Comprehensive ab initio study on the conformations of L-Threonine and L-allo-Threonine and related species in gas phase

Xu, Xuee; Lin, Zijing

doi:10.1016/j.theochem.2010.09.010

Cited by 19 publications

(27 citation statements)

References 39 publications

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“…From the G4 Gibbs free energies it is deduced a population of conformers ThrII B g− / ThrI C g+ / ThrI A g− / ThrIII C g+ at 298 K in the ratio 34/24/17/10%, the remaining 15% being shared between five minor conformers (Riffet, Frison, & Bouchoux, 2011). Comparable results based on MP2/6‐311+G(2df,p) calculations have been reported by Lin & Xu (2010). From an experimental point of view, Fourier transform microwave spectroscopy was applied to L ‐threonine vaporized by laser ablation (Alonso et al, 2009).…”

Section: Theoretical Protonation Thermochemistry Of Amino Acidssupporting

confidence: 81%

“…Conformational landscape of neutral L ‐threonine has been the subject of recent theoretical investigations (Lakard, 2004; Zhang & Lin, 2006; Szidarovsky, Czako, & Csaszar, 2009; Xu & Lin, 2010; Riffet, Frison, & Bouchoux, 2011). As expected conformational landscape of threonine strongly resemble that of serine.…”

Section: Theoretical Protonation Thermochemistry Of Amino Acidsmentioning

confidence: 99%

“…Two conformers of close energies were identified for protonated threonine (Xu & Lin, 2010; Riffet, Frison, & Bouchoux, 2011). These two structures, ThrHIg− and ThrHIg+ , are predicted to represent the equilibrium population at 298 K in the ratio of 62/38% (Riffet, Frison, & Bouchoux, 2011).…”

Section: Theoretical Protonation Thermochemistry Of Amino Acidsmentioning

confidence: 99%

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

Bouchoux

2011

Mass Spectrometry Reviews

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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.

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Section: Theoretical Protonation Thermochemistry Of Amino Acidssupporting

confidence: 81%

Section: Theoretical Protonation Thermochemistry Of Amino Acidsmentioning

confidence: 99%

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

Bouchoux

2011

Mass Spectrometry Reviews

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“…The first stage consisted of including the first ten minimum energy conformations of each amino acid (that is two hundreds conformers in all), designed and kindly provided by Zijing Lin and co-workers, into the previous training set. It is not our intention to describe here the huge computational work performed by the authors year after year, which is well documented in a number of articles, [54][55][56][57][58][59][60][61][62][63][64][65][66][67][68] but a brief account is provided in the ESI † to outline the main features of the data that were used in parametrization and refinement of the force field.…”

Section: Computational Detailsmentioning

confidence: 99%

Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

Monti

Corozzi

Fristrup

et al. 2013

Phys. Chem. Chem. Phys.

125

123

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In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector. A good agreement of ReaxFF predicted conformations and kinetics with reference data is obtained.

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“…Comparable results, based on MP2/6-311+G(2df,p) calculations, have been reported by Lin and coworkers. 39 From an experimental point of view, Fourier transform microwave spectroscopy was applied to L-threonine vaporized by laser ablation. 40 Analysis of the resulting rotational spectra leads the authors to conclude that seven conformers were present in their experimental conditions, the most abundant of which being TI C g+, TII B gÀ and TI A gÀ in excellent agreement with our expectations.…”

Section: Conformational Landscape Of Neutral Protonated and Deprotonmentioning

confidence: 99%

Acid–base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met)

Riffet

Frison

Bouchoux

2011

Phys. Chem. Chem. Phys.

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Acid-base thermochemistry of isolated amino acids containing oxygen or sulfur in their side chain (serine, threonine, cysteine and methionine) have been examined by quantum chemical computations. Density functional theory (DFT) was used, with B3LYP, B97-D and M06-2X functionals using the 6-31+G(d,p) basis set for geometry optimizations and the larger 6-311++G(3df,2p) basis set for energy computations. Composite methods CBS-QB3, G3B3, G4MP2 and G4 were applied to large sets of neutral, protonated and deprotonated conformers. Conformational analysis of these species, based on chemical approach and AMOEBA force field calculations, has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. It is observed that G4, G4MP2, G3B3, CBS-QB3 composite methods and M06-2X DFT lead to similar conformer energies. Thermochemical parameters have been computed using either the most stable conformers or equilibrium populations of conformers. Comparison of experimental and theoretical proton affinities and Δ(acid)H shows that the G4 method provides the better agreement with deviations of less than 1.5 kJ mol(-1). From this point of view, a set of evaluated thermochemical quantities for serine, threonine, cysteine and methionine may be proposed: PA = 912, 919, 903, 938; GB = 878, 886, 870, 899; Δ(acid)H = 1393, 1391, 1396, 1411; Δ(acid)G = 1363, 1362, 1367, 1382 kJ mol(-1). This study also confirms that a non-negligible ΔpS° is associated with protonation of methionine and that the most acidic hydrogen of cysteine in the gas phase is that of the SH group. In several instances new conformers were identified thus suggesting a re-examination of several IRMPD spectra.

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Comprehensive ab initio study on the conformations of L-Threonine and L-allo-Threonine and related species in gas phase

Cited by 19 publications

References 39 publications

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

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

Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

Acid–base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met)

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