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Molecular Shapes01:18

Molecular Shapes

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Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Compared to ionic bonds, which results from the transfer of electrons between metallic and nonmetallic atoms, covalent bonds result from the mutual attraction of atoms for a “shared” pair of electrons.
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Isomerism in Complexes
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Network covalent solids contain a three-dimensional network of covalently bonded atoms as found in the crystal structures of nonmetals like diamond, graphite, silicon, and some covalent compounds, such as silicon dioxide (sand) and silicon carbide (carborundum, the abrasive on sandpaper). Many minerals have networks of covalent bonds.
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The missing link: covalent linkages in structural models.

Robert A Nicholls1, Marcin Wojdyr2, Robbie P Joosten3

  • 1Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.

Acta Crystallographica. Section D, Structural Biology
|June 2, 2021
PubMed
Summary
This summary is machine-generated.

Inconsistent modeling of covalent linkages in the Protein Data Bank (PDB) leads to inaccurate structural data. This study identifies common unannotated linkages and improves the CCP4 Monomer Library (CCP4-ML) for better future modeling.

Keywords:
AceDRGCCP4 Monomer LibrarySARS-CoV-2covalent linkagerestraint dictionary

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Area of Science:

  • Structural biology
  • Computational chemistry
  • Bioinformatics

Background:

  • Covalent linkages in macromolecular models are inconsistently handled during structure determination and deposition.
  • This inconsistency arises from challenges in detecting linkages, identifying chemistry, and applying restraints.

Purpose of the Study:

  • To assess the prevalence of problems with covalent linkages in the Protein Data Bank (PDB).
  • To improve the accuracy of existing macromolecular models and inform future modeling efforts.
  • To enhance the CCP4 Monomer Library (CCP4-ML) with new linkage types.

Main Methods:

  • Analysis of covalent linkages within the Protein Data Bank (PDB).
  • Comparison of PDB data against the CCP4 Monomer Library (CCP4-ML).
  • Utilizing AceDRG for expanding CCP4-ML component and link dictionaries.

Main Results:

  • Failure to model covalent linkages results in systematically inaccurate interatomic distances.
  • A significant number of unannotated potential covalent linkages were identified in the PDB.
  • The CCP4-ML was expanded with new linkage types, improving its utility for modeling.

Conclusions:

  • Accurate modeling of covalent linkages is crucial for reliable structural data.
  • Improvements to the CCP4-ML and standardized record-keeping will enhance future macromolecular modeling.
  • A case study on viral protease inhibitors highlights the importance of comprehensive restraint dictionaries for covalent linkages.