Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography

2010 ◽  
Vol 66 (5) ◽  
pp. 558-567 ◽  
Author(s):  
Anna S. Gardberg ◽  
Alexis Rae Del Castillo ◽  
Kevin L. Weiss ◽  
Flora Meilleur ◽  
Matthew P. Blakeley ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Electron Density ◽  
Pyrococcus Furiosus ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Improved Model

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3-protonated perdeuterated crystals ofPyrococcus furiosusrubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 Å resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the σ level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 Å resolution RT neutron data for perdeuterated rubredoxin are ∼8 times more likely overall to provide high-confidence positions for D atoms than 1.1 Å resolution X-ray data at 100 K or RT. At or above the 1.0σ level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 Å resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0σ level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

scholarly journals Charge Density Study on Bullvalene (C10H10 )

1993 ◽  
Vol 48 (1-2) ◽  
pp. 55-57
Author(s):  
T. Koritsánszky ◽  
J. Buschmann ◽  
P. Luger
Keyword(s):  
Electron Density ◽  
Mean Square Displacement ◽  
Body Motion ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray ◽  
Density Maps ◽  
Anisotropic Displacement Parameters ◽  
Deformation Electron Density ◽  
Density Study

Abstract Low-temperature single-crystal neutron and X-ray diffraction data were collected for bullvalene (Figure 1). X -N Fourier and multipole static deformation electron density maps were calculated and compared. Atomic mean-square-displacement parameters were analysed in the framework of the rigid-body motion model and the residual amplitudes (UOBS - UTLS) were graphically interpreted. The preliminary results presented here reveal either a bias in the X-ray anisotropic displacement parameters (ADPs) due to improper modelling of the electron density or unresolved errors in the neutron data.

scholarly journals On avoiding negative electron density in Gram-Charlier refinements of anharmonic motion: the example of glutathione

2018 ◽  
Vol 233 (9-10) ◽  
pp. 695-706 ◽  
Author(s):  
Christian B. Hübschle ◽  
Charlotte Ruhmlieb ◽  
Anja Burkhardt ◽  
Sander van Smaalen ◽  
Birger Dittrich
Keyword(s):  
Electron Density ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Free Lunch ◽  
X Ray Diffraction ◽  
Third Order ◽  
X Ray ◽  
Density Maps ◽  
Anisotropic Displacement Parameters

Abstract The structure of glutathione, γ-l-Glutamyl-l-cysteinyl-glycine (C10H17N3O6S), was studied by multi-temperature single-crystal X-ray diffraction. Residual density maps from conventional independent atom model refinement gave indication of anharmonic motion in the molecule. This was further investigated by invariom refinement with anisotropic displacement parameters for all atoms, which described asphericity due to chemical bonding and lone pairs; afterwards only the residual-density signal of anharmonic motion remained. Treating anharmonicity with third-order Gram-Charlier displacement parameters led to regions with unphysical negative electron density. In contrast, a maximum entropy method (MEM) determination of the electron density successfully takes the features into account. Respective difference electron density plots (MEM minus prior and [Invariom+GC] minus invariom) agree well with each other. Challenges in treating and understanding the phenomenon are discussed. A procedure is proposed how unphysical negative electron density can be avoided. It is closely related to the free lunch algorithm.

scholarly journals Thermal History of Matrix Forsterite Grains from Murchison Based on High-resolution Tomography

2021 ◽  
Vol 922 (2) ◽  
pp. 256
Author(s):  
Giulia Perotti ◽  
Henning O. Sørensen ◽  
Henning Haack ◽  
Anja C. Andersen ◽  
Dario Ferreira Sanchez ◽  
...  
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Chemical Compositions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Maps ◽  
Thermally Processed ◽  
The Matrix ◽  
History Of ◽  
Chondrule Formation

Abstract Protoplanetary disks are dust- and gas-rich structures surrounding protostars. Depending on the distance from the protostar, this dust is thermally processed to different degrees and accreted to form bodies of varying chemical compositions. The primordial accretion processes occurring in the early protoplanetary disk such as chondrule formation and metal segregation are not well understood. One way to constrain them is to study the morphology and composition of forsteritic grains from the matrix of carbonaceous chondrites. Here, we present high-resolution ptychographic X-ray nanotomography and multimodal chemical microtomography (X-ray diffraction and X-ray fluorescence) to reveal the early history of forsteritic grains extracted from the matrix of the Murchison CM2.5 chondrite. The 3D electron density maps revealed, at unprecedented resolution (64 nm), spherical inclusions containing Fe–Ni, very little silica-rich glass and void caps (i.e., volumes where the electron density is consistent with conditions close to vacuum) trapped in forsterite. The presence of the voids along with the overall composition, petrological textures, and shrinkage calculations is consistent with the grains experiencing one or more heating events with peak temperatures close to the melting point of forsterite (∼2100 K), and subsequently cooled and contracted, in agreement with chondrule-forming conditions.

scholarly journals NMR and X-ray studies of apetalic acid isolated from Calophyllum brasiliense and of its chiral amides

2021 ◽  
Author(s):  
Marie-Rose Van Calsteren ◽  
Ricardo Reyes-Chilpa ◽  
Chistopher K Jankowski ◽  
Fleur Gagnon ◽  
Simón Hernández-Ortega ◽  
...  
Keyword(s):  
Antimycobacterial Activity ◽  
Side Chain ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Rain Forests ◽  
X Ray ◽  
X Ray Crystallography ◽  
Calophyllum Brasiliense ◽  
Derivatives Of

The tropical tree Calophyllum brasiliense (Clusiaceae) grows in the rain forests from Brazil to Mexico. Its leaves, as well as those of other Calophyllum species, are rich sources of chromanone acids, such as apetalic acid, isoapetalic acid, and their derivatives. Apetalic acid has shown significant antimycobacterial activity. The biological activity of apetalic acid has been related to the configuration of three asymmetric centers and the stereochemistry of the molecule; however, the C-19 configuration in the acidic side chain has not been fully resolved. For this reason, the unequivocal determination of the absolute configuration by means of X-ray crystallography in a sample of unique homogeneous apetalic acid stereoisomer was the most important point to start this study. We prepared some chiral amides using the carboxyl group. We determined the C-19 stereochemistry of apetalic acid, and its specific chiral derivatives, using NMR, X-ray diffraction methods, and molecular mechanics. Finally, we observed that steric hindrance in the side chain of apetalic acid leads to restriction of rotation around the pivotal link C-10 and C-19 establishing chiral centers at C2(R), C3(S), and C19(R). We were able to separate derivatives of these two high-rotatory-barrier conformers of apetalic acid by forming diastereoisomeric amides with phenylglycine methyl ester having a chiral center at C-2’. Our results allowed the conclusion of the existence of atropisomerism in the apetalic acid molecule.

LauePt, a graphical-user-interface program for simulating and analyzing white-beam X-ray diffraction Laue patterns

2010 ◽  
Vol 43 (4) ◽  
pp. 926-928 ◽  
Author(s):  
X. R. Huang
Keyword(s):  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
White Beam ◽  
Diffraction Geometry ◽  
Wide Range ◽  
User Friendly ◽  
Beam Diffraction ◽  
Laue Method

LauePtis a robust and extremely easy-to-use Windows application for accurately simulating, indexing and analyzing white-beam X-ray diffraction Laue patterns of any crystals under arbitrary diffraction geometry. This program has a user-friendly graphic interface and can be conveniently used by nonspecialists with little X-ray diffraction or crystallography knowledge. Its wide range of applications include (1) determination of single-crystal orientation with the Laue method, (2) white-beam topography, (3) white-beam microdiffraction, (4) X-ray studies of twinning, domains and heterostructures, (5) verification or determination of crystal structures from white-beam diffraction, and (6) teaching of X-ray crystallography.

Electron Density Distribution in LiB3O5 at 293 K

1997 ◽  
Vol 53 (6) ◽  
pp. 870-879 ◽  
Author(s):  
C. Le Hénaff ◽  
N. K. Hansen ◽  
J. Protas ◽  
G. Marnier
Keyword(s):  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hartree Fock ◽  
Density Maps ◽  
Symmetry Constraints ◽  
Net Charges ◽  
Good Agreement

The electron density distribution in lithium triborate LiB3O5 has been studied at room temperature by X-ray diffraction using Ag K \alpha radiation up to 1.02 Å−1 [1439 unique reflections with I > 3\sigma(I)]. Conventional refinements with a free-atom model yield R(F) = 0.0223, wR(F) = 0.0299, S = 1.632. Atom charge refinements show that the lithium should be considered a monovalent ion. Multipolar refinements were undertaken up to fourth order, imposing local non-crystallographic symmetry constraints in order to avoid phase problems leading to meaningless multipole populations due to the non-centrosymmetry of the structure (space group: Pn a21). The residual indices decreased to: R(F) = 0.0147, wR(F) = 0.0193, S = 1.106. The net charges are in good agreement with what can be expected in borate chemistry. Deformation density maps are analysed in terms of \sigma and \pi bonding. The experimental electron distribution in the p z orbitals of triangular B atoms and surrounding O atoms has been analysed by introducing idealized hybridized states. In parallel, the electron density has been determined from ab initio Hartree–Fock calculations on fragments of the structure. Agreement with the X-ray determination is very good and confirms the nature of bonding in the crystal. The amount of transfer of \pi electrons from the oxygen to the triangular B atoms is estimated to be 0.22 electrons by theory.

Investigation into the Crystal Structure of the Perovskite Lead Hafnate, PbHfO3

1998 ◽  
Vol 54 (1) ◽  
pp. 18-28 ◽  
Author(s):  
D. L. Corker ◽  
A. M. Glazer ◽  
W. Kaminsky ◽  
R. W. Whatmore ◽  
J. Dec ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Room Temperature ◽  
Lead Zirconate ◽  
Crystal Structure Analysis ◽  
Temperature Structure ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray

The room-temperature crystal structure of the perovskite lead hafnate PbHfO3 is investigated using both low-temperature single crystal X-ray diffraction (Mo Kα radiation, λ = 0.71069 Å) and polycrystalline neutron diffraction (D1A instrument, ILL, λ = 1.90788 Å). Single crystal X-ray data at 100 K: space group Pbam, a = 5.856 (1), b = 11.729 (3), c = 8.212 (2) Å, V = 564.04 Å3 with Z = 8, μ = 97.2 mm−1, F(000) = 1424, final R = 0.038, wR = 0.045 over 439 reflections with F >1.4σ(F). Polycrystalline neutron data at 383 K: a = 5.8582 (3), b = 11.7224 (5), c = 8.2246 (3) Å, V = 564.80 Å3 with χ2 = 1.62. Although lead hafnate has been thought to be isostructural with lead zirconate, no complete structure determination has been reported, as crystal structure analysis in both these materials is not straightforward. One of the main difficulties encountered is the determination of the oxygen positions, as necessary information lies in extremely weak l = 2n + 1 X-ray reflections. To maximize the intensity of these reflections the X-ray data are collected at 100 K with unusually long scans, a procedure which had previously been found successful with lead zirconate. In order to establish that no phase transitions exist between room temperature and 100 K, and hence that the collected X-ray data are relevant to the room-temperature structure, birefringence measurements for both PbZrO3 and PbHfO3 are also reported.

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