Arginine Zwitterion is More Stable than the Canonical Form when Solvated by a Water Molecule

Im, Suk; Jang, Sungwoo; Lee, Sungyul; Lee, Yonghoon; Kim, Bongsoo

doi:10.1021/jp801933y

Cited by 42 publications

(50 citation statements)

References 41 publications

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“…Solvation of amino acids 7-14 by water has been under intensive study both theoretically and experimentally, because the structures and stability of canonical 15-18 and zwitterionic 16,[19][20][21][22][23][24][25] forms are profoundly affected by solvent. Amino acids exist in canonical (nonzwitterionic) form in the gas phase, whereas zwitterionic (charge-separated) conformer is the predominant in aqueous solution.…”

Section: Stability Of Canonical Vs Zwitterionic Forms Of Amino Acidsmentioning

confidence: 99%

Proton Transfer in Biomolecules Facilitated by Water: Quantum Chemical Investigations

Lee¹

2011

Bulletin of the Korean Chemical Society

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We present a brief review for theoretical/computational studies of proton transfer processes of some simple biomolecules promoted by microsolvating water molecules. Focus is given on the relative stability of the canonical vs. zwitterionic forms of amino acids, tautomeric forms of the DNA base adenine, and the biologically active vs. inactive forms of nicotine. The biochemical implications of these findings are also discussed.

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Section: Stability Of Canonical Vs Zwitterionic Forms Of Amino Acidsmentioning

confidence: 99%

Proton Transfer in Biomolecules Facilitated by Water: Quantum Chemical Investigations

Lee¹

2011

Bulletin of the Korean Chemical Society

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“…Several theoretical and experimental studies were carried out on the behavior of amino acids in hydrated media. It was established that at least three water molecules were necessary to stabilize the zwitterionic character of an amino acid backbone [16][17][18][19], but it is not sufficient. Ghomi's group [10] had also confirmed these results and added that this number of solvent molecules present an adequate hydration network of NH + 3 and COO − terminals, thus avoiding the proton transfer from NH + 3 to COO − .…”

Section: Introductionmentioning

confidence: 99%

Solvent effects on the structures and vibrational features of zwitterionic dipeptides: L-diglycine and L-dialanine

2015

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Calculations were done by applying the B3LYP/6-31++G(d) method on the zwitterionic L-diglycine and L-dialanine to study the solvent effects on their structures and vibrational features. Three models of solvation (implicit, explicit, and explicit in implicit) were used and the subsequent resulting values compared. Even though both dipeptides surrounded by 12 water molecules seem sufficient to stabilize their zwitterionic characters, notably to avoid the proton transfer between the backbone (N t H[Formula: see text], COO (-)) groups, the hybrid model of solvation (explicit in implicit noted 12W/Continuum) appears to be in better agreement with available IR and Raman experiments than explicit and implicit models. The harmonic vibrational modes derived from geometry optimization of L-diglycine and L-dialanine in 12W/Continuum, agree with the available IR and Raman experimental values within 1 % for L-diglycine and 2 % for L-dialanine, and they appear more accurate than those found using the explicit model (12W). Graphical Abstract DFT/6-31++G∗ Optimized structures of L-diglycine (top) and L-dialanine (bottom) surrounded by 12 water molecules all embedded in a continuum.

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“…15 However, for this type of interaction to occur, intramolecular proton transfer is required, leading to the formation of a zwitterion, which is not trivial under isolated conditions. Under physiological conditions, polar solvent molecules and metal ions stabilize the positive and negative charges on the biomolecule 16,17 or facilitate intramolecular proton transfer by acting as a solvent bridge. 18,19 Obviously, this charge stabilizing effect is absent under isolated conditions, resembling to some extent the situation in hydrophobic protein pockets (in the absence of water molecules).…”

Section: Introductionmentioning

confidence: 99%

Gas-phase salt bridge interactions between glutamic acid and arginine

Jaeqx

Rijs

2013

Phys. Chem. Chem. Phys.

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The gas-phase side chain-side chain (SC-SC) interaction and possible proton transfer between glutamic acid (Glu) and arginine (Arg) residues are studied under low-temperature conditions in an overall neutral peptide. Conformation-specific IR spectra, obtained with the free electron laser FELIX, in combination with density functional theory (DFT) calculations, provide insight into the occurrence of intramolecular proton transfer and detailed information on the conformational preferences of the peptides Z-Glu-Ala n -Arg-NHMe (n = 0,1,3). Low-energy structures are obtained using molecular dynamics simulations via the simulated annealing approach, resulting in three types of SC-SC interactions, in particular two types of pair-wise interactions and one bifurcated interaction. These low-energy structures are optimized and frequency calculations are performed using the B3LYP functional, for structural analysis, and the M05-2x functional, for relative energies, employing the 6-311+G(d,p) basis set. Comparison of experimental and computed spectra suggests that only a single conformation was present for each of the three peptides.Despite the increasing spacing between the Glu and Arg residues, the peptides have several types of interactions in common, in particular specific SC-SC and dispersion interactions between the Arg side chain and the phenyl ring of the Z-cap. Comparison with previous experiments on Ac-Glu-Ala-Phe-Ala-Arg-NHMe as well as molecular dynamics simulations further suggest that the pairwise interaction observed here is indeed energetically most favorable for short peptide sequences.

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Arginine Zwitterion is More Stable than the Canonical Form when Solvated by a Water Molecule

Cited by 42 publications

References 41 publications

Proton Transfer in Biomolecules Facilitated by Water: Quantum Chemical Investigations

Proton Transfer in Biomolecules Facilitated by Water: Quantum Chemical Investigations

Solvent effects on the structures and vibrational features of zwitterionic dipeptides: L-diglycine and L-dialanine

Gas-phase salt bridge interactions between glutamic acid and arginine

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