Literature DB >> 12192120

Aspherical-atom scattering factors from molecular wave functions. 1. Transferability and conformation dependence of atomic electron densities of peptides within the multipole formalism.

Tibor Koritsanszky1, Anatoliy Volkov, Philip Coppens.   

Abstract

In this study, the feasibility of building a database of theoretical atomic deformation density parameters applicable to the construction of the densities of biomacromolecules and to the interpretation of their X-ray diffraction data is discussed. The procedure described involves generation of valence-only structure factors of tripeptides calculated from theoretical densities at the B3LYP level and the refinement of multipole parameters against these simulated data. Our results so far indicate that the backbone pseudoatoms extracted in such a way are highly transferable and fairly invariant with respect to rotations around single bonds in the peptide framework. The ultimate goal is to use the aspherical-atom database for improved macromolecular refinements that are based on high-resolution data and for prediction of electrostatic properties of larger molecules.

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Year:  2002        PMID: 12192120     DOI: 10.1107/s0108767302010991

Source DB:  PubMed          Journal:  Acta Crystallogr A        ISSN: 0108-7673            Impact factor:   2.290


  12 in total

1.  Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential.

Authors:  Chérif F Matta
Journal:  J Comput Chem       Date:  2014-04-29       Impact factor: 3.376

2.  Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations.

Authors:  Nicolas Muzet; Benoît Guillot; Christian Jelsch; Eduardo Howard; Claude Lecomte
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-10       Impact factor: 11.205

3.  Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme-substrate complex: influenza neuraminidase inhibition.

Authors:  Paulina M Dominiak; Anatoliy Volkov; Adam P Dominiak; Katarzyna N Jarzembska; Philip Coppens
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-04-18

4.  Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteins.

Authors:  Claude Lecomte; Christian Jelsch; Benoît Guillot; Bertrand Fournier; Angélique Lagoutte
Journal:  J Synchrotron Radiat       Date:  2008-04-18       Impact factor: 2.616

5.  Hirshfeld atom refinement.

Authors:  Silvia C Capelli; Hans-Beat Bürgi; Birger Dittrich; Simon Grabowsky; Dylan Jayatilaka
Journal:  IUCrJ       Date:  2014-08-29       Impact factor: 4.769

6.  Yes, one can obtain better quality structures from routine X-ray data collection.

Authors:  W Fabiola Sanjuan-Szklarz; Anna A Hoser; Matthias Gutmann; Anders Østergaard Madsen; Krzysztof Woźniak
Journal:  IUCrJ       Date:  2016-01-01       Impact factor: 4.769

7.  Transferable Machine-Learning Model of the Electron Density.

Authors:  Andrea Grisafi; Alberto Fabrizio; Benjamin Meyer; David M Wilkins; Clemence Corminboeuf; Michele Ceriotti
Journal:  ACS Cent Sci       Date:  2018-12-26       Impact factor: 14.553

8.  Refinement of organic crystal structures with multipolar electron scattering factors.

Authors:  Barbara Gruza; Michał Leszek Chodkiewicz; Joanna Krzeszczakowska; Paulina Maria Dominiak
Journal:  Acta Crystallogr A Found Adv       Date:  2020-01-01       Impact factor: 2.290

9.  Charge density studies of multicentre two-electron bonding of an anion radical at non-ambient temperature and pressure.

Authors:  Valentina Milašinović; Krešimir Molčanov; Anna Krawczuk; Nikita E Bogdanov; Boris A Zakharov; Elena V Boldyreva; Christian Jelsch; Biserka Kojić-Prodić
Journal:  IUCrJ       Date:  2021-06-12       Impact factor: 4.769

10.  Electron density learning of non-covalent systems.

Authors:  Alberto Fabrizio; Andrea Grisafi; Benjamin Meyer; Michele Ceriotti; Clemence Corminboeuf
Journal:  Chem Sci       Date:  2019-09-09       Impact factor: 9.825

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