Observation of Pyridine Aggregation in Aqueous Solution Using Neutron Scattering Experiments and MD Simulations

Mason, Philip E.; Neilson, G. W.; Dempsey, Christopher E.; Price, David L.; Saboungi, Marie‐Louise; Brady, John W.

doi:10.1021/jp9097827

Cited by 22 publications

(49 citation statements)

References 37 publications

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“…While the method of ICNCI is described in detail elsewhere, 15 it is necessary to declare the functions measured in this paper. The total measured intensity for the sample ( F(Q) ) is given by…”

Section: Methodsmentioning

confidence: 99%

“…If the conformation of the sugar does not change significantly with concentration, then it can be shown 15 that an appropriately scaled subtraction of these two data sets will yield a difference function that contains no correlations that are not sensitive to the concentration of the sugar. For reasons that are explained elsewhere, 15 this scaled subtraction is slightly different for the real space data than for the reciprocal space data. For the real-space data this difference can be expressed as:

Δ G_{H 5}^{X} (r) = \frac{ρ_{2}}{c_{H 5_{2}}} G_{H 5}^{X} {false(r false)}_{2} - \frac{ρ_{1}}{c_{H 5_{1}}} G_{H 5}^{X} {false(r false)}_{1} .

and for the Q space data it is expressed as:

Δ Δ S_{H 5}^{X} (Q) = \frac{1}{c_{H 5_{2}}} Δ S_{H 5}^{X} {false(Q false)}_{2} - \frac{1}{c_{H 5_{1}}} Δ S_{H 5}^{X} {false(Q false)}_{1},

…”

Section: Methodsmentioning

confidence: 99%

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A new structural technique for examining ion-neutral association in aqueous solution

et al. 2013

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The method of intramolecular coordination number concentration invariance (ICNCI) is used on neutron diffraction with isotopic substitution (NDIS) measurements of aqueous solutions to separate the intra- and intermolecular contributions to the total intensities. Molecular dynamics simulations of corresponding systems are then used to interpret the ICNCI function. It is found that the ICNCI function (characterized by two concentration measurements) is sensitive specifically to intermolecular association and that the molecular dynamics can successfully replicate this function in the cases of the neutral species xylose and pyridine in aqueous solution. ICNCI functions can also be obtained by the addition of a cosolute (such as adding GdmCl or Gdm2SO4 to pyridine solutions). In that case it is found that molecular dynamics can replicate the ICNCI function for the addition of GdmCl to pyridine, but fails to successfully replicate the same function for the addition of Gdm2SO4. This result implies that the interaction of pyridine with guanidinium sulfate is over-estimated in MD these simulations, and is of significant importance to the use of molecular dynamics simulations to elucidate an atomic level understanding of the Hofmeister series.

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Section: Methodsmentioning

confidence: 99%

Δ G_{H 5}^{X} (r) = \frac{ρ_{2}}{c_{H 5_{2}}} G_{H 5}^{X} {false(r false)}_{2} - \frac{ρ_{1}}{c_{H 5_{1}}} G_{H 5}^{X} {false(r false)}_{1} .

and for the Q space data it is expressed as:

Δ Δ S_{H 5}^{X} (Q) = \frac{1}{c_{H 5_{2}}} Δ S_{H 5}^{X} {false(Q false)}_{2} - \frac{1}{c_{H 5_{1}}} Δ S_{H 5}^{X} {false(Q false)}_{1},

…”

Section: Methodsmentioning

confidence: 99%

A new structural technique for examining ion-neutral association in aqueous solution

et al. 2013

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“…On top of that, both are liquids at room temperature with high solubilities in water. We first perform neutron diffraction with isotopic substitution (NDIS) 13,14 on aqueous solutions of both isopropyl alcohol and isopropyl amine. By direct comparison of the measured spectra of the two species, we are able to determine the pertinent differences in their hydration.…”

Section: ■ Introductionmentioning

confidence: 99%

Hydration of Hydroxyl and Amino Groups Examined by Molecular Dynamics and Neutron Scattering

et al. 2015

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Neutron diffraction with isotopic substitution was performed on aqueous solutions of isopropyl alcohol and isopropylamine. The difference between these two measurements primarily contains information about the different hydration of the alcohol and amino group. This data is used as a test of the accuracy of molecular dynamic simulations of the same systems. Having established the level of accuracy of the modeling, it is employed as an interpretive tool for the experimental data. Even though the alcohol and the amine possess comparable hydrogen bonding capabilities, consisting respectively of either two hydrogen bond acceptors and one donor, or two hydrogen bond donors and one acceptor, we find significant differences in the hydration of the hydroxyl and amino groups.

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“…For even moderately polyatomic solute molecules, including sugars and amino acids, however, such experiments are much more problematic. Recent advances in analysis of diffraction data in conjunction with computer simulations suggest the promise that such experiments might provide specific hydration information in the future (Mason et al 2010). Whether or not the information comes from simulation or experiment, knowledge of how a solute structures solvent water could potentially be exploited to understand much about the properties of that solute in solution, such as its hydrodynamics, its solubility, and its interactions with co-solutes.…”

Section: Introductionmentioning

confidence: 99%

Weakly hydrated surfaces and the binding interactions of small biological solutes

et al. 2011

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Extended planar hydrophobic surfaces, such as are found in the side chains of the amino acids histidine, phenylalanine, tyrosine, and tryptophan, exhibit an affinity for the weakly hydrated faces of glucopyranose. In addition, molecular species such as these, including indole, caffeine, and imidazole, exhibit a weak tendency to pair together by hydrophobic stacking in aqueous solution. These interactions can be partially understood in terms of recent models for the hydration of extended hydrophobic faces and should provide insight into the architecture of sugar-binding sites in proteins.

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Observation of Pyridine Aggregation in Aqueous Solution Using Neutron Scattering Experiments and MD Simulations

Cited by 22 publications

References 37 publications

A new structural technique for examining ion-neutral association in aqueous solution

A new structural technique for examining ion-neutral association in aqueous solution

Hydration of Hydroxyl and Amino Groups Examined by Molecular Dynamics and Neutron Scattering

Weakly hydrated surfaces and the binding interactions of small biological solutes

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