Water molecule adsorption on protonated dipeptides

Equilibrium constants for the adsorption of the first water molecule on six protonated dipeptides (Gly-Gly+H(+), Gly-Ala+H(+), Ala-Gly+H(+), Ala-Ala+H(+), Pro-Gly+H(+), and Gly-Trp+H(+)) have been measured as a function of temperature, and DeltaH(o) and DeltaS(o) determined. Density functional theory calculations were performed for both the unsolvated peptides and the peptide water complexes at the B3LYP/6-311++G level. MP2/6-311++G** calculations were also carried out for Gly/Ala peptides. The calculations suggest that adsorption of a water molecule by these simple dipeptides is a complex process, both the unsolvated peptide and the peptide-water complexes have multiple conformations with similar free energies. Average DeltaH(o) and DeltaS(o) values derived from the calculations are in reasonable agreement with the experimental results. According to the calculations, the dominant water adsorption process involves a significant conformational change to accommodate a bridging water molecule. DeltaH(o) is diminished for Pro-Gly+H(+) mainly because the water interacts with a secondary amine, whereas for Gly-Trp+H(+), DeltaH(o) is significantly decreased by the loss of cation-pi interactions upon water adsorption. For unsolvated peptides the proton affinities of the N-terminus and the backbone carbonyl groups are known to be similar. Addition of a single water molecule causes a significant stabilization of the N-terminus protonation site.     

Non-covalent interactions of alkali metal cations with singly charged tryptic peptides

The complexes formed by alkali metal cations (Cat(+) = Li(+), Na(+), K(+), Rb(+)) and singly charged tryptic peptides were investigated by combining results from the low-energy collision-induced dissociation (CID) and ion mobility experiments with molecular dynamics and density functional theory calculations. The structure and reactivity of [M + H + Cat](2+) tryptic peptides is greatly influenced by charge repulsion as well as the ability of the peptide to solvate charge points. Charge separation between fragment ions occurs upon dissociation, i.e. b ions tend to be alkali metal cationised while y ions are protonated, suggesting the location of the cation towards the peptide N-terminus. The low-energy dissociation channels were found to be strongly dependant on the cation size. Complexes containing smaller cations (Li(+) or Na(+)) dissociate predominantly by sequence-specific cleavages, whereas the main process for complexes containing larger cations (Rb(+)) is cation expulsion and formation of [M + H](+). The obtained structural data might suggest a relationship between the peptide primary structure and the nature of the cation coordination shell. Peptides with a significant number of side chain carbonyl oxygens provide good charge solvation without the need for involving peptide bond carbonyl groups and thus forming a tight globular structure. However, due to the lack of the conformational flexibility which would allow effective solvation of both charges (the cation and the proton) peptides with seven or less amino acids are unable to form sufficiently abundant [M + H + Cat](2+) ion. Finally, the fact that [M + H + Cat](2+) peptides dissociate similarly as [M + H](+) (via sequence-specific cleavages, however, with the additional formation of alkali metal cationised b ions) offers a way for generating the low-energy CID spectra of 'singly charged' tryptic peptides.     

Theoretical Evidence for Temperature-induced Proton Mobility in Isolated Lysine-rich Polyalanines

A multistate molecular mechanics method is introduced to model the possible competition between various protonation sites in gas-phase biomolecules with excess protons. The method relies on the Amber force field for each site and is calibrated against density-functional theory benchmark calculations at the 6-31+G(d,p) level. In its adiabatic version, where it has similarities with constant-pH algorithms, the model predicts that the small protonated Ala(4)-Lys peptide, unprotected at the N-terminus, changes protonation site above 400 K. In the larger [Ala(9)-Lys+H ](+) peptide, the proton remains at the lysine amine group in a favored charge/electric dipole conformation. In the three-state Ala(4)-Lys-Ala(4)-Lys peptide, the excess proton is found to be partially delocalized on the amine group of the first lysine and on the N-terminus. The statistical properties of the protonated peptides are found to significantly depend on the localized character of the proton. Finally, the model is extended by considering possible couplings between the protonation sites, in an empirical valence-bond version. Strong couplings can stabilize the peptides into unexpected proton-bound conformations over broad ranges of temperature.     

Gas phase hydrogen/deuterium exchange of arginine and arginine dipeptides complexed with alkali metals

The hydrogen/deuterium (H/D) exchange of protonated and alkali-metal cationized Arg-Gly and Gly-Arg peptides with D(2)O in the gas phase was studied using electrospray ionization quadropole ion trap mass spectrometry. The Arg-Gly and Gly-Arg alkali metal complexes exchange significantly more hydrogens than protonated Arg-Gly and Gly-Arg. We propose a mechanism where the peptide shifts between a zwitterionic salt bridge and nonzwitterionic charge solvated conformations. The increased rate of H/D exchange of the alkali metal complexes is attributed to the peptide metal complexes' small energy difference between the salt-bridge conformation and the nonzwitterionic charge-solvated conformation. Implications for the applicability of this mechanism to other zwitterionic systems are discussed.     

Conformational preferences of an amyloidogenic peptide: IR spectroscopy of Ac-VQIVYK-NHMe

The (306)VQIVYK(311) sequence in the tau peptide is essential for the formation of intracellular amyloid fibrils related to Alzheimer's disease, where it forms interdigitating cross-beta-structures. The inherent conformational preferences of the capped hexapeptide Ac-VQIVYK-NHMe were characterized in the gas phase. IR/UV double-resonance spectroscopy of the peptide isolated in a cold molecular beam was used to probe the conformation of the neutral peptide. The influence of protonation at the lysine side chain was investigated at 298 K by characterizing the protonated peptide ion, Ac-VQIVYK(H(+))-NHMe, with IRMPD spectroscopy in the fingerprint and amide I/II band region in an FTICR mass spectrometer. The conformations for both neutral and protonated peptides were predicted by an extensive conformational search procedure followed by cluster analysis and then DFT calculations. Comparison of the experimental and computed IR spectra, with consideration of the relative energies, was used to assign the dominant conformations observed. The neutral peptide adopts a beta-hairpin-like conformation with two loosely extended peptide chains, demonstrating the preference of the sequence for extended beta-strand-like structures. In the protonated peptide, the lysine NH3(+) disrupts this extended conformation by binding to the backbone and induces a transition to a random-coil-like structure.     

Intramolecular interactions in protonated peptides: H+ PheGlyGly and H+ GlyGlyPhe

The conformations of protonated PheGlyGly and GlyGlyPhe tripeptides, generated at temperatures approximately 300-350 K through a photochemical mechanism, were investigated in the gas phase using R-IRMPD spectroscopy in the OH and NH stretch region in combination with quantum chemistry calculations. The results aid characterisation of their conformational landscapes and specifically, help identify the intramolecular interactions that control the peptide conformations. The dominant intramolecular interaction in protonated PheGlyGly operates between the N-and C-termini but in protonated GlyGlyPhe there is a strong cation-pi interaction. The observation of a cation-pi interaction in the warm ions highlights its strong, stable nature.     

Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study

The phi,psi backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of <5 %. Trialanine samples mainly ( approximately 90%) a poly-l-proline II helix-like structure, some ( approximately 10%) beta extended structure, but no alphaR helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala(3) to Ala(7)). Trivaline samples all three major conformations significantly. Triglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala(3)-Ala(7), major differences are found for the 19mer, which significantly (30-40%) samples alphaR helical stuctures.     

Resonant infrared multiphoton dissociation spectroscopy of gas-phase protonated peptides. Experiments and Car-Parrinello dynamics at 300 K

The gas-phase structures of protonated peptides are studied by means of resonant infrared multiphoton dissociation spectroscopy (R-IRMPD) performed with a free electron laser. The peptide structures and protonation sites are obtained through comparison between experimental IR spectra and their prediction from quantum chemistry calculations. Two different analyses are conducted. It is first supposed that only well-defined conformations, sufficiently populated according to a Boltzmann distribution, contribute to the observed spectra. On the contrary, DFT-based Car-Parrinello molecular dynamics simulations show that at 300 K protonated peptides no longer possess well-defined structures, but rather dynamically explore the set of conformations considered in the first conventional approach.     

Differentiation of three pairs of Boc-beta,gamma- and gamma,beta-hybrid peptides by electrospray ionization tandem mass spectrometry

A new series of Boc-N-beta(3), gamma(4)-/gamma(4), beta(3)-isomeric hybrid peptides (containing repeats of beta(3)-Caa and gamma(4)-Caa's, Caa = C-linked carbo beta(3)-/gamma(4)-amino acids derived from D-xylose) have been differentiated by both positive and negative ion electrospray ionization (ESI) ion-trap and high resolution quadrupole time-of-flight/tandem mass spectrometry (Q-TOF MS/MS). MS(n) of protonated isomeric peptides and [M + H - Boc + H](+) produce characteristic fragmentation involving the peptide backbone, the Boc-group, and the side chain. The positional isomers are differentiated from one another by the presence of y(n) (+), b(n) (+), and other fragment ions of different m/z values. It is observed that the peptides with beta-Caa at the N-terminus produce extensive fragmentation, whereas gamma-Caa gave rise to much less fragmentation. Peptides with gamma-Caa at the N-terminus lose NH(3), whereas this process is absent for the carbopeptides with beta-Caa at the N-terminus. Two pairs of dipeptide diastereomers are clearly differentiated by the collision-induced dissociation (CID) of their protonated molecules. The loss of 2-methylprop-1-ene is more pronounced for Boc-NH-(R)-beta-Caa-(R)-gamma-Caa-OCH(3) (6) and Boc-NH-(R)-gamma-Caa-(R)-beta-Caa-OCH(3) (12), whereas it is insignificant or totally absent for its protonated diastereomeric pair Boc-NH-(S)-beta-Caa-(S)-gamma-Caa-OCH(3) (1) and Boc-NH-(S)-gamma-Caa-(S)-beta-Caa-OCH(3) (7). Further, ESI negative ion tandem mass spectrometry has also been found to be useful for differentiating these isomeric peptide acids. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides

In this work, a non‐natural amino acid, H‐propargylglycine‐OH (Pra), is chosen to examine the side‐chain effect on the backbone conformation of small peptides. The conformations of two synthesized Pra‐containing tripeptides, Ac‐Pra‐Pra‐NH₂ (PPTP) and Ac‐Pra‐Ala‐NH₂ (PATP), are examined by infrared (IR) spectroscopy in combination with molecular dynamics (MD) simulations and quantum chemical computations. By analyzing the joint distributions of backbone torsional angles, several significant conformations can be identified for the two tripeptides solvated in D₂O. At room temperature, 44 % of PPTP exists in the α‐α conformation and 33 % of PATP exists in the α‐polyproline‐II conformation. Larger structural inhomogeneity is seen in both cases by MD simulations at elevated temperatures. Thus even a small side chain, such as the propargyl group can significantly alter the peptide backbone conformations. The results suggest that there is no overwhelming conformational propensity of the Pra residue in short peptides. IR spectra simulated in the amide‐I region using two different methods, reasonably reproduce the experimental IR spectra and their temperature dependence.     

Head-to-backbone cyclization of peptides on solid support by nucleophilic aromatic substitution

A new versatile synthetic route is presented for the cyclization of tripeptides on solid support using nucleophilic aromatic substitution in the cyclization step. Identification of all conformers within a limit of 3 kcal/mol from the identified global minimum conformations by Monte Carlo conformational searching reveals that five out of six synthesized compounds have well-defined peptide backbone conformational properties. This was determined by clustering the identified conformers against a filter of seven to nine torsion angles in the peptide backbone. Thus, the results meet our goal to find synthetic routes to peptides that are conformationally sufficiently locked to serve as convenient leads for further development of pharmacophoric models. The strategy is based on Fmoc-peptide chemistry on a N-aminoethyl-substituted glycine bound to the commercially available Rink amide PS-resin. After deprotection of the N-terminus of the tripeptide, it is acylated with a fluoronitrobenzoic acid. Subsequently, a Boc group on the N-bound aminoethyl substituent is selectively deprotected allowing cyclization from the head (N-terminus) to the backbone substituent, thereby leading to the desired cyclized tripeptides. A number of representative examples of peptides cyclized by this method have been synthesized and characterized by NMR. Protecting groups that allow the incorporation of side chain functionalized amino acids have been found. Thus, the route provides access to generic libraries of conformationally restricted peptide sequences expressing a range of proteinogenic pharmacophores.     

cis‐Peptide Bonds: A Key for Intestinal Permeability of Peptides?

Recent structural studies on libraries of cyclic hexapeptides led to the identification of common backbone conformations that may be instrumental to the oral availability of peptides. Furthermore, the observation of differential Caco‐2 permeabilities of enantiomeric pairs of some of these peptides strongly supports the concept of conformational specificity driven uptake and also suggests a pivotal role of carrier‐mediated pathways for peptide transport, especially for scaffolds of polar nature. This work presents investigations on the Caco‐2 and PAMPA permeability profiles of 13 selected N‐methylated cyclic pentaalanine peptides derived from the basic cyclo(‐D ‐Ala‐Ala₄‐) template. These molecules generally showed moderate to low transport in intestinal epithelia with a few of them exhibiting a Caco‐2 permeability equal to or slightly higher than that of mannitol, a marker for paracellular permeability. We identified that the majority of the permeable cyclic penta‐ and hexapeptides possess an N‐methylated cis‐peptide bond, a structural feature that is also present in the orally available peptides cyclosporine A and the tri‐N‐methylated analogue of the Veber–Hirschmann peptide. Based on these observations it appears that the presence of N‐methylated cis‐peptide bonds at certain locations may promote the intestinal permeability of peptides through a suitable conformational preorganization.     

Dissociation of the peptide bond in protonated peptides

The dissociation of the amide (peptide) bond in protonated peptides, [M + H](+), is discussed in terms of the structures and energetics of the resulting N-terminal b(n) and C-terminal y(n) sequence ions. The combined data provide strong evidence that dissociation proceeds with no reverse barriers through interconverting proton-bound complexes between the segments emerging upon cleavage of the protonated peptide bond. These complexes contain the C-terminal part as a smaller linear peptide (amino acid if one residue) and the N-terminal part either as an oxazolone or a cyclic peptide (cyclic amide if one residue). Owing to the higher thermodynamic stability but substantially lower gas-phase basicity of cyclic peptides vs isomeric oxazolones, the N-terminus is cleaved as a protonated oxazolone when ionic (b(n) series) but as a cyclic peptide when neutral (accompanying the C-terminal y(n) series). It is demonstrated that free energy correlations can be used to derive thermochemical data about sequence ions. In this context, the dependence of the logarithm of the abundance ratio log[y(1)/b(2)], from protonated GGX (G, glycine; X, varying amino acid) on the gas-phase basicity of X is used to obtain a first experimental estimate of the gas-phase basicity of the simplest b-type oxazolone, viz. 2-aminomethyl-5-oxazolone (b(2) ion with two glycyl residues).     

某些环肽及其相应线型肽在不同溶剂中构象的CD谱研究

We used CD spectroscopy to study the conformations of three cyclic peptides (CP10E: cyclo[Glu(OBz1)-Pro-Gly-Glu(OBzl)-Gly]2, CP10K: cyclo[Lys(Z)-Pro-Gly-Lys(Z)-Gly]2, CP12K: cyclo[Phe-Lys(Z)-Pro-Gly-Lys(Z)-Gly]2 and their correspondent linear peptides (LP10E: Boc-[Glu(OBzl)-Pro-Gly-Glu(OBzl)-Gly]2-OPac, LP10K: Boc-[Lys(Z)-Pro-Lys(Z)-Pro]2-OMe, LP 12K: Bao- [-Lys(Z)-Pro-Gly-Lys(Z)-Gly]2- OMe) in three solvents of different polarity (chloroform, acetonitrile, 2,2,2-triliuroethanol), and it was found that all of linear and cyclicpeptides exists asγ-turn conformation in chloroform, however, in TFE＆ CH3CN solutions, the three linear peptides are inβ Ⅱ-turn conformations. CP10E isβI-turn conformation, CP10K ＆CP12K exists in more than one types of turn conformations. On the basis of our experiments, it was concluded: 1) In the presence of conformational constrained amino acids short linear peptides form obvious secondary structure; 2)The solvent polarity has influence on the peptide conformation and this influence on linear peptides is greater than that on cyclic peptides; 3)The backbone of cyclic peptide has constraint effect on its conformation and makes the secondary structure of cyclic peptide different from that of its relative linear peptide. This information might give some cules in the design of bioactive peptides with different receptor selectivity.     

Conformational analysis of furanoid epsilon-sugar amino acid containing cyclic peptides by NMR spectroscopy,molecular dynamics simulation,and X-ray crystallography: evidence for a novel turn structure

Sugar amino acids (SAAs) are useful building blocks for the design of peptidomimetics and peptide scaffolds. The three-dimensional structures of cyclic hybrid molecules containing the furanoid epsilon-SAA III and several amino acids were elucidated to study the preferred conformation of such an epsilon-SAA and its conformational influence on the backbone of cyclic peptides. NMR-based molecular dynamics simulations and empirical calculations of the cyclic tetramer 1, consisting of two copies of the SAA residue and two amino acids, revealed that it is conformationally restrained. The two SAA residues adopt different conformations. One of them forms an unusual turn, stabilized by an intraresidue nine-member hydrogen bond. The methylene functionalities of the other SAA residue are positioned in such a way that an intraresidue H bond is not possible. The X-ray crystal structure of 1 strongly resembles the solution conformation. Molecular dynamics calculations in combination with NMR analysis were also performed for compounds 2 and 3, which contain the RGD (Arg-Gly-Asp) consensus sequence and were previously shown to inhibit alpha(IIb)beta(3)-receptor-mediated platelet aggregation. The biologically most active compound 2 adopts a preferred conformation with the single SAA residue folded into the nine-member H bond-containing turn. Compound 3, containing an additional valine residue, as compared with compound 2, is conformational flexible. Our studies demonstrate that the furanoid epsilon-SAA III is able to introduce an unusual intraresidue hydrogen bond-stabilized beta-turn-like conformation in two of the three cyclic structures.     

The effect of fixed charge modifications on electron capture dissociation

Electron capture dissociation (ECD) studies of two modified amyloid beta peptides (20-29 and 25-35) were performed to investigate the role of H* radicals in the ECD of peptide ions and the free-radical cascade (FRC) mechanism. 2,4,6-Trimethylpyridinium (TMP) was used as the fixed charge tag, which is postulated to both trap the originally formed radical upon electron capture and inhibit the H* generation. It was found that both the number and locations of the fixed charge groups influenced the backbone and side-chain cleavages of these peptides in ECD. In general, the frequency and extent of backbone cleavages decreased and those of side-chain cleavages increased with the addition of fixed charge tags. A singly labeled peptide with the tag group farther away from the protonated site experienced a smaller abundance decrease in backbone cleavage fragments than the one with the tag group closer to the protonated site. Despite the nonprotonated nature of all charge carriers in doubly labeled peptide ions, several c and z* ions were still observed in their ECD spectra. Thus, although H* transfer may be important for the NC(alpha) bond cleavage, there also exist other pathways, which would require a radical migration via H* abstraction through space or via an amide superbase mechanism. Finally, internal fragment ions were observed in the ECD of these linear peptides, indicating that the important role of the FRC in backbone cleavages is not limited to the ECD of cyclic peptides.     

Gas-phase models of gamma turns: effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

The conformations of laser-desorbed jet-cooled short peptide chains Ac-Phe-Xxx-NH2 (Xxx=Gly, Ala, Val, and Pro) have been investigated by IR/UV double resonance spectroscopy and density-functional-theory (DFT) quantum chemistry calculations. Singly gamma-folded backbone conformations (betaL-gamma) are systematically observed as the most stable conformers, showing that in these two-residue peptide chains, the local conformational preference of each residue is retained (betaL for Phe and gamma turn for Xxx). Besides, beta turns are also spontaneously formed but appear as minor conformers. The theoretical analysis suggests negligible inter-residue interactions of the main conformers, which enables us to consider these species as good models of gamma turns. In the case of valine, two similar types of gamma turns, differing by the strength of their hydrogen bond, have been found both experimentally and theoretically. This observation provides evidence for a strong flexibility of the peptide chain, whose minimum-energy structures are controlled by side-chain/backbone interactions. The qualitative conformational difference between the present species and the reversed sequence Ac-Xxx-Phe-NH2 is also discussed.     

Probing the role of the C-H...O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides

The structural characterization in crystals of three designed decapeptides containing a double d-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all l analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed alpha-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with (D)Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-H.O hydrogen bond between residue 4 C(alpha)H and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C(alpha) atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt alpha(L) conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-H.O hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.     

Structure of cationized arginine (arg.m, m = h, li, na, k, rb, and cs) in the gas phase: further evidence for zwitterionic arginine

The gas-phase structures of cationized arginine, Arg.M(+), M = Li, Na, K, Rb, and Cs, were studied both by hybrid method density functional theory calculations and experimentally using low-energy collisionally activated and thermal radiative dissociation. Calculations at the B3LYP/LACVP++** level of theory show that the salt-bridge structures in which the arginine is a zwitterion (protonated side chain, deprotonated C-terminus) become more stable than the charge-solvated structures with increasing metal ion size. The difference in energy between the most stable charge-solvated structure and salt-bridge structure of Arg.M(+) increases from -0.7 kcal/mol for Arg.Li(+) to +3.3 kcal/mol for Arg.Cs(+). The stabilities of the salt-bridge and charge-solvated structures reverse between M = Li and Na. These calculations are in good agreement with the results of dissociation experiments. The low-energy dissociation pathways depend on the cation size. Arginine complexed with small cations (Li and Na) loses H(2)O, while arginine complexed with larger cations (K, Rb, and Cs) loses NH(3). Loss of H(2)O must come from a charge-solvated ion, whereas the loss of NH(3) can come from the protonated side chain of a salt-bridge structure. The results of dissociation experiments using several cationized arginine derivatives are consistent with the existence of these two distinct structures. In particular, arginine methyl esters, which cannot form salt bridges, dissociate by loss of methanol, analogous to loss of H(2)O from Arg.M(+); no loss of NH(3) is observed. Although dissociation experiments probe gas-phase structure indirectly, the observed fragmentation pathways are in good agreement with the calculated lowest energy isomers. The combination of the results from experiment and theory provides strong evidence that the structure of arginine-alkali metal ion complexes in the gas phase changes from a charge-solvated structure to a salt-bridge structure as the size of the metal ion increases.