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.

Insight into the Electron Density Distribution in an O,N-Heterocyclic Stannylene by High-Resolution X-ray Diffraction Analysis

2019 ◽  
Vol 2019 (6) ◽  
pp. 875-884 ◽  
Author(s):  
Maxim G. Chegerev ◽  
Alexandr V. Piskunov ◽  
Kseniya V. Tsys ◽  
Andrey G. Starikov ◽  
Klaus Jurkschat ◽  
...  
Keyword(s):  
High Resolution ◽  
Density Distribution ◽  
Diffraction Analysis ◽  
Electron Density ◽  
Electron Density Distribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Insight Into

Electron density distribution and Madelung potential in α-spodumene, LiAl(SiO3)2, from two-wavelength high-resolution X-ray diffraction data

1999 ◽  
Vol 55 (3) ◽  
pp. 273-284 ◽  
Author(s):  
Sandrine Kuntzinger ◽  
Nour Eddine Ghermani
Keyword(s):  
High Resolution ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Net Charge ◽  
X Ray ◽  
Madelung Potential ◽  
Net Charges

The electron density distribution in α-spodumene, LiAl(SiO3)2, was derived from high-resolution X-ray diffraction experiments. The results obtained from both Mo Kα- and Ag Kα-wavelength data sets are reported. The features of the Si—O and Al—O bonds are related to the geometrical parameters of the Si—O—Al and Si—O—Si bridges on the one hand and to the O...Li+ interaction on the other. Kappa refinements against the two data sets yielded almost the same net charges for the Si (+1.8 e) and O (−1.0 e) atoms in spodumene. However, the Al net charge obtained from the Ag Kα data (+1.9 e) is larger than the net charge derived from the Mo Kα data (+1.5 e). This difference correlates with a more contracted Al valence shell revealed by the shorter X-ray wavelength (κ = 1.4 for the Ag Kα data set). The derived net charges were used to calculate the Madelung potential at the spodumene atomic sites. The electrostatic energy for the chemical formula LiAl(SiO3)2 was −8.60 e2 Å−1 (−123.84 eV) from the net charges derived from the Ag Kα data and −6.97 e2 Å−1 (−100.37 eV) from the net charges derived from the Mo Kα data.

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.

Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data

2020 ◽  
Author(s):  
Jan Zaucha ◽  
Charlotte A. Softley ◽  
Michael Sattler ◽  
Grzegorz M. Popowicz
Keyword(s):  
Deep Learning ◽  
High Resolution ◽  
Electron Density ◽  
Binding Sites ◽  
Hot Spots ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Water Binding ◽  
X Ray ◽  
Deep Learning Model

ABSTRACTThe surfaces of proteins are generally hydrophilic but there have been reports of sites that exhibit an exceptionally high affinity for individual water molecules. Not only do such molecules often fulfil critical biological functions, but also, they may alter the binding of newly designed drugs. In crystal structures, sites consistently occupied in each unit cell yield electron density clouds that represent water molecule presence. These are recorded in virtually all high-resolution structures obtained through X-ray diffraction. In this work, we utilized the wealth of data from the RCSB Protein Data Bank to train a residual deep learning model named ‘hotWater’ to identify sites on the surface of proteins that are most likely to bind water, the so-called water hot spots. The model can be used to score existing water molecules from a PDB file to provide their ranking according to the predicted binding strength or to scan the surface of a protein to determine the most likely water hot-spots de novo. This is computationally much more efficient than currently used molecular dynamics simulations. Based on testing the model on three example proteins, which have been resolved using both high-resolution X-ray crystallography (providing accurate positions of trapped waters) as well as low-resolution X-ray diffraction, NMR or CryoEM (where structure refinement does not yield water positions), we were able to show that the hotWater method is able to recover in the “water-free” structures many water binding sites known from the high-resolution structures. A blind test on a newly solved protein structure with waters removed from the PDB also showed good prediction of the crystal water positions. This was compared to two known algorithms that use electron density and was shown to have higher recall at resolutions >2.6 Å. We also show that the algorithm can be applied to novel proteins such as the RNA polymerase complex from SARS-CoV-2, which could be of use in drug discovery. The hotWater model is freely available at (https://pypi.org/project/hotWater/).

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 Ultra-high resolution neutron and X-ray crystallography: structure of crambin

2014 ◽  
Vol 70 (a1) ◽  
pp. C1206-C1206
Author(s):  
Julian Chen ◽  
Bryant Hanson ◽  
S Fisher ◽  
Paul Langan ◽  
Andrey Kovalevsky ◽  
...  
Keyword(s):  
High Resolution ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Anisotropic Temperature ◽  
Exchange Patterns

Neutron diffraction data to 1.1 Å was collected on a crystal of the small protein crambin at the Protein Crystallography Station (PCS) at Los Alamos, the highest resolution neutron structure of a protein to date, and a technical benchmark for the instrument. 95 % of the hydrogen atoms in the protein structure were resolved. The data allowed for the refinement of anisotropic temperature factors for selected deuterium atoms within the protein. Hydrogen bonding networks ambiguous in room temperature, ultra-high resolution (0.84 Å) electron density maps are clarified in the nuclear density maps. The ultra-high resolution data also reveals unusual H/D exchange patterns and novel chemistry in the side chains and protein backbone. Complementary X-ray diffraction data was collected at 19-ID at the Advanced Photon Source, with extensive re-configuration of the beamline to allow for operation at higher energy settings.

scholarly journals X-ray diffraction evidence for the existence of 102.0- and 230.0-nm transverse periodicities in striated muscle.

1987 ◽  
Vol 105 (3) ◽  
pp. 1311-1318 ◽  
Author(s):  
J Bordas ◽  
G R Mant ◽  
G P Diakun ◽  
C Nave
Keyword(s):  
Electron Density ◽  
Striated Muscle ◽  
Diffraction Theory ◽  
Optical Microscope ◽  
Sartorius Muscle ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Maps ◽  
Diffraction Patterns ◽  
Integrated Intensities

Synchrotron radiation techniques have enabled us to record meridional x-ray diffraction patterns from frog sartorius muscle at resolutions ranging from approximately 2,800 to 38 nm (i.e., overlapping with the optical microscope and the region normally accessible with low angle diffraction cameras). These diffraction patterns represent the transform of the low resolution structure of muscle projected on the sarcomere axis and sampled by its repeat. Altering the sarcomere length results in the sampling of different parts of this transform, which induces changes in the positions and the integrated intensities of the diffraction maxima. This effect has been used to determine the transform of the mass projection on the muscle axis in a quasicontinuous fashion. The results reveal the existence of maxima arising from long-range periodicities in the structure. Determination of the zeroes in the transforms has been used to obtain phase information from which electron density maps have been calculated. The x-ray diffraction diagrams and the resulting electron density maps show the existence of a series of mass bands, disposed transversely to the sarcomere axis and distributed at regular intervals. A set of these transverse structures is associated with thin filaments, and their 102.0-nm repeat suggests a close structural relationship with their known molecular components. A second set, spaced by approximately 230.0 nm, is also present; from diffraction theory one has to conclude that this repeat simultaneously exists in thick and thin filament regions.

The whole range of hydrogen bonds in one crystal structure: neutron diffraction and charge-density studies of N,N-dimethylbiguanidinium bis(hydrogensquarate)

2011 ◽  
Vol 67 (6) ◽  
pp. 552-559 ◽  
Author(s):  
Mihaela-Diana Şerb ◽  
Ruimin Wang ◽  
Martin Meven ◽  
Ulli Englert
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Electron Density ◽  
Organic Salt ◽  
X Ray Diffraction ◽  
Covalent Character ◽  
X Ray

N,N-Dimethylbiguanidinium bis(hydrogensquarate) features an impressive range of hydrogen bonds within the same crystal structure: neighbouring anions aggregate to a dianionic pair through two strong O—H...O interactions; one of these can be classified among the shortest hydrogen bonds ever studied. Cations and anions in this organic salt further interact via conventional N—H...O and nonclassical C—H...O contacts to an extended structure. As all these interactions occur in the same sample, the title compound is particularly suitable to monitor even subtle trends in hydrogen bonds. Neutron and high-resolution X-ray diffraction experiments have enabled us to determine the electron density precisely and to address its properties with an emphasis on the nature of the X—H...O interactions. Sensitive criteria such as the Laplacian of the electron density and energy densities in the bond-critical points reveal the incipient covalent character of the shortest O—H...O bond. These findings are in agreement with the precise geometry from neutron diffraction: the shortest hydrogen bond is also significantly more symmetric than the longer interactions.

scholarly journals A history of experimental phasing in macromolecular crystallography

2016 ◽  
Vol 72 (3) ◽  
pp. 293-295 ◽  
Author(s):  
Neil Isaacs
Keyword(s):  
Crystal Structures ◽  
Electron Density ◽  
Diffraction Data ◽  
Fourier Transforms ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Crystal Lattices ◽  
X Ray ◽  
Experimental Phasing ◽  
History Of

It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some decades before experimental phasing methods were developed. Many scientists contributed to this development and this paper presents the author's own perspective on this history. There will be other perspectives, so what follows isahistory, rather thanthehistory, of experimental phasing.

Sign in / Sign up

Export Citation Format

Share Document