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

Li, Hongbao; Hu, Andong; Jiang, Jun; Luo, Yi

doi:10.1021/acs.jpca.7b02008

Cited by 5 publications

(3 citation statements)

References 46 publications

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“…In general, one acceptor atom (oxygen) can be bonded to no more than two donors. 58 The geometric landscape of all hydrated neutral THFA and cations and their relative energies were interpreted by computational methods. First, the structures were optimized at the B3LYP/6-311++G(d,p) level of theory and the unique conformers Fig.…”

Section: Methodsmentioning

confidence: 99%

Hydrogen bonding and dominant conformations of hydrated sugar analogue complexes using tetrahydrofurfuryl alcohol as the model sugar molecule

Jin

Wang

et al. 2018

Phys. Chem. Chem. Phys.

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Water molecules, which serve as both hydrogen bond donors and acceptors, have been found to influence the conformational landscape of gas-phase phenyl-β-d-glucopyranoside. Herein, tetrahydrofurfuryl alcohol (THFA), a sugar-like molecule without chromophores (e.g. phenyl-substitution), was used as the model sugar molecule for exploring the behaviour of water molecules on the conformational landscape of a pentose sugar such as deoxyribose. We used mass selected infrared-vacuum ultraviolet (IR-VUV) (118 nm) spectroscopy to investigate the hydrated neutral THFA and its complex cation in a supersonic jet. High level density functional theory (DFT) calculations were performed to ascertain the experimental results. The results revealed that the water molecule tends to insert into the twisted conformer at a position where two stronger intermolecular hydrogen bonds were formed by breaking the weak intramolecular interactions. We found that the twisted conformer of the hydrated neutral THFA complex is more stable than the envelope conformation, while the latter is more stable for the THFA molecule. However, the conformational landscape of the hydrated THFA complex cation did not significantly change on microsolvation with water molecules. These results indicated that the dominant structural landscape of the hydrated cationic complex is the twisted configuration with a trans-hydroxymethyl group. This finding provides valuable insight into the microsolvation of gas-phase sugar molecules.

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Section: Methodsmentioning

confidence: 99%

Hydrogen bonding and dominant conformations of hydrated sugar analogue complexes using tetrahydrofurfuryl alcohol as the model sugar molecule

Jin

Wang

et al. 2018

Phys. Chem. Chem. Phys.

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“…The equilibrium distributions of each molecule at 298 and 498 K were calculated based on the Boltzmann distribution formula in the same way as we did previously by considering the Gibbs free energy corrections. , Through anharmonic frequency calculations on the representative conformer (the global minimum) in different forms of Sec, Pyl, and their ions at the same B3LYP/6-311++G(d,p) level, the vibrational frequencies of the important conformers were calibrated by accurate scaling factors. All calculations were carried out using the Gaussian 16 software package while the DSD calculations have been done by ORCA 4.0 .…”

Section: Computational Detailsmentioning

confidence: 99%

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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“…Detection of this critical level of hydration can be performed with charged microhydrated biomolecules in the gas phase, where one can benefit from the finite size of such molecular complexes. Extensive work has been done to investigate the effect of metal cations for stabilization of SB structures of bare amino acids, − as well as of amino acids solvated by a single water molecule. − Stabilization of SB structures by microhydration of natively protonated amino acids has been studied on a few occasions theoretically − but only little experimentally. , It was shown that the zwitterionic form of the studied amino acids can be stabilized in the gas phase by complexation with metal cations and/or water molecules. Arginine is one of the amino acids that exhibits protonation of its side chain under native conditions in aqueous solution and in the gas phase.…”

Section: Introductionmentioning

confidence: 99%

Salt Bridge Structure of Microhydrated Arginine Kinetically Trapped in the Gas Phase by Evaporative Cooling

et al. 2023

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Amino acids and peptides generally exhibit zwitterionic forms with salt bridge (SB) structures in solution but charge-solvated (CS) motifs in the gas phase. Here, we report a study of non-covalent complexes of the protonated amino acid arginine, ArgH + (H 2 O) n (n = 1−5), produced in the gas phase from an aqueous solution with a controlled number of retained water molecules. These complexes were probed by cold ion spectroscopy and treated by quantum chemistry. The spectroscopic changes induced upon gradual dehydration of arginine were assigned by structural calculations to the transition from SB to CS geometries. SB conformers appear to be present for the complexes with as few as 3 retained water molecules, although energetically CS structures should become prevailing already for ArgH + with 7−8 water molecules. We attribute the revealed kinetic trapping of arginine in native-like zwitterionic forms to evaporative cooling of the hydrated complexes to as low as below 200 K.

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

Cited by 5 publications

References 46 publications

Hydrogen bonding and dominant conformations of hydrated sugar analogue complexes using tetrahydrofurfuryl alcohol as the model sugar molecule

Hydrogen bonding and dominant conformations of hydrated sugar analogue complexes using tetrahydrofurfuryl alcohol as the model sugar molecule

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

Salt Bridge Structure of Microhydrated Arginine Kinetically Trapped in the Gas Phase by Evaporative Cooling

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