Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand

We have used combined quantum mechanical and molecular mechanical (QM/MM) calculations to study the reaction mechanism of nitrogenase, assuming that none of the sulfide ligands dissociates. To avoid the problem that there is no consensus regarding the structure and protonation of the E₄ state, we start from a state where N₂ is bound to the cluster and is protonated to N₂H₂, after dissociation of H₂. We show that the reaction follows an alternating mechanism with HNNH (possibly protonated to HNNH₂) and H₂NNH₂ as intermediates and the two NH₃ products dissociate at the E₇ and E₈ levels. For all intermediates, coordination to Fe6 is preferred, but for the E₄ and E₈ intermediates, binding to Fe2 is competitive. For the E₄, E₅ and E₇ intermediates we find that the substrate may abstract a proton from the hydroxy group of the homocitrate ligand of the FeMo cluster, thereby forming HNNH₂, H₂NNH₂ and NH₃ intermediates. This may explain why homocitrate is a mandatory component of nitrogenase. All steps in the suggested reaction mechanism are thermodynamically favourable compared to protonation of the nearby His-195 group and in all cases, protonation of the NE2 atom of the latter group is preferred.     

Secondary bonding interactions in biomimetic [2Fe-2S] clusters

A series of synthetic [2Fe-2S] complexes with terminal thiophenolate ligands and tethered ether or thioether moieties has been prepared and investigated in order to provide models for the potential interaction of additional donor atoms with the Fe atoms in biological [2Fe-2S] clusters. X-ray crystal structures have been determined for six new complexes that feature appended Et (1(C)), OMe (1(O)), or SMe (1(S)) groups, or with a methylene group (2(C) ), an ether-O (2(O)), or an thioether-S (2(S)) linking two aryl groups. The latter two systems provide a constrained chelate arrangement that induces secondary bonding interactions with the ether-O and thioether-S, which is confirmed by density functional theory (DFT) calculations that also reveal significant spin density on those fifth donor atoms. Structural consequences of the secondary bonding interactions are analyzed in detail, and effects on the spectroscopic and electronic properties are probed by UV-vis, M?ssbauer, and (1)H NMR spectroscopy, as well by SQUID measurements and cyclic voltammetry. The potential relevance of the findings for biological [2Fe-2S] sites is considered.     

Chemically-assisted fragmentation combined with multi-dimensional liquid chromatography and matrix-assisted laser desorption/ionization post source decay, matrix-assisted laser desorption/ionization tandem time-of flight or matrix-assisted laser desorption/ionization tandem mass spectrometry for improved sequencing of tryptic peptides

Derivatization of tryptic peptides using an Ettan CAF matrix-assisted laser desorption/ionization (MALDI) sequencing kit in combination with MALDI-post source decay (PSD) is a fast, accurate and convenient way to obtain de novo or confirmative peptide sequencing data. CAF (chemically assisted fragmentation) is based on solid-phase derivatization using a new class of water stable sulfonation agents, which strongly improves PSD analysis and simplifies the interpretation of acquired spectra. The derivatization is performed on solid supports, ZipTip(microC18, limiting the maximum peptide amount to 5 microg. By performing the derivatization in solution enabled the labeling of tryptic peptides derived from 100 microg of protein. To increase the number of peptides that could be sequenced, derivatized peptides were purified using multidimensional liquid chromatography (MDLC) prior to MALDI sequencing. Following the first dimension strong cation exchange (SCX) chromatography step, modified peptides were separated using reversed-phase chromatography (RPC). During the SCX clean up step, positively charged peptides are retained on the column while properly CAF-derivatized peptides (uncharged) are not. A moderately complex tryptic digest, prepared from six different proteins of equimolar amounts, was CAF-derivatized and purified by MDLC. Fractions from the second dimension nano RPC step were automatically sampled and on-line dispensed to MALDI sample plates and analyzed using MALDI mass spectrometry fragmentation techniques. All proteins in the derivatized protein mixture digest were readily identified using MALDI-PSD or MALDI tandem mass spectrometry (MS/MS). More than 40 peptides were unambiguously sequenced, representing a seven-fold increase in the number of sequenced peptides in comparison to when the CAF-derivatized protein mix digest was analyzed directly (no MDLC-separation) using MALDI-PSD. In conclusion, MDLC purification of CAF-derivatized peptides significantly increases the success rate for de novo and confirmative sequencing using various MALDI fragmentation techniques. This new approach is not only applicable to single protein digests but also to more complex digests and could, thus, be an alternative to electrospray ionization MS/MS for peptide sequencing.     

Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA(-)) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More specifically, it is found that the change in the excitation energy as a consequence of the disruption of the planarity of pCA(-) inside PYP is nearly canceled out by the shift induced by the intermolecular interactions of the chromophore and the protein as a whole. These results provide important insights about the primary absorption and the tuning of the chromophore by the protein environment in PYP.     

New Reactions of Amino-Functionalized 3-Vinyl-1H-indoles and Tetrahydropyridin-4-yl Analogues with Dienophiles

Reactions of 3-[2-(morpholin-4-yl)vinyl]-1H-indole ( 1 ), the 1,2-dihydro-9H-carbazole 2 , as well as the 3-(tetrahydropyridin-4-yl)-1H-indoles 3a and 3b with some carbo- and heterodienophiles are described. The scope and limitations of the synthetic utility of these amino- (or homoamino)-functionalized 3-vinyl-1H-indoles are reported and some MO calculations for the qualitative prediction of their reactivities are presented. The reactions gave rise to substitution products, redox products, Diels-Alder adducts, ene adducts, and Michael-type adducts (Schemes 2 and 3).     

Four levels of pattern recognition

Problems of pattern recognition in chemistry and other subjects can be divided conveniently into four different types depending on the level of scope of the problem.(1) Classification into one of a number of defined classes. As an example blood samples taken from persons known to be either controls or welders are considered. The problem is whether trace element concentrations in these samples contain information on whether or not a person is a welder.(2) Level 1 plus the possibility that an object is an outlier, i.e. does not belong to any of the defined classes. As an example, the üse of ¹³C-n.m.r. data to decide whether 2-substituted norbornanes have the exo or endo structure is discussed. (2A) Level 2, asymmetric. This situation occurs when one class does not have a systematic structure, but another class is homogeneous and can be described by a level 2 model. This occurs in the classification of materials or compounds as good or bad, active or inactive, and in binary classifications. As an example the use of trace element data to classify steel samples as having good or poor properties of strength is discussed.(3) Level 2 plus the ability to relate the variables measured to external properties of continuous character. As an example, the classification of a series of chemical compounds as β -receptor blockers, β -receptor stimulants, or neither, on the basis of their structural variables is discussed. In addition, relations between these structural variables and the measured biological activity are sought within each of the two classes.(4) Level 3 with the difference that several external property variables in the objects are measured. It may be desirable to use variables of the objects both for classification and for relations to several property variables: such examples are numerous in analytical chemistry.     

The N1s ESCA Spectrum of Protonated 1,8-Bis-(Dimethylamino) Naphthalene (“proton sponge”)

The ESCA spectrum of protonated 1,8-bis-(dimethylamino) naphthalene (“proton sponge”) (I) has been recorded in the region of N1s binding energies. The results indicate that IH⁺ possesses an unsymmetrical N? H…?N hydrogen bridge.     

Reactions of Group 8, 9, and 10 monocations (Fe+, Co+, Ni+, Ru+, Rh+, Pd+, Os+, Ir+, Pt+) with phosphane in the gas phase

The reactions of Group 8, 9 and 10 monocations with phosphane were studied under single-collision conditions in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Fe(+) is completely unreactive, Co(+) reacts slowly and shows both adduct formation and P-H bond activation, and Ni(+) reacts slowly as well but shows adduct formation only. In contrast to their first-row congeners, the investigated second- and third-row transition metal monocations show facile P-H bond activations. Remarkably, extensive dehydrogenations of the collision complexes yield cations MPH(+), MP(2) (+), MP(3)H(+), MP(4) (+) and so on. Exceptional behaviour is shown by the two d(9) cations palladium (whose "dehydrogenation power" is rather limited) and platinum (which gives rise to a great manifold of only partially dehydrogenated species as well). Collision-induced dissociation experiments suggest that P(2) and PH units are formed as ligands.     

Preparation, properties, and reactions of metal-containing heterocycles: Part CV. Synthesis and structure of polyoxadiphosphaplatinaferrocenophanes

A series of novel heterobimetallic crown ether-like polyoxadiphosphaplatinaferrocenophanes cis-[1,1′-Fc(CH₂O(CH₂CH₂O)_nCH₂CH₂PPh₂)₂]PtCl₂ (n=1–3) (4a–c) was synthesized in good yield by cyclization of the bis(phosphine) ligands 1,1′-Fc(CH₂O(CH₂CH₂O)_nCH₂CH₂PPh₂)₂ (n=1–3) (3a–c) and (PhCN)₂PtCl₂ under high dilution conditions in CH₂Cl₂. The bisphosphines 3a–c are obtained by reaction of the corresponding diols 1,1′-Fc(CH₂O(CH₂CH₂O)_nCH₂CH₂OH)₂ (n=1–3) (1a–c) with: (i) CH₃SO₂Cl in CH₂Cl₂ and (ii) LiPPh₂ in THF. Although the X-ray crystal structure of 4a shows that the cavity is large enough for the encapsulation of small metal cations, inclusion experiments of 4a–c with Group 1 cations, and Mg²⁺, or NH₄⁺ in solution applying NMR titration and cyclovoltammetric methods reveal no evidence for the formation of host–guest complexes for 4a,b. In the case of 4c only the addition of Na⁺ or K⁺ leads to an insignificant effect.