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. We observe diffuse bands associated with intermolecular vibrational modes that serve as direct probes of the loose binding of water to the naphthalene surface. These signatures are poorly reproduced by static DFT or Møller-Plesset computations. Instead, a rationalization is achieved through Born-Oppenheimer Molecular Dynamics simulations, revealing the active mobility of water over the surface, even at low temperatures. Therefore, our work provides direct insights into the wetting interactions associated with shallow potential energy surfaces while simultaneously demonstrating a solid experimental-computational framework for their investigation.

Photodissociative decay pathways of the flavin mononucleotide anion and its complexes with tryptophan and glutamic acid

Flavin mononucleotide (FMN) is a highly versatile biological chromophore involved in a range of biochemical pathways including blue-light sensing proteins and the control of circadian rhythms. Questions exist about the effect of local amino acids on the electronic properties and photophysics of the chromophore. Using gas-phase anion laser photodissociation spectroscopy, we have measured the intrinsic electronic spectroscopy (3.1-5.7 eV) and accompanying photodissociative decay pathways of the native deprotonated form of FMN, i.e. [FMN-H]- complexed with the amino acids tryptophan (TRP) and glutamic acid (GLU), i.e. [FMN-H]-·TRP and [FMN-H]-·GLU, to investigate the extent to which these amino acids perturb the electronic properties and photodynamics of the [FMN-H]- chromophore. The overall photodepletion profiles of [FMN-H]-·TRP and [FMN-H]-·GLU are similar to that of the monomer, revealing that amino acid complexation occurs without significant spectral shifting of the [FMN-H]- electronic excitations over this region. Both [FMN-H]-·TRP and [FMN-H]-·GLU are observed to decay by non-statistical photodecay pathways, although the behaviour of [FMN-H]-·TRP is closer to statistical fragmentation. Long-lived FMN excited states (triplet) are therefore relatively quenched when TRP binds to [FMN-H]-. Importantly, we find that [FMN-H]-, [FMN-H]-·TRP and [FMN-H]-·GLU all decay predominantly via electron detachment following photoexcitation of the flavin chromophore, with amino acid complexation appearing not to inhibit this decay channel. The strong propensity for electron detachment is attributed to excited-state proton transfer within FMN, with proton transfer from a ribose alcohol to the phosphate preceding electron detachment.

The First Cu(I)-Peptoid Complex: Enabling Metal Ion Stability and Selectivity via Backbone Helicity

Stabilization of Cu(I) is ubiquitous within native copper proteins. Understanding how to stabilize Cu(I) within synthetic biomimetic systems is therefore desired towards biological applications. Peptoids are an important class of peptodomimetics, that can bind metal ions and stabilize them in their high oxidation state. Thus, to date, they were not used for Cu(I) binding. Here we show how the helical peptoid hexamer, having two 2,2'-bipyridine (Bipy) groups that face the same side of the helix, forms the intramolecular air stable Cu(I) complex. Further study of the binding site by rigorous spectroscopic techniques suggests that Cu(I) is tetracoordinated, binding to only three N atoms from the Bipy ligands and to the N-terminus of the peptoid's backbone. A set of control peptoids and experiments indicates that the Cu(I) stability and selectivity are dictated by the intramolecular binding, forced by the helicity of the peptoid, which can be defined as the second coordination sphere of the metal center.

UV-vis spectroscopy of gas-phase ions

Photodissociation action spectroscopy has made a great progress in expanding investigations of gas-phase ion structures. This review deals with aspects of gas-phase ion electronic excitations that result in wavelength-dependent dissociation and light emission via fluorescence, chiefly covering the ultraviolet and visible regions of the spectrum. The principles are briefly outlined and a few examples of instrumentation are presented. The main thrust of the review is to collect and selectively present applications of UV-vis action spectroscopy to studies of stable gas-phase ion structures and combinations of spectroscopy with ion mobility, collision-induced dissociation, and ion-ion reactions leading to the generation of reactive intermediates and electronic energy transfer.

Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy

Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.

Functional Nano-Objects by Electrostatic Self-Assembly: Structure, Switching, and Photocatalysis

The design of functional nano-objects by electrostatic self-assembly in solution signifies an emerging field with great potential. More specifically, the targeted combination of electrostatic interaction with other effects and interactions, such as the positioning of charges on stiff building blocks, the use of additional amphiphilic, π−π stacking building blocks, or polyelectrolytes with certain architectures, have recently promulgated electrostatic self-assembly to a principle for versatile defined structure formation. A large variety of architectures from spheres over rods and hollow spheres to networks in the size range of a few tenths to a few hundred nanometers can be formed. This review discusses the state-of-the-art of different approaches of nano-object formation by electrostatic self-assembly against the backdrop of corresponding solid materials and assemblies formed by other non-covalent interactions. In this regard, particularly promising is the facile formation of triggerable structures, i.e. size and shape switching through light, as well as the use of electrostatically assembled nano-objects for improved photocatalysis and the possible solar energy conversion in the future. Lately, this new field is eliciting an increasing amount of understanding; insights and limitations thereof are addressed in this article. Special emphasis is placed on the interconnection of molecular building block structures and the resulting nanoscale architecture via the key of thermodynamics.

Effect of ascorbic acid and citric acid on bioavailability of iron from Tegillarca granosa via an in vitro digestion/Caco-2 cell culture system

Iron deficiency anaemia (IDA) has been receiving worldwide attention. Developing safe and effective iron supplements is of great significance for IDA treatment. Tegillarca granosa (T. granosa), a traditional aquaculture bivalve species in China, is considered to be an excellent source of micronutrients, but the distribution and bioavailability of these minerals have yet to be investigated. The present research was conducted to determine the contents and in vitro enzymatic digestibility of minerals in T. granosa, using beef and wheat flour as reference foods. Meanwhile, two iron-binding proteins, hemoglobin and ferritin, were extracted from T. granosa, and their structures, iron accessibility and bioavailability were investigated. Moreover, the effects of ascorbic acid (AA) and citric acid (CA), two commonly applied dietary factors, on these parameters were evaluated. Our results indicated that the mineral levels varied significantly among different food matrices, with T. granosa showing the highest contents of the tested elements. Comparison of iron absorption of meat versus wheat flour and hemoglobin versus ferritin confirmed that heme iron exhibited higher bioavailability than non-heme iron. The addition of the two organic acids notably enhanced the cellular iron uptake of T. granosa-derived proteins. This could be because AA/CA weakened hydrogen bonds within proteins and caused disordered secondary structures, thereby improving their enzymatic digestibility and releasing more soluble iron to be available for absorption. The results of this study provided a basis for the development of T. granosa-derived protein-based iron supplements, promoting the diverse utilization of marine aquatic resources.

Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case

The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)^MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm^-1, has been obtained by combining CCSD(T)/(CBS+CV)^MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.

Probing the formation of isolated cyclo-FF peptide clusters by far-infrared action spectroscopy

Small cyclic peptides containing phenylalanine residues are prone to aggregate in the gas phase into highly hydrophobic chains. A combination of laser desorption, mass spectrometry and conformational selective IR-UV action spectroscopy allows us to obtain detailed structural insights into the formation processes of the cyclic L-phenylalanyl-L-phenylalanine dipeptide (named cyclo-FF) aggregates. The rigid properties of cyclo-FF result in highly resolved IR spectra for the smaller clusters (n ≤ 3) and corresponding conformational assignments. For the higher order clusters (n > 3) the spectra are less resolved, however the observed ratios, peak positions and trends in IR shifts are key to make predictions on their structural details. Whereas the mid-IR spectral region between 1000-1800 cm^-1 turns out to be undiagnostic for these small aggregates and the 3 μm region only for specific calculated structures, the far-IR contains valuable information that allows for clear assignments.

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.

Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy

Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.

Chiral and Isomeric Discrimination of Chiral Molecular Ions by Cold Ion Circular Dichroism Spectroscopy

Circular dichroism (CD) spectra contain information about absolute configurations and conformations of chiral compounds. However, extracting this information from CD spectra in solution is challenging, because the spectra exhibit only the averaged CD values of all different conformers. CD spectroscopy of jet-cooled molecules can provide conformation-specific CD spectra, but its application to biomolecules has been limited due to the difficulty of their production in the gas phase. Here, we obtained the first CD spectra of chiral molecular ions produced by electrospray ionization (ESI) using cold ion CD spectroscopy. Protonated l- or d-phenylalanine ions produced by ESI were stored in a cold quadrupole ion trap and irradiated by multiple laser pulses with left or right circular polarization. The CD spectra exhibited well-resolved CD bands of two conformers, whose signs were opposite to each other. This study will broaden the scope of conformation-resolved CD spectroscopy to large molecular ions without size limitations.

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.

Formation of Neutral Peptide Aggregates as Studied by Mass-Selective IR Action Spectroscopy

The spontaneous aggregation of proteins and peptides is widely studied owing to its relation to neurodegenerative diseases. To understand the underlying principles of peptide aggregation, elucidation of structure and structural changes upon their formation is key. This level of detail can be obtained by studying the peptide self‐assembly in the gas phase. Structural characterization of aggregates is mainly done on charged species, as adding charges is an intrinsic part of the technique to bring molecules into the gas phase. Studying neutral peptide aggregates will complement the existing picture. These studies are restricted to dimers due to experimental limitations. Herein, we present advances in laser desorption molecular beam spectroscopy to form neutral peptide aggregates consisting of up to 14 monomeric peptides in the gas phase. The combination of this technique with IR–UV spectroscopy allowed us to select each aggregate by size and subsequently characterize its structure.