Water-Induced Dissociative Mechanism of Carboxylate and Divalent Calcium Ions Revealed by IR Laser Spectroscopy.

The dissociation of carboxylate and divalent calcium ions is investigated at the molecular level in microsolvation experiments by gradually increasing the number of water molecules around the ions. IR photodissociation (IRPD) laser spectroscopy of H-tagged (Ca, AcO)(HO) clusters in the ν(CO) spectral range combined with RI-B97-D3-BJ-abc/TZVPPD frequency calculations is used to identify the type of ion pairs involved in this process. These results reveal that the ion dissociation follows a multistep mechanism involving in particular pseudobridged monodentate contact ion pairs (CIPs), which are found to be the first intermediate species formed from bidentate CIPs along the ion dissociation path.

Effects of sulfoxide and sulfone sidechain-backbone hydrogen bonding on local conformations in peptide models.

We examine peptide model systems designed to probe short-range N-H⋯OS sidechain-backbone hydrogen bonding involving amino acid residues with sidechain sulfoxide or sulfone functional groups and its effects on local conformations. A strong 7-membered ring hydrogen bond of this type accompanies an intra-residue N-H⋯OC interaction and stabilizes an extended backbone conformation in preference to classical folded structures.

Mobility of antimony in contrasting surface environments of a mine site: influence of redox conditions and microbial communities.

Microbial processes can influence the complex geochemical behaviour of the toxic metalloid antimony (Sb) in mining environments. The present study is aimed to evaluate the influence of microbial communities on the mobility of Sb from solid phases to water in different compartments and redox conditions of a mining site in southwest (SW) Spain. Samples of surface materials presenting high Sb concentrations, from two weathered mining waste dumps, and an aquatic sediment were incubated in slurries comparing oxic and anoxic conditions.

Stepwise hydration of [CHCOOMg] studied by cold ion trap infrared spectroscopy: insights into interactions in the magnesium channel selection filters.

The magnesium channel controls Mg concentration in the cell and plays an indispensable role in biological functions. The crystal structure of the Magnesium Transport E channel suggested that Mg hydrated by 6 water molecules is transported through a selection filter consisting of COO groups on two Asp residues. This Mg motion implies successive pairing with OOC-R and dissociation mediated by water molecules.

Length-Dependent Transition from Extended to Folded Shapes in Short Oligomers of an Azetidine-Based α-Amino Acid: The Critical Role of NH···N H-Bonds.

Hydrogen bonds (H-bonds) are ubiquitous in peptides and proteins and are central to the stabilization of their structures. Inter-residue H-bonds between non-adjacent backbone amide NH and C=O motifs lead to the well-known secondary structures of helices, turns and sheets, but it is recognized that other H-bonding modes may be significant, including the weak intra-residue H-bond (called a C5 H-bond) that implicates the NH and C=O motifs of the same amino acid residue. Peptide model compounds that adopt stable C5 H-bonds are not readily available and the so-called 2.

Non-covalent interactions reveal the protein chain conformation in a flexible single-residue model.

The conformation is a local secondary structure in proteins that implicates a π N-H⋯N interaction between a backbone N atom and the NH of the following residue. Small-molecule models thereof have been limited so far to rigid proline-type compounds. We show here that in derivatives of a cyclic amino acid with a sulphur atom in the γ-position, specific side-chain/backbone N-H⋯S interactions stabilize the conformation sufficiently to allow it to compete with classical C5 and C7 H-bonded conformers.

Evaluation of antimony availability in a mining context: Impact for the environment, and for mineral exploration and exploitation.

This work aims to establish Sb mobility, its transfer to biota and its effect on soil health in a semi-arid climate. The results show the presence of stibnite (SbS) as the main primary Sb compound, bindhemite (PbSbO(O,OH)), and minor proportions of stibiconite (Sb(Sb)O(OH)) as oxidised Sb species. This research also observes very high total Sb contents in mining materials (max: 20,000 mg kg) and soils (400-3000 mg kg), with physical dispersion around mining materials restricted to 450 m.

Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry.

The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6 and inter-residue 7 H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach.

Stepwise dissociation of ion pairs by water molecules: cation-dependent separation mechanisms between carboxylate and alkali-earth metal ions.

Microhydrated H-tagged ion pairs (Ca, AcO)(HO) and (Ba, AcO)(HO) are investigated by IR photodissociation laser spectroscopy and DFT-D frequency calculations. The detailed picture of the first steps of ion dissociation reveals two mechanisms, where water molecules promote dissociation either directly or indirectly depending on the nature of the cation.

Characterization of Asx Turn Types and Their Connate Relationship with β-Turns.

Invited for the cover of this issue are David J. Aitken, Michel Mons, and co-workers at Université Paris-Saclay. The image depicts the investigation strategies used to document the intrinsic structures of an important secondary structure in proteins, the so-called Asx turn.

Characterization of Asx Turn Types and Their Connate Relationship with β-Turns.

Models of asparagine-containing dipeptides specifically designed to favor intrinsic folding into an Asx turn were characterized both theoretically, by using quantum chemistry, and experimentally, by using laser spectroscopy in the gas phase. Both approaches provided evidence for the spontaneous folding of both the Asn-Ala and Asn-Gly dipeptide models into the most stable Asx turn, a conformation stabilized by a C10 H-bond that was very similar to a type II' β-turn. In parallel, analysis of Asx turns implicating asparagine in crystallized protein structures in the Protein Data Bank revealed a sequence-dependent behavior.

Excited States Computation of Models of Phenylalanine Protein Chains: TD-DFT and Composite CC2/TD-DFT Protocols.

The present benchmark calculations testify to the validity of time-dependent density functional theory (TD-DFT) when exploring the low-lying excited states potential energy surfaces of models of phenylalanine protein chains. Among three functionals suitable for systems exhibiting charge-transfer excited states, LC-ωPBE, CAM-B3LYP, and ωB97X-D, which were tested on a reference peptide system, we selected the ωB97X-D functional, which gave the best results compared to the approximate coupled-cluster singles and doubles (CC2) method. A quantitative agreement for both the geometrical parameters and the vibrational frequencies was obtained for the lowest singlet excited state (a ππ* state) of the series of capped peptides.

N-H⋯X interactions stabilize intra-residue C5 hydrogen bonded conformations in heterocyclic α-amino acid derivatives.

Nature makes extensive and elaborate use of hydrogen bonding to assemble and stabilize biomolecular structures. The shapes of peptides and proteins rely significantly on N-H⋯O[double bond, length as m-dash]C interactions, which are the linchpins of turns, sheets and helices. The C5 H-bond, in which a single residue provides both donor and acceptor, is generally considered too weak to force the backbone to adopt extended structures.

Ion Pair Supramolecular Structure Identified by ATR-FTIR Spectroscopy and Simulations in Explicit Solvent*.

The present work uses ATR-FTIR spectroscopy assisted by simulations in explicit solvent and frequency calculations to investigate the supramolecular structure of carboxylate alkali-metal ion pairs in aqueous solutions. ATR-FTIR spectra in the 0.25-4.

Conformational analysis by UV spectroscopy: the decisive contribution of environment-induced electronic Stark effects.

UV chromophores are frequently used as probes of the molecular structure. In particular, they are sensitive to the electric field generated by the molecular environment, resulting in the observation of Stark effects on UV spectra. While these environment-induced electronic Stark effects (EI-ESE) are already used for conformational analysis in the condensed phase, this work explores the potential of such an approach when performed at much higher conformational resolution in the gas phase.

Conformation control through concurrent N-H⋯S and N-H⋯O[double bond, length as m-dash]C hydrogen bonding and hyperconjugation effects.

In addition to the classical N-H⋯O[double bond, length as m-dash]C non-covalent interaction, less conventional types of hydrogen bonding, such as N-H⋯S, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane α-amino acid. 6-Membered ring inter-residue N-H⋯S interactions (C6), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N-H⋯O[double bond, length as m-dash]C interactions (C5) to provide a C5-C6 feature that stabilizes a planar geometry in the monomer unit.

Early control of viral load by favipiravir promotes survival to Ebola virus challenge and prevents cytokine storm in non-human primates.

Ebola virus has been responsible for two major epidemics over the last several years and there has been a strong effort to find potential treatments that can improve the disease outcome. Antiviral favipiravir was thus tested on non-human primates infected with Ebola virus. Half of the treated animals survived the Ebola virus challenge, whereas the infection was fully lethal for the untreated ones.

A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine.

S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N-H···O=C backbone interaction (C5) and an inter-residue N-H···S interaction implicating the side-chain sulfur atom (C6γ).

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues.

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems.

Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group.

A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field.

An intraresidue H-bonding motif in selenocysteine and cysteine, revealed by gas phase laser spectroscopy and quantum chemistry calculations.

Models of protein chains containing a seleno-cysteine (Sec) residue have been investigated by gas phase laser spectroscopy in order to document the effect of the H-bonding properties of the SeH group in the folding of the Sec side chain, by comparison with recent data on Ser- and Cys-containing sequences. Experimental data, complemented by quantum chemistry calculations and natural bonding orbital (NBO) analyses, are interpreted in terms of the formation of a so-called 5γ intra-residue motif, which bridges the acceptor chalcogen atom of the side chain to the NH bond of the same residue. This local structure, in which the O/S/Se atom is close to the plane of the N-terminal side amide, is constrained by local backbone-side chain hyperconjugation effects involving the S and Se atoms.

CC2 Benchmark for Models of Phenylalanine Protein Chains: 0-0 Transition Energies and IR Signatures of the ππ* Excited State.

Extensive benchmarking calculations are presented to assess the accuracy of the standard approximate coupled cluster singles and doubles method (CC2) in studying ππ* excited states properties of model protein chains containing a phenylalanine residue, namely capped peptides, whose ground state conformers adopt the prototypical secondary structural features of proteins. First, the dependence with the basis set of the CC2 excitation energies, CC2 geometry optimizations, and region frequencies of the lowest ππ* excited state in a reference system, the -acetylphenylalaninylamide, are investigated, and the results are compared with experimental data. Second, at the best level of theory determined, the CC2/aug(N,O,π)-cc-pVDZ//CC2/cc-pVDZ level, a series of capped peptides of increasing size and containing residues of different nature are investigated.