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Related Concept Videos

Entropy and Solvation02:05

Entropy and Solvation

The process of surrounding a solute with solvent is called solvation. It involves evenly distributing the solute within the solvent. The rule of thumb for determining a solvent for a given compound is that like dissolves like. A good solvent has molecular characteristics similar to those of the compound to be dissolved. For example, polar solutions dissolve polar solutes, and apolar solvents dissolve apolar solutes. A polar solvent is a solvent that has a high dielectric constant (ϵ ≥ 15); an...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
Entropy02:39

Entropy

Salt particles that have dissolved in water never spontaneously come back together in solution to reform solid particles. Moreover, a gas that has expanded in a vacuum remains dispersed and never spontaneously reassembles. The unidirectional nature of these phenomena is the result of a thermodynamic state function called entropy (S). Entropy is the measure of the extent to which the energy is dispersed throughout a system, or in other words, it is proportional to the degree of disorder of a...
Chemical Shift: Internal References and Solvent Effects01:17

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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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Enthalpy of Solution02:39

Enthalpy of Solution

There are two criteria that favor, but do not guarantee, the spontaneous formation of a solution:

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

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Published on: January 16, 2016

Treating entropy and conformational changes in implicit solvent simulations of small molecules.

David L Mobley1, Ken A Dill, John D Chodera

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA. dmobley@gmail.com

The Journal of Physical Chemistry. B
|January 4, 2008
PubMed
Summary

Implicit solvent models often neglect solute flexibility, leading to significant errors in hydration free energy calculations. Accounting for conformational changes improves accuracy in molecular simulations.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Biophysics

Background:

  • Implicit solvent models are widely used for calculating hydration free energies.
  • Current methods often assume rigid solutes, ignoring conformational changes upon solvation.

Purpose of the Study:

  • To investigate the impact of solute conformational changes on hydration free energy calculations.
  • To improve the accuracy of implicit solvent models by incorporating flexibility.

Main Methods:

  • Alchemical free energy methods were employed.
  • Solute conformational changes upon solvation were explicitly included.

Main Results:

  • Significant errors were observed when using single solute conformations.
  • Conformational entropy changes up to 2.3 kcal/mol were found upon hydration.
  • Correlation between conformational entropy and rotatable bonds was poor (R2 = 0.03).

Conclusions:

  • The assumption of rigid solutes in implicit solvent modeling leads to inaccuracies.
  • Incorporating solute flexibility is crucial for reliable hydration free energy predictions.
  • Implicit solvent models can be enhanced by removing the rigid solute approximation.