vir parameters verage of parameters. = Library. Proteins. & small compounds. Transfer. Atom types are defined ... A68, 452-463. [2] A. Poulain-Paul, A. Nassour, ...
A theoretical electron density databank using a model of spherical atoms and dummy charges NASSOUR Ayoub Laboratoire de Cristallographie
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Résonance
Magnétique
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Modélisations
UMR-CRM2 7036, NANCY
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OUTLINE Methodology Test of the virtual atom model Library building Automated refinement with software MoPro Application to UREA Conclusion 2
Methodology The Virtual atom model Ab initio calculation → Crystal09 code Density functional theory; theory; Linear combinaison of atomic orbitals; Full electron. Refinement with Program MoPro: MoPro Refinement:
X-ray structure
Deformation of the Electron Density ∆ρ = ρmolecule - ρspher-neutral-atoms Contours = +/- 0.05 eÅ-3
B3LYP/6-31G(d,p) Electron density
FT
Theoretical structure factors
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Test of the virtual atom model : confrontation with other approaches Multipolar atom model
Virtual atom model
UREA
Resorcinol Deformation of the electron density ∆ρ = ρmolecule - ρspher-neutral-atoms Contours = +/- 0.05 eÅ-3
Virtual atom model
Multipolar model
refinement vs Theo Fhkl
UREA
Resorcinol Electrostatic potential of the electron density Contours = +/- 0.05 e/Å
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Library building
Analysis of small molecules
Electron density determination by X-ray crystallography.
Average of parameters = Library
Transfer
Proteins & small compounds
Pval, Pvir κ, κ’vir parameters Atom types are defined by
Diffraction data measured at ultra high resolution (~0.5 Angstrom). Data obtained from Laboratory or IUCR journals website or from authors.
• their chemical nature (H, C, N, O, Qvir…) • the chemical nature of 1st & 2nd neighbors • the geometry of the covalent bonds
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Automated refinement with software MoPro
The fully automated electron density refinement for small molecules includes preparation of: stereochemical restraints constraints of multipoles symmetry and atoms chemical equivalence
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Application to UREA urea Molecular Dipole moments µ in Debye for urea.
Refinement vs Theo Fhkl
Electrostatic interaction energies of urea dimers in the crystal [kJ/mol] Theoretical database
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Conclusion
The theoretical databank of transferable virtual-atom model allows fast evaluation of the electrostatic interaction energies of macromolecular systems. It can be used to calculate the molecular electron density distribution and its properties.
We also note that the DB_VIR database could be used to define force fields based on off-atoms charges.
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Acknowledgements We acknowledge the CINES for computational resources. The CNRS is gratefully acknowledged for financial support . The authors thanks B. Guillot and C. Lecomte for useful discussions. Special thanks are due to C. Jelsch for valuable suggestions.
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References:
[1] N. Dadda, A. Nassour, B. Guillot, N. Benalicherif and C. Jelsch. (2012) Acta Cryst.. A68, 452-463. Paul, A. Nassour, C. Jelsch, B. Guillot, M. Kubicki and C. Lecomte. [2] A. Poulain-Paul, (2012). Acta Cryst. A68, 715-728. [3] C. Jelsch, B. Guillot, A. Lagoutte and C. Lecomte. Lecomte (2005) J. Appl. Cryst. 38, 38-54. [4] B. Guillot, C. Jelsch, A. Podjarny and C. Lecomte. (2008). Acta Cryst. D64, 567-588. 567
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