Proton transfer at the carboxylic sites of amino acids: A single water molecule catalyzed process

Yang, Gang; Wu, Xiaomin; Zu, Yuangang; Liu, Chengbu; Fu, Yujie; Zhou, Lijun

doi:10.1002/qua.21797

Cited by 10 publications

(12 citation statements)

References 51 publications

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“…In the calculations of solvent effect, polarizable continuum model (PCM) in combination with the United Atom Topological Model (UA0) was used, and dielectric constant was set to ε = 78.4 to simulate the solvent medium, although there were some limitations for the PCM calculations on the stability of glycine molecule and proton transfer. The excellent agreement of our PCM/UA0 results of these thymine tautomers with that of Rejnek et al .…”

Section: Methodssupporting

confidence: 53%

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

Chen

Zhao

et al. 2011

J of Physical Organic Chem

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Stability orderings of 150 stable complexes formed by metal ions (Na+, K+, Ca2+, Mg2+, and Zn2+) and 13 stable thymine tautomers in both solvent and gas phases are obtained, and the optimal binding site for a metal ion in a specific thymine tautomer is identified. Results indicate that the complex with the canonical thymine tautomer (T1) is more stable than those with the rare ones, and the monodentate complex M–T1o4(o2) are their ground‐state form in the solvent phase. The ground‐state thymine complexes bound by Ca2+, Mg2+, or Zn2+ become bidentate M–T3o4lo2,n3, which is derived from a rare thymine tautomer T3o4l, whereas those bound by Na+ and K+ are still monodentate complexes M–T1o4(o2), however, in the gas phase. The differences in stability are discussed in detail from the binding strength of metal ions, relative energy of the corresponding thymine tautomers, and solution effect. Copyright © 2011 John Wiley & Sons, Ltd.

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Section: Methodssupporting

confidence: 53%

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

Chen

Zhao

et al. 2011

J of Physical Organic Chem

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“…These four atoms form a hydronium ion (H 3 O + ) and are greatly stabilized by the two extra-strong hydrogen bonds of O5-H9 and O7-H11, with both distances being approximately 1.287 Å . That is, the H 7 O 3 + ion is formed, [54][55][56][57] which is further stabilized by the hydrogen bonds The reaction energy diagram of the proton transfer process is shown in Fig. 5. Step 1 is the rotation of the carboxyl O-H group, which is endothermic, with IN4 being more unstable than nBA4 by 2.68 kcal mol À1 .…”

Section: 41mentioning

confidence: 99%

The conformational analysis and proton transfer of neuraminidase inhibitors: a theoretical study

Yang

et al. 2009

Phys. Chem. Chem. Phys.

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With the aid of density functional calculations, it was revealed that neuraminidase (NA) inhibitors (Scheme 1) exist exclusively in the neutral form. However, the docking and molecular dynamics simulations indicated that the zwitterionic, rather than neutral, isomers are the active form in NA-receptors. The neutral and zwitterionic isomers of BA (Compound 7 in Scheme 1) are quite different in structure and is therefore expected to show distinct bioactivities. With the addition of four water molecules, the geometry of the neutral isomer (nBA4) is induced to resemble the zwitterion and remains rather stable throughout the proton transfer process (nBA4 --> zBA4); in addition, the energy difference between the zwitterionic vs. the neutral isomer is lowered from 24.76 to 2.54 kcal mol(-1). The zwitterion is the predominant isomer in aqueous solution, consistent with the conformational preference in NA-receptors. The proton transfer process of nBA4 --> zBA4 is divided into two elementary steps. Step 1, rather than step 2, plays a decisive role, owing to the larger energy barrier; however, step 1 is not assisted by solvent water, even if it is not water-suppressed. Accordingly, the proton transfer process that leads to the formation of zwitterions is not facilitated in aqueous solution, albeit they may be more stable than the neutral isomers. It is thus suggested that the designed antiviral inhibitors should be facile to transform into the zwitterionic form in aqueous solution. In this way, the oral bioavailability of the antiviral drugs can be improved.

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“…The presence of water solvent causes the energies of various ZnGly isomers to change within a smaller range (Table ), indicative of a broader conformational distribution. ZnD III is the least stable in the gas phase whereas has comparable stability with ZnA I by considering solvent effects, which may be due to the large dipole moment of ZnD III (39.0 Debye) . Owing to the preference of zwitterionic structures in aqueous solutions, ZnA I A I A I ranks the second most stable instead of the eighth in the gas phase.…”

Section: Resultsmentioning

confidence: 99%

Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations

et al. 2012

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Calculations were performed to study the interactions of metal ions (M) with (multiple) amino acids (AA) and fill the gap between single AA and proteins. A complete conformational search results in nine and eleven ZnGly isomers at B3P86 and MP2 levels, respectively, and four populated conformers of glycine are responsible for production of these isomers. For all M, the isomers via the OO and NO binding modes are the main constituents, and the OO mode is favored by stronger electrostatic interactions. Binding with more glycines causes larger structural distortions, improves relative stabilities of monodentate binding isomers and generates new binding modes (e.g. ZnB(III) via only the hydroxyl group). The scaling factor of Zn(Gly)(n) structures, the ratio of its binding affinity versus the sum of comprising ZnGly isomers, is linear with glycine number (n), and the linear relationship may not be altered by mutations of glycines and M. It thus allows to estimate M(AA)(n) binding affinities (n ≥ 2) from the comprising MAA structures and analyze their structures with kinetic methods. The DFT and MP2 results become comparable by increasing metal coordination, e.g. the ZnB(III) versus ZnA(I) (zwitterionic) relative energy differs by 41.9 kcal mol(-1) at B3P86 and MP2 levels and is close by addition of three water molecules (4.1 kcal mol(-1)). The presence of water solvent improves the relative stabilities of monodentate binding isomers and results in a broader conformational distribution.

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Proton transfer at the carboxylic sites of amino acids: A single water molecule catalyzed process

Cited by 10 publications

References 51 publications

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

The conformational analysis and proton transfer of neuraminidase inhibitors: a theoretical study

Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations

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