Proton Affinity of Lysine Homologues from the Extended Kinetic Method

Modulation of proton-coupled electron transfer reactions in lysine-containing alpha-helixes: alpha-helixes promoting long-range electron transfer

The proton-coupled electron transfer (PCET) reaction plays an important role in promoting many biological and chemical reactions. Usually, the rate of the PCET reaction increases with an increase in the electron transfer distance because long-range electron transfer requires more free energy barriers. Our density functional theory calculations here reveal that the mechanism of PCET occurring in lysine-containing alpha(α)-helixes changes with an increasing number of residues in the α-helical structure and the different conformations because of the modulation of the excess electron distribution by the α-helical structures. The rate constants of the corresponding PCET reactions are independent of or substantially shallower dependent on the electron transfer distances along α-helixes. This counter-intuitive behavior can be attributed to the fact that the formation of larger macro-cylindrical dipole moments in longer helixes can promote electron transfer along the α-helix with a low energy barrier. These findings may be useful to gain insights into long-range electron transfer in proteins and design α-helix-based electronics via the regulation of short-range proton transfer.

Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay

The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]⁺ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]⁺ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm^-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.

Spectroscopic Evidence for Lactam Formation in Terminal Ornithine b2+ and b3+ Fragment Ions

Infrared multiple photon dissociation action spectroscopy was performed on the AlaOrn b₂⁺ and AlaAlaOrn b₃⁺ fragment ions from ornithine-containing tetrapeptides. Infrared spectra were obtained in the fingerprint region (1000-2000 cm^-1) using the infrared free electron lasers at the Centre Laser Infrarouge d'Orsay (CLIO) facility in Orsay, France, and the free electron lasers for infrared experiments (FELIX) facility in Nijmegen, the Netherlands. A novel terminal ornithine lactam AO⁺ b₂⁺ structure was synthesized for experimental comparison and spectroscopy confirms that the b₂⁺ fragment ion from AOAA forms a lactam structure. Comparison of experimental spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory shows that AO⁺ b₂⁺ forms a terminal lactam protonated either on the lactam carbonyl oxygen or the N-terminal nitrogen atom. Several low-lying conformers of these isomers are likely populated following IRMPD dissociation. Similarly, a comparison of the experimental IRMPD spectrum with calculated spectra shows that AAO⁺ b₃⁺-ions also adopt a lactam structure, again with multiple different protonation sites, during fragmentation. This study provides spectroscopic confirmation for the lactam cyclization proposed for the "ornithine effect" and represents an alternative b_n⁺ structure to the oxazolone and diketopiperazine/macrocycle structures most often formed.

Functional Properties of Amino Acid Side Chains as Biomarkers of Extraterrestrial Life

The present study proposes to search our solar system (Mars, Enceladus, Europa) for patterns of organic molecules that are universally associated with biological functions and structures. The functions are primarily catalytic because life could only have originated within volume/space-constrained compartments containing chemical reactions catalyzed by certain polymers. The proposed molecular structures are specific groups in the side chains of amino acids with the highest catalytic propensities related to life on Earth, that is, those that most frequently participate as key catalytic groups in the active sites of enzymes such as imidazole, thiol, guanidinium, amide, and carboxyl. Alternatively, these or other catalytic groups can be searched for on non-amino-acid organic molecules, which can be tested for certain hydrolytic catalytic activities. The first scenario assumes that life may have originated in a similar manner as the terrestrial set of α-amino acids, while the second scenario does not set such a requirement. From the catalytic propensity perspective proposed in the first scenario, life must have invented amino acids with high catalytic propensity (His, Cys, Arg) in order to overcome, and be complemented by, the low catalytic propensity of the initially available abiogenic amino acids. The abiogenic and the metabolically invented amino acids with the lowest catalytic propensity can also serve as markers of extraterrestrial life when searching for patterns on the basis of the following functional propensities related to protein secondary/quaternary structure: (1) amino acids that are able to form α-helical intramembrane peptide domains, which can serve as primitive transporters in protocell membrane bilayers and catalysts of simple biochemical reactions; (2) amino acids that tend to accumulate in extremophile proteins of Earth and possibly extraterrestrial life. The catalytic/structural functional propensity approach offers a new perspective in the search for extraterrestrial life and could help unify previous amino acid-based approaches.

Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation†

Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm^-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH⁺, CavLi⁺, and CavNa⁺; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK⁺ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs⁺ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm^-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa⁺ and ArgK⁺. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na⁺, K⁺, and Cs⁺. A major difference between the zwitterionic forms of ArgM⁺ and CavM⁺ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.

Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

A method to facilitate the characterization of stapled or cyclic peptides is reported via an arginine-selective derivatization strategy coupled with MS/MS analysis. Arginine residues are converted to ornithine residues through a deguanidination reaction that installs a highly selectively cleavable site in peptides. Upon activation by CID or UVPD, the ornithine residue cyclizes to promote cleavage of the adjacent amide bond. This Arg-specific process offers a unique strategy for site-selective ring opening of stapled and cyclic peptides. Upon activation of each derivatized peptide, site-specific backbone cleavage at the ornithine residue results in two complementary products: the lactam ring-containing portion of the peptide and the amine-containing portion. The deguanidination process not only provides a specific marker site that initiates fragmentation of the peptide but also offers a means to unlock the staple and differentiate isobaric stapled peptides.

Efficient and directed peptide bond formation in the gas phase via ion/ion reactions

Amide linkages are among the most important chemical bonds in living systems, constituting the connections between amino acids in peptides and proteins. We demonstrate the controlled formation of amide bonds between amino acids or peptides in the gas phase using ion/ion reactions in a mass spectrometer. Individual amino acids or peptides can be prepared as reagents by (i) incorporating gas phase-labile protecting groups to silence otherwise reactive functional groups, such as the N terminus; (ii) converting the carboxyl groups to the active ester of N-hydroxysuccinimide; and (iii) incorporating a charge site. Protonation renders basic sites (nucleophiles) unreactive toward the N-hydroxysuccinimide ester reagents, resulting in sites with the greatest gas phase basicities being, in large part, unreactive. The N-terminal amines of most naturally occurring amino acids have lower gas phase basicities than the side chains of the basic amino acids (i.e., those of histidine, lysine, or arginine). Therefore, reagents may be directed to the N terminus of an existing "anchor" peptide to form an amide bond by protonating the anchor peptide's basic residues, while leaving the N-terminal amine unprotonated and therefore reactive. Reaction efficiencies of greater than 30% have been observed. We propose this method as a step toward the controlled synthesis of peptides in the gas phase.

The ornithine effect in peptide cation dissociation

Facile cleavage C-terminal to ornithine residues in gas phase peptides has been observed and termed the ornithine effect. Peptides containing internal or C-terminal ornithine residues, which are formed from deguanidination of arginine in solution, were fragmented to produce either a y-ion or water loss, respectively, and the complementary b-ion. The fragmentation patterns of several peptides containing arginine were compared to those of the ornithine analogues. Conversion of arginine to ornithine results in a decrease of the gas phase proton affinity of the residue, thereby increasing the mobility of the ionizing proton. This alteration allows the nucleophilic amine to facilitate a neighboring group reaction to induce a cleavage of the adjacent amide bond. The selective cleavage at the ornithine residue is proposed to result from the highly favorable generation of a six-membered lactam ring. The ornithine effect was compared with the well-known proline and aspartic acid effects in peptide fragmentation using angiotensin II, DRVYIHPF and the ornithine analogue, DOVYIHPF. Under conditions favorable to either the aspartic acid (i.e. singly protonated peptide) or proline effect (i.e. doubly protonated peptide), the ornithine effect was consistently observed to be the more favorable fragmentation pathway. The highly selective nature of the ornithine effect opens up the possibility for conversion of arginine to ornithine residues to induce selective cleavages in polypeptide ions. Such an approach may complement strategies that seek to generate non-selective cleavages of the related peptides.

Gas phase basicities of polyfunctional molecules. Part 3: Amino acids

The present article is the third part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules (first part: Mass Spectrom. Rev., 2007, 26:775-835, second part: Mass Spectrom. Rev., 2011, in press). This review is devoted to the 20 proteinogenic amino acids and is divided in two parts. In the first one, the experimental data obtained during the last 30 years using the equilibrium, thermokinetic and kinetic methods are presented. A general re-assignment of the values originating from these various experiments has been done on the basis of the commonly accepted Hunter & Lias 1998 gas-phase basicity scale in order to provide an homogeneous set of data. In the second part, theoretical investigations on gaseous neutral and protonated amino acids are reviewed. Conformational landscapes of both types of species were examined in order to provide theoretical protonation thermochemistry based on the truly identified most stable conformers. Proton affinities computed at the presently highest levels of theory (i.e. composite methods such as Gn procedures) are presented. Estimates of thermochemical parameters calculated using a Boltzmann distribution of conformers at 298K are also included. Finally, comparison between experiment and theory is discussed and a set of evaluated proton affinities, gas-phase basicities and protonation entropies is proposed.

Gas-phase acid-base properties of melamine and cyanuric acid

The thermochemical properties of melamine and cyanuric acid were characterized using mass spectrometry measurements along with computational studies. A triple-quadrupole mass spectrometer was employed with the application of the extended Cooks kinetic method. The proton affinity (PA), gas-phase basicity (GB), and protonation entropy (Δ(p)S) of melamine were determined to be 226.2 ± 2.0 kcal/mol, 218.4 ± 2.0 kcal/mol, and 26.2 ± 2.0 cal/mol K, respectively. The deprotonation enthalpy (Δ(acid)H), gas-phase acidity (Δ(acid)G), and deprotonation entropy (Δ(acid)S) of cyanuric acid were determined to be 330.7 ± 2.0 kcal/mol, 322.9 ± 2.0 kcal/mol, and 26.1 ± 2.0 cal/mol K, respectively. The geometries and energetics of melamine, cyanuric acid, and related ionic species were calculated at the B3LYP/6-31+G(d) level of theory. The computationally predicted proton affinity of melamine (225.9 kcal/mol) and gas-phase deprotonation enthalpy of cyanuric acid (328.4 kcal/mol) agree well with the experimental results. Melamine is best represented as the imide-like triazine-triamine form and the triazine nitrogen is more basic than the amino group nitrogen. Cyanuric acid is best represented as the keto-like tautomer and the N-H group is the most probable proton donor.

Gas-phase acidities of cysteine-polyglycine peptides: the effect of the cysteine position

The sequence and conformational effects on the gas-phase acidities of peptides have been studied by using two pairs of isomeric cysteine-polyglycine peptides, CysGly(3,4)NH(2) and Gly(3,4)CysNH(2). The extended Cooks kinetic method was employed to determine the gas-phase acidities using a triple quadrupole mass spectrometer with an electrospray ionization source. The ion activation was achieved via collision-induced dissociation experiments. The deprotonation enthalpies (Delta(acid)H) were determined to be 323.9 +/- 2.5 kcal/mol (CysGly(3)NH(2)), 319.2 +/- 2.3 kcal/mol (CysGly(4)NH(2)), 333.8 +/- 2.1 kcal/mol (Gly(3)CysNH(2)), and 321.9 +/- 2.8 kcal/mol (Gly(4)CysNH(2)), respectively. The corresponding deprotonation entropies (Delta(acid)S) of the peptides were estimated. The gas-phase acidities (Delta(acid)G) were derived to be 318.4 +/- 2.5 kcal/mol (CysGly(3)NH(2)), 314.9 +/- 2.3 kcal/mol (CysGly(4)NH(2)), 327.5 +/- 2.1 kcal/mol (Gly(3)CysNH(2)), and 317.4 +/- 2.8 kcal/mol (Gly(4)CysNH(2)), respectively. Conformations and energetic information of the neutral and anionic peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single point energy calculations (B3LYP/6-31+G(d)), respectively. Both neutral and deprotonated peptides adopt many possible conformations of similar energies. All neutral peptides are mainly random coils. The two C-cysteine anionic peptides, Gly(3,4)(Cys-H)(-)NH(2), are also random coils. The two N-cysteine anionic peptides, (Cys-H)(-)Gly(3,4)NH(2), may exist in both random coils and stretched helices. The two N-cysteine peptides, CysGly(3)NH(2) and CysGly(4)NH(2), are significantly more acidic than the corresponding C-terminal cysteine ones, Gly(3)CysNH(2) and Gly(4)CysNH(2). The stronger acidities of the former may come from the greater stability of the thiolate anion resulting from the interaction with the helix-macrodipole, in addition to the hydrogen bonding interactions.

A reevaluation of computed proton affinities for the common alpha-amino acids

The proton affinities of the 20 common amino acids have been computed at the G3MP2 level using structures derived from broad conformational searches at a variety of levels including G3MP2. In some cases, the conformational surveys identified more stable species than had been used in previous studies of proton affinities, though the differences in energy are sometimes rather small. The present values are likely the most reliable measure of amino acid proton affinities in the gas phase. An analysis of differences between these values and those obtained experimentally via the kinetic method indicates that the extraction of proton affinities from kinetic method data can potentially lead to large errors linked to the estimation of relative protonation entropies.

The Curtin-Hammett principle in mass spectrometry

The Curtin-Hammett principle (CHP) is an important concept in physical organic chemistry and is often utilized in the investigation of reaction mechanisms. Two reactants, A and B, in rapid equilibrium, react to form products P(A) and P(B) with rates k(A) and k(B), respectively. If the reaction is under kinetic control and the rate of equilibration between the two reactants is much faster than the reactions to form products, then the branching ratio of products P(A) and P(B) depends solely on the difference in barrier heights for the two product channels. The CHP is based on the fact that the ratio of products formed is not determined by the reactant population ratio. However, the CHP also applies to studies in other areas of chemistry, including mass spectrometry. This Account describes work from our groups in which the results must be interpreted in light of the CHP. These studies illustrate two important implications of the CHP. First, they demonstrate how product distributions cannot be used to assess reactant structure in mechanistic studies in Curtin-Hammett systems. A recent investigation of the structure of hydroxysiliconate anions demonstrated that it was not possible to distinguish between the possible reactant ion structures. A second important implication of the CHP is that the structure of the reactant does not affect the product branching ratio and therefore does not need to be a consideration if the CHP applies. We address this aspect of the discussion through kinetic method studies of the acidities of amino acids and proton affinities of bifunctional compounds. Recently reported mass spectrometric studies illustrate how the CHP puts limitations on what conclusions can be drawn from product distribution studies but also allows experimental methods, such as the kinetic method, to be carried out for complicated systems without having to know all the details of the reactant ion structures. These studies show that although the CHP is most commonly applied in mechanistic studies in physical organic chemistry, it also applies to other areas of chemistry, including mass spectrometry. Although the CHP in some cases limits the conclusions that can be drawn from an experimental study, its proper application can often be used to greatly simplify very complicated chemical systems. Therefore, it is important in mass spectrometry, and indeed, in all areas of chemistry, to recognize those systems in which the CHP should and should not apply.

Proton affinity and zwitterion stability: new results from infrared spectroscopy and theory of cationized lysine and analogues in the gas phase

The gas-phase structures of alkali metal cationized lysine (Lys), alpha-N-methyllysine (NMeLys), and epsilon-N,N-dimethyllysine (Lys(Me)(2)) are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser and ab initio calculations. The proton affinities of the compounds span a range of approximately 20 kJ/mol. For NMeLys x M(+), experiment and theory indicate that NMeLys is nonzwitterionic for M = Li and zwitterionic for M = Na and K. For Lys(Me)(2) x M(+), experiment and theory indicate that Lys(Me)(2) is zwitterionic for M = Li, Na, and K. This is the first spectroscopic observation of the zwitterionic form of an amino acid complexed with Li(+). The results are compared with IRMPD spectra reported previously for Lys and -N-methyllysine (Lys(Me)) complexed with Li, Na, and K, and new calculations performed at higher levels of theory for those ions. The combined experimental and theoretical results indicate that protonation in the zwitterionic forms of the these amino acids is favored at the more basic methylated amine site, but that any relationship between the proton affinity of the amino acid and the relative zwitterion stability of the alkali metal cationized amino acid is only indirect. These results provide additional evidence that proton affinities are not a reliable indicator of zwitterion stability for cationized amino acids because side chains can have very different effects on the stability of different conformers in the neutral, protonated, and metal cationized forms.

Theoretical and experimental investigation of the energetics of cis-trans proline isomerization in peptide models

The energetics of cis-trans proline isomerization in small peptide models have been investigated using the hybrid density functional theory method B3LYP with a 6-31+G* basis set. The molecules studied are models for the phospho-Ser/Thr-Pro substrate for Pin-1, a peptidyl-prolyl isomerase (PPIase) involved in cell division. Pin-1 requires phosphorylation of a Ser or Thr residue adjacent to a Pro residue in the substrate and catalyzes cis-trans isomerization about the proline amide bond. The dihedral angle that would correspond to the reaction coordinate for isomerization of the omega peptide bond was investigated for several small models. Relaxed potential energy scans for this dihedral angle in N-methylacetamide, 1, N,N-dimethylacetamide, 2, acetylpyrrolidine, 3 and acetylproline, 4, were carried out in 20 degrees steps using the B3LYP/6-31+G* level of theory. In addition, similar scans were carried out for 1-4 protonated on the acetylamide carbonyl oxygen. Optimized structures for 1-4 protonated on the amide nitrogen were also obtained at B3LYP/6-31+G*. Relative proton affinities were determined for each site at various angles along the reaction coordinate for isomerization. The relative proton affinities were anchored to experimental gas phase proton affinities, which were taken from the literature for 1 and 2, or determined in an electrospray ionization-quadrupole ion trap instrument using the extended kinetic method for 3 and 4. Proton affinities of 925 +/- 10 and 911 +/- 12 kJ/mol were determined for 3 and 4, respectively. These studies suggest that the nitrogen atom in these amides becomes the most basic site in the molecule at a dihedral angle of ca. 130 degrees . In addition, the nitrogen atoms in 2-4 are predicted to attain basicities in the range 920-950 kJ/mol, making them basic enough to be the preferred site for hydrogen bonding in the Pin-1 active site, in support of the proposed mechanism for PPIases.

Infrared Spectroscopy of Cationized Lysine and ε-N-methyllysine in the Gas Phase: Effects of Alkali-Metal Ion Size and Proton Affinity on Zwitterion Stability

The gas-phase structures of protonated and alkali-metal-cationized lysine (Lys) and epsilon-N-methyllysine (Lys(Me)) are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. IRMPD spectra of Lys.Li(+) and Lys.Na(+) are similar, but the spectrum for Lys.K(+) is different, indicating that the structure of lysine in these complexes depends on the metal ion size. The carbonyl stretch of a carboxylic acid group is clearly observed in each of these spectra, indicating that lysine is nonzwitterionic in these complexes. A detailed comparison of these spectra to those calculated for candidate low-energy structures indicates that the bonding motif for the metal ion changes from tricoordinated for Li and Na to dicoordinated for K, clearly revealing the increased importance of hydrogen-bonding relative to metal ion solvation with increasing metal ion size. Spectra for Lys(Me).M(+) show that Lys(Me), an analogue of lysine whose side chain contains a secondary amine, is nonzwitterionic with Li and zwitterionic with K and both forms are present for Na. The proton affinity of Lys(Me) is 16 kJ/mol higher than that of Lys; the higher proton affinity of a secondary amine can result in its preferential protonation and stabilization of the zwitterionic form.

Interaction of Guanine, Its Anions, and Radicals with Lysine in Different Charge States

Modification in DNA or protein structure can severely affect DNA-protein interactions and the functioning of biological systems. Some new insights into radiation-induced effects of guanine-lysine interactions have been obtained here by theoretical investigations. Geometries of zwitterionic and non-zwitterionic lysine in different charge states (neutral, radical cation, and protonated cation) were optimized employing the B3LYP/6-31G** and B3LYP/AUG-cc-pVDZ levels of hybrid density functional theory (DFT) and using the second-order Møller-Plesset perturbation theory along with the 6-31G** basis set. In the case of neutral lysine in the gas phase, no zwitterionic structure was obtained. The non-zwitterionic structures of lysine in radical and protonated cationic forms are appreciably more stable than the corresponding zwitterionic structures in the gas phase as obtained at all levels of theory employed here. Binding of guanine and different dehydrogenated guanine radicals with lysine in different charge states was studied at the B3LYP/6-31G** level of DFT. When guanine makes a complex with the lysine radical cation, large amounts of spin and positive charge densities are transferred from the lysine radical cation to guanine and the guanine is thus converted from its normal form to the radical cationic form. Complexation of the lysine radical cation with the H1-hydrogen-abstracted guanine radical leads to CO2 liberation and proton transfer from lysine. These results are compared with the available experimental ones.

Are Carboxyl Groups the Most Acidic Sites in Amino Acids? Gas-Phase Acidity, H/D Exchange Experiments, and Computations on Cysteine and Its Conjugate Base

Hydrogen-deuterium exchange experiments were carried out on the conjugate base of cysteine with four different deuterated alcohols. Three H/D exchanges are observed to take place in each case, and a relay mechanism which requires the SH and CO2H groups to have similar acidities and subsequently proceeds through a zwitterionic intermediate is proposed. Gas-phase acidity measurements also were carried out in a quadrupole ion trap using the extended kinetic method and in a Fourier transform mass spectrometer by an equilibrium determination. The results are in excellent accord with each other and high-level ab initio and density functional theory calculations and indicate that the side-chain thiol in cysteine is more acidic than the carboxyl group by 3.1 kcal mol-1. Deprotonated cysteine is thus predicted to be a thiolate ion. A zwitterionic species also was located on the potential energy surface, but it is energetically unfavorable (+10.1 kcal mol-1).

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.

Polar Group Enhanced Gas-Phase Acidities of Carboxylic Acids: An Investigation of Intramolecular Electrostatic Interaction

We studied the effects of polar groups on the gas-phase acidities of carboxylic acids experimentally and computationally. In this connection, the gas-phase acidities (DeltaH(acid), the enthalpy of deprotonation, and DeltaG(acid), the deprotonation free energy) of borane-complexed methylaminoacetic acid ((CH(3))2N(BH(3))CH(2)CO(2)H) and methylthioacetic acid (CH(3)S(BH(3))CH(2)CO(2)H) were measured using the kinetic method in a flowing afterglow-triple quadrupole mass spectrometer. The values of DeltaH(acid) and DeltaG(acid) of (CH(3))2N(BH(3))CH(2)CO(2)H were determined to be 328.8 +/- 1.9 and 322.1 +/- 1.9 kcal/mol, and those of CH(3)S(BH(3))CH(2)CO(2)H were determined to be 325.8 +/- 1.9 and 319.2 +/- 1.9 kcal/mol, respectively. The theoretical enthalpies of deprotonation of (CH(3))2N(BH(3))CH(2)CO(2)H (329.2 kcal/mol) and CH(3)S(BH(3))CH(2)CO(2)H (325.5 kcal/mol) were calculated at the B3LYP/6-31+G(d) level of theory. The calculated enthalpies of deprotonation of N-oxide-acetic acid (CH(3)NOCH(2)CO(2)H, 329.4 kcal/mol) and S-oxide-acetic acid (CH(3)SOCH(2)CO(2)H, 328.6 kcal/mol) are comparable to the experimental results for borane-complexed methylamino- and methylthioacetic acids. The enthalpy of deprotonation of sulfone-acetic acid (CH(3)SO2CH(2)CO(2)H, 326.1 kcal/mol) is about 2 kcal/mol lower than the S-oxide-acetic acid. The calculated enthalpy of deprotonation of sulfoniumacetic acid, (CH(3))2S+CH(2)CO(2)H, is 243.0 kcal/mol. Compared to the corresponding reference molecules, CH(3)NHCH(2)CO(2)H and CH(3)SCH(2)CO(2)H, the dipolar group and the monopolar group substituted carboxylic acids are stronger acids by 11-14 and 97 kcal/mol, respectively. We correlated the changes of the acidity upon a polar group substitution to the electrostatic free energy within the carboxylate anion. The acidity enhancements in polar group substituted carboxylic acids are the results of the favorable electrostatic interactions between the polar group and the developing charge at the carboxyl group.

Proton Affinity of Canavanine and Canaline, Oxyanalogues of Arginine and Ornithine, from the Extended Kinetic Method

The absolute proton affinities of the nonprotein amino acids canavanine and canaline have been determined using the extended kinetic method in an electrospray ionization quadrupole ion trap instrument. Canavanine results from the substitution of an oxygen atom for the delta-CH2 group in the side chain of the protein amino acid arginine, whereas canaline results from a similar substitution at the delta-CH2 group in the side chain of ornithine. Absolute proton affinities of 1001+/-9 and 950+/-7 kJ/mol are obtained for canavanine and canaline, respectively. For canaline, this proton affinity is in excellent agreement with theoretical predictions obtained using the hybrid density functional theory method B3LYP/6-311++G**//B3LYP/6-31+G*. For canavanine, theory predicts a somewhat larger proton affinity of 1015 kJ/mol. Oxygen atom substitution in these nonprotein amino acids results in a decrease in their proton affinities of 40-50 kJ/mol compared to arginine and ornithine.

Revising the proton affinity scale of the naturally occurring alpha-amino acids

The proton affinities (PA) of the 20 naturally occurring alpha-amino acids (AA) have been determined computationally by means of density functional theory (DFT) and high-level G2(MP2) calculations. These theoretical PAs, together with data that have appeared since 1997 in the literature, are used to validate the most reasonable currently available PA scale for AAs (Harrison, A. G. Mass Spectrom. Rev. 1997, 16, 201-217.). Significant scatter is observed for the PAs of Ser, Asp, Phe, Asn, Met, Pro, Gln, Glu, Trp, His, Lys, and Arg, many of which have a basic side-chain functionality. Critical review of the available data leads to new consensus PAs for Asn, Gln, Met, and Arg of 222.4, 230.5, 223.7, and 250.2 kcal/mol, respectively.

Evaluation of the protonation thermochemistry obtained by the extended kinetic method

An evaluation of the results obtained by the extended kinetic method for a series of representative bases is presented here. Analysis of the original experimental data is conducted using the orthogonal distance regression (ODR) statistical treatment. A comparison with the proton affinities and protonation entropies obtained from variable temperature equilibrium constant measurements demonstrate deviations, which may be ascribed to random and systematic errors. Considerable random errors are associated with the extended kinetic method if the number of reference bases and the range of effective temperatures are too low. It is also confirmed that large systematic errors on proton affinities and protonation entropies are obtained when large protonation entropy is associated with the considered system. It is, however, encouraging to note that the gas phase basicities obtained by the extended kinetic method are generally comparable to that obtained by other methods within a few kJ/mol.

Structures of Lithiated Lysine and Structural Analogues in the Gas Phase: Effects of Water and Proton Affinity on Zwitterionic Stability

The structures of lithiated lysine, ornithine, and related molecules, both with and without a water molecule, are investigated using both density functional theory and blackbody infrared radiative dissociation experiments. The lowest-energy structure of lithiated lysine without a water molecule is nonzwitterionic; the metal ion interacts with both nitrogen atoms and the carbonyl oxygen. Structures in which lysine is zwitterionic are higher in energy by more than 29 kJ/mol. In contrast, the singly hydrated clusters with the zwitterionic and nonzwitterionic forms of lysine are more similar in energy, with the nonzwitterionic form more stable by only approximately 7 kJ/mol. Thus, a single water molecule can substantially stabilize the zwitterionic form of an amino acid. Analogous molecules that have methyl groups attached to either the N-terminus (NMeLys) or the side-chain amine (Lys(Me)) have proton affinities greater than that of lysine. In the lithiated clusters with a water molecule attached, the zwitterionic forms of NMeLys and Lys(Me) are calculated to be approximately 4 and approximately 11 kJ/mol more stable than the nonzwitterionic forms, respectively. Calculations of the potential-energy pathway for interconversion between the different forms of lysine in the lithiated complex indicate multiple stable intermediates with an overall barrier height of approximately 83 kJ/mol between the lowest-energy nonzwitterionic form and the most accessible zwitterionic form. Experimentally determined binding energies of water are similar for all these complexes and range from 57 to 64 kJ/mol. These results suggest that loss of a water molecule from the lysine complexes is both energetically and entropically favored compared to interconversion between the nonzwitterionic and zwitterionic structures. Comparisons to calculated binding energies of water to the various structures show that the experimental results are most consistent with the nonzwitterionic forms.

Theoretical proton affinities of α1 adrenoceptor ligands

A systematic study has been performed of the proton affinity of a large family of agonists and antagonists of the alpha1-adrenoceptor at the B3LYP/6-31G* level of theory. After a conformational search, all the N atoms were considered as protonation sites and protonation energy values were determined. The inclusion of solvation by means of the Onsager model yielded stabilization in the proton affinity values obtained. In addition, a good correlation was found between the proton affinity values corresponding to the first protonation in gas phase of some of the compounds and their corresponding experimental affinity constants K(i) for the alpha1A adrenergic receptor.

Electron capture dissociation mass spectrometry of peptide cations containing a lysine homologue: a mobile proton model for explaining the observation of b-type product ions

Eleven doubly protonated peptides with a residue homologous to lysine were investigated by electron capture dissociation mass spectrometry (ECD-MS). Lysine homologues provide the unique opportunity to examine the ECD fragmentation behavior by allowing us to vary the length of the lysine side chain, with minimal structural change. The lysine homologue has a primary amine side chain with a length that successively decreases by one methylene (CH(2)) unit from the --CH(2)CH(2)CH(2)CH(2)NH(2) of lysine and the accompanying decrease of its proton affinities: lysine (K), 1006.5(+/-7.2) kJ/mol; ornithine (K(*)), 1001.1(+/-6.6) kJ/mol; 2,4-diaminobutanoic acid (K(**)), 975.8(+/-7.4) kJ/mol; 2,3-diaminopropanoic acid (K(***)), 950.2(+/-7.2) kJ/mol. In general, the lysine-homologous peptides exhibited overall ECD fragmentation patterns similar to that of the lysine-containing peptides in terms of the locations, abundances, and ion types of products, such as yielding c(+) and z(+.) ions as the dominant product ions. However, a close inspection of product ion mass spectra showed that ECD-MS for the alanine-rich peptides with an ornithinyl or 2,4-diaminobutanoyl residue gave rise to b ions, while the lysinyl-residue-containing peptides did not, in most cases, produce any b ions. The peptide selectivity in the generation of b(+) ions could be understood from within the framework of the mobile proton model in ECD-MS, previously proposed by Cooper (Ref. 29). The exact mass analysis of the resultant b ions reveals that these b ions are not radical species but rather the cationic species with R-CO(+) structure (or protonated oxozalone ion), that is, b(+) ions. The absence of [M+2H](+.) species in the ECD mass spectra and the selective b(+)-ion formation are evidence that the peptides underwent H-atom loss upon electron capture, and then the resulting reduced species dissociated following typical MS/MS fragmentation pathways. This explanation was further supported by extensive b(+) ions generated in the ECD of alanine-based peptides with extended conformations.

Proton affinity of beta-oxalylaminoalanine (BOAA): incorporation of direct entropy correction into the single-reference kinetic method

A new version of the single-reference-extended kinetic method is presented in which direct entropy correction is incorporated. Results of calibration experiments with the monodentate base pyridine and the bidentate base ethylenediamine are presented for which the method provides proton affinities in excellent agreement with published values and reasonable predictions for the protonation entropies. The method is then used to determine the proton affinity and protonation entropy of the non-protein amino acid beta-oxalylaminoalanine (BOAA). The PA of BOAA is found to be 933.1 +/- 7.8 kJ/mol and a prediction for the protonation entropy of -39 J mol(-1) K(-1) is also obtained, indicating a significant degree of intramolecular hydrogen bonding in the protonated form. These results are supported by hybrid density functional theory calculations at the B3LYP/6-311++G**//B3LYP/6-31+G* level. They indicate that the preferred site of protonation is the alpha-nitrogen atom (PA = 935.0 kJ/mol) and that protonated BOAA has a strong hydrogen bond between the hydrogen on the alpha-amino group and one of the carbonyl oxygen atoms on the side chain.

Protonation thermochemistry of alpha-aminoacids bearing a basic residue

The proton affinity, PA, and protonation entropy, Delta(p)S degree, of glycine (Gly), 1, aspartic acid (Asp), 2, asparagine (Asn), 3, histidine (His), 4, lysine (Lys), 5, glutamic acid (Glu), 6, and glutamine (Gln), 7, have been reinvestigated by the extended kinetic method, using the "isothermal point" method and the orthogonal distance regression, ODR, technique. The proton affinity values of a-aminoacids bearing a basic residue (PA = 926.8; 965.2; 996.0; 993.9; 981.8 and 988.1 kJ.mol(-1) for 2-7, respectively) show significant deviation from the tabulated values. As expected from the effect of a strong intramolecular hydrogen bond in the protonated forms of these peculiar aminoacids, negative protonation entropies are detected (Delta(p)S degree = 36; 43; 37; 29; 95 and 55 J mol(-1) K(-1) for for 27 respectively).