Nurcan Ş. Tüzün

Cyclopolymerization Reactions of Diallyl Monomers: Exploring Electronic and Steric Effects Using DFT Reactivity Indices

The regioselectivity in the cyclopolymerization of diallyl monomers is investigated using DFT-based reactivity indices. In the first part, the experimentally observed mode of cyclization (exo versus endo) of 11 selected radicals involved in this process is reproduced by the computation of activation energies, entropies, enthalpies, and Gibbs free energies for the 5- and 6-membered cyclization reactions. The application of a recently proposed energy partitioning of the activation barriers shows that the regioselectivity cannot be explained by the steric effect alone. Next, a number of relevant DFT-based reactivity indices, such as non-spin-polarized and spin-polarized Fukui functions, spin densities, and dual descriptors, were applied to probe the role of the polar and stereoelectronic effects in this reaction. The dual descriptor has been found to reproduce best the experimental trends, confirming the important role of the stereoelectronic effects.

The mechanism of copper-catalyzed azide-alkyne cycloaddition reaction: a quantum mechanical investigation.

In this study, the mechanism of CuAAC reaction and the structure of copper acetylides have been investigated with quantum mechanical methods, namely B3LYP/6-311+G(d,p). A series of possible copper-acetylide species which contain up to four copper atoms and solvent molecules as ligand has been evaluated and a four-copper containing copper-acetylide, M1A, was proposed more likely to form based on its thermodynamic stability. The reaction has been modeled with a representative simple alkyne and a simple azide to concentrate solely on the electronic effects of the mechanism. Later, the devised mechanism has been applied to a real system, namely to the reaction of 2-azido-1,1,1-trifluoroethane and ethynylbenzene in the presence of copper. The copper catalyst transforms the concerted uncatalyzed reaction to a stepwise process and lowers the activation barrier. The pre-reactive complexation of the negatively charged secondary nitrogen of azide and the positively charged copper of copper-acetylide brings the azide and the alkyne to a suitable geometry for cycloaddition to take place. The calculated activation barrier difference between the catalyzed and the uncatalyzed reactions is consistent with faster and the regioselective synthesis of triazole product.

Stereoselective propagation in free radical polymerization of acrylamides: a DFT study.

In this study stereospecific free radical polymerization of N,N-alkylamides [N,N-dimethylacrylamide (DMAAm), N-methyl-N-phenylacrylamide (MphAAm) and N,N-diphenylacrylamide (DPAAm)] is investigated with density functional theory (DFT) calculations. Model propagation reactions at dimeric stage are used to elucidate the effect of substituent bulkiness, temperature and solvent polarity on stereospecific addition modes. In calculations all the monomers favor gauche conformation in their pro-meso and pro-racemo additions in general. The DFT calculations have reproduced the stereospecificity seen in these monomers. The implicit solvent calculations performed with IEFPCM have further refined the quantitative agreement. The calculations of DMAAm in solvents of different polarity (toluene, THF, chloroform and 2-propanol) have successfully reproduced the experimental trend both qualitatively and quantitatively. Tartrate molecules as stereospecifity inducer in DMAAm are considered and the experimentally observed change in stereospecificity from iso to syn in their presence have been elucidated by modeling the possible orientations of transition states in the propagation step. The favorable stereospecific addition modes are explained via interplay between the steric effects and the hydrogen bonding interactions.

Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches, molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development

Abstract The essential biological function of phosphodiesterase (PDE) type enzymes is to regulate the cytoplasmic levels of intracellular second messengers, 3′,5′-cyclic guanosine monophosphate (cGMP) and/or 3′,5′-cyclic adenosine monophosphate (cAMP). PDE targets have 11 isoenzymes. Of these enzymes, PDE5 has attracted a special attention over the years after its recognition as being the target enzyme in treating erectile dysfunction. Due to the amino acid sequence and the secondary structural similarity of PDE6 and PDE11 with the catalytic domain of PDE5, first-generation PDE5 inhibitors (i.e. sildenafil and vardenafil) are also competitive inhibitors of PDE6 and PDE11. Since the major challenge of designing novel PDE5 inhibitors is to decrease their cross-reactivity with PDE6 and PDE11, in this study, we attempt to identify potent tadalafil-like PDE5 inhibitors that have PDE5/PDE6 and PDE5/PDE11 selectivity. For this aim, the similarity-based virtual screening protocol is applied for the “clean drug-like subset of ZINC database” that contains more than 20 million small compounds. Moreover, molecular dynamics (MD) simulations of selected hits complexed with PDE5 and off-targets were performed in order to get insights for structural and dynamical behaviors of the selected molecules as selective PDE5 inhibitors. Since tadalafil blocks hERG1 K channels in concentration dependent manner, the cardiotoxicity prediction of the hit molecules was also tested. Results of this study can be useful for designing of novel, safe and selective PDE5 inhibitors.

In silico design of novel hERG-neutral sildenafil-like PDE5 inhibitors

Cyclic nucleotide phosphodiesterase enzymes (PDEs) have functions in regulating the levels of intracellular second messengers, 3′, 5′-cyclic adenosine monophosphate (cAMP) and 3′, 5′-cyclic guanosine monophosphate (cGMP), via hydrolysis and decomposing mechanisms in cells. They take essential roles in modulating various cellular activities such as memory and smooth muscle functions. PDE type 5 (PDE5) inhibitors enhance the vasodilatory effects of cGMP in the corpus cavernosum and they are used to treat erectile dysfunction. Patch clamp experiments showed that the IC50 values of the human ether-à-go-go-related gene (hERG1) potassium (K) ion channel blocking affinity of PDE5 inhibitors sildenafil, vardenafil, and tadalafil as 33, 12, and 100 μM, respectively. hERG1 channel is responsible for the regulation of the action potential of human ventricular myocyte by contributing the rapid component of delayed rectifier K+ current (IKr) component of the cardiac action potential. In this work, interaction patterns and binding affinity predictions of selected PDE5 inhibitors against the hERG1 channel are studied. It is attempted to develop PDE5 inhibitor analogs with lower binding affinity to hERG1 ion channel while keeping their pharmacological activity against their principal target PDE5 using in silico methods. Based on detailed analyses of docking poses and predicted interaction energies, novel analogs of PDE5 inhibitors with lower predicted binding affinity to hERG1 channels without loosing their principal target activity were proposed. Moreover, molecular dynamics (MD) simulations and post-processing MD analyses (i.e. Molecular Mechanics/Generalized Born Surface Area calculations) were performed. Detailed analysis of molecular simulations helped us to better understand the PDE5 inhibitor–target binding interactions in the atomic level. Results of this study can be useful for designing of novel and safe PDE5 inhibitors with enhanced activity and other tailored properties.

Prediction of the1H NMR spectra of epoxy-fused cyclopentane derivatives by calculations of chemical shifts and spin–spin coupling constants

1H NMR spectra of epoxy-fused cyclopentane derivatives have been computationally investigated with density functional calculations in order to unravel the shielding effect of the epoxy ring on the 1H NMR chemical shifts of N-substituted epoxy-fused cyclopentane-3, 5-diol derivatives. Both 1H NMR chemical shifts and spin–spin coupling constants have been calculated with the WP04/cc-pVTZ level of theory in solution. The WP04/cc-pVTZ// B3LYP/6-31+G(d) methodology has been found to reproduce the best experimental results on epoxy-fused cyclopentane derivatives. This study is expected to lead experimentalists in their endeavour to characterize epoxy-fused cyclic systems with ease.