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Related Concept Videos

X-ray Crystallography02:18

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
Determination of Crystal Structures01:29

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...

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Updated: Jun 20, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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Polarizable atomic multipole X-ray refinement: application to peptide crystals.

Michael J Schnieders1, Timothy D Fenn, Vijay S Pande

  • 1Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

Acta Crystallographica. Section D, Biological Crystallography
|August 20, 2009
PubMed
Summary

The AMOEBA force field underestimates electron density in peptide crystals. Adding interatomic scattering sites to AMOEBA improves electron density modeling, significantly enhancing crystal structure refinement.

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Published on: April 24, 2018

Area of Science:

  • Computational chemistry
  • Structural biology
  • Crystallography

Background:

  • Advances in computational chemistry offer new force fields for biomolecular electrostatics.
  • The Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field utilizes a polarizable atomic multipole description.
  • Accurate modeling of electron density is crucial for refining molecular structures against experimental data.

Purpose of the Study:

  • To apply the AMOEBA force field to restrained refinement of peptide crystal structures using X-ray diffraction data.
  • To develop and implement a novel formalism for computing anisotropic and aspherical structure factors.
  • To evaluate the performance of the AMOEBA force field and an extended model with interatomic scattering (IAS) sites in capturing bonding electron density.

Main Methods:

  • Restrained refinement of molecular models against X-ray diffraction data.
  • Development of a fast Fourier transformation (FFT) based formalism for computing anisotropic and aspherical structure factors from Cartesian Gaussian multipoles.
  • Application of the Cartesian Gaussian multipole scattering model and the AMOEBA-IAS model to peptide crystal data.

Main Results:

  • The AMOEBA force field systematically underestimates electron density at bond centers in peptide crystals.
  • Atomic multipole expansion up to hexadecapole order is necessary to accurately describe bonding electron density for common geometries.
  • The addition of interatomic scattering (IAS) sites to the AMOEBA model captured bonding effects more effectively.
  • The AMOEBA-IAS model reduced R(free) by 20-40% compared to the spherically symmetric model for four peptide crystals.

Conclusions:

  • The standard AMOEBA force field requires augmentation to accurately model bonding electron density in peptide crystals.
  • The developed FFT-based formalism provides a significant speedup for aspherical refinement of ultrahigh-resolution crystallographic data.
  • The AMOEBA-IAS model offers a more accurate and parameter-efficient approach for crystallographic refinement, improving the quality of structural models.