Reaction Enthalpies for M+L = M++ L, Where M+= Na+and K+and L = Acetamide,N-Methylacetamide,N,N-Dimethylacetamide, Glycine, and Glycylglycine, from Determinations of the Collision-Induced Dissociation Thresholds

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.

In-Source Decay MALDI and High-Energy Collision-Induced Dissociation Mass Spectrometry of Alkali Metal-Adducted Underivatized Oligosaccharides

In-source decay (ISD) and high-energy collision-induced dissociation (HE-CID) were explored to provide structural information on alkali metal-adducted linear and stacked oligosaccharides (oligosaccharides with increased flexibility due to linkage type). These oligosaccharides include isomeric tetrasaccharides, maltoheptaose, and several human milk oligosaccharides (HMOs). Matrix-assisted laser desorption ionization (MALDI) ion production efficiency, as well as the product ion intensities, and the number of product ions formed in ISD and HE-CID of these oligosaccharides were influenced by the matrix, the ionic radius of the metal ion used for adduction, and the affinity of metal ions for specific functional groups in the oligosaccharides. 2,4,6-Trihydroxyacetophenone (THAP) was the best matrix for HE-CID of oligosaccharides, 4-dimethylaminobenzaldehyde (DMABA) worked best for ISD of tetrasaccharides and pentasaccharides, while 2,5-dihydroxybenzoic acid (DHB) was the best matrix for ISD and HE-CID of long chain oligosaccharides. In general, the number of product ions formed followed the trend Li+ > Na+ > K+ > Rb+ > Cs+, except for HMOs where Na+ ≥ Li+ > K+ > Rb+ > Cs+ occurred. The type of product ions formed and their intensities varied based on the position of the glycosidic bond linkage and the content of the monosaccharide. ISD and HE-CID produced diagnostic ions that could structurally differentiate isomers. Overall, HE-CID of alkali-metal adducted oligosaccharides produces intense glycosidic bond cleavages and low intensity cross-ring and internal cleavages. In contrast, ISD generates mainly cross-ring cleavages and internal cleavages at intensities higher than in HE-CID. In addition, ISD produced unique product ions that complement results from HE-CID.

Energetics and mechanisms for decomposition of cationized amino acids and peptides explored using guided ion beam tandem mass spectrometry

Fragmentation studies of cationized amino acids and small peptides as studied using guided ion beam tandem mass spectrometry (GIBMS) are reviewed. After a brief examination of the key attributes of the GIBMS approach, results for a variety of systems are examined, compared, and contrasted. Cationization of amino acids, diglycine, and triglycine with alkali cations generally leads to dissociations in which the intact biomolecule is lost. Exceptions include most lithiated species as well as a few examples for sodiated and one example for potassiated species. Like the lithiated species, cationization by protons leads to numerous dissociation channels. Results for protonated glycine, cysteine, asparagine, diglycine, and a series of tripeptides are reviewed, along with the thermodynamic consequences that can be gleaned. Finally, the important physiological process of the deamidation of asparagine (Asn) residues is explored by the comparison of five dipeptides in which the C-terminal partner (AsnXxx) is altered. The GIBMS thermochemistry is shown to correlate well with kinetic results from solution phase studies.

The impact of the electric field of metal ions on the vibrations and internal hydrogen bond strength in alkali metal ion di- and triglycine complexes

Using infrared predissociation spectroscopy of cryogenic ions, we revisit the vibrational spectra of alkali metal ion (Li+, Na+, K+) di- and triglycine complexes. We assign their most stable conformation, which involves metal ion coordination to all C=O groups and an internal NH⋯NH2 hydrogen bond in the peptide backbone. An analysis of the spectral shifts of the OH and C=O stretching vibrations across the different metal ions and peptide chain lengths shows that these are largely caused by the electric field of the metal ion, which varies in strength as a function of the square of the distance. The metal ion–peptide interaction also remotely modulates the strength of internal hydrogen bonding in the peptide backbone via the weakening of the amide C=O bond, resulting in a decrease in internal hydrogen bond strength from Li+ > Na+ > K+.

Potassium Binding Interactions with Aliphatic Amino Acids: Thermodynamic and Entropic Effects Analyzed via a Guided Ion Beam and Computational Study

Noncovalent interactions between alkali metals and amino acids are critical for many biological processes, especially for proper function of protein ion channels; however, many precise binding affinities between alkali metals and amino acids still need to be measured. This study addresses this need by using threshold collision-induced dissociation with a guided ion beam tandem mass spectrometer to measure binding affinities between potassium cations and the aliphatic amino acids: Gly, Ala, hAla, Val, Leu, and Ile. These measurements are supplemented by theoretical calculations and include commentary on effects of enthalpy, entropy, and structural preference. Notably, all levels of theory indicate that the lowest-lying isomers at 298 K have K⁺ binding to the carbonyl oxygen in either a monodentate ([CO]) or bidentate ([CO,OH]) fashion, isomers that are linked in a double-well potential. This complicates the analysis of the data, although does not greatly influence the final results. Analysis of the resulting cross sections includes accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates. The resulting experimental bond dissociation energies generally increase as the polarizability of the amino acid increases, results that agree well with quantum chemical calculations done at the B3LYP, B3P86, and MP2(full) levels of theory, with B3LYP-GD3BJ predicting systematically larger values.

Sodium Binding Interactions with Aliphatic Amino Acids: A Guided Ion Beam and Computational Study

Metal binding affinities play a vital role in medicinal, biological, and industrial applications. In particular, metal cation-amino acid (AA) interactions contribute to protein stability such that analyzing analogous prototypical interactions is important. Here, we present a full description of the interactions of sodium cations (Na⁺) and six aliphatic amino acids (AA), where AA = glycine (Gly), alanine (Ala), homoalanine (hAla), valine (Val), leucine (Leu), and isoleucine (Ile). Experimentally, these interactions are evaluated using threshold collision-induced dissociation carried out in a guided ion beam tandem mass spectrometer, allowing for the determination of the kinetic-energy-dependent behavior of Na⁺-AA dissociation. Analysis of these dissociation cross sections, after accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates, allows the determination of absolute Na⁺-AA bond dissociation energies (BDEs) in kJ/mol of Gly (164.0), Ala (166.9), hAla (167.9), Val (172.7), Leu (173.7), and Ile (174.6). These are favorably compared to quantum chemical calculations conducted at the B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels of theory. Our combination of structural and energetic analyses provides information regarding the specific factors responsible for Na⁺ interactions with amino acids. Specifically, we find that the BDEs increase linearly with increasing polarizability of the amino acid.

Sodium Rechargeable Batteries with Electrolytes Based on Nafion Membranes Intercalated by Mixtures of Organic Solvents

The possibilities of manufacturing batteries with Nafion 117 membranes in the Na+-form intercalated by mixtures of non-aqueous organic solvents used both as an electrolyte, separator, and binder were investigated. Electrochemical stability of various organic solvent mixtures based on N,N-dimethylacetamide, ethylene carbonate, propylene carbonate, and tetrahydrofuran were characterized. It was shown that a sodium battery based on a Nafion-Na membrane intercalated by mixture of ethylene carbonate and propylene carbonate with a Na3V1.9Fe0.1(PO4)3/C positive electrode is characterized by a discharge capacity of ≈110 mAh·g−1 (current density of 10 mA·g−1) at room temperature and shows the ability to cycle without degradation during 20 cycles. Batteries with Nafion membrane electrolytes, containing N,N-dimethylacetamide, were characterized using capacity fading during cycling, which is due to the interaction of N,N-dimethylacetamide and a negative sodium electrode.

Cationic Noncovalent Interactions: Energetics and Periodic Trends

In this review, noncovalent interactions of ions with neutral molecules are discussed. After defining the scope of the article, which excludes anionic and most protonated systems, methods associated with measuring thermodynamic information for such systems are briefly recounted. An extensive set of tables detailing available thermodynamic information for the noncovalent interactions of metal cations with a host of ligands is provided. Ligands include small molecules (H2, NH3, CO, CS, H2O, CH3CN, and others), organic ligands (O- and N-donors, crown ethers and related molecules, MALDI matrix molecules), π-ligands (alkenes, alkynes, benzene, and substituted benzenes), miscellaneous inorganic ligands, and biological systems (amino acids, peptides, sugars, nucleobases, nucleosides, and nucleotides). Hydration of metalated biological systems is also included along with selected proton-based systems: 18-crown-6 polyether with protonated peptides and base-pairing energies of nucleobases. In all cases, the literature thermochemistry is evaluated and, in many cases, reanchored or adjusted to 0 K bond dissociation energies. Trends in these values are discussed and related to a variety of simple molecular concepts.

Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field

Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K⁺, Na⁺, Ca²⁺, and Cl^–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca²⁺ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins.

Anharmonic vibrations of N-H in Cl(-)(N-methylacetamide)1(H2O)(0-2)Ar2 cluster ions. Combined IRPD experiments and BOMD simulations

Infrared Predissociation (IRPD) spectra of Cl(-)(NMA)1(H2O)0-2Ar2 combined with Born-Oppenheimer Molecular Dynamics (BOMD) IR spectra have been acquired, providing the structure and dynamics of these systems. We show that the chloride ion is bound to the hydrogen of the amide N-H group, forming a strong ionic hydrogen bond, weakening the N-H stretch, and shifting it to lower frequency. The presence of water molecules enhances the ionic hydrogen bond by binding to the amide carbonyl oxygen of NMA and shifts the N-H stretch further to lower frequency. The BOMD IR spectra can recapture all, but about 100 cm(-1), of the 600 to 700 cm(-1) shifts due to the strong N-H stretch anharmonicities observed in experiments. This residual error was found to be due to the lack of zero point energy in the classical treatment of motion in the BOMD method.

Encapsulation of metal cations by the PhePhe ligand: a cation-π ion cage

Structures and binding thermochemistry are investigated for protonated PhePhe and for complexes of PhePhe with the alkaline-earth ions Ba(2+) and Ca(2+), the alkali-metal ions Li(+), Na(+), K(+), and Cs(+), and the transition-metal ion Ag(+). The two neighboring aromatic side chains open the possibility of a novel encapsulation motif of the metal ion in a double cation-π configuration, which is found to be realized for the alkaline-earth complexes and, in a variant form, for the Ag(+) complex. Experimentally, complexes are formed by electrospray ionization, trapped in an FT-ICR mass spectrometer, and characterized by infrared multiple photon dissociation (IRMPD) spectroscopy using the free electron laser FELIX. Interpretation is assisted by thermochemical and IR spectral calculations using density functional theory (DFT). The IRMPD spectrum of protonated PhePhe is reproduced with good fidelity by the calculated spectrum of the most stable conformation, although the additional presence of the secondmost stable conformation is not excluded. All metal-ion complexes have charge-solvated binding modes, with zwitterion (salt bridge) forms being much less stable. The amide oxygen always coordinates to the metal ion, as well as at least one phenyl ring (cation-π interaction). At least one additional chelation site is always occupied, which may be either the amino nitrogen or the carboxy carbonyl oxygen. The alkaline-earth complexes prefer a highly compact caged structure with both phenyl rings providing cation-π stabilization in a "sandwich" configuration (OORR chelation). The alkali-metal complexes prefer open-cage structures with only one cation-π interaction, except perhaps Cs(+). The Ag(+) complex shows a unique preference for the closed-cage amino-bound NORR structure. Ligand-driven perturbations of normal-mode frequencies are generally found to correlate linearly with metal-ion binding energy.

A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide

Most current biomolecular simulations are based on potential energy functions that treat the electrostatic energy as a sum of pairwise Coulombic interactions between effective fixed atomic charges. This approximation, in which many-body induced polarization effects are included in an average way, is expected to be satisfactory for a wide range of systems, but less accurate for processes involving the transfer and partition of ions among heterogeneous environments. The limitations of these potential energy functions are perhaps most obvious in studies of ion permeation through membrane channels. In many cases, the pore is so narrow that the permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with protein atoms. Interactions of cations with protein backbone carbonyl oxygens, in particular, play a critical role in several important biological channels. As a first step toward meeting the challenge of developing an accurate explicit accounting for induced polarization effects, the present work combines experiments and computation to characterize the interactions of alkali and halide ions with N-methylacetamide chosen to represent the peptide bond. From solubility measurements, we extract the solvation free energies of KCl and NaCl in liquid N-methylacetamide. Polarizable models based on the Drude oscillator are then developed and compared with available experimental and ab initio data. The good agreement for a range of structural and thermodynamic properties in the gas and condensed phases suggests that the polarizable models provide an accurate representation of ion-amide interactions in biological systems.

Electrospray: from ions in solution to ions in the gas phase, what we know now

There is an advantage for users of electrospray and nanospray mass spectrometry to have an understanding of the processes involved in the conversion of the ions present in the solution to ions in the gas phase. The following processes are considered: Creation of charge droplets at the capillary tip; Electrical potentials required and possibility of gas discharges; Evolution of charged droplets, due to solvent evaporation and Coulomb explosions, to very small droplets that are the precursors of the gas phase ions; Production of gas phase ions from these droplets via the Ion Evaporation and Charge residue models; Analytical uses of ESIMS of small ions, qualitative and quantitative analysis; Effects of the ESI mechanism on the analysis of proteins and protein complexes; Determination of stability constants of protein complexes; Role of additives such as ammonium acetate on the observed mass spectra.

Determination of apparent decomposition threshold energies of lithium adducts of acylglycerols using tandem mass spectrometry and a novel derived effective reaction path length approach

Apparent decomposition threshold energies for the fragmentation pathways of lithiated acylglycerols were experimentally determined by collisional activation in a quadrupole-hexapole-quadrupole (QhQ) mass spectrometer. A previously developed 'derived effective reaction path length' approach for predicting bond dissociation energies (BDEs) of simple dissociations of electrostatic complexes such as alkali metal adducts (Li+), or halide adducts (Cl(-)) of acylglycerols, was extended to predict covalent bond apparent decomposition threshold energies of lithium adducts of a mono-acylglycerol, a 1,2-diacylglycerol, and a 1,3-diacylglycerol. The ability of the model to treat relatively large ionic systems (e.g. more than 100 atoms) represents a huge advantage of this approach. The model's calculated apparent decomposition threshold energies (Ea) are used in conjunction with the method of energy-resolved mass spectrometry, employing breakdown graphs, to give a more complete quantitative description of the fragmentation processes. Calculated Ea values allowed ranking of the 1,2-diacylglycerol as more reactive than the 1,3-diacylglycerol; the mono-acylglycerol was ranked the least reactive. The method was applied to the low molecular weight product ions generally associated with the hydrocarbon series CnH2n+1+, where two separate pathways are deduced as contributing to the production of the abundant m/z 81 fragment ion. The favored ranking of the neutral losses of fatty acyl substituents for the 1,2-diacylglycerol was determined as: loss of lithium fatty acetate > loss of fatty acid > loss of fatty acyl chain as ketene. For the 1,3-diacylglycerol, the descending order of ease of neutral loss was: loss of fatty acyl ketene > loss of lithium fatty acetate > loss of fatty acid. The results of this study demonstrate that the newly developed method is general in nature, and it can be used for the measurement of covalent bond decomposition threshold energies, as well as for the previously documented electrostatic (noncovalent) bond energies.

Nanoparticle-assisted laser desorption/ionization based mass imaging with cellular resolution

Today, two-dimensional mass spectrometry analysis of biological tissues by means of a technique called mass imaging, mass spectrometry imaging (MSI), or imaging mass spectrometry (IMS) has found application in investigating the distribution of moleculesMSI with matrix-assisted laser desorption/ionization (MALDI) and secondary ion MS (SIMS). However, the size of the matrix crystal and the migration of analytes can decrease the spatial resolution in MALDI, and SIMS can only ionize compounds with relatively low molecular weights. To overcome these problems, we developed a nanoparticle-assisted laser desorption/ionization (nano-PALDI)-based MSI. We used nano-PALDI MSI to visualize lipids and peptides at a resolution of 15 microm in mammalian tissues.

Hydration of potassiated amino acids in the gas phase

The thermochemistry of stepwise hydration of several potassiated amino acids was studied by measuring the gas-phase equilibria, AAK(+)(H(2)O)(n-1) + H(2)O = AAK(+)(H(2)O)(n) (AA = Gly, AL, Val, Met, Pro, and Phe), using a high-pressure mass spectrometer. The AAK(+) ions were obtained by electrospray and the equilibrium constants K(n-1,n) were measured in a pulsed reaction chamber at 10 mbar bath gas, N(2), containing a known partial pressure of water vapor. Determination of the equilibrium constants at different temperatures was used to obtain the DeltaH(n)(o), DeltaS(n)(o), and DeltaG(n)(o) values. The results indicate that the water binding energy in AAK(+)(H(2)O) decreases as the K(+) affinity to AA increases. This trend in binding energies is explained in terms of changes in the side-chain substituent, which delocalize the positive charge from K(+) to AA in AAK(+) complexes, varying the AAK(+)-H(2)O electrostatic interaction.

Modeling competitive interactions in proteins: vibrational spectroscopy of M+(n-methylacetamide)1(H2O)n=0-3, M=Na and K, in the 3 microm region

To properly understand the preferred structures and biological properties of proteins, it is important to understand how they are influenced by their immediate environment. Competitive intrapeptide, peptide...water, ion...water, and ion...peptide interactions, such as hydrogen bonding, play a key role in determining the structures, properties, and functionality of proteins. The primary types of hydrogen bonding involving proteins are intramolecular amide...amide (N-H...O=C) and intermolecular amide...water (O-H...O=C and H-O...H-N). n-Methylacetamide (NMA) is a convenient model for investigating these competitive interactions. An analysis of the IR photodissociation (IRPD) spectra of M+(n-methylacetamide)1(H2O)n=0-3 (M=Na and K) in the O-H and N-H spectral regions is presented. Ab initio calculations (MP2/cc-pVDZ) are used as a guide in identifying both the type and location of hydrogen bonds present. In larger clusters, where several structural isomers may be present in the molecular beam, ab initio calculations are also used to suggest assignments for the observed spectral features. The results presented offer insight to the nature of ion...NMA interactions in an aqueous environment and reveal how different ion...ligand pairwise interactions direct the extent of water...water and water...NMA hydrogen bonding observed.

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure of glycine and zwitterionic glycine

Interactions between metal ions and amino acids are common both in solution and in the gas phase. Here, the effect of metal ions and water on the structure of glycine is examined. The effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water on structures of Gly.Mn+(H2O)m and GlyZwitt.Mn+(H2O)m (m = 0, 2, 5) complexes have been determined theoretically by employing the hybrid B3LYP exchange-correlation functional and using extended basis sets. Selected calculations were carried out also by means of CBS-QB3 model chemistry. The interaction enthalpies, entropies, and Gibbs energies of eight complexes Gly.Mn+ (Mn+ = Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) were determined at the B3LYP density functional level of theory. The computed Gibbs energies DeltaG degrees are negative and span a rather broad energy interval (from -90 to -1100 kJ mol(-1)), meaning that the ions studied form strong complexes. The largest interaction Gibbs energy (-1076 kJ mol(-1)) was computed for the NiGly2+ complex. Calculations of the molecular structure and relative stability of the Gly.Mn+(H2O)m and GlyZwitt.Mn+(H2O)m (Mn+ = Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+; m = 0, 2, and 5) systems indicate that in the complexes with monovalent metal cations the most stable species are the NO coordinated metal cations in non-zwitterionic glycine. Divalent cations Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+ prefer coordination via the OO bifurcated bonds of the zwitterionic glycine. Stepwise addition of two and five water molecules leads to considerable changes in the relative stability of the hydrated species. Addition of two water molecules at the metal ion in both Gly.Mn+ and GlyZwitt.Mn+ complexes reduces the relative stability of metallic complexes of glycine. For Mn+ = Li+ or Na+, the addition of five water molecules does not change the relative order of stability. In the Gly.K+ complex, the solvation shell of water molecules around K+ ion has, because of the larger size of the potassium cation, a different structure with a reduced number of hydrogen-bonded contacts. This results in a net preference (by 10.3 kJ mol(-1)) of the GlyZwitt.K+H2O5 system. Addition of five water molecules to the glycine complexes containing divalent cations Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+ results in a net preference for non-zwitterionic glycine species. The computed relative Gibbs energies are quite high (-10 to -38 kJ mol(-1)), and the NO coordination is preferred in the Gly.Mn+(H2O)5 (Mn+ = Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) complexes over the OO coordination.

Statistical modeling of sequential collision-induced dissociation thresholds

Thermochemistry determined from careful analysis of the energy dependence of cross sections for collision-induced dissociation (CID) reactions has primarily come from the primary dissociation channel. Higher order dissociations generally have thresholds measured to be higher than the thermodynamic limit because of the unknown internal and kinetic energy distributions of the primary products. A model that utilizes statistical theories for energy-dependent unimolecular decomposition to estimate these energy distributions is proposed in this paper. This permits a straightforward modeling of the cross sections for both primary and secondary dissociation channels. The model developed here is used to analyze data for K+(NH3)x, x=2-5, complexes, chosen because the thermochemistry previously determined by threshold CID studies agrees well with values from theory and equilibrium high pressure mass spectrometry. The model is found to reproduce the cross sections with high fidelity and the threshold values for secondary processes are found to be in excellent agreement with literature values. Furthermore, relative thresholds for higher order dissociation processes appear to provide accurate thermodynamic information as well.

An electrospray ionization source for thermochemical investigation with the guided ion beam mass spectrometer

An electrospray ionization (ESI) source developed for use with the guided ion beam tandem mass spectrometer (GIBMS) is described. For accurate determination of thermochemistry using threshold collision-induced dissociation (TCID), it is essential that any source produces ions with four exacting characteristics: (1) high intensity, (2) stable signal, and well-defined energies both (3) kinetic, and (4) internal. To accomplish these objectives, the ions generated by the electrospray are collected using a radio frequency electrodynamic ion funnel and are then transferred into a hexapole ion guide where they are thermalized and subsequently passed into higher-vacuum regions for analysis. The resulting ion intensities using this source can exceed 10(6) ions/s. Stable beams (<10% variation in signal) can be generated over multiple hours. The kinetic energy distribution of ions emerging from this source has been shown to be well described by a Gaussian distribution with a full width half maximum (FWHM) of about 0.1-0.2 eV in the laboratory frame of reference. Finally, TCID results for ions generated with this source show excellent agreement with previously reported threshold values for ions generated using a variety of sources and experimental methodologies. This confirms that internal energies of the ions are well described by a Maxwell-Boltzmann distribution at room temperature.

The sodium ion affinities of simple di-, tri-, and tetrapeptides

The sodium ion affinities (binding energies) of nineteen peptides containing 2-4 residues have been determined by experimental and computational approaches. Na(+)-bound heterodimers with amino acid and peptide ligands (Pep(1), Pep(2)) were produced by electrospray ionization. The dissociations of these Pep(1)-Na(+)-Pep(2) ions to Pep(1)-Na(+) and Pep(2)-Na(+) were examined by collisionally activated dissociation to construct a ladder of relative affinities via the kinetic method. The accuracy of this ladder was subsequently ascertained by experiments using several excitation energies for four peptide pairs. The relative scale was converted to absolute affinities by anchoring the relative values to the known Na(+) affinity of GlyGly. The Na(+) affinities of AlaAla, HisGly, GlyHis, GlyGlyGly, AlaAlaAla, GlyGlyGlyGly, and AlaAlaAlaAla were also calculated at the MP2(full)/6-311 + G(2d,2p) level of ab initio theory using geometries that were optimized at the MP2(full)/6-31G(d) level for AlaAla or HF/6-31G(d) level for the other peptides; the resulting values agree well with experimental Na(+) affinities. Increasing the peptide size is found to dramatically augment the Na(+) binding energy. The calculations show that in nearly all cases, all available carbonyl oxygens are sodium binding sites in the most stable structures. Whenever side chains are available, as in HisGly and GlyHis, specific additional binding sites are provided to the cation. Oligoglycines and oligoalanines have similar binding modes for the di- and tripeptides, but differ significantly for the tetrapeptides: while the lowest energy structure of GlyGlyGlyGly-Na(+) has the peptide folded around the ion with all four carbonyl oxygens in close contact with Na(+), that of AlaAlaAlaAla-Na(+) involves a pseudo-cyclic peptide in which the C and N termini interact via hydrogen bonding, while Na(+) sits on top of the oxygens of three nearly parallel C=O bonds.

A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models

The hydration of K(+) is studied using a hierarchy of theoretical approaches, including ab initio Born-Oppenheimer molecular dynamics and Car-Parrinello molecular dynamics, a polarizable force field model based on classical Drude oscillators, and a nonpolarizable fixed-charge potential based on the TIP3P water model. While models based more directly on quantum mechanics offer the possibility to account for complex electronic effects, polarizable and fixed-charges force fields allow for simulations of large systems and the calculation of thermodynamic observables with relatively modest computational costs. A particular emphasis is placed on investigating the sensitivity of the polarizable model to reproduce key aspects of aqueous K(+), such as the coordination structure, the bulk hydration free energy, and the self diffusion of K(+). It is generally found that, while the simple functional form of the polarizable Drude model imposes some restrictions on the range of properties that can simultaneously be fitted, the resulting hydration structure for aqueous K(+) agrees well with experiment and with more sophisticated computational models. A counterintuitive result, seen in Car-Parrinello molecular dynamics and in simulations with the Drude polarizable force field, is that the average induced molecular dipole of the water molecules within the first hydration shell around K(+) is slightly smaller than the corresponding value in the bulk. In final analysis, the perspective of K(+) hydration emerging from the various computational models is broadly consistent with experimental data, though at a finer level there remain a number of issues that should be resolved to further our ability in modeling ion hydration accurately.

Properties of microsolvated ions: From the microenvironment of chromophore and alkali metal ions in proteins to negative ions in water clusters

Here we discuss the fascinating chemistry and physics of microsolvated ions that bridge the transition from bare ions in gas phase to ions in solution. Such ions occur in many situations in biochemistry and are crucial for several functions; metal ions, for example, must remove their water shell to pass through ion pumps in membranes. Furthermore, only a few water molecules are buried in the hydrophobic pockets of proteins where they are bound to charged amino acid residues or ionic chromophores. Another aspect is the reactivity of microsolvated ions and the importance in atmospheric, organic and inorganic chemistry. We close by a discussion of the stability of molecular dianions, and how hydration affects the electronic binding energy. There is a vast literature on microsolvated ions, and in this review we are far from being comprehensive, rather we mainly bring examples of our own work.

Polarization effects and charge transfer in the KcsA potassium channel

The electronic structure of the selectivity filter of KcsA K(+) channel is investigated by density functional theory (DFT/BLYP) and QM/MM methods. The quantum part includes the selectivity filter, which is polarized by the electrostatic field of the environment treated with the Amber force field. The details of the electronic structure were investigated using the maximally localized Wannier function centers of charge and Bader's atoms in molecules charge analysis. Our results show that the channel backbone carbonyl groups are largely polarized and that there is a sizeable charge transfer from the backbone to the cations. These effects are expected to be important for an accurate description of the carbonyl groups and the ion-ion electrostatic repulsion, which have been proposed to play a central role for the selectivity mechanism of the channel [S.Y. Noskov, S. Berneche, B. Roux, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834].

Small-molecule MALDI using the matrix suppression effect to reduce or eliminate matrix background interferences

The matrix suppression effect (MSE) can lead to high-quality MALDI mass spectra: strong analyte signals and weak or negligible matrix background peaks. Experiment and theory suggest that MSE should be widespread and, therefore, generally applicable to measurement of low molecular weight (LMW) substances. These are otherwise impractical with MALDI due to interference from matrix. Appropriate conditions for MSE were investigated and tested on a variety of LMW substances. Straightforward and semiautomated interpretation was possible for 87.7% of these. Another 3.5% gave poor MSE due to sodium cationization rather than protonation of the analyte, but interpretation was possible. MALDI imaging shows that MSE varies significantly across a typical sample. Selective data accumulation could further increase the utility of the method. Samples containing more than one analyte were also studied. Analyte-analyte suppression was not found to be excessive, and moderately abundant minority species can be adequately detected.

Ion formation mechanisms in UV-MALDI

Matrix Assisted Laser Desorption/Ionization (MALDI) is a very widely used analytical method, but has been developed in a highly empirical manner. Deeper understanding of ionization mechanisms could help to design better methods and improve interpretation of mass spectra. This review summarizes current mechanistic thinking, with emphasis on the most common MALDI variant using ultraviolet laser excitation. A two-step framework is gaining acceptance as a useful model for many MALDI experiments. The steps are primary ionization during or shortly after the laser pulse, followed by secondary reactions in the expanding plume of desorbed material. Primary ionization in UV-MALDI remains somewhat controversial, the two main approaches are the cluster and pooling/photoionization models. Secondary events are less contentious, ion-molecule reaction thermodynamics and kinetics are often invoked, but details differ. To the extent that local thermal equilibrium is approached in the plume, the mass spectra may be straightforwardly interpreted in terms of charge transfer thermodynamics.

Extending, and Repositioning, a Thermochemical Ladder: High-Level Quantum Chemical Calculations on the Sodium Cation Affinity Scale

High-level ab initio quantum chemical calculations, at the CP-dG2thaw level of theory, are reported for coordination of Na+ to a wide assortment of small organic and inorganic ligands. The ligands range in size from H to C6H6, and include 22 of the ligands for which precise relative sodium ion binding free energies have been determined by recent Fourier transform ion cyclotron resonance and guided ion beam studies. Agreement with the relative experimental values is excellent (+/-1.1 kJ mol(-1)), and agreement with the absolute scale (obtained when these relative values are pegged to the CH3NH2 "anchor" value measured in a high-pressure mass spectrometric study) is only marginally poorer, with CP-dG2thaw values exceeding the absolute experimental DeltaG(298) values by an average of 2.1 kJ mol(-1). The excellent agreement between experiment and the CP-dG2thaw technique also suggests that the additional 97 ligands surveyed here (which, in many cases, are not readily susceptible to laboratory investigation) can also be reliably fitted to the existing experimental scale. However, while CP-dG2thaw and the experimental ladder are in close accord, a small set of higher level ab initio calculations on sodium ion/ligand complexes (including several values obtained here using the W1 protocol) suggests that the CP-dG2thaw values are themselves too low by approximately 2.5 kJ mol(-1), thereby implying that the accepted laboratory values are typically 4.6 kJ mol(-1) too low. The present work also highlights the importance of Na+/ligand binding energy determinations (whether by experimental or theoretical approaches) on a case-by-case basis: trends in increasing binding energy along homologous series of compounds are not reliably predictable, nor are binding site preferences or chelating tendencies in polyfunctional compounds.

Carbonate, carbamate, urea, and guanidine as model species for functional groups in biological molecules — A combined density functional theory and mass spectrometry examination of polysodiation and gas-phase dissociation

Electrospray mass spectrometric analyses of carbonate, carbamate, urea, and guanidine in the presence of sodium ions results in polysodiated complexes of the type, [M – (n – 1)H + nNa]+, where M is the species analyzed and n = 2 and (or) 3. These complexes are unusual in their high sodium contents and their attractive structures. The [M – H + 2Na]+ complexes fragment to produce [Na2NH2]+, Na+, and a product ion resulting from the loss of NH3. The [M – 2H + 3Na]+ complexes dissociate to give a number of fragment ions, including [Na3O]+, [Na2OH]+, [NaOCNNa]+, [Na2NH2]+, [Na3CN2]+, and Na+, depending on the elemental composition of M. These dissociation reactions were examined both experimentally by mass spectrometry and theoretically by density functional theory. Reaction profiles as calculated at B3LYP/6-311G** for disodiated carabamate, urea, and guanidine, and for all the bases in trisodiated form are given. Both experimental and theory show [Na3CO3]+ to have high stability towards collisional activation and to preferentially dissociate to give [Na3O]+ and CO2, rather than Na+ and Na2CO3.Key words: carbonate, carbamate, urea, guanidine, electrospray, collision-induced dissociation, density functional theory, sodium ion binding energies.

An investigation of the ion–molecule interactions of protonated glycine with ammonia by high pressure mass spectrometry and ab initio calculations

The thermochemistry of gas-phase ion molecule interactions and the structures of various clusters between protonated glycine (GlyH+), glycine, and ammonia have been studied by high pressure mass spectrometry (HP-MS) and ab initio calculations. For the association reactions of GlyH+ with NH3, Gly(NH3)H+ with NH3, and (Gly)2H+ with NH3, the enthalpy changes experimentally determined are –23.2, –18.3, and –19.1 kcal mol–1 (1 cal = 4.184 J), respectively. For all clusters investigated, the measured binding enthalpies are in excellent agreement with those obtained from ab initio calculations at the B3LYP/6-311+G(d,p) level of theory. Different isomers of each of these clusters have been obtained and the corresponding binding energies have been computed. The potential energy surface for isomerization of the clusters of protonated glycine with ammonia has also been computed at the same level. For this cluster, the three most stable isomers all involve a proton transfer from protonated glycine to ammonia. According to the calculated potential energy surface, the barrier between GN4, the least stable isomer, and the most stable isomer (GN1) is 11.5 kcal mol–1 at 298 K. Thus, this isomerization will be facile given the exothermicity of the association reaction. Therefore, a statistical distribution of isomers will be present under thermal equilibrium conditions. Single point energy calculations at the MP2(full)/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level of theory reveal that the isomer GN2 in which glycine has a zwitterionic structure has the same energy as the most stable non-zwitterionic isomer GN1. NH4+ evidently may stabilize the zwitterionic structure of glycine. In contrast, N2H7+ and GlyH+ are not as effective in stabilizing the zwitterionic structure of glycine. This likely results from the more localized charge in NH4+ giving rise to stronger hydrogen bonds with the carboxylate moiety of zwitterionic glycine. This conjecture is supported by the computational results.Key words: high pressure mass spectrometry, glycine, gas-phase ion thermochemistry, ab initio calculations, cluster structure.