Molecular dynamics and EPR spectroscopic studies of 8CB liquid crystal

Chami, Fatima; Wilson, Mark R.; Oganesyan, Vasily S.

doi:10.1039/c2sm25429h

Cited by 35 publications

(40 citation statements)

References 71 publications

(100 reference statements)

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“…We have obtained reasonable results for molecular self-assembly into stacks, aggregation free energy and intermolecular distance. The GAFF force field, which has been successfully used for other chromonics, 23,61 treats the interactions between EO groups and water molecules poorly and this means the side-to-side interactions between TP6EO2M molecules are too favourable. This leads to reduced hydration of oxygens in EO side chains, too strong attraction between chromonic molecules and, as consequence, molecular aggregation into compact disorganized clusters instead of ordered stacks.…”

Section: Discussionmentioning

confidence: 99%

Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution

et al. 2015

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(2015) 'Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations.The case of TP6EO2M in aqueous solution.', Soft matter., 11 (4). pp. 680-691. Further information on publisher's website:http://dx.doi.org/10.1039/C4SM02275KPublisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. ABSTRACTAtomistic molecular dynamic simulations have been performed for the non-ionic chromonic liquid crystal 2,3,6,7,10,11-hexa-(1,4,7-trioxa-octyl)-triphenylene (TP6EO2M) in aqueous solution. TP6EO2M molecules consist of a central poly-aromatic core (a triphenylene ring) functionalized by six hydrophilic ethyleneoxy (EO) chains, and have a strong tendency to aggregate face-to-face into stacks even in very dilute solution. We have studied self-assembly of the molecules in the low concentration range corresponding to an isotropic solution of aggregates, using two force fields GAFF and OPLS. Our results reveal that the GAFF force field, even though it was successfully used previously for modelling of ionic chromonics, overestimates the attraction of TP6EO2M molecules in water. This results in an aggregation free energy which is too high, a reduced hydration of EO chains and, therefore, molecular self-assembly into compact disordered clusters instead of stacks. In contrast, use of the OPLS force field, leads to self-assembly into ordered stacks in agreement with earlier experimental studies of triphenylene-based chromonics. The free energy of association follows a "quasi-isodesmic" pattern, where the binding free energy of two molecules to form a dimer is of the order of 3 RT larger than the corresponding energy of addition of a molecule into a stack. The obtained value for the binding free energy, ∆ agg G 0 = -12 RT, is found to be in line with the published values for typical ionic chromonics (-7 to -12 RT), and agrees reasonably well with the experimental results for this system. The calculated interlayer distance between the molecules in a stack is 0.37 nm, which is at the top of the range found for typical chromonics (0.33-0.37 nm). We suggest that the relatively large layer spacing can be attributed to the repulsion between EO side chains.2

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Section: Discussionmentioning

confidence: 99%

Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution

et al. 2015

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“…Despite recent improvements in computer power, which allow for the simulation of many soft matter systems at full atomistic detail [7][8][9][10] , it is still impractical to use this technique to study large and/or slowly relaxing systems. This is especially true in the area of polymers where, for moderate chain lengths, relaxation times can easily extend beyond hundreds of nanoseconds.…”

Section: Introductionmentioning

confidence: 99%

A coarse-grained model for polyethylene glycol in bulk water and at a water/air interface

Prasitnok

Wilson

2013

Phys. Chem. Chem. Phys.

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Publisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. A coarse-grained model for polyethylene glycol (PEG) in water has been developed using a combination of the iterative Boltzmann inversion (IBI) methodology and a suitable coarse-grained water potential. The combined coarse-grained model is shown to be effective in reproducing the properties of single chains in bulk water and multiple chains across a series of chain lengths and concentrations, and is transferable to PEG chains at a water/air interface. Good agreement is achieved with both experiment and reference atomistic simulations in an explicit solvent. Simulations of a single chain in aqueous solution yield a molecular weight (M W )-radius of gyration (R g ) relation that compares favourably with the reported scaling law from experiment. Simulations of multiple chains across a wide concentration range show no concentration dependence of R g , in agreement with previous atomistic simulations. The model we develop is shown to be transferable between polymer in bulk water and at a water/air interface. For interfacial simulations, PEG chains are found to spontaneously migrate to the surface and adsorb to form a thin surface layer, which thickens with increasing surface concentration. The point at which the surface is fully saturated with polymer, and the polymer layer thicknesses obtained from simulations, are both in good agreement with experimental findings. At high surface concentrations, when the surface is fully saturated with polymer, ethylene oxide (EO) segments are found to extend into the water subphase as loop and tail conformations, with this extension increasing with further increases in the surface concentration.The coarse-grained model is noted to provide very large increases in simulation speed, with equilibration times of < 1000× the reference atomistic models. We also consider a number of different coarse-grained models for water in this study, showing that the CSJ model adopted in this work [Chiu et al., J. Chem. Theory Comput. 2010, 6, 851] is far superior for studying water at a water/air surface, than many of the previous coarse-grained models of water.

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“…These methods have been successfully applied to soft matter systems doped with nitroxide spin probes (40,41) and MTSL spin labelled proteins (4,26,28,32,38). In order to probe motions of both R1 and Rn in two different protein environments and to predict and analyse the relevant EPR spectra we have performed fully atomistic MD simualtions of all four cases of spin labelled Mb.…”

Section: Resultsmentioning

confidence: 99%

A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics

Oganesyan

Chami

White

et al. 2017

Journal of Magnetic Resonance

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EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions.

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Molecular dynamics and EPR spectroscopic studies of 8CB liquid crystal

Cited by 35 publications

References 71 publications

Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution

Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution

A coarse-grained model for polyethylene glycol in bulk water and at a water/air interface

A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics

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