Stability constant of the sodium complex with 18-crown-6 in the mixed water-ionic liquid solvent

Popov, Konstantin; Rönkkömäki, Hannu; Hannu-Kuure, M.; Kuokkanen, Toivo; Lajunen, Marja; Vendilo, A. G.; Glazkova, I.; Lajunen, Lauri H. J.

doi:10.1134/s1070328407060012

Cited by 8 publications

(2 citation statements)

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“…This choice is often not straightforward, because hydrogens are usually not resolved in X-ray crystallography and the acid dissociation constant ( K a ) values of the ionizable groups, in most cases, are not known. Therefore, the protonation state must be inferred from NMR( 8 ) or spectroscopic data,( 9 ) or from electrostatic calculations (e.g., Poisson–Boltzmann (PB) 10 , 11 or Generalized Born( 12 ) approaches). Furthermore, changes in the protonation state, either due to a change in the environment pH or in the protein conformation, as well as equilibrium protonation fluctuations leading to fractional protonation probabilities, are not taken into account by conventional simulations.…”

Section: Introductionmentioning

confidence: 99%

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

Donnini

Tegeler

Groenhof

et al. 2011

J. Chem. Theory Comput.

184

312

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pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present a method, implemented within the MD package GROMACS, for constant pH molecular dynamics simulations in explicit solvent that is based on the λ-dynamics approach. In the latter, the dynamics of the titration coordinate λ, which interpolates between the protonated and deprotonated states, is driven by generalized forces between the protonated and deprotonated states. The hydration free energy, as a function of pH, is included to facilitate constant pH simulations. The protonation states of titratable groups are allowed to change dynamically during a simulation, thus reproducing average protonation probabilities at a certain pH. The accuracy of the method is tested against titration curves of single amino acids and a dipeptide in explicit solvent.

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Section: Introductionmentioning

confidence: 99%

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

Donnini

Tegeler

Groenhof

et al. 2011

J. Chem. Theory Comput.

184

312

View full text Add to dashboard Cite

show abstract

“…Even the alkali ions are found to form weak bonds with N(Tf 2 ) - (Yan et al, 2010). An X-Ray structure of Popov et al, 2007a [BMIM] [PF 6 ] −21.0 (1.4) −25.4 (4.5) Vendilo et al, 2010 [BMPy] [BF 4 ] −47 (1) −32 (1) Popov et al, 2007a [ ]. Moreover, the observed ∆H 1 value is the highest known for CsL in both molecular solvents and RTIL.…”

Section: Thermodynamics Of Complex Formation In Rtilmentioning

confidence: 99%