Collision-induced Dissociation Cross Sections Research Articles

Methane Adducts of Gold Dimer Cations: Thermochemistry and Structure from Collision-Induced Dissociation and Association Kinetics.

The bond dissociation energies at 0 K (BDE) of Au2+-CH4 and Au2CH4+-CH4 have been determined using two separate experimental methods. Analyses of collision-induced dissociation cross sections for Au2CH4+ + Xe and Au2(CH4)2+ + Xe measured using a guided ion beam tandem mass spectrometer (GIBMS) yield BDEs of 0.71 ± 0.05 and 0.57 ± 0.07 eV, respectively. Statistical modeling of association kinetics of Au2(CH4)0-2+ + CH4 + He measured from 200 to 400 K and at 0.3-0.9 Torr using a selected-ion flow tube (SIFT) apparatus yields slightly higher values of 0.81 ± 0.21 and 0.75 ± 0.25 eV. The SIFT data also place a lower limit on the BDE of Au2C2H8+-CH4 of 0.35 eV, likely an activated isomer, not Au2(CH4)2+-CH4. Particular emphasis is placed on determining the uncertainty in the derivation from association kinetics measurements, including uncertainties in collisional energy transfer, calculated harmonic frequencies, and possible contribution of isomerization of the association complexes. This evaluation indicates that an uncertainty of ±0.2 eV should be expected and that an uncertainty of better than ±0.1 eV is unlikely to be reasonable.

Calculations of cross-sections, dissociation rate constants and transport coefficients of Xe2+ colliding with Xe.

A quantum formalism and classical treatment have been used for electrons and nuclei, respectively, in a hybrid method in order to study the dynamics of electronically ground-state ionic xenon dimer, Xe2+, in its parent gas. A semiempirical Diatomics In Molecules approach has been used to model the effective electronic Hamiltonian with different sets of input diatomic potentials (ionic and neutral). Non-reactive scattering and collision induced dissociation cross-sections have first been calculated and then injected in a Monte Carlo code for the simulations of the transport coefficients and dissociation rate constant calculated at ambient temperature and atmospheric pressure. Selected transport coefficients, such as Xe2+ mobility for which experimental measurements are available, have been compared to experimental results while transversal and longitudinal diffusion coefficients are compared to pseudo-experimental data obtained from inverse method calculations. Investigation of rotational-vibrational effects and the influence of different sets of ionic and neutral diatomic potentials have been studied.

Dissociation cross section for high energy O2-O2 collisions.

Collision-induced dissociation cross section database for high energy O2-O2 collisions (up to 30 eV) is generated and published using the quasiclassical trajectory method on the singlet, triplet, and quintet spin ground state O4 potential energy surfaces. At equilibrium conditions, these cross sections predict reaction rate coefficients that match those obtained experimentally. The main advantage of the cross section database based on ab initio computations is in the study of complex flows with high degree of non-equilibrium. Direct simulation Monte Carlo simulations using the reactive cross section databases are carried out for high enthalpy hypersonic oxygen flow over a cylinder at rarefied ambient conditions. A comparative study with the phenomenological total collision energy chemical model is also undertaken to point out the difference and advantage of the reported ab initio reaction model.

Global potential energy surface of ground state singlet spin O4.

A new global potential energy for the singlet spin state O4 system is reported using CASPT2/aug-cc-pVTZ ab initio calculations. The geometries for the six-dimensional surface are constructed using a novel point generation scheme that employs randomly generated configurations based on the beta distribution. The advantage of this scheme is apparent in the reduction of the number of required geometries for a reasonably accurate potential energy surface (PES) and the consequent decrease in the overall computational effort. The reported surface matches well with the recently published singlet surface by Paukku et al. [J. Chem. Phys. 147, 034301 (2017)]. In addition to the O4 PES, the ground state N4 PES is also constructed using the point generation scheme and compared with the existing PES [Y. Paukku et al., J. Chem. Phys. 139, 044309 (2013)]. The singlet surface is constructed with the aim of studying high energy O2-O2 collisions and predicting collision induced dissociation cross section to be used in simulating non-equilibrium aerothermodynamic flows.

An ab initio chemical reaction model for the direct simulation Monte Carlo study of non-equilibrium nitrogen flows.

A new ab initio based chemical model for a Direct Simulation Monte Carlo (DSMC) study suitable for simulating rarefied flows with a high degree of non-equilibrium is presented. To this end, Collision Induced Dissociation (CID) cross sections for N2+N2→N2+2N are calculated and published using a global complete active space self-consistent field-complete active space second order perturbation theory N4 potential energy surface and quasi-classical trajectory algorithm for high energy collisions (up to 30 eV). CID cross sections are calculated for only a selected set of ro-vibrational combinations of the two nitrogen molecules, and a fitting scheme based on spectroscopic weights is presented to interpolate the CID cross section for all possible ro-vibrational combinations. The new chemical model is validated by calculating equilibrium reaction rate coefficients that can be compared well with existing shock tube and computational results. High-enthalpy hypersonic nitrogen flows around a cylinder in the transition flow regime are simulated using DSMC to compare the predictions of the current ab initio based chemical model with the prevailing phenomenological model (the total collision energy model). The differences in the predictions are discussed.

Comparisons and scaling rules between N+N2 and N2+N2 collision induced dissociation cross sections from atomistic studies

Quantitative knowledge of elementary processes involved in plasmas are key to successfully perform accurate kinetic simulations. The issue is the huge amount of data to treat, both in the dynamical calculation and in the kinetic simulation. The aim of this paper is to study the dissociation in atom–molecule (AM) and molecule–molecule (MM) collisions involving nitrogen, obtained by molecular dynamics calculations considering vibrational states in the range 10–50 and collision energy up to 10 eV, in order to formulate suitable scaling laws resulting in less expensive computational procedures and easier to handle treatments in kinetic simulations. It is shown that, while a direct substitution of MM dissociation cross sections with AM ones might be acceptable only at very high collision energy, scaling laws application allows to obtain quite good results on almost the whole energy range of interest.

A guided-ion beam study of the collisions and reactions of I(+) and I2 (+) with I2.

Growing interest in developing and testing iodine Hall effect thrusters requires measurements of the cross sections of reactions that generate low energy plasma following discharge. Limited experimental and theoretical work necessitates a decisive experiment to elucidate the charge exchange and collision-induced dissociation channels. To this end, we have used guided-ion beam techniques to measure cross sections for both I(+) + I2 and I2 (+)+I2 collisions. We present total collision cross sections as well as collision-induced dissociation cross sections for center-of-mass collision energies ranging from 0.5 to 200 eV for molecular iodine cations. Similarly, we present total collision cross section and charge-exchange cross sections for atomic iodine cations for center-of-mass collision energies ranging from 0.67 to 167 eV. Time-of-flight measurements of the collision products allow determination of velocity distributions, which show evidence of complex formation of I3 (+) from the I(+) + I2 reaction at collision energies below 6 eV.

Thermodynamics and Mechanism of Protonated Cysteine Decomposition: A Guided Ion Beam and Computational Study

A quantitative molecular description of the decomposition of protonated cysteine, H(+)Cys, is provided by studying the kinetic energy dependence of threshold collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Primary dissociation channels are deamidation (yielding both NH3 loss and NH4(+) formation) and (H2O + CO) loss reactions, followed by an additional six subsequent decompositions. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for six different reactions after accounting for unimolecular decay rates, internal energy of reactant ions, multiple ion-molecule collisions, and competition among the decay channels. To identify the mechanisms associated with these reactions, quantum chemical calculations performed at the B3LYP/6-311 + G(d,p) level were used to locate the transition states (TSs) and intermediates for these processes. Single point energies of the reactants, products, and key optimized TSs and intermediates are calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311 + G(2d,2p) basis set. The computational characterization of the elementary steps of these reactions, including the structures of the final products, is validated by quantitative agreement with the experimental energetics. In agreement with previous work, deamidation is facilitated by anchimeric assistance of the thio group, which also leads to an interesting rearrangement of the intact amino acid identified computationally.

Silver Cation Affinities of Monomeric Building Blocks of Polyethers and Polyphenols Determined by Guided Ion Beam Tandem Mass Spectrometry

Energy-resolved collision-induced dissociation (CID) of seven silver cation-ligand complexes, Ag(+)(L), with Xe is studied using guided ion beam tandem mass spectrometry techniques. The ligands, L, investigated are monomeric building blocks of polyethers and polyphenols including phenol, 2-hydroxyphenol, 3-hydroxyphenol, 4-hydroxyphenol, 2-hydroxymethyl phenol, 3-hydroxymethyl phenol, and 4-hydroxymethyl phenol. In all cases, Ag(+) is observed as the primary CID product, corresponding to endothermic loss of the intact neutral ligand. The kinetic-energy-dependent cross sections for CID of these Ag(+)(L) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298 K Ag(+)-L bond dissociation energies (BDEs). Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of the neutral ligands and their complexes to Ag(+) using either the Stuttgart RSC 1997 valence basis set and effective core potential (SRSC ECP) or DZVP-DFT to describe Ag(+). Theoretical BDEs are determined at the B3LYP/6-311+G(2d,2p) level of theory again using the SRSC ECP or DZVP-DFT for Ag(+). For all systems, the most stable binding conformations found involve cation-π interactions when the SRSC ECP is used to describe Ag(+). When DZVP-DFT is employed, the most stable binding geometries remain cation-π complexes except for the complex to 2HP, where the ground-state conformer involves bidentate binding of Ag(+) to the hydroxyl oxygen atoms of both substituents. The agreement between the measured and calculated BDEs is excellent with a MAD of 2.9 ± 1.7 kJ/mol when the SRSC ECP is used to describe Ag(+) and less satisfactory for DZVP-DFT, which underestimates the strength of binding in these systems by ~14% or 26.0 ± 6.7 kJ/mol.

Energy-Resolved Collision-Induced Dissociation Studies of 2,2'-Bipyridine Complexes of the Late First-Row Divalent Transition-Metal Cations: Determination of the Third-Sequential Binding Energies.

The third-sequential binding energies of the late first-row divalent transition-metal cations with 2,2'-bipyridine (Bpy) are determined using guided-ion-beam tandem mass spectrometry (GIBMS) techniques. The metal cations investigated include the late first-row divalent transition-metal cations, Fe2+ , Co2+ , Ni2+ , Cu2+ , and Zn2+ . The kinetic-energy-dependent cross sections for collision-induced dissociation (CID) of the M2+ (Bpy)3 complexes are analyzed to extract absolute 0 and 298 K bond dissociation energies (BDEs) for the loss of an intact Bpy ligand. Theoretical electronic structure calculations at the B3LYP, BHandHLYP, and M06 levels of theory are performed to determine stable geometries and sequential BDEs of the M2+ (Bpy)x complexes (x=1-3). BDEs computed using the M06 functional are the largest, BHandHLYP values are intermediate, whereas B3LYP produces the smallest values. Very good agreement between the B3LYP theoretically calculated and threshold collision-induced dissociation experimentally determined BDEs is found, which suggests that the B3LYP functional is capable of accurately describing the binding in these M2+ (Bpy)3 complexes. Periodic trends in the binding of the M2+ (Bpy)x complexes are examined and compared to the analogous complexes with 1,10-phenanthroline (Phen), M2+ (Phen)x . Comparisons are also made to the analogous Bpy complexes, M+ (Bpy)x , with the late first-row monovalent transition-metal cations, Co+ , Ni+ , Cu+ , and Zn+ investigated previously.

Energy-Resolved Collision-Induced Dissociation Studies of 1,10-Phenanthroline Complexes of the Late First-Row Divalent Transition Metal Cations: Determination of the Third Sequential Binding Energies

The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated.

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(α)-AcLys), histidine (N(α)-AcHis), and arginine (N(α)-AcArg) as well as side chain acetylated lysine (N(ε)-AcLys). 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(α)-AcLys exhibits a greater 18C6 binding affinity than other protonated N(α)-AcAAs, suggesting that the side chains of Lys residues are the preferred binding sites for 18C6 complexation to peptides and proteins. N(α)-AcLys exhibits a greater 18C6 binding affinity than N(ε)-AcLys, suggesting that binding of 18C6 to the side chain of Lys residues is more favorable than to the N-terminal amino group of Lys.

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.

Thermodynamics and Mechanisms of Protonated Diglycine Decomposition: A Guided Ion Beam Study

We present a full molecular description of fragmentation reactions of protonated diglycine (H(+)GG) by studying their collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Analysis of the kinetic energy-dependent CID cross sections provides the 0K barriers for the sequential H(2)O+CO and CO+NH(3) losses from H(+)GG as well as for the reactions involved in y(1) and a(1) ion formation, after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. Here, seven energetic barriers are measured for the fragmentation processes of H(+)GG, including the loss of H(2)O and of CO at ~140 and ~156kJ/mol, the combined loss of (H(2)O+CO) and of (CO+NH(3)) at ~233 and ~185kJ/mol, and formation of y(1) and a(1) ions at ~191 and ~212kJ/mol, respectively, with a second channel for a(1) formation opening at ~326kJ/mol. Theoretical energies from the preceding paper are compared with our experimental energies and found to be in good agreement. This validates the mechanisms explored computationally, including unambiguous identification of the b(2) ion as protonated 2-aminomethyl-5-oxazolone, thereby allowing a complete characterization of the elementary steps of H(+)GG decomposition. These results also demonstrate that all reactive species are available from the ground state conformation, as opposed to involving an initial broad distribution of protonated conformers. This result verifies the utility of the "mobile proton" model for understanding the fragmentation of protonated proteins.

Thermodynamics and Mechanisms for Decomposition of Protonated Glycine and Its Protonated Dimer

We present a full molecular description of fragmentation reactions of protonated glycine (G) and its protonated dimer, H(+)G(2), by studying their collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). In contrast to previous results, it is clear that H(+)G decomposes by loss of CO followed by H(2)O. Analysis of the energy-dependent CID cross sections provides the 0 K barriers for these processes as well as for the binding energy of the dimer after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. Relaxed potential energy surface scans performed at the B3LYP/6-31G(d) level are used to map the reaction surfaces and identify the transition states (TSs) and intermediate reaction species for the reactions, structures that are further optimized at the B3LYP/6-311+G(d,p) level. Single-point energies of the key optimized structures are calculated at B3LYP and MP2(full) levels using a 6-311+G(2d,2p) basis set. These theoretical results are compared to extensive calculations in the literature and to the experimental energies. The combination of both experimental work and quantum chemical calculations allows for a complete characterization of the elementary steps of H(+)G and H(+)G(2) decomposition. These results make it clear that H(+)G is the simplest model for the ''mobile proton'', a key concept in understanding the fragmentation of protonated proteins.

Multiply charged gas-phase NaAOT reverse micelles: Formation, encapsulation of glycine, and collision-induced dissociation

We report a study of the generation and characterization of multiply charged, sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) aggregates in the gas phase, using electrospray ionization (ESI) guided-ion beam tandem mass spectrometry. It was found that distributions of gas-phase NaAOT aggregate size and charge are related to the surfactant states in electrosprayed solutions. ESI mass spectra of NaAOT/water/hexane reverse micellar solutions show the compositions of [(NaAOT) n Na z ] z+ , with the aggregation number ( n) and charge ( z) increase with increasing water content in solution. In contrast, gas-phase aggregates from NaAOT monomers in solution have smaller aggregation numbers and lower charges. Gas-phase NaAOT aggregates of n ≥ 13 could encapsulate one glycine molecule, and those of n ≥ 16 could encapsulate two glycine molecules. Up to five glycine molecules could be accommodated in single aggregates of n ≥ 24. Regardless of glycine encapsulation, no water molecules were detected within gas-phase NaAOT aggregates. Collision-induced dissociation (CID) was studied for mass-selected NaAOT aggregates with Xe, including measurements of product ion masses and CID cross-sections for both empty and glycine-encapsulating aggregates over the center-of-mass collision energy range of 0.1–8.0 eV. CID results provide a detailed probe of aggregate structures as well as the interactions between surfactants and the encapsulated glycine molecules. Specifically, the dependence of glycine encapsulation on aggregate size is observed in CID product ion mass spectra, too. The present study demonstrates that NaAOT surfactants are able to form reverse micelles in the gas phase, and gas-phase reverse micelles can act as nanometer-sized vehicles for transport of non-volatile biomolecules.

Thermodynamics and Mechanism of Protonated Asparagine Decomposition

Deamidation of the amino acid asparagine (Asn) is a primary route for spontaneous post-translational protein modification biologically and is a pH dependent process. Here we present a full molecular description of the deamidation and (H(2)O + CO) loss reactions of protonated asparagine, H(+)(Asn), by studying its collision-induced dissociation (CID) with Xe using a guided ion beam (GIB) tandem mass spectrometer. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for the deamidation and (H(2)O + CO) loss reactions after accounting for unimolecular decay rates, internal energy of reactant ions, multiple ion-molecule collisions, and competition among the decay channels. Relaxed potential energy surface scans performed at the B3LYP/6-31G(d) level identify the transition-state (TS) and intermediate reaction species for these processes, structures that are further optimized at the B3LYP/6-311+G(d,p) level. Intrinsic reaction coordinate (IRC) calculations are also performed at this level on the rate-limiting reaction TSs to validate the molecular details and energy dependence of these species. Single point energies of the key optimized TSs and intermediates are calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311+G(2d,2p) basis set. A number of alternative high-energy mechanisms for (H(2)O + CO) loss from H(+)(Asn) are also investigated. Combining both experimental work and quantum chemical calculations allows for a complete characterization of the elementary steps of these reactions as well as a comprehensive evaluation of the complex behavior of the deamidation reaction.

Experimental and Theoretical Studies of Sodium Cation Interactions with d-Arabinose, Xylose, Glucose, and Galactose

The binding of Na (+) to arabinose (Ara), xylose (Xyl), glucose (Glc), and galactose (Gal) is examined in detail by studying the collision-induced dissociation (CID) of the four sodiated monosaccharide complexes with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Analysis of the energy-dependent CID cross-sections provides 0 K sodium cation affinities for experimental complexes after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. Quantum chemical calculations for a number of geometric conformations of each Na (+)(L) complex with a comprehensive analysis of the alpha and beta anomeric forms are determined at the B3LYP/6-311+G(d,p) level with single-point energies calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. This coordinated examination of both experimental work and quantum chemical calculations allows for determination of the bond energy for both the alpha and beta forms of each monosaccharide studied here. An understanding of the energetic contributions of individual structural characteristics as well as the energetic trends in binding among the monosaccharides is developed. Structural characteristics that affect the energetics of binding involve multidentate sodium cation coordination, ring sterics, and hydrogen bonding schemes. The overall trend in sodium binding affinities for the eight ligands follows beta-Ara < alpha-Ara < beta-Xyl < beta-Glc < alpha-Glc < alpha;-Xyl < alpha-Gal < beta-Gal.

Experimental and Theoretical Studies of Potassium Cation Interactions with the Acidic Amino Acids and Their Amide Derivatives

The binding of K(+) to aspartic acid (Asp), glutamic acid (Glu), asparagine (Asn), and glutamine (Gln) is examined in detail by studying the collision-induced dissociation (CID) of the four potassium cation-bound amino acid complexes with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Formed by electrospray ionization, these complexes have energy-dependent CID cross sections that are analyzed to provide 0 K bond energies after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. Quantum chemical calculations for a number of geometric conformations of each K(+)(L) complex are determined at the B3LYP/6-311+G(d,p) level with single-point energies calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311+G(2d,2p) basis set. Theoretical bond dissociation energies are in good agreement with the experimental values. This coordinated examination of both experimental work and quantum chemical calculations allows for a comprehensive understanding of the molecular interactions of K(+) with the Asx and Glx amino acids. K(+) binding affinities for the amide complexes are systematically stronger than those for the acid complexes by 9+/-1 kJ/mol, which is attributed to an inductive effect of the OH group in the carboxylic acid side chain. Additionally, the K(+) binding affinity for the longer-chain amino acids (Glx) is enhanced by 5+/-1 kJ/mol compared to the shorter-chain Asx because steric effects are reduced. Further, a detailed comparison between experimental and theoretical results reveals interesting differences in the binding of K(+) and Na(+) to these amino acids.

Thermodynamics and Mechanism of the Deamidation of Sodium-Bound Asparagine

The deamidation of asparagine (Asn) residues is the most common type of spontaneous post-translational protein modification and plays a vital role in inflammation, protein transformation, apoptosis, aging, and a number of degenerative diseases. Here we present a full molecular description of asparagine deamidation in the Na(+)(Asn) complex by studying its collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Advanced methods for analysis of the energy-dependent CID cross section, considering both competing and sequential processes, provide the 0 K barrier for deamidation after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. Relaxed potential energy surface scans performed at the B3LYP/6-31G(d) level identify the transition state (TS) and intermediate reaction species for Na(+)(Asn) deamidation, structures that are further optimized at the B3LYP/6-311+G(d,p) level. Single-point energies of the key optimized structures are calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. This coordinated application of both experimental work and quantum chemical calculations allows for a complete characterization of the elementary steps of this reaction and identification of the rate-limiting elementary step of Asn deamidation. The latter is measured to require 1.61 +/- 0.08 eV and involves formation of a cyclic succinic ring structure.