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The supramolecular networks derived from the complexation of polyazamacrocycles with halide anions constitute fundamental building blocks of a broad range of modern materials. This study provides insights into the conformational framework that supports the binding of protonated cyclen macrocyles (1,4,7,10-Tetraazacyclododecane) by chloride anions through NH δ+ ···Cl - interactions. The isolated complex comprised of two cyclen hosts linked by one Cl - anion is characterized by means of infrared action spectroscopy and ion mobility mass spectrometry, in combination with quantum chemical computations. The Cl - anion is found to act as a hinge that bridges the protonated NH 2 + moieties of the two macrocycles leading to a molecular tweezer configuration. Different types of conformations emerge, depending on whether the trimer adopts an open arrangement, with significant freedom for internal rotation of the cyclen moieties, or it locks in a folded conformation with intermolecular H-bonds between the two cyclen backbones. The ion mobility collision cross section supports that folded configurations of the complex are dominant under isolated conditions in the gas phase. The IRMPD spectroscopy experiments suggest that two qualitatively different families of folded conformations coexist at room temperature, featuring either peripheral or inner positions of the anion with respect to the macrocycle cavities, These findings should have implications in the growth of extended networks in the nanoscale and in sensing applications.

Electrospray ionization was used to generate species such as [ZnNO 3 (CH 3 OH) 2 ] + from Zn(NO 3 ) 2 •XH 2 O dissolved in a mixture of CH 3 OH and H 2 O. Collision-induced dissociation of [ZnNO 3 (CH 3 OH) 2 ] + causes elimination of CH 3 OH to form [ZnNO 3 (CH 3 OH)] + . Subsequent collision-induced dissociation of [ZnNO 3 (CH 3 OH)] + causes elimination of 47 mass units (u), consistent with ejection of HNO 2 . The neutral loss shifts to 48 u for collision-induced dissociation of [ZnNO 3 (CD 3 OH)] + , demonstrating the ejection of HNO 2 involves intra-complex transfer of H from the methyl group methanol ligand. Subsequent collision-induced dissociation causes the elimination of 30 u (32 u for the complex with CD 3 OH), suggesting the elimination of formaldehyde (CH 2  = O). The product ion is [ZnOH] + . Collision-induced dissociation of a precursor complex created using CH 3 - 18 OH shows the isotope label is retained in CH 2  = O. Density functional theory calculations suggested that the "rearranged" product, ZnOH with bound HNO 2 and formaldehyde is significantly lower in energy than ZnNO 3 with bound methanol. We therefore used infrared multiple-photon photodissociation spectroscopy to determine the structures of both [ZnNO 3 (CH 3 OH) 2 ] + and [ZnNO 3 (CH 3 OH)] + . The infrared spectra clearly show that both ions contain intact nitrate and methanol ligands, which suggests that rearrangement occurs during collision-induced dissociation of [ZnNO 3 (CH 3 OH)] + . Based on the density functional theory calculations, we propose that transfer of H, from the methyl group of the CH 3 OH ligand to nitrate, occurs in concert with the formation of a Zn-C bond. After dissociation to release HNO 2 , the product rearranges with the insertion of the remaining O atom into the Zn-C bond. Subsequent C-O bond cleavage, with H transfer, produces an ion-molecule complex composed of [ZnOH] + and O = CH 2 .

The gas-phase structures of zinc and cadmium complexes of lysine (Lys) are investigated via a combination of infrared multiple photon dissociation action spectroscopy and ab initio quantum chemical calculations. In order to unambiguously identify the experimentally observed species, [Zn(Lys-H)] + and CdCl + (Lys), the action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using 6-311+G(d,p) and def2-TVZP basis sets for the zinc and cadmium systems, respectively. Single point energies were also calculated at the B3LYP, B3P86, MP2, and B3LYP-GD3BJ (accounting for empirical dispersion) levels of theory using larger basis sets. Identification of the experimentally formed isomers is possible through good agreement between infrared multiple photon dissociation action spectra and the theoretically predicted spectra. The [Zn(Lys-H)] + complex adopts a tridentate orientation involving the amino acid backbone amine and deprotonated carboxylic acid groups as well as the side-chain amine group, [N α ,CO - ,N ɛ ]. The CdCl + (Lys) complex similarly adopts a tridentate chelation involving the amino acid backbone amine and carbonyl groups, as well as the side-chain amine group, [N α ,CO,N ɛ ]. In both cases, the identified complexes are the lowest energy gas-phase structures at all levels of theory.

Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N-C α bond cleavages and the formation of c- and z-type fragment ions. The mechanisms involved in the formation of these ions have been the subject of much discussion. Here, we determine the molecular structures of an extensive set of c-type ions produced by ETD using infrared ion spectroscopy. Nine c 3 - and c 4 -ions are investigated to establish their C-terminal structure as either enol-imine or amide isomers by comparison of the experimental infrared spectra with quantum-chemically predicted spectra for both structural variants. The spectra suggest that all c-ions investigated possess an amide structure; the absence of the NH bending mode at approximately 1000-1200 cm -1 serves as an important diagnostic feature.

The molecular family of nucleotide triphosphates (NTPs), with adenosine 5'-triphosphate (ATP) as its best-known member, is of high biochemical importance as their phosphodiester bonds form Nature's main means to store and transport energy. Here, gas-phase IR spectroscopic studies and supporting theoretical studies have been performed on adenosine 5'-triphosphate, cytosine 5'-triphosphate and guanosine 5'-triphosphate to elucidate the intrinsic structural properties of NTPs, focusing on the influence of the nucleobase and the extent of deprotonation. Mass spectrometric studies involving collision induced dissociation showed similar fragmentation channels for the three studied NTPs within a selected charge state. The doubly charged anions exhibit fragmentation similar to the energy-releasing hydrolysis reaction in nature, while the singly charged anions show different dominant fragmentation channels, suggesting that the charge state plays a significant role in the favorability of the hydrolysis reaction. A combination of infrared ion spectroscopy and quantum-chemical computations indicates that the singly charged anions of all NTPs are preferentially deprotonated at their β-phosphates, while the doubly-charged anions are dominantly αβ-deprotonated. The assigned three-dimensional structure differs for ATP and CTP on the one hand and GTP on the other, in the sense that ATP and CTP show no interaction between nucleobase and phosphate tail, while in GTP they are hydrogen bonded. This can be rationalized by considering the structure and geometry of the NTPs where the final three dimensional structure depends on a subtle balance between hydrogen bond strength, flexibility and steric hindrance.

Crown ethers are well known as modulating agents of protein function and interactions. The action of crown ethers is driven by an alteration of the charged moieties of proteins through the capping of cationic amino acid side chains. This study evaluates the conformational features involved in the binding of crown ethers to the side chain of arginine. For this purpose, isolated complexes of methyl guanidinium with 12-crown-4 and 18-crown-6 are characterized with infrared action vibrational spectroscopy and quantum chemical computations. The conformational landscapes of the two complexes comprise an extensive ensemble of conformations close in energy. In the 12-crown-4 complex, the crown ether has the plane of its backbone approximately perpendicular to that of the guanidinium moiety and coordinates to two or three of its NH δ+ bonds. In the 18-crown-6 complex, the crown ether backbone is partially folded and tilted with respect to guanidinium and fixes its position in order to facilitate up to a four-fold coordination in the complex. The access of the complexes to multiple conformations leads to broad band structures in the N-H stretching region of their vibrational spectra., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Arginine (Arg) complexes with Zn2+ and Cd2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light from a free electron laser. Electrospray ionization generated complexes of deprotonated Arg with Zn2+, [Zn(Arg-H)]+, and Arg with CdCl+, CdCl+(Arg). Possible low-energy conformers of these species were found using quantum chemical calculations, and their calculated IR spectra were compared to experimentally measured IRMPD spectra. Calculations were performed at the B3LYP/6-311+G(d,p) level for Zn2+ complexes and B3LYP/def2-TZVP with an SDD effective core potential on cadmium for CdCl+ complexes. [Zn(Arg-H)]+ was found to adopt a charge-solvated, tridentate [N,CO-,Nω'] structure where Zn2+ binds to the backbone amine, carbonyl oxygen, and side-chain terminal guanidine nitrogen (Nω'). The CdCl+(Arg) species was suggested to be a mixture of a dominant (∼85%) charge-solvated, tridentate [N,CO,Nω'] structure where the CdCl+ binds to the backbone amine, carbonyl, and side-chain imine (Nω') and a minor (∼15%) bidentate [N,CO-](Nω'H2+) zwitterionic structure where the metal center binds to the backbone amine and carbonyl oxygen with intramolecular proton migration from the hydroxyl to the Nω' guanidine nitrogen (as designated in parenthesis).

Collision-induced dissociation of isotopically labelled protonated pentaglycine produced two abundant [b5]+ ions, the products of the loss of water from the first and second amide groups, labelled [b5]+I and [b5]+II. IRMPD spectroscopy and DFT calculations show that these two [b5]+ ions feature N1-protonated 3,5-dihydro-4H-imidazol-4-one structures. 15N-Labelling established that some interconversion occurs between these two ions but dissociations are preferred. For both ions, DFT calculations show that the barrier to interconversion is slightly higher than those to dissociation. Dehydration of protonated hexaglycine produced three imidazolone ions. Ions [b6]+I and [b6]+II exhibit analogous CID spectra to those from [b5]+I and [b5]+II; however, the spectrum of the [b6]+III ion was dramatically different, showing losses predominantly of a further water molecule or cleavage of the second amide bond to give the glycyloxazolone (a deprotonated [b2]+ ion, labelled GlyGlyox (114 Da)) from the N-terminus. Protonated polyglycines [Glyn + H]+, where n = 7-9, all readily lose at least one water molecule. The corresponding [bn]+ ions lose either a further water molecule, an oxazolone from the N-terminus or a truncated peptide from the C-terminus. The number of amino acid residues in the latter two eliminated neutral molecules provides insight into the location of the imidazolone in the peptide chain and which oxygen was lost in the initial dehydration reaction. From this analysis, it appears that water loss from the longer protonated polyglycines is predominantly from the central residues.

Chelation complexes of the histidine-containing tripeptides HisAlaAla, AlaHisAla, and AlaAlaHis with Ni(II) and Cu(II) having a -1 net charge are characterized in the gas phase by infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory calculations. We address the question of whether the gas-phase complexes carry over characteristics from the corresponding condensed-phase species. We focus particularly on three aspects of their structure: (i) square-planar chelation by the deprotonated amide nitrogens around the metal ion (low-spin for the Ni case), (ii) metal-ion coordination of the imidazole side chain nitrogen, and (iii) the exceptional preference for metal-ion chelation by peptides with His in the third position from the N-terminus, as in the amino terminal Cu and Ni (ATCUN) motif. We find that square-planar binding around the metal ion, involving bonds to both deprotonated backbone nitrogens, one of the carboxylate oxygens and the N-terminal nitrogen, is the dominant binding motif for all three isomers. In contrast to the condensed-phase behavior, the dominant mode of binding for all three isomers does not involve the imidazole side chain, which is instead placed outside the coordination zone. Only for the AlaAlaHis isomer, the imidazole-bound structure is also detected as a minority population, as identified from a distinctive short-wavelength IR absorption. The observation that this conformation exists only for AlaAlaHis correlates with condensed-phase behavior at neutral-to-basic pH, in the sense that the isomer with His in the third position is exceptionally disposed to metal ion chelation by four nitrogen atoms (4N) when compared with the other isomers. These results also emphasize the divergence between the conformational stabilities in the gas phase and in solution or crystalline environments: in the gas phase, direct metal binding of the imidazole is overall less favorable than the alternative of a remote imidazole that can act as an intramolecular H-bond donor enhancing the gas-phase stability.

Structures of deprotonated Cys, Asp, Glu, Phe, Pro, His homo dimers as well as [2Cys - 3H]-, [Asp + Glu - H]- and [2Glu - 2H + Na]- are investigated with infrared multiple-photon dissociation (IRMPD) spectroscopy between 650 and 1850 cm-1 and theory. The IRMPD spectra of all investigated complexes but [2His - H]-, [2Phe - H]- and [2Pro - H]- indicate that the structures consist of a neutral non-zwitterionic (NZ) and a deprotonated form of the amino acids. In contrast, the spectrum of [2His - H]- is complex and indicates the presence of multiple isomers and/or interactions between His and [His - H]-, so that its structure differs from that of the other deprotonated amino acid dimers. For [2Phe - H]- and especially for [2Pro - H]-, some IRMPD bands can only be explained by the presence of salt bridge (SB) structures in the dimer in which a deprotonated amino acid interacts with a zwitterionic neutral amino acid. Computational results indicate that SB structures are lower in energy at 298 K than corresponding NZ structures for neutral-anion complexes in which SB formation is not disrupted by amino acid side chains or conformational constraints, such as in [2Glu - H]- and [2Cys - 3H]- for which NZ structures are most consistent with experimental results. For deprotonated amino acid dimers in which these interfering interactions are absent, such as in [2Phe - H]- and [2Pro - H]-, the higher number of hydrogen bonds in SB compared to NZ structures stabilize the formation of zwitterionic neutral amino acids and consequently SB structures in agreement with results from IRMPD spectroscopy. These results suggest that SB structures likely occur in deprotonated peptide or protein ions at hydrophobic sites, such as protein-protein interfaces or in the interior of proteins, where interfering functional groups will not disrupt SB formation.

The identification of molecular biomarkers is critical for diagnosing and treating patients and for establishing a fundamental understanding of the pathophysiology and underlying biochemistry of inborn errors of metabolism. Currently, liquid chromatography/high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy are the principle methods used for biomarker research and for structural elucidation of small molecules in patient body fluids. While both are powerful techniques, several limitations exist that often make the identification of unknown compounds challenging. Here, we describe how infrared ion spectroscopy has the potential to be a valuable orthogonal technique that provides highly-specific molecular structure information while maintaining ultra-high sensitivity. Here, we characterize and distinguish two well-known biomarkers of inborn errors of metabolism, glutaric acid for glutaric aciduria and ethylmalonic acid for short-chain acyl-CoA dehydrogenase deficiency, using infrared ion spectroscopy. In contrast to tandem mass spectra, in which ion fragments can hardly be predicted, we show that the prediction of an IR spectrum allows reference-free identification in the case that standard compounds are either commercially or synthetically unavailable. Finally, we illustrate how functional group information can be obtained from an IR spectrum for an unknown and how this is valuable information to, for example, narrow down a list of candidate structures resulting from a database query. Early diagnosis in inborn errors of metabolism is crucial for enabling treatment and depends on the identification of biomarkers specific for the disorder. Infrared ion spectroscopy has the potential to play a pivotal role in the identification of challenging biomarkers.

Complexes of aspartic acid (Asp) cationized with Zn 2+ : Zn(Asp-H) + , Zn(Asp-H) + (ACN) where ACN = acetonitrile, and Zn(Asp-H) + (Asp); as well as with Cd 2+ , CdCl + (Asp), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. A series of low-energy conformers for each complex was found using quantum chemical calculations to identify the structures formed experimentally. The main binding motif observed for the heavy-metal complex, CdCl + (Asp)[N,CO,CO s ], is a charge-solvated, tridentate structure, where the metal center binds to the backbone amino group and carbonyl oxygens of the backbone and side-chain carboxylic acids. Likewise, the deprotonated Zn(Asp-H) + (ACN) and Zn(Asp-H) + (Asp) complexes show comparable [N,CO - ,CO s ](ACN) and [N,CO - ,CO s ][N,CO,CO s ] coordinations, respectively. Interestingly, there was only minor spectral evidence for the analogous Zn(Asp-H) + [N,CO - ,CO s ] binding motif, even though this species is predicted to be the lowest-energy conformer. Instead, rearrangement and partial dissociation of the amino acid are observed, as spectral features most consistent with the experimental spectrum are exhibited by a four-coordinate Zn(Asp-NH 4 ) + [CO 2 - ,CO s ](NH 3 ) complex. Analysis of the mechanistic pathway leading from the predicted lowest-energy conformer to the isobaric deaminated complex is explored theoretically. Further, comparison of the current work to that of Zn 2+ and Cd 2+ complexes of asparagine (Asn) allows additional conclusions regarding populated conformers and effects of carboxamide versus carboxylic acid binding to be drawn.

The following gas-phase uranyl/12-crown-4 (12C4) complexes were synthesized by electrospray ionization: [UO 2 (12C4) 2 ] 2+ and [UO 2 (12C4) 2 (OH)] + . Collision-induced dissociation (CID) of the dication resulted in [UO 2 (12C4-H)] + (12C4-H is a 12C4 that has lost one H), which spontaneously adds water to yield [UO 2 (12C4-H)(H 2 O)] + . The latter has the same composition as complex [UO 2 (12C4)(OH)] + produced by CID of [UO 2 (12C4) 2 (OH)] + but exhibits different reactivity with water. The postulated structures as isomeric [UO 2 (12C4-H)(H 2 O)] + and [UO 2 (12C4)(OH)] + were confirmed by comparison of infrared multiphoton dissociation (IRMPD) spectra with computed spectra. The structure of [UO 2 (12C4-H)] + corresponds to cleavage of a C-O bond in the 12C4 ring, with formation of a discrete U-O eq bond and equatorial coordination by three intact ether moieties. Comparison of IRMPD and computed IR spectra furthermore enabled assignment of the structures of the other complexes. Theoretical studies of the chemical bonding features of the complexes provide an understanding of their stabilities and reactivities. The results reveal bonding and structures of the uranyl/12C4 complexes and demonstrate the synthesis and identification of two different isomers of gas-phase uranyl coordination complexes.

Proton bonding drives the supramolecular chemistry of a broad range of materials with polar moieties. Proton delocalization and electronic charge redistribution have a profound impact on the structure of proton-bound molecular frameworks, and pose fundamental challenges to quantum chemical modelling. This study provides insights into the structural and spectral signatures of the intramolecular proton bond formed in a benchmark polyazamacrocycle anionophore (cyclen, 1,4,7,10-tetraazacyclododecane). Infrared action spectroscopy is employed to characterize the macrocycle, isolated in protonated form. In its most stable configuration, protonated cyclen adopts an open arrangement of Cs symmetry with a particularly strong NHδ+N bond across the cavity. The quantum chemical analysis of the infrared spectrum reveals intrinsic difficulties for the accurate description of the vibrational modes of the system. The reconciliation of the computational predictions with experiment demands a careful anharmonic treatment of the proton motion, which exposes the limitations of current methods. Best results are obtained with the incorporation of anharmonicity only to the fundamental modes directly related to motions of the proton. However, the full anharmonic treatment of the system fails to describe correctly the vibrations related to the macrocycle backbone. The results should serve as motivation for new developments in the modelling of proton bonded systems.

The recognition of arginine plays a central role in modern proteomics and genomics. Arginine is unique among natural amino acids due to the high basicity of its guanidinium side chain, which sustains specific interactions and proton exchange biochemical processes. The search for suitable macrocyclic ionophores constitutes a promising route towards the development of arginine receptors. This study evaluates the conformational features involved in the binding of free arginine by the polyether macrocycle (18-crown-6)-tetracarboxylic acid. Infrared action vibrational spectroscopy and quantum-chemical computations are combined to characterize the complexes with net charges +1 and +2. The spectrum of the +1 complex can be explained in terms of a configuration predominantly stabilized by a robust bidentate coordination of guanidinium with a carboxylate group formed from the deprotonation of one side group of the crown ether. The released proton is transferred to the amino terminus of arginine, which then coordinates with the crown ether ring. In an alternative type of conformation, partly consistent with experiment, the amino terminus is neutral and the guanidinium group inserts into the crown ether cavity. In the +2 complexes, arginine is always doubly protonated and the most stable conformations are characterized by a tripodal coordination of the ammonium -NH 3 + group of arginine with the oxygen atoms of the macrocycle ring, while the interactions of the amino acid with the side carboxylic acid groups of the crown ether acquire a remarkable lesser role.

The distinct basicity of the guanidinium side-group of arginine (Arg) sustains specific interactions involved in essential biochemical processes. The sensing of arginine is therefore key in modern biotechnology and bioanalysis. In this context, the development of molecular receptors based on crown ether building blocks has demonstrated great potential. We investigate the complexes formed by arginine with two benchmark macrocycles, 12-crown-4 (1,4,7,10-tetraoxacyclododecane) and its N-substituted analog cyclen (1,4,7,10-tetraazacyclododecane). Isolated complexes with a net charge +1 are characterized with infrared action vibrational spectroscopy and quantum mechanical computations in order to determine the most stable coordination arrangements and to elucidate the location of the protons involved. Remarkably, although arginine retains a net positive charge in its complex with 12-crown-4, it becomes zwitterionic in the cyclen complex. In this latter case, the guanidinium group remains protonated while a proton transfer from the carboxylic group occurs, leading to a charged -NH 2 + moiety in cyclen. Natural bond orbital analysis is employed to characterize the intermolecular H-bonds responsible for the stability of both complexes. Protonated arginine interacts with 12-crown-4 through the guanidinium side group, in a conformation that resembles the one expected for crown-Arg binding in peptidic chains. In contrast, the cyclen complex involves the coordination of the carboxylate anionic group with a N-H bond of the protonated amine group cyclen, and plausible but less relevant interactions with the guanidinium group.

Recent efforts to activate the strong uranium-oxygen bonds in the dioxo uranyl cation have been limited to single oxo-group activation through either uranyl reduction and functionalization in solution, or by collision induced dissociation (CID) in the gas-phase, using mass spectrometry (MS). Here, we report and investigate the surprising double activation of uranyl by an organic ligand, 3,4,3-LI(CAM), leading to the formation of a formal U 6+ chelate in the gas-phase. The cleavage of both uranyl oxo bonds was experimentally evidenced by CID, using deuterium and 18 O isotopic substitutions, and by infrared multiple photon dissociation (IRMPD) spectroscopy. Density functional theory (DFT) computations predict that the overall reaction requires only 132 kJ/mol, with the first oxygen activation entailing about 107 kJ/mol. Combined with analysis of similar, but unreactive ligands, these results shed light on the chelation-driven mechanism of uranyl oxo bond cleavage, demonstrating its dependence on the presence of ligand hydroxyl protons available for direct interactions with the uranyl oxygens.

Gas-phase ion chemistry methods that capture and characterize the degree of activation of small molecules in the active sites of homogeneous catalysts form a powerful new tool to unravel how ligand environments affect reactivity. A key roadblock in this development, however, is the ability to generate the fragile metal oxidation states that are essential for catalytic activity. Here we demonstrate the preparation of the key Ni(I) center in the widely used cyclam scaffold using ion-ion recombination as a gas-phase alternative to electrochemical reduction. The singly charged Ni + (cyclam) coordination complex is generated by electron transfer from fluoranthene and azobenzene anions to doubly charged Ni 2+ (cyclam), using the electron-transfer dissociation protocol in a commercial quadrupole ion trap instrument and in a custom-built octopole RF ion trap. The successful preparation of the Ni + (cyclam) cation is verified through analysis of its vibrational spectrum obtained using the infrared free electron laser FELIX.

Single and double protonated (E)-1,4-diamine-2-butenes were evaluated as a model system to probe isomerization during the ESI processes employing infrared multiple-photon dissociation (IRMPD) spectroscopy and density function theory (DFT) calculations, including implicit and explicit solvation models. Our results show that the preferential protonation takes place at the amines for singly protonated species and that the double bond is not protonated even under double protonation, as expected from known pK a values. This behavior was shown to reflect the (E)-(Z) interconversion rate, as no interconversion was observed nor predicted by implicit solvation model based on density (SMD) calculations even by the olefin protonation pathway. Explicit solvent calculations show that the singly protonated (E) configuration observed in the gas phase is also the most stable configuration in solution due to molecular interactions with the solvent that are absent for the (Z) configuration. The explicit solvation calculation reverts the supposed gas-phase stability of the (Z) configuration in comparison to (E) from -9 kcal mol -1 (in relative Gibbs free energy) in the gas phase to +89 kcal mol -1 (in total potential energy) as depicted by explicit Monte Carlo (MC) simulations. Together with previous results for the saturated 1,4-diamines from Morton and coworkers that show the (Z) configuration related conformation to be the most stable geometry in the gas-phase due to intermolecular hydrogen bonding, our experiments clearly show that conformational reorganizations can take place during the ESI process. These results suggest that gas-phase experiments and vacuum calculations may not be valid as evidence for conformations in solution without prior testing to check for isomerization during the ESI process.

l-Ergothioneine (ET) is a sulfur-containing derivative of the amino acid histidine that offers unique antioxidant properties. The enzyme independent redox-chemistry of ET relies on the availability of the thiol tautomer to allow oxidative formation of disulfide bridges, i.e., the tautomeric equilibrium. To study the intrinsic properties of ET the tautomeric equilibrium is studied in the gas-phase by infrared multiphoton dissociation (IRMPD) spectroscopy. The IR ion spectra of isolated molecular ions of ET and of the biosynthetic precursors of ET, i.e., hercynine and N ε -methyl-hercynine are acquired. The analyte structures are independently investigated by density functional theory (DFT) and computed linear IR-spectra of tautomer ion structures are compared with the gas-phase spectra for identification. For the molecular ion of ET the simulated IR spectra of thione and thiol structures match the recorded IRMPD spectrum and that prevents an individual structure assignment. On the other hand, theory suggests that ET adopts a thione tautomer in MeOH solution which could be carried over from the condensed phase to gas phase and could be kinetically trapped after effective electrospray phase transfer and desolvation. Such a non-thermal behavior is also found for the molecular ions of protonated hercynine and N ε -methyl-hercynine. Contrary to that, the sodium complex ions of ET, hercynine and N ε -methyl-hercynine adopt the respective ground structures predicted by theory, which are reliably identified spectroscopically. For ET the thione tautomer is by far the most stable isomer in the sodium complex molecular ion.

The effect of ionization by oxidation and protonation on the structure and IR spectrum of isolated, gas-phase triphenylamine (TPA) has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy in the fingerprint range from 600 cm -1 to 1800 cm -1 using an infrared free electron laser. IR spectra calculated using density functional theory (DFT) convincingly reproduce the experimental data. Spectral and structural differences are identified among neutral TPA, TPA˙ + and protonated TPA and qualitatively related to effects of resonance delocalization. As a consequence of electron delocalization, computed structural parameters for TPA remain virtually unchanged upon removal of an electron. Nonetheless, CC and CN stretching vibrations in the IR spectra of TPA˙ + undergo a red shift of up to 52 cm -1 as compared to those in TPA. Since ionization also strongly influences the relative band intensities, a vibrational projection analysis was used to correlate vibrational modes of TPA with those of TPA˙ + . The experimental IR spectrum of gas-phase protonated TPA indicates that protonation occurs on the nitrogen atom, despite delocalization of the lone electron pair. Upon protonation, the structure changes from the nearly planar geometry to a near-tetrahedral configuration.

Correction for 'Zn 2+ and Cd 2+ cationized serine complexes: infrared multiple photon dissociation spectroscopy and density functional theory investigations' by Rebecca A. Coates et al., Phys. Chem. Chem. Phys., 2016, 18, 22434-22445.

Correction for 'Experimental and theoretical investigations of infrared multiple photon dissociation spectra of glutamic acid complexes with Zn 2+ and Cd 2+ ' by Georgia C. Boles et al., Phys. Chem. Chem. Phys., 2017, 19, 12394-12406.

Ni(II) ions can be caged by surrounding peptide ligands in two basic binding patterns: the "iminol" (IM) binding pattern, where chelation occurs by deprotonated amide nitrogens, or the charge-solvated (CS) binding pattern, where chelation occurs by amide carbonyl oxygens. Gas-phase observation may clarify the factors affecting this choice in solution and in peptide and protein matrices. Infrared spectroscopic determination of gas-phase structures shows here how microsolvation by just one water molecule switches the balance of this choice from IM to CS for the Ni 2+ Gly 3 complex, in contrast with the always-CS structure of the Ni 2+ Gly 4 complex. Quantum-chemical calculations indicate that CS complexation is even more favored in the aqueous limit. Considering gas-phase conditions as comparable to low-pH solutions can reconcile this prediction with the common observation of IM-type binding in solutions at higher pH. This is likely the first gas-phase observation of solvation-induced IM-to-CS transition in oligopeptide complexes with doubly charged transition-metal ions.

The antibiotic activity of nonactin is sustained by its ability to transport K + across lipophilic phases, e.g., the cell membranes. Such a feature can be traced back to a specific ionophoric behavior and to a balanced hydrophobicity modulated by the formation of a cation complex. In this study, the dominant conformations and coordination arrangements in the alkali cation complexes (Na + , K + , Cs + ) of nonactin are characterized by means of action vibrational spectroscopy and quantum chemical computations. The low energy conformers of the complexes comprise compact inclusion structures, in which the cation interacts with a varying number of oxygen atoms of the carbonyl and oxolane ring groups of the nonactin macrocycle. The spectroscopy experiments indicate that the three alkali complexes explored are formed in a S 4 conformation. This is in contrast with previous crystallography studies, which concluded that the symmetry of the most stable conformer of the complex changes qualitatively with the cation size, from C 2 for Na + to S 4 for K + and Cs + . Computations with different hybrid density functionals lead to contradictory predictions that appear to be quite sensitive to the modelling of the long range interactions in the coordination arrangements. The stabilization of the nonactin-Na + complex in the C 2 or S 4 forms emerges as a subtle feature that may be tuned with an appropriate control of the environmental conditions, and constitutes a challenging benchmark to confront novel computational methods for supramolecular systems.

Small molecule identification is a continually expanding field of research and represents the core challenge in various areas of (bio)analytical science, including metabolomics. Here, we unequivocally differentiate enantiomeric N-acetylhexosamines in body fluids using infrared ion spectroscopy, providing orthogonal identification of molecular structure unavailable by standard liquid chromatography/high-resolution tandem mass spectrometry. These results illustrate the potential of infrared ion spectroscopy for the identification of small molecules from complex mixtures.

Complexes of glutamic acid (Glu) cationized with Zn 2+ and Cd 2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. Complexes of deprotonated Glu with Zn 2+ , [Zn(Glu-H)ACN] + (where ACN = acetonitrile, CH 3 CN), and intact Glu with CdCl + , CdCl + (Glu) were formed. Notably, photodissociation induces Glu fragmentation rather than ACN loss in the Zn 2+ complex. In order to identify the structures formed experimentally, the experimentally obtained spectra were compared to those calculated from optimized structures at the B3LYP/6-311+G(d,p) level for [Zn(Glu-H)ACN] + and B3LYP/def2-TZVP level with an SDD effective core potential on cadmium for the CdCl + (Glu) system. The main binding motif observed for the heavy metal complex is a charge solvated, tridentate [N,CO s ,CO] structure where the metal binds to the backbone amino group and carbonyl oxygens of the side-chain and backbone carboxylic acid groups. The Zn 2+ system similarly prefers a [N,CO - ,CO s ] binding motif, where binding is observed at one oxygen of the backbone carboxylate site along with the backbone amino and side-chain carbonyl groups. In both cases, the theoretically determined lowest-energy conformers explain the experimental [Zn(Glu-H)ACN] + and CdCl + (Glu) spectra well.

The ditopic binding of organic and inorganic anions and cations constitutes a distinct feature of polyazamacrocycles that underlies their action as intermediate docking and exchange ionophoric sites for tailored supramolecular synthesis and sensors. This work investigates the Cl - and Cs + complexes formed by hexacyclen (1,4,7,10,13,16-hexaazacyclooctadecane, ha18c6), a benchmark building block of ion-pair polyamine receptors. IR action spectroscopy is employed to characterize the anionic and cationic complexes under controlled environmental conditions in an ion trap. This allows for accurate modeling of the isolated complexes with quantum chemical computations. A comparison of the experimental and computational spectra serves to assess the low-energy conformers dominantly populated at room temperature, which comprise, in both cases, three structures of C s , C 2 , and C 3v symmetry with relative energies within about 5 kJ mol -1 . The ion-pair complex Cl - -ha18c6-Cs + is predicted to host the cation and anion on opposite sides of the macrocycle in a C 3v conformation that does not correlate with the lowest energy structures of the binary complexes. This indicates that the formation of the ion-pair complex in its most stable conformation demands a rearrangement of the hexacyclen ring structure upon the incorporation of the counterion., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The synthesis, reactivity, structures, and bonding in gas-phase binary and complex oxide anion molecules of protactinium and uranium have been studied by experiment and theory. The oxalate ions, An V O 2 (C 2 O 4 ) - , where An = Pa or U, are essentially actinyl ions, An V O 2 + , coordinated by an oxalate dianion. Both react with water to yield the pentavalent hydroxides, An V O(OH) 2 (C 2 O 4 ) - . The chemistry of Pa and U becomes divergent for reactions that result in oxidation: whereas Pa VI is inaccessible, U VI is very stable. The U V O 2 (C 2 O 4 ) - complex exhibits a remarkable spontaneous exothermic replacement of the oxalate ligand by O 2 to yield UO 4 - and two CO 2 molecules. The structure of the uranium tetroxide anion is computed to correspond to distorted uranyl, U VI O 2 2+ , coordinated in the equatorial plane by two equivalent O atoms each having formal charges of -1.5 and U-O bond orders intermediate between single and double. The unreactive nature of Pa V O 2 (C 2 O 4 ) - toward O 2 is a manifestation of the resistance toward oxidation of Pa V , and clearly reveals the disparate chemistries of Pa and U. The uranium tetroxide anion, UO 4 - , reacts with water to yield UO 5 H 2 - . Infrared spectra obtained for UO 5 H 2 - confirm the computed lowest-energy structure, UO 3 (OH) 2 - .

Complexes of asparagine (Asn) cationized with Zn 2+ and Cd 2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. Electrospray ionization yielded complexes of deprotonated Asn with Zn 2+ , [Zn(Asn-H)] + , and intact Asn with CdCl + , CdCl + (Asn). Series of low energy conformers for each complex were found using quantum chemical calculations in order to identify the structures formed experimentally. The experimentally obtained spectra were compared to those calculated from optimized structures at the B3LYP/6-311+G(d,p) level for [Zn(Asn-H)] + and the B3LYP/def2-TZVP level with an SDD effective core potential on cadmium for the CdCl + (Asn) system. The main binding motif observed for the CdCl + complex is a charge solvated, tridentate [N, CO, CO s ] structure where the metal binds to the backbone amino group and carbonyl oxygens of the carboxylic acid and side-chain amide groups. The Zn 2+ system deprotonates at the backbone carboxylic acid and prefers a [N, CO - , CO s ] binding motif, where binding was observed at the carboxylate site along with the backbone amino group and side-chain carbonyl groups. In both cases, the theoretically determined lowest-energy conformers explain the experimental [Zn(Asn-H)] + and CdCl + (Asn) spectra well. Additionally, complete mechanistic pathways were found for each of the major dissociation reactions of [Zn(Asn-H)] + (primary loss of CO 2 , followed by the sequential loss of NH 3 ) and CdCl + (Asn) (concomitant loss of NH 3 + CO).

The reactivity of the cysteine (Cys) and homocysteine (Hcy) radical cation was studied using ion-molecule reactions. The radical cations were generated via collision-induced dissociation (CID) of their S-nitrosylated precursors. Cleavage of the S-NO bond led to the formation of the radical initially positioned on the sulfur atom. The reactions of the radical cations with dimethyl disulfide revealed that the cysteine radical cation reacts more quickly than the homocysteine radical cation. Infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations were used to determine the structure of the homocysteine radical cation, which was compared to the previously published structure of the cysteine radical cation (Sinha et al. Phys. Chem. Chem. Phys. 2010, 12, 9794-9800). IRMPD spectroscopy and DFT calculations revealed that this difference in radical reactivity was not a result of a radical rearrangement for the homocysteine radical cation but rather that the reactivity was modulated by stronger hydrogen bonding.

The gas-phase IR spectrum of the protonated neurotransmitter serotonin (5-hydroxytryptamine) was measured in the fingerprint range by means of IR multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectrum was recorded in a Fourier transform ion cyclotron resonance mass spectrometer coupled to an electrospray ionization source and an IR free electron laser. Quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set yield six low-energy isomers in the energy range up to 40 kJ/mol, all of which are protonated at the amino group. Protonation at the indole N atom or the hydroxyl group is substantially less favorable. The IRMPD spectrum is rich in structure and exhibits 22 distinguishable features in the spectral range investigated (530-1885 cm(-1)). The best agreement between the measured IRMPD spectrum and the calculated linear IR absorption spectra is observed for the conformer lowest in energy at both levels of theory, denoted g-1. In this structure, one of the three protons of the ammonium group points toward the indole subunit, thereby maximizing the intramolecular NH(+)-π interaction between the positive charge of the ammonium ion and the aromatic indole ring. This mainly electrostatic cation-π interaction is further stabilized by significant dispersion forces, as suggested by the substantial differences between the DFT and MP2 energies. The IRMPD bands are assigned to individual normal modes of the g-1 conformer, with frequency deviations of less than 29 cm(-1) (average <13 cm(-1)). The effects of protonation on the geometric and electronic structure are revealed by comparison with the corresponding structural, energetic, electronic, and spectroscopic properties of neutral serotonin.

Structures of trivalent lanthanide metal cations La(3+), Ho(3+), and Eu(3+) with deprotonated Ala(n) (n = 2-5) or Leu-enk (Tyr-Gly-Gly-Phe-Leu) are investigated with infrared multiple photon dissociation (IRMPD) spectroscopy between 900 and 1850 cm(-1) and theory. In all of these complexes, a salt bridge is formed in which the metal cation coordinates to the carboxylate group of the peptide, resulting in a limited conformational space and many sharp IRMPD spectral bands. The IRMPD spectra clearly indicate that all carbonyl groups solvate the metal cation in each of the Ala(n) complexes. Due to strong vibrational coupling between the carbonyl groups, a sharp, high-energy amide I band due to in-phase stretching of all of the amide carbonyl groups bound to the metal cation is observed that is separated by approximately 50 cm(-1) from a strong, lower-energy amide I band. This extent of carbonyl coupling, which is sometimes observed in condensed-phase peptide and protein IR spectroscopy, has not been reported in IRMPD spectroscopy studies of other cationized peptide complexes. Intense bands due to carbonyl groups not associated with the metal cation are observed for Leu-enk complexes, indicating that a side chain group, such as the Tyr or Phe aromatic ring, prevents complete carbonyl coordination of the metal cation. Substitution of smaller lanthanide cations for La(3+) in these peptide complexes results only in minor structural changes consistent with the change in metal cation size. These are the first IRMPD spectra reported for lanthanide metal cationized peptides, and comparison to previously reported protonated and alkali metal or alkaline earth metal cationized peptide complexes reveals many trends consistent with the higher charge state of the lanthanide cations.