The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base

2002 ◽  
Vol 58 (5) ◽  
pp. 835-840 ◽  
Author(s):  
Harriott Nowell ◽  
J. Paul Attfield ◽  
Jason C. Cole
Keyword(s):  
Crystal Structure ◽  
Rietveld Refinement ◽  
Free Base ◽  
Final Choice ◽  
X Ray ◽  
Global Weight ◽  
Efficient Packing ◽  
Molecular Compounds

The previously unknown crystal structure of the biogenic compound tryptamine, in the form of a free base (C10H12N2), has been solved from X-ray powder diffraction data using simulated annealing followed by restrained Rietveld refinement [space group P212121, a = 12.28593 (6), b = 8.53351 (4), c = 8.49385 (4) Å, Z = 4, final reduced-χ2 = 5.255]. A restrained Rietveld refinement was carried out in which the global weight factor, f, of the stereochemical restraints was gradually lowered. The effect of the relaxation of restraints on the crystal structure and on χ2 was studied and a criterion for the final choice of f is reported. The crystal structure reported here shows efficient packing involving weak intermolecular hydrogen bonding and a herringbone-type packing pattern.

Rietveld Refinement of the Crystal Structure of α-Be3N2 and the Experimental Determination of Optical Band Gaps for Mg3N2, Ca3N2 and CaMg2N2

2003 ◽  
Vol 58 (1) ◽  
pp. 159-162 ◽  
Author(s):  
Olaf Reckeweg ◽  
Cora Lind ◽  
Arndt Simon ◽  
Francis J. DiSalvo
Keyword(s):  
Crystal Structure ◽  
Experimental Determination ◽  
Rietveld Refinement ◽  
Band Gaps ◽  
X Ray ◽  
Optical Band Gaps

Abstract α-Be3N2 powder was obtained by reacting Be metal with dry, flowing N2 at 1600 K. The product contained 5.9(7) wt.% of BeO. The anti-bixbyite structure suggested earlier was verified through Rietveld refinement on the basis of X-ray powder data (Ia3 (#206); a = 814.518(6) pm). The optical band gaps of α-Be3N2, Mg3N2 and Ca3N2 are compared with newly measured values for Mg3N2, Ca3N2 and CaMg2N2.

Crystal structure determination of molecular compounds from conventional powder diffraction data: Trimeric silver(I) 3,5-dimethylpyrazolate

1998 ◽  
Vol 13 (1) ◽  
pp. 35-40 ◽  
Author(s):  
N. Masciocchi ◽  
P. Cairati ◽  
A. Sironi
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Rietveld Method ◽  
Laboratory Data ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Difference Fourier ◽  
Molecular Compounds ◽  
Bidentate Mode

In the absence of single crystals, silver(I) 3,5-dimethylpyrazolate, [Ag(dmpz)]3, has been structurally characterized by ab initio X-ray powder diffraction, using conventional laboratory data. Its crystals are triclinic, P1¯, with a=8.0876(10), b=11.1204(13), c=11.6136(16) Å, α=68.293(6), β=78.350(7), and γ=81.243(6)°. The structure has been solved by Patterson, difference Fourier, and geometrical modeling, and ultimately refined by the Rietveld method down to Rp=0.068, Rwp=0.085, and RF=0.055, for 4300 observations in the 17<2θ<103° range. Each molecule consists of a cyclic, trimeric assembly of Ag(dmpz) fragments, with the dmpz ligand bridging, in the exo-bidentate mode, nonbonded Ag…Ag edges.

scholarly journals Synthesis and X-Ray Crystal Structure Determination of Thiotrithiazyl Iododichloride, S4N3ICl2

2002 ◽  
Vol 57 (12) ◽  
pp. 1387-1390 ◽  
Author(s):  
Stephan H. Irsen ◽  
Richard Dronskowski
Keyword(s):  
Crystal Structure ◽  
Rietveld Refinement ◽  
Structure Determination ◽  
Crystal Structure Determination ◽  
Crystal Chemical ◽  
Monoclinic System ◽  
X Ray

Thiotrithiazyl iododichloride, S4N3ICl2, has been synthesized from molecular S4N4 and liquid ICl and structurally characterized by an X-ray Rietveld refinement. S4N3ICl2 crystallizes in the monoclinic system (P21/c, a = 611.548(7), b = 877.336(8), c = 1770.12(2) pm, β = 92.3357(7)°, Z = 4), follows the crystal-chemical motif (S4N3+)(ClICl−), and is thus isotypic with (S4N3+ )(Br3− ). The crystal structure contains a planar S4N3+ ring and a linear ClICl− unit.

Single Crystal Growth of High-Pressure Phases of Ice and Salt Hydrate Far Below the Original Melting Point by Mixing Alcohol: Crystal Structure Determination of Magnesium Chloride Heptahydrate

2020 ◽  
Author(s):  
Keishiro Yamashita ◽  
Kazuki Komatsu ◽  
Hiroyuki Kagi
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Crystal Growth ◽  
Single Crystal ◽  
Room Temperature ◽  
Growth Technique ◽  
Salt Hydrate ◽  
X Ray

An crystal-growth technique for single crystal x-ray structure analysis of high-pressure forms of hydrogen-bonded crystals is proposed. We used alcohol mixture (methanol: ethanol = 4:1 in volumetric ratio), which is a widely used pressure transmitting medium, inhibiting the nucleation and growth of unwanted crystals. In this paper, two kinds of single crystals which have not been obtained using a conventional experimental technique were obtained using this technique: ice VI at 1.99 GPa and MgCl<sub>2</sub>·7H<sub>2</sub>O at 2.50 GPa at room temperature. Here we first report the crystal structure of MgCl2·7H2O. This technique simultaneously meets the requirement of hydrostaticity for high-pressure experiments and has feasibility for further in-situ measurements.

The protonation of the ethylenediphosphinetetraacetate anion and the crystal structure of the bis (hydrogen bromide) of ethylenediphosphinetetraacetic acid

1981 ◽  
Vol 46 (12) ◽  
pp. 3063-3073 ◽  
Author(s):  
Jana Podlahová ◽  
Bohumil Kratochvíl ◽  
Vratislav Langer ◽  
Josef Šilha ◽  
Jaroslav Podlaha
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Structure Determination ◽  
Free Acid ◽  
Hydrogen Bromide ◽  
Carboxyl Groups ◽  
Spectroscopic Methods ◽  
X Ray ◽  
Partial Formation

The equilibria and mechanism of addition of protons to the ethylenediphosphinetetraacetate anion (L4-) were studied in solution by the UV, IR, 1H and 31P NMR spectroscopic methods. A total of six protons can be bonded to the anion. They are added stepwise, first with partial formation of zwitterions containing P-H bonds, which then dissociate with formation of the free acid, H4L, where all four protons are bonded in carboxyl groups. The formation of zwitterions is strongly dependent on the concentration. In the final stage, the acid bonds two additional protons to form the bis-phosphonium cation, H6L2+. A number of isostructural salts containing this cation, H4L.2 HX (X = Cl, Br, I), have been prepared. The X-ray crystal structure determination of the bromide confirmed the expected arrangement. The bromide crystals are monoclinic, a = 578.2, b = 1 425.0, c = 1 046.7 pm, β = 103.07° with a space group of P21/c, Z = 2. The final R factor was 0.059 based on 1 109 observed reflections. The structure consists of H6L2+ cations containing protons bonded to phosphorus atoms (P-H distance 134 pm) and of bromide anions, located in gaps which are also sufficiently large for I- anions in the isostructural iodide. The interbonding of phosphonium cations proceeds through hydrogen bonds, C-OH...O=C, in which the O...O distance is 275.3 pm.

Crystal structure determination of the conformation of two bicyclo[3.3.1]nonan-ones

1985 ◽  
Vol 63 (6) ◽  
pp. 1166-1169 ◽  
Author(s):  
John F. Richardson ◽  
Ted S. Sorensen
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Chair Conformation ◽  
Molecular Structures ◽  
Boat Conformation ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Final Agreement

The molecular structures of exo-7-methylbicyclo[3.3.1]nonan-3-one, 3, and the endo-7-methyl isomer, 4, have been determined using X-ray-diffraction techniques. Compound 3 crystallizes in the space group [Formula: see text] with a = 15.115(1), c = 7.677(2) Å, and Z = 8 while 4 crystallizes in the space group P21 with a = 6.446(1), b = 7.831(1), c = 8.414(2) Å, β = 94.42(2)°, and Z = 2. The structures were solved by direct methods and refined to final agreement factors of R = 0.041 and R = 0.034 for 3 and 4 respectively. Compound 3 exists in a chair–chair conformation and there is no significant flattening of the chair rings. However, in 4, the non-ketone ring is forced into a boat conformation. These results are significant in interpreting what conformations may be present in the related sp2-hybridized carbocations.

scholarly journals Preparative-scale HPLC Resolution of Metallacyclic η3-Allyltricarbonyliron Complexes and Determination of the Absolute Configuration by X-Ray Crystal Structure Analysis

1999 ◽  
Vol 23 (9) ◽  
pp. 578-579
Author(s):  
Rainer Schobert ◽  
Hermann Pfab ◽  
Jutta Böhmer ◽  
Frank Hampel ◽  
Andreas Werner
Keyword(s):  
Crystal Structure ◽  
Silica Gel ◽  
Structure Analysis ◽  
Absolute Configuration ◽  
Crystal Structure Analysis ◽  
Preparative Scale ◽  
X Ray ◽  
The Absolute

Racemates of (η3-allyl)tricarbonyliron lactone complex Fe(CO)3{η1:η3-C(O)XCH2CHCMeCH2} 1a (X = O) and (η3-allyl)tricarbonyliron lactam complex 2a (X = NMe) are resolved on a preparative scale by HPLC on cellulose tris(3,5-dimethylphenyl)carbamate/silica gel RP-8 and the absolute configuration of (-)-2a is determined by X-ray crystal structure analysis.

Sign in / Sign up

Export Citation Format

Share Document