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.

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.

Wetting of a Hydrophobic Surface: Far-IR Action Spectroscopy and Dynamics of Microhydrated Naphthalene.

The interaction of water and polycyclic aromatic hydrocarbons is of fundamental importance in areas as diverse as materials science and atmospheric and interstellar chemistry. The interplay between hydrogen bonding and dipole-π interactions results in subtle dynamics that are challenging to describe from first principles. Here, we employ far-IR action vibrational spectroscopy with the infrared free-electron laser FELIX to investigate naphthalene with one to three water molecules.

A Dynamic Proton Bond: MH·HO ⇌ M·HO 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 HO, with increasing stability as the coordination number increases.

Nucleation of zeolitic imidazolate frameworks: from molecules to nanoparticles.

We have studied the clusters involved in the initial stages of nucleation of Zeolitic Imidazolate Frameworks, employing a wide range of computational techniques. In the pre-nucleating solution, the prevalent cluster is the ZnIm cluster (formed by a zinc cation, Zn, and four imidazolate anions, Im), although clusters such as ZnIm, ZnIm, ZnIm, ZnIm, ZnIm, or ZnIm have energies that are not much higher, so they would also be present in solution at appreciable quantities. All these species, except ZnIm, have a tetrahedrally coordinated Zn cation.

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.

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.

Proton in the ring: spectroscopy and dynamics of proton bonding in macrocycle cavities.

The proton bond is a paradigmatic quantum molecular interaction and a major driving force of supramolecular chemistry. The ring cavities of crown ethers provide an intriguing environment, promoting competitive proton sharing with multiple coordination anchors. This study shows that protons confined in crown ether cavities form dynamic bonds that migrate to varying pairs of coordinating atoms when allowed by the flexibility of the macrocycle backbone.

Tailoring the phase diagram of discotic mesogens.

The computational modelling of discotic molecules is a central topic in colloid science that is key for the smart design of a broad range of modern functional materials. This work lays out a versatile interaction model capable of exposing the rich mesogenic behaviour of discotics. A single coarse-grained spheroplatelet core framework is employed to generate a variety of pair interaction anisotropy classes, favouring specific relative orientations of the particles (stacked, side-side, crossed, T-shaped).

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.

Dynamics of coordination of HO and NH in crown ether cavities.

Crown ethers stand out for their ability to form inclusion complexes with metal cations and positively charged molecular moieties. Hydronium and ammonium interact strongly with crown ethers and potentially modulate their ionophoric activity in protic solvents and physiological environments commonly involved in (bio)technological applications. In this work, Born-Oppenheimer molecular dynamics (BOMD) computations are employed to gain insights into the coordination arrangements of HO and NH in the complexes with the native crown ethers 15-crown-5 (15c5) and 18-crown-6 (18c6).

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.

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.

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···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.

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.

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.

Stability of proton-bound clusters of alkyl alcohols, aldehydes and ketones in Ion Mobility Spectrometry.

Significant substances in emerging applications of ion mobility spectrometry such as breath analysis for clinical diagnostics and headspace analysis for food purity include low molar mass alcohols, ketones, aldehydes and esters which produce mobility spectra containing protonated monomers and proton-bound dimers. Spectra for all n- alcohols, aldehydes and ketones from carbon number three to eight exhibited protonated monomers and proton-bound dimers with ion drift times of 6.5-13.

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).

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.

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

The distinct basicity of the guanidinium side-group of arginine (Arg) sustains specific interactions involved in essential biochemical processes. The sensing of arginine is therefore key in modern biotechnology and bioanalysis. In this context, the development of molecular receptors based on crown ether building blocks has demonstrated great potential.

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

The antibiotic activity of nonactin is sustained by its ability to transport K across lipophilic phases, e.g., the cell membranes.

Benchmark Ditopic Binding of Cl and Cs by the Macrocycle Hexacyclen.

The ditopic binding of organic and inorganic anions and cations constitutes a distinct feature of polyazamacrocycles that underlies their action as intermediate docking and exchange ionophoric sites for tailored supramolecular synthesis and sensors. This work investigates the Cl and Cs complexes formed by hexacyclen (1,4,7,10,13,16-hexaazacyclooctadecane, ha18c6), a benchmark building block of ion-pair polyamine receptors. IR action spectroscopy is employed to characterize the anionic and cationic complexes under controlled environmental conditions in an ion trap.

On the ionophoric selectivity of nonactin and related macrotetrolide derivatives.

Nonactin and its analogs constitute a central class of macrocycles with an antibiotic activity closely related to their selective ionophoric behavior. In this study, we apply experimental and computational methods to revisit the specificity of cation binding and transport by three nactin variants differing in structural properties, such as the position of the ester linkages, the nature of the side groups, or the flexibility of the backbone. On the one hand, electrospray ionization mass spectrometry and infrared spectroscopy are employed to expose the selectivity of the liquid-liquid (water-chloroform) extraction of alkali cations by nonactin and to demonstrate that the cation complexes are partially hydrated in the organic phase.