Probing cations recognized by a crown ether with the 3D-RISM theory. II. 18-crown-6 ether

Maruyama,; Matsugami, Masaru; Ikuta,

doi:10.5488/cmp.10.3.315

Cited by 9 publications

(7 citation statements)

References 20 publications

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“…The method treats solvent and ion configurations microscopically in terms of a probabilistic distribution, so that it is capable of “detecting” the distribution of ions recognized by the binding site in telomeric DNA just as the X-ray crystallography does. The method has been applied successfully to a number of problems in biophysics and chemistry to describe the solvation phenomena as well as the molecular recognition of biomolecules in solutions. − In particular, the robustness of the method is demonstrated recently by comparing the solvation structure of DNA calculated from the theory with that from the molecular dynamics simulation . In addition, the study with 3D-RISM theory reproduced DNA B-Z transition and clarified its physical origin .…”

Section: Introductionmentioning

confidence: 99%

“…The method has been applied successfully to a number of problems in biophysics and chemistry to describe the solvation phenomena as well as the molecular recognition of biomolecules in solutions. [39][40][41][42][43][44] In particular, the robustness of the method is demonstrated recently by comparing the solvation structure of DNA calculated from the theory with that from the molecular dynamics simulation. 45 In addition, the study with 3D-RISM theory reproduced DNA B-Z transition and clarified its physical origin.…”

Section: Introductionmentioning

confidence: 99%

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Solvent and Salt Effects on Structural Stability of Human Telomere

et al. 2011

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The free energy and the solvation structures of the G-quadruplex telomeric DNA in pure water and in the 0.1 M aqueous solutions of sodium and potassium chlorides are calculated on the basis of the 3D-RISM theory. To find the most stable structure of each G-quadruplex in the aqueous solutions, the free energy is minimized in the solutions on the basis of the quasi-Newton method using the analytical derivative of the solvation free energy obtained from 3D-RISM. In pure water, the chair-type conformation was found to be the most stable structure, which is followed by basket-, hybrid-, and propeller-type structures in the order. It is clarified that the order of the stability is determined essentially by the solvation free energy, not by the conformational energy. The order of the stability changes in 0.1 M NaCl solutions from that in pure water. The basket-type structure becomes the most stable one in the electrolyte solution. The theoretical finding is consistent with the experimental observation due to NMR. The reversed order of the conformational stability was attributed to the salt effect, especially, to that from the Na(+) ions bound at interstrand spaces of DNA. Concerning the conformational stability in KCl solutions, which has not been clarified yet by experiments, our results predict that the order is not changed from that in pure water; that is, the chair-type is the most stable one. The finding suggests that the effect of the potassium ion upon the structure is not so strong as the sodium ion to change the order of the stability determined in pure water. The result is consistent with our finding for RDFs of the ions bound at the interstrand spaces in DNA, which indicates clearly that the affinity of K(+) to the binding site is weaker than that of Na(+).

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Solvent and Salt Effects on Structural Stability of Human Telomere

et al. 2011

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“…The method has been applied successfully to a number of problems in biophysics and chemistry to describe the solvation phenomena as well as the molecular recognition of biomolecules in solutions. [34][35][36][37][38][39] In particular, the robustness of the method was demonstrated recently by comparing the solvation structure of DNA calculated from the theory with that from the molecular dynamics simulation. 40…”

Section: Introductionmentioning

confidence: 99%

Revisiting the Salt-Induced Conformational Change of DNA with 3D-RISM Theory

2010

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The salt-induced conformational transition of DNA is revisited on the basis of the 3D-RISM theory with the purpose of clarifying its physical origin. To take all the contributions to the stability of the molecule into consideration, we performed the optimization of the free energy of B- and Z-DNA in aqueous solutions. Our results exhibited the transition from the B to Z forms with increasing salt concentrations, which is in qualitative accord with the experiments. The results indicate that the transition is caused by an interplay of essentially two contributions, which determine the stability of the molecules, the electrostatic repulsion among charged phosphate groups, and the negative free energy due to counterion binding to those groups. The result is consistent with one of the two models proposed earlier concerning the physical origin of the salt-induced transition of DNA, which attributes the phenomena to the screening of the electrostatic repulsion among phosphate groups, not to the "economy" of hydration, which has been proposed by Saenger et al.

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“…These types of studies on the free energy profiles of associating species have been done for hard spheres[99], LJ spheres[100], ions[61, 66, 101], molecules[101], ligand-protein systems[102] and hydrophobic plates[17] (Fig. 10).…”

Section: Resulting Liquid Structurementioning

confidence: 99%

Integral Equations in the Study of Polar and Ionic Interaction Site Fluids

Howard

Pettitt

2011

J Stat Phys

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In this review article we consider some of the current integral equation approaches and application to model polar liquid mixtures. We consider the use of multidimensional integral equations and in particular progress on the theory and applications of three dimensional integral equations. The IEs we consider may be derived from equilibrium statistical mechanical expressions incorporating a classical Hamiltonian description of the system. We give example including salt solutions, inhomogeneous solutions and systems including proteins and nucleic acids.

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Probing cations recognized by a crown ether with the 3D-RISM theory. II. 18-crown-6 ether

Cited by 9 publications

References 20 publications

Solvent and Salt Effects on Structural Stability of Human Telomere

Solvent and Salt Effects on Structural Stability of Human Telomere

Revisiting the Salt-Induced Conformational Change of DNA with 3D-RISM Theory

Integral Equations in the Study of Polar and Ionic Interaction Site Fluids

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