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We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H-X bonds of the target peptide. The cross-link positions were established from collision-induced dissociation tandem mass spectra (CID-MS3) providing sequence information on the covalent adducts. Effects of the amino acid residue (Pro or Phe) and its position in the target peptide sequence were evaluated. For proline-containing peptides, interactions resulting in covalent cross-links in these complexes became more prominent as proline was moved towards the C-terminus of the target peptide sequence. The photocross-linking yields of phenylalanine-containing peptides depended on the position of both phenylalanine and photoleucine. Density functional theory calculations were used to assign structures of low-energy conformers of the (GLPMG + GLL*LK + H)+ complex. Born-Oppenheimer molecular dynamics trajectory calculations were used to capture the thermal motion in the complexes within 100 ps and determine close contacts between the incipient carbene and the H-X bonds in the target peptide. This provided atomic-level resolution of potential cross-links that aided spectra interpretation and was in agreement with experimental data.ᅟ [ABSTRACT FROM AUTHOR]

Attractive metallophilic (aurophilic, argentophilic, cuprophilic, etc.) interactions play an important role in arrangement and stabilization of oligonuclear metal ion complexes. We report a combined experimental and theoretical assessment of aurophilic interactions in closed-shell gold(I) dimers. The experimental binding energies were obtained for charged [(LH)AuCl]+…[(L')AuCl] dimers (L is either a phosphine or an N-heterocyclic carbene ligand) in the gas phase. These energies served for benchmarking of correlated quantum chemical calculations (CCSD(T)-calibrated SCS-MP2/CBS method) that were then applied to neutral [(L)AuCl]…[(L')AuCl] dimers. The overall attractive interactions between monomeric units are in the order of 100- 165 kJ mol[sup -1] in the charged dimers and of 70-105 kJ mol[sup -1] in the corresponding neutral dimers. In the neutral dimers, pure aurophilic interactions account for 25-30 kJ mol-1, the dipole-dipole interactions for 30-45 kJ mol-1, and the L…;L' "inter-ligand" dispersion interactions for 5-25 kJ mol-1. Energy of the aurophilic interactions is thus comparable or even larger than that of strong hydrogen bonds. [ABSTRACT FROM AUTHOR]

Peptide cation-radicals containing the threonine residue undergo radical-induced dissociations upon collisional activation and photon absorption in the 210-400 nm range. Peptide cation-radicals containing a radical defect at the N-terminal residue, [•Ala-Thr-Ala-Arg+H]+, were generated by electron transfer dissociation (ETD) of peptide dications and characterized by UV-vis photodissociation action spectroscopy combined with time-dependent density functional theory (TD-DFT) calculations of absorption spectra, including thermal vibronic band broadening. The action spectrum of [•Ala-Thr-Ala-Arg+H]+ ions was indicative of the canonical structure of an N-terminally deaminated radical whereas isomeric structures differing in the position of the radical defect and amide bond geometry were excluded. This indicated that exothermic electron transfer to threonine peptide ions did not induce radical isomerizations in the fragment cation-radicals. Several isomeric structures, ion-molecule complexes, and transition states for isomerizations and dissociations were generated and analyzed by DFT and Møller-Plesset perturbational ab initio calculations to aid interpretation of the major dissociations by loss of water, hydroxyl radical, C3H6NO•, C3H7NO, and backbone cleavages. Born-Oppenheimer molecular dynamics (BOMD) in combination with DFT gradient geometry optimizations and intrinsic reaction coordinate analysis were used to search for low-energy cation-radical conformers and transition states. BOMD was also employed to analyze the reaction trajectory for loss of water from ion-molecule complexes. [ABSTRACT FROM AUTHOR]

Abstract: The N2O decomposition over Fe-ferrierite, Fe-beta, and Fe-ZSM-5 has been recently studied [K. Jisa, J. Novakova, M. Schwarze, A. Vondrova, S. Sklenak, Z. Sobalik, J. Catal. 262 (2009) 27] and a superior activity of Fe-ferrierite with respect to Fe-beta and Fe-ZSM-5 has been shown. In this study, we investigated (1) plausible active sites for the N2O decomposition over Fe-ferrierite and (2) the origin of the distinct reactivity of Fe-ferrierite, Fe-ZSM-5 and Fe-beta employing a combined theoretical (periodic DFT) and experimental (UV–vis–NIR spectroscopy, IR spectroscopy, 29Si MAS NMR spectroscopy and catalytic batch experiments) approach. We evidenced that two Fe(II) cations accommodated in two adjacent six-membered rings in the eight-membered ring channel (β sites) of Fe-ferrierite (the calculated Fe–Fe distance is 7.4Å) form the active site responsible for the superior activity of this catalyst in the N2O decomposition in the absence of NO. Similar structures can be formed in Fe-beta. However, the probability of their formation is very low. For Fe-ZSM-5, the geometrical arrangement of the cationic positions is far from that in Fe-ferrierite and it is not suitable for the N2O decomposition. Therefore, the predicted order of the activity of the Fe(II) exchanged zeolites agrees with our experimental findings and it is: Fe-ferrierite≫Fe-beta>Fe-ZSM-5. We further showed that the accommodation of divalent cations in rings forming cationic sites can lead to significant rearrangements of the local structures of the zeolite framework, and therefore, the precise structure of sites binding a divalent cation cannot be derived from results of X-ray diffraction experiments, but can be inferred from theoretical calculations. [Copyright &y& Elsevier]

Abstract: Using two different reaction methodologies, two alkali metal–magnesium alkyl bis(amide) complexes were synthesised. First the lithium magnesiate LiMg{μ-N(SiMe3)2}2( t Bu) (1) was prepared by combining equimolar quantities of t BuLi and Mg{N(SiMe3)2}2 in hydrocarbon solvent. An X-ray crystallographic study revealed that the asymmetric unit of 1 has a dinuclear arrangement, based on a planar Li–N–Mg–N four-membered ring. As a result of the presence of intermolecular agostic interactions between the Li centre of one asymmetric unit and a methyl group which is resident on the terminal tert-butyl group of another, 1 is polymeric in the solid-state. Second the sodium magnesiate NaMg{μ-N(SiMe3)2}2( t Bu)·(OEt2) (2) was prepared by reacting two molar equivalents of Na{N(SiMe3)2} with one molar equivalent of t BuMgCl in hydrocarbon/diethyl ether solution. X-ray crystallographic analysis revealed that the asymmetric unit of 2 consisted of a dinuclear molecular arrangement. As expected it is not polymeric due to the coordination of the Lewis basic ether. Stabilizing intramolecular agostic Na⋯C bonds are observed (where C is a methyl group resident on a Si atom). [Copyright &y& Elsevier]

Abstract: Quantitative surface enhanced resonance Raman scattering (SERRS) requires effective adsorption of the analyte onto the metal surface. A range of dyes incorporating the benzotriazole group has been specifically designed to achieve this and they have proved successful labels for obtaining very sensitive analysis. However, if the spectra were more fully understood, the differences between the Raman spectrum in solution and on the surface could provide unique structural information on the nature of the surface layer. Using density functional theory (DFT) calculations the Raman and Infra-red (IR) spectra of the dye 3,5-dimethoxy-4-(6′-azobenzotriazolyl)-phenylamine (ABT-DMOPA) were assigned. A good correlation was found between the computed and experimental frequencies. Two competing isomers were compared and gave a largest error in fit for any clearly assigned band in the Raman spectrum of 41cm−1 and an overall fit error of ∼15cm−1. For the IR spectrum the largest error was 24cm−1 with an overall fit error of ∼8cm−1. Comparison of resonance Raman, SERS and SERRS spectra of the dye showed intensity changes which suggest the formation of a complex with silver on the surface. In the 1600–1630cm−1 region, one vibration is reduced in intensity whilst one is greatly enhanced as surface attachment occurs, giving a good marker for surface attachment. [Copyright &y& Elsevier]

Subjecting ferrocene, ruthenocene, or osmocene to the synergic amide base sodium-magnesium tris(diisopropylamido) affords a unique homologous series of metallocene derivatives of general formula [{M(C5H3)2}Na4Mg4(i-Pr2N)8] (where M = Fe (1), Ru (2), or Os (3)). X-ray crystallographic studies of 1 - 3 reveal a common molecular "inverse crown" structure comprising a 16-membered [(NaNMgN)4]4+ "host" ring and a metallocenetetraide [M(C5H3)2]4- "guest" core, the cleaved protons of which are lost selectively from the 1, 1', 3, and 3'-positions. Variable-temperature NMR spectroscopic studies indicate that 1, 2, and 3 each exist as two distinct interconverting conformers in arene solution, the rates of exchange of which have been calculated using coalescence and EXSV NMR measurements. [ABSTRACT FROM AUTHOR]

Splitting dioxygen to yield highly active oxygen species attracts enormous attention due to its potential in direct oxidation reactions, mainly in transformation of methane into valuable products. Distant binuclear cationic Fe(II) centers in Fe‐ferrierite have recently been shown to be active in splitting dioxygen at room temperature to form very active oxygen species able to oxidize methane to methanol at room temperature as well. Computational models of the distant binuclear transition metal cationic sites (Co(II), Mn(II), and Fe(II)) stabilized in the ferrierite matrix were investigated by periodic density‐functional theory calculations including molecular dynamics simulations. The results reveal that the M(II) cations capable of the M(II) → M(IV) redox cycle with the M...M distance of ca 7.4 Å stabilized in two adjacent β sites of ferrierite can split dioxygen. Our study opens the possibility of developing tunable zeolite‐based systems for the activation of dioxygen employed for direct oxidations. [ABSTRACT FROM AUTHOR]

This article reports that alkali metal zincates are fast establishing themselves as a new vanguard class of organozinc reagent, to add to the old guard of organozinc halides and diorganozincs. Among the best developed alkali metal zincates are homoleptic triorganozincates and heteroleptic diorgano-amidozincates. In the latter category, lithium di-tert-butyltetramethylpiperidinozincate is receiving special attention in view of its high chemo-/regioselectivity in deprotonative reactions of, for example, functionalized aromatics and functionalized heteroaromatics.

Time-resolved femtosecond-stimulated Raman spectroscopy (FSRS) provides valuable information on the structural dynamics of biomolecules. However, FSRS has been applied mainly up to the nanoseconds regime and above 700 cm−1, which covers only part of the spectrum of biologically relevant time scales and Raman shifts. Here we report on a broadband (~200–2200 cm−1) dual transient visible absorption (visTA)/FSRS set-up that can accommodate time delays from a few femtoseconds to several hundreds of microseconds after illumination with an actinic pump. The extended time scale and wavenumber range allowed us to monitor the complete excited-state dynamics of the biological chromophore flavin mononucleotide (FMN), both free in solution and embedded in two variants of the bacterial light-oxygen-voltage (LOV) photoreceptor EL222. The observed lifetimes and intermediate states (singlet, triplet, and adduct) are in agreement with previous time-resolved infrared spectroscopy experiments. Importantly, we found evidence for additional dynamical events, particularly upon analysis of the low-frequency Raman region below 1000 cm−1. We show that fs-to-sub-ms visTA/FSRS with a broad wavenumber range is a useful tool to characterize short-lived conformationally excited states in flavoproteins and potentially other light-responsive proteins. [ABSTRACT FROM AUTHOR]

Melanins are highly conjugated biopolymer pigments that provide photoprotection in a wide array of organisms, from bacteria to humans. The rate-limiting step in melanin biosynthesis, which is the ortho-hydroxylation of the amino acid L-tyrosine to L-DOPA, is catalyzed by the ubiquitous enzyme tyrosinase (Ty). Ty contains a coupled binuclear copper active site that binds O2 to form a μ:η²:η²-peroxide dicopper(II) intermediate (oxy-Ty), capable of performing the regioselective monooxygenation of para-substituted monophenols to catechols. The mechanism of this critical monooxygenation reaction remains poorly understood despite extensive efforts. In this study, we have employed a combination of spectroscopic, kinetic, and computational methods to trap and characterize the elusive catalytic ternary intermediate (Ty/O2/monophenol) under single-turnover conditions and obtain molecular-level mechanistic insights into its monooxygenation reactivity. Our experimental results, coupled with quantummechanics/molecular-mechanics calculations, reveal that the monophenol substrate docks in the active-site pocket of oxy-Ty fully protonated, without coordination to a copper or cleavage of the μ:η²:η²-peroxide O-O bond. Formation of this ternary intermediate involves the displacement of active-site water molecules by the substrate and replacement of their H bonds to the μ:η²:η²-peroxide by a single H bond from the substrate hydroxyl group. This H-bonding interaction in the ternary intermediate enables the unprecedented monooxygenation mechanism, where the μ:η²:η²-peroxide O-O bond is cleaved to accept the phenolic proton, followed by substrate phenolate coordination to a copper site concomitant with its aromatic ortho-hydroxylation by the nonprotonated μ-oxo. This study provides insights into O2 activation and reactivity by coupled binuclear copper active sites with fundamental implications in biocatalysis. [ABSTRACT FROM AUTHOR]

The article explores a research designing a man-made system that mimics the enzyme functionality in the dioxygen activation using both a different mechanism and structure of the active site represents a breakthrough in catalysis. It mentions the practical importance of the system development as a potential industrial catalyst for methane utilization.

Highly active oxygen capable to selectively oxidize methane to methanol at low temperature can be prepared in transition-metal cation exchanged zeolites. Here we show that the α-oxygen stabilized by the negative charges of two framework aluminum atoms can be prepared by the dissociation of nitrous oxide over distant binuclear cation structures (M(II)...M(II), M = cobalt, nickel, and iron) accommodated in two adjacent 6-rings forming cationic sites in the ferrierite zeolite. This α-oxygen species is analogous to that known only for iron exchanged zeolites. In contrast to divalent iron cations, only binuclear divalent cobalt cationic structures and not isolated divalent cobalt cations are active. Created methoxy moieties are easily protonated to yield methanol, formaldehyde, and formic acid which are desorbed to the gas phase without the aid of water vapor while previous studies showed that highly stable methoxy groups were formed on isolated iron cations in iron exchanged ZSM-5 zeolites. Selective oxidation of methane in zeolites is economical but the details of the responsible active sites are still unclear. Here the introduction of divalent transition metal cations into the zeolite matrix generates alpha-oxygen atoms which are active species for catalytic methane oxidation. [ABSTRACT FROM AUTHOR]

Review: 242 refs. [ABSTRACT FROM AUTHOR]