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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...
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An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
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An understanding of the solvating effect helps rationalize the relation between solvation and acidity of the compound. In addition, this also explains the relative stability of conjugate bases for compounds with different pKa values. This lesson details, in-depth, the principle of solvating effects. The strength of an acid and the stability of its corresponding conjugate base are determined using pKa values. This observed relationship is a consequence of solvation, which is the interaction...
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To draw Lewis structures for complicated molecules and molecular ions, it is helpful to follow a step-by-step procedure as outlined:
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According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).
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Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.

Michael E Wall1, Gaetano Calabró2,3, Christopher I Bayly2

  • 1Computer, Computational, and Statistical Sciences Division , Los Alamos National Laboratory , Mail Stop B256 , Los Alamos , New Mexico 87545 , United States.

Journal of the American Chemical Society
|March 6, 2019
PubMed
Summary

Restrained molecular dynamics (MD) simulations accurately recover crystallographic water positions in endoglucanase. Unrestrained simulations show lower accuracy, highlighting the potential of MD for biomolecular solvation modeling.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Accurate modeling of water molecules in protein crystals is crucial for understanding biomolecular solvation.
  • Experimental methods like X-ray and neutron diffraction provide detailed structural information on water positions.

Purpose of the Study:

  • To compare experimentally determined water positions with those obtained from molecular dynamics (MD) simulations.
  • To assess the accuracy of MD simulations in reproducing crystalline water structures.

Main Methods:

  • Calculated MD models of water structure in crystalline endoglucanase using a periodic supercell with explicit solvent.
  • Computed water X-ray and neutron scattering density maps from MD trajectories.
  • Performed simulations with and without harmonic restraints biasing the protein structure toward the crystal structure.

Main Results:

  • Restrained MD simulations showed very good recall of crystallographic waters and visual agreement with neutron scattering density for hydrogen positions.
  • Unrestrained MD simulations resulted in significantly lower recall of crystallographic waters.
  • The strongest water density peaks in both simulation types corresponded to crystallographic waters.

Conclusions:

  • Restrained MD simulations are capable of recovering crystallographic water structure.
  • Unrestrained MD simulations are currently insufficient for accurately reproducing crystalline water structure.
  • Further development of MD water models is warranted for applications in crystallography and medicinal chemistry.