Glycine conformational analysis

Alparone

et al. 2008

Biophysical Chemistry

The geometries, relative energies, gas-phase static and dynamic dipole polarizabilities of the two most stable neutral forms and of the zwitterionic form of the twenty naturally occurring amino acids have been obtained by Density Functional and conventional ab initio HatreeFock theories using correlation consistent basis sets. Mean electronic polarizabilities (<α e >s) are encompassed in the 40-160 a.u. range and are little dependent on the amino acid framework conformation, structure and conformation. The relation between <α e > and the number of electrons in the molecule makes to classify the amino acids as one of the most polarizable family of compounds. Calculated <α e > values of the neutral forms linearly relate to the molecular volume and molecular hardness as well as, rather unexpectedly, with the experimental values in water solution, where amino acids are known to be in a zwitterionic form. Vibrational polarizabilities amount to 15-45 a.u.. They come essentially from the lowfrequency angular deformation modes of the -OH and -NH 2 groups.

Section: Geometries and Relative Energiessupporting

confidence: 83%

Section: Geometries and Relative Energiessupporting

confidence: 80%

Electronic and vibrational polarizabilities of the twenty naturally occurring amino acids

Alparone

et al. 2008

Biophysical Chemistry

“…[10][11][12][13][14][15][16][17][18][19][20] All calculations have been consistent in predicting that the conformer I is the most stable form. However the stability order and the structures of the other glycine conformers depended on the level of theory and the basis set used in the calculations.…”

Section: Introductionmentioning

confidence: 86%

Matrix-Isolation Infrared and Theoretical Studies of the Glycine Conformers

et al. 1998

The IR spectra of nonionized glycine and its deuterated derivatives isolated in the low-temperature argon matrices have been measured, and for the first time the infrared spectral characteristics of the three most stable conformers have been determined and assigned. Correlated level ab initio and density functional theory (DFT) calculations of IR frequencies and intensities with extended basis sets were performed and their results were employed to separate the bands of the glycine conformers in the experimental spectra and to assist the assignment. The intramolecular interconversion, conformer III w conformer I, which is observed in the matrices at temperatures higher than 13 K, was found to cause a significant decrease of the band intensities of conformer III in the spectra. This phenomenon was used to distinguish the vibrational bands of this conformer from the bands of the other conformers. The reliability of the Møller-Plesset second-order perturbation theory (MP2) method and the DFT method with the three-parameter density functional, Becke3LYP, in the prediction of the IR spectra of the nonionized glycine conformers was examined. We found that the DFT/Becke3LYP method with aug-cc-pVDZ basis set yields vibrational frequencies of the glycine conformers very similar to the MP2 results. Both DFT and MP2 results are in the excellent agreement with the experimental data.

J. Am. Soc. Mass Spectrom.

“…First, the G3MP2 global minima for neutral amino acids match structures inferred from microwave and other gas-phase spectrometric methods. The examples include glycine [3,5], alanine [11][12][13][14][15], isoleucine [16], leucine [17], serine [15,18], tryptophan [19], and valine [20,21]. However, there are some examples in the literature of global minima identified with the B3LYP functional that do not match experimental structures (although many do match).…”

Section: Assessment Of Theoretical Approachmentioning

confidence: 99%

“…For example, Paizs and coworkers concluded that glycine prefers a structure with an internal hydrogen bond between the carboxylic acid and amine groups. Highlevel ab initio, other B3LYP data [2], and experimental data suggest a structure with a syn carboxyl group and a weak interaction between the amine hydrogens and the carbonyl [3][4][5]. While the energetic impact of this problem is generally minor, we feel it is important to report values based on the most appropriate conformations that can be obtained within a computational method.…”

mentioning

confidence: 99%

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

Gronert

Simpson

Conner

2009

109

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. . As noted by these authors, there is substantial variation in the experimental values reported for these species. The origin of this variability is most likely related to the difficulties of completing thermodynamic measurements in the gas phase on materials with low volatility. As a result, many of the experimental values are from kinetic method measurements and are subject to errors associated with the kinetic method approximation (as well as cumulative errors associated with the development of ladder-type scales). Therefore, in these systems, high-level computational work offers an attractive means of resolving differences in the various experimental measurements.While working on a computational study of the conformational preferences of neutral, gaseous amino acids, we realized that it would be possible to improve on the accuracy of the proton affinities reported by Paizs and coworkers. First, their computational strategy relied on the B3LYP approach to identify global minima and, often, they identified conformations for the neutral amino acids that did not match with those reported in previous computational and experimental studies (apparently in some cases this was the result of the search strategy and in others the computational method). For example, Paizs and coworkers concluded that glycine prefers a structure with an internal hydrogen bond between the carboxylic acid and amine groups. Highlevel ab initio, other B3LYP data [2], and experimental data suggest a structure with a syn carboxyl group and a weak interaction between the amine hydrogens and the carbonyl [3][4][5]. While the energetic impact of this problem is generally minor, we feel it is important to report values based on the most appropriate conformations that can be obtained within a computational method. For the protonated amino acids, this problem is less pronounced because the hydrogen bonding interactions are much stronger; most computational methods identify similar structures as the global minimum. Second, values reported by Paizs and coworkers are at 0 K. We have added a correction for the thermal energy of a proton, which amounts to about 1.5 kcal/mol at 298 K, as well as for the neutral and protonated amino acid. Although these corrections cancel to some extent and while the ge...