Accurate modeling of infrared multiple photon dissociation spectra: the dynamical role of anharmonicities

Infrared Ion Spectroscopic Characterization of the Gaseous [Co(15-crown-5)(H2O)]2+ Complex

We report fingerprint infrared multiple-photon dissociation spectra of the gaseous monohydrated coordination complex of cobalt(II) and the macrocycle 1,4,7,10,13-pentaoxacyclopentadecane (or 15-crown-5), [Co(15-crown-5)(H2O)]2+. The metal-ligand complexes are generated using electrospray ionization, and their IR action spectra are recorded in a quadrupole ion trap mass spectrometer using the free-electron laser FELIX. The electronic structure and chelation motif are derived from spectral comparison with computed vibrational spectra obtained at the density functional theory level. We focus here on the gas-phase structure, addressing the question of doublet versus quartet spin multiplicity and the chelation geometry. We conclude that the gas-phase complex adopts a quartet spin state, excluding contributions of doublet species, and that the chelation geometry is pseudo-octahedral with the six oxygen centers of 15-crown-5 and H2O coordinated to the metal ion. We also address the possible presence of higher-energy conformers based on the IR spectral evidence and calculated thermodynamics.

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.

Facial vs. meridional coordination in gaseous Ni(II)-hexacyclen complexes revealed with infrared ion spectroscopy

We report fingerprint infrared multiple-photon dissociation (IRMPD) spectra of the isolated gaseous hexa-coordinated complex of the macrocycle hexa-aza-18-crown-6 (hexacyclen, 1,4,7,10,13,16-hexaazacyclooctadecane, 18-azacrown-6) with Ni2+. The metal-ligand complexes are generated using electrospray ionization (ESI) and IR action spectra are recorded in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR) MS coupled to the infrared free-electron laser FELIX. We investigate geometric structure of the complexes and in particular the chelation motif, by comparison with computed vibrational spectra, obtained using density functional theory (DFT) at the B3LYP/6-31++G(d,p) level. The quasi-octahedral chelation motif of the complex has been well documented in condensed-phase studies, and we focus here on the gas-phase structure, addressing in particular the question of a facial (fac) versus a meridional (mer) octahedral chelation geometry. Based on the good agreement between calculated linear IR spectra and experimental IRMPD spectra, we conclude that the gas-phase complex adopts a mer chelation geometry and we exclude significant contribution of the fac isomer, which is computed to lie about 10 kJ mol-1 higher in energy. We also address the possible presence of both meridional diastereomers and of higher energy conformers of meridional isomers. Finally, as expected for the d8 Ni2+-ion in an octahedral ligand environment, the IR spectrum also shows that the complexes are in a high-spin electron configuration.

Characterization of Elusive Reaction Intermediates Using Infrared Ion Spectroscopy: Application to the Experimental Characterization of Glycosyl Cations

A detailed understanding of the reaction mechanism(s) leading to stereoselective product formation is crucial to understanding and predicting product formation and driving the development of new synthetic methodology. One way to improve our understanding of reaction mechanisms is to characterize the reaction intermediates involved in product formation. Because these intermediates are reactive, they are often unstable and therefore difficult to characterize using experimental techniques. For example, glycosylation reactions are critical steps in the chemical synthesis of oligosaccharides and need to be stereoselective to provide the desired α- or β-diastereomer. It remains challenging to predict and control the stereochemical outcome of glycosylation reactions, and their reaction mechanisms remain a hotly debated topic. In most cases, glycosylation reactions take place via reaction mechanisms in the continuum between S_N1- and S_N2-like pathways. S_N2-like pathways proceeding via the displacement of a contact ion pair are relatively well understood because the reaction intermediates involved can be characterized by low-temperature NMR spectroscopy. In contrast, the S_N1-like pathways proceeding via the solvent-separated ion pair, also known as the glycosyl cation, are poorly understood. S_N1-like pathways are more challenging to investigate because the glycosyl cation intermediates involved are highly reactive. The highly reactive nature of glycosyl cations complicates their characterization because they have a short lifetime and rapidly equilibrate with the corresponding contact ion pair. To overcome this hurdle and enable the study of glycosyl cation stability and structure, they can be generated in a mass spectrometer in the absence of a solvent and counterion in the gas phase. The ease of formation, stability, and fragmentation of glycosyl cations have been studied using mass spectrometry (MS). However, MS alone provides little information about the structure of glycosyl cations. By combining mass spectrometry (MS) with infrared ion spectroscopy (IRIS), the determination of the gas-phase structures of glycosyl cations has been achieved. IRIS enables the recording of gas-phase infrared spectra of glycosyl cations, which can be assigned by matching to reference spectra predicted from quantum chemically calculated vibrational spectra. Here, we review the experimental setups that enable IRIS of glycosyl cations and discuss the various glycosyl cations that have been characterized to date. The structure of glycosyl cations depends on the relative configuration and structure of the monosaccharide substituents, which can influence the structure through both steric and electronic effects. The scope and relevance of gas-phase glycosyl cation structures in relation to their corresponding condensed-phase structures are also discussed. We expect that the workflow reviewed here to study glycosyl cation structure and reactivity can be extended to many other reaction types involving difficult-to-characterize ionic intermediates.

Radiative relaxation in isolated large carbon clusters: Vibrational emission versus recurrent fluorescence

Recurrent fluorescence (RF) from isolated carbon clusters containing between 24 and 60 atoms is theoretically investigated as a function of internal energy, cluster size, and structural features. The vibrational relaxation kinetics and the associated IR emission spectra are determined by means of a Monte Carlo approach with vibrational density of states computed in the harmonic approximation. RF is generally found to be highly competitive with vibrational emission. The behaviors predicted for clusters of various sizes and archetypal structures indicate that the IR emission spectra are strongly influenced by RF, an energy gap law being obtained for the evolution of the RF rate constant depending on the electronic excitation state. The present results are relevant to the photophysics of the interstellar medium and could contribute to elucidating the carriers of the extended red emission bands and the continuum emission lying below the aromatic infrared bands believed to originate from mixed aromatic–aliphatic compounds.

IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase

We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multiphoton dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm-1. Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.

Infrared spectroscopy of CO3 •-(H2O)1,2 and CO4 •-(H2O)1,2

Hydrated molecular anions are present in the atmosphere. Revealing the structure of the microsolvation is key to understanding their chemical properties. The infrared spectra of CO₃ ^•-(H₂O)_1,2 and CO₄ ^•-(H₂O)_1,2 were measured via infrared multiple photon dissociation spectroscopy in both warm and cold environments. Redshifted from the free O-H stretch frequency, broad, structured spectra were observed in the O-H stretching region for all cluster ions, which provide information on the interaction of the hydrogen atoms with the central ion. In the C-O stretching region, the spectra exhibit clear maxima, but dissociation of CO₃ ^•-(H₂O)_1,2 was surprisingly inefficient. While CO₃ ^•-(H₂O)_1,2 and CO₄ ^•-(H₂O) dissociate via loss of water, CO₂ loss is the dominant dissociation channel for CO₄ ^•-(H₂O)₂. The experimental spectra are compared to calculated spectra within the harmonic approximation and from analysis of molecular dynamics simulations. The simulations support the hypothesis that many isomers contribute to the observed spectrum at finite temperatures. The highly fluxional nature of the clusters is the main reason for the spectral broadening, while water-water hydrogen bonding seems to play a minor role in the doubly hydrated species.

IR multiple photon dissociation spectroscopy of MO2+ (M = V, Nb, Ta)

A laser vaporization cluster source is coupled to the Fourier-transform ion cyclotron resonance mass spectrometer beamline of the free-electron laser for intracavity experiments. Gas phase metal ions and their oxides (VO₂ ⁺, NbO₂ ⁺, and TaO₂ ⁺) are formed and spectroscopically characterized using IR multiple-photon dissociation spectroscopy via loss of atomic oxygen and overcoming fragmentation energies of 3 eV-6 eV. The signal is observed for all MO₂ ⁺ fundamental modes: the symmetric and anti-symmetric ν₁ and ν₃ stretch modes in the 900 cm^-1-1000 cm^-1 range and the ν₂ bending mode in the 300 cm^-1-450 cm^-1 range. A remarkable substructure is observed for the bending vibration, which is at least partly due to the rovibrational substructure.

Structural investigation of doubly-dehydrogenated pyrene cations

The vibrationally resolved spectra of the pyrene cation and doubly-dehydrogenated pyrene cation (C₁₆H₁₀˙⁺; Py⁺ and C₁₆H₈˙⁺; ddPy⁺) are presented. Infrared predissociation spectroscopy is employed to measure the vibrational spectrum of both species using a cryogenically cooled 22-pole ion trap. The spectrum of Py⁺ allows a detailed comparison with harmonic and anharmonic density functional theory (DFT) calculated normal mode frequencies. The spectrum of ddPy⁺ is dominated by absorption features from two isomers (4,5-ddPy⁺ and 1,2-ddPy⁺) with, at most, minor contributions from other isomers. These findings can be extended to explore the release of hydrogen from interstellar PAH species. Our results suggest that this process favours the loss of adjacent hydrogen atoms.

Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective

Combining the individual analytical strengths of mass spectrometry and infrared spectroscopy, infrared ion spectroscopy is increasingly recognized as a powerful tool for small-molecule identification in a wide range of analytical applications. Mass spectrometry is itself a leading analytical technique for small-molecule identification on the merit of its outstanding sensitivity, selectivity and versatility. The foremost shortcoming of the technique, however, is its limited ability to directly probe molecular structure, especially when contrasted against spectroscopic techniques. In infrared ion spectroscopy, infrared vibrational spectra are recorded for mass-isolated ions and provide a signature that can be matched to reference spectra, either measured from standards or predicted using quantum-chemical calculations. Here we present an overview of the potential for this technique to develop into a versatile analytical method for identifying molecular structures in mass spectrometry-based analytical workflows. In this tutorial perspective, we introduce the reader to the technique of infrared ion spectroscopy and highlight a selection of recent experimental advances and applications in current analytical challenges, in particular in the field of untargeted metabolomics. We report on the coupling of infrared ion spectroscopy with liquid chromatography and present experiments that serve as proof-of-principle examples of strategies to address outstanding challenges.

Impact of Sodium Cationization on Gas-Phase Conformations of DNA and RNA Cytidine Mononucleotides

Gas-phase conformations of the sodium-cationized forms of the 2'-deoxycytidine and cytidine mononucleotides, [pdCyd+Na]⁺ and [pCyd+Na]⁺, are examined by infrared multiple photon dissociation action spectroscopy. Complimentary electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory provide candidate conformations and their respective predicted IR spectra for comparison across the IR fingerprint and hydrogen-stretching regions. Comparisons of the predicted IR spectra and the measured infrared multiple photon dissociation action spectra provide insight into the impact of sodium cationization on intrinsic mononucleotide structure. Further, comparison of present results with those reported for the sodium-cationized cytidine nucleoside analogues elucidates the impact of the phosphate moiety on gas-phase structure. Across the neutral, protonated, and sodium-cationized cytidine mononucleotides, a preference for stabilization of the phosphate moiety and nucleobase orientation is observed, although the details of this stabilization differ with the state of cationization. Several low-energy conformations of [pdCyd+Na]⁺ and [pCyd+Na]⁺ involving several different orientations of the phosphate moiety and sugar puckering modes are observed experimentally.

Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility

Evolutionary algorithms such as the basin-hopping (BH) algorithm have proven to be useful for difficult non-linear optimization problems with multiple modalities and variables. Applications of these algorithms range from characterization of molecular states in statistical physics and molecular biology to geometric packing problems. A key feature of BH is the fact that one can generate a coarse-grained mapping of a potential energy surface (PES) in terms of local minima. These results can then be utilized to gain insights into molecular dynamics and thermodynamic properties. Here we describe how one can employ concepts from unsupervised machine learning to augment BH PES searches to more efficiently identify local minima and the transition states connecting them. Specifically, we introduce the concepts of similarity indices, hierarchical clustering, and multidimensional scaling to the BH methodology. These same machine learning techniques can be used as tools for interpreting and rationalizing experimental results from spectroscopic and ion mobility investigations (e.g., spectral assignment, dynamic collision cross sections). We exemplify this in two case studies: (1) assigning the infrared multiple photon dissociation spectrum of the protonated serine dimer and (2) determining the temperature-dependent collision cross-section of protonated alanine tripeptide.

Infrared multiple photon dissociation of cesium iodide clusters doped with mono-, di- and triglycine

Charged cesium iodide clusters doped with mono-, di- and triglycine serve as a model system for sea salt aerosols containing biological molecules. Here, we investigate reactions of these complexes under infrared irradiation, with spectra obtained by infrared multiple photon dissociation. The cluster ions are generated via electrospray ionization and analyzed in the cell of a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Depending on the cluster size and peptide length, loss of HI or loss of a glycine unit is observed. The experimental measurements are supported by quantum chemical calculations. We show that N-H and O-H stretching modes dominate the spectrum, with large shifts depending on local interactions, namely due to interaction with iodide anions or intramolecular hydrogen bonding. Both experiment and theory indicate that several isomers are present in the experimental mixture, with different infrared fingerprints as well as dissociation pathways.

Chiral differentiation of d- and l-isoleucine using permethylated β-cyclodextrin: infrared multiple photon dissociation spectroscopy, ion-mobility mass spectrometry, and DFT calculations

Chiral differentiation of protonated isoleucine (Ile) using permethylated β-cyclodextrin (perCD) in the gas-phase was studied using infrared multiple photon dissociation (IRMPD) spectroscopy, ion-mobility, and density functional theory (DFT) calculations. The gaseous protonated non-covalent complexes of perCD and d-Ile or l-Ile produced by electrospray ionization were interrogated by laser pulses in the wavenumber region of 2650 to 3800 cm-1. The IRMPD spectra showed remarkably different IR spectral features for the d-Ile or l-Ile and perCD non-covalent complexes. However, drift-tube ion-mobility experiments provided only a small difference in their collision cross-sections, and thus a limited separation of the d- and l-Ile complexes. DFT calculations revealed that the chiral distinction of the d- and l-complexes by IRMPD spectroscopy resulted from local interactions of the protonated Ile with perCD. Furthermore, the theoretical results showed that the IR absorption spectra of higher energy conformers (by ∼13.7 kcal mol-1) matched best with the experimentally observed IRMPD spectra. These conformers are speculated to be formed from kinetic-trapping of the solution-phase conformers. This study demonstrated that IRMPD spectroscopy provides an excellent platform for differentiating the subtle chiral difference of a small amino acid in a cyclodextrin-complexation environment; however, drift-tube ion-mobility did not have sufficient resolution to distinguish the chiral difference.

Anharmonic vibrational spectroscopy of polycyclic aromatic hydrocarbons (PAHs)

While powerful techniques exist to accurately account for anharmonicity in vibrational molecular spectroscopy, they are computationally very expensive and cannot be routinely employed for large species and/or at non-zero vibrational temperatures. Motivated by the study of Polycyclic Aromatic Hydrocarbon (PAH) emission in space, we developed a new code, which takes into account all modes and can describe all infrared transitions including bands becoming active due to resonances as well as overtone, combination, and difference bands. In this article, we describe the methodology that was implemented and discuss how the main difficulties were overcome, so as to keep the problem tractable. Benchmarking with high-level calculations was performed on a small molecule. We carried out specific convergence tests on two prototypical PAHs, pyrene (C₁₆H₁₀) and coronene (C₂₄H₁₂), aiming at optimising tunable parameters to achieve both acceptable accuracy and computational costs for this class of molecules. We then report the results obtained at 0 K for pyrene and coronene, comparing the calculated spectra with available experimental data. The theoretical band positions were found to be significantly improved compared to harmonic density functional theory calculations. The band intensities are in reasonable agreement with experiments, the main limitation being the accuracy of the underlying calculations of the quartic force field. This is a first step toward calculating moderately high-temperature spectra of PAHs and other similarly rigid molecules using Monte Carlo sampling.

Identification of the fragment of the 1-methylpyrene cation by mid-IR spectroscopy

The fragment of the 1-methylpyrene cation, C 17 H 11 + , is expected to exist in two isomeric forms, 1-pyrenemethylium PyrCH 2 + and the tropylium containing species PyrC 7 + . We measured the infrared (IR) action spectrum of cold C 17 H 11 + tagged with Ne using a cryogenic ion trap instrument coupled to the FELIX laser. Comparison of the experimental data with density functional theory calculations allows us to identify the PyrCH 2 + isomer in our experiments. The IR Multi-Photon Dissociation spectrum was also recorded following the C2H2 loss channel. Its analysis suggests combined effects of anharmonicity and isomerisation while heating the trapped ions, as shown by molecular dynamics simulations.

The structures and properties of anionic tryptophan complexes

IRMPD spectroscopy and electronic structure calculations are employed to identify π–π interactions in ionic tryptophan clusters.

Experimental and Computational Investigation of Salophen-Zn Gas Phase Complexes with Cations: A Source of Possible Interference in Anionic Recognition

We explore the possibility that protonated molecular ions might be an unexpected source of interference in the recognition process of anions and neutral species by Zn-salophen receptors. Zn-salophen complexes are known to bind anions and neutral molecules in solution. We present here evidence (from computational work and IRMPD spectroscopy) that these complexes can also be the binding site for protonated pyridine or quinuclidine. The resulting binding pattern does not involve the Zn ion, but one of the oxygen atoms directly attached to it. The resulting complex therefore turns out to have a positive charge adjacent to the Zn-salophen binding site. This finding seems to point to the existence of an interfering factor in the quantification of the experimental data about the association constant.

Effects of ESI conditions on kinetic trapping of the solution-phase protonation isomer of p-aminobenzoic acid in the gas phase

The effects of electrospray ionization (ESI) solvent and source temperature on the relative abundance of the preferred solution-phase (N-protonated; i.e. amine) versus preferred gas-phase (O-protonated; i.e., acid) isomers of p-aminobenzoic acid (PABA) were investigated. When PABA was electrosprayed from protic solvents (i.e., methanol/water), the infrared multiple photon dissociation (IRMPD) spectrum recorded was consistent with that for O-protonation, according to both calculations and previous studies. When aprotic solvent (i.e., acetonitrile) was used, a different spectrum was recorded and was assigned to the N-protonated isomer. As the amine is the preferred protonation site in solution, this suggests that an isomerization takes place under certain conditions. Photodissociation at the diagnostic band for the O-protonated isomer (NH₂ stretching mode) was used to quantify the relative contributions of each isomer to ion signal as a function of ESI conditions. For mixtures of methanol and acetonitrile, the relative contribution of the O-protonated gas-phase structure increased as a function of methanol content. Yet, substituting methanol for water resulted in a marked decrease of isomerization to the O-protonated structure. The source temperature (i.e., temperature of a heated desolvation capillary) was found to play a key role in determining the extent of isomerization, with higher temperatures yielding increased presence of gas-phase structures. These results are consistent with a protic bridge mechanism, in which the ESI droplet temperatures, dependent on endothermic desolvation and radiative heating from the capillary, may determine the isomerization yield.

Amine vs. carboxylic acid protonation in ortho-, meta-, and para-aminobenzoic acid: An IRMPD spectroscopy study

Infrared multiple photon dissociation (IRMPD) spectroscopy and computational chemistry are applied to the ortho-, meta-, and para- positional isomers of aminobenzoic acid to investigate whether the amine or the carboxylic acid are the favored sites of proton attachment in the gas phase. The NH and OH stretching modes yield distinct patterns that establish the carboxylic acid as the site of protonation in para-aminobenzoic acid, as opposed to the amine group in ortho- and meta-aminobenzoic acid, in agreement with computed thermochemistries. The trends for para- and meta-substitutions can be rationalized simplistically by inductive effects and resonant stabilization, and will be discussed in light of computed charge distributions based from electrostatic potentials. In ortho-aminobenzoic acid, the close proximity of the amine and acid groups allow a simultaneous interaction of the proton with both groups, thus stabilizing and delocalizing the charge more effectively, and compensating for some of the resonance stabilization effects.

Intramolecular cation–π interactions in protonated phenylalanine derivatives

The structures and properties of a series of phenylalanine (Phe) derivatives have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study.

Conformation of protonated glutamic acid at room and cryogenic temperatures

Linear infrared spectroscopy of protonated glutamic acid in a cryogenic ion trap allows for the clear-cut and quantitative identification of the two conformers of this fundamental biomolecule.

IRMPD Spectroscopy of Metalated Flavins: Structure and Bonding of Lumiflavin Complexes with Alkali and Coinage Metal Ions

Flavins are a fundamental class of biomolecules, whose photochemical properties strongly depend on their environment and their redox and metalation state. Infrared multiphoton dissociation (IRMPD) spectra of mass-selected isolated metal-lumiflavin ionic complexes (M⁺LF) are analyzed in the fingerprint range (800-1830 cm^-1) to determine the bonding of lumiflavin with alkali (M = Li, Na, K, Cs) and coinage (M = Cu, Ag) metal ions. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron resonance mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by comparison to quantum chemical calculations at the B3LYP/cc-pVDZ level, yielding structure, binding energy, bonding mechanism, and spectral properties of the complexes. The most stable binding sites identified in the experiments involve metal bonding to the oxygen atoms of the two available CO groups of LF. Hence, CO stretching frequencies are a sensitive indicator of both the metal binding site and the metal bond strength. More than one isomer is observed for M = Li, Na, and K, and the preferred CO binding site changes with the size of the alkali ion. For Cs⁺LF, only one isomer is identified, although the energies of the two most stable structures differ by less than 7 kJ/mol. While the M⁺-LF bonds for alkali ions are mainly based on electrostatic forces, substantial covalent contributions lead to stronger bonds for the coinage metal ions. Comparison between lumiflavin and lumichrome reveals substantial differences in the metal binding motifs and interactions due to the different flavin structures.

IR spectrum of the protonated neurotransmitter 2-phenylethylamine: dispersion and anharmonicity of the NH3(+)-π interaction

The structure and dynamics of the highly flexible side chain of (protonated) phenylethylamino neurotransmitters are essential for their function. The geometric, vibrational, and energetic properties of the protonated neutrotransmitter 2-phenylethylamine (H(+)PEA) are characterized in the N-H stretch range by infrared photodissociation (IRPD) spectroscopy of cold ions using rare gas tagging (Rg = Ne and Ar) and anharmonic calculations at the B3LYP-D3/(aug-)cc-pVTZ level including dispersion corrections. A single folded gauche conformer (G) protonated at the basic amino group and stabilized by an intramolecular NH(+)-π interaction is observed. The dispersion-corrected density functional theory calculations reveal the important effects of dispersion on the cation-π interaction and the large vibrational anharmonicity of the NH3(+) group involved in the NH(+)-π hydrogen bond. They allow for assigning overtone and combination bands and explain anomalous intensities observed in previous IR multiple-photon dissociation spectra. Comparison with neutral PEA reveals the large effects of protonation on the geometric and electronic structure.

Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals

The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

Photofragmentation mechanisms in protonated chiral cinchona alkaloids

Photo-fragmentation of protonated alkaloids results in C₈–C₉ cleavage accompanied or not by hydrogen migration, with a stereochemistry-dependent branching ratio.

The structures and properties of proton- and alkali-bound cysteine dimers

The proton-, lithium-, and sodium-bound cysteine dimers have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study.

Chirality-dependent structuration of protonated or sodiated polyphenylalanines: IRMPD and ion mobility studies

Ion mobility experiments are combined with Infra-Red Multiple Photon Dissociation (IRMPD) spectroscopy and quantum chemical calculations for assessing the role of chirality in the structure of protonated and sodiated di- or tetra-peptides. Sodiated systems show a strong chirality dependence of the competition between Na(+)O and Na(+)π interactions. Chirality effects are more subtle in protonated systems and manifest themselves by differences in the secondary interactions such hydrogen bonds between neutral groups or those involving the aromatic rings.

Going clean: structure and dynamics of peptides in the gas phase and paths to solvation

The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.

Nonlinear effects in infrared action spectroscopy of silicon and vanadium oxide clusters: experiment and kinetic modeling

Nonlinear effects in infrared action spectroscopy are experimentally quantified and successfully modeled for different inorganic clusters.

Mode-specific fragmentation of amino acid-containing clusters

Mode-specific IR-induced fragmentation is observed as a result of isomerization-induced transparency in an amino acid-containing cluster.

Structure and stability of phenoxide and fluorophenoxide anions investigated with infrared multiple-photon dissociation and detachment spectroscopy and tandem mass spectrometry

The gas-phase infrared multiple-photon dissociation and detachment (IRMPD) vibrational action spectra of the unsubstituted phenoxide anion and a series of fluorine- and trifluoromethyl-substituted phenoxide anions in the spectral region between 600 and 1800 cm(-1) are presented along with density functional theory (DFT) harmonic vibrational frequency calculations to establish the characteristic vibrations of the phenoxide functionality. The fluorophenoxide anions studied include the conjugate bases of o-, m-, and p-fluorophenol (C6H4FO(-)) as well as o-, m-, and p-α,α,α-trifluorocresol (CF3C6H4O(-)). The influence of the substituent on the characteristic vibrational frequencies is interpreted in terms of inductive and resonance shifts. In addition to the dissociation induced by infrared multiple-photon excitation, the electron detachment is also shown to play an important role in the decomposition of the unsubstituted phenoxide. It is demonstrated that the amount of electron detachment relative to dissociation is strongly mitigated by fluorination, and interpretations aided by DFT energy calculations suggest this is primarily due to the increased availability of low-energy dissociation pathways in the substituted phenoxides. Collision-induced dissociation (CID) mass spectrometry of the parent ions is used to estimate relative energies of the dissociation processes, and particular fragmentation motifs are elucidated. In particular, overall HF and CO losses provide facile decomposition pathways, yielding interesting fragment ions such as C6H(-) or C3H2FO(-) from the CF3C6H4O(-) parent anions.

Gas-phase structure of amyloid-β (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry

The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.