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A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another polar molecule, such as water (H2O), hydrogen fluoride (HF), or ammonia (NH3). The huge electronegativity difference between the H atom (2.1) and the atom to which it is bonded (4.0 for an F atom, 3.5 for an O atom, or 3.0 for an N atom), combined with the very small size of an H atom...
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Hydrogen bonds are weak attractions between atoms that have formed other chemical bonds. One of these atoms is electronegative, like oxygen, and has a partial negative charge. The other is a hydrogen atom that has bonded with another electronegative atom and has a partial positive charge.
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The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
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Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Hirshfeld atom refinement for modelling strong hydrogen bonds.

Magdalena Woińska1, Dylan Jayatilaka2, Mark A Spackman2

  • 1Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.

Acta Crystallographica. Section A, Foundations and Advances
|September 2, 2014
PubMed
Summary
This summary is machine-generated.

The new Hirshfeld atom refinement (HAR) method accurately models strong hydrogen bonds using X-ray diffraction. HAR successfully refined hydrogen atom positions and properties, matching neutron diffraction results for L-phenylalaninium hydrogen maleate.

Keywords:
Hirshfeld atom refinementaspherical scattering factorselectron densityhydrogen bondshydrogen maleatestructure refinement

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Area of Science:

  • Crystallography
  • Materials Science
  • Computational Chemistry

Background:

  • Accurate modeling of hydrogen bonds is crucial in crystal structure analysis.
  • Traditional X-ray diffraction methods often struggle to precisely determine hydrogen atom positions and properties, especially in strong hydrogen bonds.

Purpose of the Study:

  • To evaluate the efficacy of the automated iterative Hirshfeld atom refinement (HAR) procedure for modeling strong hydrogen bonds.
  • To compare HAR results with conventional X-ray refinement techniques and neutron diffraction data for L-phenylalaninium hydrogen maleate.

Main Methods:

  • High-resolution, low-temperature synchrotron X-ray diffraction data collection.
  • Application of the automated iterative Hirshfeld atom refinement (HAR) procedure.
  • Comparison with independent atom model (IAM), multipole models (MM, TAAM), and neutron diffraction data.

Main Results:

  • The HAR procedure successfully refined hydrogen atom positions and anisotropic displacement parameters (ADPs) from X-ray data.
  • HAR provided the most accurate electron density model, closely matching neutron diffraction findings, including a symmetric hydrogen bond.
  • Conventional X-ray methods (IAM, MM, TAAM) resulted in less accurate, asymmetric hydrogen positions.

Conclusions:

  • The automated iterative Hirshfeld atom refinement (HAR) is a powerful tool for accurately modeling strong hydrogen bonds using X-ray diffraction data.
  • HAR offers significant advantages over traditional refinement methods for determining precise hydrogen atom parameters.
  • This study demonstrates the first Z' > 1 application of wavefunction-based refinement methods using HAR.