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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.
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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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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.
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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,...
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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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lamaGOET: an interface for quantum crystallography.

Lorraine A Malaspina1,2, Alessandro Genoni3, Simon Grabowsky1,2

  • 1Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland.

Journal of Applied Crystallography
|June 30, 2021
PubMed
Summary
This summary is machine-generated.

The lamaGOET interface links quantum chemistry software with Tonto for advanced crystallographic refinements. This enables novel quantum crystallography techniques like Hirshfeld atom refinement.

Keywords:
Hirshfeld atom refinementX-ray constrained wavefunction fittingquantum crystallography

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Area of Science:

  • Quantum Crystallography
  • Computational Chemistry
  • Materials Science

Background:

  • Quantum crystallography requires software capable of both quantum-mechanical calculations and crystallographic refinements.
  • Currently, the Tonto program is the only software that can perform both functions.
  • Integrating quantum chemical software with crystallographic refinement tools is essential for advancing the field.

Purpose of the Study:

  • To introduce the lamaGOET interface, which bridges quantum-chemical software (Gaussian, ELMOdb) with Tonto's refinement capabilities.
  • To demonstrate the utility of lamaGOET in performing advanced quantum-crystallographic refinements.
  • To showcase three distinct quantum-crystallographic refinement methods using lamaGOET.

Main Methods:

  • Development of the lamaGOET interface to connect Gaussian and ELMOdb with Tonto.
  • Application of lamaGOET for quantum-crystallographic refinements of glycyl-l-threonine dihydrate.
  • Implementation of Hirshfeld atom refinement (HAR), HAR-ELMO, and X-ray constrained wavefunction fitting.

Main Results:

  • The lamaGOET interface successfully integrates widely used and specialized quantum-chemical software with Tonto.
  • Demonstrated the feasibility of performing diverse quantum-crystallographic refinements, including HAR, HAR-ELMO, and X-ray constrained wavefunction fitting.
  • Successfully refined the dipetide glycyl-l-threonine dihydrate using these advanced methods.

Conclusions:

  • The lamaGOET interface provides a robust solution for integrating quantum-chemical calculations and crystallographic refinements.
  • This integration facilitates novel applications in quantum crystallography, enabling more accurate and detailed structural analysis.
  • lamaGOET expands the capabilities of crystallographic software, paving the way for new theoretical and experimental investigations.