methods, M.U. Institute of Pure and Applied Sciences, Biochemistry Program, 2016.

2.     Kübra Çakır, Is the Hydride Transfer Mechanism of Monoamine Oxidase (MAO) Enzymes Single or Multiple Step? M.U. Institute of Pure and Applied Sciences, 2016.

3.     Pınar Erzincan, In Silico Design of Potential Drug Active Compounds Possessing Antioxidants and Anti-parkinson Dual Effect, M.U. Institute of Pure and Applied Sciences, Biochemistry Program, 2016.

4.     Hazal Engin, The Effect of Active Site on the Catalytic Reaction of Monoamine Oxidase B. M.U. Institute of Pure and Applied Sciences, 2015.

  1. Linda Ohanoğlu, Molecular Modeling and QSAR on Glutathione s-transferase enzyme inhibitors. M.U. Institute of Pure and Applied Sciences. 2014.

6.     Gülben Sabuncu Gürses, Computational Modeling on Axial Chirality of 2-Arylimino-3-arylthiozolidine Isomers. Institute of Pure and Applied Sciences, 2014.

7.     Seyhan Türkkan, Molecular Docking of New Pyrazole Derivatives Having Monoamine Oxidase Inhibitory Effect, M.U. Institute of Pure and Applied Sciences, 2013.

8.     Serap Salman, Investigation of Structural and Electronic Properties of Phthalocyanines by Density Functional Theory Methods, M.U. Institute of Pure and Applied Sciences, 2013.

9.     Merve Biçen, Experimental and Computational Studies of Interaction Between Small Molecules and DNA, M.U. Institute of Pure and Applied Sciences, 2011 (Co-Supervisor: Dr. N. J. Buurma. Research was conducted at Cardiff University).

10.  Özlem Sarı, Modeling the Mechanism of the Reaction Between Polyhalogenated Nitrobutadienes and Electron Deficient Anilines by Quantum Chemical Methods, M.U. Institute of Pure and Applied Sciences, 2011.

11.  Onurcan Aydın, QSAR Analysis of Hydrazone Derivative MAO Inhibitors for Rational Drug Design, M.U. Institute of Pure and Applied Sciences, 2011.

12.  Burcu Büyükmenekşe, The Investigation on the Structure-Activity Relationship of the Proposed Biradical Mechanism for Monoamine Oxidase, M.U. Institute of Pure and Applied Sciences, 2009

13.  Mehmet Ali Akyüz, Modeling of the Monoamine Oxidase Substrates in the Enzyme Active Site by QM/MM Method, M.U. Institute of Pure and  Applied Sciences, 2007.

14.  Ramazan Keleş, Investigation of the Aromaticity of Fulvene Derivatives Using NICS Method, M.U. Institute of Pure and Applied Sciences, 2007

15.  Oğuz Can, Investigation of the Structure-Activity Relationship in the Reaction of p-Substituted Benzylamines With Monoamine Oxidase, M.U. Institute of Pure and Applied Sciences, 2007

16.  Ümüt Boz, Chemical Modeling of Inhibition of MAO Enzyme Related With the Oxazolidinone and Similar Heterocyclic Compounds, M.U. Institute of Pure and Applied Sciences, 2006.

17.  Arzu (Kırsakal) Çiğit, Conformational Analysis of Model Amine Compounds Related with the Inhibition of Monoamine Oxidase, M.U. Institute of Pure and Applied Sciences, 2005.

18.  Fahriye Uyar, Modelling of Thermal Pyrolysis Mechanism of 2-acetoxy-2,6,6-trimethylbicyclo[3.1.0]hexane, M.U. Institute of Pure and Applied Sciences, 2005.

19.  Özlem Karahan, Computational Modeling of Oxidation Mechanism of Amines in MAO Enzyme, M.U. Institute of Pure and Applied Sciences, 2004.

20.  Aykut Genççakır, Investigation of the Singlet Oxygen Reactions Consisted of C-N Bond Using Computational Methods, Y.T.Ü, M.U. Institute of Pure and Applied Sciences, 2003. (co-supervisor)

21.   İbrahim Yıldız, Computational Modeling of Addition-Elimination Mechanism of Monoamine Oxidase (MAO), M.U. Institute of Pure and Applied Sciences, 2003.

22.  Mehmet Durmuş, Conformational Analysis of 2-Substitued-methylthioethylamines, M.U. Institute of Pure and Applied Sciences, 2003.

23.  Sibel Atalay, Stability of Fulvene Derivatives and Substituent Effect, M.U. Institute of Pure and Applied Sciences, 2002.

 

 

PRESENTATIONS IN SCIENTIFIC MEETINGS

 

-National meetings: Over 50 presentations.

-International meetings: Over 85 presentations

 

 

 

 

OTHER SCIENTIFIC DUTIES

Reviewer in International Journals:

 

-Journal of American Chemical Society (JACS)

-Organic and Biomolecular Chemistry (OBC)

-Physical Chemistry Chemical Physics (PCCP)

-Chemical Society Reviews

-Chemical Communications

-Journal of Chemical Information and Modeling

-Dalton Transactions

-New Journal of Chemistry

-CrystEngComm

-Turkish Journal of Chemistry

- Journal of Enzyme Inhibition and Medicinal Chemistry

- RSC Advances

- Journal of Molecular Structure

- Journal of Physical Chemistry (JPC)

-Journal of Chemical Theory and Computation

-Journal of Proteomics and Bioinformatics

-Marmara Pharmaceutical Journal

-Organic Communications

-Records of Natural Products

 

Reviewer in National/International Projects:

-TUBİTAK (Scientific and Technological Research Council of Turkey) national/joint projects

-TUBİTAK TBAG projects panel member

-FONDECYT (Chilean government Commission for Scientific and Technological Research)  projects

-Scientific Research Projects Commision (BAP) of Turkish universities

 

Member of Scientific/Organization/Advisory Committe of Scientific Meetings

-Marmara University, Faculty of Arts and Sciences, Science and Culture Days, 2011.

-Marmara University, Faculty of Arts and Sciences, Science and Culture Days, 2012.

-10th International Amine Oxidase Workshop, Kadir Has University, Istanbul, 25-29 August 2002.

-1st National Computational Chemistry Workshop, Van, 29-31 May 2014.

-2nd National Computational Chemistry Congress, Kars, 2-5 June 2015.

-4th Drug Chemistry Congress, Kuşadası, 2016.

-5th Drug Chemistry Congress, Antalya, 2017.   

 

 

ADMINISTRATIVE DUTIES

-Marmara University, Chemistry Department, Vice-chairman, 1999-2001, 2009-2010.

-Marmara University, Chemistry Department, Erasmus Coordinator, 2005- 2015.

-Marmara University, Institute of Pure and Applied Sciences, Vice-Director, 2008-2009.

-Marmara University, Institute of Pure and Applied Sciences, Administrative Board member, 2008-2009.

-Marmara University, Institute of Pure and Applied Sciences, Erasmus Coordinator, 2008-2010.

-Marmara University, Faculty of Arts and Sciences, Vice-Dean, 2010-2013.

-Marmara University, Faculty of Arts and Sciences, Administrative Board member  2011-.

-Marmara University, Faculty of Arts and Sciences, Executive Board member, 2007-2008, 2009-.

-Marmara University, Faculty of Arts and Sciences, Coordinator of Farabi Exchange Program, 2010.

-Marmara University, Faculty of Arts and Sciences, Coordinator of Mevlana Exchange Program, 2013-.

-Marmara University, Academic Awards Committe, 2011-2012.

-Marmara University, Curriculum Committe, 2012-.

-Marmara University, Board member of Scientific Research Project, 2014-

-EuCheMS Turkish delegate of Computational Chemistry Division, 2013-

 

 

AWARDS / INTERNATIONAL SCHOLARSHIPS

- Marmara University Faculty of Arts and Sciences Award for Directing National Projects, 2015.

-Visiting Scientist Fellowship, Emerson Center for Scientific Computations, Emory University, Atlanta, USA, July 2007.

-NATO-ASI, Frontiers of Chemical Dynamics Workshop, participation grand, NATO-ASI, Antalya, 5-16 Eylül 1994.

-Teaching Assistantship, Villanova University Chemistry Department, Pennysilvania, USA, 1986-1988.

 

TEACHING

Undergraduate level: Organic Chemistry I, Organic Chemistry II, Organic Chemistry III, General Chemistry I, General Chemistry II, Molecular Modelling, Drug Design in Organic Chemistry

Graduate level: Computational Organic Chemistry, Theoretical Methods in Organic Chemistry, Stereochemistry, Computer-Aided Drug Design, Physical Organic Chemistry, Applications of Computational Methods.