Supplementary data for article: Petrović, D.; Zlatović, M. Modeling Human Serum Albumin Tertiary Structure to Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics. Journal of Chemical Education 2015, 92 (7), 1233–1237. https://doi.org/10.1021/ed500358f

Supporting information for: [https://doi.org/10.1021/ed500358f]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1745

The kinetics of the reduction of the lipophilic quinone avarone by n-alkyl-1,4-dihydronicotinamides of various lipophilicities

Several NADH model compounds, N-alkyl-1,4-dihydronicotinamides, some of them possessing amphiphilic properties, have been synthesized, and the kinetics of their reaction with a biologically active liphophilic quinone, avarone, has been studied in a protic solvent both in the presence and absence of cationic, anionic or non-ionic surfactants. In the absence of micellar agents, the medium- and long-chain N-dodecyl (3) and N-heptadecyl (4) derivatives show a significant increase in the reaction rates compared to other model compounds, due to the stabilization of the semiquinone intermediate. Anionic surfactants retard the reaction, non-ionic surfactants slightly accelerate the reaction with the short-chain derivatives, and retard the reaction with the medium- and long-chain derivatives, and the cationic surfactants increase the reaction rate with all derivatives except the long-chain 4. The results support the e-p-e mechanism of the reduction of lipophilic quinones by NADH models in protic medium

Improved electrochemical epoxidation of cholesterol and avarol dimethyl ether

Electrochemical epoxidation of cholesterol and avarol dimethyl ether with bromide as heteromediator was performed, and its mechanism discussed. The influence of the solvent, the mediator concentration, and different electrolytic techniques on yield of the products was examined. Under optimal conditions, the yield of the cholesterol epoxides (5α,6α and 5β, 6β) was 88%, and of the corresponding epoxides of the avarol dimethyl ether 72%

Supplementary data for article: Petrović, D.; Zlatović, M. Modeling Human Serum Albumin Tertiary Structure to Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics. Journal of Chemical Education 2015, 92 (7), 1233–1237. https://doi.org/10.1021/ed500358f

Supporting information for: [https://doi.org/10.1021/ed500358f]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1745

Improved electrochemical epoxidation of cholesterol and avarol dimethyl ether

Electrochemical epoxidation of cholesterol and avarol dimethyl ether with bromide as heteromediator was performed, and its mechanism discussed. The influence of the solvent, the mediator concentration, and different electrolytic techniques on yield of the products was examined. Under optimal conditions, the yield of the cholesterol epoxides (5α,6α and 5β, 6β) was 88%, and of the corresponding epoxides of the avarol dimethyl ether 72%

Application of Hybrid Density Functional Theory in Calculation of Edge-to-Face Interactions of Receptor-Ligand System

Our previously described research on docking analysis of a series of isosteric N4-arylpiperazines on a model of 5-HT1A receptor was used earlier to investigate interactions of different ligands with the receptor binding site. Due to the limitations of molecular mechanics (MM) methods, docking analysis failed to give precise results about interactions that influence binding affinity of the ligands, but we presumed that aromatic-aromatic interactions, or edge-to-face, to be more precise, play an important role in the binding process. In order to further elaborate on this hypothesis, ab initio approach was used to calculate possible edge-to-face interactions on a model system and correlate them to ligand affinity. Obtained results indicate that those dispersive interactions can show notable influence on the binding of the ligands to 5-HT1A receptor. Stabilization energies of modeled receptor-ligand complex, calculated using Becke's "half-and-half" hybrid DFT method showed strong correlation with the affinity of investigated ligands towards 5-HT1A receptor

Sastav sterolne smese algi jadranskog mora Ulva lactuca, Codium dichotomum, Cystoseira adriatica i Fucus virsoides

The sterol composition of two green algae and two brown algae from the South Adriatic was determined. In the green alga Ulva lactuca, the principal sterols, were cholesterol and isofucosterol. In the brown alga Cystoseira adriatica, the main sterols were cholesterol and stigmast-5-en-3 beta-ol, while the characteristic sterol of the brown algae, fucosterol, was found only in low concentration. The sterol fractions of the green alga Codium dichotomum and the brown alga Fucus virsoides contained practically only one sterol each, comprising more than 90 % of the total sterols (clerosterol in the former and fucoserol in the latter).Određen je sastav sterolne smese dve zelene i dve mrke alge iz južnog Jadrana. U zelenoj algi Ulva lactuca glavni steroli su holesterol i izofukosterol. U mrkoj algi Cystoseira adriatica glavni steroli su holesterol i stigmast-5-en-3ß-ol, dok je fukosterol, sterol karakterističan za mrke alge, nađen samo u maloj količini. Sterolne smese zelene alge Codium dichotomum i mrke alge Fucus virsoides sastoje se praktično samo od po jednog sterola, klerosterola u prvoj i fukosterola u drugoj, koji sačinjavaju više od 90 % sterolnih frakcija

Supplementary material for the article: Ajdačić, V.; Stepanović, S.; Zlatović, M.; Gruden, M.; Opsenica, I. M. Decarbonylative Dibromination of 5-Phenylthiophene-2-Carbaldehyde with Bromine. Synthesis (Germany) 2016, 48 (24), 4423–4430. https://doi.org/10.1055/s-0035-1562615

Supplementary material for: [http://dx.doi.org/10.1055/s-0035-1562615]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2361

Uticaj disperzivnih interakcija na afinitet vezivanja liganada sa arilpiperazinskom funkcijom za dopaminski D2 receptor

Several isosteric 1,3-dihydro-5-[2-(4-aryl-l-piperazinyl)ethyl]-2H-benzinlidazole-2-thiones were used to investigate the interactions of different ligands with the binding site of the D2 receptor. Due to limitations of the simulation methods, docking analysis failed to show precisely the interactions that influence the binding affinity of the ligands. It is presumed that dispersive forces or more precisely edge-to-face interactions play an important role in the binding process, especially for the lipophilic part of the ligands. In order to confirm this hypothesis, ab initio calculations were applied on a model system in order to find the stabilization energies of potential edge-to-face interactions and then to correlate them with the ligand affinity. The obtained results indicate that there is a significant correlation between the strength of dispersive interactions and ligand affinity. It was shown that for the calculation of stabilization energies of modeled receptor-ligand complexes the Becke "half-and-half" hybrid DFT method can be used, thus speeding up the usually long calculation time and reducing the required computer strength.Nekoliko izosternih 1,3-dihidro-5-[2-(4-aril-1-piperazinil)etil]-2H-benzimidazol-2-tiona je korišćeno da bi se ispitale interakcije različitih liganada sa vezivnim mestom dopaminskog D2 receptora. Zbog ograničenja metoda korišćenih za simulaciju vezivanja, analiza ovih rezultata nije mogla da pokaže preciznije koje interakcije utiču na afinitet vezivanja liganada. Pretpostavljeno je da disperzivne sile, ili preciznije, tzv. edge-to-face interakcije, igraju značajnu ulogu u procesu vezivanja, naročito u lipofilnom delu liganda. Da bi se potvrdila ova hipoteza primenom ab initio izračunavanja na model sistem, pokušano je izračunavanje stabilizacione energije ovih interakcija i njeno dovođenje u vezu sa afinitetom liganada. Dobijeni rezultati ukazuju da postoji značajna korelacija između jačine disperzivnih interakcija i afiniteta liganda. Pokazano je da se pri izračunavanju stabilizacionih energija modelovanih kompleksa ligand-receptor može upotrebiti Beckeova 'half-and-half' hibridna DFT metoda, što značajno smanjuje vreme potrebno za izračunavanja i potrebne računarske resurse