Modeling metal cation-phosphate interactions in nucleic acids in the gas phase via alkali metal cation-triethyl phosphate complexes

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations, Na+, K+, Rb+, and Cs+, to triethyl phosphate (TEP). The primary and lowest energy dissociation pathway in all cases is the endothermic loss of the neutral TEP ligand. Theoretical electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* level of theory are used to determine the structures, molecular parameters, and theoretical estimates for the BDEs of these complexes. For the complexes to Rb+ and Cs+, theoretical calculations were performed using hybrid basis sets in which the effective core potentials and valence basis sets of Hay and Wadt were used to describe the alkali metal cation, while the standard basis sets were used for all other atoms. The agreement between theory and experiment is excellent for the complexes to Na+ and K+ and is somewhat less satisfactory for the complexes to the heavier alkali metal cations, Rb+ and Cs+, where effective core potentials were used to describe the cation. The trends in the binding energies are examined. The binding of alkali metal cations to triethyl phosphate is compared with that to trimethylphosphate.     

Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.     

Dipole effects on cation-pi interactions: absolute bond dissociation energies of complexes of alkali metal cations to N-methylaniline and N,N-dimethylaniline

Threshold collision-induced dissociation of M (+)( nMA) x with Xe is studied using guided ion beam mass spectrometry, where nMA = N-methylaniline and N, N-dimethylaniline and x = 1 and 2. M (+) includes the following alkali metal cations: Li (+), Na (+), K (+), Rb (+), and Cs (+). In all cases, the primary dissociation pathway corresponds to the endothermic loss of an intact nMA ligand. The primary cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for ( nMA) x-1 M (+)-( nMA) after accounting for the effects of multiple ion-neutral collisions, the internal and kinetic energy distributions of the reactants, and the dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes, which are also used in single-point calculations at the MP2(full)/6-311+G(2d,2p) level to determine theoretical BDEs. The results of these studies are compared to previous studies of the analogous M (+)(aniline) x complexes to examine the effects of methylation of the amino group on the binding interactions. Comparisons are also made to a wide variety of cation-pi complexes previously studied to elucidate the contributions that ion-dipole, ion-induced-dipole, and ion-quadrupole interactions make to the overall binding.     

Bond dissociation energies and equilibrium structures of Cu+(MeOH)x, x = 1-6, in the gas phase: competition between solvation of the metal ion and hydrogen-bonding interactions

The solvation of Cu+ by methanol (MeOH) was studied via examination of the kinetic energy dependence of the collision-induced dissociation of Cu+(MeOH)x complexes, where x = 1-6, with Xe in a guided ion beam tandem mass spectrometer. In all cases, the primary and lowest-energy dissociation channel observed is the endothermic loss of a single MeOH molecule. The primary cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of multiple ion-neutral collisions, kinetic and internal energy distributions of the reactants, and lifetimes for dissociation. Density functional theory calculations at the B3LYP/6-31G* level are performed to obtain model structures, vibrational frequencies, and rotational constants for the Cu+(MeOH)x complexes and their dissociation products. The relative stabilities of various conformations and theoretical BDEs are determined from single-point energy calculations at the B3LYP/6-311+G(2d,2p) level of theory using B3LYP/6-31G*-optimized geometries. The relative stabilities of the various conformations of the Cu+(MeOH)x complexes and the trends in the sequential BDEs are explained in terms of stabilization gained from sd hybridization, hydrogen-bonding interactions, electron donor-acceptor natural bond orbital stabilizing interactions, and destabilization arising from ligand-ligand repulsion.     

Tautomerization in the formation and collision-induced dissociation of alkali metal cation-cytosine complexes

Noncovalent interactions between alkali metal cations and the various low-energy tautomeric forms of cytosine are investigated both experimentally and theoretically. Threshold collision-induced dissociation (CID) of M(+)(cytosine) complexes with Xe is studied using guided ion beam tandem mass spectrometry, where M(+) = Li(+), Na(+), and K(+). In all cases, the only dissociation pathway observed corresponds to endothermic loss of the intact cytosine molecule. The cross-section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for the M(+)(cytosine) complexes after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Ab initio calculations are performed at the MP2(full)/6-31G* level of theory to determine the structures of the neutral cytosine tautomers, the M(+)(cytosine) complexes, and the TSs for unimolecular tautomerization. The molecular parameters derived from these structures are employed for the calculation of the unimolecular rates for tautomerization and the thermochemical analysis of the experimental data. Theoretical BDEs of the various M(+)(cytosine) complexes and the energy barriers for the unimolecular tautomerization of these complexes are determined at MP2(full)/6-311+G(2d,2p) level of theory using the MP2(full)/6-31G* optimized geometries. In addition, BDEs for the Li(+)(cytosine) complexes are also determined at the G3 level of theory. Based upon the tautomeric mixture generated upon thermal vaporization of cytosine, calculated M(+)-cytosine BDEs and barriers to tautomerization for the low-energy tautomeric forms of M(+)(cytosine), and measured thresholds for CID of M(+)(cytosine) complexes, we conclude that tautomerization occurs during both complex formation and CID.     

Experimental and theoretical investigation of alkali metal cation interactions with hydroxyl side-chain amino acids

Absolute bond dissociation energies of serine (Ser) and threonine (Thr) to alkali metal cations are determined experimentally by threshold collision-induced dissociation of M+AA complexes, where M+=Li+, Na+, and K+ and AA=Ser and Thr, with xenon in a guided ion beam tandem mass spectrometer. Experimental results show that the binding energies of both amino acids to the alkali metal cations are very similar to one another and follow the order of Li+>Na+>K+. Quantum chemical calculations at three different levels, B3LYP, B3P86, and MP2(full), using the 6-311+G(2d,2p) basis set with geometries and zero-point energies calculated at the B3LYP/6-311+G(d,p) level show good agreement with the experimental bond energies. Theoretical calculations show that all M+AA complexes have charge-solvated structures (nonzwitterionic) with [CO, N, O] tridentate coordination.     

The special five-membered ring of proline: An experimental and theoretical investigation of alkali metal cation interactions with proline and its four- and six-membered ring analogues

The interaction of the alkali metal cations, Li+, Na+, and K+, with the amino acid proline (Pro) and its four- and six-membered ring analogues, azetidine-2-carboxylic acid (Aze) and pipecolic acid (Pip), are examined in detail. Experimentally, threshold collision-induced dissociation of the M+(L) complexes, where M = Li, Na, and K and L = Pro, Aze, and Pip, with Xe are studied using a guided ion beam tandem mass spectrometer. From analysis of the kinetic energy dependent cross sections, M(+)-L bond dissociation energies are measured. These analyses account for unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. Ab initio calculations for a number of geometric conformations of the M+(L) complexes were determined at the B3LYP/6-311G(d,p) level with single-point energies calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. Theoretical bond energies show good agreement with the experimental bond energies, which establishes that the zwitterionic form of the alkali metal cation/amino acid, the lowest energy conformation, is formed in all cases. Despite the increased conformational mobility in the Pip systems, the Li+, Na+, and K+ complexes of Pro show higher binding energies. A meticulous examination of the zwitterionic structures of these complexes provides an explanation for the stability of the five-membered ring complexes.     

Potassium cation affinities of matrix assisted laser desorption ionization matrices determined by threshold collision-induced dissociation: application to benzoic acid derivatives

Threshold collision-induced dissociation of K+(xBA) complexes with xenon is studied using guided ion beam mass spectrometry. The xBA ligands studied include benzoic acid and all of the mono- and dihydroxy-substituted benzoic acids: 2-, 3-, and 4-hydroxybenzoic acid and 2,3-, 2,4-, 2,5-, 2,6-, 3,4-, and 3,5-dihydroxybenzoic acid. In all cases, the primary product corresponds to endothermic loss of the intact xBA ligand. The cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for K+-xBA after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of the xBA ligands and their complexes with K+. Theoretical BDEs are determined from single-point energy calculations at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels using B3LYP/6-31G* optimized geometries. Four favorable binding modes for the K+(xBA) complexes are found. In all complexes to an xBA ligand that does not have a 2-hydroxyl substituent, the most favorable binding mode corresponds to a single interaction with the carbonyl oxygen atom. Formation of a 4-membered ring via chelation interactions with both oxygen atoms of the carboxylic acid group is found to be the most favorable binding mode for all of the 2-hydroxy-substituted systems except K+(2,3-dihydroxybenzoic acid). In these complexes, a hydrogen-bonding interaction between the hydrogen atom of the carboxylic acid moiety and the oxygen atom of the 2-hydroxy substituent provides additional stabilization. Formation of a 5-membered chelation ring via interaction of K+ with the oxygen atoms of adjacent hydroxyl substituents is also favorable and corresponds to the ground-state geometry for the K+(23DHBA) complex. Formation of a 6-membered chelation ring via interaction of K+ with the carbonyl and 2-hydroxyl oxygen atoms is also quite favorable but does not correspond to the ground-state geometry for any of the systems examined here. The experimental BDEs determined here are in very good agreement with the calculated values.     

Noncovalent interactions of Cu+ with N-donor ligands (pyridine, 4,4-dipyridyl, 2,2-dipyridyl, and 1,10-phenanthroline): collision-induced dissociation and theoretical studies

Collision-induced dissociation of complexes of Cu+ bound to a variety of N-donor ligands (N-L) with Xe is studied using guided ion beam tandem mass spectrometry. The N-L ligands examined include pyridine, 4,4-dipyridyl, 2,2-dipyridyl, and 1,10-phenanthroline. In all cases, the primary and lowest-energy dissociation channel observed corresponds to the endothermic loss of a single intact N-L ligand. Sequential dissociation of additional N-L ligands is observed at elevated energies for the pyridine and 4,4-dipyridyl complexes containing more than one ligand. Ligand exchange processes to produce Cu+Xe are also observed as minor reaction pathways in several systems. The primary cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level are performed to obtain model structures, vibrational frequencies, and rotational constants for the neutral N-L ligands and the Cu+(N-L)x complexes. The relative stabilities of the various conformations of these N-L ligands and Cu+(N-L)x complexes as well as theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) level of theory using B3LYP/6-31G* optimized geometries. Excellent agreement between theory and experiment is observed for all complexes containing one or two N-L ligands, while theory systematically underestimates the strength of binding for complexes containing more than two N-L ligands. The ground-state structures of these complexes and the trends in the sequential BDEs are explained in terms of stabilization gained from sd-hybridization and repulsive ligand-ligand interactions. The nature of the binding interactions in the Cu+(N-L)x complexes are examined via natural bond orbital analyses.     

Noncovalent interactions of Zn+ with N-donor ligands (pyridine, 4,4'-dipyridyl, 2,2'-dipyridyl, and 1,10-phenanthroline): collision-induced dissociation and theoretical studies

The binding interactions in complexes of Zn(+) with nitrogen donor ligands, (N-L) = pyridine (x = 1-4), 4,4'-dipyridyl (x = 1-3), 2,2'-dipyridyl (x = 1-2), and 1,10-phenanthroline (x = 1-2), are examined in detail. The bond dissociation energies (BDEs) for loss of an intact ligand from the Zn(+)(N-L)(x) complexes are reported. Experimental BDEs are obtained from thermochemical analyses of the threshold regions of the collision-induced dissociation cross sections of Zn(+)(N-L)(x) complexes. Density functional theory calculations at the B3LYP/6-31G* level of theory are performed to determine stable structures of these species and to provide molecular parameters needed for the thermochemical analysis of experimental data. Relative stabilities of the various conformations of these N-donor ligands and their complexes to Zn(+) as well as theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) and M06/6-311+G(2d,2p) levels of theory using the B3LYP/6-31G* optimized geometries. The experimental BDEs for the Zn(+)(N-L)(x) complexes are in reasonably good agreement with values derived from density functional theory calculations. BDEs derived from M06 calculations provide better agreement with the measured values than those based on B3LYP calculations. Trends in the sequential BDEs are explained in terms of sp polarization of Zn(+) and repulsive ligand-ligand interactions. Comparisons are made to the analogous Cu(+)(N-L)(x) and Ni(+)(N-L)(x) complexes previously studied.     

Absolute thermodynamic measurements of alkali metal cation interactions with a simple dipeptide and tripeptide

Absolute bond dissociation energies (BDEs) of glycylglycine (GG) and glycylglycylglycine (GGG) to sodium and potassium cations and sequential bond energies of glycine (G) in Na+G2 were determined experimentally by threshold collision-induced dissociation (TCID) in a guided ion beam tandem mass spectrometer. Experimental results showed that the binding energies follow the order of Na+ > K+ and M+GGG > M+GG > M+G. Theoretical calculations at the B3LYP/6-311+G(d) level show that all complexes had charge-solvated structures (nonzwitterionic) with either [CO,CO] bidentate or [N,CO,CO] tridentate coordination for M+GG complexes, [CO,CO,CO] tridentate or [N,CO,CO,CO] tetradentate coordination for M+GGG complexes, and [N,CO,N,CO] tetradentate coordination for Na+G2. Ab initio calculations at three different levels of theory (B3LYP, B3P86, and MP2(full) using the 6-311+G(2d,2p) basis set with geometries and zero-point energies calculated at the B3LYP/6-311+G(d) level) show good agreement with the experimental bond energies. This study demonstrates for the first time that TCID measurements of absolute BDEs can be successfully extended to biological molecules as complex as a tripeptide.     

Sodium cation affinities of MALDI matrices determined by guided ion beam tandem mass spectrometry: application to benzoic acid derivatives

Threshold collision-induced dissociation of Na(+)(xBA) complexes with Xe is studied using guided ion beam mass spectrometry. The xBA ligands studied include benzoic acid and all of the mono- and dihydroxy-substituted benzoic acids: 2-, 3-, and 4-hydroxybenzoic acid and 2,3-, 2,4-, 2,5-, 2,6-, 3,4-, and 3,5-dihydroxybenzoic acid. In all cases, the primary product corresponds to endothermic loss of the intact xBA ligand. The cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for Na(+)-xBA after accounting for the effects of multiple ion-neutral collisions, internal and kinetic energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes and provide the molecular constants necessary for the thermodynamic analysis of the experimental data. Theoretical BDEs are determined at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels using the B3LYP/6-31G* optimized geometries. The trends in the measured BDEs suggest two very different binding modes for the Na(+)(xBA) complexes, while theory finds four. In general, the most stable binding conformation involves the formation of a six-membered chelation ring via interaction with the carbonyl and 2-hydroxyl oxygen atoms. The ground state geometries of the Na(+)(xBA) complexes in which the ligand does not possess a 2-hydroxyl group generally involve binding of Na(+) to either the carbonyl oxygen atom or to both oxygen atoms of the carboxylic acid group. These binding modes tend to be competitive because the enhancement in binding associated with the chelation interactions in the latter is mediated by steric repulsion between the hydroxyl and ortho hydrogen atoms. When possible, hydrogen bonding interactions with the ring hydroxyl group(s) enhance the stability of these complexes. The agreement between the theoretical and experimental BDEs is quite good for B3LYP and somewhat less satisfactory for MP2(full).     

Infrared multiple photon dissociation spectroscopy of cationized histidine: effects of metal cation size on gas-phase conformation

The gas phase structures of cationized histidine (His), including complexes with Li(+), Na(+), K(+), Rb(+), and Cs(+), are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser, in conjunction with quantum chemical calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) (Li(+), Na(+), and K(+) complexes) and B3LYP/HW*/6-311+G(d,p) (Rb(+) and Cs(+) complexes) levels of theory, where HW* indicates that the Hay-Wadt effective core potential with additional polarization functions was used on the metals. Single point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. On the basis of these experiments and calculations, the only conformation that reproduces the IRMPD action spectra for the complexes of the smaller alkali metal cations, Li(+)(His) and Na(+)(His), is a charge-solvated, tridentate structure where the metal cation binds to the backbone carbonyl oxygen, backbone amino nitrogen, and nitrogen atom of the imidazole side chain, [CO,N(α),N(1)], in agreement with the predicted ground states of these complexes. Spectra of the larger alkali metal cation complexes, K(+)(His), Rb(+)(His), and Cs(+)(His), have very similar spectral features that are considerably more complex than the IRMPD spectra of Li(+)(His) and Na(+)(His). For these complexes, the bidentate [CO,N(1)] conformer in which the metal cation binds to the backbone carbonyl oxygen and nitrogen atom of the imidazole side chain is a dominant contributor, although features associated with the tridentate [CO,N(α),N(1)] conformer remain, and those for the [COOH] conformer are also clearly present. Theoretical results for Rb(+)(His) and Cs(+)(His) indicate that both [CO,N(1)] and [COOH] conformers are low-energy structures, with different levels of theory predicting different ground conformers.     

Solvation of copper ions by acetone. structures and sequential binding energies of Cu+(acetone)x,x = 1-4 from collision-induced dissociation and theoretical studies

Collision-induced dissociation of Cu+(acetone)(x), x = 1-4, with Xe is studied as a function of kinetic energy using guided ion beam mass spectrometry. In all cases, the primary and lowest energy dissociation channel observed is endothermic loss of one acetone molecule. The primary cross section thresholds are interpreted to yield 0 and 298 K bond energies after accounting for the effects of multiple ion-neutral collisions, internal energy of the complexes, and dissociation lifetimes. Density functional calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes and provide molecular constants necessary for the thermodynamic analysis of the experimental data. Theoretical bond dissociation energies are determined from single point calculations at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels, using the B3LYP/6-31G* optimized geometries. The experimental bond energies determined here are in good agreement with previous experimental measurements made in a high-pressure mass spectrometer for the sum of the first and second bond energy (i.e., Cu+(acetone)2 --> Cu+ + 2 acetone) when these results are properly anchored. The agreement between theory and experiment is reasonable in all cases, but varies both with the size of the cluster and the level of theory employed. B3LYP does an excellent job for the x = 1 and 3 clusters, but is systematically low for the x = 2 and 4 clusters such that the overall trends in sequential binding energies are not parallel. In contrast, all MP2 values are somewhat low, but the overall trends parallel the measured values for all clusters. The trends in the measured Cu+(acetone), binding energies are explained in terms of 4s-3d sigma hybridization effects and ligand-ligand repulsion in the clusters.     

Sodium Cation Affinities of Commonly Used MALDI Matrices Determined by Guided Ion Beam Tandem Mass Spectrometry

The sodium cation affinities of six commonly used MALDI matrices are determined here using guided ion beam tandem mass spectrometry techniques. The collision-induced dissociation behavior of six sodium cationized MALDI matrices, Na⁺(MALDI), with Xe is studied as a function of kinetic energy. The MALDI matrices examined here include: nicotinic acid, quinoline, 3-aminoquinoline, 4-nitroaniline, picolinic acid, and 3-hydroxypicolinic acid. In all cases, the primary dissociation pathway corresponds to endothermic loss of the intact MALDI matrix. The cross section thresholds are interpreted to yield zero and 298 K Na⁺−MALDI bond dissociation energies (BDEs), or sodium cation affinities, after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* and MP2(full)/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory are used to characterized the structures and energetics for these systems. The calculated BDEs exhibit very good agreement with the measured values for most systems. The experimental and theoretical Na⁺−MALDI BDEs determined here are compared with those previously measured by cation transfer equilibrium methods.     

Metal cation dependence of interactions with amino acids: bond energies of Cs+ to Gly, Pro, Ser, Thr, and Cys

The interactions of cesium cations with five amino acids (AA) including glycine (Gly), proline (Pro), serine (Ser), threonine (Thr), and cysteine (Cys) are examined in detail. Experimentally, the bond dissociation energies (BDEs) are determined using threshold collision-induced dissociation of the Cs(+)(AA) complexes with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy-dependent cross sections include consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion-neutral collisions. Bond dissociation energies (0 K) of 93.3 ± 2.5, 107.9 ± 4.6, 102.3 ± 4.1, 105.4 ± 4.3, and 96.8 ± 4.2 kJ/mol are determined for complexes of Cs(+) with Gly, Pro, Ser, Thr, and Cys, respectively. Quantum chemical calculations are conducted at the B3LYP, B3P86, MP2(full), and M06 levels of theory with geometries and zero-point energies calculated at the B3LYP level using both HW*/6-311+G(2d,2p) and def2-TZVPPD basis sets. Results obtained using the former basis sets are systematically low compared to the experimental bond energies, whereas the latter basis sets show good agreement. For Cs(+)(Gly), theory predicts the ground-state conformer has the cesium cation binding to the carbonyl group of the carboxylic acid. For Cs(+)(Pro), the secondary nitrogen accepts the carboxylic acid hydrogen to form the zwitterionic structure, and the metal cation binds to both oxygens. Cs(+)(Ser), Cs(+)(Thr), and Cs(+)(Cys) are found to have tridentate binding at the MP2(full) level, whereas the density functional approaches slightly prefer bidentate binding of Cs(+) at the carboxylic acid moiety. Comparison of these results to those for the smaller alkali cations provides insight into the trends in binding affinities and structures associated with metal cation variations.     

Infrared multiphoton dissociation spectroscopy of cationized threonine: effects of alkali-metal cation size on gas-phase conformation

The gas-phase structures of alkali-metal cation complexes of threonine (Thr) are examined using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser in conjunction with quantum chemical calculations. Spectra of Li+(Thr) and Na+(Thr) are similar and relatively simple, whereas K+(Thr), Rb+(Thr), and Cs+(Thr) include distinctive new IR bands. Measured IRMPD spectra are compared to spectra calculated at a B3LYP/6-311+G(d,p) level to identify the structures present in the experimental studies. For the smaller metal cations, the spectra match those predicted for charge-solvated structures in which the ligand exhibits tridentate coordination, M1[N,CO,OH], binding to the amide and carbonyl groups of the amino acid backbone and to the hydroxyl group of the side chain. K+(Thr), Rb+(Thr), and Cs+(Thr) exhibit evidence of the charge-solvated complex, M3[COOH], in which the metal cation binds to the carboxylic acid group. Evidence for a small population of the zwitterionic analogue of this structure, ZW[CO2-], is also present, particularly for the Cs+ complex. Calculations indicate that the relative stability of the M3[COOH] structure is very strongly dependent on the size of the metal cation, consistent with the range of conformations observed experimentally. The present results are similar to those obtained previously for the analogous M+(Ser) complexes, although there are subtle distinctions that are discussed.     

Cation-pi interactions: structures and energetics of complexation of Na+ and K+ with the aromatic amino acids, phenylalanine, tyrosine, and tryptophan

Threshold collision-induced dissociation of M(+)(AAA) with Xe is studied using guided ion beam tandem mass spectrometry. M(+) include the alkali metal ions Na(+) and K(+). The three aromatic amino acids are examined, AAA = phenylalanine, tyrosine, or tryptophan. In all cases, endothermic loss of the intact aromatic amino acid is the dominant reaction pathway. The threshold regions of the cross sections are interpreted to extract 0 and 298 K bond dissociation energies for the M(+)-AAA complexes after accounting for the effects of multiple ion-neutral collisions, internal energy of the reactant ions, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures of the neutral aromatic amino acids and their complexes to Na(+) and K(+) and to provide molecular constants required for the thermochemical analysis of the experimental data. Theoretical bond dissociation energies are determined from single-point energy calculations at the B3LYP/6-311++G(3df,3pd) level using the B3LYP/6-31G geometries. Good agreement between theory and experiment is found for all systems. The present results are compared to earlier studies of these systems performed via kinetic and equilibrium methods. The present results are also compared to the analogous Na(+) and K(+) complexes to glycine, benzene, phenol, and indole to elucidate the relative contributions that each of the functional components of these aromatic amino acids make to the overall binding in these complexes.     

Infrared multiphoton dissociation spectroscopy of cationized serine: effects of alkali-metal cation size on gas-phase conformation

The gas-phase structures of alkali-metal cation complexes of serine (Ser) are examined using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. Spectra of Li+(Ser) and Na+(Ser) are similar and relatively simple, whereas Cs+(Ser) includes distinctive new IR bands, and K+(Ser) and Rb+(Ser) exhibit intermediate behavior. Measured IRMPD spectra are compared to spectra calculated at a B3LYP/6-311+G(d,p) level to identify the structures present in the experimental studies. On the basis of these experiments and calculations, the only conformations accessed for the complexes to the smaller alkali-metal cations, Li+ and Na+, are charge-solvated structures involving tridentate coordination to the amine and carbonyl groups of the amino acid backbone and to the hydroxyl group of the side chain, M1[N,CO,OH]. For the cesiated complex, a band corresponding to a zwitterionic structure, ZW[CO2-], is clearly visible. K+(Ser) and Rb+(Ser) exhibit evidence of the charge-solvated analogue of the zwitterions, M3[COOH], in which the metal cation binds to the carboxylic acid group. Calculations indicate that the relative stability of the M3[COOH] structure is very strongly dependent on the size of the metal cation, consistent with the range of conformations observed experimentally.     

Structural and Energetic Effects in the Molecular Recognition of Acetylated Amino Acids by 18-Crown-6

Absolute 18-crown-6 (18C6) binding affinities of four protonated acetylated amino acids (AcAAs) are determined using guided ion beam tandem mass spectrometry techniques. The AcAAs examined in this work include: N-terminal acetylated lysine (N_???CAcLys), histidine (N_???CAcHis), and arginine (N_???CAcArg) as well as side chain acetylated lysine (N_???CAcLys). The kinetic-energy-dependent cross sections for collision-induced dissociation (CID) of the (AcAA)H⁺(18C6) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298?K (AcAA)H⁺?18C6 bond dissociation energies (BDEs) after accounting for the effects of multiple collisions, kinetic and internal energy distributions of the reactants, and unimolecular dissociation lifetimes. Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AcAAs as well as the proton bound complexes of these species, (AcAA)H⁺(18C6), at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31?G* and M06/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory. For all four (AcAA)H⁺(18C6) complexes, loss of neutral 18C6 corresponds to the most favorable dissociation pathway. At elevated energies, products arising from sequential dissociation of the primary CID product, H⁺(AcAA), are also observed. Protonated N_???CAcLys exhibits a greater 18C6 binding affinity than other protonated N_???CAcAAs, suggesting that the side chains of Lys residues are the preferred binding sites for 18C6 complexation to peptides and proteins. N_???CAcLys exhibits a greater 18C6 binding affinity than N_???CAcLys, suggesting that binding of 18C6 to the side chain of Lys residues is more favorable than to the N-terminal amino group of Lys.