Our program BABELPDB allows browsing and interrogating the native and derived structural features of biological macromolecules using data obtained from the Protein Data Bank (PDB). Major features of BABELPDB are: (1) convert from PDB to other formats, (2) add or remove H atoms, (3) strip the crystallization water molecules and (4) separate the a‑carbons (Ca). The coordinates obtained with BABELPDB permit characterizing the presence of hydrogen bonds (H‑bonds). The algorithm for detecting H‑bonds is implemented in our program TOPO for the theoretical simulation of the molecular shape. An example is given to illustrate the capabilities of the software: the calculation of the fractal dimension of the lysozyme molecule with (1.908) and without (1.920) H atoms. The numbers compare well with reference calculations performed with our version of the GEPOL program and with the results from Pfeifer et al. For proteins, the Ca skeleton extracted with BABELPDB allows drawing the ribbon image, which determines the secondary structure of proteins.

In recent years, the synthesis of metal nanoparticles has attracted significant attention because of their unique properties. Although many strategies for the preparation of noble- and transition-metal nanoparticles have been published, the synthesis of indium nanoparticles (InNPs) has been scarcely reported. Most of the bottom-up methods require the use of indium salts and strong reducing agents such as sodium metal, zinc power, alkalides/electrides, or decomposition of organometallic complexes. Regrettably, some of them provide little control over particle size and size distribution of the InNPs, and the presence of stabilizing agents is generally mandatory. Recently we have been working on the simple, mild, and efficient synthesis of very reactive, monodisperse (4.0 ± 1.5 nm) spherical InNPs by fast reduction of indium(III) chloride with lithium powder and a catalytic amount of 4,4´-di-tert-butylbiphenyl (DTBB) in THF at room temperature, and in the absence of any anti-agglomeration additive or ligand. We explored the above mentioned InNPs-based reactive system for the allylation of a variety of aldehydes and ketones in a one-pot procedure, by adding allyl bromide over a suspension of InNPs followed by the addition of the corresponding carbonyl compound. For most of the compounds tested, the homoallylic alcohol product was obtained in good yields. In order to extend the scope of this indium-mediated protocol, herein, we report a comparative study on the allylation of benzaldehyde with a series of substituted allyl bromides promoted by both InNPs and In powder, in THF at room temperature. As expected, indium nanoparticles demonstrated to be much more efficient than granular indium yielding the corresponding allylic alcohols almost quantitatively. Additionally, computational studies have been applied in order to explain the differences in reactivity observed. Based on the experimental data and the DFT studies, we have proposed a possible reaction mechanism that implies the formation of a cyclic six-membered Zimmermann-Traxler-type transition state and the participation of allylindiums sesquihalides as intermediates in the indium-mediated allylation.

We have explored the use of steric hindrance on controlling the ring-chain tautomeric equilibrium of a tetrahydroquinazoline/imine system. Two imines, one of them having a bulky group (E)-N (3-((2-((4-methylphenylsulfonamido)methyl)phenylimino)methyl)pyridin-2-yl)pivalamide (H2L1SB) and the other one without bulky group (E)-N-(2-(2,3-dihydroxybenzylideneamino)-benzyl)-4-methylbenzenesulfonamide (H2L2SB) have been synthetised and spectroscopically studied by 1H NMR. Besides, the formation of the corresponding 1,2,3,4-tetrahydroquinazolines (H2L1TQ and H2L2TQ) was tested.

O-Benzyl-5-chlorsalicyl-tripeptide aldehydes are novel organic compounds aimed for inhibition of the proteasome. The inhibition of proteasome via blocking his protein recycling function is one of promising ways to treat tumor cells or multiple myeloma. In the present days a series of similar compounds are clinically used or in clinical trials (MG132, marizomib, CEP-18770, MLN-9708, ONX-0912) and some of them are already approved and available for the public (carfilzomib, bortezomib). Synthesis starts with O-benzyl-5-chlorsalicylic acid and methylesters of aminoacid hydrochlorides. The amidic bond is formed via carbodiimides (especialy EDCI∙HCl) in presence of 1‑hydroxybenzotriazole (HOBt) and N,N-diisopropylethylamine (DIPEA) to liberate the amino group. During the synthesis of the peptide backbone after joining the second amino acid a partial racemization occured. Steps have been taken to prevent this undesirable event. By adjusting the reaction conditions  92% ee was achieved. Further details will be discused in the Communication paper. The goal of my work is to prepare a series of compounds with tripeptide backbone and aldehyde or oxirane moiety and test cytotoxicity, inhibition of proteasome, inhibition of protein kinases, type of caused apoptosis and antimicrobial activity.

It is well known that heterocumulene functions are prone to participate in pericyclic processes, mainly in cycloaddition reactions. In a wide variety of such reactions, the heterocumulenic function usually acts as the two-atom component involving one of its two cumulated double bonds.   In the course of our recent research on the reactivity of heterocumulenes we have reported that ortho-(azidomethyl)phenyl carbodiimides undergo formal [3+2] intramolecular cycloaddition reactions by heating in solution to give tetrazolo[5,1-b]quinazolines. In these reactions the carbodiimide contributed with one N=C bond to the new five-membered tetrazole ring, whereas the remaining three nitrogen atoms came from the azide function. We reasoned that similar [3+2] cycloadditions could occur in related heterocumulenic compounds in which the three-atom azido component of those processes is replaced by a cyclopropane ring, thus forming a new pyrrolidine ring.  To this end we selected ortho-azidobenzylydenecyclopropane as the optimal starting material for opening the access to a variety of heterocumulenic functions via aza-Wittig reactions of its phosphazene derivative, which in turn could be prepared by the Staudinger imination reaction of triphenylphosphane with that azide.   In this communication we will disclose the successful building of the designed cyclopropane-heterocumulenes (isothiocyanates, ketenimines and carbodiimides) and the results obtained in our attempts of thermally inducing the respective intramolecular [3+2] cycloaddition reactions, that only in some instances occurred as planned.

Applying succinic acid as a versatile, bidentate ligand to coordinate to cerium, resulted to a complex. The obtained crystalline complex was characterized by IR and melting point, then calcined at a certain temperature which was found by TGA method. Since in the first step, altering organic ligand type will affect on shape of precursor and as a result on the nano oxide, and in the next step, calcination time and temperature results in different morphologies of cerium oxide,  we examine all these changes and conclude the optimum conditions and the best ligand to be succinic acid. Characterization of the nanorods of CeO₂ was performed by XRD, SEM and IR. Cerium oxide in nano-scale has many applications such as oxygen reservation capacity, conductivity, high UV absorption, high hardness, catalysis, fuel cells, sensors.  

Nitrocompounds in the triplet states have the biradical structure, with both unpaired electrons localized on the oxygen atoms. The structure is able to participate in oxidation reactions by the radical mechanisms. We have also proposed that some molecules can catalyze the nitrocompound destruction with N=O molecules formation. We have chosen the S-containing organic compounds like H2S, MeSH, and Me2S as substrates for oxidations in the presence of nitrocompounds. We performed theoretical quantum chemical studies of the most possible reaction mechanisms of the oxidation reactions using DFT B3LYP 6-311G++(d) method from the Gaussian 03 program package. We calculated the PES profiles, including intermediates and transition state structures. The activation energies of all stages involved were calculated.  We was able to show that MeSH molecule could dissociate to break the S-H bond. The hydrogen atoms formed immidiately find them to be added to the nitrocompound molecules. During further transformation H-atom could be abstracted from the methyl groups to form the S=C double bond. In the case of Me2S there are no hydrohen atoms that can be easily abstracted, and oxygen atom of nitrocompound attacks the S atom to form Me2SO has place. The last compound is able to abstract H-atom from the nitrocompound molecule and decompose to give Me2S and OH radical.

Due to the synthetic accessibility of different substituted coumarins and their biological properties, these heterocyclic compounds play an important role in the field of Medicinal Chemistry. In fact, coumarins have been previously described as anticancer, antiviral, anti-inflammatory, antimicrobial, enzymatic inhibitory and antioxidant agents. Within the field of neurodegenerative diseases are described different types and intervention processes, which include the development of acetylcholinesterase (AChE) inhibitors, which combined with another drugs are used on therapy for Alzheimer's diseases. These inhibitors allow acetylcholine levels in the brain to stabilize or even enhance them, since it's established that this enzyme is responsible for the metabolism of this important neurotransmitter. In our group, we have already synthesised multiple novel compounds incorporating the coumarin moiety with remarkable activity towards MAO and/or AChE. In this work, we continue to exploit this scaffold by the synthesis of novel 3-amidocoumarins for the treatment of neurodegenerative diseases. Following this work, pharmacological studies of the prepared compounds as AChE inhibitors are currently in progress. Some preliminary results are presented in this communication.

Density functional theory calculations and spectroscopic monitoring of the reactions of the chain tautomer N-{2-[(8-hydroxyquinolin-2-yl)methyleneamino]benzyl}-4-methylbenzene-sulfonamide (H2Lchain) and the ring tautomer 2-(3-tosyl-1,2,3,4-tetrahydroquinazolin-2-yl)quinolin-8-ol (H2Lring) against Zn(OAc)2•2H2O have been performed in order to clarify the role of the metal ion in the ring-opening/closing reaction under investigation. The results obtained show that, among the processes leading to zinc complexes that could occur, the path leading to Zn(HLring)2 is the energetically more favorable one. Thus, this path would be preferred in the presence of sufficient free ligand in solution, regardless of its tautomeric form. The latter is due to the formation of energetically similar key intermediate complexes Zn(OAc)(HLchain) and Zn(OAc)(HLring). The process to afford Zn2(Lchain)2 by dimerization of the intermediate complex Zn(OAc)(HLchain) is energetically unfavourable and is only obtained in good yield by decreasing the stoichiometry of the ligand and at high reaction temperature.

In this work the electrophilic behaviour of nitrothiophenes in polar Diels-Alder toward dienes of different nucleophilicity is studied. In thermal conditions the reactions were development in molecular solvents and in protic ionic liquids trying to compare the solvent effects on this class of reactions. In the presence of these solvents the reaction system was exposed to microwave irradiation as a complement of reaction conditions.