Infrared matrix isolation studies of amino acids. Molecular structure of proline

Reva, Igor; Stepanian, S. G.; Plokhotnichenko, A. M.; Radchenko, E. D.; Sheina, G. G.; Blagoı̆, Yu. P.

doi:10.1016/0022-2860(93)07907-e

Cited by 85 publications

(92 citation statements)

References 20 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: 63%

“…[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. A number of aliphatic amino acids as well as some of their derivatives have been investigated experimentally up to date: glycine, 4,5,[14][15][16][17][18] sarcosine (N-methylglycine), 19 N,N-dimethylglycine, 20 alanine, 6,[21][22][23] valine, 7,24 proline 8,25,26 and serine.…”

Section: Introductionmentioning

confidence: 99%

“…[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. A number of aliphatic amino acids as well as some of their derivatives have been investigated experimentally up to date: glycine, 4,5,[14][15][16][17][18] sarcosine (N-methylglycine), 19 N,N-dimethylglycine, 20 alanine, 6,[21][22][23] valine, 7,24 proline 8,25,26 and serine. 27,28 Most of these studies also reported theoretical calculations at various levels of theory.…”

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%

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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: 63%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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 first MI-IR spectroscopic investigations on amino acid residues were performed by Grenie et al (1970), who studied glycine (Gly) in an Ar matrix. Since then Gly (Grenie and Garrigou-Lagrange1972;Reva et al 1995;Stepanian et al 1998a;Ivanov et al 1997Ivanov et al , 1999Bazsó et al 2012a, b) and many other amino acids were thoroughly studied by MI-IR spectroscopy, including alanine (Rosado et al 1997;Stepanian et al 1998b;Lambie et al 2003;Bazsó et al 2013), valine (Stepanian et al 1999), leucine (Sheina et al 1988), isoleucine (Boeckx and Maes 2012a), proline (Reva et al 1994;Stepanian et al 2001), serine (Lambie et al 2004;Jarmelo et al 2005;Jarmelo et al 2006), phenylalanine (Kaczor et al 2006), tyrosine (Ramaekers et al 2005), tryptophan (Kaczor et al 2007), cysteine (Dobrowolski et al 2007), asparagine (Boeckx and Maes 2012b), lysine (Boeckx and Maes 2012c), and β-alanine (Rosado et al 1997;Dobrowolski et al 2008). In a step towards understanding the structure and folding of peptides, protected amino acids, the smallest peptide models, were also investigated by this technique, including N-formylglycine (For-Gly, Wierzejewska and OlbertMajkut 2009), N-acetylglycine (Ac-Gly, Boeckx and Maes2012d), N-acetylalanine (Ac-Ala, Boeckx and Maes 2012e), N-acetyproline (Ac-Pro, Boeckx et al 2011), N-acetylcysteine (Ac-Cys, Boeckx et al 2010), Nacetyl-N′-methyl-glycine-amide (Ac-Gly-NHMe, Grenie et al1975;Pohl et al 2007), N-acetyl-N′-methyl-Lalanine-amide (Ac-L-Ala-NHMe, Grenie et al 1975;…”

Section: Introductionmentioning

confidence: 99%

Foldamers of β-peptides: conformational preference of peptides formed by rigid building blocks. The first MI-IR spectra of a triamide nanosystem

et al. 2013

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IntroductionAlthough dynamic on a large timescale of motion, some biologically active polyamide nanosystems adopt welldefined 3D structures in a time average manner, called as globular proteins; a given name reflecting to their overall shape. Other proteins called intrinsically unstructured or dynamic (IUP or IDP) are reluctant to present such an easy to characterize structural ensemble, nicknamed as proteins with random structures. Thus, proteins exist in most phases as conformational ensembles presenting lower, while in other environment higher time average deviation from their average 3D folds. The α-amino acid sequence modification of these inherently dynamic polyamide systems can lower, or increase the amplitude and frequency of such internal motion, making the protein fold less or more -mobile‖. The chemical constitution (α) and the stereochemistry (L) of proteogenic amino acid residues are under strict evolutional conservation. Unlike L-Proline, all the remaining 19 common residues in proteins have two adjacent backbone torsional angles, φ and ψ, of high rotational freedom followed by the inflexible ω. The scenario of two flexible followed by a fixed backbone torsional angles per residue determines primarily the folding ability of a proteogenic polypeptide. Cutting of a globular fold seldom results in secondary structural elements (e.g. α-helix, β-turn) of low internal dynamics! Typically the removal of any secondary structural element from its -natural environment‖ results in polypetides of very elevated internal dynamics, often characterized as unstructured subunits. However, bioengineering requires stable toolkits to design epitopes, matching complementary folds, individual foldamers, nano-lego elements etc. of traceable shape and of low internal mobility. Shedding light on folding and stability of secondary structural elements of peptides and proteins could help to design standalone foldamers. They could be composed of β-, α-and α/β-amino acid residues, the latter called chimera. A general expectation of foldamers is to present a single time average 3D-structure of lower internal dynamics over the large timescale of picoseconds to second. These fold optimized biocompatible and nonnatural peptides often have an increased proteolytic and metabolic stability and can fulfill diverse biological functions toward DNA, RNA, ATP, etc. The improved ability of β-peptides and thus β-foldamers to rapidly and spontaneously fold (

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Ab initio and molecular mechanics conformational analysis of neutralL-proline

Ramek

Kelterer

Nikolić

1997

Int. J. Quant. Chem.

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Infrared matrix isolation studies of amino acids. Molecular structure of proline

Cited by 85 publications

References 20 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

Foldamers of β-peptides: conformational preference of peptides formed by rigid building blocks. The first MI-IR spectra of a triamide nanosystem

Ab initio and molecular mechanics conformational analysis of neutralL-proline

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