Search

An extensive and systematic conformational search was performed on the two epimers of the natural lignan 7-hydroxymatairesinol (HMR), by means of a home-made Systematic Conformational Search Analysis (SCSA) code, designed to select more and more stable conformers through sequential geometry optimization of trial structures at increasing levels of calculation theory. In the present case, the starting molecular structures were selected by the semi-empirical AM1 method and filtered – i.e. decreased in number by choosing the more stable species – on the basis of their energy calculated by the HF method and the 6-31G(d) basis set. The geometries obtained were further refined by performing density functional theory (DFT) optimizations, using the B3LYP functional and the 6-31G(d,p) basis set, both in vacuo and in ethanol solution. This procedure allowed us to isolate, at a high level of theory, three groups of epimer conformers characterized by open, semi-folded, and folded conformations. Moreover, the SCSA allowed us to describe a conformational space made-up by about 20 species for each of the two epimers. The corresponding energy content of these species was within 27 kJ mol−1 from the absolute minimum found, both in vacuo and in ethanol solution. The conformational analysis, followed by the inspection of the stereochemistry of the two most stable conformers of both epimers, provides support in rationalizing the proposed reaction mechanism of the catalytic hydrogenolysis of the HMR to matairesinol (MAT). Copyright © 2009 John Wiley & Sons, Ltd.

Two reactive pathways are described for the dissociative adsorption of a hydrogen molecule on a Pd4 pyramidal cluster, by using DFT/B3LYP and CASSCF/CASPT2 computational methods. Because of the different spin multiplicities of the cluster in the initial and final states, the reaction proceeds through a spin multiplicity change, which occurs close to the transition states. The activation energy values are very similar when the DFT method is used, whereas the CASPT2 calculations predict that the concerted mechanism is disfavored. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

An accurate crystal structure determination has provided evidence for a planar conformation for 3-acetylamino-5-methyl-1,2,4-oxadiazole (5), in agreement with quantum-mechanical calculations in the gas phase. In the crystal, a series of strong intermolecular N7H7….O9 hydrogen bonds link the amido groups of different molecules, causing the formation of infinite parallel ordered chains. The effect of the DMSO solvent on the energy and charge distribution of compound 5 and on its relevant 5− anion, involved in a fully degenerate rearrangement (FDR), has been deepened by quantum-mechanical DFT calculations. The calculated energy barrier for the FDR increases in going from in vacuo to DMSO, in agreement with previsions based on the Hughes and Ingold rules concerning the nucleophilic substitution of an anionic reagent (the deprotonated amido group in the side chain) on a neutral substrate (the 1,2,4-oxadiazole ring). Copyright © 2009 John Wiley & Sons, Ltd.

Monte Carlo algorithms and codes, used to study heterogeneous catalytic systems in the frame of the computational section of the NANOCAT project, are presented along with some exemplifying applications and results. In particular, time dependent Monte Carlo methods supported by high level quantum chemical information employed in the field of heterogeneous catalysis are focused. Technical details of the present algorithmic Monte Carlo development as well as possible evolution aimed at a deeper interrelationship of quantum and stochastic methods are discussed, pointing to two different aspects: the thermal-effect involvement and the three-dimensional catalytic matrix simulation. As topical applications, (i) the isothermal and isobaric adsorption of CO on Group 10 metal surfaces, (ii) the hydrogenation on metal supported catalysts of organic substrates in two-phase and three-phase reactors, and (iii) the isomerization of but-2-ene species in three-dimensional supported and unsupported zeolite models are presented.

This review shortly discusses recent results obtained by the application of density functional theory for the calculations of the adsorption and diffusion properties of small molecules and their reactivity on heterogenous catalytic systems, in the ambit of the Nanocat project. Particular focus has been devoted to palladium catalysts, either in atomic or small cluster form. Some protocols have been tested to obtain efficient ways able to treat the electronic and geometric influence of supports like zeolites and carbon nanotubes on the catalytic properties of palladium. The hydroisomerization of cis-but-2-ene is discussed as model reaction on supported and unsupported Pd clusters. Some preliminary results on the structural investigation of systems formed by a palladium clusters and block copolymers are also presented.

The thermal rearrangements of 3-acylamino-5-methylisoxazoles 1 have been investigated under basic and neutral conditions and interpreted with the support of computational data. The density functional theory (DFT) study on the competitive routes available for the base-catalyzed thermal rearrangement of isoxazoles 1 showed that the Boulton-Katritzky (BK) rearrangement, producing the less stable 3-acetonyl-1,2,4-oxadiazoles 5, is a much more favored process than either the migration-nucleophilic attack-cyclization (MNAC) or the ring contraction-ring expansion (RCRE). In turn, an increase in reaction temperature will promote the MNAC of oxadiazoles 5, producing the more stable 2-acylaminooxazoles 8. The thermal rearrangement of 3-acylaminoisoxazoles 1 into oxazoles 8 can therefore be interpreted in terms of a cascade BK-MNAC rearrangement involving 3-acetonyl-1,2,4-oxadiazoles 5 as ancillary intermediates.

Molecular chaperones are a class of proteins able to prevent non-specific aggregation of mitochondrial proteins and to promote their proper folding. Among them, human Hsp60 is currently considered as a ubiquitous molecule with multiple roles both in maintaining health conditions and as a trigger of several diseases. Of particular interest is its role in neurodegenerative disorders since it is able to inhibit the formation of amyloid fibrils.Hsp60 structure was considered, until recent years, analogue to the one of its bacterial homolog GroEL, one of the most investigated chaperones, whose crystallographic structure is a homo-tetradecamer, made up of two seven member rings. On the contrary, it has been recently demonstrated by some of us that Hsp60 shows an equilibrium of tetradecamers and heptamers in solution.We present the results of combined investigations including complementary approaches such as molecular dynamics (MD), circular dichroism (CD) and small-angle X-ray scattering (SAXS) concerning structure, self-organization, and stability of naive Hsp60 in solution in comparison with bacterial GroEL. We analyzed the structural differences between the two proteins in solution, evidencing their different oligomeric equilibria, too. Experiments at increasing concentrations of guanidinium hydrochloride provided further information on the stability of the oligomeric species, on the dissociation of tetradecamers into heptamers and monomers, until the unfolding. The unfolding free energy was obtained, proving that GroEL is more stable in respect to Hsp60.

In depth Monte Carlo conformational scans in combination with molecular dynamics (MD) simulations and electronic structure calculations were applied in order to study the molecular recognition process between tetrasubstituted naphthalene diimide (ND) guests and G-quadruplex (G4) DNA receptors. ND guests are a promising class of telomere stabilizers due to which they are used in novel anticancer therapeutics. Though several ND guests have been studied experimentally in the past, the protonation state under physiological conditions is still unclear. Based on chemical intuition, in the case of N-methyl-piperazine substitution, different protonation states are possible and might play a crucial role in the molecular recognition process by G4-DNA. Depending on the proton concentration, different nitrogen atoms of the N-methyl-piperazine might (or might not) be protonated. This fact was considered in our simulation in terms of a case by case analysis, since the process of molecular recognition is determined by possible donor or acceptor positions. The results of our simulations show that the electrostatic interactions between the ND ligands and the G4 receptor are maximized in the case of the protonation of the terminal nitrogen atoms, forming compact ND G4 complexes inside the grooves. The influence of different protonation states in terms of the ability to form hydrogen bonds with the sugar-phosphate backbone, as well as the importance of mediated vs. direct hydrogen bonding, was analyzed in detail by MD and relaxed force constant (compliance constant) simulations.

Two metal complexes of 2,2′:6′,2′′-terpyridine (terpy), i.e. Cd(terpy)Cl2 and Ni(terpy)Cl2·3H2O, have been prepared and extensively characterized. The interaction of Cd(terpy)Cl2 with synthetic DNA models, poly(dA-dT)·poly(dA-dT) (polyAT) and poly(dG-dC)·poly(dG-dC) (polyGC), has been studied by CD, fluorescence and UV-vis electronic absorption spectroscopy at several metal/polynucleotide–phosphate ratios and for different NaCl concentrations. All the experimental results indicate an intercalative mechanism of interaction. The optimized geometry of the cadmium complex intercalated between the sixth and seventh base pairs of (AT) and (GC) dodecanucleotide duplexes, obtained by quantum mechanics/molecular mechanics (QM/MM) calculations, lends support to the proposed mechanism. The calculated models provide some additional structural details of the intercalation complex at the molecular level. To evidence the influence of the charge and geometry of the metal complex on the mechanism of interaction with polynucleotides, the nickel complex–polyAT system has been studied to some extent by means of CD and UV-vis spectroscopy, and by thermal melting experiments. The results suggest that the octahedral complex cation [Ni(terpy)(H2O)2Cl]+ interacts with polyAT by partial intercalation assisted by electrostatic interaction with the negative charges of the backbone phosphate groups.

Conventional antibiotics might fail in the treatment of biofilm-associated infections causing infection recurrence and chronicity. The search for antimicrobial peptides has been performed with the aim to discover novel anti-infective agents active on pathogens in both planktonic and biofilm associated forms. The fragment 9-19 of human thymosin β4 was studied through 1 μs MD simulation. Two main conformations of the peptide were detected, both constituted by a central hydrophobic core and by the presence of peripheral charged residues suggesting a possible mechanism of interaction with two models of biological membranes, related to eukaryotic or bacterial membrane respectively. In addition, the peptide was chemically synthesized and its antimicrobial activity was tested in vitro against planktonic and biofilm form of a group of reference strains of Staphylococcus spp. and one P. aeruginosa strain. The human thymosin β4 fragment EIEKFDKSKLK showed antibacterial activity against staphylococcal strains and Pseudomonas aeruginosa ATCC 15442 at concentrations from 12.5 to 6.2 mg/ml and inhibited biofilm formation at sub-inhibitory concentrations (3.1-0.75 mg/ml). The activity of the fragment in inhibiting biofilm formation, could be due to the conformations highlighted by the MD simulations, suggesting its interaction with the bacterial membrane. Human thymosin β4 fragment can be considered a promising lead compound to develop novel synthetic or recombinant derivatives with improved pharmaceutical potential.

Molecular Dynamics (MD) simulations and DFT/MM calculations were performed in order to rationalize available experimental results and to provide structural details on the binding mechanism of Epolactaene (EPO) to the 60 KDa Heat Shock Protein (Hsp60). The available crystal structure of Hsp60 represents the last step of the chaperone folding cycle, while the Hsp60-EPO complex was obtained by using a homology model of Hsp60, in order to simulate a state related to the beginning of the folding cycle (Rs1). The results of MD simulations point out that EPO shows the highest binding affinity for the empty ATP binding site. The presence of ATP opens a channel that allows the entrance of both EPO diastereoisomers. However, only (15S)-EPO possesses a suitable orientation to bind its target, Cys442. A DFT/MM study was performed to investigate the structure of EPO attached through a C−S covalent bond and to estimate the binding free energy of such reaction. Interestingly, the MD simulation of Hsp60-EPO shows that the covalent bond between EPO and Cys442 hinders the conformational change leading to the R-open structure, which is involved in the formation of the Hsp60/Hsp10 complex, essential for the known chaperone activity of Hsp60.

Isoxazolo[3,4-d]pyridazin-7(6H)-one derivatives endowed with antiproliferative Activity B. Maggio1, G. Cancemi1, D. Raffa1, M. V. Raimondi1, F. Plescia1, A. D’Anneo2,M. Lauricella3, G. Barone4, R. Bonsignore4, G. Daidone1 1. Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Medicinal Chemistry and Pharmaceutical Technologies Section, University of Palermo, ViaArchirafi 32, 90123, Palermo, Italy 2. Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Laboratory of Biochemistry, University of Palermo. 3.Department of Experimental Biomedicine and Clinical Neurosciences, Laboratory of Biochemistry, University of Palermo. 4. Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo. benedetta.maggio@unipa.it A screening carried out by NCI (Bethesda, USA) on compounds available in our laboratory,in order to ascertain their antiproliferative activity against a panel of 60 human tumor cell lines, allowed to discovery the 3,4-diphenylisoxazolo[3,4-d]pyridazin-7(6H)-one 1a [1] as an hit compound, often showing GI50values at sub-micromolar level. We synthesized some analogs of 1a, i.e.1b-gand other derivatives in which the NHgroup is variably alkylated, with the aim to obtain more active compounds as well as to perform structure-activity relationship(SAR) studies. We obtained a quite active antiproliferative compound, the 3,4-di-p-tolylisoxazolo[3,4-d]pyridazin-7(6H)- one 1d, and verified the importance for the antiproliferative activity of the aril, and not alkyl, groups linked to the isoxazolo-pyridazinone moiety. Studies performed on the cell cycle progression and on some cellular target (ATM, procaspase-2 proteins and H2AX histone) demonstrated that 1d produces an increase of the cell population in pre-G0/G1 and induces cellular death by apoptosis, damaging the DNA by double strand breaks. UV-vis titration and viscosity measurement showed that the compound is able to give an interaction with the B-DNA. 1. Renzi G., Dal Piaz V. (2004)Gazz. Chim. It.95: 1478–1491

Novel nickel(II) (1) and zinc(II) (2) complexes of a Salen-like ligand, carrying a pyrimidine ring on the N,N' bridge, were synthesized and characterized. Their interaction with duplex and G-quadruplex DNA was investigated in aqueous solution through UV-visible absorption, circular dichroism and viscometry measurements. The results obtained point out that, while the zinc(II) complex does not interact with both duplex and G-quadruplex DNA, the nickel(II) complex 1 binds preferentially to G-quadruplex respect to duplex-DNA, with values of the DNA-binding constants, Kb, 2.6×10(5)M(-1) and 3.5×10(4)M(-1), respectively. Molecular dynamics simulations provided an atomic level model of the top-stacking binding occurring between 1 and hTelo (a 22-mer sequence oligonucleotide) in G-quadruplex conformation.

DNA-binding investigations showed that two different derivatives endowed with pyrene and imidazolium moieties, 1 and 2, strongly bind both double-stranded DNA and telomeric sequences in G-quadruplex (G4) conformation. The values of the DNA-binding constants indicate that 1 and 2 show preferential affinity for G4-DNA, of about one and two orders of magnitude, respectively. Moreover, 1 and 2 inhibit short and long-term proliferation of breast cancer cell lines in a time- and dose-dependent fashion. Remarkably, senescence assays indicate that telomeric G4-DNA is a possible biotarget for the cytotoxic activity of 2. Molecular dynamics simulations suggest that the stronger binding of 2 with G4-DNA and the related senescence induction, are a consequence of additional edge-to-face interactions with a base in the TTA loop.

Among computational methods, DFT (density functional theory) and TD-DFT (time-dependent DFT) are widely used in research to describe, inter alia, the optical properties of transition metal complexes. Inorganic/physical chemistry courses for undergraduate students treat such methods, but quite often only from the theoretical point of view. In the calculation exercise herein described, students are guided step by step through the computational study of the photophysics and photochemistry of polypyridyl Ru(II) d6-metal complexes. In particular, by means of DFT and TD-DFT calculations, they are asked to examine and interpret a set of experimental data describing the absorption, emission, and photochemical behavior of three structurally related ruthenium complexes, namely, [Ru(bpy)3]2+ (1), [Ru(tpy)2]2+ (2), and [Ru(bpy)2(py)2]2+ (3). These complexes are particularly suitable for an educational purpose since they exhibit distinct optical and photochemical properties despite being structurally akin to each other. In the computational chemistry laboratory, the instructor progressively guides students through the preparation of DFT and TD-DFT inputs and the use of software for the analysis of output files, including visualization of optimized geometries, absorption spectra, orbitals, and spin density surfaces. The exercise covers training of students in several key concepts concerning the photophysics and photochemistry of transition metal complexes. These include Franck-Condon transitions and the role of 3MLCT (metal-to-ligand charge transfer) and 3MC (metal-centered or ligand-field) states in luminescence and ligand photodissociation processes. Notably, the mixed character of this exercise allows its integration with theoretical and experimental activities and the design of truly multidisciplinary courses.

The experimental investigation of the base-catalyzed rearrangements of 3-acylamino-1,2,4-oxadiazoles evidenced a new reaction pathway which competes with the well-known ring-degenerate Boulton-Katritzky rearrangement (BKR). The new reaction consists of a one-atom side-chain rearrangement that is base-activated, occurs at a higher temperature than the BKR, and irreversibly leads to the corresponding 2-acylamino-1,3,4-oxadiazoles. An extensive DFT study is reported to elucidate the proposed reaction mechanism and to compare the three possible inherent routes: (i) the reversible three-atom side-chain ring-degenerate BKR, (ii) the ring contraction-ring expansion route (RCRE), and (iii) the one-atom side-chain rearrangement. The results of the computational investigation point out that the latter route is kinetically preferred over the RCRE and can be considered as the ground-state analogue of a previously proposed C(3)-N(2) migration-nucleophilic attack-cyclization (MNAC) photochemically activated pathway. The MNAC consists of the formation of a diazirine intermediate, involving the exocyclic nitrogen, that eventually evolves into a carbodiimide intermediate (migration); the latter undergoes a single intramolecular nucleophilic attack-cyclization step leading to the final 2-acylamino-1,3,4-oxadiazole.

Background: Alzheimer’s disease (AD) is the most common form of dementia that seriously affects daily life. Even if AD pathogenesis is still subject of debate, it is generally accepted that cerebral cortex plaques formed by aggregated amyloid-β (Aβ) peptides can be considered a characteristic pathological hallmark. It is well known that metal ions play an important role in the aggregation process of Aβ. Methods: This review focuses on the anti-Aβ aggregation activity of chelating ligands as well as on the use of metal complexes as diagnostic probes and as potential drugs. Conclusion: While chelating agents, such as curcumin or flavonoid derivatives, are currently used to capture metal ions responsible for Aβ aggregation, the potential application of platinum, ruthenium and cobalt complexes, among others, of several heterocyclic ligands, represents a promising new strategy to fight AD.

Subnanometric samples, containing exclusively Ag2 and Ag3 clusters, were synthesized for the first time by kinetic control using an electrochemical technique without the use of surfactants or capping agents. By combination of thermodynamic and kinetic measurements and theoretical calculations, we show herein that Ag3 clusters interact with DNA through intercalation, inducing significant structural distortion to the DNA. The lifetime of Ag3 clusters in the intercalated position is two to three orders of magnitude longer than for classical organic intercalators, such as ethidium bromide or proflavine. Fil: Buceta, David. Universidad de Santiago de Compostela; España Fil: Busto, Natalia. Universidad de Burgos; España Fil: Barone, Giampaolo. Università di Palermo; Italia Fil: Leal, José M.. Universidad de Burgos; España Fil: Domínguez, Fernando. Universidad de Santiago de Compostela; España Fil: Giovanetti, Lisandro Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; Argentina. Universidad Nacional de la Plata; Argentina Fil: Requejo, Felix Gregorio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; Argentina. Universidad Nacional de la Plata; Argentina Fil: García, Begoña. Universidad de Burgos; España Fil: López-Quintela, M. Arturo. Universidad de Santiago de Compostela; España

Premature stop codons are the result of nonsense mutations occurring within the coding sequence of a gene. These mutations lead to the synthesis of a truncated protein and are responsible for several genetic diseases. A potential pharmacological approach to treat these diseases is to promote the translational readthrough of premature stop codons by small molecules aiming to restore the full-length protein. The compound PTC124 (Ataluren) was reported to promote the readthrough of the premature UGA stop codon, although its activity was questioned. The potential interaction of PTC124 with mutated mRNA was recently suggested by molecular dynamics (MD) studies highlighting the importance of H-bonding and stacking π-π interactions. To improve the readthrough activity we changed the fluorine number and position in the PTC124 fluoroaryl moiety. The readthrough ability of these PTC124 derivatives was tested in human cells harboring reporter plasmids with premature stop codons in H2BGFP and FLuc genes as well as in cystic fibrosis (CF) IB3.1 cells with a nonsense mutation. Maintaining low toxicity, three of these molecules showed higher efficacy than PTC124 in the readthrough of the UGA premature stop codon and in recovering the expression of the CFTR protein in IB3.1 cells from cystic fibrosis patient. Molecular dynamics simulations performed with mutated CFTR mRNA fragments and active or inactive derivatives are in agreement with the suggested interaction of PTC124 with mRNA.

The heterocyclic ligands [1,2,4]triazolo-[1,5-a]pyrimidine (tp) and 5,7-dimethyl-[1,2,4]triazolo-[1,5-a]pyrimidine (dmtp), react with diorganotin dichlorides giving the addition compounds Me2SnCl2(tp)2, Et2SnCl2(tp)2, Me2SnCl2(dmtp)2, Et2SnCl2(dmtp)2, Bu2SnCl2(dmtp), Ph2SnCl2(dmtp). The organotin:ligand stoichiometry goes from 1:2 to 1:1 by increasing the steric hindrance of the organic groups bound to tin. The compounds have been characterized by means of infrared, 119Sn Mossbauer and 1H AND 13C NMR spectroscopy. The ligands presumably coordinate to tin classically through the nitrogen atom at the position 3. The 1:1 complexes adopt trigonal bipyramidal structures, with the organic groups on the equatorial plane and the ligand in the apical position. All-trans octahedral structures are inferred for the 1:2 complexes, except for Et2SnCl2(tp)2, characterized by a skew-trapezoidal structure. 119Sn Mossbauer measurements, at room temperature, in concomitance with DFT calculations, performed on isomeric structures of R2SnCl2(tp)2 (R = Me, Et), allowed us to conclude that the all-trans octahedral coordination induces self-assembly in the solid state, possibly accomplished through π–π stacking interactions among the planar ligands coordinated to the organotin(IV) compound, while the skew-trapezoidal structure attributed to Et2SnCl2(tp)2, induces the formation of monomeric adducts in the solid state. In vitro antimicrobial tests showed that [n-Bu2SnCl2(dmtp)] has interesting properties as anti Gram-positive and antibiofilm agent.

Tri-organotin(IV) complexes of the triazolo-pyrimidine derivatives 4,5-dihydro-5-oxo-[1,2,4]triazolo-[1,5 a ]pyrimidine (5HtpO), 4,7-dihydro-5-methyl-7-oxo-[1,2,4]triazolo-[1,5 a ]pyrimidine (HmtpO), and 4,5,6,7-tetrahydro-5,7-dioxo-[1,2,4]triazolo-[1,5 a ]pyrimidine (H 2 tpO 2 ), and the diorganotin derivative n -Bu 2 Sn(tpO 2 ), were synthesized and characterized by means of infrared and 119 Sn Mossbauer spectroscopy. In all the complexes obtained the triazolopyrimidines act as multidentate ligands producing polymeric structures. A trigonal bipyramidal arrangement of the ligands around the tin atom is proposed for triorganotin(IV) derivatives, with organic groups on the equatorial plane and bridging anionic ligands. DFT calculations were performed on the structure of H 2 tpO 2 and on its mono- an di-anions, to investigate their harmonic vibrational modes. The observed trend of the experimental and calculated carbonyl stretching frequencies furnishes a support for the interpretation of the structure of the organotin(IV) complexes obtained with this ligand. The structure of n -Bu 2 Sn(tpO 2 ) was elucidated by quantum chemical calculations, performed on a model system of the polymeric complex by a two layers ONIOM method. The combined experimental and theoretical results obtained support for a trans - n -Bu 2 distorted octahedral geometry, with the tpO 2 2 - units acting as bis-chelate ligands bridging the diorganotin(IV) moieties, and with the N(1)O(7) and N(4)O(5) chelating groups in the equatorial plane showing a cis -O 2 , or cis -N 2 , coordination. In vitro antimicrobial tests were performed on n -Bu 3 Sn(HtpO 2 ) and Ph 3 Sn(HtpO 2 ), and a good antifungal and antibiofilm activity was observed, in particular for n -Bu 3 Sn(HtpO 2 ).

The Systematic Conformational Search Analysis (SCSA) code was employed to study the conformational properties of the 8α-hydroxy-germacradiene-6,12-olide isomers. This procedure was extended to the trans,cis- and trans,trans-1(10),4-isomers of 8α,15-dihydroxy-germacradiene-6,12-olides and 8α-hydroxy-15-oxo-germacradiene-6,12-olides, to investigate structural and energetic analogies between these and the 8α-hydroxy-germacradiene-6,12-olide species. The calculated 13C NMR spectra, at the hybrid DFT mPW1PW91 level, showed a sound correlation with the corresponding experimental spectra, providing a valid support to the reliability of the calculated structures and to the consistence of our conformational analysis. The results presented here allowed us to support our previous mechanistic interpretation on the oxidation of 8α,15-dihydroxy-trans,trans-1(10),4-germacradiene-6,12-olides to 8α-hydroxy-15-oxo-trans,cis-1(10),4-germacradiene-6,12-olides. Copyright © 2005 John Wiley & Sons, Ltd.

DFT calculations, using an all-electron basis set and with full geometry optimization, were performed on 34 Sn(II) and Sn(IV) compounds of known structure and (119)Sn Mössbauer parameters, to obtain the theoretical values of the electric field gradient components, V(xx), V(yy), and V(zz), at the tin nucleus. These were used to determine the quantity V = V(zz)[1+ 1/3((V(xx) - V(yy))/((V(zz))(2)](1/2), for each investigated compound, which is related to the quadrupole splitting (DeltaE) parameter according to DeltaE = 1/2eQV, where e is the electronic charge and Q is the quadrupole moment of the tin nucleus. The linear fitting of the correlation plot of the experimental DeltaE, versus the corresponding calculated V values, produced a slope that is equal to 0.93 +/- 0.03 and a correlation coefficient R = 0.982. The value of Q obtained, 15.2 +/- 4.4 fm(2), is in agreement with that previously experimentally determined or calculated by analogous procedures. The calculation method is able to establish the sign of the electric field gradient component V(zz), in agreement with the sign of DeltaE determined experimentally by Mössbauer-Zeeman spectroscopy. The calculated structural parameters are in good agreement with the corresponding experimental data, determined by X-ray crystallography in the solid state, with average structural deviations of about 3 % for bond lengths and angles in the tin environment. Calculated values of DeltaE were obtained from the calibration fitting constant and from the values of V. By comparing experimental and calculated DeltaE parameters, the structure assignment of configurational isomers was successful in two test cases, in agreement with the experimental X-ray crystallographic structures. These results indicate that the method can be used as a tool to support the routine structure interpretation of tin compounds by (119)Sn Mössbauer spectroscopy.

The X-ray absorption spectra of Cu I I and Cult complexes of N,N'-1,2-phenylenebis(2-mercapto-2-methylpropionamide) were recorded and analysed in solid phase. The EXAFS spectra of the two samples were refined with full multiple scattering path. Geometry optimisations on the Cu I I and Cu I I I complexes were performed by the B3LYP density functional method, with the 6-31G(d,p) basis set, considering different spin multiplicities. The singlet state of the Cu I I I complex was shown to be more stable than the triplet state, and a good agreement between the calculated and the corresponding experimental structure was found. Further single-point calculations on the optimised geometry were carried out at the Hartree-Fock level for obtaining molecular orbital eigenvectors and eigenvalues. The latter were employed as parameters in a new fitting approach to rationalise the shape of the K-edge of the XAS spectra.

The hydrogenation of 2,4-dinitro-toluene on a Pd/C catalyst was employed as a test reaction to simulate, by the time-dependent Monte Carlo method, processes occurring in a three-phase batch reactor working at isobar and isotherm conditions. A new time-dependent Monte Carlo algorithm, including an original subroutine useful to reduce the time of the simulations, was developed and implemented in Fortran language. The paper describes the flowchart of the code together with the main technical details and the involved physical and chemical models. Computational characteristics, such as the simulated time to reach surface steady state conditions and the effects of the catalyst morphology are presented. Correlations between simulated and experimental data are summarized and current mechanistic hypotheses criticized.

The two new fluorescent ligands RosCat1 and RosCat2 contain catechol receptors connected to rosamine platforms through an amide linkage and were synthesized by using microwave-assisted coupling reactions of carboxyl- or amine-substituted rosamines with the corresponding catechol units and subsequent deprotection. RosCat1 possesses a reverse amide, whereas RosCat2 has the usual oriented amide bond (HNCO vs. CONH, respectively). The ligands were characterized by means of NMR spectroscopy, mass-spectrometry, and DFT calculations and X-ray crystallography studies for RosCat1. The influence of the amide linkage on the photophysical properties of the fluorescent ligands was assessed in different solvents and showed a higher fluorescence quantum yield for RosCat1. The coordination chemistry of these ligands with a Fe(III) center has been rationalized by mass-spectrometric analysis and semiempirical calculations. Octahedral Fe(III) complexes were obtained by the chelation of three RosCat1 or RosCat2 ligands. Interestingly, the unconventional amide connectivity in RosCat1 imposes the formation of an eight-membered ring on the chelate complex through a "salicylate-type" mode of coordination.

A new time-dependent Monte Carlo algorithm was developed to simulate isobar and isotherm three-phase batch hydrogenation of 2,4-dinitro-toluene on Pd/C catalysts. A new reaction mechanism was formulated, involving 9 and 27 toluene derivatives, in solution and adsorbed on the surface, respectively. In fact, three different ways of adsorption were considered for all surface derivatives. Microscopic mechanistic hypotheses were formulated analyzing the mimicked surface populations able to reproduce the experimental catalytic activity–selectivity patterns at different times, temperatures, reagent concentrations, and catalyst particle morphologies. The three different adsorption modes, giving rise to surface species having different steric hindrances, together with the morphology of the particle catalysts, were determinants in reproducing experimental findings.

Quantum-mechanical calculations, at HF level, were performed to gain chemical–physical basis information on the 2,4-dinitro-toluene hydrogenation occurring over palladium catalysts. To investigate the surface characteristics of the species involved in the reaction system, simplified molecular models including small metal clusters were considered. Remarkable findings, useful to elucidate the reaction mechanism and important parameters, working in time dependent Monte-Carlo simulations of the title reaction, were obtained; inter alia: the molar standard free energies of the molecules involved in the reaction, the volume occupied by the species in solution phase and the qualitative order of the desorption activation energy values, of the nitro, amino and hydroxylamino groups of the toluene fragments interacting with the Pd surface. The molecular level interaction modes of the different toluene derivatives on Pd clusters, mimicking the catalyst surface, were visualized. The results have been discussed in terms of microscopic (energetic, structural and steric hindering) factors driving the observed macroscopic reaction.

The syntheses and X-ray structures of novel heteroleptic thiolate/dithiocarbamate derivatives (Et2NCS2)2(RS)2Sn (R = Cy, CH2CF3) have been examined and their thermal decompositions compared with those of selected tin(II) and tin(IV) dithiocarbamates. The heteroleptic species decompose to SnS by initial elimination of RSSR to afford (Et2NCS2)2Sn and subsequent loss of [Et2NC(S)]2S. In contrast, (Et2NCS2)4Sn decomposes via [(Et2NCS2)2SnS]2, whose structure has been determined, and finally to SnS2 by sequential elimination of [Et2NC(S)]2S. The two families of compounds, (R2NCS2)4Sn and (Et2NCS2)2(RS)2Sn, thus provide single-source materials for bulk SnS2 and SnS, respectively, by virtue of their differing decomposition pathways. Preliminary CVD experiments with (Et2NCS2)2(CyS)2Sn are also reported.

1,3-Dipolar cycloaddition reactions can be considered a powerful synthetic tool in the building of heterocyclic rings, with applications in different fields. In this review we focus on the synthesis of biologically active compounds possessing the 1,2,3-triazole core through 1,3-dipolar cycloaddition reactions. The 1,2,3-triazole skeleton can be present as a single disubstituted ring, as a linker between two molecules, or embedded in a polyheterocycle. The cycloaddition reactions are usually catalysed by copper or ruthenium. Domino reactions can be achieved through dipolarophile anion formation, generally followed by cyclisation. The variety of attainable heterocyclic structures gives an illustration of the importance of the 1,2,3-triazole core in medicinal chemistry.

New benzothieno[3,2-d]-1,2,3-triazines, together with precursors triazenylbenzo[b]thiophenes, were designed, synthesized and screened as anticancer agents. The structural features of these compounds prompted us to investigate their DNA binding capability through UV–vis absorption titrations, circular dichroism, and viscometry, pointing out the occurrence of groove-binding. The derivative 3-(4-methoxy-phenyl)benzothieno[3,2-d]-1,2,3-triazin-4(3H)-one showed the highest antiproliferative effect against HeLa cells and was also tested in cell cycle perturbation experiments. The obtained results assessed for the first time the anticancer activity of benzothieno[3,2-d]-1,2,3-triazine nucleus, and we related it to its DNA-binding properties.

N -diphenylmethyl-2-propenamide (NDP) was synthesised and characterised. Pharmacological in vitro tests pointed out that NDP had a cytotoxic activity on a human ovarian carcinoma comparable to that of doxorubicin. Hypothesising that this in vitro cytotoxic activity could be mainly due to intercalating interactions, between the drug and DNA fragments, ab initio calculations, at the Hartree–Fock (HF) level, were performed on the structure, and on the conformational properties of NDP, whereas its interaction with an (AC)(TG) dinucleotide triphosphate duplex (DD) was studied by the ONIOM method, at HF and PM3 level for NDP and DD, respectively. The supposed intercalation process with the DNA fragment was discussed in terms of the co-planarity of the aromatic rings present in the NDP molecule.

Quantum mechanical calculations were employed to deepen information about the basic properties of the mechanism occurring in the palladium catalytic hydrogenation involving surface hydrogen species of unsaturated hydrocarbons. Activation energy values of elementary events implicated in the whole reaction were computed by potential energy surface analyses, to determine the corresponding occurrence probabilities of the same events. Different surface hydrogen species were pointed out and their relevance in the overall surface process was discussed together with their geometrical and chemical characteristics.

Quantum mechanical calculations at HF, MP2 and DFT levels were used to rationalise the surface effects of the hydrocarbon lateral interactions occurring on single planar metal surfaces or on different adjacent surfaces during the hydrogenation on palladium catalyst. The different values of electronic charge, found in the different atoms of palladium clusters, were suggested as a possible explanation of the non-homogeneous behaviour already inferred for catalyst surface sites having non-isotropic local arrangement.

A time-dependent Monte Carlo algorithm was employed to study the effects of carbonaceous surface species on the hydrogenation mechanism of acetylene–ethylene mixtures on a Pd catalyst. Simulations of tail-end and front-end mixture hydrogenation were performed employing the same set of predetermined event probabilities. The involvement of the steric hindrance of the surface species was essential to simulate the experimental data. The catalyst activity and selectivity were promoted or inhibited by different concentrations of surface polymeric species formed along with the hydrocarbon hydrogenation. Tools to get a new interpretation of the catalytic reaction mechanism and an innovative basis to perform catalyst design were suggested by the approach illustrated.

AACVD (aerosol-assisted chemical vapour deposition) using (PhS)(4)Sn as precursor leads to the deposition of Sn3O4 in the absence of H2S and tin sulfides when H2S is used as co-reactant. At 450 degreesC the film deposited consists of mainly SnS2 while at 500 degreesC SnS is the dominant component. The mechanism of decomposition of (PhS)(4)Sn is discussed and the structure of the precursor presented.

The nature of calf thymus DNA in aqueous solution, in the presence of the organotin(IV) species Sn IV Me 3 , Sn IV Me 2 and Sn IV Me, possibly partly hydrolysed and/or hydrated, was investigated by small-angle X-ray scattering (SAXS), ultraviolet spectroscopy (UV) at different temperatures and circular dichroism (CD). The results are compared with those of previous 119 Sn Mossbauer studies on condensed DNA phases. The effects of tin-phosphate oxygen bonding on the DNA melting profile in DNA-Sn IV Me systems are in agreement with previous reports on DNA-Main Group metal ion interactions. The structure and conformation of the DNA double helix are not influenced by Sn IV Me n species, even in experimental conditions near the onset of DNA condensation. Gel electrophoresis indicates that DNA is not degraded by Sn IV Me n ; the X-ray radii of gyration of the DNA cross-section and its mass per unit length, determined by SAXS from aqueous solutions, are constant and independent of the nature and concentration of the Sn IV Me n species present in the solutions. The invariance of the interparticle distances in solution at very low ionic strengths, in the presence of increasing amounts of Sn IV Me n compounds, even approaching DNA precipitation, suggests that the condensation process involves isolated DNA chains.

Synchrotron radiation small-angle X-ray scattering (SAXS) was used to investigate solutions of native DNA at different ionic strengths and temperatures. The mass per unit length, radius of gyration of the cross-section of DNA and apparent second virial coefficient (A2) were obtained from Zimm plots in the rodlike particle approximation. The values of A2 obtained in this way are positive and almost constant indicating that the repulsive interactions still influence the scattering patterns at resolutions as high as 5-8 nm. SAXS measurements in continuous temperature scans indicate that the rod approximation is valid over a wide temperature range during DNA melting and confirm that the rodlike-wormlike transition temperature increases with ionic strength.

The interaction between a dinucleotide triphosphate duplex (DD), mimicking the DNA molecule, and the dimethyltin(IV) cation is studied by the semiempirical PM3 method. The results show that the interaction can occur involving the tin atom and the electron-donor centres of DD, requiring in some cases the presence of water molecules. In particular, the binding of the dimethyltin(IV) moiety with two adjacent phosphate oxygen atoms is allowed by the presence of water molecules coordinating to the tin atom. In this case the tin environment shows a geometry in agreement with 119 Sn Mossbauer and X-ray data.

Complexes Me2SnCl(SPy) and Me2SnCl(SPym) (HSPy = 2-mercaptopyridine; HSPym = 2-mercaptopyrimidine), from ethanol solutions, interact with aqueous calf-thymus DNA yielding condensed phases with probable Me2Sn(SPy,SPym) (DNA monomer) stoichiometries of 1:1; the condensation of DNA is inferred originated from electrostatic bonding between complex cations Me2Sn(SPy,SPym)+ and the phosphate oxygen of the phosphodiester groups. Octahedral-or trigonal-bipyramidal tin environments are inferred from the point-charge model treatment of the 119Sn Mossbauer parameter nuclear quadrupole splitting, considering the bonding by S and N, or only S donor atoms from the ligand, as well as possible coordination by H2O molecules. The dynamics of tin atoms in the condensed systems Me2Sn(SPym) (DNA monomer), in both gel and lyophilized phases, have been investigated by variable-temperature 119Sn Mossbauer spectroscopy, obtaining evidence of a general correspondence as reported in the literature for the lyophilized condensates Alk2Sn(DNA monomer)2; possible analogies for Me2Sn(SPym) (DNA monomer) and Alk2Sn(DNA monomer)2 in DNA bonding, and structures of tin environments, are discussed. ‘Neutral’ complexes, such as Me2Sn(SPy)2, neither induce DNA condensation, nor bind to DNA in solution phases. Copyright © 1999 John Wiley & Sons, Ltd.

Guanidine-induced denaturation of Sulfolobus solfataricus beta-glycosidase expressed in Escherichia coli, Sbetagly, was investigated at pH 6.5 and 25 degreesC by means of circular dichroism and fluorescence measurements. The process proved reversible when the protein concentration was lower than 0.01 mg mL-1. Moreover, the transition curves determined by fluorescence did not coincide with those determined by circular dichroism, and the GuHCl concentration corresponding at half-completion of the transition increased on raising the protein concentration in the range 0.001-0.1 mg mL-1. Gel filtration chromatography experiments showed that, in the range 2-4 M GuHCl, there was an equilibrium among tetrameric, dimeric, and monomeric species. These findings, unequivocally, indicated that the guanidine-induced denaturation of Sbetagly was not a two-state transition with concomitant unfolding and dissociation of the four subunits. A mechanism involving a dimeric intermediate species was proposed and was able to fit the experimental fluorescence intensity transition profiles, allowing the estimation of the total denaturation Gibbs energy change at 25 degreesC and pH 6.5. This figure, when normalized for the number of residues, showed that, at room temperature, Sbetagly has a stability similar to that of mesophilic proteins.

The presence in the mRNA of premature stop codons (PTCs) results in protein truncation responsible for several inherited (genetic) diseases. A well-known example of these diseases is cystic fibrosis (CF), where approximately 10% (worldwide) of patients have nonsense mutations in the CF transmembrane regulator (CFTR) gene. PTC124 (3-(5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl)-benzoic acid), also known as Ataluren, is a small molecule that has been suggested to allow PTC readthrough even though its target has yet to be identified. In the lack of a general consensus about its mechanism of action, we experimentally tested the ability of PTC124 to promote the readthrough of premature termination codons by using a new reporter. The reporter vector was based on a plasmid harboring the H2B histone coding sequence fused in frame with the green fluorescent protein (GFP) cDNA, and a TGA stop codon was introduced in the H2B-GFP gene by site-directed mutagenesis. Additionally, an unprecedented computational study on the putative supramolecular interaction between PTC124 and an 11-codon (33-nucleotides) sequence corresponding to a CFTR mRNA fragment containing a central UGA nonsense mutation showed a specific interaction between PTC124 and the UGA codon. Altogether, the H2B-GFP-opal based assay and the molecular dynamics (MD) simulation support the hypothesis that PTC124 is able to promote the specific readthrough of internal TGA premature stop codons.

The in silico COMPARE analysis was performed on 8-[3-(piperidino)propyl]-4,10-dimethyl-9-phenyl-6-(methylsulfanyl)-3,4-dihydropyrimido[1,2-c]pyrrolo[3,2-e]pyrimidin-2(8H)-one, a compound with promising antiproliferative activity, previously synthetized and screened against a panel of 60 human tumor cell lines. The results evidenced that this compound matches the biological properties of Chromomycin A3 and Actinomycin D, known drugs with high DNA binding affinity. Prompted by such results, a thorough spectroscopic investigation of its DNA aqueous solutions was performed, with the aim to verify its DNA-binding properties. DNA groove-binding interaction was assigned by UV-vis spectrophotometric and circular dichroism (CD) titrations. In agreement with the spectroscopic studies, the test compound has achieved significant cell-cycle perturbation with higher accumulation of cells in G0/G1 phase. Further structure modifications of the tested compound, has led to its analogue, which showed DNA base-pairs intercalating ability. Molecular modeling studies on the annelated pyrrolo[3,2-e]pyrimidines tested were in agreement with the biological evaluation.

The rise of antibiotic-resistance as well as the reduction of investments by pharmaceutical companies in the development of new antibiotics have stimulated the investigation for alternative strategies to conventional antibiotics. Many antimicrobial peptides show a high specificity for prokaryotes and a low toxicity for eukaryotic cells and, due to their mode of action the development of resistance is considered unlikely. We recently characterized an antimicrobial peptide that was called Paracentrin 1 from the 5-kDa peptide fraction from the coelomocyte cytosol of the Paracentrotus lividus. In this study, the chemically synthesized Paracentrin 1, was tested for its antimicrobial and antibiofilm properties against reference strains of Gram positive and Gram negative. The Paracentrin 1 was active against planktonic form of staphylococcal strains (reference and isolates) and Pseudomonas aeruginosa ATCC 15442 at concentrations ranging from 12.5 to 6.2 mg/ml. The Paracentrin 1 was able to inhibit biofilm formation of staphylococcal and Pseudomonas aeruginosa strains at concentrations ranging from 3.1 to 0.75 mg/ml. We consider the tested peptide as a good starting molecule for novel synthetic derivatives with improved pharmaceutical potential.

The photophysical and DNA-binding properties of the cationic zinc(II) complex of 5-triethylammonium methyl salicylidene ortho-phenylenediiminato (ZnL 2 + ) were investi- gated by a combination of experimental and theoretical methods. DFT calculations were performed on both the ground and the first excited states of ZnL 2 + and on its possi- ble mono- and dioxidation products, both in vacuo and in selected solvents mimicked by the polarizable continuum model. Comparison of the calculated absorption and fluores- cence transitions with the corresponding experimental data led to the conclusion that visible light induces a two-elec- tron photooxidation process located on the phenylenediimi- nato ligand. Kinetic measurements, performed by monitor- ing absorbance changes over time in several solvents, are in agreement with a slow unimolecular photooxidation pro- cess, which is faster in water and slower in less polar sol- vents. Moreover, structural details of ZnL-DNA binding were obtained by DFT calculations on the intercalation complexes between ZnL and the d(ApT)2 and d(GpC)2 dinucleoside monophosphate duplexes. Two main complementary bind- ing interactions are proposed: 1) intercalation of the central phenyl ring of the ligand between the stacked DNA base pairs; 2) external electrostatic attraction between the nega- tively charged phosphate groups and the two cationic trie- thylammonium groups of the Schiff-base ligand. Such sug- gestions are supported by fluorescence titrations performed on the ZnL/DNA system at different ionic strengths and tem- peratures. In particular, the values of the DNA-binding con- stants obtained at different temperatures provided the en- thalpic and entropic contributions to the binding and con- firmed that two competitive mechanisms, namely, intercala- tion and external interaction, are involved. The two mecha- nisms are coexistent at room temperature under physiological conditions.

We present a thorough characterization of the interaction of novel nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff base complexes with native calf thymus DNA (ct-DNA), in buffered aqueous solution at pH 7.5. UV-vis absorption, circular dichroism (CD) and viscometry titrations provided clear evidence of the intercalative mechanism of the three square-planar metal complexes, allowing us to determine the intrinsic DNA-binding constants (K(b)), equal to 1.3 × 10(7), 2.9 × 10(6), and 6.2 × 10(5) M(-1) for 1, 2 and 3, respectively. Preferential affinity, of one order of magnitude, toward AT compared to GC base pair sequences was detected by UV-vis absorption titrations of 1 with [poly(dG-dC)]2 and [poly(dA-dT)]2. Structural details of the intercalation site of the three metal complexes within [dodeca(dA-dT)]2 were obtained by molecular dynamics (MD) simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations. The calculations revealed that three major intermolecular interactions contribute to the strong affinity between DNA and the three metal complexes: (1) the electrostatic attraction between the two positively charged triethylammoniummethyl groups of the metal complexes and the negatively charged phosphate groups of the DNA backbone; (2) the intercalation of the naphthalene moiety within the four nitrogen bases of the intercalation site; (3) the metal coordination by exocyclic donor atoms of the bases, specifically the carbonyl oxygen and amine nitrogen atoms. Remarkably, the Gibbs formation free energy calculated for the intercalation complexes of 1, 2 and 3 with [dodeca(dA-dT)]2 in the implicit water solution is in agreement with the experimental Gibbs free energy values obtained from the DNA-binding constants as ΔG° = -RT ln(K(b)). In particular, the DNA-binding affinity trend, 123, is reproduced. Finally, the first shell coordination distances calculated for the intercalation complex 3/[dodeca(dA-dT)]2 are in excellent agreement with the experimental distances extracted from the extended X-ray absorption fine structure (EXAFS) spectrum of the corresponding 3/ct-DNA solutions. The latter results provided the first evidence of metal ion coordination by native DNA in aqueous solution.

In this work the new protocol BIOlogical Target Assignation (BIOTA) for the prediction of the biological target from molecular structures is proposed. BIOTA is based on the Principal Components Analysis (PCA) application on a matrix of ligands versus molecular descriptors. The application of BIOTA could allow to hypothesize the mechanism of action of a candidate drug prior to its biological evaluation or to repurpose old drugs. The protocol can be fine-tuned by choosing opportune targets (biological or not) and molecular descriptors, and it can be useful in every fields in with it is possible to collect set of compounds with known properties. The robustness of the protocol depends from different factors: the correctness of biological data, the optimization of the molecular structures and their molecular descriptors calculation, the selection of the biological targets. The application of BIOTA to a new class of Hsp90 inhibitors was able to predict quite correctly their affinity for Hsp90.

A proline, a leucine, and two cysteine residues, introduced at positions 19, 28, 31, and 32 of bovine pancreatic RNase A, i.e. the positions occupied by these residues in the subunit of bovine seminal RNase, the only dimeric RNase of the pancreatic-type superfamily, transform monomeric RNase A into a dimeric RNase, endowed with the same ability of BS-RNase of swapping its N-terminal segments. The thermodynamic consequences of the progressive introduction of these four residues into RNase A polypeptide chain have been studied by comparing the temperature- and urea-induced denaturation of three mutants of RNase A with that of a stable monomeric derivative of BS-RNase. The denaturation processes proved reversible for all proteins, and well represented by the two-state N--D transition model. The progressive introduction of the four residues into RNase A led to a gradual shift of the protein stability toward that characteristic of monomeric BS-RNase, which, in turn, is markedly less stable than RNase A with respect to both temperature- and urea-induced denaturation. On the other hand, the thermal stability of a dimeric active mutant of RNase A is found to approach that of wild-type seminal RNase.