Vibrational signatures of dynamic excess proton storage between primary amine and carboxylic acid groups

Ammonium and carboxylic moieties play a central role in proton-mediated processes of molecular recognition, charge transfer or chemical change in (bio)materials. Whereas both chemical groups constitute acid-base pairs in organic salt-bridge structures, they may as well host excess protons in acidic environments. The binding of excess protons often precedes proton transfer reactions and it is therefore of fundamental interest, though challenging from a quantum chemical perspective. As a benchmark for this process, we investigate proton storage in the amphoteric compound 5-aminovaleric acid (AV), within an intramolecular proton bond shared by its primary amine and carboxylic acid terminal groups. Infrared ion spectroscopy is combined with ab initio Molecular Dynamics (AIMD) calculations to expose and rationalize the spectral signatures of protonated AV and its deuterated isotopologues. The dynamic character of the proton bond confers a fluxional structure to the molecular framework, leading to wide-ranging bands in the vibrational spectrum. These features are reproduced with remarkable accuracy by AIMD computations, which serves to lay out microscopic insights into the excess proton binding scenario.

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.

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 FE_CO 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 FE_CO 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.

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.

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

The recognition of adenosine monophosphate (AMP) by arginine-rich proteins is conditioned by the competitive binding of the guanidinium side group with metal cations, as derived from vibrational spectroscopy and modelling of mimetic complexes.

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

Small cations (K⁺, NH₄⁺) occupy the center of the valinomycin cavity. Bulkier cations like H₄PO₄⁺ stretch the valinomycin backbone, which adopts barrel-like and funnel-like configurations, depending on the dynamically varying position of the cation.

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 4aβ. 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 NH^δ+···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 NH2+ 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 NH^δ+ 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.

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.

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.

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

The binding of arginine by the 18-crown-6 tetracarboxylic ionophore relies on extensive host–guest redistribution of electronic charge and proton transfer.

Isolated complexes of the amino acid arginine with polyether and polyamine macrocycles, the role of proton transfer

Protonated arginine interacts with 12-crown-4 through the guanidinium side group. In the complex with the N-substituted analog cyclen, the dominant conformation is the result of the proton transfer from the carboxylic acid group of the amino acid to the macrocycle.

Supramolecular organization of perfluorinated 1H-indazoles in the solid state using X-ray crystallography, SSNMR and sensitive (VCD) and non sensitive (MIR, FIR and Raman) to chirality vibrational spectroscopies

The determination of the AC of three perfluorinated 1H-indazoles that resolve spontaneously as conglomerates.

Isolated alkali cation complexes of the antibiotic ionophore nonactin: correlation with crystalline structures

The stabilization of the nonactin–Na⁺ complex in a S₄ or C₂ conformation constitutes a challenging benchmark for experimental and modelling methods.

On the ionophoric selectivity of nonactin and related macrotetrolide derivatives

Microhydration determines the cation affinities of nactin macrocyles in aqueous–organic extraction processes.

Deducing the molecular properties of zwitterionic, protonated, deprotonated, and double-deprotonated forms of L-cysteine from vibrational spectroscopy (IR, Raman, VCD) and quantum chemical calculations

The behavior of L-cysteine (C3H7NO2S, (2R)-2-amino-3-sulfanylpropanoic acid) in water at different pH values was analyzed both experimentally and theoretically. The behavior was studied at pH values of 5.21 (at this pH, L-cysteine is a zwitterionic species), 1.00 (protonated species), 8.84 (monodeprotonated species), and 13.00 (dideprotonated species). We carried out a vibrational study using nonchiroptical (IR-Raman) and chiroptical (VCD) techniques complemented by quantum chemical calculations. We adopted a dual strategy, as follows. (i) The hybrid density functionals B3LYP and M062X and the ab initio MP2 method were employed, with the same 6-311++G (d,p) basis set, in order to characterize the relative energies and structures of an extensive set of conformers of L-cysteine. The presence of water was included by utilizing the IEF-PCM implicit solvation model. (ii) The vibrational analysis was made using a chirality-sensitive using a chirality-sensitive technique (VCD) and chirality-insensitive techniques (IR, including MIR and FIR, and Raman), especially in aqueous solution. The results obtained theoretically and experimentally were compared in order to deduce the most stable structures at each pH. Moreover, for the first time, the monodeprotonated anion of L-cysteine was detected in aqueous solution by means of IR, Raman and vibrational circular dichroism (VCD). Finally, analysis of the low-frequency region using the IR and Raman techniques was shown to be a very important way to understanding the conformational preference of the zwitterionic species.

Conformational preference and chiroptical response of carbohydrates D-ribose and 2-deoxy-D-ribose in aqueous and solid phases

This work targets the structural preferences of D-ribose and 2-deoxy-D-ribose in water solution and solid phase. A theoretical DFT (B3LYP and M06-2X) and MP2 study has been undertaken considering the five possible configurations (open-chain, α-furanose, β-furanose, α-pyranose, and β-pyranose) of these two carbohydrates with a comparison of the solvent treatment using only a continuum solvation model (PCM) and the PCM plus one explicit water molecule. In addition, experimental vibrational studies using both nonchiroptical (IR-Raman) and chiroptical (VCD) techniques have been carried out. The theoretical and experimental results show that α- and β-pyranose forms are the dominant configurations for both compounds. Moreover, it has been found that 2-deoxy-D-ribose presents a non-negligible percentage of open-chain forms in aqueous solution, while in solid phase this configuration is absent.