Low temperature single crystal X-ray diffraction: advantages, instrumentation and applications

The benefits of carrying out single crystal X-ray diffraction (SXRD) experiments at low temperatures have long been recognised by the scientific community, as clearly demonstrated by the massive increase in publications reporting the use of low temperature SXRD in the past 15 years. This tutorial review will summarise the advantages, many of them now often forgotten by its practitioners or never known by the newcomers to the field, of performing single crystal X-ray diffraction experiments at low temperatures. The instrumentation currently available to university laboratories, which has been greatly improved over the past 5 years, will also be briefly described and a few different examples covering a range of applications will be presented.     

Dimesitylborane monomer-dimer equilibrium in solution, and the solid-state structure of the dimer by single crystal neutron and X-ray diffraction

Dimesitylborane dimer has been shown to exist in equilibrium with dimesitylborane monomer in solution. This equilibrium has been investigated by variable concentration and variable temperature multinuclear NMR spectroscopy and values for the dissociation constant, enthalpy and entropy of dissociation were found to be K_diss=(3.2±0.4)×10⁻³ M, ΔH=70 kJ mol⁻¹, and ΔS=212 J K⁻¹mol⁻¹, respectively. Ab initio methods have been used to investigate the gas-phase structures and energies of both monomer and dimer, and calculated ¹¹B-NMR shifts are also presented. The solid-state structure of dimesitylborane dimer has been investigated by single crystal X-ray diffraction at 100 K and the position of the bridging hydrogen atoms (B---H=1.340(2), 1.342(2) Å, H---B---H=92.46(14)°) has been determined accurately, for the first time, by single crystal neutron diffraction at 20 K.     

X-ray diffraction and quantum-chemical analysis of a single crystal of 2,5-dimethyl-3,4-dihydro-2h-pyran-2-carboxylic acid

The structure of synthesized 2,5-dimethyl-3,4-dihydro-2H-pyran-2-carboxylic acid was investigated by the single crystal X-ray diffraction analysis method. It was established that the molecule of the acid exists in the form of the endo isomer while the single crystal exists as a racemate of the two enantiomeric endo stereomers. Quantum-chemical calculations of a model of the macrocell of the acid by means of the semiempirical MOPAC2009 program agree well with the X-ray diffraction data.     

2′-O,5-dimethyluridine: A total synthesis and single crystal X-ray diffraction study

A new method for the synthesis of 2′-O,5-dimethyluridine ( 5 ) has provided the title compound in a higher yield. Application of a one-pot ribosylation methodology resulted in an efficient, high yield synthesis of 5-methyluridine (ribothymine, 3b ). An X-ray diffraction analysis of 5 disclosed the conformation of the sugar moiety of this nucleoside as anti, N(3′-endo), g⁺.     

Synthesis of a new open framework cerium silicate and its structure determination by single crystal X-ray diffraction

Hydrothermal synthesis of a new open framework cerium silicate and its structure determination by single crystal X-ray diffraction are reported.     

Photodissociation reaction of 1,2-diiodoethane in solution: a theoretical and X-ray diffraction study

Various molecular species are known to form during the photoreaction of C2H4I2 in the gas phase and in solution. We have studied all species involved in this reaction by ab initio and density functional theory (DFT) calculations: Geometries, energies, and vibrational frequencies of C2H4I2, bridged C2H4I*, anti C2H4I*, C4H4, I2, I3-, and the isomer C2H4I-I were calculated. The absorption peaks and oscillator strengths of selected species along the potential energy surface (PES) were calculated using time-dependent DFT and were compared with available experimental results. The calculated PES satisfactorily describes the observed reactions of the photoexcited C2H4I2 molecule. In the gas phase, there is only one reaction pathway: the first C-I bond ruptures followed by a secondary C-I breakage in the haloethyl radical C2H4I*. In solution, by contrast, another reaction channel, which is energetically more favored over the secondary dissociation, is switched on due to a solvation effect: the bridged C2H4I* can bind to the free iodine atom to form a C2H4I-I isomer without any energy barrier. The isomer can then break into C2H4 and I2. The rotational barriers in the gas phase and in solution were also calculated and compared. To provide experimental data on the structure of C2H4I2 in solution, the ground state structure of C2H4I2 in methanol was determined from static X-ray diffraction data using 88 keV (lambda = 0.14 A) X-rays. The structural parameters are compared with those from the theoretical results.     

Reaction of ZnCl2 and HgCl2 metal salts with a bidentate Schiff base ligand in methanol solution, X-ray crystal structure, and theoretical studies

From the reaction of ZnCl₂ and HgCl₂ metal salts with (E)-4-chloro-N-(pyridine-2-ylmethylene)benzeneamine (L) in methanol solution, two binuclear Schiff base complexes were prepared. Both complexes were characterized by elemental analysis, UV–Vis, and IR spectrophotometry. X-ray crystal structure analysis showed that metal ion in the resulting centrosymmetric dinuclear ML₂Cl₄ complexes is in a distorted trigonal bipyramidal and a distorted square pyramidal coordination environment in the case of Zn(II) and Hg(II) metal ions, respectively. Three types of reaction between MCl₂ salts and ligand L producing three different types of products—ML₂ ²⁺, MLCl₂, and M₂L₂Cl₄—were simulated in both the gas phase and solution. The gas phase calculations at DFT (B3LYP) level of theory using SDD, CEP-121G, and LanL2DZ basis sets showed that the binuclear M₂L₂Cl₄ complexes are more stable than corresponding mononuclear MLCl₂ complexes. Furthermore, both the gas phase and solution studies showed that the formation of M₂L₂Cl₄ complexes from the metal cations, chloride anion, and ligand molecule is energetically more favored than that of MLCl₂ and ML₂ ²⁺ complexes.     

Synthesis and X-ray single crystal structure of a bivalent glycocluster

The crystal structure of a bivalent glycocluster containing aromatic amides reveals that alkylation of secondary amides alters amide configuration and thus carbohydrate presentation. This also facilitates non covalent interactions (azide-azide, carbonyl-pyranose and aromatic-pyranose) and thus carbohydrate-carbohydrate stacking.     

Molecular structure of a D-homoandrostanyl steroid derivative: single crystal and powder diffraction analyses

The knowledge of the structure of a molecular crystal is frequently a prerequisite for the understanding of its solid state properties. Even though single-crystal diffractometry is the method of choice when it comes to crystal structure determination, methods using powder diffraction data become more and more competitive. There has been much recent interest in the development of a new generation of "direct-space" approaches that are particularly suited for molecular crystals. The crystallographic structure of a steroid derivative molecule (17,17-di-n-propyl-17a-aza-D-homo-5alpha-androstan-3beta-ol) was obtained in two independent ways: from a single crystal by laboratory X-rays and from a polycrystalline powder by high-resolution synchrotron powder diffraction. The molecule crystallizes in the orthorhombic space group P2(1)2(1)2(1) (a = 6.5346, b = 17.6006 and c = 19.6978 A). Hydrogen bonds form infinite chains of molecules parallel to the c axis.     

Mechanochemical synthesis in copper(II) halide/pyridine systems: single crystal X-ray diffraction and IR spectroscopic studies

Whereas complexes of divalent metal halides (X = Cl, Br, I) with/from pyridine commonly crystallise as trans-[M(py)(4)X(2)]·2py, M on a site of 222 symmetry in space group Ccca, true for CuCl(2) and CuBr(2) in particular, the copper(II) iodide adduct is of the form [Cu(py)(4)I]I·2py, Cu on a site of mm2 symmetry in space group Cmcm, and five-coordinate (square-pyramidal), the same cationic species also being found in 2[Cu(py)(4)I](I(3))·[(py)(2)Cu(μ-I)(2)Cu(py)(2)] (structurally defined). Bromide or N-thiocyanate may be substituted for the unbound iodide ion in the solvated salt, resulting in complexes which crystallize in space group Ccca, but with both anions and the metal atom disordered. In [Cu(py)(4)(I(3))(2)], a pair of long Cu···I contacts approach a square-planar Cu(py)(4) array. Assignments of the ν(CuN) and ν(CuX) (X = Br, I, SCN) bands in the far-IR spectra are made, the latter with the aid of analogous assignments for [Cu(py)(2)X(2)] (X = Cl, Br), which show a dependence of ν(CuX) on the Cu-X bond length that is very similar to that determined previously for copper(i) halide complexes. The structure of the adventitious complex [(trans-)(H(2)O)(py)(4)CuClCu(py)(4)](I(3))(3)·H(2)O is also recorded, with six- and five-coordinate copper atoms; rational synthesis provides [{Cu(py)(4)}(2)(μ-Cl)](I(3))(3)·H(2)O with one water molecule less. In [{Cu(py)(4)Cl}((∞|∞))](I(3))·3py, square pyramidal [Cu(py)(4)Cl](+) cations, assisted by Cl···Cu interactions, stack to give rise to infinite polymeric strings. Several of these compounds were prepared mechanochemically, illustrating the applicability of this method to syntheses involving redox reactions as well as to complex syntheses involving up to five components. The totality of results demonstrates that the [Cu(II)(py)(4)] entity can be stabilized in an unexpectedly diverse range of mononuclear and multinuclear complexes through the presence of lattice pyridine molecules, the bulky triiodide ion, or a combination of both.     

Crystal structures of thermoelectric n- and p-type Ba8Ga16Ge30 studied by single crystal, multitemperature, neutron diffraction, conventional X-ray diffraction and resonant synchrotron X-ray diffraction

Comprehensive single-crystal structural investigations of n- and p-type Ba8Ga16Ge30 have been carried out using multitemperature neutron and conventional X-ray diffraction as well as resonant synchrotron X-ray diffraction. The data show that the guest atom positions and dynamics are very similar in the two structures, although the barium atoms are slightly more displaced from the cage centers in the p-type structure than in the n-type structure (Deltad = 0.025 A). For both structures Fourier difference maps calculated from very high-resolution neutron diffraction data (sin theta/lambda > 2 A-1) show that the Ba nuclear density at lowest temperatures (15 K) is distributed in a torus around the crystallographic 6d site with maxima in the 24j positions. At room temperature the maxima have shifted to the 24k position. Analysis of atomic displacement parameters give Einstein temperatures of approximately 60(1) K for both structures. Thus, the fundamental difference in the low temperature thermal conductivity observed for p- and n-type Ba8Ga16Ge30 appear not to be directly related to the guest atom behavior as is commonly assumed in thermoelectric research. The neutron data and the resonant synchrotron X-ray data facilitate refinement of Ga/Ge framework occupancies. The Ga atoms have a clear preference for the 6c site with the preference being somewhat stronger for the n-type structure.     

A new polymorph of methimazole: Single crystal and powder X-ray diffraction study

A new polymorph of 1-methyl-4-imidazoline-2-thione has been first discovered and studied by X-ray diffraction. The crystal of the new polymorph is monoclinic, the asymmetric part of the cell contains three independent molecules. In the crystal, the key compound is in the form of planar hydrogen-bonded dimers due to the interactions of the N-H…S type. The new modification is of an intensely yellow color in contrast to the previously known colorless forms, is characterized by a lower density but stronger hydrogen bonds; it is formed as a minor impurity to main triclinic polymorph.     

X-ray diffraction and dielectric spectroscopy studies on a partially fluorinated ferroelectric liquid crystal from the family of terphenyl esters

The fluorinated compound, (S)-4′′-(6-perfluoropentanoyoxyhexyl-1-oxy)-2′,3′-difluoro-4-(1-methylheptyloxycarbonyl)-[1,1′:4′,1′′]-terphenyl, which exhibits antiferroelectric SmC_A*, ferroelectric SmC* and paraelectric SmA* phases, has been investigated by polarising optical microscopy, differential scanning calorimetry, X-ray diffraction and frequency-dependent dielectric spectroscopy methods. X-ray studies have revealed that the layer thickness remains almost constant in the SmA* phase but within the SmC* and SmC_A* phases it decreases with decreasing temperature, a step jump being observed only at the SmA*–SmC* transition. The tilt angle in the SmC_A* phase decreases from 22.2° to 19.5°, and in the SmC* phase it decreases from 18.8° to 5.5°. Spontaneous polarisation is found to be quite high and varies between 74.1 and 118.7 nC cm^?2. The variation in ε′ and ε′′ with temperature shows a discontinuous change at the transition temperatures. Goldstone mode relaxation is only observed in the ferroelectric and antiferroelectric phases and is found to be of the Cole–Cole type. The soft mode is observed on application of a bias field near the SmC*–SmA* transition. Neither the soft mode nor the anti-phase azimuthal angle fluctuation mode is observed in SmC_A*. Rotational viscosity decreases quite rapidly with temperature but in a different manner in the ferroelectric and antiferroelectric phases. Activation energy for this process is found to be 48.14 kJ mol^?1 in the SmC* phase.     

Residue-based charge flipping: a new variant of an emerging algorithm for structure solution from X-ray diffraction data

There is currently substantial interest and activity in the development and application of a new technique, called "charge flipping" (CF), that has emerged in the past few years for carrying out structure solution from X-ray diffraction data. We report here a new variant of this technique, termed "residue-based charge flipping" (RBCF), in which the residues of calculated and experimental structure factor amplitudes, together with the corresponding electron density residues, are introduced within the CF algorithm. An important feature of this approach is that it does not require a positive threshold electron density value (delta) to be specified to control the charge-flipping step within the algorithm (in contrast, it is well established that the success of standard CF calculations can depend critically on choosing a suitable value of delta for a given structural problem). Methodological details of the RBCF algorithm are described, and the results of the application of this technique for structure solution of three test structures are reported. The RBCF technique is shown to lead to the correct structure solution in all cases, with success rates of at least 90% (for independent calculations from different sets of initial random phases). Significantly, the convergence behavior of RBCF calculations is found to contrast markedly with that generally observed for standard CF calculations. In particular, convergence (assessed from the evolution of R-factor versus iteration number) typically progresses rapidly and immediately from the earliest iterations of RBCF calculations, rather than displaying an extended plateau region. This feature, and the fact that the RBCF technique does not use the delta parameter that is required in standard CF calculations, suggest that the RBCF algorithm may be a promising approach in future applications.     

Vapor phase inclusion of ferrocene and its derivative in a microporous metal-organic porous material and its structural characterization by single crystal X-ray diffraction

The inclusion of ferrocene and its derivative in metal-organic porous material MOF-5 is achieved by vapor diffusion; single-crystal X-ray diffraction studies using synchrotron radiation of ferrocene-loaded MOF-5 reveal well-ordered guest molecules packed into the pores.     

Establishment of a new molecular model for mercury determination verified by single crystal X-ray diffraction,spectroscopic analysis and biological potentials

A wide variety of molecular probes have been developed for real-time analysis,but most of organic fluorophores possess small Stokes shifts and self-absorption or inner filter effect that could not be avoided.In this study,a new dicyanoisophorone-based derivative(E)-0-(4-(2-(3-(dicyanomethylene)-5,5-dimethylcyclohex-1-en-1-yl)vinyl)phenyl)diphenylphosphinothioate(λ_ex=405 nm,X_em=551 nm,denoted as ICM-S) with strong push-pull electron effect has been afforded and it exhibits red shift for absorption from 407 nm to 426 nm with distinct color change from pale yellow to deep yellow upon exposure to Hg~(2+).Moreover,an easily distinguishable fluorescence color change follows the route from green,yellow to red in the presence of Hg~(2+) over the range of 0-90 μmol/L(detection limit=137 nmol/L)can be observed by the naked eye under a UV lamp irradiation.Chlorodiphenylphosphine and sublimedsulfur are incorpo rated as re s ponsive sites and P-O bond has been cleaved upon the addition of mercu ry ions.During the recognition process,such dicyanoisophorone dye(ICM-S) has been evolved to 2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene) malononitrile(ICM-OH).Clear evidences in the chemical processes can be identified via single crystal X-ray diffraction,spectroscopic analysis,photophysical studies and titration experiments.With the aim of exploring its potential in biological systems,its in vitro responses to Hg~(2+) have been evaluated in 293 T cells and the effectiveness in zebrafish model has also been verified.     

Crystal structure analysis of silver oxalate,Ag2C2O4 and X-ray diffraction study of its single crystal at the initial stage of photolysis

The crystal structure of Ag₂C₂O₄ was determined; space group P2₁/c, a=3.4603(5), b=6.1972(9), c=9.548(2) Å, β=103.47(1)⁰, V=199.12(6) ų, Z=2, d_calc=5.066 g/cm³ (Syntex P2₁ automatic diffractometer, CuK_α radiation, ф/2ф scan mode with a rate of 1.98–14.5 deg/min to 2θ_max=115°, 548 measured and 274 independent I_hkl, R(F)=0.259). The structure is channel type ionic, with single-layer packing of anions in the (100) plane according to the hexagonal law. In the channels stretched along [100], there are silver dimers with the Ag?Ag distance of 2.945 Å. The C₂O ₄ ^2? anion has $\bar 1$ symmetry; the C?C bond lengths are 1.60(1) and C?O are 1.23(1) and 1.24(1) Å. The observation and X-ray diffration monitoring of the initial stage of photolysis allowed us to conclude that it proceeds in a thin surface layer and has no effect on the crystal struture. The obtained results are discussed in the light of the literature data on the photolysis and thermolysis mechanisms of Ag₂C₂O₄. The results of previous structural studies are analyzed.     

Combined optimization using Cultural and Differential Evolution: application to crystal structure solution from powder diffraction data

The principles of social and biological evolution have been combined in a Cultural Differential Evolution hybrid global optimization technique and applied to crystal structure solution.