Update 1 of: Strong Ionic Hydrogen Bonds

Mautner, M.

doi:10.1021/cr200430n

Cited by 144 publications

(98 citation statements)

References 578 publications

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“…This stronger solvent destabilization induced by carboxylates leads to cancel out most of the differences in the ion/water interaction energies U̅ iw (∞) between carboxylates and the latter cations. Hence, as experimentally reported, 49,51,52 our simulation results show that the single ion absolute solvation enthalpies ΔH g→aq , computed according to…”

Section: Theoretical Methodssupporting

confidence: 83%

Simulated Solvation of Organic Ions II: Study of Linear Alkylated Carboxylate Ions in Water Nanodrops and in Liquid Water. Propensity for Air/Water Interface and Convergence to Bulk Solvation Properties

2015

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We investigated the solvation of carboxylate ions from formate to hexanoate, in droplets of 50 to 1000 water molecules and neat water, by computations using standard molecular dynamics and sophisticated polarizable models. The carboxylate ions from methanoate to hexanoate show strong propensity for the air/water interface in small droplets. Only the ions larger than propanoate retain propensity for the interface in larger droplets, where their enthalpic stabilization by ion/water dispersion is reduced there by 3 kcal mol(-1) per CH2 group. This is compensated by entropy effects over +3.3 cal mol(-1) K(-1) per CH2 group. On the surface, the anionic headgroups are strongly oriented toward the aqueous core, while the hydrophobic alkyl chains are repelled into air and lose their structure-making effects. These results reproduce the structure-making effects of alkyl groups in solution, and suggest that the hydrocarbon chains of ionic headgroups and alkyl substituents solvate independently. Extrapolation to bulk solution using standard extrapolation schemes yields absolute carboxylate solvation energies. The results for formate and acetate yield a proton solvation enthalpy of about 270 kcal mol(-1), close to the experiment-based value. The largest carboxylate ions yield a value smaller by about 10 kcal mol(-1), which requires studies in much larger droplets.

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Section: Theoretical Methodssupporting

confidence: 83%

Simulated Solvation of Organic Ions II: Study of Linear Alkylated Carboxylate Ions in Water Nanodrops and in Liquid Water. Propensity for Air/Water Interface and Convergence to Bulk Solvation Properties

2015

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“…The similarity of partial and full solvation enthalpies also applies to further alkylammonium ions from NH 4 + to (Et) 3 NH + , as well as to oxonium ions. 3,15,18 There seems to be little physical interpretation of the above solvation effects, except some early analysis of solvation terms. 7,18 Compared to monatomic ions, the solvation of alkylammonium ions has been much less investigated using theoretical approaches, and most of the reported studies concern NH 4 + (see refs 19−22).…”

Section: Introductionmentioning

confidence: 99%

Simulated Solvation of Organic Ions: Protonated Methylamines in Water Nanodroplets. Convergence toward Bulk Properties and the Absolute Proton Solvation Enthalpy

2014

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We applied an alternative, purely theoretical route to estimate thermodynamical properties of organic ions in bulk solution. The method performs a large ensemble of simulations of ions solvated in water nanodroplets of different sizes, using a polarizable molecular dynamics approach. We consider protonated ammonia and methylamines, and K(+) for comparison, solvated in droplets of 50-1000 water molecules. The parameters of the model are assigned from high level quantum computations of small clusters. All the bulk phase results extrapolated from droplet simulations match, and confirm independently, the relative and absolute experiment-based ion solvation energies. Without using experiment-based parameters or assumptions, the results confirm independently the solvation enthalpy of the proton, as -270.3 ± 1.1 kcal mol(-1). The calculated relative solvation enthalpies of these ions are constant from small water clusters, where only the ionic headgroups are solvated, up to bulk solution. This agrees with experimental thermochemistry, that the relative solvation energies of alkylammonium ions by only four H2O molecules reproduce the relative bulk solvation energies, although the small clusters lack major bulk solvation factors. The droplet results also show a slow convergence of ion solvation properties toward their bulk limit, and predict that the stepwise solvation enthalpies of ion/water droplets are very close to those of pure neutral water droplets already after 50 water molecules. Both the ionic and neutral clusters approach the bulk condensation energy very gradually up to 10,000 water molecules, consistent with the macroscopic liquid drop model for pure water droplets. Compared to standard computational methods based on infinite periodic systems, our protocol represents a new purely theoretical approach to investigate the solvation properties of ions. It is applicable to the solvation of organic ions, which are pivotal in environmental, industrial, and biophysical chemistry but have been little investigated theoretically up to the present.

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“…We identified potential salt bridge-forming residues within the sialidase BPD interface at topologically identical positions that we suspect could be involved in protein folding and stability, enzyme activation, and biomolecular recognition (Breuker et al, 2011;Buschiazzo and Alzari, 2008;Meot-Ner Mautner, 2012;Wilks et al, 1988). In addition, we established differences in both ATCC 33277 and W50 b2D444-b6K338 distance measurements, whereby strain ATCC 33277 does not favor salt bridge formation while strain W50 favors salt bridge formation.…”

Section: Discussionmentioning

confidence: 89%

Structural Significance of the β1K396 Residue Found in thePorphyromonas gingivalisSialidase β-Propeller Domain: A Computational Study with Implications for Novel Therapeutics Against Periodontal Disease

Cueno

Kamio²,

Imai³

et al. 2014

OMICS: A Journal of Integrative Biology

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Porphyromonas gingivalis sialidase activity is associated with virulence and initiated by sialic acid (SA) binding to the b-propeller domain (BPD). Sialidase BPD is structurally conserved in various bacterial species and the protein binding interfaces have the tendency to form salt bridges, whereas uncommitted charged residues may affect binding and protein structure. However, it is not clear whether the sialidase BPD of varying strains of the same bacterial species differ, particularly with regards to salt bridge formation. Here, we determined the P. gingivalis ATCC 33277 and W50 sialidase homology models and sialidase activities, while the putative salt bridge residues found in the sialidase BPDs were compared. We established that both ATCC 33277 and W50 have different sialidase homology models and activities, whereas, the BPD (b1-6) is structurally conserved with most salt bridge-forming residues following a common orientation. Moreover, b2D444-b6K338 distance measurement in ATCC 33277 (5.99 Å ) and W50 (3.09 Å ) differ, while b1K396A substitution alters the b2D444-b6K338 distance measurements in ATCC 33277 (3.09 Å ) and W50 (3.01 Å ) consequentially affecting each model. P. gingivalis plays a major role in periodontitis induction and its virulence is greatly influenced by the sialidase enzyme wherein the sialidase BPD is highly conserved. Our results suggest that alterations in the salt bridge formation within the BPD interface may affect the P. gingivalis sialidase structure. This would imply that disrupting the salt bridge formation within the P. gingivalis sialidase BPD could serve as a potential therapeutic strategy for the treatment of P. gingivalis-related periodontitis.

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Update 1 of: Strong Ionic Hydrogen Bonds

Cited by 144 publications

References 578 publications

Simulated Solvation of Organic Ions II: Study of Linear Alkylated Carboxylate Ions in Water Nanodrops and in Liquid Water. Propensity for Air/Water Interface and Convergence to Bulk Solvation Properties

Simulated Solvation of Organic Ions II: Study of Linear Alkylated Carboxylate Ions in Water Nanodrops and in Liquid Water. Propensity for Air/Water Interface and Convergence to Bulk Solvation Properties

Simulated Solvation of Organic Ions: Protonated Methylamines in Water Nanodroplets. Convergence toward Bulk Properties and the Absolute Proton Solvation Enthalpy

Structural Significance of the β1K396 Residue Found in thePorphyromonas gingivalisSialidase β-Propeller Domain: A Computational Study with Implications for Novel Therapeutics Against Periodontal Disease

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