Thermodynamics of water entry in hydrophobic channels of carbon nanotubes

Self Cite

We report spontaneous translocation of small interfering RNA (siRNA) inside carbon nanotubes (CNTs) of various diameters and chirality using all atom molecular dynamics (MD) simulations with explicit solvent. We use Umbrella sampling method to calculate the free energy landscape of the siRNA entry and translocation event. Free energy profiles shows that siRNA gains free energy while translocating inside CNT and barrier for siRNA exit from CNT ranges from 40 to 110 kcal/mol depending on CNT chirality and salt concentration. The translocation time τ decreases with the increase of CNT diameter with a critical diameter of 24Å for the translocation. In contrast, double strand DNA (dsDNA) of the same sequence does not translocate inside CNT due to large free energy barrier for the translocation. This study helps in understanding the nucleic acid transport through nanopores at microscopic level and may help designing carbon nanotube based sensor for siRNA.

“…The 2PT method has found successful application in several related problems [38][39][40][43][44][45].…”

Section: A Translocation Of Sirna Inside Cntsmentioning

confidence: 99%

Translocation and encapsulation of siRNA inside carbon nanotubes

Mogurampelly¹,

Maiti²

2013

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“…Despite extensive studies, there are conflicting views of whether filling is driven by the entropy or energy of transfer. 3,16,20,21 The magnitude and even the sign of the entropy of single-file water remain contentious. An early study by Vaitheeswaran et al 3 reported a near-zero entropy of transfer from bulk into a quasi-infinite nanotube obtained by periodic replication of a finite nanotube segment.…”

Section: Introductionmentioning

confidence: 99%

“…In more recent studies, density of states formalisms were used to estimate the translational and rotational contributions to the entropy, producing positive transfer entropies for model TIP3P and SPC/E water in (6,6) carbon nanotubes. 20,21 To resolve these discrepancies in the calculated entropies of single-file water, we here use the most direct method to determine the entropy of transfer, by examining the thermodynamics of filling an open carbon nanotube in equilibrium with bulk TIP3P water in molecular dynamics (MD) simulations over a range of temperatures. We first describe the simulation setup and the analysis methods, including those for periodically replicated nanotubes (with the issue of the bulk reference discussed in the Appendix).…”

Section: Introductionmentioning

confidence: 99%

Entropy of single-file water in (6,6) carbon nanotubes

Waghe

Rasaiah

Hummer

2012

We used molecular dynamics simulations to investigate the thermodynamics of filling of a (6,6) open carbon nanotube (diameter D = 0.806 nm) solvated in TIP3P water over a temperature range from 280 K to 320 K at atmospheric pressure. In simulations of tubes with slightly weakened carbonwater attractive interactions, we observed multiple filling and emptying events. From the water occupancy statistics, we directly obtained the free energy of filling, and from its temperature dependence the entropy of filling. We found a negative entropy of about −1.3 k B per molecule for filling the nanotube with a hydrogen-bonded single-file chain of water molecules. The entropy of filling is nearly independent of the strength of the attractive carbon-water interactions over the range studied. In contrast, the energy of transfer depends strongly on the carbon-water attraction strength. These results are in good agreement with entropies of about −0.5 k B per water molecule obtained from grand-canonical Monte Carlo calculations of water in quasi-infinite tubes in vacuum under periodic boundary conditions. Overall, for realistic carbon-water interactions we expect that at ambient conditions filling of a (6,6) carbon nanotube open to a water reservoir is driven by a favorable decrease in energy, and opposed by a small loss of water entropy.

“…The 2PT method has been shown to be accurate and efficient in determining the entropy of pure liquids from classical MD simulations of bulk water in good agreement with more expensive method 5,6 and to access the thermodynamics of water under hydrophobic confinement and surfaces. 8 It has also recently been applied to understanding the thermodynamics of hydrocarbons at high temperatures and pressures and of metal alloys using BOMD simulations. 9 A closely related technique to calculate the entropy based on the partial pair correlation function has been recently devised by Chakravarty and co-workers.…”

Section: Introductionmentioning

confidence: 99%

On the absolute thermodynamics of water from computer simulations: A comparison of first-principles molecular dynamics, reactive and empirical force fields

Pascal

Schärf

Jung

et al. 2012

We present the absolute enthalpy, entropy, heat capacity, and free energy of liquid water at ambient conditions calculated by the two-phase thermodynamic method applied to ab initio, reactive and classical molecular dynamics simulations. We find that the absolute entropy and heat capacity of liquid water from ab initio molecular dynamics (AIMD) is underestimated, but falls within the range of the flexible empirical as well as the reactive force fields. The origin of the low absolute entropy of liquid water from AIMD simulations is due to an underestimation of the translational entropy by 20% and the rotational entropy by 40% compared to the TIP3P classical water model, consistent with previous studies that reports low diffusivity and increased ordering of liquid water from AIMD simulations. Classical MD simulations with rigid water models tend to be in better agreement with experiment (in particular TIP3P yielding the best agreement), although the TIP4P-ice water model, the only empirical force field that reproduces the experimental melting temperature, has the lowest entropy, perhaps expectedly. This reiterates the limitations of existing empirical water models in simultaneously capturing the thermodynamics of solid and liquid phases. We find that the quantum corrections to heat capacity of water can be as large as 60%. Although certain water models are computed to yield good absolute free energies of water compared to experiments, they are often due to the fortuitous enthalpy-entropy cancellation, but not necessarily due to the correct descriptions of enthalpy and entropy separately.