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Cisplatin, (NH3)2PtCl2, has been known as a successful metal-based anticancer drug for more than half a century. Its analogue, Argplatin, arginine-linked cisplatin, (Arg)PtCl2, is being investigated because it exhibits reactivity towards DNA and RNA that differs from that of cisplatin. In order to understand the basis for its altered reactivity, the deprotonated and sodium cationized forms of Argplatin, [(Arg-H)PtCl2]− and [(Arg)PtCl2 + Na]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy in the IR fingerprint and hydrogen-stretching regions. Complementary electronic structure calculations are performed using density functional theory approaches to characterize the stable structures of these complexes and to predict their infrared spectra. Comparison of the theoretical IR spectra predicted for various stable conformations of these Argplatin complexes to their measured IRMPD spectra enables determination of the binding mode(s) of Arg to the Pt metal center to be identified. Arginine is found to bind to Pt in a bidentate fashion to the backbone amino nitrogen and carboxylate oxygen atoms in both the [(Arg-H)PtCl2]− and [(Arg)PtCl2 + Na]+ complexes, the NO− binding mode. The neutral side chain of Arg also interacts with the Pt center to achieve additional stabilization in the [(Arg-H)PtCl2]− complex. In contrast, Na+ binds to both chlorido ligands in the [(Arg)PtCl2 + Na]+ complex and the protonated side chain of Arg is stabilized via hydrogen-bonding interactions with the carboxylate moiety. These findings are consistent with condensed-phase results, indicating that the NO− binding mode of arginine to Pt is preserved in the electrospray ionization process even under variable pH and ionic strength. [ABSTRACT FROM AUTHOR]

The gas-phase conformations of the protonated forms of thymidine-5′-monophosphate and uridine-5′-monophosphate, [pdThd+H]+ and [pUrd+H]+, are investigated by infrared multiple photon dissociation (IRMPD) action spectroscopy and electronic structure calculations. The IRMPD action spectra of [pdThd+H]+ and [pUrd+H]+ are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Low-energy conformations of [pdThd+H]+ and [pUrd+H]+ and their relative stabilities are computed at the MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers indicate that the dominant conformers of [pdThd+H]+ and [pUrd+H]+ populated in the experiments are protonated at the phosphate oxo oxygen atom, with a syn nucleobase orientation that is stabilized by strong P=OH+…O2 and P–OH…O4′ hydrogen-bonding interactions, and C2′-endo sugar puckering. Minor abundance of conformers protonated at the O2 carbonyl of the nucleobase residue may also contribute for [pdThd+H]+, but do not appear to be important for [pUrd+H]+. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of thymidine and uridine, [dThd+H]+ and [Urd+H]+, and the deprotonated forms of pdThd and pUrd, [pdThd−H]− and [pUrd−H]−, provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Most interestingly, the thymine and uracil nucleobases remain in their canonical forms for [pdThd+H]+ and [pUrd+H]+, unlike [dThd+H]+ and [Urd+H]+, where protonation occurs on the nucleobases and induces tautomerization of the thymine and uracil residues. [ABSTRACT FROM AUTHOR]

Uridine (Urd) is one of the naturally occurring pyrimidine nucleosides of RNA. 2′-Deoxyuridine (dUrd) is a naturally occurring modified form of Urd, but is not one of the canonical DNA nucleosides. In order to understand the effects of sodium cationization on the conformations and energetics of Urd and dUrd, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and density functional theory (DFT) calculations are performed. By comparing the calculated IR spectra of [Urd+Na]+ and [dUrd+Na]+ with the measured IRMPD spectra, the stable low-energy conformers populated in the experiments are determined. Anti oriented bidentate O2 and O2′ binding conformers of [Urd+Na]+ are the dominant conformers populated in the experiments, whereas syn oriented tridentate O2, O4′, and O5′ binding conformers of [dUrd+Na]+ are dominantly populated in the experiments. The 2′-hydroxyl substituent of Urd stabilizes the anti oriented O2 binding conformers of [Urd+Na]+. Significant differences between the measured IRMPD and calculated IR spectra for complexes of [Urd+Na]+ and [dUrd+Na]+ involving minor tautomeric forms of the nucleobase make it obvious that none are populated in the experiments. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized Urd and dUrd follow the order: [dUrd+H]+ ＜ [Urd+H]+ ＜ [dUrd+Na]+ ＜ [Urd+Na]+. The 2′-deoxy modification is found to weaken the glycosidic bond of dUrd versus that of Urd for the sodium cationized uridine nucleosides. [ABSTRACT FROM AUTHOR]

Infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of 2′-deoxyguanosine-5′-monophosphate and guanosine-5′-monophosphate, [pdGuo+H]+ and [pGuo+H]+, are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Electronic structure calculations are performed to generate low-energy conformations of [pdGuo+H]+ and [pGuo+H]+ and determine their relative stabilities at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparative analyses of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers are performed to determine the most favorable site of protonation and the conformers present in the experiments. These comparisons and the computed energetics find that N7 protonation is considerably preferred over O6 and N3, and the N7 protonated ground-state conformers of [pdGuo+H]+ and [pGuo+H]+ are populated in the experiments. The 2′-hydroxyl substituent does not significantly impact the stable low-energy conformers of [pdGuo+H]+vs. those of [pGuo+H]+. The effect of the 2′-hydroxyl substituent is primarily reflected in the relative intensities of the measured IRMPD bands, as the IRMPD profiles of [pdGuo+H]+ and [pGuo+H]+ are quite similar. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of the guanine nucleosides, [dGuo+H]+ and [Guo+H]+, and deprotonated forms of the guanine nucleotides, [pdGuo–H]− and [pGuo–H]−, provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Protonation is found to induce base rotation of the guanine residue to an anti orientation vs. the syn orientation found for the deprotonated forms of the guanine nucleotides. [ABSTRACT FROM AUTHOR]

The gas-phase conformations of protonated uridine, [Urd+H]+, and its modified form, protonated 2′-deoxyuridine, [dUrd+H]+, generated by electrospray ionization are investigated using infrared multiple photon dissociation (IRMPD) action spectroscopy techniques. IRMPD action spectra of [Urd+H]+ and [dUrd+H]+ are measured over the IR fingerprint and hydrogen-stretching regions. [Urd+H]+ and [dUrd+H]+ exhibit very similar IRMPD spectral profiles. However, the IRMPD yields of [Urd+H]+ exceed those of [dUrd+H]+ in both the IR fingerprint and hydrogen-stretching regions. The measured spectra are compared to the linear IR spectra predicted for the stable low-energy structures of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the tautomeric conformations populated by electrospray ionization. Both B3LYP and MP2 methods find O4 and O2 protonated canonical as well as 2,4-dihydroxy tautomers among the stable low-energy structures of [Urd+H]+ and [dUrd+H]+. Comparison between the measured IRMPD and calculated linear IR spectra suggests that these species exist in their ring-closed forms and that both 2,4-dihydroxy tautomers as well as O4 protonated canonical conformers coexist in the population generated by electrospray ionization for both [Urd+H]+ and [dUrd+H]+. The 2′-deoxy modification of [dUrd+H]+ reduces the variety of 2,4-dihydroxy tautomers populated in the experiments vs. those of [Urd+H]+. [ABSTRACT FROM AUTHOR]

Glutathione is a biologically abundant and redox active tripeptide that serves to protect cells from oxidative stress and rid the body of toxic heavy metals. The present study examines the coordination complexes of glutathione (GSH) with metals that are central to redox processes in biology, Zn, Cu, and Fe, using infrared multiple photon dissociation (IRMPD) action spectroscopy with a free electron laser. For all three metals, a complex between the metal dication and deprotonated GSH was formed, M(GSH-H) + . The experimental IRMPD spectra were compared to scaled harmonic vibrational spectra calculated at the MP2/6-311+G(d,p) level of theory after thorough exploration of conformational space using a simulated annealing protocol. Interestingly, spectra calculated at the B3LYP or ωB97XD level do not match experiment as well. These findings offer the first gas-phase spectroscopic evidence for how the biologically relevant metal ions coordinate with glutathione. There are spectral features that are common to all three metals, however, noting the differences in the strengths of the common features between the three metals enables an assessment of the preference or specificity that each individual metal has for a given coordination site. Additionally, all three metals form structures where the deprotonated thiol of the cysteine side chain coordinates with the metal center, which is consistent with the involvement of the thiol site in biologically relevant redox chemistry.

Infrared emission features are observed towards diverse astronomical objects in the interstellar medium (ISM). Generally, the consensus is that these IR features originate from polycyclic aromatic hydrocarbons (PAHs) and are hence named aromatic infrared bands (AIBs). More recently, it has been suggested that nitrogen substituted PAHs (PANHs) contribute to the AIBs as well and it has even been shown that nitrogen inclusion in PAHs can improve the match with the AIBs, specifically around the 6.2 μm feature. In order to determine which specific molecules or functional groups are at the origin of the AIBs, IR spectra of various PA(N)Hs are experimentally and computationally studied. In this work we expand on the spectroscopic investigation of PANHs by presenting the gas-phase mid-IR spectra of 1,5,9-triazacoronene˙ + ( TAC˙ + , m / z 303), a threefold nitrogenated congener of coronene˙ + , its protonated derivative TACH + ( m / z 304) and the product that forms when water adds to dehydrogenated TAC˙ + [TAC-H + H 2 O] + ( m / z 320). We analyze the mid-IR spectra by comparing them with vibrational modes calculated at the B3LYP/6-311++G(d,p) level a theory and we present a possible geometry for [TAC-H + H 2 O] + . The TAC˙ + mid-IR spectrum is compared to that of coronene˙ + and is demonstrated to be remarkably similar. We put TAC˙ + and TACH + into astronomical context by comparing their recorded mid-IR spectra to observed ISM spectra of four spectral classes. From this we conclude that TAC˙ + and TACH + could both contribute to the AIBs, with TACH + being a more likely contributor than TAC˙ + .

Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born-Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH] + ·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO] - ·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations.

Sinapoyl malate, naturally present in plants, has proved to be an exceptional UV filter and molecular heater for plants. Although there are nowadays industrially relevant sustainable synthetic routes to sinapoyl malate, its incorporation into certain cosmetic formulations, as well as its adsorption on plant leaves, is limited by its hydrophilicity. To overcome these obstacles, it is important to find a way to effectively control the hydrophilic-lipophilic balance of sinapoyl malate to make it readily compatible with the cosmetic formulations and stick on the waxy cuticle of leaves. To this end, herein, we describe a highly regioselective chemo-enzymatic synthesis of sinapoyl malate analogues possessing fatty aliphatic chains of variable length, enabling the lipophilicity of the compounds to be modulated. The potential toxicity ( i.e. , mutagenicity, carcinogenicity, endocrine disruption, acute and repeated-dose toxicity), bioaccumulation, persistence and biodegradability potential of these new analogues were evaluated in silico , along with the study of their transient absorption spectroscopy, their photostability as well as their photodegradation products., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The amino acid arginine plays a key role in the interaction of proteins with adenosine phosphates, as its protonated guanidinium side group is capable of building multipodal H-bonding interactions with the oxygen atoms of the phosphate, phosphoester and ribose moieties and with the nitrogen atoms of adenine. Protein interactions often take place in competition with other ionic species, typically metal cations, which are prone to build concerted coordination arrangements with the same centers of negative charge as guanidinium. We report on a vibrational spectroscopy and computational investigation of a positively charged ternary complex formed by adenosine monophosphate (AMP) with methyl guanidinium and Na + . Following a bottom-up approach, an analogous complex with ribose phosphate is characterized as well, which serves to assess the individual role of the phosphate, sugar and adenine moieties in the binding process and to compare, within a single complex, the interactions associated with diffuse versus localized charge distributions of guanidinium and the alkali cation, respectively. The results indicate that Na + is preferentially hosted in a semi-rigid pocket formed by the phosphoester-adenosine backbone of AMP and displaces guanidinium to a peripheral binding to the phosphate anionic end group. This suggests that the control of the salt concentration may constitute an effective route to modulate protein-AMP complexation.

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 Ni 2+ . 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 d 8 Ni 2+ -ion in an octahedral ligand environment, the IR spectrum also shows that the complexes are in a high-spin electron configuration.

The gas-phase structures of cationized glycine (Gly), including complexes with Li + , Na + , K + , Rb + , and Cs + , are examined using infrared multiple-photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) for the Li + , Na + , and K + complexes and at B3LYP/def2TZVP for the Rb + and Cs + complexes. Single-point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set for Li + , Na + , K + and the def2TZVPP basis set for Rb + and Cs + . The Li + and Na + complexes are identified as metal cation coordination to the amino nitrogen and carbonyl oxygen, [N,CO]-tt, although Na + (Gly) may have contributions from additional structures. The heavier metal cations coordinate to either the carbonyl oxygen, [CO]-cc, or the carbonyl oxygen and hydroxy oxygen, [CO,OH]-cc, with the former apparently preferred for Rb + and Cs + and the latter for K + . These two structures reside in a double-well potential and different levels of theory predict very different relative stabilities. Some experimental evidence is provided that MP2(full) theory provides the most accurate relative energies.

The biological activity of the macrocycle nonactin is intimately related to its ionophore properties and ability to act as a selective cation carrier. While the focus of most investigations on nonactin has been on the binding of metal cations and small molecular ions, this study pursues the characterization of its inclusion complexes with primary amines with bulky structured side groups of different polarity. To this end, the complexes of nonactin with aniline and with the amino acid L-serine, both in protonated form, are considered as case studies and their relevant coordination arrangements are assessed by means of infrared action spectroscopy, quantum chemical density functional theory and Born-Oppenheimer molecular dynamics. The study suggests that the oxygen atoms from the oxolane (tetrahydrofuran) groups of nonactin constitute the preferential docking sites of the ammonium moiety of the guest cation, although conformational constraints promote interactions with the ester carbonyl backbone groups. In the aniline complex, the benzyl side ring is oriented outwards from the cavity, whereas in the case of L-serine, the side carboxylic acid and alcohol groups participate actively in the coordination process. Interestingly, the accommodation of L-serine is favoured when nonactin adopts an enantiomeric-selective folding, that promotes the tripodal coordination of the protonated amine group with oxolane rings from three nonactinic acid blocks with enantiomeric sequence (+)-(-)-(+), which allows for a facile coordination of the serine side groups. This is recognized as a general feature associated with the alternation of chiral domains in globally achiral natural nonactin, yielding mirror-symmetric complexes with the enantiomers of chiral amines.

The gas-phase structures of protonated unsymmetrical 1,1-dimethylhydrazine (UDMH) and the proton-bound dimers of UDMH and hydrazine are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser and an optical parametric oscillator laser system. To identify the structures present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP-GD3BJ/6-311+G(d,p) level of theory. These comparisons show that protonated UDMH binds the proton at the methylated nitrogen atom (α) with two low-lying α conformers probably being populated. For (UDMH) 2 H + , the proton is shared between the methylated nitrogen atoms with several low-lying α conformers likely to be populated. Higher-lying conformers of (UDMH) 2 H + in which the proton is shared between α and β (unmethylated) nitrogen atoms cannot be ruled out on the basis of the IRPMD spectrum. For (N 2 H 4 ) 2 H + , there are four low-lying conformers that all reproduce the IRMPD spectrum reasonably well. As hydrazine and UDMH see usage as fuels for rocket engines, such spectra are potentially useful as a means of remotely monitoring rocket launches, especially in cases of unsuccessful launches where environmental hazards need to be assessed.

Infrared ion spectroscopy is increasingly recognized as a method to identify mass spectrometry-detected analytes in many (bio)chemical areas and its integration in analytical laboratories is now on the horizon. Commercially available quadrupole ion trap mass spectrometers are attractive ion spectroscopy platforms but operate at relatively high pressures. This promotes collisional deactivation which directly interferes with the multiple-photon excitation process required for ion spectroscopy. To overcome this, infrared lasers having a high instantaneous power are required and therefore a majority of analytical studies have been performed at infrared free electron laser facilities. Proliferation of the technique to routine use in analytical laboratories requires table-top infrared lasers and optical parametric oscillators (OPOs) are the most suitable candidates, offering both relatively high intensities and reasonable spectral tuning ranges. Here, we explore the potential of a range of commercially available high-power OPOs for ion spectroscopy, comparing systems with repetition rates of 10 Hz, 20 kHz, 80 MHz and a continuous-wave (cw) system. We compare the performance for various molecular ions and show that the kHz and MHz repetition-rate systems outperform cw and 10 Hz systems in photodissociation efficiency and offer several advantages in terms of cost-effectiveness and practical implementation in an analytical laboratory not specialized in laser spectroscopy.

Cisplatin, (NH 3 ) 2 PtCl 2 , has been known as a successful metal-based anticancer drug for more than half a century. Its analogue, Argplatin, arginine-linked cisplatin, (Arg)PtCl 2 , is being investigated because it exhibits reactivity towards DNA and RNA that differs from that of cisplatin. In order to understand the basis for its altered reactivity, the deprotonated and sodium cationized forms of Argplatin, [(Arg-H)PtCl 2 ] - and [(Arg)PtCl 2 + Na] + , are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy in the IR fingerprint and hydrogen-stretching regions. Complementary electronic structure calculations are performed using density functional theory approaches to characterize the stable structures of these complexes and to predict their infrared spectra. Comparison of the theoretical IR spectra predicted for various stable conformations of these Argplatin complexes to their measured IRMPD spectra enables determination of the binding mode(s) of Arg to the Pt metal center to be identified. Arginine is found to bind to Pt in a bidentate fashion to the backbone amino nitrogen and carboxylate oxygen atoms in both the [(Arg-H)PtCl 2 ] - and [(Arg)PtCl 2 + Na] + complexes, the NO - binding mode. The neutral side chain of Arg also interacts with the Pt center to achieve additional stabilization in the [(Arg-H)PtCl 2 ] - complex. In contrast, Na + binds to both chlorido ligands in the [(Arg)PtCl 2 + Na] + complex and the protonated side chain of Arg is stabilized via hydrogen-bonding interactions with the carboxylate moiety. These findings are consistent with condensed-phase results, indicating that the NO - binding mode of arginine to Pt is preserved in the electrospray ionization process even under variable pH and ionic strength.

The proton bond is a paradigmatic quantum molecular interaction and a major driving force of supramolecular chemistry. The ring cavities of crown ethers provide an intriguing environment, promoting competitive proton sharing with multiple coordination anchors. This study shows that protons confined in crown ether cavities form dynamic bonds that migrate to varying pairs of coordinating atoms when allowed by the flexibility of the macrocycle backbone. Prototypic native crown ethers (12-crown-4, 15-crown-5 and 18-crown-6) and aza-crown ethers (cyclen, 1-aza-18-crown-6 and hexacyclen) are investigated. For each system, Infrared action spectroscopy experiments and ab initio Molecular Dynamics computations are employed to elucidate the structural effects associated with proton diffusion and its entanglement with the conformational and vibrational dynamics of the protonated host.

We present the gas-phase infrared spectra of the phenyl cation, phenylium, in its perprotio (C6H5+) and perdeutero (C6D5+) forms, in the 260-1925 cm-1 (5.2-38 μm) spectral range, and investigate the observed photofragmentation. The spectral and fragmentation data were obtained using Infrared Multiple Photon Dissociation (IRMPD) spectroscopy within a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR MS) located inside the cavity of the free electron laser FELICE (Free Electron Laser for Intra-Cavity Experiments). The 1A1 singlet nature of the phenylium ion is ascertained by comparison of the observed IR spectrum with DFT calculations, using both harmonic and anharmonic frequency calculations. To investigate the observed loss of predominantly [2C,nH] (n = 2-4) fragments, we explored the potential energy surface (PES) to unravel possible isomerization and fragmentation reaction pathways. The lowest energy pathways toward fragmentation include direct H elimination, and a combination of facile ring-opening mechanisms (≤2.4 eV), followed by elimination of H or CCH2. Energetically, all H-loss channels found are more easily accessible than CCH2-loss. Calculations of the vibrational density of states for the various intermediates show that at high internal energies, ring opening is thermodynamically the most advantageous, eliminating direct H-loss as a competing process. The observed loss of primarily [2C,2H] can be explained through entropy calculations that show favored loss of [2C,2H] at higher internal energies.

Long-range electron transfer in proteins can be rationalized as a sequential short-distance electron-hopping processes via amino acid residues having low ionization energy as relay stations. Tyrosine residues can serve as such redox-active intermediates through one-electron oxidation to form a π-radical cation at its phenol side chain. An electron transfer from a vicinal functional group to this π-electron hole completes an elementary step of charge migration. However, transient oxidized/reduced intermediates formed at those relay stations during electron transfer processes have not been observed. In this study, formation of analog reactive intermediates via electron donor-acceptor coupling is observed by using IRMPD action spectroscopy. An elementary charge migration at the molecular level in model tyrosine-containing peptide radical cations [M]˙+ in the gas phase is revealed with its unusual Cα-Cβ bond cleavage at the side chain of the N-terminal residue. This reaction is induced by the radical character of the N-terminal amino group (-NH2˙+) resulting from an n → π+ interaction between the nonbonding electron pair of NH2 (n) and the π-electron hole at the Tyr side chain (π+). The formation of -NH2˙+ is supported by the IRMPD spectrum showing a characteristic NH2 scissor vibration coupled with Tyr side-chain stretches at 1577 cm-1. This n → π+ interaction facilitates a dissociative electron transfer with NH2 as the relay station. The occurrence of this side-chain cleavage may be an indicator of the formation of reactive conformers featuring the n → π+ interaction.

The macrocycle valinomycin displays an outstanding ability in cation binding and carriage across hydrophobic environments (e.g., cell membranes) and constitutes a central landmark for the design of novel ionophores for the regulation of biochemical processes. Most previous investigations have focused on the capture of metal cations (primarily K+). Here, we address the versatility of valinomycin in the encapsulation of molecular ions of small and moderate size, with NH4+ and H4PO4+ as case studies. A combination of infrared action vibrational spectroscopy and quantum chemical computations of molecular structure and dynamics is employed with the two-fold aim of assessing the dominant H-bonding coordination networks in the complexes and of characterizing the positional and rotational freedom of the guest cations inside the cavity of the macrocycle. Valinomycin binds NH4+ with only moderate distortion of the C3 configuration adopted in the complexes with the metal cations. The ammonium cation occupies the center of the cavity and displays two low-energy coordination arrangements that are dynamically connected through a facile rotation of the cation. The inclusion of the bulkier phosphoric acid cation demands significant stretching of the valinomycin backbone. Interestingly, the H4PO4+ cation achieves ample positional and rotational mobility inside valinomycin. The valinomycin backbone is capable of adopting barrel-like configurations when the cation occupies a region close to the center of the cavity, and funnel-like configurations when it diffuses to positions close to the exit face. This can accommodate the cation in varying coordination arrangements, characterized by different H-bonding between the four POH arms and the ester carbonyl groups of the macrocycle.

A key decay pathway by which organic sunscreen molecules dissipate harmful UV energy involves excited-state hydrogen atom transfer between proximal enol and keto functional groups. Structural modifications of this molecular architecture have the potential to block ultrafast decay processes, and hence promote direct excited-state molecular dissociation, profoundly affecting the efficiency of an organic sunscreen. Herein, we investigate the binding of alkali metal cations to a prototype organic sunscreen molecule, oxybenzone, using IR characterization. Mass-selective IR action spectroscopy was conducted at the free electron laser for infrared experiments, FELIX (600-1800 cm-1), on complexes of Na+, K+ and Rb+ bound to oxybenzone. The IR spectra reveal that K+ and Rb+ adopt binding positions away from the key OH intermolecular hydrogen bond, while the smaller Na+ cation binds directly between the keto and enol oxygens, thus breaking the intramolecular hydrogen bond. UV laser photodissociation spectroscopy was also performed on the series of complexes, with the Na+ complex displaying a distinctive electronic spectrum compared to those of K+ and Rb+, in line with the IR spectroscopy results. TD-DFT calculations reveal that the origin of the changes in the electronic spectra can be linked to rupture of the intramolecular bond in the sodium cationized complex. The implications of our results for the performance of sunscreens in mixtures and environments with high concentrations of metal cations are discussed.

Distinguishing positional isomers, such as compounds having different substitution patterns on an aromatic ring, presents a significant challenge for mass spectrometric analyses and is a frequently encountered difficulty in, for example, drug metabolism research. In contrast to mass spectrometry, IR spectroscopy is a well-known and powerful tool in the distinction of ortho-, meta- and para-isomers, but is not applicable to low-abundance compounds in complex mixtures such as often targeted in bioanalytical studies. Here, we demonstrate the use of infrared ion spectroscopy (IRIS) as a novel method that facilitates the differentiation between positional isomers of disubstituted phenyl-containing compounds and that can be applied in mass spectrometry-based complex mixture analysis. By analyzing different substitution patterns over several sets of isomeric compounds, we show that IRIS is able to consistently probe the diagnostic CH out-of-plane vibrations that are sensitive to positional isomerism. We show that these modes are largely independent of the chemical functionality contained in the ring substituents and of the type of ionization. We also show that IRIS spectra often identify the positional isomer directly, even in the absence of reference spectra obtained from physical standards or from computational prediction. We foresee that this method will be generally applicable to the identification of disubstituted phenyl-containing compounds.

Microspheres containing radioactive 166 holmium-acetylacetonate are employed in emerging radionuclide therapies for the treatment of malignancies. At the molecular level, details on the coordination geometries of the Ho complexes are however elusive. Infrared ion spectroscopy (IRIS) was used to characterize several 165 Ho-acetylacetonate complexes derived from non-radioactive microspheres. The coordination geometry of four distinct ionic complexes were fully assigned by comparison of their measured IR spectra with spectra calculated at the density functional theory (DFT) level. The coordination of each acetylacetonate ligand is dependent on the presence of other ligands, revealing an asymmetric chelation motif in some of the complexes. A fifth, previously unknown constituent of the microspheres was identified as a coordination complex containing an acetic acid ligand. These results pave the way for IRIS-based identification of microsphere constituents upon neutron activation of the metal center.

We report herein the first detailed study of the mechanism of redox reactions occurring during the gas-phase dissociative electron transfer of prototypical ternary [Cu II (dien)M]˙ 2+ complexes (M, peptide). The two final products are (i) the oxidized non-zwitterionic π-centered [M]˙ + species with both the charge and spin densities delocalized over the indole ring of the tryptophan residue and with a C-terminal COOH group intact, and (ii) the complementary ion [Cu I (dien)] + . Infrared multiple photon dissociation (IRMPD) action spectroscopy and low-energy collision-induced dissociation (CID) experiments, in conjunction with density functional theory (DFT) calculations, revealed the structural details of the mass-isolated precursor and product cations. Our experimental and theoretical results indicate that the doubly positively charged precursor [Cu II (dien)M]˙ 2+ features electrostatic coordination through the anionic carboxylate end of the zwitterionic M moiety. An additional interaction exists between the indole ring of the tryptophan residue and one of the primary amino groups of the dien ligand; the DFT calculations provided the structures of the precursor ion, intermediates, and products, and enabled us to keep track of the locations of the charge and unpaired electron. The dissociative one-electron transfer reaction is initiated by a gradual transition of the M tripeptide from the zwitterionic form in [Cu II (dien)M]˙ 2+ to the non-zwitterionic M intermediate, through a cascade of conformational changes and proton transfers. In the next step, the highest energy intermediate is formed; here, the copper center is 5-coordinate with coordination from both the carboxylic acid group and the indole ring. A subsequent switch back to 4-coordination to an intermediate IM1, where attachment to GGW occurs through the indole ring only, creates the structure that ultimately undergoes dissociation.

A charge-tagged phenyl pyruvic acid derivative was investigated by tandem-MS, infrared (IR) ion spectroscopy and theory. The tailor-made precursor ions efficiently lose CO 2 in collision induced dissociation (CID) experiments, offering access to study the secondary decay reactions of the product ions. IR ion spectroscopy provides evidence for the formation of an enol acid precursor ion structure in the gas phase and indicates the presence of enol products formed after CO 2 loss. Extensive DFT computations however, suggest intermediate generation of hydroxycarbene products, which in turn rearrange in a secondary process to the enol ions detected by IR ion spectroscopy. Quantum mechanical tunneling of the hydroxycarbene can be excluded since no evidence for aldehyde product ion formation could be found. This finding is in contrast to the behavior of methylhydroxycarbene, which cleanly penetrates the energy barrier to form exclusively acetaldehyde at cryogenic temperatures in an argon matrix via quantum mechanical hydrogen tunneling. The results presented here are attributed to the highly excited energy levels of the product ions formed by CID in combination with different barrier heights of the competing reaction channels, which allow exclusive access over one energy barrier leading to the formation of the enol tautomer ions observed.

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.

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.

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.

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.

Polycyclic aromatic hydrocarbons (PAHs) have been shown to be ubiquitous in a large variety of distinct astrophysical environments and are therefore of great interest to astronomers. The majority of these findings are based on theoretically predicted spectra, which make use of scaled DFT harmonic frequencies for band positions and the double harmonic approximation for intensities. However, these approximations have been shown to fail at predicting high-resolution gas-phase infrared spectra accurately, especially in the CH-stretching region (2950-3150 cm -1 , 3 μm). This is particularly worrying for the subset of hydrogenated or methylated PAHs to which astronomers attribute the observed non-aromatic features that appear in the CH-stretching region of spectral observations of the interstellar medium (ISM). In our previous work, we presented the anharmonic theoretical spectra of three linear PAHs and five non-linear PAHs, demonstrating the importance of including anharmonicities into theoretical calculations. In this work we extend these techniques to two methylated PAHs (9-methylanthracene, and 9,10-dimethylanthracene) and four hydrogenated PAHs (9,10-dihydroanthracene, 9,10-dihydrophenanthrene, 1,2,3,4-tetrahydronaphthalene, and 1,2,3,6,7,8-hexahydropyrene) in order to better understand the aliphatic IR features of substituted PAHs. The theoretical spectra are compared with the spectra obtained under matrix isolation low-temperature conditions for the full vibrational fundamental range and under high-resolution, low-temperature gas-phase conditions for the CH-stretching region. Excellent agreement is observed between the theoretical and high-resolution experimental spectra with a deviation of 0.00% ± 0.17%, and changes to the spectra of PAHs upon methylation and hydrogenated are tracked accurately and explained.

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.

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.

Uridine (Urd) is one of the naturally occurring pyrimidine nucleosides of RNA. 2'-Deoxyuridine (dUrd) is a naturally occurring modified form of Urd, but is not one of the canonical DNA nucleosides. In order to understand the effects of sodium cationization on the conformations and energetics of Urd and dUrd, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and density functional theory (DFT) calculations are performed. By comparing the calculated IR spectra of [Urd+Na] + and [dUrd+Na] + with the measured IRMPD spectra, the stable low-energy conformers populated in the experiments are determined. Anti oriented bidentate O2 and O2' binding conformers of [Urd+Na] + are the dominant conformers populated in the experiments, whereas syn oriented tridentate O2, O4', and O5' binding conformers of [dUrd+Na] + are dominantly populated in the experiments. The 2'-hydroxyl substituent of Urd stabilizes the anti oriented O2 binding conformers of [Urd+Na] + . Significant differences between the measured IRMPD and calculated IR spectra for complexes of [Urd+Na] + and [dUrd+Na] + involving minor tautomeric forms of the nucleobase make it obvious that none are populated in the experiments. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized Urd and dUrd follow the order: [dUrd+H] + < [Urd+H] + < [dUrd+Na] + < [Urd+Na] + . The 2'-deoxy modification is found to weaken the glycosidic bond of dUrd versus that of Urd for the sodium cationized uridine nucleosides.

Correction for 'Structural characterization of gas-phase cysteine and cysteine methyl ester complexes with zinc and cadmium dications by infrared multiple photon dissociation spectroscopy' by Rebecca A. Coates et al., Phys. Chem. Chem. Phys., 2015, 17, 25799-25808.

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.

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.

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.

Energetic processing of gaseous polycyclic aromatic hydrocarbons (PAHs) plays a pivotal role in the chemistries of inter- and circumstellar environments, certain planetary atmospheres, and also in the chemistry of combustion and soot formation. Although the precursor PAH species have been extensively characterized, the products from these gaseous breakdown reactions have received far less attention. It has been particularly challenging to accurately determine their molecular structure in gas-phase experiments, where comparisons against theoretical modeling are best made. Here we report on a combined experimental and theoretical study of the dissociative ionization of two nitrogen containing polycyclic aromatic hydrocarbons of C 13 H 9 N composition, acridine and phenanthridine. The structures of HCN-loss fragments are resolved by infrared multiple-photon dissociation (IRMPD) spectroscopy of the mass-isolated products in an ion trap mass spectrometer. Quantum-chemical computations as well as reference IRMPD spectra are employed to unambiguously identify the molecular structures. Furthermore, computations at the density functional level of theory provide insight into chemical pathways leading to the observed products. Acenaphthylene˙ + and benzopentalene˙ + - two aromatic species containing pentagons - are identified as the main products, suggesting that such species are easily formed and may be abundant in regions where thermal or photoprocessing of polyaromatics occurs.

Understanding of the nature and extent of chemical bonding in uranyl coordination complexes is crucial for the design of new ligands for nuclear waste separation, uranium extraction from seawater, and other applications. We report here the synthesis, infrared spectroscopic characterization, and quantum chemical studies of a molecular uranyl-di-15-crown-5 complex. The structure and bonding of this unique complex featuring a distinctive 6-fold coplanar coordination staggered sandwich structure and an unusual non-perpendicular orientation of the uranyl moiety are evaluated using density functional theory and chemical bonding analyses. The results provide fundamental understanding of the coordination interaction of uranyl with oxygen-donor ligands.

The observed variety of metal-ion complexation sites offered by peptides reflects a basic tension between charge solvation of the ion by Lewis-basic chelating groups versus amide nitrogen deprotonation and formation of metal-nitrogen bonds. Gas-phase models of metal-ion coordination can illuminate the factors governing this choice in condensed-phase proteins and enzymes. Here, structures of gas-phase complexes of Ni(ii) and Cu(ii) with tri- and tetra-peptide ligands are mapped out using a combination of Infrared Multiple Photon Dissociation (IRMPD) spectroscopy and density functional theory (DFT) computations. The two binding modes give distinctive IRMPD signatures, particularly in the diagnostic region 1500-1550 cm -1 . Previous observations have suggested that Ni(ii) complexes preferentially show the iminol rearrangement pattern (Im) giving low-spin square-planar geometries with metal-ion bonds to deprotonated amide nitrogens. In contrast, alkaline earth metal ion complexes prefer amide carbonyl oxygens chelating the metal ion with pyramidal geometry (charge-solvation, CS). Surprisingly, it is shown here that the Gly 4 complexes are CS bound, in contrast with the expectation of Im binding. It is suggested that CS binding is actually a normal Ni(ii) and Cu(ii) binding mode to simple peptides lacking participating side chains. Three factors are suggested to influence the choice between CS and Im binding patterns: (1) presence of an accessible side-chain Lewis-basic proton interaction site (FGGF, FGG and HAA complexes); (2) short chain length of the peptide leading to a shortage of accessible carbonyl oxygen sites for CS binding, (AAA, FGG and HAA complexes); (3) outright deprotonation of the ligand giving net negatively charged Im[Ni 2+ (Gly 4 -3H + )] - and Im[Ni 2+ (Ala 3 -3H + )] - complexes, which have a triply-deprotonated ligand. IRMPD spectra of [Cu 2+ Gly 4 ] 2+ and [Cu 2+ (Gly 4 -3H + )] - complexes suggest that their structures are similar to their Ni 2+ analogs.

The gas-phase structures of zinc and cadmium dications bound to serine (Ser) are investigated by infrared multiple photon dissociation (IRMPD) action spectroscopy using the free electron laser FELIX, in combination with ab initio calculations. To identify the structures of the experimentally observed species, [Zn(Ser-H)CH3CN](+) and CdCl(+)(Ser), the measured action spectra are compared to linear absorption spectra calculated at the B3LYP/6-311+G(d,p) level for Zn(2+) containing complexes and B3LYP/def2-TZVP levels for Cd(2+) containing complexes. Good agreement between the observed IRMPD spectra and the predicted spectra allows identification of the isomers present. The intact amino acid interacting with cadmium chloride adopts a tridentate chelation involving the amino acid backbone amine and carbonyl groups as well as the hydroxyl group of the side-chain, [N,CO,OH]. The presence of two low-energy conformers is observed for the deprotonated serine-zinc complex, with the same tridentate coordination as for the cadmium complex but proton loss occurs at both the hydroxyl side-chain, [N,CO,O(-)], and the carboxylic acid of the amino acid backbone, [N,CO(-),OH]. These results are profitably compared with the analogous results previously obtained for comparable complexes with cysteine.

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.

Although acetylene loss is well known to constitute the main breakdown pathway of polycyclic aromatic hydrocarbon (PAH) species, the molecular structure of the dissociation products remains only poorly characterized. For instance, the structure of the C8H6 product ion formed upon acetylene loss from the smallest PAH naphthalene (C10H8) has not been experimentally established. Several C8H6(+) isomers are conceivable, including phenylacetylene, benzocyclobutadiene, pentalene as well as a number of a-cyclic products. Here we present infrared (IR) spectroscopic evidence for the formation of the (anti-aromatic) pentalene structure using a combination of tandem mass spectrometry and IR laser spectroscopy. The formation of pentalene is suggestive of facile 6- to 5-membered ring conversion, which possibly has implications for the PAH/fullerene interrelationship in energetic settings such as the interstellar medium and combustion environments.

The formation of a salt bridge in deprotonated glycine dimer anions in a solvent-free environment is investigated using both infrared multiple photon dissociation spectroscopy between 600 and 1800 cm(-1) and theory. The zwitterionic and nonzwitterionic forms of glycine in this complex are computed to be nearly iso-energetic, yet predominantly the zwitterionic form is observed experimentally. The zwitterion stability is attributed to both the Coulombic attraction and the high stabilization from intramolecular hydrogen bonding that drives the energetic cost of proton transfer in a solvent free environment. These results show that there is a fine balance between the stabilities of these two forms of the anion. Elucidating the role of intrinsic factors, such as hydrogen bonding, can lead to a better understanding of the stabilities of salt bridges in the interiors of large proteins or at protein interfaces.