Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation

In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.

A Kinetic Investigation of Metal-Dipeptide Complex with Ninhydrin in the Absence and Presence of CTAB Micelles

This paper presents the results of a kinetic study performed between ninhydrin and a Ni(II) dipeptide complex under various conditions. The rate of formation of the imine adduct was measured spectrophotometrically both in plain aqueous media and in aqueous micellar media in which CTAB (cetyltrimethylammonium bromide) is used as the surfactant. These studies were carried out at pH 5 and over a temperature a range of 50 to 70°C. Studies were also conducted to elucidate the effect of some organic sodium salts on the rate of this reaction. In these studies, it was found that the formation of imine adduct followed a first-order kinetics with respect to [Ni(II)-Gly-Leu]⁺ in both aqueous and micellar medium. A fractional-order kinetics was observed with respect to ninhydrin, again in both aqueous and micellar media. Increase in the total concentration of CTAB from 0 to 40×10^-3 mol dm^-3 resulted in approximately two folds increase in the pseudo-first-order rate constant (k_ψ). The rate constant (k_Ψ) in micellar medium first increased with increase in CTAB concentration, reached a maximum value, and finally, with further increase in CTAB concentration, a decreasing effect was observed. Quantitative kinetic analysis of k_ψ-[CTAB] data was performed on the basis of the pseudo-phase model of the micelles. The rate profile in presence of CTAB suggests a cooperative effect in the enhanced formation of the imine adduct as is commonly found in enzyme catalyzed reactions. Addition of organic sodium salts (such as benzoate, salicylate and tosylate) enhanced the rate at lower concentrations but rates start to decrease at higher concentrations. This suggests that tightly binding organic counter-anions were the most effective. Viscosity of the reaction media seems to affect the kinetic behavior in micellar media.

Metal-Templated, Tight Loop Conformation of a Cys-X-Cys Biomimetic Assembles a Dimanganese Complex

With the goal of generating anionic analogues to MN₂ S₂ ⋅Mn(CO)₃ Br we introduced metallodithiolate ligands, MN₂ S₂ ^2- prepared from the Cys-X-Cys biomimetic, ema^4- ligand (ema=N,N'-ethylenebis(mercaptoacetamide); M=Ni^II , [V^IV ≡O]²⁺ and Fe^III ) to Mn(CO)₅ Br. An unexpected, remarkably stable dimanganese product, (H₂ N₂ (CH₂ C=O(μ-S))₂ )[Mn(CO)₃ ]₂ resulted from loss of M originally residing in the N₂ S₂ ^4- pocket, replaced by protonation at the amido nitrogens, generating H₂ ema^2- . Accordingly, the ema ligand has switched its coordination mode from an N₂ S₂ ^4- cavity holding a single metal, to a binucleating H₂ ema^2- with bridging sulfurs and carboxamide oxygens within Mn-μ-S-CH₂ -C-O, 5-membered rings. In situ metal-templating by zinc ions gives quantitative yields of the Mn₂ product. By computational studies we compared the conformations of "linear" ema^4- to ema^4- frozen in the "tight-loop" around single metals, and to the "looser" fold possible for H₂ ema^2- that is the optimal arrangement for binucleation. XRD molecular structures show extensive H-bonding at the amido-nitrogen protons in the solid state.

Matrix-assisted nanoelectrospray mass spectrometry for soft ionization of metal(i)–protein complexes

Metal ions play significant roles in biological processes, and investigation of metal–protein interactions provides a basis to understand the functions of metal ions in such systems.

Structures and Dissociation Products of Ce/Peptide Complexes: Competition between Coordination and Charge Delocalization

Structures of [Ce(GGG)]³⁺ and [Ce(GGG ? H)]²⁺ have been investigated by DFT calculations. The two lowest-energy structures of the triply charged metal complex have the peptide in either the iminol or conventional zwitterionic form, and these ions have almost identical energies. In the doubly charged complex, the iminol and charge-solvated structures are the best structures on the potential energy surface, but the latter is favored. In both iminol structures, the metal ion coordinates to the iminol oxygen rather than to the nitrogen, unlike in previously reported iminol-containing complexes. Triply charged [Ce(peptide)]³⁺ complexes are fragile and not easily isolated in a mass spectrometer, whereas the doubly charged [Ce(peptide ? H)]²⁺ complexes are more robust. Here, we studied the fragmentations of 37 [Ce(peptide ? H)]²⁺ and 30 [Ce(peptide)(peptide ? H)]²⁺ complexes and the results are systematically summarized. Losses of CO and/or H₂O are the most commonly observed fragmentation channels for [Ce(peptide ? H)]²⁺ complexes and these dissociation pathways are modeled by DFT calculations. For [Ce(peptide)(peptide ? H)]²⁺ complexes the neutral peptide plays the role of a solvent molecule but, unlike in the dissociations of [Ce(CH₃CN)(peptide ? H)]²⁺ complexes, the loss of the solvent molecule is not observed. Instead, fragmentation occurs by cleavage of the second amide bond of the solvating peptide molecule.

Gas-Phase Infrared Ion Spectroscopy Characterization of Cu(II/I)Cyclam and Cu(II/I)2,2'-Bipyridine Redox Pairs

We report the fingerprint IR spectra of mass-isolated gaseous coordination complexes of 2,2′-bipyridine (bpy) and 1,4,8,11-tetra-azacyclotetradecane (cyclam) with a copper ion in its I and II oxidation states. Experiments are carried out in a quadrupole ion trap (QIT) mass spectrometer coupled to the FELIX infrared free-electron laser. Dications are prepared using electrospray ionization (ESI), while monocations are generated by charge reduction of the dication using electron transfer-reduction (ETR) in the QIT. Interestingly, [Cu(bpy)₂]⁺ can also be generated directly using ESI, so that its geometries as produced from ETR and ESI can be compared. The effects of charge reduction on the IR spectra are investigated by comparing the experimental spectra with the IR spectra modeled by density functional theory. Reduction of Cu(II) to the closed-shell Cu(I) ion retains the square-planar geometry of the Cu–cyclam complex. In contrast, for the bis–bpy complex with Cu, charge reduction induces a conversion from a near-square-planar to a tetrahedral geometry. The geometry of [Cu(bpy)₂]⁺ is identical to that of the complex generated directly from ESI as a native structure, which indicates that the ETR product ion thermalizes. For [Cu(cyclam)]⁺, however, the square-planar geometry of the 2+ complex is retained upon charge reduction, although a (distorted) tetrahedral geometry was predicted to be lower in energy. These differences are attributed to different barriers to rearrangement.

Gas-phase metal ion chelation investigated with IRMPD spectroscopy: A brief review of Robert Dunbar's contributions

With the passing of Prof. Robert C. Dunbar on 31 October 2017, the field of ion chemistry lost one of its modern heroes. Throughout his career in mass spectrometry, two of his main research interests involved the interaction of trapped ions with electromagnetic radiation and the chelation motifs of metal ions with organic ligands. The focus of his early career was on the fundamental processes that take place in molecules upon ultraviolet and infrared excitation. From 2003 to 2017, his scientific interests shifted to more structural questions, notably to resolving the structures and binding motifs of metal ion chelation complexes by application of infrared photodissociation spectroscopy. These experiments were carried out during numerous visits to the (Free Electron Laser for Infrared eXperiments) (FELIX) facility in the Netherlands and were complemented by extensive theoretical investigations by Rob. As a tribute to our friend, we present in this contribution a brief review of this work.

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

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

Experimental and theoretical investigations of infrared multiple photon dissociation spectra of lysine complexes with Zn2+ and Cd2

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.

Replacing H+ by Na+ or K+ in phosphopeptide anions and cations prevents electron capture dissociation

By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.

Binding of Divalent Metal Ions with Deprotonated Peptides: Do Gas-Phase Anions Parallel the Condensed Phase?

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.

Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules

Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules.

Water Microsolvation Can Switch the Binding Mode of Ni(II) with Small Peptides

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 Ni²⁺Gly₃ complex, in contrast with the always-CS structure of the Ni²⁺Gly₄ 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.