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    Comparison of binding properties of a novel non-steroidal anti-inflammatory agent and ibuprofen to cyclooxygenase-1 and cyclooxygenase-2 enzymes by saturation transfer difference nuclear magnetic resonance
    (Canadian Science Publishing, Nrc Research Press, 2018) Binbay, Nil E.; Ziyadanogullari, Berrin
    Saturation transfer difference nuclear magnetic resonance is a ligand-based screening technique that focuses directly on the physical interaction of a macromolecule (protein, enzyme, etc.) and a small ligand. It is a powerful tool in pharmaceutical research. Here, a comparison is reported of the binding characteristics of ibuprofen and a novel anti-inflammatory agent to cyclooxygenase-1 and cyclooxygenase-2 enzymes as an application of saturation transfer difference nuclear magnetic resonance. It has been shown that this novel agent is capable of binding to both isoforms of the cyclooxygenase enzymes. It has also been reported that novel agent binds better to cyclooxygenase-2.
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    Effect of initial configuration on DFT calculations for transition metal complexes
    (Osman SAĞDIÇ, 2019) Binbay, Nil E.; Binbay, Veysel; Aydemir, Murat; Durap, Feyyaz; Meriç, Nermin; Kayan, Cezmi; Arslan, Nevin
    Computational methods, which solves the Schrödinger’s equation for molecules, have become an indispensable tool in last decades.And Density Functional Theory is one of the most used, and most effective computational method.Transition Metal complexes, on the other hand, have been being used extensively in many important applications in many fields, suchas chemical catalysts, atomic thin films, and pharmaceutical industry. Applying computational methods to transition metal complexeshas become inevitable to understand better, to control and to design these compounds.As it is known, it is very difficult to handle transition metals computationally, mostly due to near degeneracy in their electronic states.The computational algorithms usually cannot achieve as successive result as they can do for other typical elements, like carbon ornitrogen for instance. Computational methods are needed to be improved for properly deal with transition metal complexes. To findcomputationally cheaper but still effective methods to deal with these complexes is a major challenge.Unlike the analogue calculations, computational methods solve all equations iteratively, so there are major differences between thesetwo calculation types. The starting point in state space (the assumed initial conformation of molecule) is could have a stronger effectthen the expected, on the flow of the iterative solving algorithm of the computational approach.Here we present a comparative study for a Ruthenium complex. We have optimised the molecule several times. Each of the optimisationsstarted from different initial molecular conformations. Then we have compared the result in different ways, like calculation times andminimum energy that had reached, to see effect of starting configurations on the calculation.It is showed that, starting configuration is an important parameter for computational calculations of transition metal complexes, and itis needed to be carefully chosen to improve success of calculations.
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    Effect of Polarisation Functions on to Errors of Ab-initio Calculations for Ibuprofen
    (2019) Binbay, Veysel; Binbay, Nil E.
    Computational algorithms, which aimed to solve quantum mechanical equations for molecules, usually produces more errors about thebonds which involves Hydrogens, than the others. Actually this fact is more or less expected, due to unique properties of Hydrogenatoms, such as carrying just single electron for making bonds with other atoms.Computational approaches, unlike the analogue solutions, usually neglect many parameters, under some reasonable assumptions ofcourse, to reduce complexity of quantum systems to some computable ranges. Actually all practical quantum computations can beconsidered as managing the “neglecting process”, by keeping the balance between reduced complexity and acceptable correctness.Polarisation is one of those parameters that usually neglected, for quantum molecular computations about molecules.On the other hand, Hydrogen has a serious capability of being strongly polarised, due to possibility of existence of semi or fully nakedprotons, when it constructs a bond structure.Within this point of view, it is needed to analyse the effect of adding polarisation functions, on to calculation errors, especially forhydrogens, by hoping to reduce big calculation errors about them.Here, we added polarisation functions to optimisation calculations of ibuprofen molecule, to see the effect of polarisation functions tothe errors of computed bond lengths. We have compared the results to X-RAY data.Finally it is concluded that, more polarisation function reduces the calculation errors, but it is not worth to increased computationalcosts.