Identification of ion pairs in solution by IR spectroscopy: crucial contributions of gas phase data and simulations

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 H2-tagged (Ca2+, AcO-)(H2O)n=8-21 clusters in the ν(CO2-) 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. Altogether, structural assignments suggest a sequence of simple reactions in the first coordination shell of the carboxylate group, leading us to propose two possible dissociation paths. The appearance threshold of monodentate structures is measured at n = 10, with that of solvent-shared ion pairs (SIPs) being potentially at n = 18. By showing in detail how solvation progressively takes over from the ionic interaction in shaping these supramolecular structures, this study can serve as a reference for solving ion-pairing/dissociation problems.

Deciphering the Effect of Microstructural Modification in Sodium Alginate-Based Solid Polymer Electrolyte by Unlike Anions

Microstructure modification in sodium alginate (NaAlg)-based solid polymer electrolytes by the perchlorate (ClO4-) and acetate (CH3COO-) anions of sodium salts has been reported. ClO4- participates in the structure-breaking effect via inter/intramolecular hydrogen bond breaking, while CH3COO- changes the amorphous phase, as evident from X-ray diffraction studies. The larger size and negative charge delocalization of ClO4- have a plasticizing effect, resulting in a lower glass transition temperature (Tg) compared to CH3COO-. Decomposition temperature is strongly dependent on the type of anion. Scanning electron microscopy images showed divergent modifications in the surface morphology in both electrolyte systems, with variations in salt content. The mechanical properties of the NaAlg-NaClO4 electrolyte systems are better than those of the NaAlg-CH3 COONa system, indicating weak interactions in the latter. Although most of the studies focus on the cation influence on conductivity, the interaction of the anion and its size certainly have an influence on the properties of solid polymer electrolytes, which will be of interest in the near future for sodium ion-based electrolytes in energy storage devices.

Stepwise hydration of [CH3COOMg]+ studied by cold ion trap infrared spectroscopy: insights into interactions in the magnesium channel selection filters

The magnesium channel controls Mg2+ concentration in the cell and plays an indispensable role in biological functions. The crystal structure of the Magnesium Transport E channel suggested that Mg2+ hydrated by 6 water molecules is transported through a selection filter consisting of COO- groups on two Asp residues. This Mg2+ motion implies successive pairing with -OOC-R and dissociation mediated by water molecules. For another divalent ion, however, it is known that RCOO-⋯Ca2+ cannot be separated even with 12 water molecules. From this discrepancy, we probe the structure of Mg2+(CH3COO-)(H2O)4-17 clusters by measuring the infrared spectra and monitoring the vibrational frequencies of COO- with the help of quantum chemistry calculations. The hydration by (H2O)6 is not enough to induce ion separation, and partially-separated or separated pairs are formed from 10 water molecules at least. These results suggest that the ion separation between Mg2+ and carboxylate ions in the selection-filter of the MgtE channel not only results from water molecules in their first hydration shell, but also from additional factors including water molecules and protein groups in the second solvation shell of Mg2+.

Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins

Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5-10 millihartrees and 5 cm-1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.

Lamellarity-Driven Differences in Surface Structural Features of DPPS Lipids: Spectroscopic, Calorimetric and Computational Study

Although single-lipid bilayers are usually considered models of eukaryotic plasma membranes, their research drops drastically when it comes to exclusively anionic lipid membranes. Being a major anionic phospholipid in the inner leaflet of eukaryote membranes, phosphatidylserine-constituted lipid membranes were occasionally explored in the form of multilamellar liposomes (MLV), but their inherent instability caused a serious lack of efforts undertaken on large unilamellar liposomes (LUVs) as more realistic model membrane systems. In order to compensate the existing shortcomings, we performed a comprehensive calorimetric, spectroscopic and MD simulation study of time-varying structural features of LUV made from 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS), whereas the corresponding MLV were examined as a reference. A substantial uncertainty of UV/Vis data of LUV from which only T_m was unambiguously determined (53.9 ± 0.8 °C), along with rather high uncertainty on the high-temperature range of DPPS melting profile obtained from DSC (≈50-59 °C), presumably reflect distinguished surface structural features in LUV. The FTIR signatures of glycerol moiety and those originated from carboxyl group serve as a strong support that in LUV, unlike in MLV, highly curved surfaces occur continuously, whereas the details on the attenuation of surface features in MLV were unraveled by molecular dynamics.

Raman Spectroscopic Studies on Aqueous Sodium Formate Solutions and DFT Calculations

NaHCOO(aq) and NaDCOO(aq) solutions were measured using Raman spectroscopy from dilute to concentrated solutions at 23 °C in water and heavy water from 50 to 4300 cm−1. A concentrated NaHCOO solution in heavy water was also measured. The Raman band parameters of HCOO−(aq) and DCOO−(aq) such as peak position, full width at half maximum (fwhm), integrated intensities, and depolarization values were determined. From the Raman spectroscopic data, it was concluded that the HCOO−(aq) and DCOO−(aq) symmetry is lower than C2v and probably as low as C1. In contrast to the solution state, $$\tt \normalsize \tt \normalsize {\text{HCO}}_{2}^{ - }$$ HCO 2 - ($$\tt \normalsize\tt\normalsize {\text{DCO}}_{2}^{ - }$$ DCO 2 - ) possess C2v symmetry in the gas phase and the DFT frequencies are given. DFT frequencies on a cluster of HCOO−/DCOO− with five implicit water molecules in the first sphere and placed in a polarizable continuum deviate not more than 1–2% from the measured ones. In the Raman spectrum in NaHCOO(aq), a band doublet at 2730 cm−1 and 2820 cm−1 occurs instead of a single band. The band doublet is due to Fermi resonance and results from the interaction of the overtone of the bending C–H mode, 2ν6 at 1382 cm−1 and ν1. The undisturbed C–H stretching mode, ν1 amounts to 2785 cm−1. In DCOO−(aq), a Fermi doublet was also observed at 2030.5 and 2116.5 cm−1, and the undisturbed wavenumber position amounts to 2101 cm−1. Furthermore, a solution of HCOO− in D2O showed slightly changed frequencies compared with the ones in water caused by the solvent isotope effect. Ion pairing between Na+ and HCOO− characterizes the Raman spectrum at high solute concentrations which are melt-like enabling direct contact between the ions. A NaHCOO solution with high amounts of LiCl added showed large perturbations of the HCOO− bands especially νsCOO− and δ COO− of HCOO−and revealed a stronger affinity of Li+ toward HCOO−. The ion pairs formed are most likely contact ion pairs between Li+ and HCOO− which have different stoichiometry of Li+: HCOO− such as 1:1 and 2:1.

Graphical Abstract

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

Microhydrated H₂-tagged ion pairs (Ca²⁺, AcO^-)(H₂O)_n=0-8 and (Ba²⁺, AcO^-)(H₂O)_n=0-5 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.

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 0.25-4.0 M concentration range displayed cation-specific behaviors, which enabled the measurement of the appearance concentration thresholds of contact ion pairs between 1.9 and 2.6 M depending on the cation. Conformational explorations performed using a non-local optimization method associated to a polarizable force-field (AMOEBA), followed by high quantum chemistry level (RI-B97-D3/dhf-TZVPP) optimizations, mode-dependent scaled harmonic frequency calculations and electron density analyses, were used to identify the main supramolecular structures contributing to the experimental spectra. A thorough analysis enables us to reveal the mechanisms responsible for the spectroscopic sensitivity of the carboxylate group and the respective role played by the cation and the water molecules, highlighting the necessity of combining advanced experimental and theoretical techniques to provide a fair and accurate description of ion pairing.

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. By investigating model alkali benzylacetate and 4-phenylbutyrate ion pairs, where the electric field applied to the phenyl ring is chemically tuned by changing the nature of the alkali cation, this work demonstrates that precise conformational assignments can be proposed based on the correlation between the conformation-dependent calculated electric fields and the frequency of the electronic transitions observed in the experimental UV spectra. Remarkably, the sole analysis of Stark effects and fragmentation patterns in mass-selected UV spectra provided an accurate and complete conformational analysis, where spectral differences as small as a few cm-1 between electronic transitions were rationalized. This case study illustrates that the identification of EI-ESE together with their interpretation at the modest cost of a ground state electric field calculation qualify UV spectroscopy as a powerful tool for conformational analysis.

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. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

In Situ Differentiation of Multiplex Noncovalent Interactions Using SERS and Chemometrics

Probing changes of noncovalent interactions is crucial to study the binding efficiencies and strengths of (bio)molecular complexes. While surface-enhanced Raman scattering (SERS) offers unique molecular fingerprints to examine such interactions in situ, current platforms are only able to recognize hydrogen bonds because of their reliance on manual spectral identification. Here, we differentiate multiple intermolecular interactions between two interacting species by synergizing plasmonic liquid marble-based SERS platforms, chemometrics, and density functional theory. We demonstrate that characteristic 3-mercaptobenzoic acid (probe) Raman signals have distinct peak shifts upon hydrogen bonding and ionic interactions with tert-butylamine, a model interacting species. Notably, we further quantify the contributions from each noncovalent interaction coexisting in different proportions. As a proof-of-concept, we detect and categorize biologically important nucleotide bases based on molecule-specific interactions. This will potentially be useful to study how subtle changes in biomolecular interactions affect their structural and binding properties.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

Electronic Stark Effect in Isolated Ion Pairs

Stark spectral shifts of a molecular probe are commonly used to estimate the local electric field in condensed media. The very large fields reported, typically in the 0.1-10 GV m^-1 range, are, however, difficult to reproduce in a controlled manner, limiting the calibration of these molecular probes to ranges below 0.1 GV m^-1. In this context, we investigated gas-phase, isolated, molecular ion pairs, where a phenyl ring is immersed in the electric field produced by the nearby ionic groups. The intensity of the electric field is chemically tuned in the 1 GV m^-1 range by changing the nature of the cations, and the phenyl ring response is monitored by UV spectroscopy. A quadratic Stark effect is observed, demonstrating the possibility to characterize molecular probes in a solvent-free environment and in the very large field range they typically meet in condensed media such as biological environments.