The role of dimerization on the structure transformation of arginine in gas phase

Li, Hongbao; Lin, Zijing; Luo, Yi

doi:10.1016/j.cplett.2014.06.019

Cited by 7 publications

(13 citation statements)

References 27 publications

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“…This leads to some changes in the theoretical total spectrum (SUM) (for example, the three peaks at around 2829 cm À1 in group Z). Similar to arginine, 53 although the dispersion interactions are included in the M062X functional, it does not introduce effective changes in spectra.…”

Section: Chemical Structure: Infrared Spectramentioning

confidence: 99%

Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

Jiang

et al. 2015

Phys. Chem. Chem. Phys.

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The energy differences between canonical and zwitterionic isomers of arginylglycine (ArgGly) at the CCSD/aug-cc-pVDZ level are too small (less than 1 kcal mol(-1)) to determine the dominant form in the gas phase from the energetic point of view. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of neutral ArgGly. Noticeable spectral differences were found which enable the unambiguous identification of different neutral groups. We thus demonstrate X-ray spectroscopy as a powerful technique to study the conformation dependent chemical and electronic properties of neutral ArgGly.

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Section: Chemical Structure: Infrared Spectramentioning

confidence: 99%

Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

Jiang

et al. 2015

Phys. Chem. Chem. Phys.

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“…But these two peaks are totally absent in the zwitterions. Two strong peaks at 1666 and 1693 cm –1 appeared in the IR experiment of gaseous arginine at 443 K and have been explained by a combination of the three neutral arginine isomers . For R 1 , the experimental peak (at 1693 cm –1 ) red-shifted to 1678 cm –1 , with the contributions from the CN stretching mode and NH 2 scissoring mode of the guanidine group.…”

Section: Resultsmentioning

confidence: 96%

“…Arg has three different neutral isomers in the gas phase: two are canonical forms and one is a zwitterion. ,, To achieve reliable structural information, the most stable monomers of arginine in each neutral isomer should be included. Arg contains three unique functional groups: the carboxylate group, the amino group, and the guanidine group in the side chain.…”

Section: Computational Detailsmentioning

confidence: 99%

“…The counterpoise procedure was employed for the hydrated clusters to estimate the BSSE values . The calculated vibrational frequencies of the hydrated conformers are all scaled by uniform factors of 0.9813 , and 0.954 ,, for the B3LYP and M062X methods, respectively. The transition states for the transformation from the most populated canonical conformers to the zwitterion were identified at the B3LYP/6-311++G(d,p) level of theory.…”

Section: Computational Detailsmentioning

confidence: 99%

“…It can also affect the stability of the zwitterionic form of amino acids and peptides, which is one of the most intriguing examples of dramatic effects of water on biomolecules. It is well-known that the charge-separated zwitterionic conformers mostly exist in solid state or in solution within a narrow pH range and can hardly be found dominantly in the gas phase. − Therefore, the canonical-to-zwitterionic structure transition of amino acids becomes an important issue of biological phenomena triggered by the presence of water molecules. − This also raises the question of how many water molecules are required to induce such structure transition for a given amino acid molecule …”

Section: Introductionmentioning

confidence: 99%

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Systematic Study on Hydrated Arginine: Clear Theoretical Evidence for the Canonical-to-Zwitterionic Structure Transition

Jiang

et al. 2017

J. Phys. Chem. A

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Extensive ab initio investigations have been performed to characterize the stable conformers of hydrated arginine (Arg-HO). Many new low-energy canonical Arg-HO conformers were identified and they are more stable than previous results. The large energy differences (more than 5.00 kcal mol) between the canonical and zwitterionic Arg-HO isomers calculated by the composite CBS-QB3 method confirmed the dominance of the zwitterions. The micro effects of corrections of the zero-point energy and the basis set superposition error on the stability of hydrated isomers were carefully examined for the first time. The infrared (IR) spectra were simulated at a recommended temperature and the notable spectral differences enable the unambiguous identification of the different hydrated forms. Further transition state calculations revealed that the canonical Arg-HO can be transformed to the zwitterions using the amino group as a bridge. Our study thus shows valuable insights into the hydration of large flexible molecules and provides solid theoretical evidence for the canonical-to-zwitterionic structure transition of hydrated arginine.

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A fragment based step-by-step strategy for determining the most stable conformers of biomolecules

Li¹,

Lin²,

Luo³

2014

Chemical Physics Letters

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The role of dimerization on the structure transformation of arginine in gas phase

Cited by 7 publications

References 27 publications

Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

Systematic Study on Hydrated Arginine: Clear Theoretical Evidence for the Canonical-to-Zwitterionic Structure Transition

A fragment based step-by-step strategy for determining the most stable conformers of biomolecules

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