Mobile-BAT-A Novel Ultra-Low Power Wildlife Tracking System.

We introduce a novel ultra-low power system for tracking animal movements over long periods with an unprecedented high-temporal-resolution. The localization principle is based on the detection of cellular base stations using a miniaturized software-defined radio, weighing 2.0 g, including the battery, and having a size equivalent to two stacked 1-euro cent coins. Therefore, the system is small and lightweight enough to be deployed on small, wide-ranging, or migrating animals, such as European bats, for movement analysis with an unprecedented spatiotemporal resolution. The position estimation relies on a post-processing probabilistic RF pattern-matching method based on the acquired base stations and power levels. In several field tests, the system has been successfully verified, and a run-time of close to one year has been demonstrated.

Protocols for Understanding the Redox Behavior of Copper-Containing Systems.

Suitability of single-reference density functional theory (DFT) methods for the calculation of redox potentials of copper-containing macrocycle complexes was confirmed by the use of T 1 diagnostics along with a verification of negligible spin contamination or wave function instability. When examining the effect of improvement in the cc-pVnZ basis set series on calculated redox potentials, the results readily converged at the cc-pVTZ level. The all-electron Def2-TZVPP basis set is shown to be a suitable choice of a basis set for the calculation of redox potentials when utilizing a cc-pVTZ geometry. The best-performing model chemistries are determined to be the M06/polarizable continuum model (PCM); therefore, a scheme for redox potential calculations of copper macrocycles using either M06/cc-pVTZ with PCM solvation is proposed to reliably reproduce experimental trends.

Metformin selectively targets redox control of complex I energy transduction.

Many guanide-containing drugs are antihyperglycaemic but most exhibit toxicity, to the extent that only the biguanide metformin has enjoyed sustained clinical use. Here, we have isolated unique mitochondrial redox control properties of metformin that are likely to account for this difference. In primary hepatocytes and H4IIE hepatoma cells we found that antihyperglycaemic diguanides DG5-DG10 and the biguanide phenformin were up to 1000-fold more potent than metformin on cell signalling responses, gluconeogenic promoter expression and hepatocyte glucose production. Each drug inhibited cellular oxygen consumption similarly but there were marked differences in other respects. All diguanides and phenformin but not metformin inhibited NADH oxidation in submitochondrial particles, indicative of complex I inhibition, which also corresponded closely with dehydrogenase activity in living cells measured by WST-1. Consistent with these findings, in isolated mitochondria, DG8 but not metformin caused the NADH/NAD+ couple to become more reduced over time and mitochondrial deterioration ensued, suggesting direct inhibition of complex I and mitochondrial toxicity of DG8. In contrast, metformin exerted a selective oxidation of the mitochondrial NADH/NAD+ couple, without triggering mitochondrial deterioration. Together, our results suggest that metformin suppresses energy transduction by selectively inducing a state in complex I where redox and proton transfer domains are no longer efficiently coupled.

Biomolecular mode of action of metformin in relation to its copper binding properties.

Metformin (Metf), the most commonly used type 2 diabetes drug, is known to affect the cellular housekeeping of copper. Recently, we discovered that the structurally closely related propanediimidamide (PDI) shows a cellular behavior different from that of Metf. Here we investigate the binding of these compounds to copper, to compare their binding strength. Furthermore, we take a closer look at the electronic properties of these compounds and their copper complexes such as molecular orbital interactions and electrostatic potential surfaces. Our results clearly show that the copper binding energies cannot alone be the cause of the biochemical differentiation between Metf and PDI. We conclude that other factors such as pKa values and hydrophilicity of the compounds play a crucial role in their cellular activity. Metf in contrast to PDI can occur as an anion in aqueous medium at moderate pH, forming much stronger complexes particularly with Cu(II) ions, suggesting that biguanides but not PDI may induce easy oxidation of Cu(I) ions extracted from proteins. The higher hydrophobicity and the lack of planarity of PDI may further differentiate it from biguanides in terms of their molecular recognition characteristics. These different properties could hold the key to metformin's mitochondrial activity because they suggest that the drug could act at least in part as a pro-oxidant of accessible protein-bound Cu(I) ions.

Indole based cyclooxygenase inhibitors: synthesis, biological evaluation, docking and NMR screening.

The close structural similarity between the two cyclooxygenase (COXs) isoforms and the absence of selective inhibitors without side effects continues to stimulate the development of novel approaches towards selective anti-inflammatory drugs. In the present study a small library of new indolic compounds involving two different substitutions patterns at the indole scaffold was synthesized. In order to establish a relation between the spatial distribution of known functional groups related with inhibitory activity, two substitution patterns were explored: one with substituents at N-1, C-3, C-5 positions and another at C-2, C-3 and C5 positions. Accordingly, indole positions C-5, C-3 and N-1 were substituted with: sulfonamide or methylsulfone at C-5, p-halo-benzyl group at C-3, and an alkyl chain with a trifluoromethyl group at N-1. Alternatively, a p-halo-benzyl group was introduced at C-2, leaving the indolic nitrogen free. Inhibitory studies were performed and the activity results obtained against both COXs isoforms were rationalized based on docking and NMR studies. Docking studies show that dialkyation at C-2 and C-3 favors a binding with an orientation similar to that of the known selective inhibitor SC-558. From the tested compounds, this substitution pattern is correlated with the highest inhibitory activity and selectivity: 70% COX-2 inhibition at 50 µM, and low COX-1 inhibition (18 ± 9%). Additionally, Saturation Transfer Difference NMR experiments reveal different interaction patterns with both COXs isoforms that may be related with different orientations of the sulfonamide group in the binding pocket. Despite the moderated inhibitory activities found, this study represents an innovative approach towards COXs inhibitory activity rationalization and to the design of anti-inflammatory drugs.

Platinated DNA affects zinc finger conformation. Interaction of a platinated single-stranded oligonucleotide and the C-terminal zinc finger of nucleocapsid protein HIVNCp7.

This paper describes for the first time the intimate molecular details of the association between a platinated oligonucleotide and a zinc finger peptide. Site-specific platination of the guanine in a single-stranded hexanucleotide gave {[Pt(dien)d(5'-TACGCC-3')], Pt(dien)(6-mer)} (II) characterized by mass spectrometry and (1)H nuclear magnetic resonance (NMR) spectroscopy. The work extends the study of platinum-nucleobase complex-zinc finger interactions using small molecules such as [Pt(dien)(9-EtGua)](2+) (I). The structure of the (34-52) C-terminal finger of HIV nucleocapsid protein HIVNCp7 (ZF1) was characterized by (1)H NMR spectroscopy and compared with that of the N-terminal single finger and the two-finger "intact" NCp7. Interaction of II with ZF1 results in significant changes in comparison to the "free" uncomplexed hexanucleotide; the major changes occurring for Trp37 resonances that are broadened and moved upfield, and other major shifts are for Gln45 (Hε21, Hγ3, Qß), Met46 (NH, Hγ2), Lys47 (NH, Qγ), and Glu50 (Hγ2, Hγ3). The Zn-Cys/His chemical shifts show only marginal deviations. The solution structures of ZF1 and the 6-mer-ZF1 and II-ZF1 adducts were calculated from the nuclear Overhauser effect spectroscopy-derived distance constraints. The DNA position in the II-ZF1 adduct is completely different than in the absence of platinum. Major differences are the appearance of new Met46-Cyt6 H5 and Trp37-Cyt5 H5 contacts but severe weakening of the Trp37-Gua4 contact, attributed to the steric effects caused by Gua4 platination, accompanied by a change in the position of the aromatic ring. The results demonstrate the feasibility of targeting specific ZF motifs with DNA-tethered coordination compounds, such as Pt compounds and Co macrocycles, with implications for drug targetting and indeed the intimate mechanisms of DNA repair of platinated DNA.

Experimental and computational investigation of C-N bond activation in ruthenium N-heterocyclic carbene complexes.

A combination of experimental studies and density functional theory calculations is used to study C-N bond activation in a series of ruthenium N-alkyl-substituted heterocyclic carbene (NHC) complexes. These show that prior C-H activation of the NHC ligand renders the system susceptible to irreversible C-N activation. In the presence of a source of HCl, C-H activated Ru(I(i)Pr(2)Me(2))'(PPh(3))(2)(CO)H (1, I(i)Pr(2)Me(2) = 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene) reacts to give Ru(I(i)PrHMe(2))(PPh(3))(2)(CO)HCl (2, I(i)PrHMe(2) = 1-isopropyl-4,5-dimethylimidazol-2-ylidene) and propene. The mechanism involves (i) isomerization to a trans-phosphine isomer, 1c, in which hydride is trans to the metalated alkyl arm, (ii) C-N cleavage to give an intermediate propene complex with a C2-metalated imidazole ligand, and (iii) N-protonation and propene/Cl(-) substitution to give 2. The overall computed activation barrier (ΔE(++)(calcd)) corresponds to the isomerization/C-N cleavage process and has a value of +24.4 kcal/mol. C-N activation in 1c is promoted by the relief of electronic strain arising from the trans disposition of the high-trans-influence hydride and alkyl ligands. Experimental studies on analogues of 1 with different C4/C5 carbene backbone substituents (Ru(I(i)Pr(2)Ph(2))'(PPh(3))(2)(CO)H, Ru(I(i)Pr(2))'(PPh(3))(2)(CO)H) or different N-substituents (Ru(IEt(2)Me(2))'(PPh(3))(2)(CO)H) reveal that Ph substituents promote C-N activation. Calculations confirm that Ru(I(i)Pr(2)Ph(2))'(PPh(3))(2)(CO)H undergoes isomerization/C-N bond cleavage with a low barrier of only +21.4 kcal/mol. Larger N-alkyl groups also facilitate C-N bond activation (Ru(I(t)Bu(2)Me(2))'(PPh(3))(2)(CO)H, ΔE(++)(calcd) = +21.3 kcal/mol), and in this case the reaction is promoted by the formation of the more highly substituted 2-methylpropene.

Competing C-F activation pathways in the reaction of Pt(0) with fluoropyridines: phosphine-assistance versus oxidative addition.

A survey of computed mechanisms for C-F bond activation at the 4-position of pentafluoropyridine by the model zero-valent bis-phosphine complex, [Pt(PH3)(PH2Me)], reveals three quite distinct pathways leading to square-planar Pt(II) products. Direct oxidative addition leads to cis-[Pt(F)(4-C5NF4)(PH3)(PH2Me)] via a conventional 3-center transition state. This process competes with two different phosphine-assisted mechanisms in which C-F activation involves fluorine transfer to a phosphorus center via novel 4-center transition states. The more accessible of the two phosphine-assisted processes involves concerted transfer of an alkyl group from phosphorus to the metal to give a platinum(alkyl)(fluorophosphine), trans-[Pt(Me)(4-C5NF4)(PH3)(PH2F)], analogues of which have been observed experimentally. The second phosphine-assisted pathway sees fluorine transfer to one of the phosphine ligands with formation of a metastable metallophosphorane intermediate from which either alkyl or fluorine transfer to the metal is possible. Both Pt-fluoride and Pt(alkyl)(fluorophosphine) products are therefore accessible via this route. Our calculations highlight the central role of metallophosphorane species, either as intermediates or transition states, in aromatic C-F bond activation. In addition, the similar computed barriers for all three processes suggest that Pt-fluoride species should be accessible. This is confirmed experimentally by the reaction of [Pt(PR3)2] species (R = isopropyl (iPr), cyclohexyl (Cy), and cyclopentyl (Cyp)) with 2,3,5-trifluoro-4-(trifluoromethyl)pyridine to give cis-[Pt(F){2-C5NHF2(CF3)}(PR3)2]. These species subsequently convert to the trans-isomers, either thermally or photochemically. The crystal structure of cis-[Pt(F){2-C5NHF2(CF3)}(P iPr3)2] shows planar coordination at Pt with r(F-Pt) = 2.029(3) A and P(1)-Pt-P(2) = 109.10(3) degrees. The crystal structure of trans-[Pt(F){2-C5NHF2(CF3)}(PCyp3)2] shows standard square-planar coordination at Pt with r(F-Pt) = 2.040(19) A.

Computational study of the reaction of C6F6 with [IrMe(PEt3)3]: identification of a phosphine-assisted C-F activation pathway via a metallophosphorane intermediate.

Density functional theory calculations have been used to model the reaction of C6F6 with [IrMe(PEt3)3], which proceeds with both C-F and P-C bond activation to yield trans-[Ir(C6F5)(PEt3)2(PEt2F)], C2H4, and CH4 (Blum, O.; Frolow, F.; Milstein, D. J. Chem. Soc., Chem. Commun. 1991, 258). Using a model species, trans-[IrMe(PH3)2(PH2Et)], a low-energy mechanism involving nucleophilic attack of the electron-rich Ir metal center at C6F6 with displacement of fluoride has been identified. A novel feature of this process is the capture of fluoride by a phosphine ligand to generate a metallophosphorane intermediate [Ir(C6F5)(Me)(PH3)2(PH2EtF)]. These events occur in a single step via a 4-centered transition state, in a process that we have termed "phosphine-assisted C-F activation". Alternative mechanisms based on C-F activation via concerted oxidative addition or electron-transfer processes proved less favorable. From the metallophosphorane intermediate the formation of the final products can be accounted for by facile ethyl group transfer from phosphorus to iridium followed by beta-H elimination of ethene and reductive elimination of methane. The interpretation of phosphine-assisted C-F activation in terms of nucleophilic attack is supported by the reduced activation barriers computed with the more electron-rich model reactant trans-[IrMe(PMe3)2(PMe2Et)] and the higher barriers found with lesser fluorinated arenes. Reactivity patterns for a range of fluoroarenes indicate the dominance of the presence of ortho-F substituents in promoting phosphine-assisted C-F activation, and an analysis of the charge distribution and transition state geometries indicates that this process is controlled by the strength of the Ir-aryl bond that is being formed.

Mechanisms of catalyst poisoning in palladium-catalyzed cyanation of haloarenes. remarkably facile C-N bond activation in the [(Ph3P)4Pd]/[Bu4N]+ CN- system.

Reaction paths leading to palladium catalyst deactivation during cyanation of haloarenes (eq 1) have been identified and studied. Each key step of the catalytic loop (Scheme 1) can be disrupted by excess cyanide, including ArX oxidative addition, X/CN exchange, and ArCN reductive elimination. The catalytic reaction is terminated via the facile formation of inactive [(CN)4Pd]2-, [(CN)3PdH]2-, and [(CN)3PdAr]2-. Moisture is particularly harmful to the catalysis because of facile CN- hydrolysis to HCN that is highly reactive toward Pd(0). Depending on conditions, the reaction of [(Ph3P)4Pd] with HCN in the presence of extra CN- can give rise to [(CN)4Pd]2- and/or the remarkably stable new hydride [(CN)3PdH]2- (NMR, X-ray). The X/CN exchange and reductive elimination steps are vulnerable to excess CN- because of facile phosphine displacement leading to stable [(CN)3PdAr]2- that can undergo ArCN reductive elimination only in the absence of extra CN-. When a quaternary ammonium cation such as [Bu4N]+ is used as a phase-transfer agent for the cyanation reaction, C-N bond cleavage in the cation can occur via two different processes. In the presence of trace water, CN- hydrolysis yields HCN that reacts with Pd(0) to give [(CN)3PdH]2-. This also releases highly active OH- that causes Hofmann elimination of [Bu4N]+ to give Bu3N, 1-butene, and water. This decomposition mode is therefore catalytic in H2O. Under anhydrous conditions, the formation of a new species, [(CN)3PdBu]2-, is observed, and experimental studies suggest that electron-rich mixed cyano phosphine Pd(0) species are responsible for this unusual reaction. A combination of experimental (kinetics, labeling) and computational studies demonstrate that in this case C-N activation occurs via an S(N)2-type displacement of amine and rule out alternative 3-center C-N oxidative addition or Hofmann elimination processes.

Model studies of beta-scission ring-opening reactions of cyclohexyloxy radicals: application to thermal rearrangements of dispiro-1,2,4-trioxanes.

A DFT study of model cyclohexyloxy radicals (8a-c, 9) show that (a) the presence of an adjacent oxygen atom, and (b) alpha-substituents on the cyclohexyl ring, particularly methoxy, accelerate the rate of beta-scission ring-opening reactions. Consistent with theoretical results, thermolysis of the methoxy-substituted dispiro-1,2,4-trioxane 10 afforded the structurally novel, 14-membered macrocyclic keto lactone 11 as the major isolable product.

The conformations of 13-vertex ML2C2B10 metallacarboranes: experimental and computational studies.

The docosahedral metallacarboranes 4,4-(PMe(2)Ph)2-4,1,6-closo-PtC(2)B(10)H(12), 4,4-(PMe(2)Ph)2-4,1,10-closo-PtC(2)B(10)H(12), and [N(PPh(3))2][4,4-cod-4,1,10-closo-RhC(2)B(10)H(12)] were prepared by reduction/metalation of either 1,2-closo-C(2)B(10)H(12) or 1,12-closo-C(2)B(10)H(12). All three species were fully characterized, with a particular point of interest of the latter being the conformation of the {ML2} fragment relative to the carborane ligand face. Comparison with conformations previously established for six other ML(2)C(2)B(10) species of varying heteroatom patterns (4,1,2-MC(2)B(10), 4,1,6-MC(2)B(10), 4,1,10-MC(2)B(10), and 4,1,12-MC(2)B(10)) reveals clear preferences. In all cases a qualitative understanding of these was afforded by simple MO arguments applied to the model heteroarene complexes [(PH3)2PtC(2)B(4)H(6)]2- and [(PH3)2PtCB(5)H(6)]3-. Moreover, DFT calculations on [(PH3)2PtC(2)B(4)H(6)]2- in its various isomeric forms approximately reproduced the observed conformations in the 4,1,2-, 4,1,6-, and 4,1,10-MC(2)B(10) species, although analogous calculations on [(PH3)2PtCB(5)H(6)]3- did not reproduce the conformation observed in the 4,1,12-MC(2)B(10) metallacarborane. DFT calculations on (PH3)2PtC(2)B(10)H(12) yielded good agreement with experimental conformations in all four isomeric cases. Apparent discrepancies between observed and computed Pt-C distances were probed by further refinement of the 4,1,2- model to 1,2-(CH2)3-4,4-(PMe3)2-4,1,2-closo-PtC(2)B(10)H(10). This still has a more distorted structure than measured experimentally for 1,2-(CH2)3-4,4-(PMe(2)Ph)2-4,1,2-closo-PtC(2)B(10)H(10), but the structural differences lie on a very shallow potential energy surface. For the model compound a henicosahedral transition state was located 8.3 kcal mol(-1) above the ground-state structure, consistent with the fluxionality of 1,2-(CH2)3-4,4-(PMe(2)Ph)2-4,1,2-closo-PtC(2)B(10)H(10) in solution.

A challenge to chemical intuition: donor-acceptor interactions in H3B-L and H2B+-L (L=CO; EC5H5, E=N-Bi).

The equilibrium geometries and bond energies of the complexes H(3)B-L and H(2)B(+)-L (L=CO; EC(5)H(5): E=N, P, As, Sb, Bi) have been calculated at the BP86/TZ2P level of theory. The nature of the donor-acceptor bonds was investigated by energy decomposition analysis (EDA). The bond strengths of H(3)B-L have the order CO>N>P>As>Sb>Bi. The calculated values are between D(e)=37.1 kcal mol(-1) for H(3)B-CO and D(e)=6.9 kcal mol(-1) for H(3)B-BiC(5)H(5). The bond dissociation energies of the cations H(2)B(+)-CO and H(2)B(+)-EC(5)H(5) are larger than for H(3)B--L, particularly for complexes of the heterobenzene ligands. The calculated values are between D(e)=51.9 kcal mol(-1) for H(2)B(+)-CO and D(e)=122.1 kcal mol(-1) for H(2)B(+)-NC(5)H(5). The trend of the BDE of H(2)B(+)-CO and H(2)B(+)-EC(5)H(5) is N>P>As>Sb>Bi>CO. A surprising result is found for H(2)B(+)-CO, which has a significantly stronger and yet substantially longer bond than H(3)B-CO. The reason for the longer but stronger bond in H(2)B(+)-CO compared with that in H(3)B-CO comes mainly from the change in electrostatic attraction and pi bonding at shorter distances, which increases more in the neutral system than in the cation, and to a lesser extent from the deformation energy of the fragments. The H(2)B(+)<--NC(5)H(5) pi( perpendicular) donation plays an important role for the stronger interactions at shorter distances compared with those in H(3)B-NC(5)H(5). The attractive interaction in H(2)B(+)--CO further increases at bond lengths that are shorter than the equilibrium value, but this is compensated by the energy which is necessary to deform BH(2) (+) from its linear equilibrium geometry to the bent form in the complex. The EDA shows that the contributions of the orbital interactions to the donor-acceptor bonds are always larger than the classical electrostatic contributions, but the latter term plays an important role for the trend in bond strength. The largest contributions to the orbital interactions come from the sigma orbitals. The EDA calculations suggest that heterobenzene ligands may become moderately strong pi donors in complexes with strong Lewis acids, while CO is only a weak pi donor. The much stronger interaction energies in H(2)B(+)-EC(5)H(5) compared with those in H(3)B-EC(5)H(5) are caused by the significantly larger contribution of the pi(perpendicular) orbitals in H(2)B(+)-EC(5)H(5) and by the increase of the binding interactions of the sigma+pi( parallel) orbitals.

A water sluice is generated in the active site of bovine lens leucine aminopeptidase.

Nature has provided the binuclear zinc based active site of bovine lens leucine aminopeptidase (blLAP) with two water channels: one for substrate docking and a much smaller one (function unknown) above Zn1. In addition, Zn1 possesses an unusual pentacoordinate geometry with a loosely bound carbonyl ligand (Ala333). Extensive DFT calculations on a model of the active site provide first mechanistic implications for these structural features. The weakly bound carbonyl ligand is capable of functioning as a "traffic cop" to direct water molecules coming from the small channel into the heart of the active site. A water sluice is thus generated that is capable of repeatedly providing a series of nucleophilic active "Zn-OH" functionalities.

Metal-mediated reactions modeled after nature.

The Collaborative Research Center (CRC) 436 'Metal-Mediated Reactions Modeled after Nature' was founded for the express purpose of analyzing the catalytic principles of metallo-enzymes in order to construct efficient catalysts on a chemical basis. The structure of the active center and neighboring chemical environment in enzymes serves as a focal point for developing reactivity models for the chemical redesign of catalysts. Instead of simply copying enzyme construction, we strive to achieve new chemical intuition based on the results of long-lasting natural evolution. We hope for success, since nature uses a limited set of building blocks, whereas we can apply the full repertoire of chemistry. Key substrates in this approach are small molecules, such as CO2, O2 NO3- and N2. Nature complexes these substrates, activates them and performs chemical transformations--all within the active center of a metalloenzyme. In this article, we report on some aspects and first results of the Collaborative Research Center (CRC) 436, such as nitrate reductase, sphingolipid desaturase, carbonic anhydrase, leucine aminopeptidase and dopamine beta-monooxygenase.