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Related Concept Videos

Lattice Centering and Coordination Number02:33

Lattice Centering and Coordination Number

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The structure of a crystalline solid, whether a metal or not, is best described by considering its simplest repeating unit, which is referred to as its unit cell. The unit cell consists of lattice points that represent the locations of atoms or ions. The entire structure then consists of this unit cell repeating in three dimensions. The three different types of unit cells present in the cubic lattice are illustrated in Figure 1.
Types of Unit Cells
Imagine taking a large number of identical...
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Ionic Crystal Structures02:42

Ionic Crystal Structures

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Ionic crystals consist of two or more different kinds of ions that usually have different sizes. The packing of these ions into a crystal structure is more complex than the packing of metal atoms that are the same size.
Most monatomic ions behave as charged spheres, and their attraction for ions of opposite charge is the same in every direction. Consequently, stable structures for ionic compounds result (1) when ions of one charge are surrounded by as many ions as possible of the opposite...
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Structures of Solids02:22

Structures of Solids

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Solids in which the atoms, ions, or molecules are arranged in a definite repeating pattern are known as crystalline solids. Metals and ionic compounds typically form ordered, crystalline solids. A crystalline solid has a precise melting temperature because each atom or molecule of the same type is held in place with the same forces or energy. Amorphous solids or non-crystalline solids (or, sometimes, glasses) which lack an ordered internal structure and are randomly arranged. Substances that...
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Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

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Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
26.9K
Crystal Field Theory - Tetrahedral and Square Planar Complexes02:46

Crystal Field Theory - Tetrahedral and Square Planar Complexes

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Tetrahedral Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
43.2K
Metallic Solids02:37

Metallic Solids

18.5K
Metallic solids such as crystals of copper, aluminum, and iron are formed by metal atoms. The structure of metallic crystals is often described as a uniform distribution of atomic nuclei within a “sea” of delocalized electrons. The atoms within such a metallic solid are held together by a unique force known as metallic bonding that gives rise to many useful and varied bulk properties.
All metallic solids exhibit high thermal and electrical conductivity, metallic luster, and malleability....
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Updated: Jul 26, 2025

Methods of Ex Situ and In Situ Investigations of Structural Transformations: The Case of Crystallization of Metallic Glasses
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Methods of Ex Situ and In Situ Investigations of Structural Transformations: The Case of Crystallization of Metallic Glasses

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Efficient structure-factor modeling for crystals with multiple components.

Pavel V Afonine1, Paul D Adams1, Alexandre G Urzhumtsev2

  • 1Molecular Biophysics and Integrated Bioimaging Department, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA.

Acta Crystallographica. Section A, Foundations and Advances
|June 20, 2023
PubMed
Summary
This summary is machine-generated.

This study presents an efficient computational solution for modeling complex diffraction data in crystallography. The new algorithms enable more accurate analysis of macromolecular structures by accounting for multiple components beyond simple atomic models.

Keywords:
bulk solventdensity mapsmultiple componentsrefinementscattering functionsstructure factors

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Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Chemistry

Background:

  • Diffraction intensities in crystallography reflect contributions from the entire unit cell, including macromolecules, solvent, and other compounds.
  • Current atomic models often fail to accurately represent disordered entities like solvent, lipid belts, or polymer loops, necessitating advanced modeling approaches.

Purpose of the Study:

  • To develop and present an efficient computational solution for handling multi-component structure factors in crystallographic data analysis.
  • To address the algorithmic and computational challenges associated with modeling more than two components in structure factors.

Main Methods:

  • Implementation of novel algorithms within the computational crystallography toolbox (CCTBX) and Phenix software.
  • Development of general algorithms applicable to various molecule types and sizes, without specific assumptions about components.

Main Results:

  • An efficient solution for modeling multiple contributions to structure factors has been developed.
  • The implemented algorithms provide a general framework for detailed modeling of disordered regions in crystallographic experiments.

Conclusions:

  • The proposed methods offer a more accurate and detailed approach to modeling crystallographic data, particularly for regions with disorder.
  • The developed algorithms enhance the capabilities of crystallographic software like Phenix for advanced structural analysis.