Synthesis, Characterization, Catalytic Activity, and DFT Calculations of Zn(II) Hydrazone Complexes.

Two new Zn(II) complexes with tridentate hydrazone-based ligands (condensation products of 2-acetylthiazole) were synthesized and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy and single crystal X-ray diffraction methods. The complexes 1, 2 and recently synthesized [ZnL3(NCS)2] (L3 = (E)-N,N,N-trimethyl-2-oxo-2-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)ethan-1-aminium) complex 3 were tested as potential catalysts for the ketone-amine-alkyne (KA2) coupling reaction. The gas-phase geometry optimization of newly synthesized and characterized Zn(II) complexes has been computed at the density functional theory (DFT)/B3LYP/6-31G level of theory, while the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO and LUMO) energies were calculated within the time-dependent density functional theory (TD-DFT) at B3LYP/6-31G and B3LYP/6-311G(d,p) levels of theory. From the energies of frontier molecular orbitals (HOMO-LUMO), the reactivity descriptors, such as chemical potential (µ), hardness (η), softness (S), electronegativity (χ) and electrophilicity index (ω) have been calculated. The energetic behavior of the investigated compounds (1 and 2) has been examined in gas phase and solvent media using the polarizable continuum model. For comparison reasons, the same calculations have been performed for recently synthesized [ZnL3(NCS)2] complex 3. DFT results show that compound 1 has the smaller frontier orbital gap so, it is more polarizable and is associated with a higher chemical reactivity, low kinetic stability and is termed as soft molecule.

Complexes of Zn(II)-Triazoles with CO2 and H2O: Structures, Energetics, and Applications.

Using a first-principle methodology, we investigate the stable structures of the nonreactive and reactive clusters formed between Zn2+-triazoles ([Zn2+-Tz]) clusters and CO2 and/or H2O. In sum, we characterized two modes of bonding of [Zn2+-Tz] with CO2/H2O: the interaction is established through (i) a covalent bond between Zn2+ of [Zn2+-Tz] and oxygen atoms of CO2 or H2O and (ii) hydrogen bonds through N-H or C-H of [Zn2+-Tz] and oxygen atoms of H2O or CO2, N-H···O. We also identified intramolecular proton transfer processes induced by complexation. Indeed, water drastically changes the shape of the energy profiles of the tautomeric phenomena through strong lowering of the potential barriers to tautomerism. The comparison to [Zn2+-Im] subunits formed with Zn2+ and imidazole shows that the efficiency of Tz-based compounds for CO2 capture and uptake is due to the incorporation of more accessible nitrogen donor sites in Tzs compared to imidazoles. Since [Zn2+-Tz] clusters are subunits of an organometallic nanoporous materials and Zn-proteins, our data are useful for deriving force fields for macromolecular simulations of these materials. Our work also suggests the consideration of traces of water to better model the CO2 sequestration and reactivity on macromolecular entities such as pores or active sites.

Selenazolyl-hydrazones as Novel Selective MAO Inhibitors With Antiproliferative and Antioxidant Activities: Experimental and In-silico Studies.

The novel approach in the treatment of complex multifactorial diseases, such as neurodegenerative disorders and cancer, requires a development of efficient multi-targeting oriented drugs. Since oxidative stress significantly contributes to the pathogenesis of cancer and neurodegenerative disorders, potential drug candidates should possess good antioxidant properties. Due to promising biological activities shown for structurally related (1,3-thiazol-2-yl)hydrazones, a focused library of 12 structurally related benzylidene-based (1,3-selenazol-2-yl)hydrazones was designed as potential multi-targeting compounds. Monoamine oxidases (MAO) A/B inhibition properties of this class of compounds have been investigated. Surprisingly, the p-nitrophenyl-substituted (1,3-selenazol-2-yl)hydrazone 4 showed MAO B inhibition in a nanomolar concentration range (IC50 = 73 nM). Excellent antioxidant properties were confirmed in a number of different in vitro assays. Antiproliferative activity screening on a panel of six human solid tumor cell lines showed that potencies of some of the investigated compounds was comparable or even better than that of the positive control 5-fluorouracil. In-silico calculations of ADME properties pointed to promising good pharmacokinetic profiles of investigated compounds. Docking studies suggest that some compounds, compared to positive controls, have the ability to strongly interact with targets relevant to cancer such as 5'-nucleotidase, and to neurodegenerative diseases such as the small conductance calcium-activated potassium channel protein 1, in addition to confirmation of inhibitory binding at MAO B.

Assessing the dispersive and electrostatic components of the selenium-aromatic interaction energy by DFT.

Selenium has been increasingly recognized as an important element in biological systems, which participates in numerous biochemical processes in organisms, notably in enzyme reactions. Selenium can substitute sulfur of cysteine and methionine to form their selenium analogues, selenocysteine (Sec) and selenomethionine (SeM). The nature of amino acid pockets in proteins is dependent on their composition and thus different non-covalent forces determine the interactions between selenium of Sec or SeM and other functional groups, resulting in specific biophysical behavior. The discrimination of selenium toward sulfur has been reported. In order to elucidate the difference between the nature of S-π and Se-π interactions, we performed extensive DFT calculations of dispersive and electrostatic contributions of Se-π interactions in substituted benzenes/hydrogen selenide (H2Se) complexes. The results are compared with our earlier reported S-π calculations, as well as with available experimental data. Our results show a larger contribution of dispersive interactions in Se-π systems than in S-π ones, which mainly originate from the attraction between Se and substituent groups. We found that selenium exhibits a strong interaction with aromatic systems and may thus play a significant role in stabilizing protein folds and protein-inhibitor complexes. Our findings can also provide molecular insights for understanding enzymatic specificity discrimination between single selenium versus a sulfur atom, notwithstanding their very similar chemical properties.

Co(iii) complexes of (1,3-selenazol-2-yl)hydrazones and their sulphur analogues.

The first Co(iii) complexes with (1,3-selenazol-2-yl)hydrazones as an unexplored class of ligands were prepared and characterized by NMR spectroscopy and X-ray diffraction analysis. The novel ligands act as NNN tridentate chelators forming octahedral Co(iii) complexes. The impact of structural changes on ligands' periphery as well as that of isosteric replacement of sulphur with selenium on the electrochemical and electronic absorption features of complexes are explored. To support the experimental data, density functional theory (DFT) calculations were also conducted. Theoretical NMR chemical shifts, the relative energies and natural bond orbital (NBO) analysis are calculated within the DFT approach, while the singlet excited state energies and HOMO-LUMO energy gap were calculated with time-dependent density functional theory (TD-DFT). The electrophilic f- and nucleophilic f+ Fukui functions are well adapted to find the electrophile and nucleophile centres in the molecules. Both (1,3-selenazol-2-yl)- and (1,3-thiazol-2-yl)hydrazone Co(iii) complexes showed potent antimicrobial and antioxidant activity. A significant difference among them was a smaller cytotoxicity of selenium compounds.

Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides.

Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 310- and/or α-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i → i + 3 and i → i + 4 hydrogen bonds characterizing 310 and α-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides.

Palladium(II) complexes with N-heteroaromatic bidentate hydrazone ligands: the effect of the chelate ring size and lipophilicity on in vitro cytotoxic activity.

Novel Pd(II) complex with N-heteroaromatic Schiff base ligand, derived from 8-quinolinecarboxaldehyde (q8a) and ethyl hydrazinoacetate (haOEt), was synthesized and characterized by analytical and spectroscopy methods. The structure of novel complex, as well as structures of its quinoline and pyridine analogues, was optimized by density functional theory calculations, and theoretical data show good agreement with experimental results. A cytotoxic action of the complexes was evaluated on cultures of human promyelocytic leukemia (HL-60), human glioma (U251), rat glioma (C6), and mouse fibrosarcoma (L929) cell lines. Among investigated compounds, only complexes with quinoline-based ligands reduce the cell numbers in a dose-dependent manner in investigated cell lines. The observed cytotoxic effect of two isomeric quinoline-based complexes is predominantly mediated through the induction of apoptotic cell death in HL-60 cell line. The cytotoxicity of most efficient novel Pd(II) complex is comparable to the activity of cisplatin, in all cell lines investigated.

An improved AMBER force field for α,α-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems.

α,α-Dialkylated amino acid residues have acquired considerable importance as effective means for introducing backbone conformation constraints in synthetic peptides. The prototype of such a class of residues, namely Aib (α-aminoisobutyric acid), appears to play a dominant role in determining the preferred conformations of host proteins. We have recently introduced into the standard AMBER force field some new parameters, fitted against high-level quantum mechanical (QM) data, for simulating peptides containing α,α-dialkylated residues with cyclic side chains, such as TOAC (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) and Ac6c (Ac6c = 1-aminocyclohexaneacetic acid). Here, we show that in order to accurately reproduce the observed conformational geometries and structural fluctuations of linear α,α-dialkylated peptides based on Aib, further improvements of the non-bonding and side chain torsion potential parameters have to be considered, due to the expected larger structural flexibility of linear residues with respect to cyclic ones. To this end, we present an extended set of parameters, which have been optimized by fitting the energies of multiple conformations of the Aib dipeptide analogue to corresponding QM calculations that properly account for dispersion interactions (B3LYP-D3). The quality, transferability and size-consistency of the proposed force field have been assessed both by considering a series of poly-Aib peptides, modeled at the same QM level, and by performing molecular dynamics simulations in solvents with high and low polarity. As a result, the present parameters allow one to reproduce with good reliability the available QM and experimental data, thus representing a notable improvement over current force field especially in the description of the α/310-helix conformational equilibria of α,α-dialkylated peptides with linear and cyclic side chains.

Extension of the AMBER force field to cyclic α,α dialkylated peptides.

The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing α,α dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac-Ac(6)C-NMe (Ac = acetyl, Ac(6)C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac-TOAC-NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac-TOAC-NMe dipeptide and double spin-labeled heptapeptide Fmoc-(Aib-Aib-TOAC)(2)-Aib-OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, α-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 3(10) helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 3(10)- and α-helical structures is established in aqueous solution, in agreement with EPR data.

Van der Waals interactions at surfaces by density functional theory using Wannier functions.

The method, recently developed to include van der Waals interactions in the density functional theory by using the maximally localized Wannier functions, is extended to the case of atoms and fragments weakly bonded (physisorbed) to metal and semimetal surfaces, thus opening the way to realistic simulations of surface-physics processes, where van der Waals interactions play a key role. Successful applications to the case of Ar on graphite and of Ar, He, and H(2) on the Al(100) surface are presented.

Conformational analysis of octa- and tetrabromo tetraphenylporphyrins and their Ni(II) and Tb(III) complexes.

Molecular mechanics (MM) calculations were used to analyze the puckering of metalloporphyrins as a function of metal ion size and the position of substituents on the porphyrin periphery, on a three series of octa- and tetrabromo tetraphenylporphyrins: without metal, and with Ni(II), and Tb(III) as representative small and large metal ions, respectively. Molecular energy optimization calculations were carried out using the Consistent Force Field (CFF) program, with the parameters developed previously and new parameters for bromine atom. Normal-coordinate structural decomposition (NSD) analysis was performed on the equilibrium structures obtained by MM calculations. The conformers are also stereochemically characterized, compared with available X-ray structures and with the conformers obtained in our previous MM study using chloro instead of bromo beta-pyrrole substituents.