A multiscale approach to model hydrogen bonding: The case of polyamide

Gowers, Richard; Carbone, Paola

doi:10.1063/1.4922445

Cited by 81 publications

(97 citation statements)

References 51 publications

(66 reference statements)

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“…In our analysis, we identified a hydrogen bond when

θ_{OH - O} > 130 °

and d HO < 0.24 nm. These criteria are similar to those used in other simulations with water and were verified using 2D contour plots (see SI 11), which is a common method to determine the geometric criteria for dilute and condensed polymer systems. As there are two layers of water within the channel, an additional criterion was used to differentiate between hydrogen bonds that are within a layer (intralayer) and between the layers (interlayer).…”

Section: Resultsmentioning

confidence: 60%

Why different water models predict different structures under 2D confinement

2018

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Experiments of nanoconfined water between graphene sheets at high pressure suggest that it forms a square ice structure (Algara-Siller et al., Nature, 2015, 519, 443). Molecular dynamics (MD) simulations have been used to attempt to recreate this structure, but there have been discrepancies in the structure formed by the confined water depending on the simulation set-up that was employed and particularly on the choice of water model. Here, using classical molecular dynamics simulations, we have systematically investigated the effect that three different water models (SPC/E, TIP4P/2005 and TIP5P) have on the structure of water confined between two rigid graphene sheets with a 0.9 nm separation. We show that the TIP4P/2005 and the TIP5P water models form a hexagonal AA-stacked structure, whereas the SPC/E model forms a rhombic AB-stacked structure. Our work demonstrates that the formation of these structures is driven by differences in the strength of hydrogen bonds predicted by the three water models, and that the nature of the graphene/water interaction only mildly affects the phase diagram. Considering the available experimental data and first-principle simulations we conclude that, among the models tested, the TIP4P/2005 and TIP5P force fields are for now the most reliable when simulating water under confinement. © 2018 Wiley Periodicals, Inc.

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“…In our analysis, we identified a hydrogen bond when

θ_{OH - O} > 130 °

Section: Resultsmentioning

confidence: 60%

Why different water models predict different structures under 2D confinement

2018

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“…The hydrogen bonding lifetime calculations show the average bonding time between the atoms, which represents the average strength of the hydrogen bonds. The MD Analysis H-bond autocorrelation package generated the hydrogen bonding lifetimes, which were calculated in a series of four separate simulations with different time steps and run times [57][58][59]. Four simulations with varying time steps were utilized because it provided accurate hydrogen bonding lifetimes by minimizing the error in the time integration, especially in the case of the short hydrogen bonding lifetimes.…”

Section: Simulation Methods and Detailsmentioning

confidence: 99%

Insight into Cellulose Dissolution with the Tetrabutylphosphonium Chloride–Water Mixture using Molecular Dynamics Simulations

Crawford¹,

Ismail²

2020

Polymers

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All-atom molecular dynamics simulations are utilized to determine the properties and mechanisms of cellulose dissolution using the ionic liquid tetrabutylphosphonium chloride (TBPCl)–water mixture, from 63.1 to 100 mol % water. The hydrogen bonding between small and large cellulose bundles with 18 and 88 strands, respectively, is compared for all concentrations. The Cl, TBP, and water enable cellulose dissolution by working together to form a cooperative mechanism capable of separating the cellulose strands from the bundle. The chloride anions initiate the cellulose breakup, and water assists in delaying the cellulose strand reformation; the TBP cation then more permanently separates the cellulose strands from the bundle. The chloride anion provides a net negative pairwise energy, offsetting the net positive pairwise energy of the peeling cellulose strand. The TBP–peeling cellulose strand has a uniquely favorable and potentially net negative pairwise energy contribution in the TBPCl–water solution, which may partially explain why it is capable of dissolving cellulose at moderate temperatures and high water concentrations. The cellulose dissolution declines rapidly with increasing water concentration as hydrogen bond lifetimes of the chloride–cellulose hydroxyl hydrogens fall below the cellulose’s largest intra-strand hydrogen bonding lifetime.

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“…Effective contact lifetimes are estimated by way of an autocorrelation function analogous to that defined for hydrogen bonds by Gowers and Carbone 67 :where:…”

Section: Methodsmentioning

confidence: 99%

Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope

et al. 2018

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Transient interactions in which binding partners retain substantial conformational disorder play an essential role in regulating biological networks, challenging the expectation that specificity demands structurally defined and unambiguous molecular interactions. The monoclonal antibody 6D8 recognises a completely conserved continuous nine-residue epitope within the intrinsically disordered malaria antigen, MSP2, yet it has different affinities for the two allelic forms of this antigen. NMR chemical shift perturbations, relaxation rates and paramagnetic relaxation enhancements reveal the presence of transient interactions involving polymorphic residues immediately C-terminal to the structurally defined epitope. A combination of these experimental data with molecular dynamics simulations shows clearly that the polymorphic C-terminal extension engages in multiple transient interactions distributed across much of the accessible antibody surface. These interactions are determined more by topographical features of the antibody surface than by sequence-specific interactions. Thus, specificity arises as a consequence of subtle differences in what are highly dynamic and essentially non-specific interactions.

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A multiscale approach to model hydrogen bonding: The case of polyamide

Cited by 81 publications

References 51 publications

Why different water models predict different structures under 2D confinement

Why different water models predict different structures under 2D confinement

Insight into Cellulose Dissolution with the Tetrabutylphosphonium Chloride–Water Mixture using Molecular Dynamics Simulations

Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope

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