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  4. Libraries of Extremely Localized Molecular Orbitals. 3. Construction and Preliminary Assessment of the New Databanks
 
research article

Libraries of Extremely Localized Molecular Orbitals. 3. Construction and Preliminary Assessment of the New Databanks

Meyer, Benjamin  
•
Genoni, Alessandro
November 15, 2018
The Journal of Physical Chemistry A

The fast and reliable determination of wave functions and electron densities of macromolecules has been one of the goals of theoretical chemistry for a long time, and in this context, several linear scaling techniques have been successfully devised over the years. Different approaches have been adopted to tackle this problem, and one of them exploits the fact that, according to the traditional chemical perception, molecules can be seen as constituted of recurring units (e.g., functional groups) with well-defined chemical features. This has led to the development of methods in which the global wave functions or electron densities of macromolecules are obtained by simply transferring density matrices or fuzzy electron densities associated with molecular fragments. In this context, we propose an alternative strategy that aims at quickly reconstructing wave functions and electron densities of proteins through the transfer of extremely localized molecular orbitals (ELMOs), which are orbitals strictly localized on small molecular units and, for this reason, easily transferable from molecule to molecule. To accomplish this task we have constructed original libraries of ELMOs that cover all the possible elementary fragments of the 20 natural amino acids in all their possible protonation states and forms. Our preliminary test calculations have shown that, compared to more traditional methods of quantum chemistry, the transfers from the novel ELMO databanks allow to obtain wave function and electron densities of large polypeptides and proteins at a significantly reduced computational cost. Furthermore, notwithstanding expected discrepancies, the obtained electron distributions and electrostatic potentials are in very good agreement with those obtained at Hartree-Fock and density functional theory (DFT) levels. Therefore, the results encourage to use the new libraries as alternatives to the popular pseudoatom-databases of crystallography in the refinement of crystallographic structures of macromolecules. In particular, in this context, we have already envisaged the coupling of the ELMO databanks with the promising Hirshfeld atom refinement technique to extend the applicability of the latter to very large systems.

  • Details
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Type
research article
DOI
10.1021/acs.jpca.8b09056
Web of Science ID

WOS:000451101200019

Author(s)
Meyer, Benjamin  
Genoni, Alessandro
Date Issued

2018-11-15

Publisher

AMER CHEMICAL SOC

Published in
The Journal of Physical Chemistry A
Volume

122

Issue

45

Start page

8965

End page

8981

Subjects

Chemistry, Physical

•

Physics, Atomic, Molecular & Chemical

•

Chemistry

•

Physics

•

kernel energy method

•

atom scattering factors

•

x-ray-diffraction

•

electronic-structure calculations

•

charge-density refinement

•

theoretical data-bank

•

ab-initio treatment

•

wave-functions

•

tailoring approach

•

electrostatic potentials

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCMD  
Available on Infoscience
December 13, 2018
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/152403
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