scholarly journals NMR crystallography, diffraction and modeling of small organic molecules

2014 ◽  
Vol 70 (a1) ◽  
pp. C1088-C1088
Author(s):  
Luís Miguel Monteiro Mafra
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Crystal Packing ◽  
Computational Study ◽  
Chemical Shifts ◽  
Hybrid Approach ◽  
X Ray Diffraction ◽  
Structure Solution ◽  
Nmr Crystallography

Solid-state NMR (SSNMR) is a powerful atomic-level characterization technique able to study the local chemical environment of a nucleus in crystalline/amorphous solids. Toward a better understanding of how small molecules self-assemble in the solid-state and reorganizes to produce its hydrate/anhydrous forms, an experimental SSNMR, X-ray diffraction (XRD), and computational study of the supramolecular assemblies of selected small pharmaceuticals is presented. The effect of crystal packing on the 1H and 13C chemical shifts including nonconventional hydrogen bonds, pi···pi and CH···pi contacts, is studied through computer simulations. It will be shown that NMR chemical shifts are sensitive detectors of hydration/dehydration states in highly insoluble antibiotics.[1] Recently, SSNMR became an important gadget in the process of crystal structure solution in powders. This is a non-trivial task and using powder XRD methods alone may often lead to the wrong structure solution. In this talk, a new hybrid approach for structure determination of crystalline solids, will be presented, based on the combination of SSNMR, XRD and an ensemble of computational-assisted structure solution tools including a genetic algorithm based on evolution-inspired operators repeatedly applied to populations of possible crystal structure solutions that evolve to eventually produce the best new offspring candidates. Such methodologies are successfully applied to challenging cases involving multiple component crystals composed by flexible molecules such as a trihydrate β-lactamic antibiotic [2] and an azole-based co-crystal featuring an hydrogen bond network of α-helixes involving NH···N/CH···π intermolecular interactions. ACKNOLEDGEMENTS: Supported by Fundação para a Ciência e a Tecnologia (FCT), Portuguese National NMR Network (RNRMN), CICECO (PEst-C/CTM/LA0011/2013), FEDER, COMPETE, and University of Aveiro. FCT is greatly acknowledge for the consolidation grant IF/01401/2013.

Low-temperature crystallization and structure determination of N-(trifluoromethyl)formamide, N-(2,2,2-trifluoroethyl)formamide and 2,2,2-trifluoroethyl isocyanide

1999 ◽  
Vol 55 (1) ◽  
pp. 70-77 ◽  
Author(s):  
G. J. Perpétuo ◽  
J. Buschmann ◽  
P. Luger ◽  
D. Lentz ◽  
D. Dreissig
Keyword(s):  
Crystal Structure ◽  
Low Temperatures ◽  
Crystal Packing ◽  
Crystal Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Low Temperature Crystallization ◽  
Temperature Crystallization

Crystals of N-(trifluoromethyl)formamide, C2H2F3NO, (I), N-(2,2,2-trifluoroethyl)formamide, C3H4F3NO, (II), and 2,2,2-trifluoroethyl isocyanide, C3H2F3N, (III), were grown in situ on an X-ray diffractometer and analysed by single-crystal X-ray diffraction methods at low temperatures. Crystal data: (I) orthorhombic, P212121, a = 4.547 (2) Å, b = 5.947 (3) Å, c = 14.731 (9) Å, V = 398.3 (4) Å3, Z = 4, M r = 113.05, T = 143 K, D x = 1.885 Mg m−3; (II) monoclinic, P21/n, a = 4.807 (1) Å, b = 16.707 (3) Å, c = 6.708 (1) Å, β = 109.90 (1)°, V = 506.6 (2) Å3, Z = 4, M r = 127.07, T = 141 K, D x = 1.666 Mg m−3; (III) orthorhombic, P212121, a = 5.668 (2) Å, b = 9.266 (3) Å, c = 8.626 (2) Å, V = 453.0 (2) Å3, Z = 4, M r = 109.06, T = 163 K, D x = 1.599 Mg m−3. The results showed that in the crystal both formamides (I) and (II) are exclusively present in the form of the Z isomer, although measurements of solutions of (I) have shown that the E isomer prevails [Lentz et al. (1987). Angew. Chem. 99, 951–953]. In addition ab initio calculations for (I) predicted the E isomer to be the more stable one. In compound (III) the isocyanide group is staggered with respect to the trifluoroethyl group. In the crystal packing of (I) and (II) intermolecular N—H\cdotsO hydrogen bonds generate infinite chains. In (I), these chains are linked to form sheets by C—H\cdotsO contacts. In the crystal structure of (III) each isocyanide dipole is surrounded by four electronegative F atoms with intermolecular C\cdotsF contacts between 3.4 and 3.5 Å.

scholarly journals Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil

2017 ◽  
Vol 73 (3) ◽  
pp. 149-156 ◽  
Author(s):  
Ann-Christin Pöppler ◽  
Emily K. Corlett ◽  
Harriet Pearce ◽  
Mark P. Seymour ◽  
Matthew Reid ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Chemical Shifts ◽  
Magic Angle Spinning ◽  
Mas Nmr ◽  
Double Quantum ◽  
Magic Angle ◽  
X Ray Diffraction ◽  
X Ray ◽  
Nmr Crystallography

A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile–4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental 1H and 13C chemical shifts are determined from two-dimensional 1H–13C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C—H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a 1H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the 1H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N—H...O and C—H...O hydrogen bonding, while changes of −2.7 and −1.5 ppm are due to ring current effects associated with C—H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.

scholarly journals Characterizing the Turbostratic Disorder in COF-5 with NMR Crystallography

2020 ◽  
Author(s):  
Giovanna Pope ◽  
Demetrius Vazquez ◽  
Fernando Uribe-Romo ◽  
James K. Harper
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Chemical Shifts ◽  
X Ray Diffraction ◽  
Space Groups ◽  
Turbostratic Disorder ◽  
Characteristic Features ◽  
Nmr Crystallography ◽  
Pure Phases ◽  
Three Space

Since its initial synthesis in 2005, COF-5 has been known to have intrinsic disorder in the placement of the 2D layers relative to one another (i.e. turbostratic disorder). Prior studies of have demonstrated that the eclipsed layering found in the space group originally assigned to COF-5 (<i>P</i>6<i>/mmm</i>) is inconsistent with energy considerations. Herein it is demonstrated that eclipsed layers are also inconsistent with<sup> 13</sup>C solid-state NMR data. Crystal structure predictions are made in five alternative space groups and good agreement is obtained in <i>P</i>21<i>/m</i>, <i>Cmcm</i>, and <i>C</i>2<i>/m</i>. We posit that all three space groups are present within the stacked 2D layers and show that this conclusion is consistent with evidence from <sup>13</sup>C solid-state NMR linewidths and chemical shifts, powder x-ray diffraction data and energy considerations. An alternative explanation involving a mixture of multiple pure phases is rejected because the observed NMR spectra don’t exhibit the characteristic features of such mixed phase materials.

Determination of Crystal Structure of Cd3(BO3)2 by Powder X-Ray Diffraction

1991 ◽  
Vol 6 (1) ◽  
pp. 28-30 ◽  
Author(s):  
Y. Laureiro ◽  
M.L. Veiga ◽  
M.L. López ◽  
S. García-Martín ◽  
A. Jerez ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Low Temperatures ◽  
Rietveld Analysis ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Orthorhombic System ◽  
X Ray ◽  
Cell Parameters

AbstractCd3(BO3)2 was prepared by a solid state reaction between B(OH)3 and Cd(OH)2 at low temperatures ranging between 523° and 623° and at a pressure of 10−4 – 10−5 Hg mm. The crystal structure has been refined by Rietveld analysis of X-ray powder diffraction data. The compound crystallizes in the orthorhombic system, space group Pnnm, Z = 2, with cell parameters of a = 5.967(5) Å, b = 4.78 (0) Å and c = 9.009(5) Å.

scholarly journals Formation and structure of the first metal complexes comprising amidinoguanidinate ligands

2016 ◽  
Vol 72 (11) ◽  
pp. 1526-1531 ◽  
Author(s):  
Farid M. Sroor ◽  
Phil Liebing ◽  
Cristian G. Hrib ◽  
Daniel Gräsing ◽  
Liane Hilfert ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Metal Complexes ◽  
Solid State Reaction ◽  
The Novel ◽  
X Ray Diffraction ◽  
Reaction Conditions ◽  
X Ray

The first metal complexes comprising amidinoguanidinate ligands have been prepared and structurally characterized, namely bis[μ-N,N′,N′′,N′′′-tetraisopropyl-1-(1-butylamidinato)guanidinato-κ3N1,N2:N2]bis[(tetrahydrofuran)lithium], [Li2(C18H37N4)2(C4H8O)2], (2), and [bis(tetrahydrofuran)lithium]-di-μ-chlorido-{(N,N′-dicyclohexyl-1-butylamidinato-κ2N1,N2)[N,N′,N′′,N′′′-tetracyclohexyl-1-(1-butylamidinato)guanidinato-κ2N1,N2]holmate(III)}, [HoLiCl2(C4H8O)2(C17H31N2)(C30H53N4)], (3). The novel lithium amidinoguanidinate precursors Li[nBuC(=NR)(NR)C(NR)2] [1:R= Cy (cyclohexyl),2:R=iPr) were obtained by treatment ofN,N′-diorganocarbodiimides,R—N=C=N—R(R=iPr, Cy), with 0.5 equivalents ofn-butyllithium under well-defined reaction conditions. An X-ray diffraction study of2revealed a ladder-type dimeric structure in the solid state. Reaction of anhydrous holmium(III) chloride within situ-prepared2afforded the unexpected holmium `ate' complex [nBuC(=NCy)(NCy)C(NCy)2]Ho[nBuC(NCy)2](μ-Cl)2Li(THF)2(3) in 71% yield. An X-ray crystal structure determination of3showed that this complex contains both an amidinate ligand and the new amidinoguanidinate ligand.

A Coordination Polymer of Bis-[2-(dimethylamino)ethanolato]dimethylsilane with a Lithium Chloride Dimer

2009 ◽  
Vol 64 (3) ◽  
pp. 343-346
Author(s):  
Michael Hagemann ◽  
Tania Pape ◽  
Norbert W. Mitzel
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Nmr Spectroscopy ◽  
Coordination Polymer ◽  
Lithium Chloride ◽  
X Ray Diffraction ◽  
X Ray ◽  
Chloride Adduct

The reaction of lithium 2-(dimethylamino)ethanolate with Me2SiCl2 yielded a lithium chloride adduct of Me2Si- (OCH2CH2NMe2)2. Despite the application of an excess of Me2SiCl2, the formation of ClMe2SiOCH2CH2NMe2 was not observed. [Me2Si(OCH2CH2NMe2)2・Li2Cl2] was characterised by NMR spectroscopy and determination of its crystal structure by X-ray diffraction. In the solid state it forms endless chains consisting of Li2Cl2 rhombi, with the lithium atoms chelated by the O and N atom of one OCH2- CH2NMe2 substituent of Me2Si(OCH2CH2NMe2)2 units.

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