Design and structural bioinformatic analysis of polypeptide antigens useful for the SRLV serodiagnosis.

Due to their intrinsic genetic, structural and phenotypic variability the Lentiviruses, and specifically small ruminant lentiviruses (SRLV), are considered viral quasispecies with a population structure that consists of extremely large numbers of variant genomes, termed mutant spectra or mutant cloud. Immunoenzymatic tests for SRLVs are available but the dynamic heterogeneity of the virus makes the development of a diagnostic "golden standard" extremely difficult. The ELISA reported in the literature have been obtained using proteins derived from a single strain or they are multi-strain based assay that may increase the sensitivity of the serological diagnosis. Hundreds of SRLV protein sequences derived from different viral strains are deposited in GenBank. The aim of this study is to verify if the database can be exploited with the help of bioinformatics in order to have a more systematic approach in the design of a set of representative protein antigens useful in the SRLV serodiagnosis. Clustering, molecular modelling, molecular dynamics, epitope predictions and aggregative/solubility predictions were the main bioinformatic tools used. This approach led to the design of SRLV antigenic proteins that were expressed by recombinant DNA technology using synthetic genes, analyzed by CD spectroscopy, tested by ELISA and preliminarily compared to currently commercially available detection kits.

Bis(CBT)palladium(II) Derivatives (CBT = m-carborane-1-thiolate): Synthesis, Molecular Structure, and Physicochemical Properties of cis-[(bipy)Pd(CBT)2] and trans-[(py)2Pd(CBT)2].

The new synthesized PdII complex cis-[(bipy)Pd(CBT)2] (bipy = 2,2'-bipyridyl; CBT = m-carborane-1-thiolate anion), which is a potential BNCT (boron neutron capture therapy) agent and of structure elucidated by single-crystal X-ray work, has been studied by infrared (IR) and ultraviolet-visible light (UV-vis) spectra and its properties compared with those of the previously reported and also the structurally characterized analogue trans-[(py)2Pd(CBT)2]. This trans species, prepared via a direct method, was previously isolated from a pyridine solution, consequent to the occurring releasing of the external Pd(CBT)2 moieties of the porphyrazine macrocycle [{Pd(CBT)2}4LZn]·xH2O (L = tetrakis-2,3-[5,6-di(2-pyridyl)pyrazino]porphyrazinato anion), which is an active photosensitizer in photodynamic therapy (PDT) and a potential bimodal PDT/BNCT agent. The UV-vis spectral behavior of both cis and trans species in CHCl3 solution and in the gas phase has been examined in detail by density functional theory (DFT) and time-dependent density functional theory (TDDFT) studies devoted to explain their distinct behavior observed in the region of 400-500 nm, as determined by the presence in the cis structure of a vicinal arrangement of the two CBT groups, an ensemble of results closely similar to those observed for the macrocycles [{Pd(CBT)2}4LM]·xH2O (M = MgII(H2O), ZnII, PdII). It has also been experimentally proved the tendency of the cis isomer in CHCl3/pyridine solution to be changed to the respective trans analogue, with conversion occurring in two steps, as interpreted by detailed DFT studies.

Photoconductive Properties and Electronic Structure in 3,5-Disubstituted 2-(2'-Pyridyl)Pyrroles Coordinated to a Pd(II) Salicylideneiminate Synthon.

The synthesis and the electrochemical, photophysical, structural, and photoconductive properties of three new heteroleptic Pd(II) complexes with various 3',5'- disubstituted-2-(2'-pyridil) pyrroles H(N^N) as coordinated ligands are reported. The coordination of the metal center was completed by a functionalized Schiff base H(O^N) used as an ancillary ligand. The [(N^N)Pd(O^N)] complexes showed highly interesting photoconductive properties which have been correlated to their electronic and molecular structures. Theoretical density functional theory (DFT) and time-dependent DFT calculations were performed, and the results were confronted with the organization in crystalline phase, allowing to point out that the photoconductive properties are mainly a consequence of an efficient intramolecular ligand-to-metal charge transfer, combined to the proximity between the central metal and the donor moieties in the solid-state molecular stacks. The reported results confirm that these new Pd(II) complexes form a novel class of organometallic photoconductors with intrinsic characteristics suitable for molecular semiconductors applications.

Origin of the Enhanced Binding Capability toward Axial Nitrogen Bases of Ni(II) Porphyrins Bearing Electron-Withdrawing Substituents: An Electronic Structure and Bond Energy Analysis.

Axial coordination to metalloporphyrins is important in many biological and catalytic processes. Experiments found the axial coordination of nitrogenous bases to nickel(II) porphyrins to be strongly favored by electron-withdrawing substituents such as perfluorophenyls at the meso carbon positions. Careful analysis of the electronic structure reveals that the natural explanation in terms of density change of the nickel(II) porphyrin system (in particular the metal), does not apply. Electron density changes, by the assumed inductive or polarizing effects on the metal or on the porphyrin ring system, are slight. The effect is caused by a remarkable through-space electric field effect on the metalloporphyrin system, originating from the charge distribution inside the perfluorphenyl groups (mostly the C-F dipoles).

Linkage Isomerism in Silver Acylpyrazolonato Complexes and Correlation with Their Antibacterial Activity.

Novel silver(I) acylpyrazolonato coordination polymers of formula [Ag(Q(R))]n (1-3) have been synthesized by interaction of silver nitrate with HQ(R) in methanol in the presence of an equivalent quantity of KOH (in general HQ(R) = 1-phenyl-3-methyl-4-RC(═O)-5-pyrazolone, in detail HQ(fb), R = -CF2CF2CF3; HQ(cy), R = -cyclo-C6H11; HQ(be), R = -C(H)═C(CH3)2). [Ag(Q(R))]n react with 2-ethylimidazole (2EtimH), 1-methylimidazole (Meim), and triphenylphosphine (PPh3), affording the mononuclear Ag(Q(fb))(EtimH) (4), Ag(Q(cy))(Meim)2 (5), Ag(Q(be))(Meim) (6), and Ag(Q(R))(PPh3)2 (7-9). All complexes have been analytically and spectroscopically characterized, and for some of them the X-ray crystal structure has been resolved. In particular, the single crystal molecular structure determination of Ag(Q(fb))(EtimH) and Ag(Q(be))(PPh3)2 has confirmed the different coordination modes of the HQ(fb) and HQ(be) acylpyrazolone ligands, the former being bound to the silver(I) ion in a monodentate fashion while the latter in the O2-chelating mode. Density functional theory computations suggest new insights about metal-ligand interactions and the observed linkage isomerism. While phosphine-containing complexes Ag(Q(R))(PPh3)2 (7-9) seem not to be able to efficiently inhibit the growth of Escherichia coli and Staphylococcus aureus, the polynuclear complexes [Ag(Q(R))]n (1-3) and the mononuclear Ag(Q(fb))(EtimH) (4), Ag(Q(cy))(Meim)2 (5), and Ag(Q(be))(Meim) (6) show a high and almost steady in time antibacterial activity, comparable to that of AgNO3. This activity is likely related to the degree of saturation of the silver center and to the presence of different ancillary ligands in the diverse typologies of complexes.

Non-symmetrical aryl- and arylethynyl-substituted thioalkyl-porphyrazines for optoelectronic materials: synthesis, properties, and computational studies.

A series of novel non-symmetrically substituted mono ß-aryl and ß-arylethynyl (alkylsulfanyl)porphyrazines and the corresponding Ni(ii) complexes have been prepared by the Suzuki-Miyaura and Sonogashira cross-coupling reactions with the aim to investigate substituent effects on their electronic and aggregation properties. Spectroscopic, electrochemical and computational investigations show that in both aryl and arylethynyl compounds efficient electron transfer between the aryl and macrocycle moieties occurs. The highest perturbation of the porphyrazine π-electron core is provided by strong electron-donating (NMe2) and electron withdrawing (NO2) aryl substituents, which increase and decrease the macrocycle electron density, respectively. Moreover, while in most of the compounds the LUMOs and HOMOs are mainly localized on the porphyrazine ring, in the amino-substituted derivatives the HOMO is localized on the peripheral aryl moieties and the LUMO is localized on the macrocycle. Charge-transfer electronic excitations give rise to absorptions in UV-Vis spectra of both amino- and nitro-substituted compounds. In the former such excitations occur from aryl-localized to macrocycle-localized orbitals, while backward excitations occur in the latter. Therefore, the porphyrazine ring shows an ambivalent behavior, acting as an electron acceptor in the case of the NMe2-substituted compounds and as an electron donor in the NO2-substituted derivative. In these derivatives, even macrocycle mono-substitution provides unconventional "push-pull" systems suitable for NLO. Columnar discotic mesophases are also shown by thio-octyl arylethynyl derivatives, allowing us to envisage the possibility to achieve compounds both suitable for optoelectronic applications and endowed with self-aggregation properties.

An interplay between infrared multiphoton dissociation Fourier-transform ion cyclotron resonance mass spectrometry and density functional theory computations in the characterization of a tripodal quinolin-8-olate Gd(III) complex.

A new hexadentate, tripodal 8-hydroxyquinoline based ligand (QH3) and its gadolinium(III) tris-chelated (GdQ) complex with hemicage structure was investigated by using high resolution Fourier-transform ion cyclotron resonance mass spectrometry (FTICRMS). The protonated adduct of the free ligand and its hemicage tripodal Gd(III) complex, [GdQ + H](+), were first observed in experiments of electrospray ionization (ESI) with a linear ion trap (LTQ) mass spectrometer and further investigated by using high resolution FTICRMS. Gas-phase dissociation of the protonated Gd(III) complex, by infrared multiphoton dissociation (IRMPD) FTICR MS, demonstrated a fragmentation pattern with six main product cluster ions labeled as [Fn](+) (n = 1 up to 6). These product ions suggest the elimination of 7-amino-alkyl or 7-alkyl chains of the hemicage moiety. High resolution MS conditions allowed the elucidation of the fragmentation pattern and product ion structures along with the determination, among the isotopic pattern of Gd, of the chemical compositions of closely related species, which differ in terms of hydrogen content. Among the Gd six naturally stable isotopes, (158)Gd is the most abundant, and its peak within each cluster was used as a reference for distinguishing each product ions. Computational DFT investigations were applied to give support to some hypothesis of fragmentation pathways, which could not have been easily justified on the basis of the experimental work. Furthermore, computational studies suggested the coordination geometry of the protonated parent complex and the five- and four-coordinated complexes, which derive from its fragmentation. Furthermore, experimental and computational evidences were collected about the octet spin state of the parent compound.

Cyclometalated Pt(IV) trans-diiodo adducts: experimental and computational studies within an homologous series of compounds.

Four cyclometalated Pt(IV) compounds, 1a,b and 2a,b, were successfully obtained by oxidative addition of I(2) to 2-phenylpyridinate (PhPy) and Nile Red (NR) derived Pt(II) complexes with acetylacetonate (acac) or hexafluoroacetylacetonate (hacac) ancillary ligands. Single crystal X-ray diffraction, electrochemical, photophysical and computational studies have been performed in comparison with the analogues Pt(II) compounds, shedding new light on the role of the oxidation state of the metal centre towards both the luminescence properties and the dioxygen quenching.

Organometallic red-emitting chromophores: a computational and experimental study on cyclometallated Nile Red complexes of palladium(II) and platinum(II) acetylacetonates and hexafluoroacetylacetonates.

A comparative photophysical, electrochemical and computational study of a series of Nile Red cyclopalladated and newly synthesised cycloplatinated complexes is reported. All complexes are luminescent at room temperature and the emission properties are governed by the nature of the cyclometallated dye. However, the presence of platinum(II) as metal centre decreases severely the emission quantum yield, while the electronegativity of the ancillary hexafluoroacetylacetonato ligand enhanced the emission properties of the Nile Red complexes.

Spectroscopy and electrochemical properties of a homologous series of acetylacetonato and hexafluoroacetylacetonato cyclopalladated and cycloplatinated complexes.

A photophysical, electrochemical and computational study has been performed on a homologous series of cyclometallated Pd(II) (1a-f) and Pt(II) (2a-f) complexes of general formula [(C,N)M(O,O)]; (H(C,N) = azobenzene, 2-phenylpyridine, benzo[h]quinoline; M = Pd, Pt; H(O,O) = acetylacetone, hexafluoroacetylacetone). Experimental and computational data have shown the strong influence exerted by electronegativity of the ancillary ligand on the frontier orbitals of the complexes, such an effect being enhanced for the Pt(II) species.

8-hydroxyquinoline monomer, water adducts, and dimer. Environmental influences on structure, spectroscopic properties, and relative stability of cis and trans conformers.

The low fluorescence quantum yield of 8-hydroxyquinoline cannot be correctly interpreted without knowing the form that such a compound assumes in different environments. The commonly accepted emission-quenching excited-state proton transfer can follow different reaction paths if 8-hydroxyquinoline is dimeric or monomeric or if it exists in the form of cis and trans conformers; in this light, the knowledge of the compound form in a particular environment is basic. We have performed a spectroscopic and computational investigation aimed at the determination of the form of 8-hydroxyquinoline in different solvents. UV-vis, fluorescence, and IR spectral features have been assigned by ab initio computations based on the density functional theory and time-dependent density functional theory; the density functional theory and MP2 computations have been applied to the determination of the relative stability of the dimeric and monomeric cis and trans forms of 8-hydroxyquinoline in different solvents. Molecular dynamics computations have been used to determine the compound behavior in water solutions. According to our results, 8-hydroxyquinoline shows a clear preference for the cis conformation (as dimer or monomer), but, in water solutions, a small fraction of the trans conformation is also present.

Experimental and computational evidence of the intermolecular motifs in the crystal packing of luminescent pentacoordinated gallium(III) complexes.

This paper reports the synthesis, characterization, photophysical and structural properties of the homologous series of good emitting pentacoordinated GaQ'2L complexes 1-3, where Q' is 2-methyl-quinolin-8-olate and L is a phenolate substituted in para position with respect to the oxygen donor atom. A combined approach between the experimental structural analysis (i.e. the molecular fragments involved in intermolecular pi-pi interactions) and the computational study (i.e. the nature of the molecular orbitals residing therein) is discussed in order to compare the charge transport aptitude of complexes 1-3, in relation to the facing of their LUMO/LUMO, HOMO/HOMO and HOMO/LUMO arising from the molecular packing. The different phenolate ligands significantly change the packing characteristics of 1-3, with indirect effects on the electron hopping kinetics responsible for conduction in amorphous thin films. The observed preference for pyridyl-pyridyl stacking proves a faster electron conduction in comparison to hole conduction in the three complexes studied.

Synthesis of heteroaryl imines: theoretical and experimental approach to the determination of the configuration of C=N double bond.

The reaction between an iminophosphorane with furan-2-carbaldehyde, thiophene-2-carbaldehyde, furan-3-carbaldehyde, and thiophene-3-carbaldehyde at 60 degrees C gives the corresponding trans imines in 53-84% yields, while the same reaction at 100 degrees C gives a mixture of the corresponding trans and cis imines. Whether the iminophosphorane reacted with 5-nitrofuran-2-carbaldehyde or 5-nitrothiophene-2-carbaldehyde only the trans imines were obtained in 85-89% yields. The irradiation of the imines obtained from thiophene-2-carbaldehyde and thiophene-3-carbaldehyde gave the corresponding photocyclization products. Cis/trans stereochemistry of the imines can be assigned simulating the UV-vis spectra. In the case of the imine from furan-2-carbaldehyde the computed spectra are characterized by an intense absorption at 361 and 357 nm respectively for the trans-1 and trans-2 structures. No other absorptions of comparable intensity have been predicted: the agreement with the experimental spectrum can be considered good. Furthermore, the experimental weak peaks at 280 and 270 nm can be associated to the computed transitions at 278 and 260 nm for the trans-1 isomer. Several minima of the energy surface can be assigned to the cis isomer, and they all present a very similar energy. The structures of the cis-1 and cis-2 isomers present quite coincident computed electronic spectra. In both cases, the computed spectrum shows two principal features. For the cis-1 structure, the first characteristic absorption is located at 414 nm and the second one at 284 nm. For the cis-2 structure, the first feature is located at 412 nm and the second one at 286 nm. The second transition is computed somewhat more intense. The experimental spectrum could be the consequence of similar populations of the planar cis structure (cis-3) and nonplanar cis structures (cis-1, cis-2, and their enantiomers).

Blue emitting pentacoordinated Al(III) complexes based on 2-methylquinolin-8-olate and substituted phenolate ligands. The role of phenolate derivatives on emission and absorption properties.

This paper reports the synthesis, characterisation and photophysical investigation of the homologous series of blue-emitting pentacoordinated AlQ'(2)L complexes 1-6, where Q' is 2-methylquinolin-8-olate and L is a phenolate substituted in para to the oxygen donor atom. Both electron attracting and electron releasing substituents have been considered. Also binuclear complexes of formula Q'(2)Al-L'-AlQ'(2), where L' = OC(6)H(4)C(6)H(4)O, OC(6)H(4)(CH(2))(3)C(6)H(4)O and OC(6)H(4)C(CH(3))(2)C(6)H(4)C(CH(3))(2)C(6)H(4)O have been synthesised and characterised. These are interesting blue-emitting materials for OLED (organic light emitting diode) fabrication. A comparison between computational and experimental results allowed the description of the absorption and fluorescence processes. A study of the frontier orbitals involved in the electric conduction and fluorescence emission has been performed. Influences of the phenolate-based ligands on the compounds spectroscopy have been particularly taken into account.

Two-electron reduction of alkyl(sulfanyl)porphyrazines: a route to free-base and peripherally metallated asymmetric porphyrazines.

Treatment of octakis(octylthio)porphyrazine (H(2)OOSPz) with cis-bis(benzonitrile)dichloroplatinum(II) in a 1,2,4-trichlorobenzene (TCB)-n-BuOH mixture at 190 degree C affords the asymmetric porphyrazine 2H-heptakis(octylthio)porphyrazine, H(2)HOSPz, in ca. 40% yield. In the key synthetic step the two-electron reduced diprotonated porphyrazine, [H(2)OOPz(4-)(H(+))(2)](hemiporphyrazinogen), forms in nearly quantitative yield. This species undergoes nucleophilic substitution of an octylsulfide group by H(-), affording the asymmetric porphyrazine, this process being favoured by the high-temperature induced charge and structural intramolecular rearrangements. The resulting molecule shows mesomorphic behaviour. Interestingly, in the presence of sodium acetate, or in neat TCB, the asymmetric porphyrazine does not form at all. Under these conditions, a PtCl(2) molecular fragment coordinates both to a porphyrazine aza bridge and to a thioether moiety leading to the formation of the [H(2)OOSPz]PtCl(2) complex. The S,N-coordination of the PtCl(2) unit was proved by (1)H, (195)Pt[(1)H], and (13)C NMR spectroscopy, and supported by DFT (B3LYP) calculations. The complex conjugates high asymmetry with strong solvatochromism and, therefore, it is potentially interesting for nonlinear optics.

Investigations on the electronic effects of the peripheral 4'-group on 5-(4'-substituted)phenylazo-8-hydroxyquinoline ligands: zinc and aluminium complexes.

A new series of 5-(4'-substituted)phenylazo-8-hydroxyquinolines (H[L-R]; R = N(CH(3))(2), C(2)H(5), n-C(4)H(9), C(CH(3))(3), H, and F, ) has been prepared and the corresponding Zn[L-R](2) (1a-6a) and Al[L-R](3) (1b-6b) complexes successfully synthesized. These compounds have been studied in order to design new molecular materials with enhanced electron transport properties. The obtained species have been extensively characterized by absorption and emission spectra and by cyclic voltammetric measurements. Experimental and computational results show that the Zn[L-N(CH(3))(2)].2H(2)O (1a) and Al[L-N(CH(3))(2)](1b) complexes only feature luminescence (at 620 and 600 nm), respectively. The unique effects, which are induced by the N=N-C(6)H(4)-N(CH(3))(2) group, are further proved by a reversible electron transfer process detected by cyclic voltammetry. These outcomes, discussed on the basis of theoretical calculations performed on the (H[L-N(CH3)2])-, H[L-N(CH3)2] and (H[L-N(CH3)(2)])+ species, suggest that metal complexes formed by 5-(4'-N,N-dimethylamino)phenylazo-8-hydroxyquinoline should be considered as electron transport materials suitable for applications in photonic devices.