scholarly journals Temperature dependence of Uiso constraints in riding hydrogen treatments

2014 ◽  
Vol 70 (a1) ◽  
pp. C286-C286
Author(s):  
Jens Luebben ◽  
Simon Grabowsky ◽  
Alison Edwards ◽  
Wolfgang Morgenroth ◽  
George Sheldrick ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Structure Refinement ◽  
Heavy Atom ◽  
Data Sets ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Structure Determinations ◽  
Thermal Displacements ◽  
Conventional Structure ◽  
Oniom Approach

"Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of ""riding"" hydrogen atoms are frequently constrained to values of their ""parent"" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR [1], Invariom refinement [2], time-of-flight Neutron diffraction and the TLS+ONIOM approach [3]. In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations."

scholarly journals Why direct and post-refinement determinations of absolute structure may give different results

2016 ◽  
Vol 72 (5) ◽  
pp. 661-683 ◽  
Author(s):  
David John Watkin ◽  
Richard Ian Cooper
Keyword(s):  
Recent Literature ◽  
Structure Refinement ◽  
Direct Determination ◽  
Standard Uncertainty ◽  
Data Sets ◽  
Normal Probability Plot ◽  
Normal Probability ◽  
Structure Determinations ◽  
Absolute Structure

Direct determination of the Flack parameter as part of the structure refinement procedure usually gives different, though similar, values to post-refinement methods. The source of this discrepancy has been probed by analysing a range of data sets taken from the recent literature. Most significantly, it was observed that the directly refined Flack (x) parameter and its standard uncertainty are usually not much influenced by changes in the refinement weighting schemes, but if they are then there are probably problems with the data or model. Post-refinement analyses give Flack parameters strongly influenced by the choice of weights. Weights derived from those used in the main least squares lead to post-refinement estimates of the Flack parameters and their standard uncertainties very similar to those obtained by direct refinement. Weights derived from the variances of the observed structure amplitudes are more appropriate and often yield post-refinement Flack parameters similar to those from direct refinement, but always with lower standard uncertainties. Substantial disagreement between direct and post-refinement determinations are strongly indicative of problems with the data, which may be difficult to identify. Examples drawn from 28 structure determinations are provided showing a range of different underlying problems. It seems likely that post-refinement methods taking into account the slope of the normal probability plot are currently the most robust estimators of absolute structure and should be reported along with the directly refined values.

scholarly journals Exploiting subtle structural differences in heavy-atom derivatives for experimental phasing

2014 ◽  
Vol 70 (7) ◽  
pp. 1873-1883 ◽  
Author(s):  
Jimin Wang ◽  
Yue Li ◽  
Yorgo Modis
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Data Sets ◽  
Diarrhea Virus ◽  
Isomorphous Replacement ◽  
Experimental Phasing ◽  
Structural Differences ◽  
Structure Determinations ◽  
Weak Derivatives ◽  
Viral Diarrhea Virus

Structure determination using the single isomorphous replacement (SIR) or single-wavelength anomalous diffraction (SAD) methods with weak derivatives remains very challenging. In a recent structure determination of glycoprotein E2 from bovine viral diarrhea virus, three isomorphous uranium-derivative data sets were merged to obtain partially interpretable initial experimental maps. Small differences between them were then exploited by treating them as three independent SAD data sets plus three circular pairwise SIR data sets to improve the experimental maps. Here, how such subtle structural differences were exploited for experimental phasing is described in detail. The basis for why this approach works is also provided: the effective resolution of isomorphous signals between highly isomorphous derivatives is often much higher than the effective resolution of the anomalous signals of individual derivative data sets. Hence, the new phasing approaches outlined here will be generally applicable to structure determinations involving weak derivatives.

Structure, Stereochemistry and Novel 'Hydrogen Bonding' in Two Bipyridinium Salts of the B10H102- Anion

1987 ◽  
Vol 40 (12) ◽  
pp. 2097 ◽  
Author(s):  
DJ Fuller ◽  
DL Kepert ◽  
BW Skelton ◽  
AH White
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Charge Transfer ◽  
Single Crystal ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
X Ray ◽  
Structure Determinations ◽  
Positively Charged

Crystal structure determinations of (LH)2(B10H10), (1), and (LH2)(B10H10), (2), L = 2,2'- bipyridine , have been carried out by single-crystal X-ray diffraction methods at 295 K, being refined by full-matrix least squares to residuals of 0.041, 0.047 for 1758, 1771 'observed' independent reflections respectively. Crystals of (1) are monoclinic, P21/n, a 12.040(7), b 17.71(1), c 11.142(4) �, β 101.78(4)�, Z 4. Crystals of (2) are monoclinic, P21/c, a 9.937(4), b 10.837(3), c 14.856(5) �, β 109 2l(3)�, Z 4. The colour of the compounds is accounted for by charge-transfer interactions of a novel type, namely between the positively charged cationic acid hydrogen atoms and the negatively charged non-apical hydrogen atoms of the anion. In yellow (1), these distances are 2.26(5) �, while in red (2), they are much shorter, being 1.89(4), 1.97(3) �.

scholarly journals Anisotropic displacement parameters for H atoms using an ONIOM approach

2006 ◽  
Vol 62 (5) ◽  
pp. 875-888 ◽  
Author(s):  
Andrew E. Whitten ◽  
Mark A. Spackman
Keyword(s):  
Neutron Diffraction ◽  
Charge Density ◽  
Ab Initio ◽  
Diffraction Data ◽  
Heavy Atom ◽  
Molecular Crystals ◽  
X Ray ◽  
Density Analysis ◽  
Anisotropic Displacement Parameters ◽  
Oniom Approach

X-ray diffraction data cannot provide anisotropic displacement parameters (ADPs) for H atoms, a major outstanding problem in charge-density analysis of molecular crystals. Although neutron diffraction experiments are the preferred source of this information, for a variety of reasons they are possible only for a minority of materials of interest. To date, approximate procedures combine rigid-body analysis of the molecular heavy-atom skeleton, based on ADPs derived from the X-ray data, with estimates of internal motion provided by spectroscopic data, analyses of neutron diffraction data on related compounds, or ab initio calculations on isolated molecules. Building on these efforts, an improved methodology is presented, incorporating information on internal vibrational motion from ab initio cluster calculations using the ONIOM approach implemented in GAUSSIAN03. The method is tested by comparing model H-atom ADPs with reference values, largely from neutron diffraction experiments, for a variety of molecular crystals: benzene, 1-methyluracil, α-glycine, xylitol and 2-methyl-4-nitroaniline. The results are impressive and, as the method is based on widely available software, and is in principle widely applicable, it offers considerable promise in future charge-density studies of molecular crystals.

A simple approach to estimate isotropic displacement parameters for hydrogen atoms

2015 ◽  
Vol 71 (2) ◽  
pp. 169-174 ◽  
Author(s):  
Anders Østergaard Madsen ◽  
Anna Agnieszka Hoser
Keyword(s):  
Structure Refinement ◽  
Simple Approach ◽  
Large Temperature ◽  
Neutron Diffraction Data ◽  
Hydrogen Atoms ◽  
Temperature Dependent ◽  
X Ray ◽  
Common Structure ◽  
Additive Term ◽  
Simple Combination

A simple combination of riding motion and an additive term is sufficient to estimate the temperature-dependent isotropic displacement parameters of hydrogen atoms, for use in X-ray structure refinements. The approach is validated against neutron diffraction data, and gives reasonable estimates in a very large temperature range (10–300 K). The model can be readily implemented in common structure refinement programs without auxiliary software.

Influence of surface relaxations on X-ray intensities of microcrystals

1995 ◽  
Vol 210 (6) ◽  
Author(s):  
R. B. Neder
Keyword(s):  
Volume Fraction ◽  
Structure Refinement ◽  
Perfect Crystal ◽  
Data Sets ◽  
Near Surface ◽  
X Ray ◽  
Simulation Techniques ◽  
Small Crystals ◽  
Structure Simulation ◽  
Standard Structure

AbstractThe influence of surface relaxations on the intensity of microcrystals was investigated. Since the volume fraction of near surface atoms becomes appreciable for submicrometer crystals, it is important to estimate whether observed intensities of submicrometer crystals can be interpreted with standard structure refinement methods or whether surface relaxations produce a significant deviation from the intensities of the perfect crystal.Structure simulation techniques were applied in order to calculate the intensity of microcrystals of various sizes. Different models of surface relaxations were applied. Structure refinements on the data sets calculated for these models showed that submicrometer crystals down to 0.5 μm in diameter are not affected by surface relaxations. Smaller crystals below 0.1 μm in diameter are significantly affected by surface relaxations. Great care will have to be taken when refining observed intensities of these small crystals.

scholarly journals Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase

2015 ◽  
Vol 71 (8) ◽  
pp. 1072-1077 ◽  
Author(s):  
Mats Ohlin ◽  
Laura von Schantz ◽  
Tobias E. Schrader ◽  
Andreas Ostermann ◽  
Derek T. Logan ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Structure Refinement ◽  
Carbohydrate Binding ◽  
Initial Structure ◽  
Data Sets ◽  
Rhodothermus Marinus ◽  
Structural Determinants ◽  
X Ray ◽  
Carbohydrate Binding Modules ◽  
Hydrolyzing Enzymes

Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate–protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A ofRhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm3) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement usingphenix.refineshowed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein–carbohydrate binding interactions.

scholarly journals Studies of azo and azoxy dyestuffs. Part 17. Synthesis and structure determination of isomeric α and β phenylazoxypyridines, N-oxides, and methiodides. A reexamination of the oxidation of phenylazopyridines and X-ray structure analyses of 4-(phenyl-α-azoxy)pyridinium methiodide and 4-(phenyl-β-azoxy)pyridine-N-oxide

1984 ◽  
Vol 62 (8) ◽  
pp. 1628-1639 ◽  
Author(s):  
E. Buncel ◽  
S. R. Keum ◽  
M. Cygler ◽  
K. I. Varughese ◽  
G. I. Birnbaum
Keyword(s):  
Crystal Structure ◽  
Least Squares ◽  
Inductive Effect ◽  
Heavy Atom ◽  
Direct Methods ◽  
X Ray ◽  
Proton Donors ◽  
Structure Determinations ◽  
Heavy Atom Method

In an extension of Wallach rearrangement studies into the phenylazoxypyridine series, an investigation of 4-, 3-, and 2-phenylazoxypyridines, the N-oxides, and methiodides is reported. Oxidation of 4- and 3-phenylazopyridine with peracetic acid gives rise to the α and β phenylazoxypyridine-N-oxides, contrary to previous literature reports on the obtention solely of the α isomers. 2-Phenylazopyridine, however, yields only the 2-(phenyl-α-azoxy)pyridine-N-oxide. These results are rationalized on the basis of field, resonance, and steric effects. An unprecedented reactivity difference has been observed in the reactions of the α,β isomers of phenylazoxypyridines under conditions of the Wallach rearrangement. This reactivity difference permits the isolation of the α-azoxy isomers from the α,β mixtures. Unequivocal confirmation of the structures has been obtained from X-ray crystal structure determinations of two representative compounds in this series, viz. 4-(phenyl-β-azoxy)pyridine-N-oxide (11) and 4-(phenyl-α-azoxy)pyridinium methiodide (12), which itself was formed by deoxygenation of 4-(phenyl-α-azoxy)pyridine-N-oxide, followed by methylation with methyl iodide. The crystal structure of 11 was solved by direct methods and refined by block-diagonal least squares to R = 0.041 for 2479 observed reflections. The asymmetric unit contains two independent molecules, both of which are planar. The structure of 12 was determined by the heavy-atom method and refined by full-matrix least squares to R = 0.043 for 1718 observed reflections. The molecules are not planar, the pyridine ring being rotated by 36.5° from the phenylazoxy plane. Evidence is presented for the existence of intramolecular [Formula: see text] and [Formula: see text] bonds in crystal structures of trans-azoxyarenes. The carbon atoms involved in these hydrogen bonds are ortho to the azoxy group and can act as proton donors as a result of the inductive effect of the adjacent nitrogen.

The Crystal and Molecular Structure of trans-Dichloro-mer-trans-bis (triisopropylphosphine)(phosphine)hydridoiridium(III)

1995 ◽  
Vol 48 (7) ◽  
pp. 1277 ◽  
Author(s):  
EJ Ditzel ◽  
GB Robertson
Keyword(s):  
Molecular Structure ◽  
Transition Metal ◽  
Crystal And Molecular Structure ◽  
Structure Refinement ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
X Ray ◽  
Molecular Dimensions

The structure of mer-trans-(PPri3)2(PH3)H-trans-Cl2IrIII (1) (Pri = isopropyl), the second third-row transition-metal-PH3 complex to be so characterized, has been determined by single-crystal X-ray diffraction analysis. Crystals are monoclinic, space group C 2/c with a 21.701(2), b 8.735(1), c 15.594(1) Ǻ, β 119.57(1)° and Z 4. Structure refinement by full-matrix least-squares analysis (2811 reflections, 113 parameters) converged with R = 0.016 and Rw = 0.022. Molecules exhibit crystallographically imposed C2 symmetry. The C2 axis passes through the iridium, hydride and PH3 phosphorus atoms, and requires the PH3 hydrogen atoms to be disordered. Important molecular dimensions are Ir-PPri3 2.371(1) Ǻ, Ir-PH3 2.362(1) Ǻ, Ir-Cl 2.374(1) Ǻ and P- Ir -P(trans) 163.21(3)°.

Lewis-Base Adducts of Lead(II) Compounds. X. Synthetic and Structural Studies of Some 1:1 Adducts of 'tet-b' With Lead(II) (Pseudo-)Halides

1996 ◽  
Vol 49 (10) ◽  
pp. 1067 ◽  
Author(s):  
JM Harrowfield ◽  
H Miyamae ◽  
BW Skelton ◽  
AA Soudi ◽  
AH White
Keyword(s):  
Hydrogen Bonding ◽  
Room Temperature ◽  
Lewis Base ◽  
Double Salt ◽  
Rear Side ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Hydrogen Bonding Interactions ◽  
Structure Determinations ◽  
Pseudo Halides

Syntheses and room-temperature single-crystal X-ray structure determinations are recorded for 1 : 1 adducts of (7R*,14R*)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane (' tet -b') with a variety of lead(II) salts. [( tet -b)PbCl2] is monoclinic, P 21/c, a 7.183(3), b 12.425(2), c 24.418(2) Ǻ, β 95.32(3)°, Z = 4; conventional R on |F| was 0.044 for 3188 independent, 'observed' (I > 3σ(I)) reflections. [( tet -b)PbI2] is monoclinic, P 21/c, a 19.920(5), b 7.772(5), c 15.605(6) Ǻ, β 108.39(2)°, Z = 4; R 0.051 for No 2507. [( tet -b) Pb (NCS)2] is orthorhombic, P 212121, a 36.99(1), b 8.996(5), c 6.964(3) Ǻ, Z = 4; R 0.043 for No 2100. All are discrete mononuclear [( tet -b)PbX2] entities in which the macrocyclic N4 ligand occupies one 'face' of the N4PbX2 coordination sphere, the thiocyanate ligands being N-bonded, with Pb -N-C angles of 116(2) and 118(1)°; interesting hydrogen-bonding interactions are found, columns of molecules being formed by way of hydrogen bonding between the coordinated (pseudo-)halides and the NH hydrogen atoms which project to the 'rear' face of the ligand of the next molecule, opposite the metal. In contrast to these, the bromide analogue, monoclinic, P21, a 9.342(3), b 12.720(5), c 18.845(5) Ǻ, β 103.17(2)°, Z = 4, R 0.035 for No 3593, is best formulated as [( tet -b) PbBr ] Br, one only of the bromide entities being bound to the lead, the other being fully dissociated by hydrogen bonding/ion pairing to the 'rear' side of adjacent ligands , forming hydrogen-bonded sheets rather than columns. This formulation has been extended to provide a description of an analogous mixed chloride- perchlorate 'double salt', [( tet -b) PbCl ] (ClO4).CH3OH, which is orthorhombic, P 212121, a 19.475(2), b 18.73(1), c 6.820(2) Ǻ, Z = 4, R 0.054 for No 3075. However, another double salt, modelled in refinement as Pb ( tet -b)Cl0.5(ClO4)1.5.H2O, orthorhombic Pnma , a 20.640(5), b 26.16(1), c 8.937(4) Ǻ, Z = 4 dimers , R 0.074 for No 1769, is in this case more appropriately described as [( tet -b) Pb (OClO2O)2Pb( tet -b)] (ClO4) Cl.H2O with perchlorate rather than halide coordinated, and an incipiently dimeric cation, as in the parent [( tet -b) Pb (OClO3)]2 (ClO4)2.2H2O.

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