Corrosion inhibition in acidic environments: key interfacial insights with photoelectron spectroscopy.

In many engineering scenarios, surface-active organic species are added to acidic solutions to inhibit the corrosion of metallic components. Given suitable selection, such corrosion inhibitors are highly effective, preventing significant degradation even in highly aggressive environments. Nevertheless, there are still considerable gaps in fundamental knowledge of corrosion inhibitor functionality, severely restricting rational development. Here, we demonstrate the capability of X-ray photoelectron spectroscopy (XPS), supported by ab initio modelling, for revealing key details of inhibited substrates. Attention is focussed on the corrosion inhibition of carbon steel through the addition of an exemplar imidazoline-based corrosion inhibitor (OMID) to aqueous solutions of both HCl and H2SO4. Most notably, it is demonstrated that interfacial chemistry varies with the identity of the acid. High resolution Fe 2p, O 1s, N 1s, and Cl 2p XPS spectra, acquired from well-inhibited carbon steel in 1 M HCl, show that there are two different singly protonated OMID species bound directly to the metallic carbon steel substrate. In sharp contrast, in 0.01 M H2SO4, OMID adsorbs onto an ultra-thin surface film, composed primarily of a ferric sulfate (Fe2(SO4)3)-like phase. Such insight is essential to efforts to develop a mechanistic description of corrosion inhibitor functionality, as well as knowledge-based identification of next generation corrosion inhibitors.

Application of a peptide-based assay to characterize inhibitors targeting protein kinases from yeast.

Chemical molecules that inhibit protein kinase activity are important tools to assess the functions of protein kinases in living cells. To develop, test and characterize novel inhibitors, a convenient and reproducible kinase assay is of importance. Here, we applied a biotinylated peptide-based method to assess adenosine triphosphate-competitive inhibitors that target the yeast kinases Hog1, Elm1 and Elm1-as. The peptide substrates contained 13 amino acids, encompassing the consensus sequence surrounding the phosphorylation site. To test whether the lack of distal sites affects inhibitor efficacy, we compared the peptide-based assay with an assay using full-length protein as substrate. Similar inhibitor efficiencies were obtained irrespective of whether peptide or full-length protein was used as kinase substrates. Thus, we demonstrate that the peptide substrates used previously (Dinér et al. in PLoS One 6(5):e20012, 2011) give accurate results compared with protein substrates. We also show that the peptide-based method is suitable for selectivity assays and for inhibitor screening. The use of biotinylated peptide substrates provides a simple and reliable assay for protein kinase inhibitor characterization. The utility of this approach is discussed.

Determination of primary sequence specificity of Arabidopsis MAPKs MPK3 and MPK6 leads to identification of new substrates.

MAPKs (mitogen-activated protein kinases) are signalling components highly conserved among eukaryotes. Their diverse biological functions include cellular differentiation and responses to different extracellular stress stimuli. Although some substrates of MAPKs have been identified in plants, no information is available about whether amino acids in the primary sequence other than proline-directed phosphorylation (pS-P) contribute to kinase specificity towards substrates. In the present study, we used a random positional peptide library to search for consensus phosphorylation sequences for Arabidopsis MAPKs MPK3 and MPK6. These experiments indicated a preference towards the sequence L/P-P/X-S-P-R/K for both kinases. After bioinformatic processing, a number of novel candidate MAPK substrates were predicted and subsequently confirmed by in vitro kinase assays using bacterially expressed native Arabidopsis proteins as substrates. MPK3 and MPK6 phosphorylated all proteins tested more efficiently than did another MAPK, MPK4. These results indicate that the amino acid residues in the primary sequence surrounding the phosphorylation site of Arabidopsis MAPK substrates can contribute to MAPK specificity. Further characterization of one of these new substrates confirmed that At1g80180.1 was phosphorylated in planta in a MAPK-dependent manner. Phenotypic analyses of Arabidopsis expressing phosphorylation site mutant forms of At1g80180.1 showed clustered stomata and higher stomatal index in cotyledons expressing the phosphomimetic form of At1g80180.1, providing a link between this new MAPK substrate and the defined role for MPK3 and MPK6 in stomatal patterning.

Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCO by Klenow fragment.

Studies of the mechanisms by which DNA polymerases select the correct nucleotide frequently employ fluorescently labeled DNA to monitor conformational rearrangements of the polymerase-DNA complex in response to incoming nucleotides. For this purpose, fluorescent base analogs play an increasingly important role because they interfere less with the DNA-protein interaction than do tethered fluorophores. Here we report the incorporation of the 5'-triphosphates of two exceptionally bright cytosine analogs, 1,3-diaza-2-oxo-phenothiazine (tC) and its oxo-homolog, 1,3-diaza-2-oxo-phenoxazine (tC(O)), into DNA by the Klenow fragment. Both nucleotide analogs are polymerized with slightly higher efficiency opposite guanine than cytosine triphosphate and are shown to bind with nanomolar affinity to the DNA polymerase active site, according to fluorescence anisotropy measurements. Using this method, we perform competitive binding experiments and show that they can be used to determine the dissociation constant of any given natural or unnatural nucleotide. The results demonstrate that the active site of the Klenow fragment is flexible enough to tolerate base pairs that are size-expanded in the major groove. In addition, the possibility to enzymatically polymerize a fluorescent nucleotide with high efficiency complements the tool box of biophysical probes available to study DNA replication.

Positional scanning peptide libraries for kinase substrate specificity determinations: straightforward and reproducible synthesis using pentafluorophenyl esters.

An efficient method to synthesize positional scanning synthetic combinatorial libraries (PS-SCLs) for studying the specificity of protein kinases is presented. Isokinetic ratios for pentafluorophenyl esters were determined iteratively using a new approach incorporating high performance liquid chromatography (HPLC) quantification and statistical experimental design. In the development process a large amount of work was put in to find efficient ways of screening for new isokinetic mixtures and to optimize the process of PS-SCL synthesis. The newly developed methods for the screening of isokinetic mixtures could be used for the screening of other interesting mixtures, but more importantly, the isokinetic ratios determined for the preactivated pentafluorophenyl esters were incorporated into a new efficient protocol. This straightforward protocol allows for a convenient synthesis of high quality PS-SCLs regardless of previous experience in solid phase synthesis.

Membrane-anchored DNA assembly for energy and electron transfer.

In this work we examine the trapping and conversion of visible light energy into chemical energy using a supramolecular assembly. The assembly consists of a light-absorbing antenna and a porphyrin redox center, which are covalently attached to two complementary 14-mer DNA strands, hybridized to form a double helix and anchored to a lipid membrane. The excitation energy is finally trapped in the lipid phase of the membrane as a benzoquinone radical anion that could potentially be used in subsequent chemical reactions. In addition, in this model complex, the hydrophobic porphyrin moiety acts as an anchor into the liposome positioning the DNA construct on the lipid membrane surface. The results show the suitability of our system as a prototype for DNA-based light-harvesting devices, in which energy transfer from the aqueous phase to the interior of the lipid membrane is followed by charge separation.

Triplet excitation energy transfer in porphyrin-based donor--bridge--acceptor systems with conjugated bridges of varying length: an experimental and DFT study.

A series of donor--bridge--acceptor (D--B--A) systems with varying donor-acceptor distances have been studied with respect to their triplet energy transfer properties. The donor and acceptor moieties, zinc(II), and free-base porphyrin, respectively, were separated by 2-5 oligo-p-phenyleneethynylene units (OPE) giving rise to edge-to-edge separations ranging between 12.7 and 33.4 A. The study was performed in 2-MTHF at 150 K and it was established that triplet excitation energy transfer occurs with high efficiency in all of the studied D--B--A systems. The distance dependence was exponential with an attenuation factor, beta, equal to 0.45 +/- 0.015 A(-1). The experimental study was also supported by quantum mechanical DFT and TD-DFT calculations on a series of closely related model systems. A thorough analysis of the OPE-bridge conformational dynamics led to an equation that quantitatively models the distance dependence of the electronic coupling found in the experimental study.

Functionalized nanostructures: redox-active porphyrin anchors for supramolecular DNA assemblies.

We have synthesized and studied a supramolecular system comprising a 39-mer DNA with porphyrin-modified thymidine nucleosides anchored to the surface of large unilamellar vesicles (liposomes). Liposome porphyrin binding characteristics, such as orientation, strength, homogeneity, and binding site size, was determined, suggesting that the porphyrin is well suited as a photophysical and redox-active lipid anchor, in comparison to the inert cholesterol anchor commonly used today. Furthermore, the binding characteristics and hybridization capabilities were studied as a function of anchor size and number of anchoring points, properties that are of importance for our future plans to use the addressability of these redox-active nodes in larger DNA-based nanoconstructs. Electron transfer from photoexcited porphyrin to a lipophilic benzoquinone residing in the lipid membrane was characterized by steady-state and time-resolved fluorescence and verified by femtosecond transient absorption.

A membrane anchored DNA-based energy/electron transfer assembly.

In this work the trapping and conversion of visible light energy into chemical energy is examined using a supramolecular assembly. This consists of a light absorbing antenna and a porphyrin redox centre both covalently attached to a DNA strand, which in turn is bound to a lipid membrane. The excitation energy is finally trapped as a benzoquinone radical anion that could potentially be used in subsequent chemical reactions.

Charge recombination versus charge separation in donor-bridge-acceptor systems.

Optimizing the ratio of the rates for charge separation (CS) over charge recombination (CR) is crucial to create long-lived charge-separated states. Mastering the factors that govern the electron transfer (ET) rates is essential when trying to achieve molecular-scale electronics, artificial photosynthesis, and also for the further development of solar cells. Much work has been put into the question of how the donor-acceptor distances and donor-bridge energy gaps affect the electronic coupling, V(DA), and thus the rates of ET. We present here a unique comparison on how these factors differently influence the rates for CS and CR in a porphyrin-based donor-bridge-acceptor model system. Our system contains three series, each of which focuses on a separate charge-transfer rate-determining factor, the donor-acceptor distance, the donor-bridge energy gap, and last, the influence of the electron acceptor on the rate for charge transfer. In these three series both CS and CR are governed by superexchange interactions which make a CR/CS comparative study ideal. We show here that the exponential distance dependence increases slightly for CR compared to that for CS as a result of the increased tunneling barrier height for this reaction, in accordance with the McConnell superexchange model. We also show that the dependence on the tunneling barrier height is different for CS and CR. This difference is highly dependent on the electron acceptor and thus cannot solely be explained by the differences in the frontier orbitals of the electron donor in these porphyrin systems.

Interplay between barrier width and height in electron tunneling: photoinduced electron transfer in porphyrin-based donor-bridge-acceptor systems.

The rate of electron tunneling in molecular donor-bridge-acceptor (D-B-A) systems is determined both by the tunneling barrier width and height, that is, both by the distance between the donor and acceptor as well as by the energy gap between the donor and bridge moieties. These factors are therefore important to control when designing functional electron transfer systems, such as constructs for photovoltaics, artificial photosynthesis, and molecular scale electronics. In this paper we have investigated a set of D-B-A systems in which the distance and the energy difference between the donor and bridge states (DeltaEDB) are systematically varied. Zinc(II) and gold(III) porphyrins were chosen as electron donor and acceptor because of their suitable driving force for photoinduced electron transfer (-0.9 eV in butyronitrile) and well-characterized photophysics. We have previously shown, in accordance with the superexchange mechanism for electron transfer, that the electron transfer rate is proportional to the inverse of DeltaEDB in a series of zinc/gold porphyrin D-B-A systems with bridges of constant edge to edge distance (19.6 A) and varying DeltaEDB (3900-17 600 cm(-1)). Here, we use the same donor and acceptor but the bridge is shortened or extended giving a set of oligo-p-phenyleneethynylene bridges (OPE) with four different edge to edge distances ranging from 12.7 to 33.4 A. These two sets of D-B-A systems-ZnP-RB-AuP+ and ZnP-nB-AuP+-have one bridge in common, and hence, for the first time both the distance and DeltaEDB dependence of electron transfer can be studied simultaneously in a systematic way.

Solvent and base dependence of copper-free palladium-catalyzed cross-couplings between terminal alkynes and arylic iodides: development of efficient conditions for the construction of gold(III)/free-base porphyrin dimers.

In this paper, our attempts to optimize the Heck alkynylation (copper-free Sonogashira) reaction are presented. An efficient copper-free coupling protocol was needed for the synthesis of gold/zinc porphyrin dimers because previous methods had failed. Previous studies have usually focused on ligands, whereas this work focuses on the choice of solvent and base. The catalytic system throughout the investigation was formed from the stable precursor [Pd2(dba)3.CHCl3] together with the ligand triphenylarsine, an easy-to-handle, air-stable ligand. A model study was conducted to examine the dependence of the Heck alkynylation on the solvent and base. The most successful modification proved to be the addition of methanol, as a cosolvent, in combination with a nucleophilic tertiary base. The success of the methanol additive is hypothesized to be caused by the presence of a rate-determining deprotonation step featuring a charge-separated transition state. Finally, the very high yielding and successful synthesis of a series of porphyrin systems using these new conditions is presented. For the first time, gold porphyrin substrates could efficiently be coupled in Heck alkynylation reactions.

Singlet energy transfer in porphyrin-based donor-bridge-acceptor systems: interaction between bridge length and bridge energy.

Singlet excitation energy transfer is governed by two donor-acceptor interactions, the Coulombic and exchange interactions giving rise to the Förster and Dexter mechanisms, respectively, for singlet energy transfer. In transfer between colliding molecules or between a donor (D) and acceptor (A) connected in donor-bridge-acceptor (D-B-A) system by an inert spacer (B), the distinction between these two mechanisms is quite clear. However, in D-B-A systems connected by a pi-conjugated bridge, the exchange interaction between the donor and acceptor is mediated by the virtual low-lying excited states (unoccupied orbitals) of that bridge and, as a consequence, becomes much more long-range in character. Thus, the clear distinction to the Coulombic mechanism is lost. This so-called superexchange mechanism for singlet energy transfer has been shown to make a significant contribution to the energy transfer rates in several D-B-A systems, and its D-A distance as well as D-B energy gap dependencies have been studied. We here demonstrate that in a series of oligo-p-phenyleneethynylene (OPE) bridged porphyrin-based D-B-A systems with varying D-A distances the Förster and through-bond (superexchange) mechanisms both make considerable contributions to the observed singlet energy transfer rates. The donor is either a zinc porphyrin or a zinc porphyrin with a pyridine ligand, and the acceptor is a free base porphyrin. By comparison to a homologous series where only the D-B energy gaps varies, a separation between the two energy transfer mechanisms was possible and, moreover, an interplay between distance and energy gap dependencies was noted. The distance dependence was shown to be approximately exponential with an attenuation factor beta=0.20 A-1. If the effect of the varying D-B energy gaps in the OPE series was taken into account, a slightly higher beta-value was obtained. Ground-state absorption, steady-state, and time-resolved emission spectroscopy were used. The experimental study is accompanied by time-dependent density functional theory (TD-DFT) calculations of the electronic coupling, and the experimental and theoretical results are in excellent qualitative agreement (same distance dependence).

Triplet photophysics of gold(III) porphyrins.

Gold porphyrins are often used as electron-accepting chromophores in donor-acceptor complexes for the study of photoinduced electron transfer, and they can also be involved in triplet-triplet energy-transfer interactions with other chromophores. Since the lowest excited singlet state is very short-lived (240 fs), the triplet state is usually the starting point for the transfer reactions, and it is therefore crucial to understand its photophysics. The triplet state of various gold porphyrins has been reported to have a lifetime of around 1.5 ns at room temperature and to have a biexponential decay both in emission and in transient absorption with decay times of around 10 and 100 micros at 80 K. In this paper, the triplet photophysics of two gold porphyrins (Au(III) 5,15-bis(3,5-di-tert-butylphenyl)-2,8,12,18-tetraethyl-3,7,13,17-tetramethylporphyrin and Au(III) 5,10,15,20-tetra(3,5-di-tert-butylphenyl)porphyrin) are studied by steady-state and time-resolved absorption and emission spectroscopy over a wide temperature range (4-300 K). The study reveals the existence of a dark state with an approximate lifetime of 50 ns, which was not previously observed. This state acts as an intermediate between the short-lived singlet and the triplet state manifold. In addition, we present DFT calculations, in which the core electrons of the central metal were replaced by a pseudopotential to account for the relativistic effects, which suggest that the lowest excited singlet state is an optically forbidden ligand-to-metal charge-transfer (LMCT) state. This LMCT state is an obvious candidate for the experimentally observed dark state, and it is shown to dictate the photophysical properties of gold porphyrins by acting as a gate for triplet state formation versus direct return to the ground state.