scholarly journals Hirshfeld atom refinement

IUCrJ ◽  
2014 ◽  
Vol 1 (5) ◽  
pp. 361-379 ◽  
Author(s):  
Silvia C. Capelli ◽  
Hans-Beat Bürgi ◽  
Birger Dittrich ◽  
Simon Grabowsky ◽  
Dylan Jayatilaka
Keyword(s):  
Hydrogen Atom ◽  
Diffraction Data ◽  
Iterative Procedure ◽  
Structural Parameters ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Electron Densities ◽  
X Ray ◽  
Bond Lengths ◽  
Better Than

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-madeab initioquantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustratedviathe example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–L-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

2020 ◽  
Vol 76 (3) ◽  
pp. 296-306 ◽  
Author(s):  
Kunal Kumar Jha ◽  
Barbara Gruza ◽  
Prashant Kumar ◽  
Michal Leszek Chodkiewicz ◽  
Paulina Maria Dominiak
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Bond Lengths ◽  
Atom Model ◽  
User Friendly

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

scholarly journals Hydrogen atoms in bridging positions from quantum crystallographic refinements: influence of hydrogen atom displacement parameters on geometry and electron density

CrystEngComm ◽  
2020 ◽  
Vol 22 (28) ◽  
pp. 4778-4789 ◽  
Author(s):  
Lorraine A. Malaspina ◽  
Anna A. Hoser ◽  
Alison J. Edwards ◽  
Magdalena Woińska ◽  
Michael J. Turner ◽  
...  
Keyword(s):  
Hydrogen Atom ◽  
Electron Density ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Atom Displacement

Hydrogen atom positions can be obtained accurately from X-ray diffraction data of hydrogen maleate salts via Hirshfeld atom refinement.

scholarly journals Multipole electron densities and structural parameters from synchrotron powder X-ray diffraction data obtained with a MYTHEN detector system (OHGI)

2021 ◽  
Vol 77 (2) ◽  
Author(s):  
Bjarke Svane ◽  
Kasper Tolborg ◽  
Kenichi Kato ◽  
Bo Brummerstedt Iversen
Keyword(s):  
Single Crystal ◽  
Electron Density ◽  
Diffraction Data ◽  
Structural Parameters ◽  
Detector System ◽  
X Ray Diffraction ◽  
Electron Densities ◽  
X Ray ◽  
Peak Overlap ◽  
Microstrip Detectors

Powder X-ray diffraction has some inherent advantages over traditional single-crystal X-ray diffraction in accurately determining electron densities and structural parameters due to the lower requirements for sample crystallinity, simpler corrections and measurement simultaneity. For some simple inorganic materials, it has been shown that these advantages can compensate for disadvantages such as peak overlap and error-prone background subtraction. Although it is challenging to extend powder X-ray diffraction-based electron-density studies to organic materials with significant peak overlap, previous results using a dedicated vacuum diffractometer with a large image-plate camera (AVID) demonstrated that it can be done. However, the vacuum setup with the off-line detector system was found to prohibit a widespread use. Fast microstrip detectors, which have been employed at a number of powder diffraction beamlines, have the potential to facilitate electron-density studies. Nevertheless, no electron-density studies even for materials with slight peak overlap have been performed with microstrip detectors. One of the most critical problems has been a difference in sensitivity between microstrip channels, which substantially defines the dynamic range of a detector. Recently, a robust approach to this problem has been developed and applied to a total scattering measurement system (OHGI) with 15 MYTHEN microstrip modules. In the present study, synchrotron powder X-ray diffraction data obtained with OHGI are evaulated in terms of multipole electron densities and structural parameters (atomic positions and displacement parameters). These results show that, even without a dedicated setup and perfect samples, electron-density modelling can be carried out on high-quality powder X-ray diffraction data. However, it was also found that the required prior information about the sample prohibits widespread use of the method. With the presently obtainable data quality, electron densities of molecular crystals in general are not reliably obtained from powder data, but it is an excellent, possibly superior, alternative to single-crystal measurements for small-unit-cell inorganic solids. If aspherical atomic scattering factors can be obtained from other means (multipole databases, theoretical calculations), then atomic positions (including for hydrogen) and anisotropic atomic displacement parameters (non-hydrogen atoms) of excellent accuracy can be refined from synchrotron powder X-ray diffraction data on organic crystals.

The first proof of protonated anion tetrahedra in the tsumcorite-type compounds

2004 ◽  
Vol 68 (5) ◽  
pp. 757-767 ◽  
Author(s):  
T. Mihajlović ◽  
H. Effenberger
Keyword(s):  
Crystal Structure ◽  
Hydrothermal Synthesis ◽  
Single Crystal ◽  
Diffraction Data ◽  
Title Compound ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Synthetic Compounds ◽  
X Ray

AbstractHydrothermal synthesis produced the new compound SrCo2(AsO4)(AsO3OH)(OH)(H2O). The compound belongs to the tsumcorite group (natural and synthetic compounds with the general formula M(1)M(2)2(XO4)2(H2O,OH)2; M(1)1+,2+,3+ = Na, K, Rb, Ag, NH4, Ca, Pb, Bi, Tl; M(2)2+,3+ = Al, Mn3+, Fe3+, Co, Ni, Cu, Zn; and X5+,6+ = P, As, V, S, Se, Mo). It represents (1) the first Sr member, (2) the until now unknown [7]-coordination for the M(1) position, (3) the first proof of (partially) protonated arsenate groups in this group of compounds, and (4) a new structure variant.The crystal structure of the title compound was determined using single-crystal X-ray diffraction data. The compound is monoclinic, space group P21/a, with a = 9.139(2), b = 12.829(3), c = 7.522(2) Å, β = 114.33(3)°, V = 803.6(3) Å3, Z = 4 [wR2 = 0.065 for 3530 unique reflections]. The hydrogen atoms were located experimentally.

scholarly journals Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

2017 ◽  
Vol 23 (19) ◽  
pp. 4605-4614 ◽  
Author(s):  
Birger Dittrich ◽  
Jens Lübben ◽  
Stefan Mebs ◽  
Armin Wagner ◽  
Peter Luger ◽  
...  
Keyword(s):  
Single Crystal ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Bond Lengths

(Ph4P)2 Mn2Br6 und (Ph3PCH2Ph)2Mn2I6 (Ph = C6H5) / (Ph4P)2Mn2Br6 and (Ph 3PCH2Ph)2Mn2I6 (Ph = C6H5

1988 ◽  
Vol 43 (2) ◽  
pp. 171-174 ◽  
Author(s):  
Siegfried Pohl ◽  
Wolfgang Saak ◽  
Peter Stolz
Keyword(s):  
Single Crystal ◽  
Diffraction Data ◽  
Unit Cell ◽  
Formula Unit ◽  
X Ray Diffraction ◽  
Triclinic Space Group ◽  
X Ray ◽  
Bond Lengths ◽  
The Mean ◽  
The Difference

(Ph4P)2Mn2Br6 (1) and (Ph3PCH2Ph)2Mn2I6 (2) were prepared from the reaction of manganese dihalide with the corresponding phosphonium halide in CH2Cl2.The structures of 1 and 2 were determined from single crystal X-ray diffraction data.Both compounds crystallize in the triclinic space group P 1 with one formula unit per unit cell.1:a = 998.1(1), b = 1005.7(1), c = 1313.3(2) pm, α = 108.51(1), β = 94.25(1), γ = 100.36(1)°.2: a = 1058.6(2), b = 1236.3(2), c = 1248.4(3) pm, α = 63.53(1), β = 74.15(1), γ = 74.65(1)°.The structures of 1 and 2 exhibit discrete, dimeric anions formed by the fusion of two identical tetrahedral-like units with a common halogen-halogen edge. The mean Mn-Hal bond lengths were found to be 251.8 pm (Mn-Br) and 272.2 pm (Mn-I). The difference between the bridging and terminal Mn-Hal bond lengths is about 12-13 pm in both compounds

Formamidinhim-Hexachloroferrat(III) Synthese und Kristallstruktur / Formamidinium-Hexachloroferrate(III) Synthesis and Crystal Structure

1985 ◽  
Vol 40 (3) ◽  
pp. 443-446 ◽  
Author(s):  
Udo Demant ◽  
Elke Conradi ◽  
Ulrich Müller ◽  
Kurt Dehnicke
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
The Other ◽  
X Ray Diffraction ◽  
Synthesis And Crystal Structure ◽  
Space Group ◽  
X Ray ◽  
Positional Disorder ◽  
Lattice Constants ◽  
Bond Lengths

[HC(NH2)2]3FeCl6 was obtained together with other products from the reaction of S4N4 with HCl in H2CCl2 in the presence of FeCl3. Its crystal structure was determined from X-ray diffraction data (473 independent observed reflexions, R = 0.047). Lattice constants: a = 961.6, c = 876.4 pm; tetragonal, space group P42/m, Z = 2. Of the two crystallographically independent formamidinium ions HC(NH2)2⊕, one exhibits positional disorder; the other one has C-N bond lengths of 128 pm. The FeCl63⊖ ions have symmetry C2h, but the deviation from Oh is small.

VALTOPO: a program for the determination of atomic and molecular properties from experimental electron densities

2005 ◽  
Vol 38 (1) ◽  
pp. 232-236 ◽  
Author(s):  
Riccardo Bianchi ◽  
Alessandra Forni
Keyword(s):  
Quantum Theory ◽  
Diffraction Data ◽  
Molecular Properties ◽  
Atoms In Molecules ◽  
X Ray Diffraction ◽  
Electron Densities ◽  
X Ray ◽  
Electrostatic Properties ◽  
Multipole Refinement

VALTOPOis a program for the multipole refinement of accurate X-ray diffraction data and for the determination of electrostatic properties. It is a new version ofVALRAY, including the quantum theory of atoms in molecules analysis as implemented in theTOPOND98program. Two test structures, L-alanine and the complex of (E)-1,2-bis(4-pyridyl)ethylene with 1,4-diiodotetrafluorobenzene, have been analysed in order to illustrate some of the potentialities of the program.

scholarly journals TAAM: a reliable and user-friendly tool for hydrogen-atom location using X-ray diffraction data

2019 ◽  
Vol 75 (a2) ◽  
pp. e453-e453
Author(s):  
Michal Chodkiewicz ◽  
Kunal Jha ◽  
Barbara Gruza ◽  
Paulina Dominiak
Keyword(s):  
Hydrogen Atom ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
User Friendly

Crystal structure of low-cristobalite-type Al0.5Ga0.5PO4: A combined Rietveld refinement of neutron and X-ray diffraction data

2005 ◽  
Vol 20 (3) ◽  
pp. 207-211 ◽  
Author(s):  
S. N. Achary ◽  
A. K. Tyagi ◽  
S. K. Kulshreshtha ◽  
O. D. Jayakumar ◽  
P. S. R. Krishna ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Tetrahedral Coordination ◽  
X Ray Diffraction ◽  
Rietveld Refinements ◽  
X Ray ◽  
Cell Parameters ◽  
Bond Lengths

The low-cristobalite-type modification of Al0.5Ga0.5PO4 is prepared by annealing the amorphous precipitate of stoichiometric phosphate at 1300 °C. The phase purity of the sample is ascertained by powder X-ray diffraction. The crystal structure is refined by Rietveld refinements of the neutron and X-ray diffraction data of the polycrystalline powder. This compound crystallizes in an orthorhombic lattice with unit cell parameters, a=7.0295(8), b=7.0132(8), and c=6.9187(4) Å, V=341.08(6) Å3, Z=4 (Space group C 2221, No. 20). The crystal structure analysis reveals the random distribution of the Al3+ and Ga3+ having tetrahedral coordination with typical M–O (M=Al3+:Ga3+) bond lengths as 1.74 Å. Similarly, the P5+ have tetrahedral coordination with typical P–O bond lengths 1.52–1.54 Å. The Mo4 and PO4 tetraheda are linked by common corners forming a three-dimensional framework lattice. The details of the crystal structure are presented in this paper.

Sign in / Sign up

Export Citation Format

Share Document