Conformational landscapes in amino acids: infrared and ultraviolet ion-dip spectroscopy of phenylalanine in the gas phase

Snoek, Lavina C.; Robertson, Evan G.; Kroemer, Romano T.; Simons, John P.

doi:10.1016/s0009-2614(00)00320-1

Cited by 243 publications

(380 citation statements)

References 32 publications

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“…27,28 Most of these studies also reported theoretical calculations at various levels of theory. [5][6][7][8][9][10][11][12][13]15,17,[19][20][21][22][23][24][25][26][27][28] In general, the gas-phase results are qualitatively consistent with the matrix-isolation data, despite van der Waals forces appearing in the solid matrix between the sample and inner gas molecules. The most stable structures of aliphatic amino acids have been found to be stabilized by a bifurcated H-bond linking the carboxylic oxygen atom and the hydrogen atoms of the amino group.…”

Section: Introductionmentioning

confidence: 62%

“…In proteins, amino acids occur as residues of neutral L-R forms, whereas the zwitterionic structures are found in the crystalline state and in solution. [1][2][3] Amino acids adopt their neutral form also in the gas phase [4][5][6][7][8][9][10][11][12][13] and in low-temperature inert matrixes. [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28] Therefore, the structures of these compounds have been extensively studied in both these media.…”

Section: Introductionmentioning

confidence: 99%

“…However, existence of other conformers has been proven experimentally for all molecules studied hitherto. [4][5][6][7][8][9][10][11][12][13][15][16][17][18][21][22][23][24][25][26][27][28] The conformational distribution of amino acids depends strongly on the experimental conditions, because they have low conformational interconversion barriers. Low barriers have been predicted theoretically for glycine and alanine (for alanine, as low as 129 cm -1 and less than 35 cm -1 for the internal rotations around C-N and C-C(dO) bonds, respectively).…”

Section: Introductionmentioning

confidence: 99%

“…Due to the presence of UV chromophores in their structures, these compounds have been extensively studied in the gaseous phase by laser spectroscopy. 9,11,12,[29][30][31][32] However, according to our best knowledge, only two studies have been reported until now, which investigated the fingerprint region of the IR spectra of these compounds (Trp and Phe) in the gaseous phase. 31,33 For Phe, the IR spectrum was recorded, 33 but the experimental approach used was not conformationally selective.…”

Section: Introductionmentioning

confidence: 99%

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Importance of Entropy in the Conformational Equilibrium of Phenylalanine: A Matrix-Isolation Infrared Spectroscopy and Density Functional Theory Study

et al. 2006

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The conformational behavior and infrared spectrum of L-phenylalanine were studied by matrix-isolation infrared spectroscopy and DFT [B3LYP/6-311++G(d,p)] calculations. The fourteen most stable structures were predicted to differ in energy by less than 10 kJ mol -1 , eight of them with abundances higher than 5% at the temperature of evaporation of the compound (423 K). Experimental results suggest that six conformers contribute to the spectrum of the isolated compound, whereas two conformers (IIb 3 and IIIb 3 ) relax in matrix to a more stable form (IIb 2 ) due to low energy barriers for conformational isomerization (conformational cooling). The two lowest-energy conformers (Ib 1 , Ia) differ only in the arrangement of the amino acid group relative to the phenyl ring; they exhibit a relatively strong stabilizing intramolecular hydrogen bond of the O-H‚‚‚N type and the carboxylic group in the trans configuration (OdC-O-H dihedral angle ca. 180°). Type II conformers have a weaker H-bond of the N-H‚‚‚OdC type, but they bear the more favorable cis arrangement of the carboxylic group. Being considerably more flexible, type II conformers are stabilized by entropy and the relative abundances of two conformers of this type (IIb 2 and IIc 1 ) are shown to significantly increase with temperature due to entropic stabilization. At 423 K, these conformers are found to be the first and third most abundant species present in the conformational equilibrium, with relative populations of ca. 15% each, whereas their populations could be expected to be only ca. 5% if entropy effects were not taken into consideration. Indeed, phenylalanine can be considered a notable example of a molecule where entropy plays an essential role in determining the relative abundance of the possible low-energy conformational states and then, the thermodynamics of the compound, even at moderate temperatures. Upon UV irradiation (λ > 235 nm) of the matrix-isolated compound, unimolecular photodecomposition of phenylalanine is observed with production of CO 2 and phenethylamine.

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Section: Introductionmentioning

confidence: 62%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Importance of Entropy in the Conformational Equilibrium of Phenylalanine: A Matrix-Isolation Infrared Spectroscopy and Density Functional Theory Study

et al. 2006

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“…It is observed that the conformation has a strong influence on the spectra. The experimental results are combined with density functional theory (DFT) calculations, and unique information on the structures of the individual conformers is obtained.IR absorption spectra of gas phase species can be obtained by ion-or fluorescence-dip spectroscopy [6,7,10], a technique that has been applied to various interesting systems, such as isolated [11] or paired nucleobases [12], to the amino acids phenylalanine and tryptophan [13,14], and to -sheet model systems [15,16]. These experiments have all been performed using laser systems that cover the near-and mid-IR and are limited to wavelengths shorter than about 7 m. In this range, X-H (X C;O; N), and C --O stretching vibrations are probed and the experiments provide insight into the conformational arrangement, as transitions exhibit shifts in absorption frequency and changes in intensity in the presence of, for instance, intramolecular hydrogen bonds or solvating molecules.…”

mentioning

confidence: 99%

Fingerprint IR Spectroscopy to Probe Amino Acid Conformations in the Gas Phase

Bakker

Aleese

Meijer³

et al. 2003

Phys. Rev. Lett.

137

192

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We report the infrared (IR) absorption spectra of different conformational isomers of gas phase amino acid molecules in the molecular fingerprint region of 330-1500 cm ÿ1 . The IR absorption spectra for three conformers of the amino acid tryptophan show absorption bands that uniquely identify the conformational structure of the molecule and that are well matched by density functional theory calculations. The present observations hold great promise for future identification of conformational folding of larger molecules by means of their IR absorption characteristics. DOI: 10.1103/PhysRevLett.91.203003 PACS numbers: 33.20.Ea, 31.15.Ew, 33.15.Bh, 33.20.Tp Over the past 20 years, sophisticated techniques have been developed to bring intact large biomolecules into the gas phase. The techniques most widely used today are matrix-assisted laser desorption ionization (MALDI) [1] and electrospray ionization (ESI) [2]. Because of their ability to provide mass and sequence information of biological samples, both techniques have revolutionized analytical biochemistry. However, inferring structural information on gas phase ions and molecules is often a difficult task. The knowledge of the gas phase structure can provide important insight into fundamental intramolecular interactions and can serve as a calibration point for theoretical models. While elaborate tools for solid and liquid samples exist, most of them cannot be applied to gas phase samples. One of the few techniques that can provide direct structural information on gas phase species is ion mobility, in which large ionized molecules are mass selected and pass through a drift cell filled with a buffer gas [3,4]. The molecular ions will arrive at the end of the drift cell after a period of time which depends on their collisional cross section. Information can also be obtained using spectroscopic methods, either in the ultraviolet (UV) [5] or in the infrared (IR) [6,7]. The IR absorption spectrum is a unique identifier for the structure: line intensities and frequencies give direct information on the forces that hold the molecule together. Recently, it was experimentally demonstrated that additional information can be obtained by the direct measurement of the direction of the vibrational transition dipole moment of isolated species [8]. Selective IR induced isomerization in the gas phase is another interesting technique that provides structural and dynamical information [9]. We here present IR absorption spectra for three conformers of tryptophan in the gas phase over a wide frequency range, from 330 to 1500 cm ÿ1 . It is observed that the conformation has a strong influence on the spectra. The experimental results are combined with density functional theory (DFT) calculations, and unique information on the structures of the individual conformers is obtained.IR absorption spectra of gas phase species can be obtained by ion-or fluorescence-dip spectroscopy [6,7,10], a technique that has been applied to various interesting systems, such as isolated [11] or paired nucl...

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Alkali Metal Ion Binding to Amino Acids Versus Their Methyl Esters: Affinity Trends and Structural Changes in the Gas Phase

et al. 2002

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The relative alkali metal ion (M+) affinities (binding energies) between seventeen different amino acids (AA) and the corresponding methyl esters (AAOMe) were determined in the gas phase by the kinetic method based on the dissociation of AA–M+–AAOMe heterodimers (M=Li, Na, K, Cs). With the exception of proline, the Li+, Na+, and K+ affinities of the other aliphatic amino acids increase in the order AAAAOMe is already observed for K+. Proline binds more strongly than its methyl ester to all M+ except Li+. Ab initio calculations on the M+ complexes of alanine, β‐aminoisobutyric acid, proline, glycine methyl ester, alanine methyl ester, and proline methyl ester show that their energetically most favorable complexes result from charge solvation, except for proline which forms salt bridges. The most stable mode of charge solvation depends on the ligand (AA or AAOMe) and, for AA, it gradually changes with metal ion size. Esters chelate all M+ ions through the amine and carbonyl groups. Amino acids coordinate Li+ and Na+ ions through the amine and carbonyl groups as well, but K+ and Cs+ ions are coordinated by the O atoms of the carboxyl group. Upon consideration of these differences in favored binding geometries, the theoretically derived relative M+ affinities between aliphatic AA and AAOMe are in good overall agreement with the above given experimental trends. The majority of side chain functionalized amino acids studied show experimentally the affinity order AAAAOMe. The latter ranking is attributed to salt bridge formation.

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Conformational landscapes in amino acids: infrared and ultraviolet ion-dip spectroscopy of phenylalanine in the gas phase

Cited by 243 publications

References 32 publications

Importance of Entropy in the Conformational Equilibrium of Phenylalanine: A Matrix-Isolation Infrared Spectroscopy and Density Functional Theory Study

Importance of Entropy in the Conformational Equilibrium of Phenylalanine: A Matrix-Isolation Infrared Spectroscopy and Density Functional Theory Study

Fingerprint IR Spectroscopy to Probe Amino Acid Conformations in the Gas Phase

Alkali Metal Ion Binding to Amino Acids Versus Their Methyl Esters: Affinity Trends and Structural Changes in the Gas Phase

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