Thermodynamic Stability of [60]Fullerene and γ-Cyclodextrin Complex in Aqueous Solution: Free Energy Simulation

2014 ◽  
Vol 118 (23) ◽  
pp. 12555-12561 ◽  
Author(s):  
Shunsuke Mieda ◽  
Atsushi Ikeda ◽  
Yasushi Shigeri ◽  
Wataru Shinoda
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Thermodynamic Stability ◽  
Energy Simulation ◽  
Cyclodextrin Complex

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

The Generation of a Carbon Nanotube- Cyclodextrin Complex

2001 ◽  
Vol 703 ◽  
Author(s):  
G.F. Farrell ◽  
G. Chambers ◽  
A.B Dalton ◽  
E. Cummins ◽  
M. McNamara ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Aqueous Solution ◽  
Raman Spectroscopy ◽  
Carbon Nanotube ◽  
Intermolecular Interaction ◽  
Intermolecular Interactions ◽  
Small Diameter ◽  
Cyclodextrin Complex ◽  
Yellow Solution ◽  
Single Wall Nanotubes

ABSTRACTIn this study the intermolecular interactions of small diameter (∼0.7nm) carbon nanotubes and γ-cyclodextrin were examined. Four samples of γ cyclodextrin and HiPco carbon nanotubes were prepared. The first, by grinding the tubes and the cyclodextrin (1:30 ratio) together in a dry mixture, the second was prepared in a similar fashion but was ground in the presence of water (1ml). Finally an aqueous solution of γ-cyclodextrin (0.3M) and HiPco carbon nanotubes (5mg) was prepared by refluxing for ∼100 hours, forming a pale yellow solution from which a number of crystals were produced, both the solution and the recrystallised material were analysed. The samples were analysed using UV-Vis-NIR and Raman spectroscopy. The results presented are the first spectroscopic evidence of an intermolecular interaction between γ-cyclodextrin and single wall nanotubes.

Sorption of Pb(II) by poly(hydroxamic acid) grafted oil palm empty fruit bunch

2011 ◽  
Vol 63 (8) ◽  
pp. 1788-1793
Author(s):  
M. J. Haron ◽  
M. Tiansin ◽  
N. A. Ibrahim ◽  
A. Kassim ◽  
W. M. Z. Wan Yunus ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Oil Palm ◽  
Hydroxamic Acid ◽  
Sorption Process ◽  
Enthalpy Change ◽  
Langmuir Model ◽  
Order Kinetic ◽  
Empty Fruit Bunch ◽  
Order Kinetic Model

This paper describes the sorption of Pb(II) from aqueous solution. Oil palm empty fruit bunch (OPEFB) fiber was first grafted with poly(methylacrylate) and then treated with hydroxylammonium chloride in alkaline medium to produce hydroxamic acid (PHA) grafted OPEFB. Sorption of Pb(II) by PHA-OPEFB was maximum at pH 5. The sorption followed the Langmuir model with maximum capacityof 125.0 mg g−1 at 25°C. The sorption process was exothermic, as shown by the negative value of enthalpy change, ΔH0. The free energy change (ΔG0) for the sorption was negative, showing that the sorption process was spontaneous. A kinetic study showed that the Pb(II) sorption followed a second order kinetic model.

Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics

1997 ◽  
Vol 37 (6) ◽  
pp. 1018-1024 ◽  
Author(s):  
Jérôme Baudry ◽  
Serge Crouzy ◽  
Benoît Roux ◽  
Jeremy C. Smith
Keyword(s):  
Free Energy ◽  
Quantum Chemical ◽  
Simulation Analysis ◽  
Energy Simulation
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