Rigaku Rotating Anodes: Powerful and Reliable Sources for Seamless and High-throughput Small Molecule Structure Solution

Interesting structures from our users

Some of our RAG users have provided their peer-reviewed publications to show the range of samples that can analyzed and the diversity of research topics that can be addressed when using Rigaku microfocus rotating anode diffractometers. We provide a summary for each of them below. These results span the last 15-20 years, demonstrating that using RAGs for small molecule crystallography is not just a recent occurrence.

Ethylene Tetramerization:  A New Route to Produce 1-Octene in Exceptionally High Selectivities, J. Am. Chem. Soc., 2004, 126, 45, 14712.

Annette Bollmann*, Kevin Blann, John T. Dixon, Fiona M. Hess, Esna Killian, David H. Morgan, Arno Neveling, Stefanus Otto, Hulisani Maumela, Matthew Overett, David S. McGuinness: Sasol Technology (Pty) Ltd., South Africa and U.K.; Alexandra M. Z. Slawin (crystallographer): University of St. Andrews, Scotland; Peter Wasserscheid and Sven Kuhlmann: University of Erlangen-Nuernberg, Germany

A new synthetic route to the synthesis of 1-octene with good selectivity of up to 
70% via ethylene tetramerization was discovered. A complex of Cr(III) with 
diphosphinamine ligands ((R^a)₂P)₂-NR^b catalyzes the reaction . In addition to discussing the effect of the nature of the R^a and R^b substituents on 1-octene synthetic selectivity, the authors discovered that the catalyst didn’t have to be synthesized in situ for the reaction to occur. Instead, they demonstrated that the catalytic reactions can also be conducted using a pre-synthesized Cr(III) complex. The unambiguous characterization of the catalyst formed in such a way came from X-ray analysis. The crystal structure of the derivative with Ra = Rb = phenyl was obtained and showed that it is a chlorine-bridged dimer [Cr(((R^a)₂P)₂-NR^b)Cl₂(µ-Cl)]₂.

Metal–Organic Frameworks from Edible Natural Products, Angew. Chem. Int. Ed., 2010, 49, 8630.

Ronald A. Smaldone, Ross S. Forgan, Jeremiah J. Gassensmith, J. Fraser Stoddart*: Northwestern University, USA; Alexandra M. Z. Slawin (crystallographer): University of St. Andrews, Scotland; Hiroyasu Furukawa, Omar M. Yaghi: University of California Los Angeles, USA.

These authors report the successful synthesis of a Metal-Organic Framework 
(MOF) from a renewable, naturally available  building block: γ-cyclodextrin (γ-CD), 
an additive commonly used in the food industry as well as a solubilizing and 
stabilizing agent in drug delivery. A series of CD-MOFs were synthesized, using 
various metals: K⁺, Na⁺, Rb⁺ and Cs⁺. The use of inexpensive, non-hazardous and readily available natural products aims to address the growing desire to avoid relying on organic building blocks derived from non-renewable petrochemical feedstocks. The CD-MOFs described in this work can be prepared entirely from edible ingredients: food-grade γ-CD, salt substitute (KCl) or potassium benzoate (food additive E212) in bottled water and Everclear® grain spirit (EtOH), making virtually edible MOFs. A detailed analysis of the crystal structure of the K⁺ MOF derivative is used to explain the success of synthesizing and obtaining crystalline CD-MOFs. Additional structural analyses were performed on crystals of CD-MOFs soaked in the dye Rhodamine B. However, while the presence of the dye molecules was evident from the crystals turning red and was confirmed by ¹H NMR, the crystal structures could not definitively reveal all counterions or guest molecules, indicating a likely heavy disorder of the guest molecules.

Molecular Trefoil Knot from a Trimeric Circular Helicate, J. Am. Chem. Soc., 2018, 140, 4982.

Liang Zhang, David P. August, Jiankang Zhong, George F. S. Whitehead (crystallographer), Iñigo J. Vitorica-Yrezabal, and David A. Leigh*: University of Manchester, U.K.

A novel two-step synthesis of a molecular trefoil knot is described, based on the self assembly of a 12-component trimeric circular zinc helicate, followed by ring closing metathesis of six pendant alkene chains. Only three designed synthetic routes had been reported to date and they involved complex intermediates and lengthy syntheses. In contrast, this was one of the shortest and highest yielding designed routes to a trefoil knot developed to date. The crystal structure of the intermediate compound unambiguously established its trimeric circular zinc helicate nature and showed how the alkyl chains are well ordered in the solid state and positioned such that joining each of them to their nearest neighbor generates a trefoil knot. The crystal structure of the trefoil knot revealed an 84-atom-long closed loop that weaves a continuous path around the three zinc centers, with the strand crossing over or under itself at each zinc atom.

Isoreticular two-dimensional magnetic coordination polymers prepared through pre-synthetic ligand functionalization, Nature Chemistry, 2018, 10, 1001.

J. López-Cabrelles, S. Mañas-Valero, G. Mínguez Espallargas* and E. Coronado*: University of Valencia, Spain; I. J. Vitórica-Yrezábal (crystallographer): University of Manchester, U.K.; P. J. Bereciartua: Polytechnic University of Valencia, Spain; J. A. Rodríguez-Velamazá: Institut Laue-Langevin, France; J. C. Waerenborgh and B. J. C. Vieira: University of Lisbon, Portugal; D. Davidovikj, P. G. Steeneken and H. S. J. van der Zant: Delft University of Technology, The Netherlands

The authors describe a novel method to synthesize 2D materials with specific 
physical and chemical properties whereby organic ligands are covalently functionalized before the synthesis of the layered coordination polymers used in the preparation of 2D crystalline materials. Pre-synthetic ligand functionalization is a better way to preserve the long-range structural order of materials, unlike post-synthetic functionalization where molecules are anchored on a 2D crystal post-exfoliation to engineer their surface and tune their properties. A series of five isostructural layered magnetic coordination polymers between Fe(II) centers and different benzimidazole derivatives (bearing a Cl, H, CH₃, Br or NH2 side group) were prepared and used to produce the final material by mechanical exfoliation. The crystal structures of two of the compounds were determined from synchrotron data, while data collected on a Rigaku FR-X RAG led to the crystal structure of the other three. X-Ray analyses established the layered nature of the compounds, showed they were all isostructural and provided a path to explaining their magnetic properties. 

First Synthesis and Characterization of CH₄@C₆₀, Angew. Chem. Int. Ed., 2019, 58, 5038.

Sally Bloodworth, Gabriela Sitinova, Shamim Alom, Sara Vidal, George R. Bacanu, Stuart J. Elliott, Mark E. Light, Julie M. Herniman, G. John Langley, Malcolm H. Levitt, and Richard J. Whitby*: University of Southampton, U.K.

The first complete chemical synthesis of the endohedral fullerene CH₄@C₆₀ 
in which each C₆₀ fullerene entity encapsulates a single methane molecule, is 
reported. While the opening of a fullerene by a chemical route, to allow a small 
molecule to insert itself, was known, the critical step of suturing the fullerene 
to imprison the small molecule had remained elusive. This work describes the 
first successful closure of any A@C₆₀ compound, where A is methane, a molecule thought to be one of the largest possible guests for C₆₀. The crystal structure of the nickel(II) octaethylporphyrin/benzene solvate of CH₄@C₆₀ critically shows an additional spherical electron density blob inside C₆₀, demonstrating that methane has indeed been encapsulated. Moreover, a faint shell of electron density symmetrically distributed around the central carbon is also observed 1.03 Å away from it and attributed to the methane hydrogens,. This shell of electron density corresponds to the delocalized nuclear wavefunction of the methane hydrogens, as expected for a quantum description of the freely rotating molecule and as has been previously established for the analogous systems H₂@ C₆₀, H₂O@C₆₀, and HF@C₆₀.

Understanding the interactions between the bis(trifluoromethylsulfonyl)imide anion and absorbed CO₂ using X-ray diffraction analysis of a soft crystal surrogate, Commun. Chem., 2020, 3, Article #143

Xin Zheng; Katsuo Fukuhara; Yuh Hijikata; Jenny Pirillo; Kiyonori Takahashi; Shin-ichiro Noro and Takayoshi Nakamura: Hokkaido University, Japan; Hiroyasu Sato: Rigaku Corporation, Japan.

In today’s world where the threat from global warming increases rapidly, interests 
in ionic liquids (IL) has increased because of their capacity to selectively absorb 
carbon dioxide (CO₂). CO₂ absorption in ILs is known to be primarily dependent on 
the nature of the anion, where fluorinated anions have been identified as superior 
absorbers relative to those lacking that specific halogen. In that regard, the bis(trifluoromethylsulfonyl)imide (NTf2-) anion, made of two CF₃SO₂ moieties linked by a nitrogen center, has attracted much of the research effort. A clear understanding of the reasons for the superior CO₂ absorption capabilities remains elusive, given the lack of structural data on these liquid compounds. In this work, the authors propose to use soft crystals, materials that can switch between crystalline and soft states under the action of a chemical or physical stimulus, as solid-state models for ILs available for single crystal X-ray crystallography. They synthesized soft crystals of a (NTf²⁻) salt of a Cu²⁺ metal-organic cluster. The ligand on the Cu²⁺ cation consists of two pyridyl groups linked by a propane chain similar to alkyl chains found in ILs. The crystal structure of the guest-free and CO₂-loaded species demonstrates how the compound switches from a closely-packed to an open, porous arrangement, principally due to a change of conformation of the (NTf²⁻) moiety. Indeed, (NTf²⁻) switches from a cis to trans conformation relative to the central S-N bond to form a cavity which encloses two CO₂ molecules. Additional structural and theoretical calculation details are provided, along with results from experiments that show that the soft crystals specifically absorb CO₂, but not nitrogen or argon gases.

Magnet Creation by Guest Insertion into a Paramagnetic Charge-Flexible Layered Metal–Organic Framework, J. Am. Chem. Soc., 2021, 143, 7021.

Jun Zhang, Wataru Kosaka, and Hitoshi Miyasaka*:  Tohoku University, Japan; Hiroyasu Sato: Rigaku Corporation, Japan

Three collaborating groups at Tohoku University in Japan propose to chemically 
alter the magnetic properties of molecular materials through the lens of Metal-
Organic Frameworks (MOFs). First, they synthesized a MOF where Ru-based 
clusters are linked by single molecules of tetracyanoquinone(TCNQ)-ether, forming 
a 2D-layered framework. The solvent-free paramagnetic MOF compound is a 
charge-transfer complex which undergoes an electron transfer from the electron-rich TCNQ moiety to the electron-accepting Ru cluster at 380 K via a structural transition. Then, the authors were able to initiate the same electron transfer and trigger a non-magnetic to magnetic transition at temperatures between 70 K and 92 K by inserting molecules of various organic solvents into the MOF. Remarkably, they were able to tune the magnetic properties of the solvated compounds to ferrimagnetic or antiferromagnetic upon inserting guest molecules of benzene, xylene, dichloroethane and dichloromethane vs. carbon disulfide, respectively. High-quality rotating anode data were collected on the non-solvated and solvated crystals at various temperatures and allowed for the careful analysis of the crystal arrangements as well as relevant interatomic distances, such as the C-N triple bonds of the TCNQ moiety, to estimate the electronic charge borne by various parts of the MOF. X-ray data and results from differential scanning calorimetry, infrared and Raman measurements are used to discuss in detail the structure-properties relationships in this charge-flexible MOF material.

Uncovering a Functional Motif of Nonlinear Optical Materials by In Situ Electron Density and Wavefunction Studies Under Laser Irradiation, Angew. Chem. Int. Ed., 2021, 60, 11799.

Guo-Cong Guo, Xiao-Ming Jiang, Shu-Juan Lin, Chao He and Bin-Wen Liu: Fujian Institute of Research on the Structure of Matter, China

Thanks to their capabilities to generate tunable laser sources via second harmonic 
generation, nonlinear optical materials (NLO) are of great interest for a wide range 
of applications in medicine, the military, and in communication networks. Understanding the mechanisms leading to NLO activities, and thus designing better materials, resides upon the identification of the Functional Motif (FM) responsible for the optical response and upon the study of how its molecular topology and electronic structure may change under the stress of external fields. The authors of this work set out to achieve, for the first time, the experimental identification of the FM of a NLO material. To that effect, they selected the archetypical NLO material LiB₃O₅ and used the Mo radiation of their rotating anode diffractometer to collect very high-resolution single-crystal X-ray diffraction data, both in the dark and under a laser beam with wavelength of 360 nm or 1064 nm at 85 K. The systematic study of the topological changes in the electron density distribution and wavefunction of LiB₃O₅ established that laser irradiation significantly alters the atomic and bond properties of the [B₃O₅]- unit, due to electron movement from oxygen atoms to boron atoms. As it is fully in line with what was known about [B₃O₅]- being the FM of NLO material LiB₃O₅, it is hoped that this work represents a new method to determine the structural origin of optical efficiency in NLO materials.

Geometric Frustration Suppresses Long-Range Structural Distortions in NbₓV₁₋ₓO₂, J. Phys. Chem. C 2022, 126, 2049−2061.

Top B. Rawot Chhetri, Tyra C. Douglas, Matthew A. Davenport, Stephan Rosenkranz, Raymond Osborn, Matthew J. Krogstad and Jared M. Allred: University of Alabama, USA.

Certain transition metal dioxides, such as VO₂ and NbO₂, undergo simultaneous 
structural and electronic transitions, inducing a metal-to-insulator transition 
(MIT) at 340 K and 1073 K respectively for VO₂ and NbO₂. The dependency of 
the MIT temperature on pressure and on small amounts of other metals such 
as Nb (for VO₂), Mo, W, Cr and Al makes these materials good candidates as 
temperature sensors, optical switches, memory devices, smart windows, etc. 
However, the forces driving the MIT transitions are not well misunderstood. So, researchers at the University of Alabama undertook the determination of the phase diagram for the alloy NbₓV₁₋ₓO₂  using total X-ray scattering and 3D-difference pair distribution function (3D-ΔPDF) methods. In their total X-ray scattering experiments, they used the power of the Rigaku dual source Cu/Mo rotating anode in the Mo Kα mode and the extremely low electronic noise and high sensitivity of the Hybrid Photon Counting detector HyPix-6000HE to study the weak, but obvious, diffuse scattering features present across all samples and temperatures, albeit at varying levels of intensity and complexity. They discovered two separate short-range ordered phases, one of which has not been observed before. These short-range orders, probably both two-dimensional, suggest that the MIT mechanism is likely related to the geometric frustration of displacement models, suppressing long-range structural order in these materials.