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Related Concept Videos

X-ray Crystallography02:18

X-ray Crystallography

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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...
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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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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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Crystal structure of 2-oxo-2<i>H</i>-chromen-7-yl tri-fluoro-methane-sulfonate.

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The [M<sub>6</sub>(S<sub>2</sub>C<sub>2</sub>Ph<sub>2</sub>)<sub>6</sub>] (M = Ni, Pd, Pt) Series: Multielectron Reservoirs That Sustain Ligand-Based Oxidations and Metal-Based Reductions.

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Bis[1,2-bis-(4-fluoro-phen-yl)ethyl-ene-1,2-di-thiol-ato(1-)]nickel(II).

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Bis[1,2-bis-(3,5-di-methyl-phen-yl)ethyl-ene-1,2-di-thiol-ato(1-)]nickel(II).

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Derivatization of Protein Crystals with I3C using Random Microseed Matrix Screening
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Derivatization of Protein Crystals with I3C using Random Microseed Matrix Screening

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The single-atom R1: a new optimization method to solve crystal structures.

Xiaodong Zhang1, James P Donahue1

  • 1Chemistry Department, Tulane University, 6400 Freret Street, New Orleans, Louisiana 70118, USA.

Acta Crystallographica. Section A, Foundations and Advances
|March 18, 2024
PubMed
Summary

The single-atom R1 (sR1) method refines crystal structure analysis by optimizing atom positions sequentially. This approach, validated with experimental data, effectively solves complex crystal structures, revealing atomic arrangements step-by-step.

Keywords:
global minimizationmolecular replacementsingle-atom R1structure solution

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Area of Science:

  • Crystallography
  • Materials Science
  • Computational Chemistry

Background:

  • Crystal structure determination is crucial for understanding material properties.
  • Traditional methods face challenges with complex structures and large unit cells.

Purpose of the Study:

  • To introduce and validate a novel method for crystal structure solution.
  • To improve the efficiency and accuracy of determining atomic positions in crystal structures.

Main Methods:

  • Development of the single-atom R1 (sR1) factor, a modified R1 factor.
  • Optimization of the sR1 function to determine fractional coordinates of individual atoms.
  • Iterative structure building starting from a single atom, guided by user input.

Main Results:

  • The sR1 method successfully solves crystal structures up to 156 non-hydrogen atoms.
  • Experimental data confirms the presence of 'holes' near missing atoms using sR1.
  • The strategy for structure solution using sR1 has been optimized for efficiency.

Conclusions:

  • The sR1 method is a viable and effective tool for crystal structure solution.
  • The gradual structure revelation approach enhances model quality with user guidance.
  • sR1 offers a robust alternative for complex crystallographic challenges.