Shape of Glycine

Godfrey, Peter D.; Brown, R. D.

doi:10.1021/ja00112a015

Cited by 247 publications

(195 citation statements)

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“…Type III conformers are ''missing'' in the supersonic expansion for all ␣-amino acids with nonpolar side chains studied up to now (19-25, 27-30, 34-36). This has been attributed to relaxation to configuration I, which is supported by the relatively small III 3 I interconversion barriers determined for glycine and alanine (19)(20)(21)(22)(23)(24)27). Contrary to the previously described experimental behavior, type III conformers have been observed in serine.…”

Section: Resultsmentioning

confidence: 52%

Revealing the multiple structures of serine

Blanco

Sanz

López

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

117

141

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We explored the conformational landscape of the proteinogenic amino acid serine [CH2OHOCH(NH2)OCOOH] in the gas phase. Solid serine was vaporized by laser ablation, expanded in a supersonic jet, and characterized by Fourier transform microwave spectroscopy. In the isolation conditions of the jet there have been discovered up to seven different neutral (non-zwitterionic) structures of serine, which are conclusively identified by the comparison between the experimental values of the rotational and quadrupole coupling constants with those predicted by ab initio calculations. These seven forms can serve as a basis to represent the shape of serine in the gas phase. From the postexpansion abundances we derived the conformational stability trend, which is controlled by the subtle network of intramolecular hydrogen bonds formed between the polar groups in the amino acid backbone and the hydroxy side chain. It is proposed that conformational cooling perturbs the equilibrium conformational distribution; thus, some of the lower-energy forms are ''missing'' in the supersonic expansion.amino acids ͉ conformations ͉ laser ablation ͉ microwave spectroscopy ͉ supersonic expansion A mino acids are distinguished by an outstanding conformational flexibility originating from multiple torsional degrees of freedom, which makes folding and functionality of proteins possible (1). Whereas covalent forces determine the molecular skeleton, conformational isomerism is controlled by weaker nonbonded interactions within the molecule, especially hydrogen bonding. Amino acids are also very sensitive to the chemical medium chosen for their study. In traditional studies in the condensed phase, the extensive intermolecular hydrogen bond interactions fix amino acids as doubly charged zwitterions (2, 3), wiping out the conformational variety of these molecules. The intrinsic structural preferences of amino acids can be revealed only when they are studied as free species in the gas phase, where neutral forms (present in polypeptide chains) are the most stable in detriment of ionic or zwitterionic forms. Levy and coworkers (4) were the first to measure highly resolved electronic spectra of amino acids in the gas phase by seeding tryptophan in a supersonic expansion. Since then, different experimental methods have been used to investigate the electronic spectrum of amino acids and a variety of biological molecules in the gas phase (5-7). The electronic spectrum is interpreted with the help of theoretical calculations to identify different conformations with a high degree of confidence. However, the use of electronic spectroscopy is limited to favorable cases that present aromatic chromophores. Only three of the 20 natural amino acids have aromatic side chains that meet this criterion: phenylalanine, tyrosine, and tryptophan (4,(8)(9)(10)(11)(12)(13)(14).Microwave spectroscopy, often considered the most definitive gas-phase structural probe, can distinguish unambiguously between different conformational structures and provide accurate structural inform...

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Section: Resultsmentioning

confidence: 52%

Revealing the multiple structures of serine

Blanco

Sanz

López

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

117

141

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“…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

J. Am. Soc. Mass Spectrom.

109

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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...

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“…We now consider these results in the context of two important experimental observations: ͑1͒ When the glycine molecules are evaporated at ϳ500 K and subjected to free-jet expansion in a stream of argon gas, conformer III is not observed using microwave spectroscopy. 16 ͑2͒ When glycine molecules are evaporated at 410-440 K and deposited in a matrix of Ne, Ar, or Kr atoms on a sufficiently cold substrate ͑Ͻ13 K͒, conformer III is conclusively observed using IR spectroscopy. 18 To explain observation ͑1͒, conformer III was concluded to have undergone total interconversion during free-jet expansion in the Ar carrier gas, 17 which suggests that during expansion, glycine-Ar collisions occur at sufficient energy to facilitate III→ I interconversion.…”

Section: Detection Of Conformer IVmentioning

confidence: 99%

Collision-induced conformational changes in glycine

Miller

Clary

Meijer

2005

The Journal of Chemical Physics

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We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes ͑III→ I and IV→ I͒, we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters, conformer III has been consistently observed, but conformer IV has yet to be conclusively detected. Because of the calculated thermodynamic stability of conformer IV, its elusiveness has been attributed to the IV→ I conformer interconversion process. However, our calculations present little indication that IV→ I interconversion occurs more readily than III→ I interconversion. Although we cannot determine whether conformer IV interconverts during experimental Ne-and Ar-matrix depositions, our evidence suggests that the conformer should be present in helium droplets. Anharmonic vibrational frequency calculations illustrate that previous efforts to detect conformer IV may have been hindered by the overlap of its IR-absorption bands with those of other conformers. We propose that the redshifted symmetric −CH 2 stretch of conformer IV provides a means for its conclusive experimental detection.

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Shape of Glycine

Cited by 247 publications

References 0 publications

Revealing the multiple structures of serine

Revealing the multiple structures of serine

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

Collision-induced conformational changes in glycine

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