Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

Li, Hongbao; Li, Leilei; Jiang, Jun; Lin, Zijing; Luo, Yi

doi:10.1039/c5cp03729h

Cited by 7 publications

(11 citation statements)

References 50 publications

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“…Briefly speaking, the whole molecule was divided into two parts by the amide bond: the first one is the main-chain part, including the carboxyl group, the amino group and four methylene groups and the second one is the side-chain part, mainly including the amide bond and the pyrroline ring. The rotational details are similar to our previous work on several large flexible molecules. , …”

Section: Computational Detailssupporting

confidence: 58%

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Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine

Hua

Wang

et al. 2020

J. Phys. Chem. A

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The chemical and electronic structures of the 21st and 22nd proteinogenic amino acid selenocysteine (Sec), pyrrolysine (Pyl), and their derivatives (deprotonated and protonated ions) were extensively characterized for the first time. Through the fragment based step-by-step research on their potential energy surface (PES), electronic energies of the most stable conformers of Sec, Pyl and the related ions were finally determined at the advanced CBS-QB3 and DSD-PBEP86-D3(BJ)/ aug-cc-pVTZ levels, respectively, with the identification of many new low-energy conformers. The infrared spectra (IR) at 298 K of the most abundant conformers in different forms were scaled by comparison with the anharmonic frequency calculations and analyzed comparing with the experimental spectra of similar molecules. The characteristic soft X-ray spectra (including X-ray photoelectron spectra (XPS) and near-edge X-ray absorption finestructure spectra (NEXAFS)) of the most stable conformers at 498 K were also simulated. In particular, the two possible protonated configurations of Pyl can be clearly distinguished by their different spectral features. Furthermore, a small binding energy intersection appeared around 293 eV at the C 1s edge between the canonical and protonated Pyl conformers, which is different from all the previous studies. This work thus filled the gap in our knowledge by providing detailed information on the chemical and electronic structures of Sec and Pyl and will be a useful guidance for future experimental research.

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Section: Computational Detailssupporting

confidence: 58%

“…The latter vibration red-shifted ca. 52 cm −1 compared with that of several similar molecules, 18,36,55 mainly due to the strong interaction between the carboxyl group and the amide bond in Pyl. For its deprotonated form, the peaks around 700−900 cm −1 are similar to that of the canonical form.…”

Section: Resultsmentioning

confidence: 90%

Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine

Hua

Wang

et al. 2020

J. Phys. Chem. A

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“…It is found that the global minimum is still the zwitterionic conformer R z1 . Furthermore, it is interesting to find that the energy differences between the zwitterionic and canonical forms become larger with the improved theoretical methods (more than 3.18 and 5.00 kcal mol –1 ), which is opposite to the situation on dipeptide arginylglycine . It seems that with the improvement in the computational accuracy, the identification of the dominant form from the energetic point of view becomes possible for the hydrated molecules.…”

Section: Resultsmentioning

confidence: 98%

“…Furthermore, it is interesting to find that the energy differences between the zwitterionic and canonical forms become larger with the improved theoretical methods (more than 3.18 and 5.00 kcal mol −1 ), which is opposite to the situation on dipeptide arginylglycine. 12 It seems that with the improvement in the computational accuracy, the identification of the dominant form from the energetic point of view becomes possible for the hydrated molecules. Therefore, we believed that, at least for this hydrated molecule, calculations at the CCSD/6-311++G(d,p) are good enough to give reliable theoretical values.…”

mentioning

confidence: 99%

“…27,41 At present, both the measurement of energy in several kcal mol −1 and probing the molecular geometry of the isomers are still difficult in experiment. So various spectroscopic techniques 1,[10][11][12][13]42 should be applied to identify the dominant form in future experiment. The simulated spectral differences between the canonical and zwitterionic isomers can help one to deeply understand the structure−property relationship.…”

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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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Identification of the smallest peptide with a zwitterion as the global minimum: a first-principles study on arginine-containing peptides

Jiang

Luo

2017

Phys. Chem. Chem. Phys.

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Zwitterions are believed to play an important role in determining the structures, properties and functions of peptides and proteins. However, the smallest peptide with a zwitterionic structure as the global minimum in the gas phase is still not yet identified. In this study, an effective step-by-step strategy has been used to characterize the stable conformers of arginine-containing peptides arginylalanine (ArgAla) and arginylserine (ArgSer). Energy calculations at the DSD-PBEP86-D3BJ/aug-cc-pVTZ level and further extrapolation to the complete basis set (CBS) limit have confirmed, for the first time, that ArgSer appears to be a promising candidate as the smallest peptide with a zwitterionic global minimum structure. 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 these arginine-containing peptides. Notable spectral differences were found which enable the unambiguous identification of different neutral forms in future experiments. Our study thus provides valuable insights into the structural stability of zwitterions with the increase of molecular size and illustrates the competition between the canonical and zwitterionic isomers.

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Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

Cited by 7 publications

References 50 publications

Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine

Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine

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

Identification of the smallest peptide with a zwitterion as the global minimum: a first-principles study on arginine-containing peptides

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