Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid.

Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born-Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH]+·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO]-·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations.

Sulfonate-Based Triazine Multiple-Electron Anolyte for Aqueous Organic Flow Batteries.

A new highly soluble triazine derivative (SPr)34TpyTz showing three reversible redox processes with fast kinetics and high diffusion coefficients has been synthesized using an efficient, low-cost, and straightforward synthetic route. Concentrated single cell tests and DFT studies reveal a tendency of the reduced triazine species to form aggregates which could be avoided by tuning the supporting electrolyte concentration. Under the right conditions, (SPr)34TpyTz shows no capacity decay and good Coulombic, voltage, and energy efficiencies for the storage of two electrons. The storage of further electrons leads to a higher capacity decay and an increase of the electrolyte pH, suggesting the irreversible protonation of the generated species. So, a plausible mechanism has been proposed. A higher concentration of (SPr)34TpyTz shows slightly higher capacity decay and lower efficiencies due to the aggregate formation.

Clean H2 Production by Lignin-Assisted Electrolysis in a Polymer Electrolyte Membrane Flow Reactor.

Biomass-derived products, such as lignin, are interesting resources for energetic purposes. Lignin is a natural polymer that, when added to the anode of an alkaline exchange membrane water electrolyser, enhances H2 production rates and efficiencies due to the substitution of the oxygen evolution reaction. Higher efficiencies are reported when different catalytic materials are employed for constructing the lignin anolyte, demonstrating that lower catalytic loadings for the anode improves the H2 production when compared to higher loadings. Furthermore, when a potential of -1.8 V is applied, higher gains are obtained than when -2.3 V is applied. An increase of 200% of H2 flow rates with respect to water electrolysis is reported when commercial lignin is used coupled with Pt-Ru at 0.09 mg cm-2 and E = -1.8 V is applied at the cathode. This article provides deep information about the oxidation process, as well as an optimisation of the method of the lignin electro-oxidation in a flow-reactor as a pre-step for an industrial implementation.

Strategies to Enhance CO2 Electrochemical Reduction from Reactive Carbon Solutions.

CO2 electrochemical reduction (CO2 ER) from (bi)carbonate feed presents an opportunity to efficiently couple this process to alkaline-based carbon capture systems. Likewise, while this method of reducing CO2 currently lags behind CO2 gas-fed electrolysers in certain performance metrics, it offers a significant improvement in CO2 utilization which makes the method worth exploring. This paper presents two simple modifications to a bicarbonate-fed CO2 ER system that enhance the selectivity towards CO. Specifically, a modified hydrophilic cathode with Ag catalyst loaded through electrodeposition and the addition of dodecyltrimethylammonium bromide (DTAB), a low-cost surfactant, to the catholyte enabled the system to achieve a FECO of 85% and 73% at 100 and 200 mA·cm-2, respectively. The modifications were tested in 4 h long experiments where DTAB helped maintain FECO stable even when the pH of the catholyte became more alkaline, and it improved the CO2 utilization compared to a system without DTAB.

A Dynamic Proton Bond: MH+·H2O ⇌ M·H3O+ Interconversion in Loosely Coordinated Environments.

The interaction of organic molecules with oxonium cations within their solvation shell may lead to the emergence of dynamic supramolecular structures with recurrently changing host-guest chemical identity. We illustrate this phenomenon in benchmark proton-bonded complexes of water with polyether macrocyles. Despite the smaller proton affinity of water versus the ether group, water in fact retains the proton in the form of H3O+, with increasing stability as the coordination number increases. Hindrance in many-fold coordination induces dynamic reversible (ether)·H3O+ ⇌ (etherH+)·H2O interconversion. We perform infrared action ion spectroscopy over a broad spectral range to expose the vibrational signatures of the loose proton bonding in these systems. Remarkably, characteristic bands for the two limiting proton bonding configurations are observed in the experimental vibrational spectra, superimposed onto diffuse bands associated with proton delocalization. These features cannot be described by static equilibrium structures but are accurately modeled within the framework of ab initio molecular dynamics.

Insights into the binding of arginine to adenosine phosphate from mimetic complexes.

The amino acid arginine plays a key role in the interaction of proteins with adenosine phosphates, as its protonated guanidinium side group is capable of building multipodal H-bonding interactions with the oxygen atoms of the phosphate, phosphoester and ribose moieties and with the nitrogen atoms of adenine. Protein interactions often take place in competition with other ionic species, typically metal cations, which are prone to build concerted coordination arrangements with the same centers of negative charge as guanidinium. We report on a vibrational spectroscopy and computational investigation of a positively charged ternary complex formed by adenosine monophosphate (AMP) with methyl guanidinium and Na+. Following a bottom-up approach, an analogous complex with ribose phosphate is characterized as well, which serves to assess the individual role of the phosphate, sugar and adenine moieties in the binding process and to compare, within a single complex, the interactions associated with diffuse versus localized charge distributions of guanidinium and the alkali cation, respectively. The results indicate that Na+ is preferentially hosted in a semi-rigid pocket formed by the phosphoester-adenosine backbone of AMP and displaces guanidinium to a peripheral binding to the phosphate anionic end group. This suggests that the control of the salt concentration may constitute an effective route to modulate protein-AMP complexation.

Alpha-Germanium Nanolayers for High-Performance Li-ion Batteries.

The exfoliation of tridimensional crystal structures has recently been considered a new source of bidimensional materials. The new approach offers the possibility of dramatically enlarging the library of bidimensional materials, but the number of nanolayers produced so far is still limited. Here, we report for the first time the use of a new type of material, α-germanium nanolayers (2D α-Ge). The 2D α-Ge is obtained by exfoliating crystals of α-germanium in a simple one-step procedure assisted by wet ball-milling (gram-scale fabrication). The α-germanium nanolayers have been tested as anode material for high-performance LIBs. The results show excellent performance in semi-cell configuration with a high specific capacity of 1630 mAh g-1 for mass loading of 1 mg cm-2 at 0.1 C. The semi-cell was characterized by a constant current rate of 0.5 C during 400 cycles and different scan rates (0.1 C, 0.5 C, and 1 C). Interestingly, the structural characterization, including Raman spectroscopy, XRPD, and XPS, concludes that 2D α-Ge largely retains its crystallinity after continuous cycling. These results can be used to potentially apply these novel 2D germanium nanolayers to high-performance Li-ion batteries.

Inclusion complexes of the macrocycle nonactin with benchmark protonated amines: aniline and serine.

The biological activity of the macrocycle nonactin is intimately related to its ionophore properties and ability to act as a selective cation carrier. While the focus of most investigations on nonactin has been on the binding of metal cations and small molecular ions, this study pursues the characterization of its inclusion complexes with primary amines with bulky structured side groups of different polarity. To this end, the complexes of nonactin with aniline and with the amino acid L-serine, both in protonated form, are considered as case studies and their relevant coordination arrangements are assessed by means of infrared action spectroscopy, quantum chemical density functional theory and Born-Oppenheimer molecular dynamics. The study suggests that the oxygen atoms from the oxolane (tetrahydrofuran) groups of nonactin constitute the preferential docking sites of the ammonium moiety of the guest cation, although conformational constraints promote interactions with the ester carbonyl backbone groups. In the aniline complex, the benzyl side ring is oriented outwards from the cavity, whereas in the case of L-serine, the side carboxylic acid and alcohol groups participate actively in the coordination process. Interestingly, the accommodation of L-serine is favoured when nonactin adopts an enantiomeric-selective folding, that promotes the tripodal coordination of the protonated amine group with oxolane rings from three nonactinic acid blocks with enantiomeric sequence (+)-(-)-(+), which allows for a facile coordination of the serine side groups. This is recognized as a general feature associated with the alternation of chiral domains in globally achiral natural nonactin, yielding mirror-symmetric complexes with the enantiomers of chiral amines.

Gas-phase hydration of nopinone: the interplay between theoretical methods and experiments unveils the conformational landscape.

The structure of microsolvated nopinone formed in the supersonic jet expansion is investigated in the gas phase. The rotational spectra of nopinone(H2O)n (n = 1, 2, 3) were analysed by means of Fourier transform microwave spectroscopy. In the present study, three monohydrates, two dihydrates and two trihydrates were observed and characterized. The observed structures are the lowest energy conformers predicted by quantum chemical calculations. In all the observed hydrates of nopinone, water was found to be linked to the ketone group (C[double bond, length as m-dash]O) with a strong hydrogen bond (ONOPHW) and finishing with a dispersive one (OWHNOP). The structure of nopinone was found to alter the structure of water dimer and water trimer, which make nopinone be surrounded with a chain of water molecules. A remarkable decrease in the H-bonding length was observed when the number of attached water molecules is increased. Different DFT and ab initio calculations at the equilibrium structure allowed the identification of the observed conformers. Evaluation of the B3LYP-D3 and ωB97X-D results revealed deficiencies in reproducing the structure of one observed monohydrated structure while MP2 and M06-2X reproduce all the three observed structures. A comparison with similar bicyclic ketones highlights how a small change in the bicyclic ring leads to different effects in the microsolvation of biogenic VOCs. This study presents the first step of molecular aggregation to understand the atmospheric formation of aerosols at the molecular scale.

Molecular Characterization of Nonvolatile Fractions of Algerian Petroleum with High-Resolution Mass Spectrometry.

Algerian crude oil displays a marked propensity for asphaltene precipitation, leading to solid deposits during extraction, transportation, and storage. The relationship between precipitation and chemical composition is unclear; in fact, Algerian crude oil actually features a low asphaltene concentration, despite its relatively large rate of deposit formation. The rationalization of the precipitation process and its remediation should benefit from a molecular characterization of the crude oil. In this study, two unstable asphaltene fractions (A1 and A2) from two different deposits, and two resin crude oil fractions (R1 and R2) from the Hassi-Messaoud Algerian field have been characterized at the molecular level by means of high-resolution mass spectrometry with an Atmospheric Pressure Chemical Ionization (APCI) source. Positively and negatively charged compounds with molecular weights 200-1200 m/z were detected. Several thousand molecular stoichiometries were identified and classified for each sample, in terms of heteroatom content and aromaticity, searching for trends characteristic of the two asphaltenes and of the associated resins. The A2 asphaltene, from a downstream storage tank, displays a higher aromaticity and O-heteroatom content, which correlates with an enhanced aggregation propensity, in comparison to the A1 fraction, collected at the well bore. The resin fractions are found to be abundant in aliphatic hydrocarbons and heteroatomic compounds of moderate aromaticity. The more polar resin fraction, R2, is enriched in N-containing species, with respect to the less polar resin fraction R1, which correlates with the stabilizing function observed in previous works. The results stress the view of crude oil fractions as complex mixtures, rather than in terms of average prototypical compounds, when facing the understanding of asphaltene deposition conditions.

Multipodal coordination and mobility of molecular cations inside the macrocycle valinomycin.

The macrocycle valinomycin displays an outstanding ability in cation binding and carriage across hydrophobic environments (e.g., cell membranes) and constitutes a central landmark for the design of novel ionophores for the regulation of biochemical processes. Most previous investigations have focused on the capture of metal cations (primarily K+). Here, we address the versatility of valinomycin in the encapsulation of molecular ions of small and moderate size, with NH4+ and H4PO4+ as case studies. A combination of infrared action vibrational spectroscopy and quantum chemical computations of molecular structure and dynamics is employed with the two-fold aim of assessing the dominant H-bonding coordination networks in the complexes and of characterizing the positional and rotational freedom of the guest cations inside the cavity of the macrocycle. Valinomycin binds NH4+ with only moderate distortion of the C3 configuration adopted in the complexes with the metal cations. The ammonium cation occupies the center of the cavity and displays two low-energy coordination arrangements that are dynamically connected through a facile rotation of the cation. The inclusion of the bulkier phosphoric acid cation demands significant stretching of the valinomycin backbone. Interestingly, the H4PO4+ cation achieves ample positional and rotational mobility inside valinomycin. The valinomycin backbone is capable of adopting barrel-like configurations when the cation occupies a region close to the center of the cavity, and funnel-like configurations when it diffuses to positions close to the exit face. This can accommodate the cation in varying coordination arrangements, characterized by different H-bonding between the four POH arms and the ester carbonyl groups of the macrocycle.

The synergy of different solid-state techniques to elucidate the supramolecular assembly of two 1H-benzotriazole polymorphs.

1H-Benzotriazole crystallizes as two different polymorphs, namely 4aα and 4aß. One polymorph is chiral and it resolves spontaneously as conglomerates. The other polymorph crystallizes in a centrosymmetric space group and it is therefore achiral. In both polymorphs supramolecular structures are formed starting from achiral monomers. An analysis of these two polymorphs of 1H-benzotriazole has been carried out by a complete strategy involving different solid-state experimental techniques and quantum chemical calculations (DFT, Density Functional Theory). In particular, X-ray crystallography, NMR spectroscopy and vibrational spectroscopy techniques (FarIR, IR and Raman) that are not sensitive to chirality have been used to characterize the two polymorphs structurally. Vibrational spectroscopy (VCD, Vibrational Circular Dichroism) that is sensitive to chirality was employed to determine the absolute configuration (M or P helices) of the chiral supramolecular structure of 4aα.

Insights into the Recognition of Phosphate Groups by Peptidic Arginine from Action Spectroscopy and Quantum Chemical Computations.

The side group of the amino acid arginine is typically in its guanidinium protonated form under physiological conditions and participates in a broad range of ligand binding and charge transfer processes of proteins. The recognition of phosphate moieties by guanidinium plays a particularly key role in the interactions of proteins with ATP and nucleic acids. Moreover, it has been recently identified as the driving force for the inhibition of kinase phosphorilation activity by guanidinium derivatives devised as potential anticancer agents. We report on a fundamental investigation of the interactions and coordination arrangements formed by guanidinium with phosphoric, phosphate, and pyrophosphate groups. Action vibrational spectroscopy and ab initio quantum chemical computations are employed to characterize the conformations of benchmark positively charged complexes isolated in an ion trap. The multidentate structure of guanidinium and of the phosphate groups gives rise to a rich conformational landscape with a particular relevance of tweezer-like configurations, where phosphate is effectively trapped by two guanidinium cations. The pyrophosphate complex incorporates a Na+ cation, which serves to compare the interactions associated with the localized versus diffuse charge distributions of the alkali cation and guanidinium, respectively, within a common supramolecular framework.

A Cl- Hinge for Cyclen Macrocycles: Ionic Interactions and Tweezer-Like Complexes.

The supramolecular networks derived from the complexation of polyazamacrocycles with halide anions constitute fundamental building blocks of a broad range of modern materials. This study provides insights into the conformational framework that supports the binding of protonated cyclen macrocyles (1,4,7,10-Tetraazacyclododecane) by chloride anions through NHδ+···Cl- interactions. The isolated complex comprised of two cyclen hosts linked by one Cl- anion is characterized by means of infrared action spectroscopy and ion mobility mass spectrometry, in combination with quantum chemical computations. The Cl- anion is found to act as a hinge that bridges the protonated NH 2 + moieties of the two macrocycles leading to a molecular tweezer configuration. Different types of conformations emerge, depending on whether the trimer adopts an open arrangement, with significant freedom for internal rotation of the cyclen moieties, or it locks in a folded conformation with intermolecular H-bonds between the two cyclen backbones. The ion mobility collision cross section supports that folded configurations of the complex are dominant under isolated conditions in the gas phase. The IRMPD spectroscopy experiments suggest that two qualitatively different families of folded conformations coexist at room temperature, featuring either peripheral or inner positions of the anion with respect to the macrocycle cavities, These findings should have implications in the growth of extended networks in the nanoscale and in sensing applications.

Preferential host-guest coordination of nonactin with ammonium and hydroxylammonium.

The biological activity of the macrocycle nonactin is intimately related to its ionophore properties and ability to act as a selective cation carrier. The competitive binding of small protonated amines constitutes a particularly key issue in the biochemistry of nonactin, which finds application in sensing and extraction technologies. In this study, isolated complexes of nonactin with ammonium and hydroxylammonium are investigated with infrared action spectroscopy and quantum chemical computations. The focus of the investigation is on the coordination achieved by the protonated guest with the oxygen atoms of either the oxolane groups or the carboxyl groups in the ester linkages of the macrocyle host and their relative contributions to the stability of the complexes. The experimental and computational data converge to a preferred coordination arrangement associated with a tight binding of the N-H δ+ bonds with the oxolane groups. In the N H 4 + complex, this results in a compact complex of S 4 symmetry. In contrast, symmetry is disrupted in the NH3OH+ complex, as it incorporates a bifurcated coordination of the -OH bond with a carbonyl group and an oxolane group of the host, involving also a more stretched arrangement of the nonactin backbone. These gas-phase conformations are in agreement with the structures postulated for these complexes in condensed phases, from previous Raman and crystallographic experiments.

Conformational aspects of polymorphs and phases of 2-propyl-1H-benzimidazole.

This paper reports on the polymorphism of 2-propyl-1H-benzimidazole (2PrBzIm) induced by temperature change. Upon heating, an irreversible reconstructive-type phase transition at T = 384 K from the ordered form I (P212121) to a new polymorph, form II HT (Pcam), was observed. The structural transformation between forms I and II involves significant changes in the crystal packing, as well as a key conformational variation around the propyl chain of the molecule. After the first irreversible phase transition, the II HT form undergoes two further (reversible) phase transitions upon cooling at 361 K (II RT) and 181 K (II LT). All three phases (forms II HT, II RT and II LT) have almost identical crystal packing and, given the reversibility of the conversions as a function of temperature, they are referred to as form II temperature phases. They differ, however, with respect to conformational variations around the propyl chain of 2PrBzIm. Energy calculations of the gas-phase conformational energy landscape of this compound about its flexible bonds allowed us to classify the observed conformational variations of all forms into changes and adjustments of conformers. This reveals that forms I and II are related by conformational change, and that two of the form II phases (HT and RT) are related by conformational adjustment, whilst the other two (RT and LT) are related by conformational change. We introduce the term 'conformational phases' for different crystal phases with almost identical packing but showing changes in conformation.

Complexes of Crown Ether Macrocycles with Methyl Guanidinium: Insights into the Capture of Charge in Peptides.

Crown ethers are well known as modulating agents of protein function and interactions. The action of crown ethers is driven by an alteration of the charged moieties of proteins through the capping of cationic amino acid side chains. This study evaluates the conformational features involved in the binding of crown ethers to the side chain of arginine. For this purpose, isolated complexes of methyl guanidinium with 12-crown-4 and 18-crown-6 are characterized with infrared action vibrational spectroscopy and quantum chemical computations. The conformational landscapes of the two complexes comprise an extensive ensemble of conformations close in energy. In the 12-crown-4 complex, the crown ether has the plane of its backbone approximately perpendicular to that of the guanidinium moiety and coordinates to two or three of its NHδ+ bonds. In the 18-crown-6 complex, the crown ether backbone is partially folded and tilted with respect to guanidinium and fixes its position in order to facilitate up to a four-fold coordination in the complex. The access of the complexes to multiple conformations leads to broad band structures in the N-H stretching region of their vibrational spectra.

Intra-cavity proton bonding and anharmonicity in the anionophore cyclen.

Proton bonding drives the supramolecular chemistry of a broad range of materials with polar moieties. Proton delocalization and electronic charge redistribution have a profound impact on the structure of proton-bound molecular frameworks, and pose fundamental challenges to quantum chemical modelling. This study provides insights into the structural and spectral signatures of the intramolecular proton bond formed in a benchmark polyazamacrocycle anionophore (cyclen, 1,4,7,10-tetraazacyclododecane). Infrared action spectroscopy is employed to characterize the macrocycle, isolated in protonated form. In its most stable configuration, protonated cyclen adopts an open arrangement of Cs symmetry with a particularly strong NHδ+N bond across the cavity. The quantum chemical analysis of the infrared spectrum reveals intrinsic difficulties for the accurate description of the vibrational modes of the system. The reconciliation of the computational predictions with experiment demands a careful anharmonic treatment of the proton motion, which exposes the limitations of current methods. Best results are obtained with the incorporation of anharmonicity only to the fundamental modes directly related to motions of the proton. However, the full anharmonic treatment of the system fails to describe correctly the vibrations related to the macrocycle backbone. The results should serve as motivation for new developments in the modelling of proton bonded systems.

A vibrational circular dichroism (VCD) methodology for the measurement of enantiomeric excess in chiral compounds in the solid phase and for the complementary use of NMR and VCD techniques in solution: the camphor case.

For the first time, the success of a methodology for the determination of enantiomeric excess (% ee) in chiral solid samples by vibrational circular dichroism (VCD) spectroscopy is reported. We have used camphor to determine the % ee in a blind sample constituted by a mixture of its two enantiomers as a test for the validity of our approach. IR and VCD spectra of different enantiomeric mixtures of R/S-camphor in Nujol mulls were recorded and linear regressions of VCD intensities (ΔAbs.) vs. % ee for selected bands were found. Finally, the VCD intensities of a blind sample were interpolated in these linear regressions, obtaining its % ee with a rms of 2.4. These results in the solid phase were complemented with the determination of % ee in the liquid phase by VCD and NMR techniques, which are proved to be complementary techniques to carry out this kind of analysis. In the same way as in the VCD solid phase, linear regressions of ΔAbs. vs. % ee for selected bands were established, obtaining a rms of 1.1 in the % ee determination of a blind sample. 1H NMR experiments at 600 MHz using the chiral solvating agent, (S,S)-ABTE, allow the determination of the proportions of enantiomers in CD2Cl2 solution with great accuracy. 13C CPMAS NMR spectra prove that this technique cannot be used for conglomerates and/or solid solutions.

Guanidinium/ammonium competition and proton transfer in the interaction of the amino acid arginine with the tetracarboxylic 18-crown-6 ionophore.

The recognition of arginine plays a central role in modern proteomics and genomics. Arginine is unique among natural amino acids due to the high basicity of its guanidinium side chain, which sustains specific interactions and proton exchange biochemical processes. The search for suitable macrocyclic ionophores constitutes a promising route towards the development of arginine receptors. This study evaluates the conformational features involved in the binding of free arginine by the polyether macrocycle (18-crown-6)-tetracarboxylic acid. Infrared action vibrational spectroscopy and quantum-chemical computations are combined to characterize the complexes with net charges +1 and +2. The spectrum of the +1 complex can be explained in terms of a configuration predominantly stabilized by a robust bidentate coordination of guanidinium with a carboxylate group formed from the deprotonation of one side group of the crown ether. The released proton is transferred to the amino terminus of arginine, which then coordinates with the crown ether ring. In an alternative type of conformation, partly consistent with experiment, the amino terminus is neutral and the guanidinium group inserts into the crown ether cavity. In the +2 complexes, arginine is always doubly protonated and the most stable conformations are characterized by a tripodal coordination of the ammonium -NH3+ group of arginine with the oxygen atoms of the macrocycle ring, while the interactions of the amino acid with the side carboxylic acid groups of the crown ether acquire a remarkable lesser role.