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

Insights into the terahertz response of L-glutamic acid and its receptor

L-Glutamic acid (L-Glu) is a basic unit of proteins and also serves as an important neurotransmitter in the central nervous system. Its structural properties are critical for biological functions and selective receptor recognition. Although this molecule has been extensively studied, the low frequency vibrational behavior that is closely related to conformational changes and the intermolecular interactions between L-Glu and its receptors are still unclear. In this study, we acquired the fingerprint spectrum of L-Glu by using air plasma terahertz (THz) time-domain spectroscopy in the 0.5-18 THz range. The low frequency vibrational characteristics of L-Glu were investigated through density functional theory (DFT) calculations. The THz responses of the ligand binding domain of the NMDAR-L-Glu complex were studied by the ONIOM method, with a focus on discussing the normal modes and interactions of ligand L-Glu and water molecules. The results illustrate that THz spectroscopy exhibits a sensitive response to the influence of L-Glu on the structure of the NMDAR. The water molecules in proteins have various strong vibration modes in the THz band, showing specificity, diversity and complexity of vibrational behavior. There is potential for influencing and regulating the structural stability of the NMDAR-L-Glu complex through water molecules.

Boosting the Modeling of Infrared and Raman Spectra of Bulk Phase Chromophores with Machine Learning

In the field of vibrational spectroscopy simulation, hybrid approximations to Kohn-Sham density-functional theory (KS-DFT) are often considered computationally prohibitive due to the significant effort required to evaluate the exchange-correlation potential in planewave codes. In this Letter, we show that by leveraging the porting of KS-DFT on GPU and incorporating machine-learning techniques, simulating IR and Raman spectra of real-life chromophores in bulk aqueous solution becomes a routine application at this level of theory.

Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers

Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.

Conformational Mapping, Interactions, and Fluorine Impact by Combined Spectroscopic Approaches and Quantum Chemical Calculations

Noncovalent interactions and their careful variation can be crucial in understanding molecular structures, conformational topographies, and properties. Here, we examine the fluorination impact on the structure and conformational behavior of 2-(2-fluorophenyl)ethyl alcohol (2-FPEAL) by monitoring the first individual ionization-loss-stimulated Raman spectra of the jet-cooled molecule. The comparison of two different broad-range spectra and predicted equivalents discloses two distinct structures. One possesses a folded side chain (gauche) and the other an extended chain (anti) with the terminal hydrogen atom pointing opposite or toward the fluorine side, indicating the improper previous tentative assignment of the latter. These conformers resemble and differ from the nonfluorinated analogue structures. Theoretical analyses reveal interconversion pathways of 2-FPEAL conformers during expansion and the delicate balance between attractive (C-H···F and O-H···π) and repulsive interactions. These findings show the achievements of our integrated approach, suggesting its potential for overcoming future structural challenges.

Searching low-energy conformers of neutral and protonated di-, tri-, and tetra-glycine using first-principles accuracy assisted by the use of neural network potentials

In the last ten years, combinations of state-of-the-art gas-phase spectroscopies and quantum chemistry calculations have suggested several intuitive trends in the structure of small polypeptides that may not hold true. For example, the preference for the cis form of the peptide bond and multiple protonated sites was proposed by comparing experimental spectra with low-energy minima obtained from limited structural sampling using various density functional theory methods. For understanding the structures of polypeptides, extensive sampling of their configurational space with high-accuracy computational methods is required. In this work, we demonstrated the use of deep-learning neural network potential (DL-NNP) to assist in exploring the structure and energy landscape of di-, tri-, and tetra-glycine with the accuracy of high-level quantum chemistry methods, and low-energy conformers of small polypeptides can be efficiently located. We hope that the structures of these polypeptides we found and our preliminary analysis will stimulate further experimental investigations.

The infrared absorption spectrum of phenylacetylene and its deuterated isotopologue in the mid- to far-IR

Anharmonicity strongly influences the absorption and emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules. Here, IR-UV ion-dip spectroscopy experiments together with detailed anharmonic computations reveal the presence of fundamental, overtone, as well as 2- and 3-quanta combination band transitions in the far- and mid-infrared absorption spectra of phenylacetylene and its singly deuterated isotopologue. Strong absorption features in the 400-900 cm-1 range originate from CH(D) in-plane and out-of-plane wags and bends, as well as bending motions including the C≡C and CH bonds of the acetylene substituent and the aromatic ring. For phenylacetylene, every absorption feature is assigned either directly or indirectly to a single or multiple vibrational mode(s). The measured spectrum is dense, broad, and structureless in many regions but well characterized by computations. Upon deuteration, large isotopic shifts are observed. At frequencies above 1500 cm-1 for d1-phenylacetylene, a one-to-one match is seen when comparing computations and experiments with all features assigned to combination bands and overtones. The C≡C stretch observed in phenylacetylene is not observed in d1-phenylacetylene due to a computed 40-fold drop in intensity. Overall, a careful treatment of anharmonicity that includes 2- and 3-quanta modes is found to be crucial to understand the rich details of the infrared spectrum of phenylacetylene. Based on these results, it can be expected that such an all-inclusive anharmonic treatment will also be key for unraveling the infrared spectra of PAHs in general.

Efficient Prediction of Mole Fraction Related Vibrational Frequency Shifts

While so far it has been possible to calculate vibrational spectra of mixtures at a particular composition, we present here a novel cluster approach for a fast and robust calculation of mole fraction dependent infrared and vibrational circular dichroism spectra at the example of acetonitrile/(R)-butan-2-ol mixtures. By assigning weights to a limited number of quantum chemically calculated clusters, vibrational spectra can be obtained at any desired composition by a weighted average of the single cluster spectra. In this way, peak positions carrying information about intermolecular interactions can be predicted. We show that mole fraction dependent peak shifts can be accurately modeled and, that experimentally recorded infrared spectra can be reproduced with high accuracy over the entire mixing range. Because only a very limited number of clusters is required, the presented approach is a valuable and computationally efficient tool to access mole fraction dependent spectra of mixtures on a routine basis.

Design and characterization of an optical-fiber-coupled laser-induced desorption source for gas-phase dynamics experiments

Preparation of neutral non-volatile molecules intact in the gas phase for mass spectrometry or chemical dynamics experiments remains a challenge for many classes of molecules. Here, we report the design and characterization of a fiber-coupled laser-based thermal desorption source capable of preparing intact neutral molecules at high molecular densities in the gas phase for use in velocity-map imaging experiments. Within this source, the sample is deposited onto a thin tantalum foil. Irradiation of the foil from the reverse side by a focused laser beam leads to highly localized heating of the sample, resulting in desorption of a plume of molecules into the gas phase. The fiber-coupled design simplifies the alignment of the desorption laser beam, and the ability to rotate the foil relative to the fixed laser beam allows the sample to be continually refreshed under vacuum. We use 118 nm photoionization of three test molecules-uracil, adenine, and phenylalanine-to characterize the source and to demonstrate various aspects of its performance. These include the dependence of the velocity-map imaging performance on the size of the interaction region and the dependence of the laser-induced desorption source emission on desorption laser power and heating time. Signal levels recorded in these measurements are comparable to those we typically obtain in similar experiments using a pulsed supersonic molecular beam, and we, therefore, believe that the source has considerable potential for use in a wide range of chemical dynamics and other experiments.

DFT and ab initio molecular dynamics simulation study of the infrared spectrum of the protic ionic liquid 2-hydroxyethylammonium formate

Protic ionic liquids (PILs) typically show a complex band shape in their infrared (IR) spectra in the high-frequency range due to the hydrogen stretching vibrations of functional groups forming rather strong hydrogen bonds (H-bonds). In the low-frequency range, the intermolecular stretching mode of the H-bond leaves a mark in the far-IR spectrum of PILs. In this study, the IR spectrum of the PIL 2-hydroxyethylammonium formate, [HOCH2CH2NH3][HCOO], is investigated in order to identify the different modes that contribute to the high-frequency band shape, i.e. the cation ν(NH), ν(OH), and ν(CH) modes, and the anion ν(CH) mode, as well as the intermolecular mode of the strongest H-bond in the far-IR spectrum. The assignment is validated by quantum chemistry calculations of clusters at the density functional theory (DFT) level for four ionic pairs and by ab initio molecular dynamics (AIMD) simulations of ten ionic pairs. There is good agreement between the vibrational frequencies obtained from DFT and AIMD simulations for both the high- and low-frequency ranges. Based on the calculations, the strong H-bond interaction between the cation -NH3 group and [HCOO]- gives a broad band envelope associated with the ν(NH) mode in the high-frequency range of the IR spectrum on which there are narrower peaks corresponding to the ν(OH) and ν(CH) modes. In the far-IR (FIR) spectrum, the anions' rattling motion gives a broad feature with a maximum at 160 cm-1, while the H-bond's intermolecular NH⋯O stretching mode appears as a peak at 255 cm-1.

Synergistic Spectroscopic and Computational Characterization Evidencing the Preservation or Flipping of the Hydroxyl Group of 2-Phenylethyl Alcohol upon Single and Double Hydration

Even apparently simple, obtaining and analyzing observations on molecules and clusters and unambiguously assigning their structures is challenging. We report here the first ionization-loss Raman spectra compared to quantum chemical predictions for establishing the structural preferences of hydrates of the neurotransmitters hydroxy analogue, 2-phenylethyl alcohol (PEAL). The spectra encode two monohydrates and two previously unnoticed dihydrates, consequences of water insertion and sidewise attachment to the O-H group of gauche PEALs, in PEAL-H2O and PEAL-(H2O)2, or the higher-energy gauche-trans PEAL in the latter. The electronic structures retain the stable PEAL or flip its O-H to convert the gauche-trans PEAL conformer to the global minimum-energy dihydrate. We disclose conventional and bifurcated hydrogen bonds and electron steric repulsions by noncovalent interaction analysis and correlations between the experimental O-H stretching vibrational frequencies and the O-H and H···X bond lengths and electron densities, pointing to implications on hydrate forms and our approach virtue.

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.

FTIR study on the CO interactions of benzeneacetamide in solution

The main attention of present work is to study how benzeneacetamide interacts with other molecules in organic solvents. The frequencies of CO groups in 18 solvents were obtained by using infrared spectroscopy. The empirical parameters of the solvents as the acceptor number (AN), the van der Waals interaction parameters (S_VW) and the linear solvation energy relationships (LSER) were correlated with the frequencies of carbonyl stretching vibration (ν(CO)) of benzeneacetamide to estimate the contributions in intermolecular interactions. The results showed that solvent effects on the frequencies of CO stretching vibrations of benzeneacetamide were obvious. Self-association of alkanol leads to enhancement of O-H⋯O=C hydrogen bond strength and red-shift of the ν(CO) peak. The ν(CO) of benzeneacetamide is more vulnerable to the acidity of the hydrogen bond donor of the solvent. This research contributes to a thorough understanding of the molecular interactions and microstructures in the liquid mixtures.

Ionization energies and ionization-induced structural changes in 2-phenylethylamine and its monohydrate

We report the resonance-enhanced two-photon ionization combined with various detection approaches and quantum chemical calculations of biologically relevant neurotransmitter prototypes, the most stable conformer of 2-phenylethylamine (PEA), and its monohydrate, PEA-H₂O, to reveal the possible interactions between the phenyl ring and amino group in the neutral and ionic species. Extracting the ionization energies (IEs) and appearance energy was achieved by measuring the photoionization and photodissociation efficiency curves of the PEA parent and photofragment ions, together with velocity and kinetic energy-broadened spatial map images of photoelectrons. We obtained coinciding upper bounds for the IEs for PEA and PEA-H₂O of 8.63 ± 0.03 and 8.62 ± 0.04 eV, within the range predicted by quantum calculations. The computed electrostatic potential maps show charge separation, corresponding to a negative charge on phenyl and a positive charge on the ethylamino side chain in the neutral PEA and its monohydrate; in the cations, the charge distributions naturally become positive. The significant changes in geometries upon ionization include switching of the amino group orientation from pyramidal to nearly planar in the monomer but not in the monohydrate, lengthening of the N-H⋯π hydrogen bond (HB) in both species, C_α-C_β bond in the side chain of the PEA⁺ monomer, and the intermolecular O-H⋯N HB in PEA-H₂O cations, leading to distinct exit channels.

Influence of the environment on the infrared spectrum of alanine: An effective mode analysis

The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000-2000 cm^-1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.

Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble

Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.

Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures

Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this work, we address the challenging task of efficiently sampling realistic low-lying peptide coordinates by resorting to a surrogate based genetic algorithm (GA)/density functional theory (DFT) approach (sGADFT) in which promising candidates provided by the GA are ultimately optimized with DFT. We provide a benchmark of several computational methods (GAFF, AMOEBApro13, PM6, PM7, DFTB3-D3(BJ)) as possible prescanning surrogates and apply sGADFT to two test case systems that are (i) two isomer families of the protonated Gly-Pro-Gly-Gly tetrapeptide (Masson, A.; J. Am. Soc. Mass Spectrom.2015, 26, 1444-1454) and (ii) the doubly protonated cyclic decapeptide gramicidin S (Nagornova, N. S.; J. Am. Chem. Soc.2010, 132, 4040-4041). We show that our GA procedure can correctly identify low-energy minima in as little as a few hours. Subsequent refinement of surrogate low-energy structures within a given energy threshold (≤10 kcal/mol (i), ≤5 kcal/mol (ii)) via DFT relaxation invariably led to the identification of the most stable structures as determined from high-resolution infrared (IR) spectroscopy at low temperature. The sGADFT method therefore constitutes a highly efficient route for the screening of realistic low-lying peptide structures in the gas phase as needed for instance for the interpretation and assignment of experimental IR spectra.

Hydration dynamics and IR spectroscopy of 4-fluorophenol

Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of para-fluorophenol (F-PhOH) and phenol (PhOH) is investigated in the gas phase and in water using a combination of experiment and molecular dynamics (MD) simulations. The gas phase and solvent dynamics around F-PhOH and PhOH is characterized from atomistic simulations using empirical energy functions with point charges or multipoles for the electrostatics, Machine Learning (ML) based parametrizations and with full ab initio (QM) and mixed Quantum Mechanical/Molecular Mechanics (QM/MM) simulations with a particular focus on the CF- and OH-stretch region. The CF-stretch band is heavily mixed with other modes whereas the OH-stretch in solution displays a characteristic high-frequency peak around 3600 cm-1 most likely associated with the -OH group of PhOH and F-PhOH together with a characteristic progression below 3000 cm-1 due to coupling with water modes which is also reproduced by several of the simulations. Solvent and radial distribution functions indicate that the CF-site is largely hydrophobic except for simulations using point charges which renders them unsuited for correctly describing hydration and dynamics around fluorinated sites. The hydrophobic character of the CF-group is particularly relevant for applications in pharmaceutical chemistry with a focus on local hydration and interaction with the surrounding protein.

Stacking Is Favored over Hydrogen Bonding in Azaphenanthrene Dimers

N-Doped polycyclic aromatic hydrocarbons have recently emerged as potential organic electronic materials. The function of such materials is determined not only by the intrinsic electronic properties of individual molecules but also by their supramolecular interactions in the solid state. Therefore, a proper characterization of the interactions between the individual units is of interest to materials science since they ultimately govern properties such as excitons and charge transfer. Here, we report a joint experimental and computational study of two azaphenanthrene dimers to determine the structure and the nature of supramolecular interactions in the aggregates. IR/UV double-resonance experiments were carried out using far- and mid-infrared free-electron laser radiation. The experimental spectra are compared with quantum chemical calculations for the lowest-energy π-stacked and hydrogen-bonded structures. The data reveal a preference of the π-stacked structure for the benzo[f]quinoline and the phenanthridine dimer.

Do Stereochemical Effects Overcome a Charge-Induced Perturbation in Isolated Protonated Cyclo(Tyr-Tyr)?

Two diastereomers of the protonated diketopiperazine (DKP) dipeptide cyclo(Tyr-Tyr), namely, cyclo(LTyr-LTyr)H⁺ and cyclo(LTyr-DTyr)H⁺, are studied in a cryogenic ion trap by means of IR photodissociation spectroscopy combined with quantum chemical calculations. The two diastereomers have similar structures in which one of the rings is folded over the DKP ring and the other one is extended in a trans geometry, allowing a strong OH⁺···π interaction to take place. This contrasts to the observation of a stacked geometry for neutral cyclo(LTyr-LTyr) only under supersonic expansion conditions that do not exist for cyclo(LTyr-DTyr). In the protonated form, the strength of the OH⁺···π interaction is different for the two diastereomers, resulting in a ∼110 cm^-1 difference in the ν(OH⁺) frequency and a smaller but clearly identifiable difference in the protonated amide ν(NH) frequency. Stereochemical effects are therefore still evidenced despite the strong perturbation due to the excess charge.

How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer

The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.

Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides

Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 2₇-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.

Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry and artificial intelligence: the puzzling case of homocysteine

An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm. In this step, last generation semiempirical methods are exploited together with hybrid and double-hybrid density functionals. Next, the barriers ruling the interconversion between the low-lying conformers are evaluated in order to unravel possible fast relaxation paths. The relative stabilities and spectroscopic parameters of the ``surviving' conformers are then refined using state-of-the-art composite schemes. The reliability of the computational procedure is further improved by the inclusion of vibrational and thermal effects. The final step of the strategy is the comparison between experiment and theory without any ad hoc adjustment, which allows an unbiased assignment of the spectroscopic features in terms of different conformers and their spectroscopic parameters. The proposed approach has been tested and validated for homocysteine, a highly flexible non-proteinogenic alpha-amino acid. The synergism of the integrated strategy allowed the characterization of five conformers stabilized by bifurcated N-H-O=C hydrogen bonds, together with an additional conformer involving a more conventional HNH-O hydrogen bond. The stability order estimated from the experimental intensities as well as the number and type of conformers observed in the gas phase are in full agreement with the theoretical predictions. Analogously, a good match has been found for the spectroscopic parameters.

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.

Experimental/Computational Study on the Impact of Fluorine on the Structure and Noncovalent Interactions in the Monohydrated Cluster of ortho-Fluorinated 2-Phenylethylamine

Fluorine-containing medicinal compounds frequently allow modulation of physical-chemical properties. Here, we address the effect of fluorine, near the ethylamino side chain, on conformational flexibility and noncovalent interactions (NCIs) of the selected jet-cooled monohydrated cluster of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) by mass-selected resonance-enhanced two-photon ionization and ionization-loss stimulated Raman spectroscopies. Our results show that Raman spectral signatures of the 2-FPEA-H₂O cluster match the scaled harmonic vibrational Raman frequencies, resulting from density functional theory calculations of the most stable 2-FPEA gauche conformer hydrogen-bonded (HB) to water, confirming the three-dimensional cluster structure. This predicted electronic structure, together with NCI analysis, allows visualization and assessment of the attractive and repulsive interactions. The comparison of the NCIs and revealed red (O-H and N-H stretches) and blue shifts (C-H stretches and CH₂ out-of-plane bends) of the cluster to other class members confirm O-H···N, N-H···π, C-H···O, and C-H···F HB formation and their contribution to structure stabilization, uncovering the potential of the approach.

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.

Investigating Membrane‐Mediated Antimicrobial Peptide Interactions with Synchrotron Radiation Far‐Infrared Spectroscopy

Synchrotron radiation‐based Fourier transform infrared spectroscopy enables access to vibrational information from mid over far infrared to even terahertz domains. This information may prove critical for the elucidation of fundamental bio‐molecular phenomena including folding‐mediated innate host defence mechanisms. Antimicrobial peptides (AMPs) represent one of such phenomena. These are major effector molecules of the innate immune system, which favour attack on microbial membranes. AMPs recognise and bind to the membranes whereupon they assemble into pores or channels destabilising the membranes leading to cell death. However, specific molecular interactions responsible for antimicrobial activities have yet to be fully understood. Herein we probe such interactions by assessing molecular specific variations in the near‐THz 400–40 cm⁻¹ range for defined helical AMP templates in reconstituted phospholipid membranes. In particular, we show that a temperature‐dependent spectroscopic analysis, supported by 2D correlative tools, provides direct evidence for the membrane‐induced and folding‐mediated activity of AMPs. The far‐FTIR study offers a direct and information‐rich probe of membrane‐related antimicrobial interactions.

Setting up the HyDRA blind challenge for the microhydration of organic molecules

The procedure leading to the first HyDRA blind challenge for the prediction of water donor stretching vibrations in monohydrates of organic molecules is described. A training set of 10 monohydrates...

Revealing the Structure and Noncovalent Interactions of Isolated Molecules by Laser-Desorption/Ionization-Loss Stimulated Raman Spectroscopy and Quantum Calculations

The structural and dynamical characteristics of isolated molecules are essential, yet obtaining this information is difficult. We demonstrate laser-desorption jet-cooling/ionization-loss stimulated Raman spectroscopy to obtain Raman spectral signatures of nonvolatile molecules in the gas phase. The vibrational features of a test substance, the most abundant conformer of tryptamine, are compared and found to match those resulting from the scaled harmonic Raman spectrum obtained by density functional theory calculations. The vibrational signatures serve to identify the most prominent gauche conformer and evaluate its predicted electronic structure. These findings, together with noncovalent interaction (NCI) analysis, provide new insights into electron densities and reduced density gradients, assessing the hydrogen bonds (N-H···π and C-H···H-C) and interplay between attractive and repulsive NCIs affecting the structure. This approach accesses vibrational signatures of isolated nonvolatile molecules by tabletop lasers at uniform resolution and in a broad frequency range, promising great benefit to future studies.

Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go

We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.

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.

A New Solid-State Proton Conductor: The Salt Hydrate Based on Imidazolium and 12-Tungstophosphate

We report the structure and charge transport properties of a novel solid-state proton conductor obtained by acid–base chemistry via proton transfer from 12-tungstophosphoric acid to imidazole. The resulting material (henceforth named Imid₃WP) is a solid salt hydrate that, at room temperature, includes four water molecules per structural unit. To our knowledge, this is the first attempt to tune the properties of a heteropolyacid-based solid-state proton conductor by means of a mixture of water and imidazole, interpolating between water-based and ionic liquid-based proton conductors of high thermal and electrochemical stability. The proton conductivity of Imid₃WP·4H₂O measured at truly anhydrous conditions reads 0.8 × 10^–6 S cm^–1 at 322 K, which is higher than the conductivity reported for any other related salt hydrate, despite the lower hydration. In the pseudoanhydrous state, that is, for Imid₃WP·2H₂O, the proton conductivity is still remarkable and, judging from the low activation energy (E_a = 0.26 eV), attributed to structural diffusion of protons. From complementary X-ray diffraction data, vibrational spectroscopy, and solid-state NMR experiments, the local structure of this salt hydrate was resolved, with imidazolium cations preferably orienting flat on the surface of the tungstophosphate anions, thus achieving a densely packed solid material, and water molecules of hydration that establish extremely strong hydrogen bonds. Computational results confirm these structural details and also evidence that the path of lowest energy for the proton transfer involves primarily imidazole and water molecules, while the proximate Keggin anion contributes with reducing the energy barrier for this particular pathway.

Broadband terahertz signatures and vibrations of dopamine

Dopamine (DA) is an essential neurotransmitter and hormone of the nervous system, its structural and conformational properties play critical roles in biological functions and signal transmission processes. Although this neuroactive molecule has been studied extensively, the low-frequency vibration features that are closely related to the conformation and molecular interactions in the terahertz (THz) band still remain unclear. In this study, a broadband THz time-domain spectroscopy (THz-TDS) system in the frequency band of 0.5-18 THz was used to characterize the unique THz fingerprint of DA. In addition, density functional theory (DFT) calculations were performed to analyze the vibrational properties of DA. The results suggest that each THz resonant absorption peak of DA corresponds to specific vibrational modes, and the collective vibration also exists in the broadband THz range. Moreover, the interactions between the DA ligand and the D2 and D3 receptors were investigated by docking, and the simulated THz spectra were obtained. The results indicate the dominant role of hydrogen bonding interactions and the specificity of molecular conformation. This work may help to understand the resonance coupling between THz electromagnetic waves and neurotransmitters.

My Trajectory in Molecular Reaction Dynamics and Spectroscopy

This is the story of a career in theoretical chemistry during a time of dramatic changes in the field due to phenomenal growth in the availability of computational power. It is likewise the story of the highly gifted graduate students and postdoctoral fellows that I was fortunate to mentor throughout my career. It includes reminiscences of the great mentors that I had and of the exciting collaborations with both experimentalists and theorists on which I built much of my research. This is an account of the developments of exciting scientific disciplines in which I was involved: vibrational spectroscopy, molecular reaction mechanisms and dynamics, e.g., in atmospheric chemistry, and the prediction of new, exotic molecules, in particular noble gas molecules. From my very first project to my current work, my career in science has brought me the excitement and fascination of research. What a wonderful pursuit!

Ultra-broadband terahertz fingerprint spectrum of melatonin with vibrational mode analysis

Melatonin (MLT), as a neurotransmitter and an endogenous neurohormone, plays an important role in physiological functions through interactions with specific receptors. The conformations of MLT are closely related to its biological activities and functions. However, the internal relationship between the structure and interaction of MLT and its allosteric transition remains unclear. In this work, we obtain the broadband fingerprint terahertz (THz) spectrum of MLT in the range of 0.5-18 THz using the air-plasma terahertz time-domain spectroscopy (THz-TDS) system. DFT calculations are employed to analyze the vibration characteristics of MLT. The result shows that the low-frequency vibrations mainly come from the strong coupling between inter- and intramolecular vibrations, and the contribution of intramolecular vibrations gradually dominates with increasing frequency. Meanwhile, the local vibrations of the different functional groups distribute widely in the THz low-frequency band, relating to the diversity of conformational changes in the molecule. The intermolecular hydrogen bonds (HBs) have distinct resonant responses and play critical roles in the THz low-frequency vibrations. The study reveals the complex characteristics of the resonant coupling of MLT with THz electromagnetic waves. The results will help to understand the conformational preferences of MLT in neural signal transmission processes.

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.

Far-IR Absorption of Neutral Polycyclic Aromatic Hydrocarbons (PAHs): Light on the Mechanism of IR-UV Ion Dip Spectroscopy

Gas-phase IR-UV double-resonance laser spectroscopy is an IR absorption technique that bridges the gap between experimental IR spectroscopy and theory. The IR experiments are used to directly evaluate predicted frequencies and potential energy surfaces as well as to probe the structure of isolated molecules. However, a detailed understanding of the underlying mechanisms is, especially in the far-IR regime, still far from complete, even though this is crucial for properly interpreting the recorded IR absorption spectra. Here, events occurring upon excitation to vibrational levels of polycyclic aromatic hydrocarbons by far-IR radiation from the FELIX free electron laser are followed using resonance-enhanced multiphoton ionization spectroscopy. These studies provide detailed insight into how ladder climbing and anharmonicity influence IR-UV spectroscopy and therefore the resulting IR signatures in the far-IR region. Moreover, the potential energy surfaces of these low-frequency delocalized modes are investigated and shown to have a strong harmonic character.

Crucial effect of transverse vibrations on the transport through polymer chains

The low temperature transport of electron, or vibrational or electronic exciton toward polymer chains, turns out to be dramatically sensitive to its interaction with transverse acoustic vibrations. We show that this interaction leads to a substantial polaron effect and decoherence, which are generally stronger than those associated with longitudinal vibrations. For site-dependent interactions, transverse phonons form subohmic bath leading to the quantum phase transition accompanied by full suppression of the transport at zero temperature and fast decoherence characterized by temperature dependent rate k₂ ∝ T^3/4 at low temperature, while k₂ ∝ T² for site-independent interactions. The latter dependence was used to interpret recent measurements of temperature dependent vibrational energy transport in polyethylene glycol oligomers.