Structural Evidence for Inter-Residue Hydrogen Bonding Observed for Cellobiose in Aqueous Solution

O’Dell, William B.; Baker, David C.; McLain, Sylvia E.

doi:10.1371/journal.pone.0045311

Cited by 36 publications

(32 citation statements)

References 67 publications

(92 reference statements)

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“…NDIS is a well-established technique which has been used successfully to determine the atomistic interactions between a range of molecules and water in solution. [18][19][20][23][24][25][26][27][28][29] Neutron diffraction measurements provide a direct measure of the structure in reciprocal space -the static structure factor, F(Q). F(Q) can be written as:…”

Section: Neutron Diffraction With Isotopic Substitutionmentioning

confidence: 99%

On the atomic structure of cocaine in solution

Johnston

Büsch

Pardo

et al. 2016

Phys. Chem. Chem. Phys.

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Cocaine is an amphiphilic drug which has the ability to cross the blood-brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ∼5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Å of cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function.

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Section: Neutron Diffraction With Isotopic Substitutionmentioning

confidence: 99%

On the atomic structure of cocaine in solution

Johnston

Büsch

Pardo

et al. 2016

Phys. Chem. Chem. Phys.

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“…These data show the expected strong hydrogen bonds between the NH 3 group and the water molecules (H N ···O w 1.75 Å; N···O w 2.75 Å) and the OH group and the water molecules (H OH ···O w 1.76 Å; O···O w 2.76 Å) and are in good agreement with radial distribution functions between similar functional groups with water. 29,50 The first peak in the H w ···O pair correlation shows that the hydroxyl groups also accept hydrogen bonds from the water molecules (H w ···O 1.86 Å). The difference of ∼1 Å between the H···O w /H···O distances and the N···O w /O···O w distances indicates predominantly linear hydrogen bonding.…”

Section: B Dopamine-water Intermolecular Interactionsmentioning

confidence: 99%

Conformation and interactions of dopamine hydrochloride in solution

Callear

Johnston

McLain

et al. 2015

The Journal of Chemical Physics

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The aqueous solution of dopamine hydrochloride has been investigated using neutron and X-ray total scattering data together with Monte-Carlo based modelling using Empirical Potential Structure Refinement. The conformation of the protonated dopamine molecule is presented and the results compared to the conformations found in crystal structures, dopamine-complexed protein crystal structures and predicted from theoretical calculations and pharmacophoric models. It is found that protonated dopamine adopts a range of conformations in solution, highlighting the low rotational energy barrier between different conformations, with the preferred conformation being trans-perpendicular. The interactions between each of the species present (protonated dopamine molecules, water molecules, and chloride anions) have been determined and are discussed with reference to interactions observed in similar systems both in the liquid and crystalline state, and predicted from theoretical calculations. The expected strong hydrogen bonds between the strong hydrogen bond donors and acceptors are observed, together with evidence of weaker CH hydrogen bonds and π interactions also playing a significant role in determining the arrangement of adjacent molecules.

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“…These observations concerning solvent‐exposed H‐bonding are particularly important considering that experimental techniques such as nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy permit nowadays the detection of individual H‐bonds in solvated (bio)molecules, see e.g . Refs . for NMR studies, Refs .…”

Section: Introductionmentioning

confidence: 99%

“…for other approaches. In these studies as well as in related theoretical work, high‐occurrence (so‐called persistent) solvent‐exposed H‐bonds are often automatically regarded as conformationally determinant . However, the above discussion suggests that in aqueous solution, they are rather opportunistic, even if their detection may still represent an interesting structural probe for the dominant conformations.…”

Section: Introductionmentioning

confidence: 99%

Solvent‐Modulated Influence of Intramolecular Hydrogen‐Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study

Lonardi

Oborský

Hünenberger

2016

Helvetica Chimica Acta

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Intramolecular hydrogen‐bonding (H‐bonding) is commonly regarded as a major determinant of the conformation of (bio)molecules. However, in an aqueous environment, solvent‐exposed H‐bonds are likely to represent only a marginal (possibly adverse) conformational driving as well as steering force. For example, the hydroxymethyl rotamers of glucose and galactose permitting the formation of an intramolecular H‐bond with the adjacent hydroxyl group are not favored in water but, in the opposite, least populated. This is because the solvent‐exposed H‐bond is dielectrically screened as well as subject to intense H‐bonding competition by the water molecules. In the present study, the effect of a decrease in the solvent polarity on this rotameric equilibrium is probed using molecular dynamics simulation. This is done by considering six physical solvents (H2O, DMSO, MeOH, CHCl3, CCl4, and vacuum), along with 19 artificial water‐like solvent models for which the dielectric permittivity and H‐bonding capacity can be modulated independently via a scaling of the O–H distance and of the atomic partial charges. In the high polarity solvents, the intramolecular H‐bond is observed, but arises as an opportunistic consequence of the proximity of the H‐bonding partners in a given rotameric state. Only when the polarity of the solvent is decreased does the intramolecular H‐bond start to induce a conformational pressure on the rotameric equilibrium. The artificial solvent series also reveals that the effects of the solvent permittivity and of its H‐bonding capacity mutually enhance each other, with a slightly larger influence of the permittivity. The hydroxymethyl conformation in hexopyranoses appears to be particularly sensitive to solvent‐polarity effects because the H‐bond involving the hydroxymethyl group is only one out of up to five H‐bonds capable of forming a network around the ring.

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Structural Evidence for Inter-Residue Hydrogen Bonding Observed for Cellobiose in Aqueous Solution

Cited by 36 publications

References 67 publications

On the atomic structure of cocaine in solution

On the atomic structure of cocaine in solution

Conformation and interactions of dopamine hydrochloride in solution

Solvent‐Modulated Influence of Intramolecular Hydrogen‐Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study

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