Methane-to-methanol oxidation by the hydrated iron(IV) oxo species in aqueous solution: a combined DFT and car-parrinello molecular dynamics study

Previously, we have shown that the ferryl ion ([FeIVO]2+) is easily produced from Fenton's reagent (i.e., a mixture of Fe2+ ions and H2O2 in aqueous solution), using DFT and Car-Parrinello MD calculations. To verify that the ferryl ion can indeed act as the active species in oxidation reactions with Fenton's reagent, we study in the present paper the reactivity of the ferryl ion toward an organic substrate, in particular the oxidation of methane to methanol. In the first part of this paper, we perform static DFT calculations on the reaction of CH4 with the [(H2O)5FeIVO]2+ complex in vacuo that show a strong prevalence of the oxygen-rebound mechanism over the methane coordination mechanism. This is in agreement with the static DFT results for methane oxidation by biocatalysts MMO and P450, but not with those for methane oxidation by bare metal-oxo ions, where the methane coordination mechanism prevails. The highest energy barrier in the oxygen-rebound mechanism is only 3 kcal/mol in vacuo, whereas in the methane coordination mechanism the highest barrier is 23 kcal/mol. Overall the oxidation reaction energy is downhill by 47 kcal/mol. We conclude that the ferryl ion can indeed act as the oxidative intermediate in the Fenton oxidation of organic species. In the second part of this paper, we perform a preliminary assessment of solvent effects on the oxidation by the ferryl ion in aqueous solution using the method of constrained (first principles) molecular dynamics. The free energy barrier of the H-abstraction reaction from methane by the ferryl ion (i.e., the first step in the rebound mechanism) in aqueous solution is, with 22 kcal/mol in solution, significantly higher than in vacuo. Given the fact that methane has a relatively strong C-H bond (ca. 10 kcal/mol stronger than the C-H bonds in the more typical Fenton's reagent substrates), we infer that for many organic substrates oxidation with the ferryl ion as an active intermediate may be a perfectly viable route.     

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 ).     

Dramatic 5'-residue effect on conformer distribution of short oligonucleotide retro models of the cisplatin-DNA cross-link: implications for the Lippard and cross-link distorted base pair steps present in cisplatin-DNA duplex adducts

The cisplatin anticancer drug preferentially attacks the GG sequence of DNA duplexes. Virtually all DNAs containing the key G*G* lesion (G* = N7 platinated G) have large distortions in the cross-link (G*G*) base pair (bp) step and also in the adjacent Lippard (XG*) bp step, making the adducts very different from B-form DNA in the XG*G* region. The XG*G* strand in duplexes also differs in several ways from single-strand (ss) models with G*G* and XG*G* sequences. In the duplex, the X residue has an N sugar, the 5'-G* and 3'-G* bases have slight "R" canting (3'-G* H8 atom toward the 5'-G* base), and there is no or weak H-bonding by the NH3 ligands. In most XG*G* ss models, X has an S sugar, the 5'-G* base normally cants strongly toward the 3'-G* base (L canting), and the NH3 forms an H-bond. Well-defined ss models exist in the solid state, but dynamic motion obscures the properties of the ss models in solution. In this work, we employ retro models (better defined, less dynamic ss models) to understand the differences between duplex and ss models. The retro models in this study lack carrier ligand NH's, thus eliminating H-bonding. To correlate previous ss solid-state models with our solution work, we constructed hybrid molecules by overlaying parts of known structures. The combined model and experimental information indicates that the X N-pucker is not favorable in L-canted ss models, that X residue steric effects (not H-bonding) favor L canting in ss models, that X N-pucker is needed for favorable WC hydrogen bonding and stacking interactions in duplexes, and that X N-pucker minimizes X base clashes with bases in the complementary strand in duplexes. The R canting minimizing clashes between the X and G* residues of the Lippard bp step (independent of X pucker) and the repositioning of the X residue base caused by the change from S-pucker to N-pucker together lead to the unusual features of the Lippard bp step in the duplex.     

M(R-dmet)2] bis(1,2-dithiolenes): a promising new class intermediate between [M(dmit)2] and [M(R,R'-timdt)2] (M = Ni, Pd, Pt)

We report the first examples of metal dithiolenes belonging to the class [M(R-dmet)(2)] [R-dmet = formally monoreduced N-substituted thiazolidine-2,4,5-trithione; R = Et, M = Ni (1), Pd (2), Pt (3)]. A comparative spectroscopic, electrochemical, and density functional theory theoretical investigation indicates that [M(R-dmet)(2)] complexes show features intermediate between those of the dithiolenes belonging to the previously reported classes [M(R,R'-timdt)(2)] and [M(dmit)(2)] (R,R'-timdt = formally monoreduced N,N'-disubstituted imidazolidine-2,4,5-trithione; dmit = 2-thioxo-1,3-dithiole-4,5-dithiolato). UV-vis-near-IR spectroscopy and cyclic voltammetry/differential pulsed voltammetry measurements performed on 1 and 3 proved that the new dithiolenes are stable as neutral, monoanionic, and bianionic species and feature a near-IR electrochromic absorption falling at about 1000 and 1250 nm for neutral and monoanionic species, respectively.     

Photoinduced electroreduction of chlorophyllide on alkanethiol-coated mercury

Monolayers of n-alkanethiols of chain length from C12 to C18 were self-assembled on a hanging mercury drop electrode, and a film of chlorophyllide (Chlide) was adsorbed on top of them. The reduction photocurrents following illumination of the Chlide film were measured over the potential range in which the Chlide is electroinactive in the dark, and their action spectra were determined. Plotting the derivative of the photocurrents with respect to the applied potential against potential yields bell-shaped curves that can be fitted to a Gaussian. The potential of the Gaussian maximum was used to determine the reorganization energy lambda for the Chlide electroreduction process. An increase in the thiol chain length causes lambda to decrease regularly and the photocurrent to decay exponentially with the monolayer thickness, with a decay constant beta of about 0.17 A(-1).     

Syntheses and crystal structures of dinuclear complexes containing d-block and f-block luminophores. Sensitization of NIR luminescence from Yb(III), Nd(III), and Er(III) centers by energy transfer from Re(I)- and Pt(II)-bipyrimidine metal centers

Mononuclear complexes [Re(bpym)(CO)(3)Cl] and [Pt(bpym)(CC-C(6)H(4)CF(3))(2)] (bpym = 2,2'-bipyrimidine), in which one of the bipyrimidine sites is vacant, have been used as "complex ligands" to prepare heterodinuclear d-f complexes in which a lanthanide tris(1,3-diketonate) unit is attached to the secondary bipyrimidine site to evaluate the ability of d-block chromophores to act as antennae for causing sensitized near-infrared (NIR) luminescence from adjacent lanthanide(III) centers. The two sets of complexes so prepared are [Re(CO)(3)Cl(mu-bpym)Ln(fod)(3)] (abbreviated as Re-Ln; where Ln = Yb, Nd, Er) and [(F(3)C-C(6)H(4)-CC)(2)Pt(mu-bpym)Ln(hfac)(3)] (abbreviated as Pt-Ln; where Ln = Nd, Gd). Members of both series have been structurally characterized; the metal-metal separation across the bipyrimidine bridge is approximately 6.3 A in each case. In these complexes, the (3)MLCT (MLCT = metal to ligand charge-transfer) luminescences of the mononuclear [Re(bpym)(CO)(3)Cl] and [Pt(bpym)(CC-C(6)H(4)CF(3))(2)] complexes are quenched by energy transfer to those lanthanides (Ln = Yb, Nd, Er) that have low-lying f-f states capable of NIR luminescence; as a result, sensitized NIR luminescence is seen from the lanthanide center following excitation of the d-block unit. In the solid state, quenching of the luminescence from the d-block chromophore is complete, indicating efficient d --> f energy transfer, as a result of the short metal-metal separation across the bipyrimidine bridge. In a CH(2)Cl(2) solution, partial dissociation of the dinuclear complexes into the mononuclear units occurs, with the result that some (3)MLCT luminescence is observed from mononuclear [Re(bpym)(CO)(3)Cl] or [Pt(bpym)(CC-C(6)H(4)CF(3))(2)] present in the equilibrium mixture. Solution UV-vis and luminescence titrations, carried out by the addition of portions of Ln(fod)(3)(H(2)O)(2) or Ln(hfac)(3)(H(2)O)(2) to the d-block complex ligands, indicate that binding of the lanthanide tris(1,3-diketonate) unit at the secondary bipyrimidine site to give the d-f dinuclear complexes occurs with an association constant of ca. 10(5) M(-)(1).     

Ion pairing, H-bonding, and π–π interactions in copper(II) complex-organo-networks derived from a proton-transfer compound of the 1,10-phenanthroline-2,9-dicarboxylic acid

The one-pot reaction between the novel proton transfer compound (pydaH₂)²⁺(phendc)²⁻, LH₂, and Cu(II) afforded the compounds (pydaH)₂[Cu(phendc)₂]·10H₂O, 1, and (pydaH)₂[Cu(phendc)(phendcH)]₂·5H₂O, 2, where pyda=2,6-diaminopyridine, and phendcH₂=1,10-phenanthroline-2,9-dicarboxylic acid. The single crystal X-ray diffraction analysis of 1 and 2 revealed that these are two novel self-assembled 3D Cu(II) complex-organo-networks, in which (pydaH)⁺ ions and [Cu(phendc)₂]²⁻ or complex units are held together by ion pairing, H-bonding, and π–π interactions. Magnetic measurements over the temperature range 1.8–310 K revealed no significant magnetic coupling between Cu(II) centers in 1 or 2.     

The rise of lignin biorefinery

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Binuclear wirelike dimers based on ruthenium(II)-bipyridine units linked by ethynylene-oligothiophene-ethynylene bridges

The syntheses, structural characteristics, electrochemical behavior, ground-state spectra, photophysical properties, and transient absorption (TA) spectra in CH(3)CN solvent are reported for binuclear [(bpy)(2)Ru(bpy-E(T)(n)()E-bpy)Ru(bpy)(2)](4+) complexes, Ru(bpyT(n)bpy)Ru, where the Ru-based units are connected by alternating 3,4-dibutylthiophene (DBT')/thiophene (T') fragments linked via ethynyl groups (E) to bpy ligands at the 5-position (bpy is 2,2'-bipyridine). The ligand bpyT(3)bpy represents a module containing DBT'/T'/DBT' subunits, and bpyT(5)bpy accounts for a DBT'/T'/DBT'/T'/DBT' pattern. The syntheses and electrochemical and spectroscopic (emission and TA) properties in CH(2)Cl(2) solvent of the bpyT(n)()bpy ligands are likewise reported. The behavior of the Ru(bpyT(n)bpy)Ru dimers has been compared to that of the bpyT(n)bpy ligands and to that of a related mononuclear complex, [(bpy)(2)Ru(bpy-E-DBT')](2+), Ru(bpyDBT'). For the dimeric complexes, the electrochemical results show that the first reduction step takes place at the bpy ligand(s) bearing an ethynylene group, the first oxidation step is thiophene-centered, and further oxidation involves the metal centers, which are only weakly interacting. The photophysical and TA results for the Ru(bpyT(n)bpy)Ru dimers account for the presence of low-lying oligothiophene-centered (3)pi,pi levels, while higher-lying metal-ligand charge transfer ((3)MLCT) levels are thermally accessible only for the case of Ru(bpyT(3)bpy)Ru; the possible role of charge separation (CS) levels (from oxidation at the thiophene bridge and reduction at one of the coordinated bpy's) is also discussed.     

An infrared spectroscopic investigation on N-methyl-1,3-thiazolidine-2-thione and -2-selone

An infrared investigation cm N-methyl-1,3-thiazolidine-2-thione and -2-selone in the range 4000-200 cm^?1 is reported. The v CS and v CSe vibrations give contributions to the absorptions around 1000 cm^?1 and below 600 cm^?1. The assignments are supported by comparison of their ir spectra with those of S- and Se-methiodides. The π-bond orders of the thio- and seleno-ketonic links in these compounds are higher than those found for 1,3-imidazolidine-2-thione and -2-selone.