An Experimental and Ab Initio Study of the Nature of the Binding in Gas-Phase Complexes of Sodium Ions

McMahon, T. B.; Ohanessian, Gilles

doi:10.1002/1521-3765(20000818)6:16<2931::aid-chem2931>3.0.co;2-7

Cited by 123 publications

(242 citation statements)

References 16 publications

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“…As for alkali metal cation systems [24,49,50], BSSE corrections for DFT calculations on H ϩ (Asn) are small, 2.0 to 3.4 kJ/mol, whereas those for MP2 calculations are larger, here 8 to 14 kJ/mol. Feller and coworkers [51,52], and Ohanessian and coworkers [53,54] have previously commented that the full counterpoise approximation to BSSE for MP2 calculations can provide worse agreement with experiment than MP2 values without BSSE corrections. Because of this possibility for BSSE to overcorrect the MP2 calculations, both values are reported here.…”

Section: Computational Detailsmentioning

confidence: 71%

Thermodynamics and mechanism of protonated asparagine decomposition

Heaton

Armentrout

2009

J. Am. Soc. Mass Spectrom.

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Deamidation of the amino acid asparagine (Asn) is a primary route for spontaneous posttranslational protein modification biologically and is a pH dependent process. Here we present a full molecular description of the deamidation and (H 2 O ϩ CO) loss reactions of protonated asparagine, H ϩ (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 ϩ 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/6-311ϩG(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 6-311ϩG(2d,2p) basis set. A number of alternative high-energy mechanisms for (H 2 O ϩ CO) loss from H ϩ (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. (J Am Soc Mass Spectrom 2009, 20, 852-866)

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Section: Computational Detailsmentioning

confidence: 71%

Thermodynamics and mechanism of protonated asparagine decomposition

Heaton

Armentrout

2009

J. Am. Soc. Mass Spectrom.

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“…Ab initio calculations were carried out at levels which have been shown in previous work to provide reasonably accurate geometries and sodium ion affinities [37]. Geometries were optimized at the HF/6-31G(d) level; vibrational analyses were carried out at the same level to determine zero-point vibrational energies, thermal corrections to total energies, and entropies.…”

Section: Calculationsmentioning

confidence: 99%

The sodium ion affinities of simple Di-, Tri-, and tetrapeptides

Wang

Wesdemiotis

Kapota

et al. 2007

J. Am. Soc. Mass Spectrom.

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The sodium ion affinities (binding energies) of nineteen peptides containing 2-4 residues have been determined by experimental and computational approaches. Na ϩ -bound heterodimers with amino acid and peptide ligands (Pep 1 , Pep 2 ) were produced by electrospray ionization. The dissociations of these Pep 1 -Na ϩ -Pep 2 ions to Pep 1 -Na ϩ and Pep 2 -Na ϩ 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 ϩ affinity of GlyGly. The Na ϩ affinities of AlaAla, HisGly, GlyHis, GlyGlyGly, AlaAlaAla, GlyGlyGlyGly, and AlaAlaAlaAla were also calculated at the MP2(full)/6-311 ϩ 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 ϩ affinities. Increasing the peptide size is found to dramatically augment the Na ϩ 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 ϩ has the peptide folded around the ion with all four carbonyl oxygens in close contact with Na ϩ , that of AlaAlaAlaAla-Na ϩ involves a pseudo-cyclic peptide in which the C and N termini interact via hydrogen bonding, while Na ϩ sits on top of the oxygens of three nearly parallel CϭO bonds. (J Am Soc Mass Spectrom 2007, 18, 541-552)

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“…Gas-phase measurements of ion/molecule equilibriums have generated vast amount of different affinity (acidity and basicity) scales, which have been widely used for the studies of the reaction energetics and their utilization in different fields [1][2][3][4][5].…”

Section: Introductionmentioning

confidence: 59%