Polarizable AMOEBA force field predicts thin and dense hydration layer around monosaccharides
Luke A Newman1,2, Mackenzie G Patton3, Breyanna A Rodriguez4
1Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA. vwelborn@vt.edu.
Chemical Communications (Cambridge, England)
|November 15, 2024
Summary
New polarizable force field parameters for six monosaccharides improve molecular dynamics simulations. This advancement resolves non-physical aggregation issues in carbohydrate modeling, particularly for glucose in water.
Area of Science:
- Biophysics
- Computational Chemistry
- Molecular Modeling
Background:
- Polarizable force fields are essential for accurate macromolecular simulations in polar environments.
- Existing models face challenges in simulating carbohydrate behavior, leading to artifacts like aggregation.
Purpose of the Study:
- To develop and validate new parameters for the AMOEBA polarizable force field to model six common monosaccharides.
- To address the long-standing issue of non-physical aggregation in molecular dynamics (MD) simulations of carbohydrates.
Main Methods:
- Development of novel AMOEBA force field parameters for six monosaccharides.
- Molecular dynamics simulations of monosaccharides in polar media, specifically water.
- Analysis of hydration layer properties and aggregation behavior.
Main Results:
- The new parameters produce a thinner yet denser hydration layer around monosaccharides compared to previous models.
- This refined hydration shell effectively eliminates the non-physical aggregation of glucose in aqueous solutions.
- Improved accuracy in modeling carbohydrate-water interactions.
Conclusions:
- The enhanced AMOEBA force field parameters provide a more accurate representation of monosaccharides in polar environments.
- This work overcomes a significant hurdle in the MD simulation of carbohydrates, enabling more reliable studies.
- The developed parameters are crucial for advancing research in glycobiology and related fields.
Related Concept Videos
03:37Molecular Shape and Polarity
59.7K
Dipole Moment of a Molecule
59.7K
02:42Aqueous Solutions and Heats of Hydration
14.4K
Water and other polar molecules are attracted to ions. The electrostatic attraction between an ion and a molecule with a dipole is called an ion-dipole attraction. These attractions play an important role in the dissolution of ionic compounds in water.
When ionic compounds dissolve in water, the ions in the solid separate and disperse uniformly throughout the solution because water molecules surround and solvate the ions, reducing the strong electrostatic forces between them. This process...
When ionic compounds dissolve in water, the ions in the solid separate and disperse uniformly throughout the solution because water molecules surround and solvate the ions, reducing the strong electrostatic forces between them. This process...
14.4K
03:13Intermolecular Forces
57.7K
Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen...
57.7K
02:36Molecular Geometry and Dipole Moments
12.6K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
12.6K
01:29Potential Due to a Polarized Object
367
A neutral atom consists of a positively charged nucleus surrounded by a negatively charged electron cloud. When placed in an external electric field, the external electric force pulls the electrons and nucleus apart, opposite to the intrinsic attraction between the nucleus and the electrons. The opposing forces balance each other with a slight shift between the center of masses of the nucleus and the electron cloud, resulting in a polarized atom. On the other hand, a few molecules, like water,...
367
02:18Fischer Projections
13.0K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines.
13.0K