Accurate charge density of the tripeptide Ala-Pro-Ala with the maximum entropy method (MEM): influence of data resolution

Abstract

The accurate electron density of Ala-Pro-Ala is determined by the maximum entropy method (MEM), employing the same reflection data measured at 100 K which was used for a multipole refinement by Kalinowski et al. [(2007), Acta Cryst. Accepted for publication]. Properties of the electron density are compared with the corresponding properties of the static electron density from the multipole model and to the dynamic MEM electron density of trialanine at 20 K. It is thus shown that the increased thermal smearing at 100 K leads to lower electron densities in the bond critical points and atomic charges closer to zero for Ala-Pro-Ala than has been obtained for trialanine at 20 K. The influence of the resolution of the data is investigated by a series of MEM calculations. Atomic charges and atomic volumes are found not to depend on the resolution, but the charge density in the BCPs decreases with decreasing resolution of the dataset. The origin of this dependence is found to lie mostly in the more accurate estimate of the atomic displacement parameters (ADPs) for the higher-resolution datasets. If these effects are taken into account, meaningful information on chemical bonding can be obtained with data at a resolution better than d(min) = 0.63 A. Alternatively, low-resolution X-ray diffraction data can be used in accurate electron-density studies by the MEM, if another source of accurate values of the ADPs is available, e.g. from refinements with multipole parameters from a database of transferable multipole parameters.

Experimental evidence of orbital order inα-B12andγ-B28Mondal1, Smaalen2, Parakhonskiy3 et al. 2013Phys. Rev. BSelf Cite2914340View full textAdd to dashboardCite

“…The final choice of χ 2 aim = 1.60 and the choice of the weighting scheme H 4 were made according to procedures discussed elsewhere. 32,[34][35][36] 2D contour maps were plotted using the program JANA2006. 37…”

Electron densities by the maximum entropy method (MEM) for various types of prior densities: a case study on three amino acids and a tripeptide

“…Several extensions have been introduced into the MEM aimed at removing these problems, but which, at the same time, introduce a structure model into the calculation . Although successful to a large extent, unexplained discrepancies have remained between, especially, Laplacians at bond critical points (BCPs) from MP models and MEM densities (Hofmann, Kalinowski et al, 2007;Hofmann, Netzel & van Smaalen, 2007;Netzel et al, 2008). Here we present a systematic study of the dependence of MEM densities on the kind of structure model employed as prior in the calculation of the MEM.…”

“…They have proposed that noise and artifacts in MEM densities can be reduced by using prior densities as close as possible to the true densities. Until now, dynamic densities of independent atom models (IAMs) have been used as prior for electron-density studies using the MEM (de Vries et al, 1996;Papoular et al, 2002;Takata, 2008;Hofmann, Kalinowski et al, 2007;Hofmann, Netzel & van Smaalen, 2007;Netzel et al, 2008). We have recently established a procedure to obtain dynamic model densities of both the MP model and the IAM (Mondal et al, 2012).…”

How to easily replace the independent atom model – the example of bergenin, a potential anti-HIV agent of traditional Asian medicine

“…Recently, the maximum entropy method (MEM) has been used in a number of cases (van Smaalen et al, 2003;Hofmann, Kalinowski et al, 2007;Hofmann, Netzel & van Smaalen, 2007;Netzel et al, 2008) as an alternative to the multipole model. Since MEM also requires high-order data, the experimental challenge still remains.…”