Photochemistry of Dihydrido(hydrotris(3,5-dimethylpyrazolyl)borato)(Z-cyclooctene)iridium. Synthetic Intermediates and Mechanism of the Photochemical Formation of Hydridophenyl(hydrotris(3,5-dimethylpyrazolyl)borato)(trimethyl phosphite)iridium

The photolysis of a benzene solution of [Tp(Me2)IrH(2)(COE)], 1 (Tp(Me2) = hydrotris(3,5-dimethylpyrazolyl)borate, COE = Z-cyclooctene), in the presence of P(OMe)(3), gives the stable novel complex [Tp(Me2)IrH(C(6)H(5))(P(OMe)(3))], 3a. The photochemical syntheses of [Tp(Me2)IrH(2)(P(OMe)(3))], from 1 and P(OMe)(3) in diethyl ether, and [Tp(Me2)IrH(2)(CH(2)=CHCOO(t)Bu)], from 1 in tert-butyl acrylate, are also reported. The above reactions and several experiments using C(6)D(6) and P(OCD(3))(3) show that, in all cases, the primary photoproduct is the 16-electron, five-coordinate iridium(III) intermediate {Tp(Me2)IrH(2)}, 6a, produced by loss of COE from 1. The above experiments also allow the postulation of a mechanistic pathway for the formation of 3a which involves the oxidative addition of an aromatic C-H bond by 6a. Furthemore, the photochemical reaction of 1 in the presence of P(OCD(3))(3) shows that, under the reaction conditions used, oxidative addition of C-H bonds of P(OMe)(3) and of coordinated Tp(Me2)-ligands, presumably, to the intermediates 6a and {Tp(Me2)IrH(C(6)H(5))}, also occurs. Thus, coordinatively unsaturated iridium(III) species readily activate C-H bonds.     

The role of the Zn(II) binding domain in the mechanism of E. coli DNA topoisomerase I

Background  

Escherichia coli DNA topoisomerase I binds three Zn(II) with three tetracysteine motifs which, together with the 14 kDa C-terminal region, form a 30 kDa DNA binding domain (ZD domain). The 67 kDa N-terminal domain (Top67) has the active site tyrosine for DNA cleavage but cannot relax negatively supercoiled DNA. We analyzed the role of the ZD domain in the enzyme mechanism.     

Synthesis and Characterization of Pyrrolthiosemicarbazone Complexes of Palladium(II). Crystal Structures of [{Pd[C4H4NC(H)=NNC(S)NHMe](Cl)}2{μ‐Ph2P(CH2)3PPh2}] and [Pd{C4H4NC(H)=NNC(S)NHMe}{Ph2P(CH2)2PPh2‐P,P}](Cl)

Reaction of the thiosemicarbazone ligands C₄H₄NC(H)=NN(H)C(S)NHR (R = Me, a ; Et, b ) with Li₂[PdCl₄] gave the dinuclear complexes [Pd{C₄H₄NC(H)=NNC(S)NHR}(μ‐Cl)]₂ (R = Me, 1a ; Et, 1b ) with a central Pd₂Cl₂ core and with deprotonation of the thiosemicarbazones at the hydrazinic nitrogen atom. Treatment of 1a and 1b with triphenylphosphine gave the mononuclear compounds [Pd{C₄H₄C(H)=NNC(S)NHR}(Cl)(PPh₃)] (R = Me, 2a ; Et, 2b ), whereas reaction of 1a and 1b with tertiary diphosphines gave mono‐ and dinuclear compounds, as appropriate, with the corresponding diphosphine acting as a monodentate ( 6b ), chelating ( 3a ) and bridging ligand ( 4a, 5a , 4b, 5b ). Treatment of 1a and 1b with (Ph₂PCH₂CH₂PPh₂)W(CO)₅ gave the new heterobimetallic complexes 7a and 7b . The crystal structures of complexes 3a and 4a are described.     

New Furano-sesquiterpenoids from Mediterranean Sponges

A mixture of sponges of the East Pyrenean Mediterranean is shown to contain the known sponge products longifolin ( 1 ), avarol ((+)- 3 ), and avarone ( 4 ) and the terrestrial-plant product sesquirosefuran ( 2 ), besides to the new furano-sesquiterpenoids tavacfuran (= 3-methyl-2-[(3′Z)-3′-methyl-4″-methyl-2″-furyl-3′-butenyl]furan; ( 5 ) and tavacpallescensin (= 5,10-dihydro-6,9-dimethyl-4H-benzo[5,6]cyclohepta[1,2-b]furan; 6 ) and the new furano-butenolide sesquiterpenoids tavacbutenolide-1 (= (±-4-ethoxy-2-methyl-4-)[(2′E)-2′-methyl-4′-(3″-methyl-2″-furyl)-2′-butenyl]-2-buten-4-olide; (±)- 7 ) and tavacbutenolide-2 (= (±)-4-ethoxy-3-methyl-4-[2′E)-3′-methyl-4′-(4″-methyl-2″-furyl)-2′-butenyl]-2-buten-4-olide; (±)- 8 ). Structural assignments are based on NMR data and on the synthesis of the (E)-isomer of 5 . The sponge Dysidea tupha of the same area is also shown to contain the two sesquiterpenoids ent-furodysinin ((?)- 14 ), which is enantiomeric to a product of a Dysidea sp. of Australian waters, and tuphabutenolide ((+)- 15 ).     

Pseudo-MS3 in a MALDI orthogonal quadrupole-time of flight mass spectrometer

Both the matrix selected and the laser fluence play important roles in MALDI-quadrupole/time of flight (QqTOF) fragmentation processes. "Hot" matrices, such as alpha-cyano4-hydroxycinnamic acid (HCCA), can increase fragmentation in MS spectra. Higher laser fluence also increases fragmentation. Typical peptide fragment ions observed in the QqTOF are a, b, and y ion series, which resemble low-energy CID product ions. This fragmentation may occur in the high-pressure region before the first mass-analyzing quadrupole. Fragment ions can be selected by the first quadrupole (Q1), and further sequenced by conventional MS/MS. This allows pseudo-MS3 experiments to be performed. For peptides of higher molecular weight, pseudo-MS3 can extend the mass range beyond what is usually accessible for sequencing, by allowing one to sequence a fragment ion of lower molecular weight instead of the full-length peptide. Peptides that predominantly show a single product ion after MS/MS yield improved sequence information when this technique is applied. This method was applied to the analysis of an in vitro phosphorylated peptide, where the intact enzymatically-generated peptide showed poor dissociation via MS/MS. Sequencing a fragment ion from the phosphopeptide enabled the phosphorylation site to be unambiguously determined.     

Selective synthesis of 14β-amino taxanes

The base induced deprotonation of H-14 of 7-triethylsilyl- (7-TES-) and 7-tert-butoxycarbonyl- (7-BOC-) protected 13-oxo-baccatins gave the corresponding enolates, which were selectively aminated with electrophilic nitrogen donors, such as azodicarboxylates and tosyl azide. In particular, tosyl azide gave the corresponding 7-BOC- and 7-TES-13-oxo-14β-azido-baccatin III. Alternatively, the last compound was prepared via NaN₃ induced azidation of the 13-silyl enol ether of 7-TES-13-oxo-baccatin III under oxidative (cerium ammonium nitrate) conditions. The 13-silyl enol ether was obtained in a multistep process by DBU induced silylation of 7-TES-13-oxo-baccatin III. The 7-TES-13-oxo-14β-azido-baccatin III was used as a key intermediate for the synthesis of a new family of antitumour taxanes containing amino based functional groups at the C-14 position, such as: 14β-azido, 14β-amino, 14β-amino 1, 14-carbamate, 14β-amino 1, 14-thiocarbamate, and 14β-amino N-tert-butoxycarbonyl-1,14-carbamate.     

Infrared matrix isolation and quantum chemical studies of the nitrous acid complexes with water

The 1:1 and 2:1 complexes between water and trans- and cis-isomers of nitrous acid have been isolated in argon matrices and studied using FTIR spectroscopy and DFT(B3LYP) calculations with a 6-311++G(2d,2p) basis set. The analysis of the experimental spectra indicate that 1:1 complexes trapped in solid argon involve very strong hydrogen bond in which acid acts as the proton donor and water as the proton acceptor. The perturbed OH stretches are −248, −228 cm⁻¹ red shifted from their free-molecules values in complexes formed by trans- and cis-HONO isomers, respectively. The calculated spectral parameters for the two complexes are in good agreement with experimental data. The calculations also predict stability of two more 1:1 weakly bound complexes formed by each isomer. In these the water acts as the proton donor and one of the two oxygen atoms of the acid as the acceptor. The experimental spectra demonstrate also formation of 2:1 complex between water and trans-HONO isomer in an argon matrix. The performed calculations indicate that the complex involves a seven-membered ring in which OH group of HONO forms very strong hydrogen bond with the oxygen atom of one water molecule and nitrogen atom acts as a weak proton acceptor for the hydrogen atom of the second water molecule of the water dimer. The observed perturbations of the OH stretch of trans-HONO (750 cm⁻¹ red shift) is much larger than that predicted by calculations (556 cm⁻¹ red shift); this difference is attributed to strong solvation effect of argon matrix on very strong hydrogen bond.     

Raspailynes,Novel Long-Chain Acetylenic Enol Ethers of Glycerol from the Marine Sponges Raspailia pumila and Raspailia ramosa

The sponges Raspailia pumila and ramosa (Demospongiae, Tetractinomorpha, Axinellida) from the North-East Atlantic are shown to contain a series of novel long-chain enol ethers of glycerol where the enol ether C?C bond is conjugated, in sequence, to both an acetylenic and an olefinic bond. Polar extracts give raspailynes hydroxylated at their (1Z5Z)-1,5-alkadien-3-ynyl chain, like raspailyne Al ( = (+)-(S)-3-[((1Z,5Z)-16-hydroxy-hexadeca-1,5-dien-3-ynyl)oxy]-1,2-propanediol; (+ 2 ) and isoraspailyne A ( = (+)-3-[((1Z,5Z)-17-hydroxyocta-deca-1,5-dien-3-ynyl)oxy]-1,2-[propanediol; (+)- 3 ). Less polar extracts give 3 different types of raspailynes not hydroxylated at the chain. Raspailynes of the first type have either the (1Z,5Z)-configuration in a linear chain such as raspailyne B2 (( = (?)-(s)-3-[((1Z,5Z)-trideca-1,5-dien-3-ynyl)oxy]-1,2-propanediol; (?)-4), raspailyne Bl ( = (?)-3-[((1Z,5Z)-tetradeca-1,5-dien-3-ynyl)oxy]-1,2-propanediol;(?)- 5 ), and raspailyne B ( = 3-[((1Z,5Z)-pentadeca-1,5-dien-3-ynyl)oxy]-1,2-propanediol; 6 ) or the (1Z,5Z)-pentadeca-1,5-dien-3-ynyl)oxy]-1,2-propanediol; 6 )or the (1Z,5Z)-configuration in a chain ending with an isopropyl group, like isoraspailyne Bl ( = 3-[((1Z,5Z)-12-methyltrideca-1,5-dien-3-ynyl)oxy]-1,2-propanediol; 7 ) and isoraspailyne B ( = 3-[((1Z,5Z)-13-methyltetradeca-1,5-dien-3-ynyl)oxy]-1,2-propanediol; 8 ). Raspailynes of the second type have the (1Z,5E)-configuration, like isoraspailyne Bla ( =3-[((1Z,5E)-tetradeca-1,5-dien-3-ynyl)oxy]-1,2-propanediol; 9 ) and isoraspailyne Ba ( = 3-[((1Z,5E)-13-methyltetradeca-1,5-dien-3-ynyl)oxy]-1,2-propanediol; 10 ). Raspailynes of the third type have the (1E,5Z)-configuration, like isoraspailyne Blb ( = 3-[((1E,5Z)-tetradeca-1,5-dien-3-ynyl)oxy]-1,2,-propanediol; 11 ). The (S)-configuration for (+)- 1 ,((+)- 2 , and (?)- 4 is derived from chemical correlations.     

Novel feature extraction technique for fuzzy relational clustering of a flexible dopamine reuptake inhibitor

This paper describes a novel clustering methodology for classifying over 700 conformations of a flexible analogue of GBR 12909, a dopamine reuptake inhibitor that has completed phase I clinical trials as a treatment for cocaine abuse. The major aspect of the clustering methodology includes an efficient data-conditioning scheme where a systematic feature extraction procedure based on the structural properties of the molecule was used to reduce the associated feature space. This allowed region-specific clustering that focused on individual pharmacophore elements of the molecule. For clustering of the reduced feature set, the fuzzy clustering partitional method was utilized. Due to the relational nature of the feature data, fuzzy relational clustering was employed, and it successfully detected natural groups defined by rotational minima around N(sp(3))-C(sp(3)), O(sp(3))-C(sp(3)), and C(sp(3))-C(sp(2)) bonds. The proposed clustering methodology also employed several cluster validity measures, which corroborated the partitions produced by the clustering technique and agreed with the results of hierarchical clustering using the XCluster program. Representative structures which exhibited a reasonable spread of energies and showed good spatial coverage of the conformational space were identified for use as putative bioactive conformations in a future Comparative Molecular Field Analysis of GBR 12909 analogues. The clustering methodology developed here is capable of handling other computational chemistry problems, and the feature extraction technique can be easily generalized to other molecules.     

Reaction of electrochemically produced radical cations with organic monomers

The reactivity of free radical cations, produced by anodic oxidation of 9, 10-diphenylanthracene (and perylene), with polymerizable organic monomers has been investigated by amperometry.It results that the radical cations, which are relatively stable in acetonitrile and nitrobenzene, decay with the monomer substrate by either an addition reaction or an electron transfer process. The cationic species of the monomer thus produced by catalyze the cationic polymerization of the substrate.The cationic polymerization initiated in this way has been investigated in the case of styrene: this reaction shows some similarity with the process initiated by perchloric acid, but carbonium ion carriers seem to give the main contribution to the propagation stage.