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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http://dx.doi.org/10.1107/s0108767302010991 | DOI Listing |
IUCrJ
September 2024
Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
Acta Crystallogr C Struct Chem
July 2024
Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland.
3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data.
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May 2024
Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom.
Over 30 years ago, it was shown that bonding between atoms has a noticeable effect on convergent beam electron diffraction patterns. The paper by Olech et al. [(2024).
View Article and Find Full Text PDFIUCrJ
May 2024
Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland.
Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al.
View Article and Find Full Text PDFRSC Adv
February 2024
Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
Applications of 9-aminoacridine (9aa) and its derivatives span fields such as chemistry, biology, and medicine, including anticancer and antimicrobial activities. Protonation of such molecules can alter their bioavailability as weakly basic drugs like aminoacridines exhibit reduced solubility at high pH levels potentially limiting their effectiveness in patients with elevated gastric pH. In this study, we analyse the influence of protonation on the electronic characteristics of the molecular organic crystals of 9-aminoacridine.
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